Academic literature on the topic 'Antibiotic resistance transmission'

Antibiotic resistance represents a global health concern. Soil, water, livestock and plant foods are directly or indirectly exposed to antibiotics due to their agricultural use or contamination. This selective pressure has acted synergistically to bacterial competition in nature to breed antibiotic-resistant (AR) bacteria. Research over the past few decades has focused on the emergence of AR pathogens in food products that can cause disease outbreaks and the spread of antibiotic resistance genes (ARGs), but One Health approaches have lately expanded the focus to include commensal bacteria as ARG donors. Despite the attempts of national and international authorities of developed and developing countries to reduce the over-prescription of antibiotics to humans and the use of antibiotics as livestock growth promoters, the selective flow of antibiotic resistance transmission from the environment to the clinic (and vice-versa) is increasing. This review focuses on the mechanisms of ARG transmission and the hotspots of antibiotic contamination resulting in the subsequent emergence of ARGs. It follows the transmission of ARGs from farm to plant and animal food products and provides examples of the impact of ARG flow to clinical settings. Understudied and emerging antibiotic resistance selection determinants, such as heavy metal and biocide contamination, are also discussed here.

AbstractAntibiotic resistance is a global threat to public health. The use of antibiotics at sub-inhibitory concentrations has been recognized as an important factor in disseminating antibiotic resistance via horizontal gene transfer. Although non-antibiotic, human-targeted pharmaceuticals are widely used by society (95% of the pharmaceuticals market), the potential contribution to the spread of antibiotic resistance is not clear. Here, we report that commonly consumed, non-antibiotic pharmaceuticals, including nonsteroidal anti-inflammatories (ibuprofen, naproxen, diclofenac), a lipid-lowering drug (gemfibrozil), and a β-blocker (propranolol), at clinically and environmentally relevant concentrations, significantly accelerated the dissemination of antibiotic resistance via plasmid-borne bacterial conjugation. Various indicators were used to study the bacterial response to these drugs, including monitoring reactive oxygen species (ROS) and cell membrane permeability by flow cytometry, cell arrangement, and whole-genome RNA and protein sequencing. Enhanced conjugation correlated well with increased production of ROS and cell membrane permeability. Additionally, these non-antibiotic pharmaceuticals induced responses similar to those detected when bacteria are exposed to antibiotics, such as inducing the SOS response and enhancing efflux pumps. The findings advance understanding of the transfer of antibiotic resistance genes, emphasizing the concern that non-antibiotic, human-targeted pharmaceuticals enhance the spread of antibiotic resistance among bacterial populations.

SUMMARY Antibiotics have always been considered one of the wonder discoveries of the 20th century. This is true, but the real wonder is the rise of antibiotic resistance in hospitals, communities, and the environment concomitant with their use. The extraordinary genetic capacities of microbes have benefitted from man's overuse of antibiotics to exploit every source of resistance genes and every means of horizontal gene transmission to develop multiple mechanisms of resistance for each and every antibiotic introduced into practice clinically, agriculturally, or otherwise. This review presents the salient aspects of antibiotic resistance development over the past half-century, with the oft-restated conclusion that it is time to act. To achieve complete restitution of therapeutic applications of antibiotics, there is a need for more information on the role of environmental microbiomes in the rise of antibiotic resistance. In particular, creative approaches to the discovery of novel antibiotics and their expedited and controlled introduction to therapy are obligatory.

Antibiotic resistance has become a global health problem requiring urgent intervention. The pace of development and frequency of transmission of antimicrobial resistance have tremendously surpassed the number of antibiotics developed in the past few decades. Emergence and transmission of multidrug-resistant genes, for example, mcr-1 and mcr-5.3, against the last resort of antibiotics has challenged the treatment options. Vaccination is a promising approach with no instance of antimicrobial resistance generation or transmission reported so far. The time required for developing a vaccine, extensive pre- and post-licensure studies and the financial constraints for the R&D has hampered vaccine development over the past few decades. Vaccine can prove to be an effective future strategy for combating antimicrobial resistance.

Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes (ARGs) are found in human hosts, plants, and animals and virtually all natural environments. Their migration and transmission in different environmental media are often more harmful than antibiotics themselves. ARGs mainly move between different microorganisms through a variety of mobile genetic elements (MGEs), such as plasmids and phages. The soil environment is regarded as the most microbially active biosphere on the Earth’s surface and is closely related to human activities. With the increase in human activity, soils are becoming increasingly contaminated with antibiotics and ARGs. Soil plasmids play an important role in this process. This paper reviews the current scenario of plasmid-mediated migration and transmission of ARGs in natural environments and under different antibiotic selection pressures, summarizes the current methods of plasmid extraction and analysis, and briefly introduces the mechanism of plasmid splice transfer using the F factor as an example. However, as the global spread of drug-resistant bacteria has increased and the knowledge of MGEs improves, the contribution of soil plasmids to resistance gene transmission needs to be further investigated. The prevalence of multidrug-resistant bacteria has also made the effective prevention of the transmission of resistance genes through the plasmid-bacteria pathway a major research priority.

In this paper, we propose and study a transmission model among individuals in a hospital of antibiotic-resistant bacteria considering dysbiosis. The transmission of such bacteria in a hospital setting has been the focus of several previous researches. However, the aspect and contribution of antibioticinduced dysbiosis was not considered in the existing literature. Antibiotics impact the human intestinal microbiome for it unintentionally affects the needed gut microbiota diversity which are fundamental drivers of health and disease in humans. This unintentional destabilization of the healthy human microbiome results in microbial imbalance called dysbiosis. The goal of this paper is to analyze the dynamics of the proposed model in order to come up with insights and possible strategies to control antibiotic-resistant bacterial transmission among individuals in a hospital considering dysbiosis. Possible equilibria of the model system include the resistance-free equilibrium and the endemic equilibrium. The stability of the former means that the antibiotic resistance dies out, while the stability of the latter implies that the antibiotic resistance persists. We determined using sensitivity analysis that the most infl uential parameter is the drug 1 treatment rate. Moreover, we found a threshold value for this parameter, using numerical continuation, where the antibiotic resistance persists. These results provide insights on how to strategize to control the transmission of antibiotic-resistant bacteria in this setting.

ABSTRACTThe rapid horizontal transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. Plasmid-carrying donor strains are constructed in high-throughput. We then mix the resistance plasmid-carrying donors with recipients in a design where only transconjugants can reproduce, measure growth in dense intervals, and extract transmission times as the growth lag. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within Escherichia coli populations, by screening the Keio deletion collection in high replication. We recover all seven known chromosomal gene mutants affecting conjugation as donors and identify many novel mutants, all of which diminish antibiotic resistance transmission. We validate nine of the novel genes’ effects in liquid mating assays and complement one of the novel genes’ effect on conjugation (rseA). The new framework holds great potential for exhaustive disclosing of candidate targets for helper drugs that delay resistance development in patients and societies and improve the longevity of current and future antibiotics. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains.IMPORTANCE The rapid transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within E. coli populations. We recover all previously known and many novel chromosomal gene mutants that affect conjugation efficiency. The new framework holds great potential for rapid screening of compounds that decrease transmission. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains.

For some time now, antibiotic-resistant bacterial strains have been found in the human population, in foods, in livestock and wild animals, as well as in surface waters. The entry of antibiotics and resistant bacterial strains into the environment plays an important role in the spread of antibiotic resistance. The goal of the present study was to monitor the entry of antibiotic resistances into the environment through the contamination of wastewater. To assess the extent of transmission of antibiotic resistances from human sources into the environment, the resistance patterns of Escherichia coli strains isolated from human patients have been compared to those found in strains isolated from sewage sludge. Our results may indicate if resistances to particular antibiotics are more prone than others to spread into the environment. To monitor the increase of specific resistances over time, samples taken in the years 2000 and 2009 were analysed. Our study shows that for some antibiotics a parallel development of resistance patterns has taken place in both patient and environmental samples over time. For other sets of antibiotics, independent developments have occurred in the samples. A clear increase of multi-resistant E. coli strains over time was observed in samples from both sources.

The evolution of antibiotic resistance in opportunistic pathogens such as Streptococcus pneumoniae , Escherichia coli or Staphylococcus aureus is a major public health problem, as infection with resistant strains leads to prolonged hospital stay and increased risk of death. Here, we develop a new model of the evolution of antibiotic resistance in a commensal bacterial population adapting to a heterogeneous host population composed of untreated and treated hosts, and structured in different host classes with different antibiotic use. Examples of host classes include age groups and geographic locations. Explicitly modelling the antibiotic treatment reveals that the emergence of a resistant strain is favoured by more frequent but shorter antibiotic courses, and by higher transmission rates. In addition, in a structured host population, localized transmission in host classes promotes both local adaptation of the bacterial population and the global maintenance of coexistence between sensitive and resistant strains. When transmission rates are heterogeneous across host classes, resistant strains evolve more readily in core groups of transmission. These findings have implications for the better management of antibiotic resistance: reducing the rate at which individuals receive antibiotics is more effective to reduce resistance than reducing the duration of treatment. Reducing the rate of treatment in a targeted class of the host population allows greater reduction in resistance, but determining which class to target is difficult in practice.

Antibiotic resistance is a growing threat to human health and is defined by the World Health Organization as a crisis that must be managed with the utmost urgency. Antibiotic resistant bacteria increase both mortality and morbidity and have a great impact on the global economy. Resistance is not confined to human health care, but is present also among animals and in our environment at large. Indeed, resistant bacterial strains have now been found in virtually all parts of the world, even in locations without direct human contact. The human gastrointestinal tract is populated by a complex, dynamic, diverse and highly interactive collection of microorganisms, including bacteria, archaea, fungi, yeasts and viruses, which constitutes our gastrointestinal microbiota. This microbiota is an important reservoir of resistance genes (our gastrointestinal resistome) and a “melting pot” for transfer of resistance genes between microbes, including potential pathogens. In this thesis I investigated the prevalences of two clinically important kinds of antibiotic resistance: extended-spectrum β-lactamases (ESBL) and vancomycin-resistant enterococci (VRE), as well as asymptomatic carriage of potential enteropathogens among healthy preschool children in Uppsala. Fecal samples from unidentified, individual diapers were collected in 2010 (125+313 samples) and in 2016 (334 samples). In addition, 204 environmental samples from the children’s preschools were collected in autumn 2016. A prevalence of 2.9% ESBL-producing Enterobactericeae was demonstrated in the first samples from 2010. No VRE were found and the occurrence of enteropathogens were reassuringly low. Results on ESBL prevalence in 2016 and transmission of resistance between children will be presented when the manuscript is published and at the dissertation.

Anthropozoonotic diseases, defined as infectious diseases caused by pathogens transmitted from humans to wildlife, pose a significant health threat to wildlife populations. Many of these pathogens are also able to move from wildlife reservoirs to humans, termed zoonotic diseases, creating the possibility for bi-directional transmission between humans and wildlife. Recent studies show that a significant proportion of emerging infectious diseases in humans originate in wildlife reservoirs and that the frequency of emergence is increasing, yet the specific transmission pathways still remain speculative in most cases. Human fecal waste is persistent across human-modified landscapes and has been identified as a potential source of disease exposure for wildlife populations living near humans. As part of a long-term study of banded mongoose (Mungos mungo) that live in close association with humans and human fecal waste I used Escherichia coli and banded mongoose (Mungos mungo) for evaluating exchange of fecal waste-borne microorganisms at the human-wildlife interface. Antibiotic resistance was found in 57.5% ° 10.3% (n=87) of mongoose fecal samples and 37.2% ° 5.9% of isolates (n=253). Multidrug resistance was detected in 13.8% ° 4.2% of isolates (n=253). Mongoose and human fecal waste isolates consistently clustered together in phylogenetic analyses and statistical analysis of genetic variation showed no significant differences (p=0.18) between E. coli from human and mongoose populations. These results suggest that human fecal waste contamination is an important mechanism for the transmission of pathogens to both humans and animals, including the spread of antibiotic resistance in the environment, an emerging global health threat.
Master of Science

Whole genome sequencing (WGS) has transformed molecular infectious diseases epidemiology in the last five years, and represents a high resolution means by which to catalogue the genetic content and variation in bacterial pathogens. This thesis utilises WGS to enhance our understanding of antimicrobial resistance in two clinically important members of the Enterobacteriaceae family of bacteria, namely Escherichia coli and Klebsiella pneumoniae. These organisms cause a range of clinical infections globally, and are increasing in incidence. The rapid emergence of multi-drug resistance in association with infections caused by them represents a major threat to the effective management of a range of clinical conditions. The reliability of sequencing and bioinformatic methods in the analysis of E. coli and K. pneumoniae sequence data is assessed in chapter 4, and provides a context for the subsequent study chapters, investigating resistance genotype prediction, outbreak epidemiology in two different contexts, and population structure of an important global drug-resistant E. coli lineage, ST131 (5-8). In these, the advantages (and limitations) of short-read, high-throughput, WGS in defining resistance gene content, associated mobile genetic elements and host bacterial strains, and the relationships between them, are discussed. The overarching conclusion is that the dynamic between all the components of the genetic hierarchy involved in the transmission of important antimicrobial resistance elements is extremely complicated, and encompasses almost every imaginable scenario. Complete/near-complete assessment of the genetic content of both chromosomal and episomal components will be a prerequisite to understanding the evolution and spread of antimicrobial resistance in these organisms.

[eng] Chronic respiratory infection (CRI) by Pseudomonas aeruginosa is the main cause of morbidity and mortality in cystic fibrosis (CF). During the progression from early infection to chronic non-eradicable colonization P. aeruginosa undergoes a complex evolutionary adaptation and diversification process which eventually leads to a mixed and persistent infecting population in which multidrug resistant variants frequently rise compromising the selection of appropriate antibiotic therapies. In this work the interplay between three key microbiological aspects of these infections was investigated: the occurrence of transmissible and persistent strains, the emergence of variants with enhanced mutation rates (mutators) and the evolution of resistance to antibiotics. Clonal epidemiology, antibiotic susceptibility profiles, contribution of P. aeruginosa classical resistance mechanisms and the role of mutator variants were investigated in two large collections of CF P. aeruginosa isolates from the Balearic Islands and Spain. As well, whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, within-host evolution, WGS mutator genotypes (mutome) and resistome of widespread P. aeruginosa clonal complex 274 (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. Finally, due to the Chronic respiratory infection (CRI) by Pseudomonas aeruginosa is the main cause of morbidity and mortality in cystic fibrosis (CF). During the progression from early infection to chronic non-eradicable colonization P. aeruginosa undergoes a complex evolutionary adaptation and diversification process which eventually leads to a mixed and persistent infecting population in which multidrug resistant variants frequently rise compromising the selection of appropriate antibiotic therapies. In this work the interplay between three key microbiological aspects of these infections was investigated: the occurrence of transmissible and persistent strains, the emergence of variants with enhanced mutation rates (mutators) and the evolution of resistance to antibiotics. Clonal epidemiology, antibiotic susceptibility profiles, contribution of P. aeruginosa classical resistance mechanisms and the role of mutator variants were investigated in two large collections of CF P. aeruginosa isolates from the Balearic Islands and Spain. As well, whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, within-host evolution, WGS mutator genotypes (mutome) and resistome of widespread P. aeruginosa clonal complex 274 (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. Finally, due to the relevance of aminoglycosides in the management of CF-CRI, the dynamics of P. aeruginosa resistance development to aminoglycosides was also studied in vitro by WGS approaches. Despite discrepancies between molecular genotyping methods, a high degree of genetic diversity was documented among CF isolates from the Balearic Islands and Spain with scarce representation of CF epidemic strains. However, for the first time in Spain, we documented a superinfection with the multidrug resistant Liverpool Epidemic Strain (LES) in a chronically colonized patient. As well, P. aeruginosa CC274, previously detected in several CF individuals from Austria, Australia and France, was detected in 5 unrelated chronically colonized patients from the Balearic Islands and, therefore, this clone-type should be added to the growing list of CF epidemic clones. Subsequent analysis of the whole genomes sequences of P. aeruginosa isolates from the CC274 P. aeruginosa collection provides evidence of interpatient dissemination of mutator sublineages and denotes their potential for unexpected short-term sequence type (ST) evolution and antibiotic resistance spread, illustrating the complexity of P. aeruginosa population biology in CF. As well, epidemiological studies demonstrated the coexistence of two divergent lineages but without evident geographical barrier. Antibiotic resistance significantly accumulated overtime accompanied by hypersusceptibility to certain antibiotics such as aztreonam, which can be explained in terms of collateral susceptibility. Correlation between phenotypes and WGS genotypes of clonal isolates from the CC274 collection allowed us to define the mutational resistome of CF P. aeruginosa which extends beyond the classical mutational resistance mechanisms. Among the new chromosomic resistance determinants encountered, mutations within the penicillin-binding-protein 3 (PBP3), shaping up beta-lactam resistance, are noteworthy as well as mutations within the fusA1 gene, coding for elongation factor G, which along with MexXY overexpresion contribute to high-level aminoglycoside resistance. Strikingly, we encountered that MexXY overexpression is dispensable for in vitro resistance development to aminoglycosides which suggests an evolutionary advantage of its overexpression in the CF respiratory tract. Altogether this work demonstrates that clonal epidemiology and antibiotic resistance evolution in the CF setting results from the complex interplay among mutation-driven resistance mechanisms, within host diversification and interpatient transmission of epidemic strains.
[spa] La infección respiratoria crónica por P. aeruginosa es la principal causa de morbilidad y mortalidad en pacientes con fibrosis quística (FQ). Durante la progresión desde la infección temprana a la colonización crónica, P. aeruginosa experimenta un complejo proceso adaptativo y de diversificación que resulta en una población heterogénea y persistente en la que la aparición de resistencias a los antibióticos comprometen la selección de terapias apropiadas. En este trabajo se investigó la interacción entre tres aspectos microbiológicos clave de estas infecciones: la presencia de cepas transmisibles y persistentes, la aparición de variantes con tasas de mutación incrementadas y la evolución de la resistencia a los antibióticos. La epidemiología clonal, los perfiles de sensibilidad antibiótica, la contribución de los mecanismos clásicos de resistencia de P. aeruginosa y el papel de las variantes hipermutadoras se estudiaron en dos grandes colecciones de aislados procedentes de pacientes con fibrosis quística de las Islas Baleares y España. Asimismo, mediante secuenciación de genoma completo, se determinó la filogenia, diseminación interpaciente, evolución intrapaciente, genotipo hipermutador y resistoma de una colección de aislados clonales pertenecientes al complejo clonal 274 (CC274), proviniendo dichos aislados de dos países muy distantes, Australia y España, y cubriendo un período de 18 años. Finalmente, dada la relevancia de los aminoglucósidos en el manejo de estos pacientes, se estudió la dinámica del desarrollo de resistencia a aminoglucósidos in vitro mediante secuenciación de genoma completo. A pesar de encontrarse discrepancias entre los métodos de genotipado molecular, se documentó un alto grado de diversidad genética en las colecciones de las Islas Baleares y España, siendo escasa la representación de cepas epidémicas. No obstante, por primera vez en España, se documentó un caso de sobreinfección con el clon epidémico multirresistente de Liverpool. Además, en 5 pacientes de Baleares, crónicamente colonizados y sin aparente relación epidemiológica, se detectó el CC274. Puesto que este complejo clonal también ha sido detectado en pacientes de países como Austria, Australia y Francia, éste debería incluirse en la creciente lista de cepas epidémicas. El análisis posterior de las secuencias de genoma completo de los aislados del CC274 evidenció la diseminación interpaciente de un sublinaje hipermutador, denotando además el potencial de estas variantes para la inesperada evolución a corto plazo del secuenciotipo y la rápida diseminación de resistencias. Además, los estudios epidemiológicos demostraron la coexistencia de dos linajes divergentes, no evidenciándose barrera geográfica. Asimismo se documentó una tendencia generalizada a la acumulación de resistencias a los antibióticos en el tiempo, acompañada de hipersensibilidad a ciertos antibióticos como aztreonam, lo cual se puede explicar en términos de sensibilidad colateral. La correlación entre los fenotipos y genotipos determinados mediante secuenciación del genoma completo de los aislados pertenecientes al CC274 nos permitió definir el resistoma mutacional de P. aeruginosa en la FQ, el cual se extiende más allá de los mecanismos mutacionales clásicos. Entre los nuevos determinantes de resistencia cromosómica encontrados caben destacar tanto las mutaciones en la proteína fijadora de penicilina PBP3, que confieren resistencia a betalactámicos, como las mutaciones en fusA1, que codifica para el factor de elongación G, y que junto con la hiperexpresión de MexXY contribuyen a la resistencia de alto nivel a aminoglucósidos. Paradójicamente, encontramos que la hiperexpresión de MexXY es prescindible para el desarrollo de resistencia in vitro a aminoglucósidos, lo que sugiere que dicha hiperexpresión confiere una ventaja evolutiva in vivo. En conjunto, este trabajo demuestra que, en la FQ, la epidemiología clonal y la evolución de la resistencia a los antibióticos son el resultado de una compleja interacción entre los mecanismos de resistencia mutacionales, la diversificación de la población infectante y la transmisión interpaciente de cepas epidémicas.
[cat] La infecció respiratòria crònica per P. aeruginosa és la principal causa de morbiditat i mortalitat en els pacients amb fibrosi quística (FQ). Durant la progressió des de la infecció primerenca a la colonització crònica, P. aeruginosa experimenta un complexe procés adaptatiu i de diversificació que resulta en una població heterogènia i persistent en la qual l'aparició de variants resistents a múltiples antibiòtics comprometen la selecció de teràpies antibiòtiques apropiades. En aquest treball es va investigar la interacció entre tres aspectes microbiològics clau: la presència de soques transmissibles i persistents, l'aparició de variants amb taxes de mutació incrementades i l'evolució de la resistència als antibiòtics. L'epidemiologia clonal, els perfils de sensibilitat antibiòtica, la contribució dels mecanismes clàssics de resistència i el paper de les variants hipermutadores es van estudiar en dos grans col·leccions d'aïllats procedents de pacients amb FQ de les Illes Balears i Espanya. Així mateix, mitjançant seqüenciació del genoma complet, es va determinar la filogènia, disseminació interpacient, evolució intrapacient, genotip hipermutador i resistoma d'una col·lecció d'aïllats pertanyents al complexe clonal 274 (CC274), provenint de dos països molt distants, Austràlia i Espanya, i cobrint un període de 18 anys. Finalment, donada la rellevància dels aminoglicòsids en el maneig d’aquests pacients, es va estudiar la dinàmica del desenvolupament de resistència a aminoglicòsids in vitro mitjançant seqüenciació de genoma complet. Tot i trobar discrepàncies entre els mètodes de genotipat molecular, es va documentar un alt grau de diversitat genètica en les col·leccions de les Illes Balears i Espanya, sent escassa la representació de soques epidèmiques. No obstant això, per primera vegada a Espanya, es va documentar un cas de sobreinfecció amb el clon epidèmic multiresistent de Liverpool. A més, en 5 pacients de les Illes Balears, crònicament colonitzats i sense aparent relació epidemiològica, es va detectar el CC274. Ja que aquest complexe clonal també ha estat detectat en països com Àustria, Austràlia i França, aquest clon hauria d'incloure a la creixent llista de soques epidèmiques. L'anàlisi posterior de les seqüències de genoma complet dels aïllats pertanyents al CC274, va evidenciar la disseminació interpaciente d'un subllinatge hipermutador, denotant a més el potencial d'aquestes variants per a la inesperada evolució a curt termini del sequenciotip i per a la ràpida disseminació de la resistència antibiòtica. A més, els estudis epidemiològics van demostrar la coexistència de dos llinatges divergents, no existint barrera geogràfica. Així mateix es va evidenciar una tendència generalitzada a l'acumulació de resistències en el temps, acompanyada d'hipersensibilitat a certs antibiòtics com l’aztreonam, la qual cosa es pot explicar en termes de sensibilitat col·lateral. La correlació entre els fenotips i genotips determinats mitjançant seqüenciació del genoma complet dels aïllats pertanyents al CC274 ens va permetre definir el resistoma mutacional de P. aeruginosa en la FQ, el qual s'estén més enllà dels mecanismes de resistència mutacionals clàssics. Entre els nous determinants de resistència cromosòmica trobats cal destacar tant les mutacions en la proteïna fixadora de penicil·lina PBP3, que confereixen resistència a betalactàmics, així com les mutacions en fusA1, que codifica per al factor d'elongació G, i que juntament amb la hiperexpressió de MexXY contribueixen a la resistència d'alt nivell a aminoglucòsids. Paradoxalment, vam trobar a més que la hiperexpressió de MexXY és prescindible per al desenvolupament de resistència in vitro a aminoglucòsids, el que suggereix que aquesta hiperexpressió suposa un avantatge evolutiu in vivo. En conjunt, aquest treball demostra que l'epidemiologia clonal i l'evolució de la resistència als antibiòtics en el context de la FQ són el resultat d'una complexa interacció entre els mecanismes de resistència mutacionals, la diversificació de la població infectant i la transmissió interpaciente de ceps epidèmiques.

L’émergence et la dissémination des bactéries résistantes aux antibiotiques sont préoccupantes. L’infection causée par les bactéries multi-résistantes (BMR) aggrave le pronostic des malades infectés et augmente les dépenses liées à leur prise en charge. Parmi les BMR, les bactéries à Gram négatif (BGN), plus particulièrement les entérobactéries productrices de béta-lactamase à spectre étendu (E-BLSE) sont les plus fréquemment isolées. La résistance aux antibiotiques pourrait avoir un impact sur la morbidité et la mortalité dans les pays à revenu faible ou intermédiaire (PRFI) en raison du potentiel d’émergence et de diffusion de bactéries résistantes aux antibiotiques, et du fardeau des infections bactériennes dans ces pays. Cependant, les données sur la résistance bactérienne sont rares et très majoritairement hospitalières dans les PRFI. De plus, dans ces pays, les infections bactériennes néonatales sévères (septicémies, pneumonies et méningites) représentent encore les principales causes de décès chez les nouveau-nés. Les entérobactéries sont majoritairement responsables de ces infections néonatales. Ainsi, investiguer la transmission d'E-BLSE chez le nouveau-né permettrait de proposer des stratégies de prévention. Ce travail de recherche s’est appuyé sur le programme BIRDY (Bacterial Infections and antibiotic Resistant Diseases among Young children in low-income countries). Le premier objectif était d’estimer la prévalence de la colonisation par des E-BLSE chez les femmes enceintes à Madagascar ainsi que les facteurs favorisant cette colonisation. Les résultats ont montré une prévalence globale de colonisation de 18.5% [IC à 95% 14.5-22.6]. Des facteurs reflétant un niveau socioéconomique plus élevé comme l’accès privatif à l’eau de boisson et avoir une maison individuelle sont associés à la colonisation. Le second objectif de ce travail était d'étudier l'incidence de la première colonisation par des E-BLSE chez les nouveau-nés en milieu communautaire et d'identifier les facteurs de risque d'acquisition. Les résultats révèlent une incidence globale d'acquisitions d'E-BLSE de 10.4 pour 1000 nouveau-nés-jours [IC à 95% : 8.0; 13.4]. Par ailleurs, nous avons mis en évidence que le faible poids à la naissance HR ajusté 2.7 [IC à 95% 1.2 ; 5.9], l'accouchement par césarienne HR ajusté 3.4 [IC à 95% 1.7 ; 7.1], la prise maternelle d'antibiotique à l'accouchement HR ajusté 2.2 [IC à 95% 1.1 ; 4.5] étaient des facteurs de risque d'acquisition d'E-BLSE. Le troisième objectif était de documenter les infections néonatales. Nous avons trouvé une incidence d'infections néonatales de 30.6 cas pour 1000 naissances vivantes [IC à 95%: 23.4 ; 40.1].Nos résultats montrent que les mesures de santé publique devraient axer sur l’amélioration de la prise en charge de la grossesse et sur le diagnostic précoce des infections néonatales
The emergence and spread of antibiotic-resistant bacteria is a concern. Infection caused by multidrug-resistant bacteria (MDR) worsens the prognosis of infected patients and increases the costs associated with their management. Among the MDRs, Gram-negative bacteria (GNB), especially extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) are the most frequently isolated. Antibiotic resistance may have an impact on morbidity and mortality in low- and middle-income countries (LMICs) because of the potential for emergence and spread of antibiotic-resistant bacteria, and the burden of bacterial infections in these countries. However, data on bacterial resistance are scarce or came from the hospital, for the great majority, in LMICs. In these settings, severe neonatal bacterial infections (sepsis, pneumoniae and meningitis) still represent the leading causes of death in newborns. Enterobacteriaceaeare responsible for a great part of these neonatal infections. Thus, investigating the transmission of ESBL-PE in newborns would make it possible to propose prevention strategies. This work was based on the BIRDY program (Bacterial Infections and Antibiotic Resistant Diseases among Young Children in Low-Income Countries). The first objective was to estimate the prevalence of colonization by ESBL-PE in pregnant women in Madagascar as well as the risk factors of this colonization. The results showed an overall colonization prevalence of 18.5% [95% CI 14.5-22.6]. Factors reflecting a higher socioeconomic level such as private access to drinking water and having a house are associated with colonization. The second objective of this work was to study the incidence of ESBL-PE colonization in community-based infants and to identify acquisition risk factors. The results reveal an overall incidence of ESBL-PE acquisition of 10.4 per 1000 newborn-days [95% CI: 8.0; 13.4]. In addition, we found that low birth weight adjusted HR 2.7 [95% CI 1.2; 5.9], cesarean section delivery adjusted HR 3.4 [95% CI 1.7; 7.1], maternal intake of antibiotic at delivery adjusted HR 2.2 [95% CI 1.1; 4.5] were risk factors for the acquisition of ESBL-PE. The third objective was to document neonatal infections. We found an incidence of neonatal infections of 30.6 cases per 1000 live births [95% CI: 23.4; 40.1]. Our results suggest that public health measures should focus on the improvement of pregnancy follow-up and early diagnosis of neonatal infections

Comprendre l'émergence et la propagation des maladies infectieuses chez les animaux sauvages est devenue une priorité en santé publique et en conservation. En combinant la collecte de données et le développement de modèles épidémiologiques, cette thèse s'est focalisée sur la compréhension de deux phénomènes clés: (i) étudier comment l'hétérogénéité au niveau des individus, des groupes, de la population et de l'environnement influence la propagation de parasites et (ii) quantifier la transmission de bactéries résistantes aux antibiotiques depuis l'homme vers les animaux sauvages dans trois aires protégées d'Afrique (Tsaobis NP- Namibie, Lopé NP-Gabon et Dzanga-Ndoki NP- République Centrafricaine). Les principaux résultats de ce travail montrent que : (1) De multiples facteurs incluant la température, la pluie, l'utilisation du territoire, le genre, l'âge et la condition physique influencent la richesse spécifique de parasites gastro-intestinaux chez le babouin chacma, (2) Les contacts entre animaux autour des points d'attractions de l'habitat peuvent influencer de manière importante la propagation spatio-temporelle d'une maladie, (3) La transmission d'entérobactéries résistantes semble avoir lieu depuis les humains ou le bétail vers les animaux sauvages dans des zones où le contact entre ces populations est élevé, (4) Le gradient de densité de gorilles produit par la chasse peut générer une augmentation de prévalence d'un parasite avec la distance au point d'introduction. Les conclusions de ce travail ouvrent de nouvelles possibilités pour l'étude des maladies émergentes chez les animaux sauvages
Understanding the emergence and spread of infectious disease in wild animal populations has become an important priority for both public health and animal conservation. Combining the collection of empirical data with the development of epidemiological models, this thesis focuses on understanding two key issues of wildlife epidemiology: (i) how heterogeneity at the individual, group, population and landscape level affects parasite spread (ii) investigating whether transmission of antibiotic resistant bacteria from humans to wildlife is occurring within three protected areas of Africa (Tsaobis NP-Namibia, Lope NP-Gabon and Dzanga-Ndoki NP-Central African Republic). The main findings of this work indicated that: (1) multiple-scale factors including temperature, rainfall, home range use, sex, age and body condition influence gastro-intestinal parasite richness among wild baboons; (2) animal contacts around ‘habitat hotspots' can substantially influence the spatio-temporal dynamics of a disease; (3) antibiotic resistant enterobacteria seem to be spreading from humans/livestock to wildlife when the territory overlap between these two populations is expected to be high; (4) gradients in gorilla density created by bushmeat hunting can reverse the expected pattern of decreasing parasite prevalence with distance to human-spillover. The conclusions of this work open new possibilities for studying the mechanisms explaining the spread of emerging infectious diseases among wild animals

The two objectives of ensuring early appropriate antimicrobial treatment for septic patients on the intensive care unit (ICU), and limiting emergence and spread of antimicrobial resistance are both complicated and potentially conflicting. Increasingly unpredictable resistance, particularly amongst Gram-negative bacteria, through both local selection and transmission, and importation of globally successful resistant clones encourages the use of broad-spectrum empiric antimicrobials for septic patients, including in combination. This may lead to a vicious cycle whereby increasing antibiotic use increases resistance, which in turn leads to higher levels of inappropriate therapy. In response, the multi-disciplinary ICU-team implements infection prevention and control, and antimicrobial stewardship programmes. Antimicrobial stewardship programmes provide interventions and guidance to optimize appropriate therapy,whilelimiting unnecessary use through a variety of measures. The development of rapid molecular testing for bacterial identification and antimicrobial susceptibility prediction could potentially bring useful microbiological information to the bedside at the time of therapeutic decision making.

Tularemia, caused by the gram-negative coccobacillus Francisella tularensis, is an extremely infectious bacterial zoonosis. Symptoms depend on site of exposure; they can be nonspecific and may include fever, lymphadenopathy, ulcer or papule, and nausea/vomiting. Natural transmission occurs via small mammals, such as rabbits, or arthropod bites. IV or IM antibiotics are preferred over oral forms. Supportive care is also critical; some patients may require respiratory support. If used as a biological weapon, aerosolized F. tularensis would be the most likely route of transmission. Clinical symptoms would include those of pneumonic tularemia. In the event of a bioterrorist attack, oral administration antibiotics can be used, as the health care system may not be able to accommodate intravenous or intramuscular treatment. Antibiotic resistance should also be considered if patients deteriorate despite use of recommended antibiotics.

The Manual of Infection Prevention and Control provides practical guidance on all aspects of healthcare-associated infections (HAIs). It outlines the basic concepts of infection prevention and control (IPC), modes of transmission, surveillance, control of outbreaks, epidemiology, and biostatistics. The book provides up-to-date advice on the triage and isolation of patients and on new and emerging infectious diseases, and with the use of illustrations, it provides a step-by-step approach on how to perform hand hygiene and how to don and take off personal protective equipment correctly. In addition, this section also outlines how to minimize cross-infection by healthcare building design and prevent the transmission of various infectious diseases from infected patients after death. The disinfection and sterilization section reviews how to risk assess, disinfect and/or sterilize medical items and equipment, antimicrobial activities, and the use of various chemical disinfectants and antiseptics, and how to decontaminate endoscopes. The section on the prevention of HAIs reviews and updates IPC guidance on the prevention of the most common HAIs, i.e. surgical site infections, infections associated with intravascular and urinary catheters, and hospital- and ventilator-acquired pneumonias. In view of the global emergence of antimicrobial resistance to the various pathogens, the book examines and provides practical advice on how to implement an antibiotic stewardship programme and prevent cross-infection against various multi-drug resistant pathogens. Amongst other pathogens, the book also reviews IPC precautions against various haemorrhagic and bloodborne viral infections. The section on support services discusses the protection of healthcare workers, kitchen, environmental cleaning, catering, laundry services, and clinical waste disposal services.

Abstract Nussbaum’s capability theory by drawing attention to multiple determinants of wellbeing provides a rich and relevant evaluative space for framing antibiotic resistance. I consider the implications of antibiotic resistance for child development and adult capabilities. There are common risk factors for childhood growth stunting and the spread of infectious diseases in both antibiotic sensitive and resistant forms. The interaction between infectious diseases, antibiotic resistance and growth stunting illustrates a clustering of disadvantage. The control of antibiotic resistance requires wide-ranging cooperative action. Cooperation is predicated on an expectation of equitable access to effective antibiotics. This expectation is confounded by inequality both in access to antibiotics, and in the risk that available antibiotics will be ineffective. Securing child development (and adult capabilities) requires that inequalities both in access to antibiotics and in risk factors for the dissemination and transmission of antibiotic resistance are addressed. Inequality undermines the cooperative activity that is control of infectious diseases and compounds the threat to the securing of capabilities that arises from antibiotic resistance.

Abstract In this chapter we review the development of hospital infection prevention and control (IPC) since the nineteenth century and its increasingly important role in reducing the spread of antibiotic resistance (ABR). Excessive rates of hospital-acquired infection (HAI) fell dramatically, towards the end of the nineteenth century, because of improved hygiene and surgical antisepsis, but treatment remained rudimentary until effective antibiotics became widely available in the mid-twentieth century. While antibiotics had profound clinical benefits, their widespread appropriate and inappropriate use in humans and animals inevitably led to the emergence of antibiotic resistance (ABR). Within 50 years, this could no longer be offset by a reliable supply of new drugs, which slowed to a trickle in the 1980s. In hospitals, particularly, high rates of (often unnecessary) antibiotic use and ABR are exacerbated by person-to-person transmission of multi-drug resistant organisms (MDRO), which have, so far, largely resisted the introduction of antimicrobial stewardship (AMS) programs and repeated campaigns to improve infection prevention and control (IPC). Despite clear evidence of efficacy in research settings, both AMS and IPC programs are often ineffective, in practice, because of, inter alia, insufficient resourcing, poor implementation, lack of ongoing evaluation and failure to consult frontline staff. In this chapter we review reasons for the relatively low priority given to preventive programs despite the ethical obligation of healthcare organisations to protect current and future patients from preventable harm. The imminent threat of untreatable infections may provide an impetus for a shared organisational and professional commitment to promoting the cultural and behavioural changes needed to successfully reduce the burdens of ABR and drug-resistant HAIs.

Abstract Drug-resistant bacterial infections constitute a major threat to global public health. Several key bacteria that are becoming increasingly resistant are among those that are ubiquitously carried by human beings and usually cause no symptoms (i.e. individuals are asymptomatic carriers) until a precipitating event leads to symptomatic infection (and thus disease). Carriers of drug-resistant bacteria can also transmit resistant pathogens to others, thus putting the latter at risk of infections that may be difficult or impossible to treat with currently available antibiotics. Accumulating evidence suggests that such transmission occurs not only in hospital settings but also in the general community, although much more data are needed to assess the extent of this problem. Asymptomatic carriage of drug-resistant bacteria raises important ethical questions regarding the appropriate public health response, including the degree to which it would be justified to impose burdens and costs on asymptomatic carriers (and others) in order to prevent transmission. In this paper, we (i) summarize current evidence regarding the carriage of key drug-resistant bacteria, noting important knowledge gaps and (ii) explore the implications of existing public health ethics frameworks for decision- and policy-making regarding asymptomatic carriers. Inter alia, we argue that the relative burdens imposed by public health measures on healthy carriers (as opposed to sick individuals) warrant careful consideration and should be proportionate to the expected public health benefits in terms of risks averted. We conclude that more surveillance and research regarding community transmission (and the effectiveness of available interventions) will be needed in order to clarify relevant risks and design proportionate policies, although extensive community surveillance itself would also require careful ethical consideration.

Objectives: This study aims to characterize at the molecular level the genes encoding resistance in Salmonella and explain the molecular mechanisms underlying resistance to ceftriaxone, cefepime, amoxicillin-clavulanate, tetracycline, trimethoprim-sulfamethoxazole, chloramphenicol, colistin and azithromycin in Salmonella. It aims as well to characterize the 16S rRNA gene region by restriction fragment length polymorphism (RFLP) to investigate if this region constitutes an appropriate ‘coincidental’ marker to distinguish important pathogenic Salmonella species. Finally, determine the lineages of Salmonella species and evolutionary relationships among bacteria classified within the same genus. Methodology: 246 Salmonella isolates were collected from children under 16 years old during Jan. 2018 - Dec 2019, presented with gastroenteritis at Hamad Medical Corporation. Isolates were tested for antibiotic susceptibility against nineteen relevant antibiotics using E-test. Isolates that harbor antibiotic resistance were confirmed using PCR specific primers for 38 genes. In addition, the variable region of class 1 and 2 integrons were identified by PCR among amoxicillin-clavulanate (AMC) resistant samples. RFLP targeting16S rRNAwas performed using seven restriction enzymes including AluI, Bgl I, Bgl II, EcoR I, SmaI, Hinf I & Hae III. Results: Resistance was detected against 15 antibiotics and (38.2%) of isolates were resistant to at least one antibiotic. Overall, high resistance was reported to tetracycline (23.9%), ampicillin (21.1%), AMC (18.7%) and sulfamethoxazoletrimethoprim (13%). Further, 22.4% of the isolates were multidrug-resistant (MDR), with 4.1% being ESBL producers. 90 % of ESBL producers had one of bla CTX-M-Group. Class (1) AMC resistant samples showed the highest resistance to different antibiotics. 16S rRNA-RFLP analysis divided Salmonella isolates into two main groups. Conclusion: Our results indicate a high antimicrobial resistance pattern of Salmonella, which necessities the development of regulatory programs to combats antimicrobial resistance. In particular, our results showed high resistance to Class (1) AMC cassette that involves the transmission and expression of the resistance. This might lead to a concern of increased multidrug resistance in the future. This study provides evidence guidance to activate and implement the pillars of an antimicrobial stewardship program in animal and human health to reduce MDR salmonellosis.

Salmonella is a zoonotic disease that is transmitted from animal products by contact with sick animals or the environments where these animals are living. The mathematical model of transmission disease improve the students' understanding of pathogen dynamics, the role of factors that influence the transmission and control of a specific pathogen and the trend of antimicrobial resistance for this pathogen. The tendency to increase of resistance of Salmonella to antibiotic and combination of antibiotics suggest that models are useful in simulation of different scenarios for dynamic of transmission of this disease. There are two main Salmonella types: Typhimurium serotype and Enteritidis serotype. Both types are included in the software toolbox in a tutorial and interactive manners. The three models of Salmonella compartmental are presented in friendly manner to user with possibility to automatically generation of system equations using built-in templates. Tools that calculate the R0 number and stability analysis are provided as modules in order to evaluate how the experimental data are fit to model or to evaluate the influence of constant coefficients over mathematical model. Because Salmonella typhi bacteria is responsible for a communicable disease, Typhoid fever, an optional module is append to main software in order to give to student the possibility to improve the knowledge with mathematical model of this disease as direct result of a particular bacteria from a larger group of bacteria. The educational software has a friendly GUI (Graphic User Interface) that help student to understand better the dynamic of a specific pathogen modeled by class of larger mathematical models, the compartmental models.

Research For children, the excessive use of antibiotics treatment will damage the liver and kidney functions of children, produce drug resistance, affect the health of children, and traditional Chinese medicine has the characteristics of safety, effective and green, among which children moxibustion application has been widely recognized, and the family traditional Chinese medicine health equipment for children is of great significance. Current studies believe that moxibustion plays the function of dredging meridians and regulating the whole body through three aspects: thermal action, near infrared action and biochemical action. But for children, the skin is delicate, and the nerve is weak. The traditional diagnosis and treatment method of moxibustion has some problems, such as heavy smoke smell, difficult time and temperature control, and complex operation. Besides, the quality of electronic moxibustion products on the market is uneven, and children have not been subdivided. The product design of moxibustion instrument that fully considers the physiological and psychological characteristics of users can have good physiotherapy effect and user experience.Research objective: Emotional design has three different dimensions, namely instinct, behavior and reflection, to study the cognitive response and psychological experience of users to products and apply it in design. This paper aims to explore children as the target user group, focus on the specific situation of home care, summarize and analyze the characteristics and needs of users, design a wearable children's home moxibustion instrument that acts on the body surface and acupoints, and create a good physiotherapy experience for users through visual information and interesting design.Research methods: Based on emotional design, this paper discusses the three-level theory method of products and applies it to the design of wearable children's home moxibustion instrument. This paper mainly from three parts: firstly, population analysis and demand exploration. In this study, the characteristics of children groups are summarized by means of observation and user interview, and the internal needs of related users in the home environment are analyzed. The physical and behavioral characteristics of children are fully considered, the psychological and emotional needs of children are studied, and the three-level theory of emotional design is combined to create an interesting physiotherapy experience. Secondly, summarize the application of pediatric moxibustion in daily health care. Summarize the main health needs of users through preliminary investigation, study the multiple diseases in the childhood stage, and sort out the corresponding treatment methods as the theoretical basis of health care. Thirdly, analyze the transmission mode of information and design visualization. In the design, the wearable sensor and communication equipment are investigated and analyzed, and the user's psychology and interaction scenarios were studied through role-playing, service blueprint and other methods, to design the information interface and product interaction mode.Conclusion: This design starts from the collection of users' physiological signals, receives and transforms them into visual information, puts forward health care plan based on children's moxibustion as a theoretical basis, and adjusts users' physical conditions by applying moxibustion patches in line with children's group characteristics to the surface acupoints. Through the three-level theory of emotional design, users are centered, and emotions are taken as the starting point to analyze the group characteristics and potential needs of users, so as to provide design help for providing positive emotional guidance, creating good experience and satisfying deep needs.

This human campylobacteriosis sentinel surveillance project was based at two sites in Oxfordshire and North East England chosen (i) to be representative of the English population on the Office for National Statistics urban-rural classification and (ii) to provide continuity with genetic surveillance started in Oxfordshire in October 2003. Between October 2015 and September 2018 epidemiological questionnaires and genome sequencing of isolates from human cases was accompanied by sampling and genome sequencing of isolates from possible food animal sources. The principal aim was to estimate the contributions of the main sources of human infection and to identify any changes over time. An extension to the project focussed on antimicrobial resistance in study isolates and older archived isolates. These older isolates were from earlier years at the Oxfordshire site and the earliest available coherent set of isolates from the national archive at Public Health England (1997/8). The aim of this additional work was to analyse the emergence of the antimicrobial resistance that is now present among human isolates and to describe and compare antimicrobial resistance in recent food animal isolates. Having identified the presence of bias in population genetic attribution, and that this was not addressed in the published literature, this study developed an approach to adjust for bias in population genetic attribution, and an alternative approach to attribution using sentinel types. Using these approaches the study estimated that approximately 70% of Campylobacter jejuni and just under 50% of C. coli infection in our sample was linked to the chicken source and that this was relatively stable over time. Ruminants were identified as the second most common source for C. jejuni and the most common for C. coli where there was also some evidence for pig as a source although less common than ruminant or chicken. These genomic attributions of themselves make no inference on routes of transmission. However, those infected with isolates genetically typical of chicken origin were substantially more likely to have eaten chicken than those infected with ruminant types. Consumption of lamb’s liver was very strongly associated with infection by a strain genetically typical of a ruminant source. These findings support consumption of these foods as being important in the transmission of these infections and highlight a potentially important role for lamb’s liver consumption as a source of Campylobacter infection. Antimicrobial resistance was predicted from genomic data using a pipeline validated by Public Health England and using BIGSdb software. In C. jejuni this showed a nine-fold increase in resistance to fluoroquinolones from 1997 to 2018. Tetracycline resistance was also common, with higher initial resistance (1997) and less substantial change over time. Resistance to aminoglycosides or macrolides remained low in human cases across all time periods. Among C. jejuni food animal isolates, fluoroquinolone resistance was common among isolates from chicken and substantially less common among ruminants, ducks or pigs. Tetracycline resistance was common across chicken, duck and pig but lower among ruminant origin isolates. In C. coli resistance to all four antimicrobial classes rose from low levels in 1997. The fluoroquinolone rise appears to have levelled off earlier and among animals, levels are high in duck as well as chicken isolates, although based on small sample sizes, macrolide and aminoglycoside resistance, was substantially higher than for C. jejuni among humans and highest among pig origin isolates. Tetracycline resistance is high in isolates from pigs and the very small sample from ducks. Antibiotic use following diagnosis was relatively high (43.4%) among respondents in the human surveillance study. Moreover, it varied substantially across sites and was highest among non-elderly adults compared to older adults or children suggesting opportunities for improved antimicrobial stewardship. The study also found evidence for stable lineages over time across human and source animal species as well as some tighter genomic clusters that may represent outbreaks. The genomic dataset will allow extensive further work beyond the specific goals of the study. This has been made accessible on the web, with access supported by data visualisation tools.

Mycoplasma iowae (Mi) is a pathogenic avian mycoplasma which causes mortality in turkey embryos and as such has clinical and economic significance for the turkey breeder industry. Control of Mi infection is severely hampered by lack of adequate diagnostic tests, together with resistance to most antibiotics and resilience to environment. A markedly high degree of intra-species antigenic variation also contributes to difficulties in detection and control of infection. In this project we have designed an innovative gene-based diagnostic test based on specific amplification of the 16S rRNA gene of Mi. This reaction, designed Multi-species PCR-RFLP test, also amplifies the DNA of the pathogenic avian mycoplasmas M. gallisepticum (Mg) and M. synoviae (Ms). This test detects DNA equivalent to about 300 cfu Mi or either of the other two target mycoplasmas, individually or in mixed infection. It is a quick test, applicable to a wide variety of clinical samples, such as allantoic fluid or tracheal or cloacal swab suspensions. Differential diagnosis is carried out by gel electro-phoresis of the PCR amplicon digested with selected restriction enzymes (Restriction Fragment Length Polymorphism). This can also be readily accomplished by using a simple Dot-Blot hybridization assay with digoxigenin-labeled oligonucleotide probes reacting specifically with unique Mi, Mg or Ms sequences in the PCR amplicon. The PCR/OLIGO test increased sensitivity by at least 10-fold with a capacity for rapid testing of large numbers of samples. Experimental infection trials were carried out to evaluate the diagnostic tools and to study pathogenesis of Mi infection. Field studies and experimental infection of embryonated eggs indicated both synergistic and competitive interaction of mycoplasma pathogens in mixed infection. The value of the PCR diagnostic tests for following the time course of egg transmission was shown. A workable serological test (Dot Immunobinding Assay) was also developed but there was no clear-cut evidence that infected turkeys develop an immune response. Typing of a wide spectrum of Mi field isolates by a variety of gene-based molecular techniques indicated a higher degree of genetic homogeneity than predicted on the basis of the phenotypic variability. All known strains of Mi were detected by the method developed. Together with an M. meleagridis-PCR test based on the same gene, the Multi-species PCR test is a highly valuable tool for diagnosis of pathogenic mycoplasmas in single or mixed infection. The further application of this rapid and specific test as a part of Mi and overall mycoplasma control programs will be dependent on developments in the turkey industry.