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1
Gao, Crystal, Zheng Jie Lim, Brendan Freestone, Kristy Austin, and Rob McManus. "Use of a Novel Electronic Patient Care Record System at Mass Gathering Events by St. John Ambulance Victoria." Prehospital and Disaster Medicine 34, s1 (May 2019): s88. http://dx.doi.org/10.1017/s1049023x19001845.
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Introduction:The growing number of mass gathering events (MGEs) in Victoria has seen an increase in demand for event health services and the need for real-time reporting of medical incidents at these events.Aim:Since 2016, St. John Ambulance Victoria has introduced an electronic patient care record (ePCR) system with the aim of improving patient care and satisfaction. It appears that this ePCR system is the first of its kind to be trialed at MGEs by a volunteer organization.Methods:A qualitative study was conducted to determine strengths and limitations of the ePCR system by compiling results of surveys and interviews and through anonymous feedback from volunteers and patrons (event organizers, patients). This study is ongoing.Results:It was found that the use of ePCR: 1.Allowed for collection of relevant data to assist in future planning of MGEs2.Aids the overall coordination of first aid delivery at MGEs -faster relaying of patient information to event commanders-reduction of paperwork-improved ability to locate first aid crews using GPS tracking3.Received positive feedback from first aiders, event organizers, and patrons4.Was deemed easy-to-use (4/5), acceptable (4.3/5), and helpful (4.1/5) by our membersDiscussion:These experiences demonstrate that ePCR is well-received, easy to use, and leads to improved patient satisfaction and treatment outcomes at MGEs. Furthermore, the ability to collect and analyze real-time data such as GPS location tracking, incidence heat maps, and patient demographics facilitate future event planning and resource allocation at MGEs. It is acknowledged that this study is preliminary, and the trialed use of an ePCR system has been limited to metropolitan areas and MGEs with <1 million patrons. The intent is to continue this study and explore the use of ePCRs at larger MGEs and events in rural or regional areas.
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Johansson, Markus H. K., Frank M. Aarestrup, and Thomas N. Petersen. "Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world." PLOS ONE 18, no. 10 (October 19, 2023): e0293169. http://dx.doi.org/10.1371/journal.pone.0293169.
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We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.
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Sáenz, Airo, Schulze-Makuch, Schloter, and Vestergaard. "Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert." Diversity 11, no. 11 (October 31, 2019): 205. http://dx.doi.org/10.3390/d11110205.
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Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.
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Guillén-Chable, Francisco, Johnny Omar Valdez Iuit, Luis Alejandro Avila Castro, Carlos Rosas, Enrique Merino, Zuemy Rodríguez-Escamilla, and Mario Alberto Martínez-Núñez. "Geographical distribution of mobile genetic elements in microbial communities along the Yucatan coast." PLOS ONE 19, no. 4 (April 29, 2024): e0301642. http://dx.doi.org/10.1371/journal.pone.0301642.
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Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan’s microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It’s important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.
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Newell, Alaina M., Jessie M. VanSwearingen, Elizabeth Hile, and Jennifer S. Brach. "The Modified Gait Efficacy Scale: Establishing the Psychometric Properties in Older Adults." Physical Therapy 92, no. 2 (February 1, 2012): 318–28. http://dx.doi.org/10.2522/ptj.20110053.
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BackgroundPerceived ability or confidence plays an important role in determining function and behavior. The modified Gait Efficacy Scale (mGES) is a 10-item self-report measure used to assess walking confidence under challenging everyday circumstances.ObjectiveThe purpose of this study was to determine the reliability, internal consistency, and validity of the mGES as a measure of gait in older adults.DesignThis was a cross-sectional study.MethodsParticipants were 102 community-dwelling older adults (mean [±SD] age=78.6±6.1 years) who were independent in ambulation with or without an assistive device. Participants were assessed using the mGES and measures of confidence and fear, measures of function and disability, and performance-based measures of mobility. In a subsample (n=26), the mGES was administered twice within a 1-month period to establish test-retest reliability through the intraclass correlation coefficient (ICC [2,1]). The standard error of measure (SEM) was determined from the ICC and standard deviation. The Cronbach α value was calculated to determine internal consistency. To establish the validity of the mGES, the Spearman rank order correlation coefficient was used to examine the association with measures of confidence, fear, gait, and physical function and disability.ResultsThe mGES demonstrated test-retest reliability within the 1-month period (ICC=.93, 95% confidence interval=.85, .97). The SEM of the mGES was 5.23. The mGES was internally consistent across the 10 items (Cronbach α=.94). The mGES was related to measures of confidence and fear (r=.54–.88), function and disability (Late-Life Function and Disability Instrument, r=.32–.88), and performance-based mobility (r=.38–.64).LimitationsThis study examined only community-dwelling older adults. The results, therefore, should not be generalized to other patient populations.ConclusionThe mGES is a reliable and valid measure of confidence in walking among community-dwelling older adults.
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Rocha, Eduardo P. C., and David Bikard. "Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?" PLOS Biology 20, no. 1 (January 13, 2022): e3001514. http://dx.doi.org/10.1371/journal.pbio.3001514.
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Prokaryotes have numerous mobile genetic elements (MGEs) that mediate horizontal gene transfer (HGT) between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control, or inactivate them. Recent studies have shown that prophages, conjugative elements, their parasites (phage satellites and mobilizable elements), and other poorly described MGEs encode defense systems homologous to those of bacteria. These constitute a significant fraction of the repertoire of cellular defense genes. As components of MGEs, these defense systems have presumably evolved to provide them, not the cell, adaptive functions. While the interests of the host and MGEs are aligned when they face a common threat such as an infection by a virulent phage, defensive functions carried by MGEs might also play more selfish roles to fend off other antagonistic MGEs or to ensure their maintenance in the cell. MGEs are eventually lost from the surviving host genomes by mutational processes and their defense systems can be co-opted when they provide an advantage to the cell. The abundance of defense systems in MGEs thus sheds new light on the role, effect, and fate of the so-called “cellular defense systems,” whereby they are not only merely microbial defensive weapons in a 2-partner arms race, but also tools of intragenomic conflict between multiple genetic elements with divergent interests that shape cell fate and gene flow at the population level.
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Patil, Pooja D., Ana Clara Melo, Brian M. Westwood, E. Ann Tallant, and Patricia E. Gallagher. "A Polyphenol-Rich Extract from Muscadine Grapes Prevents Hypertension-Induced Diastolic Dysfunction and Oxidative Stress." Antioxidants 11, no. 10 (October 14, 2022): 2026. http://dx.doi.org/10.3390/antiox11102026.
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Muscadine grapes are abundant in dietary polyphenols, but their effect on hypertension-induced cardiac damage is limited. This study assessed whether a muscadine grape skin/seed extract supplement (MGES) prevents hypertension-induced cardiac damage and oxidative stress. Male Sprague Dawley rats were treated for four weeks with drinking water, angiotensin II (Ang II) to induce hypertension, MGES, or both Ang II and MGES. Cardiac function assessed by echocardiography showed that Ang II increased systolic blood pressure while MGES alone or in combination with Ang II had no effect. Ang II increased E/e′, an indicator of left ventricular filling pressure and diastolic dysfunction, by 41% compared to Control and co-treatment with MGES prevented the Ang II-mediated increase, suggesting that the extract attenuated hypertension-induced diastolic function. Ang II infusion increased urinary 8-hydroxy-2′-deoxyguanosine and cardiac 4-hydroxynonenal and malondialdehyde, which were prevented by the extract. The antioxidant enzymes catalase and superoxide dismutase 1 activity and mRNA were increased significantly in animals treated with MGES alone or in combination with Ang II, suggesting that the extract upregulates oxidative stress defense mechanisms in cardiac tissue. Thus, MGES may serve as a medical food to protect the heart from hypertension-induced diastolic dysfunction caused in part by excessive reactive oxygen species production.
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Kwun, Min Jung, Marco R. Oggioni, Stephen D. Bentley, Christophe Fraser, and Nicholas J. Croucher. "Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae." Genes 10, no. 9 (September 13, 2019): 707. http://dx.doi.org/10.3390/genes10090707.
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A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the transformation machinery has been proposed to limit vertical transmission of chromosomally integrated MGEs. This work describes how these mechanisms can act in concert. Experimental data demonstrate RMS phase variation occurs at a sub-maximal rate. Simulations suggest this may be optimal if MGEs are sometimes vertically inherited, as it reduces the probability that an infected cell will switch between RMS variants while the MGE is invading the population, and thereby undermine the restriction barrier. Such vertically inherited MGEs can be deleted by transformation. The lack of between-strain transformation hotspots at known prophage att sites suggests transformation cannot remove an MGE from a strain in which it is fixed. However, simulations confirmed that transformation was nevertheless effective at preventing the spread of MGEs into a previously uninfected cell population, if a recombination barrier existed between co-colonising strains. Further simulations combining these effects of phase variable RMSs and transformation found they synergistically inhibited MGEs spreading, through limiting both vertical and horizontal transmission.
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Rodríguez-Beltrán, Jerónimo, Vidar Sørum, Macarena Toll-Riera, Carmen de la Vega, Rafael Peña-Miller, and Álvaro San Millán. "Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria." Proceedings of the National Academy of Sciences 117, no. 27 (June 22, 2020): 15755–62. http://dx.doi.org/10.1073/pnas.2001240117.
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Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.
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Dokland, Terje. "Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements." Viruses 11, no. 11 (October 31, 2019): 1003. http://dx.doi.org/10.3390/v11111003.
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Horizontal transfer of mobile genetic elements (MGEs) is a key aspect of the evolution of bacterial pathogens. Transduction by bacteriophages is especially important in this process. Bacteriophages—which assemble a machinery for efficient encapsidation and transfer of genetic material—often transfer MGEs and other chromosomal DNA in a more-or-less nonspecific low-frequency process known as generalized transduction. However, some MGEs have evolved highly specific mechanisms to take advantage of bacteriophages for their own propagation and high-frequency transfer while strongly interfering with phage production—“molecular piracy”. These mechanisms include the ability to sense the presence of a phage entering lytic growth, specific recognition and packaging of MGE genomes into phage capsids, and the redirection of the phage assembly pathway to form capsids with a size more appropriate for the size of the MGE. This review focuses on the process of assembly redirection, which has evolved convergently in many different MGEs from across the bacterial universe. The diverse mechanisms that exist suggest that size redirection is an evolutionarily advantageous strategy for many MGEs.
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Rhoads, Douglas D., Jeff Pummil, Nnamdi S. Ekesi, and Adnan A. K. Alrubaye. "Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis." PLOS ONE 18, no. 7 (July 5, 2023): e0283914. http://dx.doi.org/10.1371/journal.pone.0283914.
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Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17–19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.
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Gao, Crystal, Zheng Jie Lim, Sabrina Yeh, Scott Santinon, Scott De Haas, and Kristy Austin. "Assessing the Efficacy of a One-day Structured Induction Program in Orienting Clinical Staff to a Novel Prehospital Medical Deployment Model." Prehospital and Disaster Medicine 34, s1 (May 2019): s102—s103. http://dx.doi.org/10.1017/s1049023x19002127.
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Introduction:St. John Ambulance Victoria provides first aid and medical services at a variety of mass gathering events (MGEs) throughout Victoria. Volunteer healthcare professionals and students (termed “volunteers”) form Medical Assistance Teams (MAT) at these MGEs. MAT deployments manage a variety of patient presentations which include critically ill patients. This reduces high acuity patient transfers to the hospital and, where possible, avoid ambulance and hospital utilization.Aim:To determine the effectiveness of interdisciplinary prehospital simulation workshops in preparing volunteers for MAT deployment at MGEs.Methods:A one-day, simulation-based training session within the MAT environment was implemented to introduce volunteers to the management of various scenarios faced at MGEs. All volunteers were provided an orientation to the equipment and setting up MAT deployments at MGEs. Volunteers then participated in interdisciplinary group-based scenarios such as cardiac arrest management, drug intoxication, spinal injuries, agitated patients, and airway management. To determine the effectiveness of this training session, volunteers were invited to participate in a post-training survey, comprising of Likert scores and open-ended responses.Results:Seventeen volunteers attended the training session with 10 (58.8%) completing the post-training survey. Volunteers were satisfied with environment familiarization in the MAT (Average 4.47/5.00) and found the simulation-based training helpful (Average 3.67/4.00). The induction overall was well-received (4.60/5.00) with volunteers feeling more confident in being deployed at MGEs (4.20/5.00).Discussion:The results of the simulation-based training session were positive with volunteers receptive to the need for a training day prior to MAT deployment at MGEs. The simulation session enables volunteers to be comfortable with working in MAT and managing a diverse range of patients at MGEs. This session is likely to improve interdisciplinary communication and teamwork in the MAT. Future research is aimed at following these volunteers after several MAT deployments to improve the training session for future participants.
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Johansson, Markus H. K., Valeria Bortolaia, Supathep Tansirichaiya, Frank M. Aarestrup, Adam P. Roberts, and Thomas N. Petersen. "Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder." Journal of Antimicrobial Chemotherapy 76, no. 1 (October 3, 2020): 101–9. http://dx.doi.org/10.1093/jac/dkaa390.
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Abstract Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.
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Zhang, Xiaolei Brian, Grace Oualline, Jim Shaw, and Yun William Yu. "skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements." Bioinformatics 40, Supplement_2 (September 1, 2024): ii155—ii164. http://dx.doi.org/10.1093/bioinformatics/btae398.
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Abstract Motivation: Mobile genetic elements (MGEs) are as ubiquitous in nature as they are varied in type, ranging from viral insertions to transposons to incorporated plasmids. Horizontal transfer of MGEs across bacterial species may also pose a significant threat to global health due to their capability to harbor antibiotic resistance genes. However, despite cheap and rapid whole-genome sequencing, the varied nature of MGEs makes it difficult to fully characterize them, and existing methods for detecting MGEs often do not agree on what should count. In this manuscript, we first define and argue in favor of a divergence-based characterization of mobile-genetic elements. Results: Using that paradigm, we present skandiver, a tool designed to efficiently detect MGEs from whole-genome assemblies without the need for gene annotation or markers. skandiver determines mobile elements via genome fragmentation, average nucleotide identity (ANI), and divergence time. By building on the scalable skani software for ANI computation, skandiver can query hundreds of complete assemblies against >65 000 representative genomes in a few minutes and 19 GB memory, providing scalable and efficient method for elucidating mobile element profiles in incomplete, uncharacterized genomic sequences. For isolated and integrated large plasmids (>10 kb), skandiver’s recall was 48% and 47%, MobileElementFinder was 59% and 17%, and geNomad was 86% and 32%, respectively. For isolated large plasmids, skandiver’s recall (48%) is lower than state-of-the-art reference-based methods geNomad (86%) and MobileElementFinder (59%). However, skandiver achieves higher recall on integrated plasmids and, unlike other methods, without comparing against a curated database, making skandiver suitable for discovery of novel MGEs. Availability and implementation https://github.com/YoukaiFromAccounting/skandiver
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Pant, Archana, Satyabrata Bag, Bipasa Saha, Jyoti Verma, Pawan Kumar, Sayantan Banerjee, Bhoj Kumar, et al. "Molecular insights into the genome dynamics and interactions between core and acquired genomes ofVibrio cholerae." Proceedings of the National Academy of Sciences 117, no. 38 (September 1, 2020): 23762–73. http://dx.doi.org/10.1073/pnas.2006283117.
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Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome ofVibrio choleraeharbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome ofV. choleraeand examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages. Recombinant vectors carrying the integration module of these GIs, ICE and CTXΦ, helped us to understand the efficiency of integrations of MGEs in theV. choleraechromosome. We have deleted more than 250 acquired genes from 6 different loci in theV. choleraechromosome and showed contribution of CTX prophage in the essentiality of SOS response master regulator LexA, which is otherwise not essential for viability in other bacteria, includingEscherichia coli. In addition, we observed that the core genome-encoded RecA helps CTXΦ to bypassV. choleraeimmunity and allow it to replicate in the host bacterium in the presence of similar prophage in the chromosome. Finally, our proteomics analysis reveals the importance of MGEs in modulating the levels of cellular proteome. This study engineered the genome ofV. choleraeto remove all of the GIs, ICEs, and prophages and revealed important interactions between core and acquired genomes.
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Mazzamurro, Fanny, Jason Baby Chirakadavil, Isabelle Durieux, Ludovic Poiré, Julie Plantade, Christophe Ginevra, Sophie Jarraud, Gottfried Wilharm, Xavier Charpentier, and Eduardo P. C. Rocha. "Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species." PLOS Biology 22, no. 10 (October 14, 2024): e3002814. http://dx.doi.org/10.1371/journal.pbio.3002814.
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Natural transformation is the only mechanism of genetic exchange controlled by the recipient bacteria. We quantified its rates in 786 clinical strains of the human pathogens Legionella pneumophila (Lp) and 496 clinical and environmental strains of Acinetobacter baumannii (Ab). The analysis of transformation rates in the light of phylogeny revealed they evolve by a mixture of frequent small changes and a few large quick jumps across 6 orders of magnitude. In standard conditions close to half of the strains of Lp and a more than a third in Ab are below the detection limit and thus presumably non-transformable. Ab environmental strains tend to have higher transformation rates than the clinical ones. Transitions to non-transformability were frequent and usually recent, suggesting that they are deleterious and subsequently purged by natural selection. Accordingly, we find that transformation decreases genetic linkage in both species, which might accelerate adaptation. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these transitions and a GWAS confirmed systematic negative associations between transformation and MGEs: plasmids and other conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the hypothesis of modulation of transformation rates by genetic conflicts, transformable strains have fewer MGEs in both species and some MGEs inactivate genes implicated in the transformation with heterologous DNA (in Ab). Innate defense systems against MGEs are associated with lower transformation rates, especially restriction-modification systems. In contrast, CRISPR-Cas systems are associated with higher transformation rates suggesting that adaptive defense systems may facilitate cell protection from MGEs while preserving genetic exchanges by natural transformation. Ab and Lp have different lifestyles, gene repertoires, and population structure. Nevertheless, they exhibit similar trends in terms of variation of transformation rates and its determinants, suggesting that genetic conflicts could drive the evolution of natural transformation in many bacteria.
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Redhead, Sky, Jeroen Nieuwland, Sandra Esteves, Do-Hoon Lee, Dae-Wi Kim, Jordan Mathias, Chang-Jun Cha, et al. "Fate of antibiotic resistant E. coli and antibiotic resistance genes during full scale conventional and advanced anaerobic digestion of sewage sludge." PLOS ONE 15, no. 12 (December 1, 2020): e0237283. http://dx.doi.org/10.1371/journal.pone.0237283.
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Antibiotic resistant bacteria (ARB) and their genes (ARGs) have become recognised as significant emerging environmental pollutants. ARB and ARGs in sewage sludge can be transmitted back to humans via the food chain when sludge is recycled to agricultural land, making sludge treatment key to control the release of ARB and ARGs to the environment. This study investigated the fate of antibiotic resistant Escherichia coli and a large set of antibiotic resistance genes (ARGs) during full scale anaerobic digestion (AD) of sewage sludge at two U.K. wastewater treatment plants and evaluated the impact of thermal hydrolysis (TH) pre-treatment on their abundance and diversity. Absolute abundance of 13 ARGs and the Class I integron gene intI1 was calculated using single gene quantitative (q) PCR. High through-put qPCR analysis was also used to determine the relative abundance of 370 ARGs and mobile genetic elements (MGEs). Results revealed that TH reduced the absolute abundance of all ARGs tested and intI1 by 10–12,000 fold. After subsequent AD, a rebound effect was seen in many ARGs. The fate of ARGs during AD without pre-treatment was variable. Relative abundance of most ARGs and MGEs decreased or fluctuated, with the exception of macrolide resistance genes, which were enriched at both plants, and tetracyline and glycopeptide resistance genes which were enriched in the plant employing TH. Diversity of ARGs and MGEs decreased in both plants during sludge treatment. Principal coordinates analysis revealed that ARGs are clearly distinguished according to treatment step, whereas MGEs in digested sludge cluster according to site. This study provides a comprehensive within-digestor analysis of the fate of ARGs, MGEs and antibiotic resistant E. coli and highlights the effectiveness of AD, particularly when TH is used as a pre-treatment, at reducing the abundance of most ARGs and MGEs in sludgeand preventing their release into the environment.
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Andryukov, B. G., N. N. Besednova, and T. S. Zaporozhets. "Mobile Genetic Elements of Prokaryotes and Their Role in the Formation of Antibiotic Resistance in Pathogenic Bacteria." Antibiotics and Chemotherapy 67, no. 1-2 (April 16, 2022): 62–74. http://dx.doi.org/10.37489/0235-2990-2022-67-1-2-62-74.
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The emergence and spread of antibiotic-resistant pathogenic bacterial strains in recent decades is an alarming trend and a serious challenge for the future of mankind around the world. The horizontal transfer and spread of antibiotic resistance genes among microorganisms through mobile genetic elements (MGEs), an extremely diverse group of prokaryotic mobilomas capable of moving DNA molecules intra- or intercellularly, aggravate the situation. MGEs play a central role in the phenotypic adaptation of bacteria, providing resistance to antibiotics and physical parameters of the environment, acquiring pathogenicity factors, and transforming metabolic pathways. However, the importance of MGEs is often overlooked when planning the strategies to contain the spread of antimicrobial resistance in pathogens. The aim of this review is to briefly characterize the main types of MGEs (plasmids, transposons, bacteriophages, integrons, and introns) involved in the formation of antibiotic resistance in pathogenic bacteria, with an emphasis on the members of the Enterobacteriaceae family. In the final part of the review, promising modern strategies for combating antimicrobial resistance based on the use of antiplasmid approaches and CRISPR/Cas technologies are considered.
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Delany, Catherine, Julia Crilly, and Jamie Ranse. "Drug and Alcohol Related Patient Presentations to Emergency Departments during Sporting Mass-Gathering Events: An Integrative Review." Prehospital and Disaster Medicine 35, no. 3 (March 25, 2020): 298–304. http://dx.doi.org/10.1017/s1049023x20000357.
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AbstractBackground:Drug and alcohol consumption at sporting mass-gathering events (MGEs) has become part of the spectator culture in some countries. The direct and indirect effects of drug and alcohol intoxication at such MGEs has proven problematic to in-event health services as well as local emergency departments (EDs). With EDs already under significant strain from increasing patient presentations, resulting in access block, it is important to understand the impact of sporting and other MGEs on local health services to better inform future planning and provision of health care delivery.Aim:The aim of this review was to explore the impact of sporting MGEs on local health services with a particular focus on drug and alcohol related presentations.Method:A well-established integrative literature review methodology was undertaken. Six electronic databases and the Prehospital and Disaster Medicine (PDM) journal were searched to identify primary articles related to the aim of the review. Articles were included if published in English, from January 2008 through July 2019, and focused on a sporting MGE, mass-gathering health, EDs, as well as drug and alcohol related presentations.Results:Seven papers met the criteria for inclusion with eight individual sporting MGEs reported. The patient presentation rate (PPR) to in-event health services ranged from 0.18/1,000 at a rugby game to 41.9/1,000 at a recreational bicycle ride. The transport to hospital rate (TTHR) ranged from 0.02/1,000 to 19/1,000 at the same events. Drug and alcohol related presentations from sporting MGEs contributed up to 10% of ED presentations. Alcohol was a contributing factor in up to 25% of cases of ambulance transfers.Conclusions:Drug and alcohol intoxication has varying levels of impact on PPR, TTHR, and ED presentation numbers depending on the type of sporting MGE. More research is needed to understand if drug and alcohol intoxication alone influences PPR, TTHR, and ED presentations or if it is multifactorial. Inconsistent data collection and reporting methods make it challenging to compare different sporting MGEs and propose generalizations. It is imperative that future studies adopt more consistent methods and report drug and alcohol data to better inform resource allocation and care provision.
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Guo, Tengfei, Zhaoyi Li, Yanqiu Shao, Yanli Fu, Weiyi Zhang, Yingying Shao, and Ying Zhu. "Effects of Oxytetracycline/Lead Pollution Alone and in the Combined Form on Antibiotic Resistance Genes, Mobile Genetic Elements, and Microbial Communities in the Soil." International Journal of Environmental Research and Public Health 19, no. 23 (November 24, 2022): 15619. http://dx.doi.org/10.3390/ijerph192315619.
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The application of livestock manure is the leading cause of antibiotic and heavy metal pollution in agricultural soil. However, the effects of oxytetracycline (OTC) and lead (Pb) pollution in the single or combined form on antibiotic resistance genes (ARGs) in the soil need to be further studied. This study was planned to investigate the effects of OTC and Pb application on ARGs, mobile genetic elements (MGEs), and bacterial abundance in the soil. The relative abundance of ARGs and MGEs increased by 0.31-fold and 0.03-fold after the addition of 80 mg kg−1 Pb to the soil, and by 0.49-fold and 0.03-fold after the addition of 160 mg kg−1 Pb. In addition, under the premise of the existence of OTC, the inhibitory effect of a low concentration of Pb on ARG is stronger than that of a high concentration of Pb, resulting in a lower abundance of ARGs. The abundance of ARGs and MGEs increased by 0.11-fold and 0.17-fold after the addition of OTC (30 mg kg−1) to the soil at a Pb concentration of 80 mg kg−1 and by 0.18-fold and 0.04-fold at a Pb concentration of 160 mg kg−1. The addition of OTC and Pb in the soil also decreased the many bacterial communities such as Bacteroidetes, Proteobacteria, Acidobacteria, and Firmicutes. Redundancy analysis (RDA) showed that organic matter content and pH were positively correlated with the abundance of ARGs and MGEs. At the same time, electrical conductivity (EC) had a negative correlation with the abundance of ARGs and MGEs in the soil. Intl1 was significantly associated with tetB, sul1, tetQ, sul2, and sul3. Network analysis illustrated that Actinobacteria, Bacteroidetes, and Proteobacteria were the main host bacteria causing changes in the abundance of ARGs and MGEs, and they were also predominant phylum in the culture environment. This conclusion can provide a reference for the related research of ARGs in soil.
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Pidpala, O. V., and L. L. Lukash. "Analysis of nucleotide sequences of bacterial retrointrons for the presence of homology to eukaryotic MGE." Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv 22, no. 1-2 (January 1, 2025): 4–9. https://doi.org/10.7124/visnyk.utgis.22.1-2.1683.
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Aims. To analyze the sequences of bacterial retrointrons for the presence of homology to representatives of various classes of eukaryotic mobile genetic elements (MGE). Methods. Nucleotide sequences of bacterial group II introns were taken for analysis from the Database for Bacterial Group II Introns. The results of the search and identification of MGE have been realized by CENSOR program. Results. In the analyzed sequences of bacterial retrointrons, fragments of sequences of both classes of eukaryotic MGEs were found in various combinations: non-LTR; LTR; DNA; non-LTR+LTR; non-LTR+DNA; LTR+DNA; non-LTR+LTR+DNA. The largest group of retrointrons contains MGEs of various classes. Conclusions. Bacterial retrointrons can be not only ancestors of non-LTR retroelements, but also carriers of fragmentary nucleotide sequences for the formation of various eukaryotic MGEs.
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Minnick, Michael F. "Functional Roles and Genomic Impact of Miniature Inverted-Repeat Transposable Elements (MITEs) in Prokaryotes." Genes 15, no. 3 (March 3, 2024): 328. http://dx.doi.org/10.3390/genes15030328.
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Prokaryotic genomes are dynamic tapestries that are strongly influenced by mobile genetic elements (MGEs), including transposons (Tn’s), plasmids, and bacteriophages. Of these, miniature inverted-repeat transposable elements (MITEs) are undoubtedly the least studied MGEs in bacteria and archaea. This review explores the diversity and distribution of MITEs in prokaryotes and describes what is known about their functional roles in the host and involvement in genomic plasticity and evolution.
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Xanthopoulou, Kyriaki, Alessandra Carattoli, Julia Wille, Lena M. Biehl, Holger Rohde, Fedja Farowski, Oleg Krut, et al. "Antibiotic Resistance and Mobile Genetic Elements in Extensively Drug-Resistant Klebsiella pneumoniae Sequence Type 147 Recovered from Germany." Antibiotics 9, no. 10 (October 5, 2020): 675. http://dx.doi.org/10.3390/antibiotics9100675.
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Mobile genetic elements (MGEs), especially multidrug-resistance plasmids, are major vehicles for the dissemination of antimicrobial resistance determinants. Herein, we analyse the MGEs in three extensively drug-resistant (XDR) Klebsiella pneumoniae isolates from Germany. Whole genome sequencing (WGS) is performed using Illumina and MinION platforms followed by core-genome multi-locus sequence typing (MLST). The plasmid content is analysed by conjugation, S1-pulsed-field gel electrophoresis (S1-PFGE) and Southern blot experiments. The K. pneumoniae isolates belong to the international high-risk clone ST147 and form a cluster of closely related isolates. They harbour the blaOXA-181 carbapenemase on a ColKP3 plasmid, and 12 antibiotic resistance determinants on an multidrug-resistant (MDR) IncR plasmid with a recombinogenic nature and encoding a large number of insertion elements. The IncR plasmids within the three isolates share a high degree of homology, but present also genetic variations, such as inversion or deletion of genetic regions in close proximity to MGEs. In addition, six plasmids not harbouring any antibiotic resistance determinants are present in each isolate. Our study indicates that genetic variations can be observed within a cluster of closely related isolates, due to the dynamic nature of MGEs. The mobilome of the K. pneumoniae isolates combined with the emergence of the XDR ST147 high-risk clone have the potential to become a major challenge for global healthcare.
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Selle, Kurt, Todd R. Klaenhammer, and Rodolphe Barrangou. "CRISPR-based screening of genomic island excision events in bacteria." Proceedings of the National Academy of Sciences 112, no. 26 (June 15, 2015): 8076–81. http://dx.doi.org/10.1073/pnas.1508525112.
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Genomic analysis ofStreptococcus thermophilusrevealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk. Clustered regularly interspaced short palindromic repeats–CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPR-Cas systems and MGEs is one of the driving forces governing genome homeostasis in this genus. To investigate the genetic outcomes resulting from CRISPR-Cas targeting of integrated MGEs,in silicoprediction revealed four genomic islands without essential genes in lengths from 8 to 102 kbp, totaling 7% of the genome. In this study, the endogenous CRISPR3 type II system was programmed to target the four islands independently through plasmid-based expression of engineered CRISPR arrays. TargetinglacZwithin the largest 102-kbp genomic island was lethal to wild-type cells and resulted in a reduction of up to 2.5-log in the surviving population. Genotyping of Lac−survivors revealed variable deletion events between the flanking insertion-sequence elements, all resulting in elimination of the Lac-encoding island. Chimeric insertion sequence footprints were observed at the deletion junctions after targeting all of the four genomic islands, suggesting a common mechanism of deletion via recombination between flanking insertion sequences. These results established that self-targeting CRISPR-Cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling.
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Berbel, Dàmaris, Jordi Càmara, Aida González-Díaz, Meritxell Cubero, Guillem López de Egea, Sara Martí, Fe Tubau, M. Angeles Domínguez, and Carmen Ardanuy. "Deciphering mobile genetic elements disseminating macrolide resistance in Streptococcus pyogenes over a 21 year period in Barcelona, Spain." Journal of Antimicrobial Chemotherapy 76, no. 8 (May 20, 2021): 1991–2003. http://dx.doi.org/10.1093/jac/dkab130.
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Abstract Objectives To phenotypically and genetically characterize the antibiotic resistance determinants and associated mobile genetic elements (MGEs) among macrolide-resistant (MR) Streptococcus pyogenes [Group A streptococci (GAS)] clinical isolates collected in Barcelona, Spain. Methods Antibiotic susceptibility testing was performed by microdilution. Isolates were emm and MLST typed and 55 were whole-genome sequenced to determine the nature of the macrolide resistance (MR) determinants and their larger MGE and chromosomal context. Results Between 1998 and 2018, 142 of 1028 GAS (13.8%) were MR. Among 108 isolates available for molecular characterization, 41.7% had cMLSB, 30.5% iMLSB and 27.8% M phenotype. Eight erm(B)-containing strains were notable in having an MDR phenotype conferred by an MGE encoding several antibiotic resistance genes. MR isolates were comprised of several distinct genetic lineages as defined by the combination of emm and ST. Although most lineages were only transiently present, the emm11/ST403 clone persisted throughout the period. Two lineages, emm9/ST75 with erm(B) and emm77/ST63 with erm(TR), emerged in 2016–18. The erm(B) was predominantly encoded on the Tn916 family of transposons (21/31) with different genetic contexts, and in other MGEs (Tn6263, ICESpHKU372 and one harbouring an MDR cluster called ICESp1070HUB). The erm(TR) was found in ICESp2905 (8/17), ICESp1108-like (4/17), ICESpHKU165 (3/17) and two structures described in this study (IMESp316HUB and ICESp3729HUB). The M phenotype [mef(A)-msr(D)] was linked to phage φ1207.3. Eight integrative conjugative element/integrative mobilizable element (ICE/IME) cluster groups were classified on the basis of gene content within conjugation modules. These groups were found among MGEs, which corresponded with the MR-containing element or the site of integration. Conclusions We detected several different MGEs harbouring erm(B) or erm(TR). This is the first known description of Tn6263 in GAS and three MGEs [IMESp316HUB, ICESp3729HUB and ICESp1070HUB] associated with MR. Periods of high MR rates in our area were mainly associated with the expansion of certain predominant lineages, while in low MR periods different sporadic and low prevalence lineages were more frequent.
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Wang, You, Quanchao Cui, Yuliang Hou, Shunfu He, Wenxin Zhao, Zhuoma Lancuo, Kirill Sharshov, and Wen Wang. "Metagenomic Insights into the Diverse Antibiotic Resistome of Non-Migratory Corvidae Species on the Qinghai–Tibetan Plateau." Veterinary Sciences 12, no. 4 (March 23, 2025): 297. https://doi.org/10.3390/vetsci12040297.
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Antibiotic resistance represents a global health crisis with far-reaching implications, impacting multiple domains concurrently, including human health, animal health, and the natural environment. Wild birds were identified as carriers and disseminators of antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). A majority of studies in this area have concentrated on migratory birds as carriers for the spread of antibiotic resistance over long distances. However, there has been scant research on the resistome of non-migratory Corvidae species that heavily overlap with human activities, which limits our understanding of antibiotic resistance in these birds and hinders the development of effective management strategies. This study employed a metagenomics approach to examine the characteristics of ARGs and mobile genetic elements (MGEs) in five common Corvidae species inhabiting the Qinghai–Tibetan Plateau. The ARGs were classified into 20 major types and 567 subtypes. Notably, ARGs associated with multidrug resistance, including to macrolide–lincosamide–streptogramins, tetracyclines, beta-lactam, and bacitracin, were particularly abundant, with the subtypes acrB, bacA, macB, class C beta-lactamase, and tetA being especially prevalent. A total of 5 types of MGEs (166 subtypes) were identified across five groups of crows, and transposase genes, which indicated the presence of transposons, were identified as the most abundant type of MGEs. Moreover, some common opportunistic pathogens were identified as potential hosts for these ARGs and MGEs. Procrustes analysis and co-occurrence network analysis showed that the composition of the gut microbiota shaped the ARGs and MGEs, indicating a substantial association between these factors. The primary resistance mechanisms of ARGs in crows were identified as multidrug efflux pumps, alteration of antibiotic targets, and enzymatic inactivation. High-risk ARGs which were found to potentially pose significant risks to public health were also analyzed and resulted in the identification of 81 Rank I and 47 Rank II ARGs. Overall, our study offers a comprehensive characterization of the resistome in wild Corvidae species, enhancing our understanding of the potential public health risks associated with these birds.
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Lau, Chun H., Ryan Reeves, and Edward L. Bolt. "Adaptation processes that build CRISPR immunity: creative destruction, updated." Essays in Biochemistry 63, no. 2 (June 11, 2019): 227–35. http://dx.doi.org/10.1042/ebc20180073.
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Abstract Prokaryotes can defend themselves against invading mobile genetic elements (MGEs) by acquiring immune memory against them. The memory is a DNA database located at specific chromosomal sites called CRISPRs (clustered regularly interspaced short palindromic repeats) that store fragments of MGE DNA. These are utilised to target and destroy returning MGEs, preventing re-infection. The effectiveness of CRISPR-based immune defence depends on ‘adaptation’ reactions that capture and integrate MGE DNA fragments into CRISPRs. This provides the means for immunity to be delivered against MGEs in ‘interference’ reactions. Adaptation and interference are catalysed by Cas (CRISPR-associated) proteins, aided by enzymes well known for other roles in cells. We survey the molecular biology of CRISPR adaptation, highlighting entirely new developments that may help us to understand how MGE DNA is captured. We focus on processes in Escherichia coli, punctuated with reference to other prokaryotes that illustrate how common requirements for adaptation, DNA capture and integration, can be achieved in different ways. We also comment on how CRISPR adaptation enzymes, and their antecedents, can be utilised for biotechnology.
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Weltzer, Michael L., and Daniel Wall. "Social Diversification Driven by Mobile Genetic Elements." Genes 14, no. 3 (March 4, 2023): 648. http://dx.doi.org/10.3390/genes14030648.
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Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient’s social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.
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Han, Il, and Keunje Yoo. "Metagenomic Profiles of Antibiotic Resistance Genes in Activated Sludge, Dewatered Sludge and Bioaerosols." Water 12, no. 6 (May 26, 2020): 1516. http://dx.doi.org/10.3390/w12061516.
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Wastewater treatment plants (WWTPs) have been considered hotspots for the development and dissemination of antibiotic resistance in the environment. Although researchers have reported a significant increase in bioaerosols in WWTPs, the associated bacterial taxa, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) remain relatively unknown. In this study, we have investigated the abundance and occurrences of ARGs and MGEs, as well as the bacterial community compositions in activated sludge (AS), dewatered sludge (DS) and bioaerosols (BA) in a WWTP. In total, 153 ARG subtypes belonging to 19 ARG types were identified by the broad scanning of metagenomic profiles obtained using Illumina HiSeq. The results indicated that the total occurrences and abundances of ARGs in AS and DS samples were significantly higher than those in BA samples (p < 0.05). However, some specific ARG types related to sulfonamide, tetracycline, macrolide resistance were present in relatively high abundance in BA samples. Similar to many other full-scale WWTPs, the Proteobacteria (58%) and Bacteroidetes (18%) phyla were dominant in the AS and DS samples, while the Firmicutes (25%) and Actinobacteria (20%) phyla were the most dominant in the BA samples. Although the abundance of genes related to plasmids and integrons in bioaerosols were two to five times less than those in AS and DS samples, different types of MGEs were observed in BA samples. These results suggest that comprehensive analyses of resistomes in BA are required to better understand the emergence of both ARGs and MGEs in the wastewater treatment process due to the significant increase of scientific attention toward bioaerosols effects.
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Sow, Demba. "Blind Signature Scheme Based on MGES." International Journal of Scientific Research and Engineering Trends 9, no. 5 (November 20, 2023): 1–8. http://dx.doi.org/10.61137/ijsret.vol.9.issue5.103.
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Fang, Hao, Nan Ye, Kailong Huang, Junnan Yu, and Shuai Zhang. "Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture." Water 13, no. 11 (May 23, 2021): 1461. http://dx.doi.org/10.3390/w13111461.
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Shrimp aquaculture environments are a natural reservoir of multiple antibiotic resistance genes (ARGs) due to the overuse of antibiotics. Nowadays, the prevalence of these kinds of emerging contaminants in shrimp aquaculture environments is still unclear. In this study, high-throughput sequencing techniques were used to analyze the distribution of ARGs and mobile genetic elements (MGEs), bacterial communities, and their correlations in water and sediment samples in two types of typical shrimp (Procambarus clarkii and Macrobrachium rosenbergii) freshwater aquaculture environments. A total of 318 ARG subtypes within 19 ARG types were detected in all the samples. The biodiversity and relative abundance of ARGs in sediment samples showed much higher levels compared to water samples from all ponds in the study area. Bacitracin (17.44–82.82%) and multidrug (8.57–49.70%) were dominant ARG types in P. clarkii ponds, while sulfonamide (26.33–39.59%) and bacitracin (12.75–37.11%) were dominant ARG types in M. rosenbergii ponds. Network analysis underlined the complex co-occurrence patterns between bacterial communities and ARGs. Proteobacteria, Cyanobacteria, and Actinobacteria exhibited a high abundance in all samples, in which C39 (OTU25355) and Hydrogenophaga (OTU162961) played important roles in the dissemination of and variation in ARGs based on their strong connections between ARGs and bacterial communities. Furthermore, pathogens (e.g., Aeromonadaceae (OTU195200) and Microbacteriaceae (OTU16033)), which were potential hosts for various ARGs, may accelerate the propagation of ARGs and be harmful to human health via horizontal gene transfer mediated by MGEs. Variation partitioning analysis further confirmed that MGEs were the most crucial contributor (74.76%) driving the resistome alteration. This study may help us to understand the non-ignorable correlations among ARGs, bacterial diversity, and MGEs in the shrimp freshwater aquaculture environments.
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Lee, Jung Hun, Nam-Hoon Kim, Kyung-Min Jang, Hyeonku Jin, Kyoungmin Shin, Byeong Chul Jeong, Dae-Wi Kim, and Sang Hee Lee. "Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa." International Journal of Molecular Sciences 24, no. 20 (October 15, 2023): 15209. http://dx.doi.org/10.3390/ijms242015209.
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Pseudomonas aeruginosa is the primary opportunistic human pathogen responsible for a range of acute and chronic infections; it poses a significant threat to immunocompromised patients and is the leading cause of morbidity and mortality for nosocomial infections. Its high resistance to a diverse array of antimicrobial agents presents an urgent health concern. Among the mechanisms contributing to resistance in P. aeruginosa, the horizontal acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) has gained recognition as a substantial concern in clinical settings, thus indicating that a comprehensive understanding of ARG dissemination within the species is strongly required for surveillance. Here, two approaches, including a systematic literature analysis and a genome database survey, were employed to gain insights into ARG dissemination. The genome database enabled scrutinizing of all the available sequence information and various attributes of P. aeruginosa isolates, thus providing an extensive understanding of ARG dissemination within the species. By integrating both approaches, with a primary focus on the genome database survey, mobile ARGs that were linked or correlated with MGEs, important sequence types (STs) carrying diverse ARGs, and MGEs responsible for ARG dissemination were identified as critical factors requiring strict surveillance. Although human isolates play a primary role in dissemination, the importance of animal and environmental isolates has also been suggested. In this study, 25 critical mobile ARGs, 45 critical STs, and associated MGEs involved in ARG dissemination within the species, are suggested as critical factors. Surveillance and management of these prioritized factors across the One Health sectors are essential to mitigate the emergence of multidrug-resistant (MDR) and extensively resistant (XDR) P. aeruginosa in clinical settings.
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McFarlane, S. Eryn, Jamieson C. Gorrell, David W. Coltman, Murray M. Humphries, Stan Boutin, and Andrew G. McAdam. "The nature of nurture in a wild mammal's fitness." Proceedings of the Royal Society B: Biological Sciences 282, no. 1806 (May 7, 2015): 20142422. http://dx.doi.org/10.1098/rspb.2014.2422.
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Genetic variation in fitness is required for the adaptive evolution of any trait but natural selection is thought to erode genetic variance in fitness. This paradox has motivated the search for mechanisms that might maintain a population's adaptive potential. Mothers make many contributions to the attributes of their developing offspring and these maternal effects can influence responses to natural selection if maternal effects are themselves heritable. Maternal genetic effects (MGEs) on fitness might, therefore, represent an underappreciated source of adaptive potential in wild populations. Here we used two decades of data from a pedigreed wild population of North American red squirrels to show that MGEs on offspring fitness increased the population's evolvability by over two orders of magnitude relative to expectations from direct genetic effects alone. MGEs are predicted to maintain more variation than direct genetic effects in the face of selection, but we also found evidence of maternal effect trade-offs. Mothers that raised high-fitness offspring in one environment raised low-fitness offspring in another environment. Such a fitness trade-off is expected to maintain maternal genetic variation in fitness, which provided additional capacity for adaptive evolution beyond that provided by direct genetic effects on fitness.
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Avelino, Patrick Roberto, Kênia Kiefer Parreiras de Menezes, Lucas Rodrigues Nascimento, Iza Faria-Fortini, Christina Danielle Coelho de Morais Faria, Aline Alvim Scianni, and Luci Fuscaldi Teixeira-Salmela. "Adaptação transcultural da Modified Gait Efficacy Scale para indivíduos pós-acidente vascular encefálico." Revista de Terapia Ocupacional da Universidade de São Paulo 29, no. 3 (November 30, 2018): 230–36. http://dx.doi.org/10.11606/issn.2238-6149.v29i3p230-236.
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A Modified Gait Efficacy scale (mGES) avalia a percepção do indivíduo sobre o seu nível de confiança na marcha, em circunstâncias desafiadoras. Para sua aplicação na população brasileira, é necessário que seja realizada a sua adaptação transcultural. Este estudo objetivou realizar a adaptação transcultural do mGES para uso no Brasil. O processo de adaptação seguiu diretrizes padronizadas, sendo realizado em cinco etapas: tradução, retrotradução, síntese das traduções, avaliação pelo comitê de especialistas e teste da versão pré final. A versão pré final foi aplicada em 12 indivíduos pós-Acidente Vascular Encefálico (AVE), que foram indagados sobre como interpretaram cada item. O processo de adaptação seguiu todas as recomendações propostas, sendo necessárias apenas pequenas alterações em três itens, para possibilitar melhor compreensão. Resultados satisfatórios foram obtidos no teste da versão pré final, uma vez que não houve nenhum problema quanto à redação e clareza dos itens ou ao objetivo da escala. A versão final da mGES-Brasil demonstrou satisfatório grau de equivalência semântica, conceitual e cultural, em relação à versão original, e pode, ser utilizada em contextos clínicos e de pesquisa no Brasil, para avaliar o nível de confiança na marcha de indivíduos pós-AVE.
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Zhao, Fuzheng, Bo Wang, Kailong Huang, Jinbao Yin, Xuechang Ren, Zhu Wang, and Xu-Xiang Zhang. "Correlations among Antibiotic Resistance Genes, Mobile Genetic Elements and Microbial Communities in Municipal Sewage Treatment Plants Revealed by High-Throughput Sequencing." International Journal of Environmental Research and Public Health 20, no. 4 (February 17, 2023): 3593. http://dx.doi.org/10.3390/ijerph20043593.
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Municipal sewage treatment plants (MSTPs) are environmental pools for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which is cause for growing environmental-health concerns. In this study, the effects of different wastewater treatment processes on microbial antibiotic resistance in four MSTPs were investigated. PCR, q-PCR, and molecular cloning integrally indicated that the tetracycline resistance (tet) genes significantly reduced after activated-sludge treatment. Illumina high-throughput sequencing revealed that the broad-spectrum profile of ARGs and mobile element genes (MGEs) were also greatly decreased by one order of magnitude via activated sludge treatment and were closely associated with each other. Correlations between ARGs and bacterial communities showed that potential ARB, such as Acinetobacter, Bacteroides, and Cloaibacterium, were removed by the activated-sludge process. Sedimentation processes cannot significantly affect the bacterial structure, resulting in the relative abundance of ARGs, MGEs, and ARB in second-clarifier effluent water being similar to activated sludge. A comprehensive study of ARGs associated with MGEs and bacterial structure might be technologically guided for activated sludge design and operation in the MSTPs, to purposefully control ARGs carried by pathogenic hosts and mobility.
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Qiu, Yunjing (Shirley), Julia Crilly, Peta-Anne Zimmerman, and Jamie Ranse. "The Impact of Mass Gatherings on Emergency Department Patient Presentations with Communicable Diseases Related to Syndromic Indicators: An Integrative Review." Prehospital and Disaster Medicine 35, no. 2 (February 19, 2020): 206–11. http://dx.doi.org/10.1017/s1049023x20000151.
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AbstractBackground:Mass-gathering events (MGEs) are commonly associated with a higher than average rate of morbidity. Spectators, workers, and the substantial number of MGE attendees can increase the spread of communicable diseases. During an MGE, emergency departments (EDs) play an important role in offering health care services to both residents of the local community and event attendees. Syndromic indicators (SIs) are widely used in an ED surveillance system for early detection of communicable diseases.Aim:This literature review aimed to develop an understanding of the effect of MGEs on ED patient presentations with communicable diseases and their corresponding SIs.Method:An integrative literature review methodology was used. Online databases were searched to retrieve relevant academic articles that focused on MGEs, EDs, and SIs. Inclusion/exclusion criteria were applied to screen articles. The Standard Quality Assessment Criteria for Evaluating Primary Research (QualSyst) assessment tool was used to assess the quality of included papers.Results:Eleven papers were included in this review; all discussed the impact of an MGE on patient presentations with communicable diseases at EDs/hospitals. Most included studies used the raw number of patients who presented or were admitted to EDs/hospitals to determine impact. Further, the majority of studies focused on either respiratory infections (n = 4) or gastrointestinal infections (n = 2); two articles reported on both. Eight articles mentioned SIs; however, such information was limited. The quality of evidence (using QualSyst) ranged from 50% to 90%.Conclusions:Limited research exists on the impact of MGEs on ED presentations with communicable diseases and related SIs. Recommendations for future MGE studies include assessing differences in ED presentations with communicable diseases regarding demographics, clinical characteristics, and outcomes before, during, and after the event. This would benefit health care workers and researchers by offering more comprehensive knowledge for application into practice.
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Kerkvliet, Jesse J., Alex Bossers, Jannigje G. Kers, Rodrigo Meneses, Rob Willems, and Anita C. Schürch. "Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements." PeerJ 12 (January 4, 2024): e16695. http://dx.doi.org/10.7717/peerj.16695.
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Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.
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Sato, Yu, Masashi Taniguchi, Yoshihiro Fukumoto, Shogo Okada, Zimin Wang, Kaede Nakazato, Nanami Niiya, Yosuke Yamada, Misaka Kimura, and Noriaki Ichihashi. "Age‐related change in gait efficacy and predictors of its decline: A 3‐year longitudinal study." Geriatrics & Gerontology International, December 16, 2023. http://dx.doi.org/10.1111/ggi.14767.
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AimThis study aimed to calculate the minimal clinically important difference (MCID) for a modified Gait Efficacy Scale (mGES) over 3 years and to clarify the predictors of mGES decline.MethodsIn total, 87 community‐dwelling older adults were enrolled in this 3‐year longitudinal study. The mGES, fall history and physical function (chair stand frequency, open‐eyes one‐leg stand, open–close stepping test, walking speed, walking endurance [shuttle stamina walk test] and physical activity) were assessed at baseline. After a 3‐year follow‐up period, the mGES and Global Rating of Change Scale were assessed. The MCID was calculated using anchor‐based methods, with the Global Rating of Change Scale as an anchor. The participants were classified into the decline and keep groups based on whether the changes in the mGES were greater than the MCID. A logistic regression analysis was conducted using the mGES as the dependent variable and physical characteristics, fall history, and physical function as independent variables.ResultsThe MCID for the mGES over 3 years was −7.38 points. A logistic regression analysis identified low open–close stepping (odds ratio, 0.87; 95% confidence interval, 0.782–0.985; P = 0.027) and the shuttle stamina walk test (odds ratio, 0.974; 95% confidence interval, 0.949–1.000; P = 0.049) as predictors of the mGES decline.ConclusionThese findings suggest that a change of 7.38 points in the mGES was clinically significant and that poor agility and walking endurance can predict future decline in the mGES. Geriatr Gerontol Int 2023; ••: ••–••.
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Tokuda, Maho, and Masaki Shintani. "Microbial evolution through horizontal gene transfer by mobile genetic elements." Microbial Biotechnology, January 16, 2024. http://dx.doi.org/10.1111/1751-7915.14408.
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AbstractMobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini‐review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Haudiquet, Matthieu, Jorge Moura de Sousa, Marie Touchon, and Eduardo P. C. Rocha. "Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations." Philosophical Transactions of the Royal Society B: Biological Sciences 377, no. 1861 (August 22, 2022). http://dx.doi.org/10.1098/rstb.2021.0234.
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Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell–MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
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Chen, Fangzhou, Peng Wang, Zhe Yin, Huiying Yang, Lingfei Hu, Ting Yu, Ying Jing, Jiayao Guan, Jiahong Wu, and Dongsheng Zhou. "VIM-encoding IncpSTY plasmids and chromosome-borne integrative and mobilizable elements (IMEs) and integrative and conjugative elements (ICEs) in Pseudomonas." Annals of Clinical Microbiology and Antimicrobials 21, no. 1 (March 9, 2022). http://dx.doi.org/10.1186/s12941-022-00502-w.
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Abstract Background The carbapenem-resistance genes blaVIM are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic elements (MGEs). However, there are few reports on detailed genetic dissection of blaVIM-carrying MGEs in Pseudomonas. Methods This study presented the complete sequences of five blaVIM-2/-4-carrying MGEs, including two plasmids, two chromosomal integrative and mobilizable elements (IMEs), and one chromosomal integrative and conjugative element (ICE) from five different Pseudomonas isolates. Results The two plasmids were assigned to a novel incompatibility (Inc) group IncpSTY, which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups IncpSTY-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative IncpSTY plasmids, two Tn6916-related IMEs, two Tn6918-related IMEs, and eight Tn6417-related ICEs and ten of these 15 MGEs were first time identified. At least 22 genes involving resistance to seven different categories of antibiotics and heavy metals were identified within these 15 MGEs, and most of these resistance genes were located within the accessory modules integrated as exogenous DNA regions into these MGEs. Especially, eleven of these 15 MGEs carried the blaVIM genes, which were located within 11 different concise class 1 integrons. Conclusion These blaVIM-carrying integrons were further integrated into the above plasmids, IMEs/ICEs with intercellular mobility. These MGEs could transfer between Pseudomonas isolates, which resulted in the accumulation and spread of blaVIM among Pseudomonas and thus was helpful for the bacteria to survival from the stress of antibiotics. Data presented here provided a deeper insight into the genetic diversification and evolution of VIM-encoding MGEs in Pseudomonas.
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Wang, Pengxia, Xiaofei Du, Yi Zhao, Weiquan Wang, Tongxuan Cai, Kaihao Tang, and Xiaoxue Wang. "Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria." Applied and Environmental Microbiology, March 18, 2024. http://dx.doi.org/10.1128/aem.00095-24.
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ABSTRACT Horizontal gene transfer, facilitated by mobile genetic elements (MGEs), is an adaptive evolutionary process that contributes to the evolution of bacterial populations and infectious diseases. A variety of MGEs not only can integrate into the bacterial genome but also can survive or even replicate like plasmids in the cytoplasm, thus requiring precise and complete removal for studying their strategies in benefiting host cells. Existing methods for MGE removal, such as homologous recombination-based deletion and excisionase-based methods, have limitations in effectively eliminating certain MGEs. To overcome these limitations, we developed the Cas9-NE method, which combines the CRISPR/ Cas9 system with the n atural e xcision of MGEs. In this approach, a specialized single guide RNA (sgRNA) element is designed with a 20-nucleotide region that pairs with the MGE sequence. This sgRNA is expressed from a plasmid that also carries the Cas9 gene. By utilizing the Cas9-NE method, both the integrative and circular forms of MGEs can be precisely and completely eliminated through Cas9 cleavage, generating MGE-removed cells. We have successfully applied the Cas9-NE method to remove four representative MGEs, including plasmids, prophages, and genomic islands, from Vibrio strains. This new approach not only enables various investigations on MGEs but also has significant implications for the rapid generation of strains for commercial purposes. IMPORTANCE Mobile genetic elements (MGEs) are of utmost importance for bacterial adaptation and pathogenicity, existing in various forms and multiple copies within bacterial cells. Integrated MGEs play dual roles in bacterial hosts, enhancing the fitness of the host by delivering cargo genes and potentially modifying the bacterial genome through the integration/excision process. This process can lead to alterations in promoters or coding sequences or even gene disruptions at integration sites, influencing the physiological functions of host bacteria. Here, we developed a new approach called Cas9-NE, allowing them to maintain the natural sequence changes associated with MGE excision. Cas9-NE allows the one-step removal of integrated and circular MGEs, addressing the challenge of eliminating various MGE forms efficiently. This approach simplifies MGE elimination in bacteria, expediting research on MGEs.
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Wang, Bo, Wenjie Chen, Chula Sa, Xin Gao, Su Chang, Yuquan Wei, Ji Li, et al. "Dynamics of antibiotic resistance genes and the association with bacterial community during pig manure composting with chitin and glucosamine addition." Frontiers in Microbiology 15 (May 22, 2024). http://dx.doi.org/10.3389/fmicb.2024.1384577.
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In modern ecological systems, the overuse and misuse of antibiotics have escalated the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), positioning them as emerging environmental contaminants. Notably, composting serves as a sustainable method to recycle agricultural waste into nutrient-rich fertilizer while potentially reducing ARGs and MGEs. This study conducted a 47-day composting experiment using pig manure and corn straw, supplemented with chitin and N-Acetyl-D-glucosamine, to explore the impact of these additives on the dynamics of ARGs and MGEs, and to unravel the interplay between these genetic elements and microbial communities in pig manure composting. Results showed that adding 5% chitin into composting significantly postponed thermophilic phase, yet enhanced the removal efficiency of total ARGs and MGEs by over 20% compared to the control. Additionally, the addition of N-Acetyl-D-glucosamine significantly increased the abundance of tetracycline-resistant and sulfonamide-resistant genes, as well as MGEs. High-throughput sequencing revealed that N-Acetyl-D-glucosamine enhanced bacterial α-diversity, providing diverse hosts for ARGs and MGEs. Resistance mechanisms, predominantly efflux pumps and antibiotic deactivation, played a pivotal role in shaping the resistome of composting process. Co-occurrence network analysis identified the key bacterial phyla Proteobacteria, Firmicutes, Gemmatimonadota, and Myxococcota in ARGs and MGEs transformation and dissemination. Redundancy analysis indicated that physicochemical factors, particularly the carbon-to-nitrogen ratio emerged as critical variables influencing ARGs and MGEs. The findings lay a foundation for the developing microbial regulation method to reduce the risks of ARGs in animal manure composts.
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Li, Shaoting, Shaokang Zhang, Leen Baert, Balamurugan Jagadeesan, Catherine Ngom-Bru, Taylor Griswold, Lee S. Katz, Heather A. Carleton, and Xiangyu Deng. "Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations." Applied and Environmental Microbiology 85, no. 24 (October 4, 2019). http://dx.doi.org/10.1128/aem.01985-19.
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ABSTRACT Single-nucleotide polymorphisms (SNPs) are widely used for whole-genome sequencing (WGS)-based subtyping of foodborne pathogens in outbreak and source tracking investigations. Mobile genetic elements (MGEs) are commonly present in bacterial genomes and may affect SNP subtyping results if their evolutionary history and dynamics differ from that of the bacterial chromosomes. Using Salmonella enterica as a model organism, we surveyed major categories of MGEs, including plasmids, phages, insertion sequences, integrons, and integrative and conjugative elements (ICEs), in 990 genomes representing 21 major serotypes of S. enterica. We evaluated whether plasmids and chromosomal MGEs affect SNP subtyping with 9 outbreak clusters of different serotypes found in the United States in 2018. The median total length of chromosomal MGEs accounted for 2.5% of a typical S. enterica chromosome. Of the 990 analyzed S. enterica isolates, 68.9% contained at least one assembled plasmid sequence. The median total length of assembled plasmids in these isolates was 93,671 bp. Plasmids that carry high densities of SNPs were found to substantially affect both SNP phylogenies and SNP distances among closely related isolates if they were present in the reference genome for SNP subtyping. In comparison, chromosomal MGEs were found to have limited impact on SNP subtyping. We recommend the identification of plasmid sequences in the reference genome and the exclusion of plasmid-borne SNPs from SNP subtyping analysis. IMPORTANCE Despite increasingly routine use of WGS and SNP subtyping in outbreak and source tracking investigations, whether and how MGEs affect SNP subtyping has not been thoroughly investigated. Besides chromosomal MGEs, plasmids are frequently entangled in draft genome assemblies and yet to be assessed for their impact on SNP subtyping. This study provides evidence-based guidance on the treatment of MGEs in SNP analysis for Salmonella to infer phylogenetic relationship and SNP distance between isolates.
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Weisberg, Alexandra J., and Jeff H. Chang. "Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution." Annual Review of Microbiology 77, no. 1 (July 12, 2023). http://dx.doi.org/10.1146/annurev-micro-032521-022006.
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Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Dimitriu, Tatiana. "Evolution of horizontal transmission in antimicrobial resistance plasmids." Microbiology 168, no. 7 (July 18, 2022). http://dx.doi.org/10.1099/mic.0.001214.
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Mobile genetic elements (MGEs) are one of the main vectors for the spread of antimicrobial resistance (AMR) across bacteria, due to their ability to move horizontally between bacterial lineages. Horizontal transmission of AMR can increase AMR prevalence at multiple scales, from increasing the prevalence of infections by resistant bacteria to pathogen epidemics and worldwide spread of AMR across species. Among MGEs, conjugative plasmids are the main contributors to the spread of AMR. This review discusses the selective pressures acting on MGEs and their hosts to promote or limit the horizontal transmission of MGEs, the mechanisms by which transmission rates can evolve, and their implications for limiting the spread of AMR, with a focus on AMR plasmids.
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Contarin, Rachel, Antoine Drapeau, Pauline François, Jean-Yves Madec, Marisa Haenni, and Emilie Dordet-Frisoni. "The interplay between mobilome and resistome in Staphylococcus aureus." mBio, September 17, 2024. http://dx.doi.org/10.1128/mbio.02428-24.
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ABSTRACT Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S . aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus , emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer. IMPORTANCE The research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus , a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.
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Valentin-Alvarado, Luis E., Ling-Dong Shi, Kathryn E. Appler, Alexander Crits-Christoph, Valerie De Anda, Benjamin A. Adler, Michael L. Cui, et al. "Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements." Genome Research, October 15, 2024. http://dx.doi.org/10.1101/gr.279480.124.
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Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.
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da Silva, Giarlã Cunha, Osiel Silva Gonçalves, Jéssica Nogueira Rosa, Kiara Campos França, Janine Thérèse Bossé, Mateus Ferreira Santana, Paul Richard Langford, and Denise Mara Soares Bazzolli. "Mobile Genetic Elements Drive Antimicrobial Resistance Gene Spread in Pasteurellaceae Species." Frontiers in Microbiology 12 (January 6, 2022). http://dx.doi.org/10.3389/fmicb.2021.773284.
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Mobile genetic elements (MGEs) and antimicrobial resistance (AMR) drive important ecological relationships in microbial communities and pathogen-host interaction. In this study, we investigated the resistome-associated mobilome in 345 publicly available Pasteurellaceae genomes, a large family of Gram-negative bacteria including major human and animal pathogens. We generated a comprehensive dataset of the mobilome integrated into genomes, including 10,820 insertion sequences, 2,939 prophages, and 43 integrative and conjugative elements. Also, we assessed plasmid sequences of Pasteurellaceae. Our findings greatly expand the diversity of MGEs for the family, including a description of novel elements. We discovered that MGEs are comparable and dispersed across species and that they also co-occur in genomes, contributing to the family’s ecology via gene transfer. In addition, we investigated the impact of these elements in the dissemination and shaping of AMR genes. A total of 55 different AMR genes were mapped to 721 locations in the dataset. MGEs are linked with 77.6% of AMR genes discovered, indicating their important involvement in the acquisition and transmission of such genes. This study provides an uncharted view of the Pasteurellaceae by demonstrating the global distribution of resistance genes linked with MGEs.
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Kreuze, Kim, Ville-Petri Friman, and Tommi Vatanen. "Mobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly?" Microbiome Research Reports 3, no. 4 (November 9, 2024). http://dx.doi.org/10.20517/mrr.2024.51.
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The gut microbiota is important for healthy infant development. Part of the initial colonizing microbial strains originate from the maternal gut, and undergo a selective event, termed the “colonization bottleneck”. While vertical mother-to-infant inheritance and subsequent colonization of bacteria have previously been studied, the role of mobile genetic elements (MGEs) in the infant gut microbiota assembly is unclear. In this perspective article, we discuss how horizontally and vertically transmitted phages and conjugative elements potentially have important roles in infant gut microbiota assembly and colonization through parasitic and mutualistic interactions with their bacterial hosts. While some of these MGEs are likely to be detrimental to their host survival, in other contexts, they may help bacteria colonize new niches, antagonize other bacteria, or protect themselves from other parasitic MGEs in the infant gut. As a result, the horizontal transfer of MGEs likely occurs at high rates in the infant gut, contributing to gene transfer between bacteria and affecting which bacteria can pass the colonization bottleneck. We conclude by highlighting the potential in silico , in vitro , and in vivo methodological approaches that could be employed to study the transmission and colonization dynamics of MGEs and bacteria in the infant gut.