RÉSUMÉ
Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005-2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.
Sujet(s)
Traçage des contacts/méthodes , Épidémiologie moléculaire/méthodes , Typage moléculaire/méthodes , Mycobacterium/classification , Mycobacterium/génétique , Tuberculose/épidémiologie , Séquençage du génome entier/méthodes , Transmission de maladie infectieuse , Génotype , Humains , Mycobacterium/isolement et purification , Tuberculose/transmission , Territoire du Yukon/épidémiologieRÉSUMÉ
Few studies have used genomic epidemiology to understand tuberculosis (TB) transmission in rural and remote settings - regions often unique in history, geography and demographics. To improve our understanding of TB transmission dynamics in Yukon Territory (YT), a circumpolar Canadian territory, we conducted a retrospective analysis in which we combined epidemiological data collected through routine contact investigations with clinical and laboratory results. Mycobacterium tuberculosis isolates from all culture-confirmed TB cases in YT (2005-2014) were genotyped using 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) and compared to each other and to those from the neighbouring province of British Columbia (BC). Whole genome sequencing (WGS) of genotypically clustered isolates revealed three sustained transmission networks within YT, two of which also involved BC isolates. While each network had distinct characteristics, all had at least one individual acting as the probable source of three or more culture-positive cases. Overall, WGS revealed that TB transmission dynamics in YT are distinct from patterns of spread in other, more remote Northern Canadian regions, and that the combination of WGS and epidemiological data can provide actionable information to local public health teams.
Sujet(s)
Génome bactérien , Mycobacterium tuberculosis/génétique , Tuberculose/transmission , Adolescent , Adulte , Sujet âgé , Sujet âgé de 80 ans ou plus , Colombie-Britannique , Enfant , Enfant d'âge préscolaire , Femelle , Humains , Nourrisson , Nouveau-né , Mâle , Adulte d'âge moyen , Répétitions minisatellites , Tuberculose/microbiologie , Séquençage du génome entier , Jeune adulte , Territoire du YukonRÉSUMÉ
Mycobacterium tuberculosis isolates of the Manila sublineage are genetically homogeneous. In this study, we used whole-genome sequencing (WGS) to type a collection of 36 M. tuberculosis isolates of the Manila family. WGS enabled the subtyping of these 36 isolates into at least 10 distinct clusters. Our results indicate that WGS is a powerful approach to determining the relatedness of Manila family M. tuberculosis isolates.
Sujet(s)
ADN bactérien/génétique , Génome bactérien , Typage moléculaire/méthodes , Mycobacterium tuberculosis/classification , Mycobacterium tuberculosis/génétique , Analyse de séquence d'ADN/méthodes , Analyse de regroupements , ADN bactérien/composition chimique , Génotype , Humains , Épidémiologie moléculaire/méthodesRÉSUMÉ
Resistance to rifampin (RIF) and rifabutin (RFB) in Mycobacterium tuberculosis is associated with mutations within an 81-bp region of the rpoB gene (RIF resistance-determining region [RRDR]). Previous studies have shown that certain mutations in this region are more likely to confer high levels of RIF resistance, while others may be found in phenotypically susceptible isolates. In this study, we sought to determine the relationship between the MICs of RIF and RFB and rpoB RRDR mutations in 32 multidrug-resistant (MDR), 4 RIF-monoresistant, and 5 susceptible M. tuberculosis clinical isolates. The MICs were determined using the MGIT 960 system. Mutations in the rpoB RRDR were determined by Sanger sequencing. RpoB proteins with mutations S531L (a change of S to L at position 531), S531W, H526Y, and H526D and the double mutation D516A-R529Q were associated with high MICs for RIF and RFB. Five isolates carrying the mutations L511P, H526L, H526N, and D516G-S522L were found to be susceptible to RIF. Several mutations were associated with resistance to RIF and susceptibility to RFB (F514FF, D516V, and S522L). Whole-genome sequencing of two MDR isolates without rpoB RRDR mutations revealed a mutation outside the RRDR (V146F; RIF MIC of 50 µg/ml). The implications of the polymorphisms identified in the second of these isolates in RIF resistance need to be further explored. Our study further establishes a correlation between the mutations and the MICs of RIF and, also, RFB in M. tuberculosis. Several rpoB mutations were identified in RIF- and RFB-susceptible isolates. The clinical significance of these findings requires further exploration. Until then, a combination of phenotypic and molecular testing is advisable for drug susceptibility testing.
Sujet(s)
Antituberculeux/pharmacologie , Protéines bactériennes/génétique , DNA-directed RNA polymerases/génétique , Mutation , Mycobacterium tuberculosis/génétique , Rifabutine/pharmacologie , Rifampicine/pharmacologie , Génome bactérien , Humains , Tests de sensibilité microbienne , Mycobacterium tuberculosis/effets des médicaments et des substances chimiques , Mycobacterium tuberculosis/isolement et purification , Analyse de séquence d'ADN , Tuberculose/microbiologieRÉSUMÉ
BACKGROUND: In Canada, tuberculosis (TB) rates are at a historic low, with the remaining risk concentrated in a few vulnerable population subgroups. OBJECTIVES: To describe the epidemiology of TB in the Canadian province of Ontario and to characterise risk factors associated with transmission events, identified using genetic typing techniques. DESIGN: Retrospective analysis of 2186 culture-positive TB cases between August 2007 and December 2011. Temporal trends and risk of spatiotemporal and genotypic clustering were evaluated using Poisson and logistic regression models. RESULTS: Being in a spatiotemporal cluster was associated with Aboriginal status (odds ratio [OR] 3.63, 95% confidence interval [CI] 1.23-10.71). Cases in genotypic clusters were more likely to report homelessness as a risk factor (adjusted OR [aOR] 2.92, 95%CI 1.74-4.90) or be male (aOR 1.35, 95%CI 1.09-1.68), and were less likely to be aged ≥ 65 years (aOR 0.63, 95%CI 0.49-0.82), foreign-born (aOR 0.32, 95%CI 0.24-0.43) or Aboriginal (aOR 0.40, 95%CI 0.16-0.99). The Beijing lineage had an annual rate of increase of almost 10% (P = 0.047), and was associated with genotypic clustering (aOR 2.84, 95%CI 2.19-3.67). CONCLUSION: Genotypic data suggest that disease clusters are smaller, but far more common, than would be estimated using spatiotemporal clustering.
Sujet(s)
/statistiques et données numériques , Indiens d'Amérique Nord/statistiques et données numériques , Mycobacterium tuberculosis/isolement et purification , Tuberculose/épidémiologie , Adulte , Facteurs âges , Sujet âgé , Techniques de typage bactérien , Analyse de regroupements , Femelle , Génotype , Humains , Modèles logistiques , Mâle , Adulte d'âge moyen , Mycobacterium tuberculosis/génétique , Ontario/épidémiologie , Loi de Poisson , Facteurs de risque , Facteurs sexuels , Analyse spatio-temporelle , Tuberculose/ethnologie , Tuberculose/microbiologieRÉSUMÉ
Toronto has been the site of a recent extended tuberculosis (TB) outbreak in the homeless or under-housed population. Genotyping has identified a unique strain that continues to circulate within this population, with spread to individuals with no links to the shelter system, and anecdotally appears to progress rapidly from infection to active disease in some cases. The recent appearance and transmission of another unique strain was also identified, indicating that TB transmission continues to be a problem within the under-housed population. Enhanced surveillance utilizing molecular epidemiology is a useful tool to assist in TB control in vulnerable populations.
Sujet(s)
/statistiques et données numériques , Mycobacterium tuberculosis/génétique , Tuberculose/microbiologie , Tuberculose/transmission , Population urbaine/statistiques et données numériques , Adulte , Loi du khi-deux , Contrôle des maladies transmissibles/méthodes , Épidémies de maladies , Femelle , Génotype , Humains , Mâle , Adulte d'âge moyen , Mycobacterium tuberculosis/classification , Ontario/épidémiologie , Phénotype , Surveillance de la population , Santé publique , Tuberculose/épidémiologieRÉSUMÉ
BP3385 has been proposed as a diagnostic PCR target for discriminating between Bordetella pertussis and other Bordetella species that also infect humans. Our results demonstrate that this gene is also present in some strains of Bordetella hinzii and Bordetella bronchiseptica.
Sujet(s)
Protéines bactériennes/génétique , Techniques bactériologiques/méthodes , Bordetella pertussis/isolement et purification , Réaction de polymérisation en chaîne/méthodes , Coqueluche/diagnostic , Séquence nucléotidique , Bordetella bronchiseptica/génétique , Bordetella pertussis/génétique , ADN bactérien/composition chimique , ADN bactérien/génétique , Humains , Données de séquences moléculaires , Sensibilité et spécificité , Alignement de séquences , Analyse de séquence d'ADNRÉSUMÉ
Bordetella holmesii is a human pathogen found mainly in immunocompromised patients. A specific real-time PCR assay was developed and successfully used to identify specimens from which B. holmesii was misidentified as Bordetella pertussis and to establish the prevalence of B. holmesii in Ontario patients with pertussis-like symptoms.
Sujet(s)
Bordetelloses/épidémiologie , Bordetelloses/microbiologie , Bordetella/isolement et purification , Réaction de polymérisation en chaîne/méthodes , Bordetella/classification , Bordetelloses/anatomopathologie , Humains , Ontario/épidémiologie , Prévalence , Sensibilité et spécificitéRÉSUMÉ
This study utilized the Bordetella pertussis single-copy PCR target BP3385 as a means of confirming IS481 PCR-positive reactions with cycle threshold (C(T)) values of >35. IS481 PCRs with C(T) values of >35 cycles may represent PCR conditions where there is <1 CFU of B. pertussis per PCR.