published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

published_or_final_version / Microbiology / Master / Master of Philosophy

The introduction of the polymerase chain reaction (PCR) into the diagnostic setting has provided unprecedented opportunities in the field of respiratory medicine, not only because pathogens need no longer be cultivable for detection but also through improved sensitivity, specificity and turnaround time compared with traditional methods. The recent discovery of several novel respiratory viruses, such as human metapneumovirus (HMPV), human bocavirus and human coronaviruses (HCoVs) NL63 and HKU1 has nevertheless created significant challenges in respiratory diagnostics, as identification of which pathogens should be tested for is increasingly difficult. The recent discovery of two novel respiratory coronaviruses (HCoV-HKU1 and HCoV-NL63) presented the opportunity to undertake large scale clinical and epidemiologic study of these alongside two previously known respiratory coronaviruses, HCoV-229E and HCoV-OC43. Over 12,000 samples collected over three years were screened using a novel four-way multiplex real-time reverse transcription-PCR (RTPCR). Clinically, coronaviruses were similar to viruses currently included in routine diagnostics, with the exception of HCoV-229E which was identified as an opportunistic pathogen in immunocompromised hosts. Variability in detection frequencies of HCoVHKU1 and HCoV-OC43 was evident. The low detection frequencies of HCoVs, comparable to those of parainfluenza viruses 1 and 2 (which are included in the routine diagnostic screening panel) indicate a borderline case for inclusion of these pathogens in routine respiratory diagnostics. To investigate the epidemiology and clinical correlates of HMPV in Edinburgh, large scale retrospective screening of over 7000 respiratory samples collected over two years was conducted. Nucleotide sequencing of HMPV-positive samples was undertaken to determine phylogenetic relationships of circulating HMPV strains. HMPV comprises two genotypes, A and B. Comparisons of the clinical presentations of the two genotypes revealed little difference, with only the observation that sub-genotype B2 was more frequently associated with infection of immunocompromised patients. Detection frequencies and symptomatology associated with HMPV infections were comparable to respiratory viruses currently included in the routine diagnostic panel, mandating its inclusion in future diagnostic screening. A switch of the predominantly circulating genotype of HMPV was observed between respiratory seasons. This is a phenomenon more widely reported for the closely related respiratory syncytial virus (HRSV), which also comprises two circulating groups. To further investigate subtype (HRSV)/ genotype (HMPV) switching, evolutionary analyses of nucleotide sequence data generated from isolates collected from geographically disparate referral centres was undertaken. The fusion and attachment (G) genes were targeted, as these encode major surface proteins and are immunogenic. Analyses were by MCMC analyses using Bayesian Evolutionary Analyses of Sampling Trees (BEAST) software. Identification of positively selected sites was performed using Phylogenetic Analysis Maximum Likelihood (PAML). Switching of the predominantly circulating lineage does not arise for either virus due to emergence of novel strains, but through fluctuating circulation frequencies of pre-existing lineages which have been circulating for several decades, indicated by the time since the most recent common ancestor. Two HRSV-A lineages comprising genotypes undergoing turnover and replacement were identified. This finding is agreeable with serologic studies of the 1970s which reported three HRSV serogroups, two within HRSV-A and one within HRSV-B. HMPV and HRSV have similar mutation rates. Positively selected sites identified within the HRSV G gene were incongruent with those identified in a previous study, generating the hypothesis that immune evasion occurs within linear epitopes rather than at specific sites. A great deal of clinical and epidemiologic data was generated through this work, parallel studies of other respiratory viruses and through diagnostic screening results. To provide a robust indication of where resources should be diverted in terms of diagnostics, therapeutics and vaccine development, and to inform infection control measures and public health policy planning, quantification of the relative disease burden attributable to the most commonly detected respiratory viruses was calculated using the World Health Organization- endorsed Disability Adjusted Life Year (DALY) model. Relative disease burden was calculated in an age stratified manner to reflect the differences in sampling in different age groups. HRSV and influenza A were consistently one of the greatest causes of disease regardless of sampled population, although HRSV caused more disease in children under 5 than influenza A and B combined. Rhinoviruses and PIV-3 were significant pathogens in all groups except those aged 16-64 years; rhinoviruses were the leading cause of disease in the immunocompromised patient group. The potential for patient-specific diagnostic screening and guidance of interventions such as patient cohorting were clear.

Résumé : Le Campylobacter est la première cause de gastro-entérites bactériennes dans les pays industrialisés. La grande majorité des cas sont des infections sporadiques dont la source est rarement identifiée. Le Campylobacter fait partie de la flore intestinale normale d’une large diversité d’animaux et peut également se retrouver dans l’eau. Le but de mon projet de recherche était d’étudier l’épidémiologie clinique et moléculaire des infections à Campylobacter en Estrie afin de déterminer les principales sources d’infections sporadiques et de comparer les génotypes des isolats de Campylobacter selon les différentes niches écologiques. Nous avons déterminé le profil de sensibilité aux antibiotiques d’isolats de différentes sources. Nous avons observé un haut taux de résistance à l’érythromycine et à la tétracycline et un faible taux de résistance à la ciprofloxacine chez les isolats de poulet, pouvant refléter l’utilisation de ces antibiotiques dans cet élevage. Le fait que le taux de résistance à l’érythromycine parmi les isolats humains soit significativement moins élevé que chez les isolats de poulet suggérait l’importance d’autres sources de Campylobacter chez l’humain. Afin de déterminer quelle méthode de typage moléculaire serait la mieux adaptée pour notre devis de recherche, nous avons comparé quatre méthodes (AFLP, MLST, typage du gène fla et EGCP). Seul le MLST a pu attribuer des isolats humains à des niches écologiques particulières comme le poulet, le lait cru et l’eau. Afin d’optimiser la technique de MLST, nous avons développé un système complémentaire basé sur le HRM, qui est beaucoup plus rapide et moins coûteux que le MLST. Nous avons démontré que le HRM a le potentiel de complémenter les méthodes d’analyses basées sur du séquençage pour l’étude des mutations ponctuelles et de faciliter une vaste gamme d’études basées sur des méthodes génotypiques, telle la détection de mutations ponctuelles qui confèrent de la résistance aux antibiotiques. Nous avons entrepris par la suite une étude cas-cas et un vaste projet d’isolement et de caractérisation moléculaire de souches de Campylobacter en Estrie, afin de véritablement cerner les mécanismes de transmission de la bactérie et de comparer les sources d’infections sporadiques chez les cas acquis en régions rurales vs urbaines. Nous avons confirmé que le poulet était responsable de la majorité des cas de campylobactérioses. Cependant, nos résultats suggèrent que la saisonnalité ainsi que le gradient urbain-rural de la campylobactériose sont dus à l’exposition aux souches bovines, particulièrement chez le groupe d’âge des 15-34 ans via l’exposition professionnelle. Par la détermination des sources d’infections, nous avons établi des pistes d’interventions utilisables par les autorités de santé publique, afin de diminuer l’incidence de la campylobactériose au Québec. / Abstract : Campylobacteriosis is the leading notifiable enteric disease in industrialised countries. It colonizes a wide range of animal which in turn spread the disease. The majority of campylobacteriosis cases are sporadic infections for which the source is rarely apparent. The main goal of my research project is to determine contamination sources of Campylobacter in the Eastern Townships, to identify the sources and routes of transmission and to establish the main sources of sporadic infections. We determined antimicrobial susceptibility profiles of Campylobacter isolates in order to predict which bacterial population will be resistant, caused by antimicrobial selective pressure administered to the host. High levels of resistance of chicken isolates to erythromycin and tetracycline, and low levels of resistance to ciprofloxacin reflect the use of the former antibiotics in animal husbandry. The fact that the erythromycin and tetracycline resistance levels were significantly lower among human isolates suggests that other transmission sources are important for human infection. In order to determine which molecular typing method will be the most relevant for our research design, we compared four typing methods (AFLP, MLST,/7a typing and PFGE). Only MLST has the potential to link isolates to a particular ecological niche, such as chicken, raw milk and water. In order to optimize MLST, we developed a complementary system based on HRM. We demonstrated that HRM has the potential to complement the analysis methods based on sequencing for SNP and facilitate a wide range of studies based on genotypic methods. We have subsequently undertaken a major project of isolation and molecular characterization of Campylobacter in the Eastern Townships, in order to truly understand the mechanisms of transmission of the bacteria and determine the source of sporadic cases. We confirmed that chicken was responsible for the majority of cases of campylobacteriosis. However, we have shown that the urban-rural gradient of campylobacteriosis in the Eastern Townships could be explained by exposure to bovine, especially for the 15-34 year old age group through occupational exposure. By the identification of infection sources, we proposed courses of action that could be used by public health authorities to reduce the incidence of campylobacteriosis in Quebec.

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.

A raiva é uma antropozoonose com alta letalidade, acomete todos os animais de sangue quente, essa doença causa enormes prejuízos econômicos ao rebanho pecuário nacional, é impossível estimar os custos reais com controle dessa doença, em decorrência do grande número de subnotificações. O uso de ferramentas moleculares permite identificar as linhagens virais circulantes, facilitando desse modo à compreensão da epidemiologia da raiva. A técnica de RT-PCR para amplificação parcial dos genes N e G, foi aplicada em 60 amostras positivas para o vírus da raiva pelas provas de imunofluorescência direta e prova biológica, procedentes dos Estados do Pará, Tocantins, Rondônia e Acre das espécies bovina, equídea, bubalina e suína. As sequências nucleotídicas obtidas para os genes N (41 amostras) e G (17 amostras) foram analisadas pelo algoritmo Neighbor-Joining e modelo evolutivo Kimura 2-parâmetros. Essa análise permitiu identificar distintas linhagens circulantes nas regiões estudadas, foi evidenciado ainda, um padrão de distribuição geográfico dessas linhagens. Além disso, este estudo possibilitou identificar marcadores moleculares para diferentes regiões geográficas, promovendo um melhor entendimento da epidemiologia molecular da raiva das linhagens circulantes da região em estudo. / Rabies is an anthropozoonosis with high mortality, affects all warm-blooded animals, this disease causes major economic losses to livestock. It is difficult to estimate the actual costs of disease control, due to sub notification of cases. Molecular techniques allow identification of genetic viral strains circulating, improving rabies epidemiology comprehension. Sixty rabies virus isolates from bovines, equines, swine and buffaloes coming from the states of Pará, Tocantins, Rondônia and Acre were analyzed in the present study. All samples were previously submitted to direct immunofluorescence test and inoculation in mice, afterwards were submitted to RT-PCR for amplification of partial Nucleoprotein and Glycoprotein genes. Nucleotide sequences from nucleoprotein (41 samples) and glycoprotein G (17 samples) genes were analyzed by Neighbor-joining algorithm and Kimura two-parameter model. This analysis allowed to identify different genetic strains circulating and its geographic distribution patterns. Moreover this study revealed molecular markers for different geographic regions, promoting a better understanding of rabies molecular epidemiology of circulating strains of study area.

Gastroenterites são uma das causas mais comuns e importantes de morbidade e mortalidade entre animais neonatos e juvenis, em muitos casos, ocasionadas por uma infecção intestinal múltipla, sendo os principais agentes virais entéricos em bovinos o rotavírus e o coronavírus bovino (BCoV). O BCoV tem distribuição mundial e causa gastroenterites em bezerros, disenteria de inverno em bovinos adultos e processos patológicos respiratórios, enquanto que nos equinos os coronavírus causam enterocolite neonatal em potros. Considerando-se que o coronavírus bovino é mais estudado do que os coronavírus equinos, havendo possibilidade de transmissão interespécies, o presente trabalho teve por objetivo a comparação multigênica do coronavírus em bovinos adultos com disenteria de inverno e bezerros com diarréia neonatal e em equinos do Brasil, com base em sequências parciais dos genes codificadores das proteínas hemagluninina-esterase (HE), espícula (S) e nucleoproteína (N). Foram utilizadas amostras fecais de 11 vacas leiteiras de um surto de disenteria de inverno e de 27 equinos testadas quanto a presença de Betacoronavirus com uma RT-PCR dirigida ao gene RdRp; em seguida, as amostras positivas foram submetidas as reações parciais de PCR para os genes N, HE e S, e posterior sequenciamento e análise genealógica. Além destas amostras, foram utilizadas 15 amostras fecais de bezerros, já estudadas parcialmente quanto ao gene S, submetidas as reações de RT-PCR para N e HE, e posterior sequenciamento e análise genealógica. Sequências representativas da população em estudo foram obtidas para todos os genes. Pode-se concluir que a genealogia de amostras entéricas de BCoV detectadas em bovinos jovens e adultos é diretamente associada a padrões geográficos quando se consideram os genes S e HE, sendo a genealogia de menor resolução para os genes HE e nucleoproteína N, para a qual há uma tendência a segregação por faixa etária do hospedeiro e que equinos podem apresentar Betacoronavirus indistinguíveis daqueles encontrados em bovinos. / Gastroenteritis is one of the leading causes of morbidity and mortality amongst young and newborn animals, often caused by multiple intestinal infections, being rotavirus and Bovine coronavirus (BCoV) the main viral causes in cattle. BCoV has a worldwide distribution and caused diarrhea in calves, winter dysentery in adult cattle and respiratory disease, while in horses coronaviruses lead to neonatal enterocolitis in foals. Taking into account that BCoV is more largely studied than equine coronaviruses and the possibility of interspecies transmission of these viruses, this research aimed to assess a multigenic comparison of coronaviruses from adult cattle with winter dysentery and calves with neonatal diarrhea as well as from equines, all from Brazil, based on partial sequences of the hemagglutinin-esterase (HE), spike (S) and nucleoprotein (N) genes. To this end, 11 samples from dairy cows with winter dysentery and 27 from horses were tested for Betacoronavirus using an RT-PCR targeted to the RdRp gene and the positive samples were next submitted to RT-PCRs to the partial amplification and sequencing of N, HE and S genes for genealogic analysis. Besides, 15 calves samples previously studied for the same S gene region were also submitted to the N and HE genes RT-PCRs and sequencing for genealogic analysis. Sequences representative of the population under study were obtained for all genes. It could be concluded that enteric BCoV genealogy from newborn and adult cattle is directly associated to geographic patterns when S and HE genes are taken into account, with a less-resolved genealogy for the HE and N genes, with a trend for an age-related segregation pattern for the last and also that horses might present Betacoronavirus undistinguishable from those found in cattle, a fact previously unknown.

Staphylococcus aureus é um patógeno versátil, capaz de causar uma grande variedade de infecções. Nos últimos anos, ocorreu um aumento da proporção de infecções causadas por S. aureus resistentes a meticilina (MRSA). A resistência a meticilina deve-se à presença do gene mecA, carreado no cassete cromossômico estafilocócico (SCCmec). Pacientes infectados ou colonizados por MRSA são reservatórios e fontes de disseminação deste microorganismo, em instituições de cuidado à saúde, principalmente através de profissionais transitoriamente colonizados. Freqüentemente, a infecção por MRSA é precedida por um período de colonização. Em 2003 foi observado um aumento das taxas de infecções hospitalares por S. aureus na Enfermaria de Dermatologia do Hospital das Clínicas (EDER), em relação aos cinco anos anteriores. Os objetivos do presente estudo foram avaliar a transmissão hospitalar de MRSA, entre os pacientes da EDER e caracterizar os isolados de MRSA, obtidos de pacientes e funcionários colonizados, presentes nessa unidade. Foi realizada a detecção dos pacientes colonizados por MRSA, através de culturas de vigilância das narinas e, quando possível, culturas de vigilância das lesões de pele, num período de seis meses. A identificação fenotípica foi confirmada por reação em cadeia da polimerase (PCR) multiplex para detecção dos genes mecA e coa. Posteriormente, os isolados de MRSA foram submetidos ao teste de sensibilidade aos antimicrobianos pelo método de microdiluição em caldo, PCR multiplex para determinação do tipo de SCCmec e tipagem molecular por eletroforese em campo pulsado (PFGE). Quarenta e cinco por cento dos pacientes eram portadores de MRSA. No início do estudo, 14% dos funcionários eram portadores de MRSA, no fim eram 18%. Foram obtidas 105 amostras de MRSA, sendo que 11 foram isoladas de funcionários da EDER e 94 isoladas de 64 pacientes que eram portadores deste microorganismo.Sessenta e um por cento dos pacientes classificados como portadores de MRSA, eram positivos na primeira coleta realizada e 39% foram identificados durante o seguimento, nas coletas posteriores. O gene da coagulase foi detectado em todas as 105 amostras e o gene mecA em 101. Todos os isolados foram sensíveis a vancomicina e resistentes a oxacilina e penicilina. Trinta e três por cento dos isolados eram multirresistentes, apresentaram SCCmec tipo IIIA e um perfil PFGE predominante. SCCmec tipo IV foi observado em 59% dos isolados. Não foi possível determinar o tipo de SCCmec de quatro isolados. Na PFGE, o perfil B1 foi o mais prevalente, apresentado por isolados de MRSA SCCmec tipo IV, obtidos de nove pacientes e de três funcionários. A transmissão hospitalar foi caracterizada em 39% dos pacientes portadores. Foi possível observar a participação dos funcionários, na transmissão cruzada de MRSA, na EDER. A colonização por MRSA, dos profissionais de cuidado à saúde, foi transitória. Além da transmissão hospitalar de MRSA, foi possível detectar pacientes que eram portadores de MRSA na admissão / Staphylococcus aureus is a versatile pathogen capable of causing a wide variety of infections. The proportion of nosocomial and community-acquired methicillinresistant Staphylococcus aureus (MRSA) infections has increased in the last years. Methicillin resistance is mediated by the mecA gene which is carried on the Staphylococcal Cassette Chromosome mec (SCCmec). In heath care settings, patients who are colonized or infected with MRSA constitute a reservoir and a source of spread of this microorganism, mainly through transiently colonized health care workers (HCWs). MRSA infections are usually preceded by a period of colonization. In 2003, an increase in the rates of MRSA nosocomial infection in the Dermatology ward of Hospital das Clínicas was observed, in comparison with the five previous years. The aims of this study were to evaluate the nosocomial transmission of MRSA in the Dermatology ward and to characterize MRSA isolates obtained from patients and HCWs. Surveillance cultures of the anterior nares and skin lesions were performed to identify patients who were MRSA carriers, during a period of six months. The phenotypic identification was confirmed by multiplex polymerase chain reaction (PCR), to detect mecA and coa genes. Subsequently, MRSA isolates were submitted to antimicrobial susceptibility testing by microdilution method, multiplex PCR for SCCmec typing and molecular typing by pulsed-field gel electrophoresis (PFGE). Forty-five percent of the patients were MRSA carriers. 14% of the HCWs were MRSA carriers at the beginning of the study and 18% at the end. One hundred and five MRSA isolates were obtained, 11 from HCWs and 94 from 64 patients who were MRSA carriers. Sixty-one percent of the patients, classified as MRSA carriers, were positive on the first culture and 39% were identified during the follow up period in the subsequent cultures. The coagulase gene was detected in all 105 isolates and the mecA gene in 101. All MRSA isolates were susceptible to vancomycin and resistant to oxacillin and penicillin. Thirty-three percent of the isolates were multiresistant, presented SCCmec Type IIIA and showed a predominant PFGE type. The SCCmec type IV was found in 59% of the isolates. It was not possible to determine the SCCmec type of four isolates. The B1 PFGE pattern was the most prevalent, presented by MRSA SCCmec type IV isolates, obtained from nine patients and three HCWs. Nosocomial transmission occurred in 39% of the MRSA carriers. It was possible to observe HCWs MRSA cross- transmission in the Dermatology ward. HCWs were transiently colonized. In addition to nosocomial transmission of MRSA, it was possible to detect patients who were MRSA carriers on admission

Picobirnavirus (PBV) pertencem à família Picobirnaviridae, divididos em duas espécies Human Picobirnavirus e Rabbit Picobirnavirus. São pequenos vírus constituídos de genoma bissegmentado de cadeia dupla de RNA (dsRNA), não envelopados, com capsídeo de simetria icosaédrica, sendo divididos em dois genogrupos, GI e GII. Já foram detectados em fezes humanas e de uma ampla gama de espécies animais, com ou sem sinais diarreicos, sendo considerados agentes emergentes e oportunistas, e seu potencial zoonótico foi sugerido. Entretanto, os estudos epidemiológicos e moleculares de PBV em bovinos são raros na literatura nacional e internacional. Devido à carência de dados a respeito de PBV em bovinos, o presente estudo foi realizado objetivando-se a detecção e caracterização moleculares de cepas de PVB bovinos dos genogrupos GI e GII em amostras fecais de bovinos com ou sem sintomatologia diarreica de diferentes idades e regiões do Brasil. O estudo foi conduzido a partir de 77 animais, obtendo-se 18 (23,3%) amostras positivas para GI, compreendendo animais provenientes dos estados de São Paulo, Minas Gerais e Goiás. Não foram detectadas amostras positivas para GII. A identidade nucleotídica das amostras obtidas apresentou média de 67,4% quando comparadas uma com as outras e de até 83,77% quando comparadas com amostras de PBV de referência. Na reconstrução filogenética, três amostras agruparam-se em clado de PVB humano e somente uma agrupou-se em clado de PVB bovino. Em síntese, os resultados obtidos indicam, de maneira inédita, a circulação de PVB bovino pertencente ao genogrupo GI em diferentes estados brasileiros, com perfis filogenéticos heterogêneos. / Picobirnavirus (PBV) belong to the Picobirnaviridae family, divides into two species Human Picobirnavirus and Rabbit Picobirnavirus. They are small, non-enveloped, bisegmented double-stranded RNA (dsRNA) virus with an icosahedral capsid, being divided into two genogroups, GI and GII. They have been detected in feces of humans and many animal species, with or without diarrheal signs and are considered emerging and opportunistic agents, and its zoonotic potential has been suggested. However, epidemiological and molecular studies of bovine PBV are rare in the national and international literature. Due to lack of data on PBV in cattle, this study was conducted aiming to detect and molecularly characterize bovine PBV strains of GI and GII genogroups in feces from animals with or without diarrheal signs of different ages and regions of Brazil. Seventy-seven animals were sampled, resulting in 18 (23.3%) positive samples for GI, including animals from the states of São Paulo, Minas Gerais and Goiás. There were no positive samples for GII. The nucleotide identity of the samples obtained showed a mean of 67.4% compared to each other and up to 83.77% compared to PBV reference samples. In phylogenetic reconstruction, three samples were grouped in the human PBV clade and only one sample was clustered in the bovine PVB clade. In summary, the results indicate in an unprecedented way the circulation of the bovine PBV belong to GI genogroup in different Brazilian states, with heterogeneous phylogenetic profiles.

Le complexe Mycobacterium abscessus (MABSC) fait partie des mycobactéries non tuberculeuses. C’est un pathogène opportuniste environnemental pouvant causer des infections pulmonaires chroniques, en particulier chez les patients atteints de mucoviscidose, et extra-pulmonaires sévères. Il est également résistant à la plupart des antibiotiques, et ne connait pas de traitement efficace. Il se divise en trois sous-espèces : Mycobacterium abscessus subsp. abscessus, Mycobacterium subsp. massiliense et Mycobacterium subsp. bolletii, Ces trois sous espèces possèdent des différences cliniques et de résistance aux antibiotiques, une identification sûre et rapide est don essentielle. De plus, son épidémiologie reste peu connue, notamment au sein des patients atteints de mucoviscidose.Dans un premier temps, nous avons évalué la performance d’identification au sein du MABSC et la caractérisation des principales résistances du kit Genotype NTM-DR. Celui-ci s’est révélé extrêmement efficace, avec une réussite de 100% d’identification de la sous-espèce mais aussi pour la caractérisation des résistances à la clarithromycine et à l’amikacine, qui sont les antibiotiques recommandés pour le traitement d’une infection à MABSC. Ce kit est donc une alternative rapide et robuste aux principales méthodes d’identification et de caractérisation de la résistance chez MABSC.Dans un second temps, nous avons testé l’efficacité de deux molécules différentes, la clofazimine et la tigecycline, en synergie. Une synergie a pu être mise en évidence sur 42 % des isolats, et la présence de clofazimine a permis d’abaisser la concentration minimale inhibitoire de la tigecycline pour 52 % des isolats. Cette association pourrait constituer une alternative thérapeutique efficace et mieux supportable pour le patient.Enfin, nous avons réalisé deux études épidémiologiques : au Vietnam, chez des patients possédant une condition pulmonaire inflammatoire, et en France, chez des patients atteints de la mucoviscidose dans cinq centres hospitaliers différents. En France, un suivi longitudinal a pu être réalisé sur 7 patients de deux centres différents.Le Vietnam présentait un grand nombre de Sequence Type (ST) nouveaux (29/38) ainsi qu’une grande diversité génotypique (0.72 pour 53 isolats). Une majorité de M. massiliense a été mis en évidence. De plus, des ST responsables d’épidémies dans différents pays ont aussi été retrouvés (ST 23 et ST 117). Trois complexes clonaux ont été identifiés, reflétant la grande diversité du complexe M. abscessus dans ce pays. Deux de ces complexes clonaux étaient constitués de M. abscessus subsp. massiliense contenaient les ST 23 et 117. Le grand nombre de nouveaux génotype est dû au manque de données au Vietnam, il s’agit là de la première étude épidémiologique dans ce pays.En France, on retrouvait un plus grand nombre de sequence type connus (20/31), certainement dû au nombre d’études existantes dans cette région. Une majorité de M. abscessus subsp. abscessus a été retrouvé. Sept sequence type d’importance épidémiologique ont été retrouvés, dont le ST 23. Le suivi longitudinal montre que : le risque d’infection exogène est grand ; le pool de génotypes à Brest est plus important qu’à Montpellier, même si les ST persistent chez un même patient, on ne peut exclure le risque d’une infection exogène. Enfin, l’analyse VNTR des isolats des cinq centres suggère une possible transmission nosocomiale ainsi que la diffusion de génotypes en France.En conclusion, ce travail de thèse a permis d’améliorer l’approche de l’identification et du traitement des infections du complexe M. abscessus, en plus d’explorer et de comparer son épidémiologie dans deux populations différentes. Nous montrons la présence ubiquitaire de certains génotypes d’importance cliniques, une grande diversité génotypique, une variabilité du portage chez le patient mucoviscidose ainsi qu’un risque d’infections exogènes et de transmission chez cette population. / The Mycobacterium abscessus complex is a nontuberculous mycobacteria. It is an environmental opportunistic pathogen that can cause chronic lung infections, especially in patients with cystic fibrosis, and severe extra-pulmonary infections. It is also resistant to most antibiotics, and does not have an effective treatment. It is divided into three subspecies: Mycobacterium abscessus subsp. abscessus, Mycobacterium subsp. massiliense and Mycobacterium subsp. bolletii, These three subspecies have clinical and antibiotic resistance differences, Thus, a safe and rapid identification is essential. In addition, little is known about its epidemiology, particularly among patients with cystic fibrosis.First, we assessed the identification performance within the M. abscessus complex and the characterization of the main resistances of a commercial assay (Genotype NTM-DR). The kit was highly efficient, with 100% success in identifying the subspecies and also in characterizing resistance to clarithromycin and amikacin, which are the recommended antibiotics for the treatment of complex M. abscessus infection. This kit is therefore a fast and robust alternative to the main methods for identifying and characterizing resistance in the M. abscessus complex.Secondly, we tested the efficacy of two different molecules, clofazimine and tigecycline, in synergy. Synergy was demonstrated in 42% of the isolates, and the presence of clofazimine reduced the minimum inhibitory concentration of tigecycline in 52% of the isolates. This combination could be an effective and more tolerable therapeutic alternative for the patient.Finally, we carried out two epidemiological studies: in Vietnam, in patients with inflammatory lung disease, and in France, in patients with cystic fibrosis in five different hospitals. In France, longitudinal follow-up was carried out on 7 patients from two different centres, Brest and Montpellier. Two different typing tools were used: MLST and VNTR.Vietnam had a large number of new Sequence Type (ST) (29/38) and a high genotypic diversity (0.72 for 53 isolates). A majority of M. abscessus subsp. massiliense was found. In addition, STs responsible for epidemics in different countries have also been found (ST 23 and ST 117). Three clonal complexes have been identified, reflecting the great diversity of the M. abscessus complex in this country. Two of these clonal complexes were composed of M. abscessus subsp. massiliense containing ST 23 and 117. The large number of new genotypes is due to the lack of data in Vietnam, this is the first epidemiological study in this country.In France, there was a greater number of known sequence type (20/31), certainly due to the number of existing studies in this region. A majority of M. abscessus subsp. abscessus was found. Seven sequence type of epidemiological importance were found, including ST 23. Longitudinal monitoring shows a high variability of the ST in Brest compared to Montpellier, which is confirmed by the VNTR. This follow-up shows that: the risk of exogenous infection is high; the genotype pool in Brest is greater than in Montpellier, even if STs persist in the same patient, the risk of exogenous infection cannot be excluded. Finally, the VNTR analysis of isolates from the five centres suggests possible nosocomial transmission and the spread of genotypes in France.In conclusion, this thesis work has improved the approach to the identification and treatment of M. abscessus complex infections, as well as exploring and comparing its epidemiology in two different populations. We show the ubiquitous presence of certain clinically important genotypes, a high genotypic diversity, a variability in carrying in the cystic fibrosis patient as well as a risk of exogenous infections and transmission in this population