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Academic literature on the topic 'Achromobacter spp, cystic fibrosis, genomic analysis'
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Journal articles on the topic "Achromobacter spp, cystic fibrosis, genomic analysis"
1
Bocharova, Y. A., T. A. Saviniova, A. V. Chaplin, Artem V. Lyamin, O. V. Kondratenko, S. V. Polikarpova, S. V. Zhilina, et al. "Genomic properties in Achromobacter spp. strains from cystic fibrosis patients in Russia." Clinical Microbiology and Antimicrobial Chemotherapy 23, no. 3 (2021): 220–25. http://dx.doi.org/10.36488/cmac.2021.3.220-225.
Full textAbstract:
Objective. To determine species, sequence-types, antimicrobial resistance and virulence genes in Achromobacter spp. isolates obtained from cystic fibrosis (CF) patients in Russia. Materials and Methods. Samples (sputum, nasopharyngeal swab) from 168 CF patients from 48 regions were studied. Whole-genome sequencing (WGS) was performed on MGISEQ-2000 platform. SPAdes software, Galaxy, ResFinder, Integrall, PubMLST were used for analysis of WGS data. Results. A total of 18 strains of Achromobacter spp. were isolated from 16 of 168 CF patients.Achromobacter xylosoxidans was the most prevalent and detected in 13⁄18 cases (72%). Studied Achromobacter spp. isolates belonged to 14 sequence types, including 8 new sequence types. An adaptive resistance gene carriage was a rare phenomenon (1⁄18 isolates). Conclusions. The Achromobacter spp. colonization rate of respiratory system in CF patients in Russia corresponds to the data reported in other countries. A. xylosoxidans isolates were the most prevalent (72%). Achromobacter spp. isolates from CF patients in Russia and show a high clonal diversity.
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Chan, Hiu Tat, Heng Ku, Ying Ping Low, Steven Batinovic, Mwila Kabwe, Steve Petrovski, and Joseph Tucci. "Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient." Viruses 12, no. 10 (October 8, 2020): 1138. http://dx.doi.org/10.3390/v12101138.
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Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.
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Veschetti, Laura, Angela Sandri, Cristina Patuzzo, Paola Melotti, Giovanni Malerba, and Maria M. Lleò. "Mobilome Analysis of Achromobacter spp. Isolates from Chronic and Occasional Lung Infection in Cystic Fibrosis Patients." Microorganisms 9, no. 1 (January 8, 2021): 130. http://dx.doi.org/10.3390/microorganisms9010130.
Full textAbstract:
Achromobacter spp. is an opportunistic pathogen that can cause lung infections in patients with cystic fibrosis (CF). Although a variety of mobile genetic elements (MGEs) carrying antimicrobial resistance genes have been identified in clinical isolates, little is known about the contribution of Achromobacter spp. mobilome to its pathogenicity. To provide new insights, we performed bioinformatic analyses of 54 whole genome sequences and investigated the presence of phages, insertion sequences (ISs), and integrative and conjugative elements (ICEs). Most of the detected phages were previously described in other pathogens and carried type II toxin-antitoxin systems as well as other pathogenic genes. Interestingly, the partial sequence of phage Bcep176 was found in all the analyzed Achromobacter xylosoxidans genome sequences, suggesting the integration of this phage in an ancestor strain. A wide variety of IS was also identified either inside of or in proximity to pathogenicity islands. Finally, ICEs carrying pathogenic genes were found to be widespread among our isolates and seemed to be involved in transfer events within the CF lung. These results highlight the contribution of MGEs to the pathogenicity of Achromobacter species, their potential to become antimicrobial targets, and the need for further studies to better elucidate their clinical impact.
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Veschetti, Laura, Angela Sandri, Cristina Patuzzo, Paola Melotti, Giovanni Malerba, and Maria M. Lleò. "Mobilome Analysis of Achromobacter spp. Isolates from Chronic and Occasional Lung Infection in Cystic Fibrosis Patients." Microorganisms 9, no. 1 (January 8, 2021): 130. http://dx.doi.org/10.3390/microorganisms9010130.
Full textAbstract:
Achromobacter spp. is an opportunistic pathogen that can cause lung infections in patients with cystic fibrosis (CF). Although a variety of mobile genetic elements (MGEs) carrying antimicrobial resistance genes have been identified in clinical isolates, little is known about the contribution of Achromobacter spp. mobilome to its pathogenicity. To provide new insights, we performed bioinformatic analyses of 54 whole genome sequences and investigated the presence of phages, insertion sequences (ISs), and integrative and conjugative elements (ICEs). Most of the detected phages were previously described in other pathogens and carried type II toxin-antitoxin systems as well as other pathogenic genes. Interestingly, the partial sequence of phage Bcep176 was found in all the analyzed Achromobacter xylosoxidans genome sequences, suggesting the integration of this phage in an ancestor strain. A wide variety of IS was also identified either inside of or in proximity to pathogenicity islands. Finally, ICEs carrying pathogenic genes were found to be widespread among our isolates and seemed to be involved in transfer events within the CF lung. These results highlight the contribution of MGEs to the pathogenicity of Achromobacter species, their potential to become antimicrobial targets, and the need for further studies to better elucidate their clinical impact.
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Shadrina, V. V., V. D. Sherman, and E. G. Furman. "Effect of respiratory tract infections on the costs of cystic fibrosis therapy." Voprosy praktičeskoj pediatrii 17, no. 3 (2022): 40–46. http://dx.doi.org/10.20953/1817-7646-2022-3-40-46.
Full textAbstract:
Cystic fibrosis (CF) is a severe progressive disease in which the control of respiratory infection determines the disease prognosis. Objective. To assess the impact of different respiratory tract infections on the costs of antibiotic therapy in children with CF, depending on their age. Patients and methods. Patients were divided into three groups (0–3 years, 4–10 years, and 11–18 years) for the costeffectiveness analysis; mean body weight was calculated for each group. Current regulatory documents were used to evaluate antibacterial therapy. The State Register of Medicines was used to calculate the costs of each drug. Results. We found that the highest costs were associated with inhaled antibiotics used for the eradication therapy in patients with P. aeruginosa and Achromobacter spp. infections (up to 1,152,000 RUB per year), chronic P. aeruginosa and Achromobacter spp. infections (up to 2,304,000 RUB per year), and infections caused by Burkholderia cepacia complex (up to 750,178 RUB per year). In case of intravenous antibiotics, the highest costs were associated with the treatment of infections caused by Burkholderia cepacia complex (up to 790,236 RUB per year). Conclusion. Patients with CF require regular microbiological monitoring to ensure timely detection of pathogenic microorganisms and respiratory tract infections. Early initiation of adequate antibacterial therapy in accordance with clinical guidelines is necessary to prevent chronic infections. Key words: antibacterial drugs, children, cystic fibrosis, therapy cost
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Neidhöfer, Claudio, Christina Berens, and Marijo Parčina. "An 18-Year Dataset on the Clinical Incidence and MICs to Antibiotics of Achromobacter spp. (Labeled Biochemically or by MAL-DI-TOF MS as A. xylosoxidans), Largely in Patient Groups Other than Those with CF." Antibiotics 11, no. 3 (February 25, 2022): 311. http://dx.doi.org/10.3390/antibiotics11030311.
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Achromobacter spp. are intrinsically multidrug-resistant environmental microorganisms which are known to cause opportunistic, nosocomial, and sometimes chronic infections. The existing literature yields scarcely any larger datasets, especially with regard to the incidence in patient groups other than those with cystic fibrosis. The aim of this study was to fill this gap. We present a retrospective analysis of 314 clinical and 130 screening isolates detected in our diagnostic unit between 2004 and 2021, combined with patients’ demographic and clinical information (ward type and length of hospitalization), and the results of routine diagnostic antibiotic MIC determination. We found the apparent increase in prevalence in our diagnostic unit, in which cystic fibrosis patients are an underrepresented group, in large part to be attributable to an overall increase in the number of samples and, more importantly, changes in the diagnostic setting, such as the introduction of rigorous screening for Gram-negative multidrug-resistant pathogens. We found these Achromobacter spp. to be most commonly detected in urine, stool, wounds and airway samples, and found the resistance rates to vary strongly between different sample types. Intestinal carriage is frequently not investigated, and its frequency is likely underestimated. Isolates resistant to meropenem can hardly be treated.
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Kondratieva, E. I., S. V. Trishina, A. V. Yurieva, N. V. Komlev, V. A. Tanaga, V. A. Terentiev, A. Yu Voronkova, et al. "Characteristics of mukoviscisidosis in the southern regions of Russia." Meditsinskiy sovet = Medical Council, no. 4 (April 6, 2022): 108–19. http://dx.doi.org/10.21518/2079-701x-2022-16-4-108-119.
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Introduction. Cystic fibrosis (CF) is a hereditary disease with genetic heterogeneity and clinical polymorphism. Expanding the range of knowledge about the characteristics of the course of the disease in different regions is important to achieve the goal of improving the quality and life expectancy.Purpose. Comparative analysis of the features of the course of CF in the subjects of the Southern Federal District, Stavropol Territory.Methods. Data from the National Register of Patients of the RF MV 2016 were used. Results: there are clinical and genetic features between the regions of the Southern Federal District and the Stavropol Territory of the North Caucasus Federal District and in general with the Russian Federation. Analysis of the data showed differences in indicators: the proportion of patients aged ≥ 18 is the lowest in the Republic of Crimea (14.9%), in the Rostov region the lowest average age of patients (9.0 ± 6.3), and the lowest age of diagnosis 2.2 ± 3.1 years. Late terms of diagnosis were revealed in the Stavropol Territory (4.0 ± 8.0 years), but here there is one of the highest average age of CF patients (14.1 ± 11.5), the proportion of adult patients (23.3%) and the lowest allelic frequency of F508del, which is determined by the high number of patients with a “soft” genotype. There is a high proportion of patients with an undetermined genotype. A low proportion of two identified genetic variants of the CFTR gene is registered in patients of the Republic of Crimea. A low frequency of Burkholderia cepacia complex and Achromobacter spp was revealed, and a high infection with non-tuberculous mycobacteria was revealed in the Rostov region. FEV1 in children and adults was lower in Rostov Region and Stavropol Territory. In all regions, there is a discrepancy between the seeding of flora and azithromycin therapy and the severity of the genotype with the use of pancreatic enzymes.Conclusions. Analysis of the data of the registry, which allows substantiating the need to study the regional characteristics of the course of CF in order to differentiate the planning of measures to improve the quality of medical care for patients with CF.
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Price, Erin P., Valentina Soler Arango, Timothy J. Kidd, Tamieka A. Fraser, Thuy-Khanh Nguyen, Scott C. Bell, and Derek S. Sarovich. "Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp." Microbial Genomics 6, no. 7 (July 1, 2020). http://dx.doi.org/10.1099/mgen.0.000406.
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Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans . Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans , with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non- Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.
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Okoliegbe, Ijeoma N., Karolin Hijazi, Kim Cooper, Corinne Ironside, and Ian M. Gould. "Longitudinal Surveillance and Combination Antimicrobial Susceptibility Testing of Multidrug-Resistant Achromobacter Species from Cystic Fibrosis Patients." Antimicrobial Agents and Chemotherapy 64, no. 11 (August 17, 2020). http://dx.doi.org/10.1128/aac.01467-20.
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ABSTRACT Achromobacter spp. are recognized as emerging pathogens in patients with cystic fibrosis (CF). Though recent works have established species-level identification using nrdA sequencing, there is a dearth in knowledge relating to species-level antimicrobial susceptibility patterns and antimicrobial combinations, which hampers the use of optimal antimicrobial combinations for the treatment of chronic infections. The aims of this study were to (i) identify at species-level referred Achromobacter isolates, (ii) describe species-level antimicrobial susceptibility profiles, and (iii) determine the most promising antimicrobial combination for chronic Achromobacter infections. A total of 112 multidrug-resistant (MDR) Achromobacter species isolates from 39 patients were identified using nrdA sequencing. Antimicrobial susceptibility and combination testing were carried out using the Etest method. We detected six species of Achromobacter and found that Achromobacter xylosoxidans was the most prevalent species. Interestingly, sequence analysis showed it was responsible for persistent infection (18/28 patients), followed by Achromobacter ruhlandii (2/3 patients). Piperacillin-tazobactam (70.27%) and co-trimoxazole (69.72%) were the most active antimicrobials. Differences were observed in species-level susceptibility to ceftazidime, carbapenems, ticarcillin-clavulanate, and tetracycline. Antimicrobial combinations with co-trimoxazole or tobramycin demonstrate the best synergy, while co-trimoxazole gave the best susceptibility breakpoint index values. This study enriches the understanding of MDR Achromobacter spp. epidemiology and confirms prevalence and chronic colonization of A. xylosoxidans in CF lungs. It presents in vitro data to support the efficacy of new combinations for use in the treatment of chronic Achromobacter infections.
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Garrigos, Thomas, Manon Dollat, Arnaud Magallon, Anaïs Folletet, Julien Bador, Maryam Abid, Marlène Amara, et al. "Distribution of Achromobacter Species in 12 French Cystic Fibrosis Centers in 2020 by a Retrospective MALDI-TOF MS Spectrum Analysis." Journal of Clinical Microbiology, May 5, 2022. http://dx.doi.org/10.1128/jcm.02422-21.
Full textAbstract:
Achromobacter spp. are nonfermenting Gram-negative bacilli mainly studied among cystic fibrosis (CF) patients. The identification of the 19 species within the genus is time-consuming ( nrdA -sequencing), thus data concerning the distribution of the species are limited to specific studies.
Dissertations / Theses on the topic "Achromobacter spp, cystic fibrosis, genomic analysis"
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laura, Veschetti. "Achromobacter spp. in Cystic Fibrosis Patients: A Genomic-Based Approach to Unravel Microbe-Host Adaptation." Doctoral thesis, 2022. http://hdl.handle.net/11562/1073346.
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Bacteria belonging to the genus Achromobacter are widely distributed in natural environments and have been recognized as emerging nosocomial pathogens for their contribution to a wide range of human infections. Achromobacter spp. can establish chronic infections associated with inflammation, produce biofilm, resist common disinfectants, readily acquire antibiotic resistance and outcompete resident microbiota. In particular, cystic fibrosis (CF) patients with lung disease are the most frequently colonized and infected by Achromobacter species usually developing persistent respiratory tract infections. In the last five years the number of publications regarding these pathogens has doubled in comparison to the preceding five-year period and their whole genome sequencing data availability has seen a steep increase, underlining both the growing research interest for these microorganisms as well as their emergence in the clinical setting. Nonetheless, many clinical aspects and pathogenic mechanisms still remain to be elucidated. The main focus of this thesis has been to unravel underlying key processes and to investigate the adaptive mechanisms exploited by these microorganisms during lung infection in CF patients. This has been pursued by analysing both genomic and phenotypic data of 103 Achromobacter spp. clinical isolates from 40 CF patients followed at the CF centres in Verona (Italy), Rome (Italy), and Copenhagen (Denmark). The work presented in this thesis provides new knowledge on the onset of Achromobacter spp. infections and their adaptation to the CF lung environment. With further genomic and phenotypic studies it will be possible to translate these results into the clinical setting, leading to better predictions of the infection course and improvement of treatment strategies to the benefit of CF patients.