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1.
J Infect Dis ; 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38456644

ABSTRACT

Epidemiologic research on zoonotic tuberculosis historically used Mycobacterium bovis as a surrogate measure, however, increased reports of human tuberculosis caused by other animal-associated Mycobacterium tuberculosis complex members like Mycobacterium orygis necessitates their inclusion. We performed a retrospective cohort study including persons infected with any animal-lineage M. tuberculosis complex species in Alberta, Canada, from January 1995 to July 2021, identifying 42 patients (20 M. bovis, 21 M. orygis, one M. caprae). Demographic, epidemiologic and clinical characteristics were compared against persons with culture-confirmed M. tuberculosis infection. The proportion of culture-positive infections caused by M. orygis increased continuously from 2016-2020. Significantly more females at a higher median age were impacted by M. orygis, with all patients originating from South Asia. M. bovis caused significantly more extra-pulmonary disease, and disproportionately impacted young females, particularly those pregnant or post-partum. All infections were acquired abroad. These findings can aid in developing targeted public health interventions.

2.
J Infect Dis ; 2024 Aug 27.
Article in English | MEDLINE | ID: mdl-39189818

ABSTRACT

BACKGROUND: Mycobacterium abscessus complex (MABC), an opportunistic nontuberculous mycobacteria (NTM), can lead to poor clinical outcomes in pulmonary infections. Conflicting data exist on person-to-person transmission of MABC within and across healthcare facilities. To investigate further, a comprehensive retrospective study across five healthcare institutions on the Island of Montréal was undertaken. METHODS: We analyzed the genomes of 221 MABC isolates obtained from 115 individuals (2010-2018) to identify possible links. Genetic similarity, defined as ≤25 single-nucleotide polymorphisms (SNPs), was investigated through a blinded epidemiological inquiry. RESULTS: Bioinformatics analyses identified 28 sequence types (STs), including globally observed dominant circulating clones (DCCs). Further analysis revealed 210 isolate pairs within the SNP threshold. Among these pairs, there was one possible lab contamination where isolates from different patients processed in the same lab differed by only 2 SNPs. There were 37 isolate pairs from patients who had provided specimens from the same hospital; however, epidemiological analysis found no evidence of healthcare-associated person-to-person transmission between these patients. Additionally, pan-genome analysis showed higher discriminatory power than core genome analysis for examining genomic similarity. CONCLUSIONS: Genomics alone is insufficient to establish MABC transmission, particularly considering the genetic similarity and wide distribution of DCCs, although pan-genome analysis has the potential to add further insight. Our findings indicate that MABC infections in Montréal are unlikely attributable to healthcare-associated person-to-person transmission.

3.
Int J Mol Sci ; 25(11)2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38892433

ABSTRACT

Phenotypic susceptibility testing of the Mycobacterium tuberculosis complex (MTBC) isolate requires culture growth, which can delay rapid detection of resistant cases. Whole genome sequencing (WGS) and data analysis pipelines can assist in predicting resistance to antimicrobials used in the treatment of tuberculosis (TB). This study compared phenotypic susceptibility testing results and WGS-based predictions of antimicrobial resistance (AMR) to four first-line antimicrobials-isoniazid, rifampin, ethambutol, and pyrazinamide-for MTBC isolates tested between the years 2018-2022. For this 5-year retrospective analysis, the WGS sensitivity for predicting resistance for isoniazid, rifampin, ethambutol, and pyrazinamide using Mykrobe was 86.7%, 100.0%, 100.0%, and 47.8%, respectively, and the specificity was 99.4%, 99.5%, 98.7%, and 99.9%, respectively. The predictive values improved slightly using Mykrobe corrections applied using TB Profiler, i.e., the WGS sensitivity for isoniazid, rifampin, ethambutol, and pyrazinamide was 92.31%, 100%, 100%, and 57.78%, respectively, and the specificity was 99.63%. 99.45%, 98.93%, and 99.93%, respectively. The utilization of WGS-based testing addresses concerns regarding test turnaround time and enables analysis for MTBC member identification, antimicrobial resistance prediction, detection of mixed cultures, and strain genotyping, all through a single laboratory test. WGS enables rapid resistance detection compared to traditional phenotypic susceptibility testing methods using the WHO TB mutation catalog, providing an insight into lesser-known mutations, which should be added to prediction databases as high-confidence mutations are recognized. The WGS-based methods can support TB elimination efforts in Canada and globally by ensuring the early start of appropriate treatment, rapidly limiting the spread of TB outbreaks.


Subject(s)
Antitubercular Agents , Microbial Sensitivity Tests , Mycobacterium tuberculosis , Whole Genome Sequencing , Whole Genome Sequencing/methods , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/drug effects , Antitubercular Agents/pharmacology , Humans , Microbial Sensitivity Tests/methods , Retrospective Studies , Drug Resistance, Bacterial/genetics , Genome, Bacterial , Ethambutol/pharmacology , Isoniazid/pharmacology , Pyrazinamide/pharmacology , Tuberculosis/microbiology , Tuberculosis/drug therapy , Rifampin/pharmacology
4.
J Clin Microbiol ; 61(11): e0026023, 2023 11 21.
Article in English | MEDLINE | ID: mdl-37877705

ABSTRACT

A recently described member of the Mycobacterium tuberculosis complex (MTBC) is Mycobacterium orygis, which can cause disease primarily in animals but also in humans. Although M. orygis has been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphism (SNP) analysis using whole genome sequencing (WGS) that can accurately identify M. orygis and differentiate it from other members of the MTBC species. WGS-based SNP analysis was performed for 61 isolates from different provinces in Canada that were identified as M. orygis. A total of 56 M. orygis sequences from the public databases were also included in the analysis. Several unique SNPs in the gyrB, PPE55, Rv2042c, leuS, mmpL6, and mmpS6 genes were used to determine their effectiveness as genetic markers for the identification of M. orygis. To the best of our knowledge, five of these SNPs, viz., gyrB 277 (A→G), gyrB 1478 (T→C), leuS 1064 (A→T), mmpL6 486 (T→C), and mmpS6 334 (C→G), are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that the studied genomes were genetically diverse and clustered with M. orygis sequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high-confidence identification of M. orygis from MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.


Subject(s)
Mycobacterium tuberculosis , Mycobacterium , Tuberculosis , Animals , Humans , Phylogeny , Tuberculosis/diagnosis , Tuberculosis/microbiology , Whole Genome Sequencing , Polymorphism, Single Nucleotide , Mycobacterium tuberculosis/genetics
5.
Can J Infect Dis Med Microbiol ; 2022: 3505142, 2022.
Article in English | MEDLINE | ID: mdl-36046174

ABSTRACT

Tuberculosis is a significant cause of morbidity worldwide and is a priority at the provincial and federal levels in Canada. It is known that tuberculosis transmission networks are complex and span many years as well as different jurisdictions and countries. MIRU-VNTR is a universal tuberculosis genotyping method that utilizes a 24-loci pattern and it has shown promise in identifying inter and intrajurisdictional clusters within Canada. MIRU-VNTR data collected over 10 years from the National Reference Centre for Mycobacteriology (NRCM) were analyzed in this study. Some clusters were unique to a single province/territory, while others spanned multiple provinces and/or territories in Canada. The use of a universal laboratory test can enhance contact tracing, provide geographical information on circulating genotypes, and hence, aid in tuberculosis investigation by public health. The housing of all data on one platform, technical ease of the method, easy exchange of data between jurisdictions, and strong collaboration with laboratories and surveillance units at the provincial and federal levels have the potential to identify possible outbreaks in real time.

6.
BMC Infect Dis ; 20(1): 944, 2020 Dec 10.
Article in English | MEDLINE | ID: mdl-33302900

ABSTRACT

BACKGROUND: Mycobacterium abscessus is a rapidly growing mycobacteria involved in severe infections of the lung, skin, or soft tissue. Macrolides such as clarithromycin are the recommended first line drugs for treatment of M. abscessus infections. However, M. abscessus has dual mechanisms of resistance to macrolides, making treatment by macrolides difficult. A functional erm(41) gene confers for inducible resistance while acquired mutations on the 23S rRNA rrl gene confer for constitutive resistance. METHODS: We have developed a real-time PCR assay to detect both inducible and acquired resistance to clarithromycin, and compared the results to traditional erm(41) and rrl sequencing and phenotypic susceptibility testing using Sensititre™ plates. RESULTS: Of the total 126 M. abscessus isolates tested, truncated erm(41) was found in 23/126 (18.3%) of the samples, 27/126 (21.4%) had a T28C mutation in erm(41), and 2/126 (1.6%) had an acquired A2058C mutation in rrl. The phenotypic results correlated with the expected sequencing results in 121/126 samples (96%). Phenotypic testing compared to real-time PCR resolved 2 of these discrepancies by showing the existence of both erm(41) alleles in the isolates that sequencing missed. One culture was found to be mixed with two M. abscessus subsp. as per hsp65 sequencing and 2 isolates had discordance between molecular and phenotypic results. It was presumed that 3 isolates showed discrepancy between sequencing and real-time PCR, but one culture was mixed and other 2 detected both alleles by real-time PCR leading to 100% concordance when compared to sequencing. CONCLUSION: In conclusion, real-time PCR is more accurate for detection of both acquired and induced clarithromycin resistance, specifically when mixed genic profiles are present in a sample.


Subject(s)
Anti-Bacterial Agents/pharmacology , Clarithromycin/pharmacology , Drug Resistance, Bacterial/drug effects , Drug Resistance, Bacterial/genetics , Mycobacterium Infections, Nontuberculous/microbiology , Mycobacterium abscessus/drug effects , Mycobacterium abscessus/genetics , Real-Time Polymerase Chain Reaction/methods , Genes, Bacterial , Humans , Microbial Sensitivity Tests , Mutation , RNA, Ribosomal, 23S/genetics
7.
Proc Natl Acad Sci U S A ; 112(44): 13609-14, 2015 Nov 03.
Article in English | MEDLINE | ID: mdl-26483462

ABSTRACT

Nunavik, Québec suffers from epidemic tuberculosis (TB), with an incidence 50-fold higher than the Canadian average. Molecular studies in this region have documented limited bacterial genetic diversity among Mycobacterium tuberculosis isolates, consistent with a founder strain and/or ongoing spread. We have used whole-genome sequencing on 163 M. tuberculosis isolates from 11 geographically isolated villages to provide a high-resolution portrait of bacterial genetic diversity in this setting. All isolates were lineage 4 (Euro-American), with two sublineages present (major, n = 153; minor, n = 10). Among major sublineage isolates, there was a median of 46 pairwise single-nucleotide polymorphisms (SNPs), and the most recent common ancestor (MRCA) was in the early 20th century. Pairs of isolates within a village had significantly fewer SNPs than pairs from different villages (median: 6 vs. 47, P < 0.00005), indicating that most transmission occurs within villages. There was an excess of nonsynonymous SNPs after the diversification of M. tuberculosis within Nunavik: The ratio of nonsynonymous to synonymous substitution rates (dN/dS) was 0.534 before the MRCA but 0.777 subsequently (P = 0.010). Nonsynonymous SNPs were detected across all gene categories, arguing against positive selection and toward genetic drift with relaxation of purifying selection. Supporting the latter possibility, 28 genes were partially or completely deleted since the MRCA, including genes previously reported to be essential for M. tuberculosis growth. Our findings indicate that the epidemiologic success of M. tuberculosis in this region is more likely due to an environment conducive to TB transmission than a particularly well-adapted strain.


Subject(s)
Mycobacterium tuberculosis/genetics , Genes, Bacterial , Genetics, Population , Humans , Inuit , Polymorphism, Single Nucleotide , Quebec/epidemiology , Selection, Genetic , Tuberculosis/epidemiology , Tuberculosis/transmission
8.
BMC Microbiol ; 16(1): 164, 2016 07 26.
Article in English | MEDLINE | ID: mdl-27459848

ABSTRACT

BACKGROUND: The increasing emergence of drug-resistant tuberculosis presents a threat to the effective control of tuberculosis (TB). Rapid detection of drug-resistance is more important than ever to address this scourge. The purpose of this study was to genotypically characterize the first-line antitubercular drug-resistant isolates collected over 11 years in Quebec. RESULTS: The main mutations found in our resistant strains collection (n = 225) include: the S315T substitution in katG (50.2 %), the -15 C/T mutation in the inhA promoter (29 %); the S531L substitution in rpoB (43 %); the deletion 8 bp 446 / + R140S in pncA (72.9 %); the M306I (35.7 %) and M306V (21.4 %) substitutions in embB. Ten of the mutations in katG and 4 mutations identified in pncA were previously undescribed. CONCLUSION: Screening of mutations conferring resistance to first-line antituberculous drugs using DNA-sequencing approach seems to be feasible and would drastically shorten the time to determine the resistance profile compared to the proportion method.


Subject(s)
Mycobacterium tuberculosis/genetics , Tuberculosis, Multidrug-Resistant/microbiology , Amidohydrolases/genetics , Antitubercular Agents/pharmacology , Bacterial Proteins/genetics , Catalase/genetics , DNA, Bacterial/genetics , DNA-Directed RNA Polymerases/genetics , Genome, Bacterial , Genotype , Humans , Microbial Sensitivity Tests , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/isolation & purification , Oxidoreductases/genetics , Pentosyltransferases/genetics , Quebec , Sequence Analysis, DNA , Sequence Deletion , Tuberculosis/microbiology
9.
J Infect Dis ; 211(12): 1905-14, 2015 Jun 15.
Article in English | MEDLINE | ID: mdl-25576599

ABSTRACT

BACKGROUND: Between November 2011 and November 2012, a Canadian village of 933 persons had 50 culture-positive cases of tuberculosis, with 49 sharing the same genotype. METHODS: We performed Illumina-based whole-genome sequencing on Mycobacterium tuberculosis isolates from this village, during and before the outbreak. Phylogenetic trees were generated using the maximum likelihood method. RESULTS: Three distinct genotypes were identified. Strain I (n = 7) was isolated in 1991-1996. Strain II (n = 8) was isolated in 1996-2004. Strain III (n = 62) first appeared in 2007 and did not arise from strain I or II. Within strain III, there were 3 related but distinct clusters: IIIA, IIIB, and IIIC. Between 2007 and 2010, cluster IIIA predominated (11 of 22 vs 2 of 40; P < .001), whereas in 2011-2012 clusters IIIB (n = 18) and IIIC (n = 20) predominated over cluster IIIA (n = 11). Combined evolutionary and epidemiologic analysis of strain III cases revealed that the outbreak in 2011-2012 was the result of ≥6 temporally staggered events, spanning from 1 reactivation case to a point-source outbreak of 20 cases. CONCLUSIONS: After the disappearance of 2 strains of M. tuberculosis in this village, its reemergence in 2007 was followed by an epidemiologic amplification, affecting >5% of the population.


Subject(s)
Communicable Diseases, Emerging/epidemiology , Disease Outbreaks , Tuberculosis/epidemiology , Adolescent , Adult , Arctic Regions , Canada/epidemiology , Communicable Diseases, Emerging/microbiology , Female , Genome, Bacterial , Genotype , Humans , Male , Mycobacterium tuberculosis/classification , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/isolation & purification , Phylogeny , Sequence Analysis, DNA , Tuberculosis/microbiology , Young Adult
10.
J Clin Microbiol ; 52(11): 3973-7, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25210065

ABSTRACT

Mycobacterium xenopi is an opportunistic mycobacterial pathogen of increasing clinical importance. Surveillance of M. xenopi is hampered by the absence of tools for genotyping and molecular epidemiology. In this study, we describe the development and evaluation of an effective multilocus sequence typing strategy for M. xenopi.


Subject(s)
Multilocus Sequence Typing/methods , Mycobacterium Infections, Nontuberculous/microbiology , Mycobacterium xenopi/classification , Mycobacterium xenopi/genetics , Humans , Molecular Epidemiology/methods , Mycobacterium Infections, Nontuberculous/epidemiology
11.
Antibiotics (Basel) ; 13(7)2024 Jul 04.
Article in English | MEDLINE | ID: mdl-39061306

ABSTRACT

In Mycobacterium tuberculosis, molecular predictions of ethambutol resistance rely primarily on the detection of mutations within embB. However, discordance between embB406 mutations and gold standard phenotypic drug sensitivity testing (DST) questions the significance of embB406 mutations used in molecular DST. This study tabulates embB mutations found in Canadian M. tuberculosis isolates and evaluates the impact of specific mutations on ethambutol resistance. The National Reference Centre for Mycobacteriology culture collection (n = 2796) was screened for isolates with embB mutations. Phenotypic DST was performed on the BACTEC™ MGIT™ 960 at ethambutol concentrations of 2-5 µg/mL. Whole genome sequencing was used for drug resistance predictions, phylogenomics and single nucleotide polymorphism analysis. Detection of resistance-associated embB mutations corresponded to a positive predictive value of 64.3%, negative predictive value of 99.2%, 98.7% specificity, and 73.3% sensitivity compared to phenotypic DST. Two embB406 mutation subtypes (Gly406Asp, Gly406Ala) were found among 16 isolates, of which 12 were sensitive at 5 µg/mL ethambutol with variable resistance between 2-4 µg/mL. A novel frameshift mutation in regulator embR (Gln258fs) was found in nine isolates. Mutations in embB406 were associated with low-level ethambutol resistance undetectable at the recommended critical concentration (5 µg/mL). These novel mutations may exacerbate variability in ethambutol resistance.

12.
Antimicrob Agents Chemother ; 57(10): 4911-9, 2013 Oct.
Article in English | MEDLINE | ID: mdl-23877698

ABSTRACT

The broad-spectrum fluoroquinolone ciprofloxacin is a bactericidal antibiotic targeting DNA topoisomerase IV and DNA gyrase encoded by the parC and gyrA genes. Resistance to ciprofloxacin in Streptococcus pneumoniae mainly occurs through the acquisition of mutations in the quinolone resistance-determining region (QRDR) of the ParC and GyrA targets. A role in low-level ciprofloxacin resistance has also been attributed to efflux systems. To look into ciprofloxacin resistance at a genome-wide scale and to discover additional mutations implicated in resistance, we performed whole-genome sequencing of an S. pneumoniae isolate selected for resistance to ciprofloxacin in vitro (128 µg/ml) and of a clinical isolate displaying low-level ciprofloxacin resistance (2 µg/ml). Gene disruption and DNA transformation experiments with PCR fragments harboring the mutations identified in the in vitro S. pneumoniae mutant revealed that resistance is mainly due to QRDR mutations in parC and gyrA and to the overexpression of the ABC transporters PatA and PatB. In contrast, no QRDR mutations were identified in the genome of the S. pneumoniae clinical isolate with low-level resistance to ciprofloxacin. Assays performed in the presence of the efflux pump inhibitor reserpine suggested that resistance is likely mediated by efflux. Interestingly, the genome sequence of this clinical isolate also revealed mutations in the coding region of patA and patB that we implicated in resistance. Finally, a mutation in the NAD(P)H-dependent glycerol-3-phosphate dehydrogenase identified in the S. pneumoniae clinical strain was shown to protect against ciprofloxacin-mediated reactive oxygen species.


Subject(s)
Anti-Bacterial Agents/pharmacology , Ciprofloxacin/pharmacology , Streptococcus pneumoniae/drug effects , Streptococcus pneumoniae/metabolism , Genome, Bacterial/genetics , Microbial Sensitivity Tests , Mutation , Reactive Oxygen Species/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Streptococcus pneumoniae/genetics
13.
Can J Microbiol ; 58(8): 953-64, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22803574

ABSTRACT

Nontuberculosis mycobacteria (NTM) are an important cause of human disease and infections. Though less notorious than tuberculosis, these infections are clinically significant and have been associated with outbreaks in various settings. To accommodate outbreak investigations for the numerous species of NTM, we evaluated a DiversiLab repetitive-sequence-based PCR (rep-PCR) kit for genotyping of mycobacteria. This kit was used to genotype both rapidly and slowly growing mycobacteria and was compared with other PCR-based genotyping methods, including random amplified polymorphic DNA (RAPD) analysis, hsp65 gene sequencing, and mycobacterial interspersed repetitive unit - variable number of tandem repeat (MIRU-VNTR) analysis. Compared with RAPD analysis, rep-PCR achieved better reproducibility in testing. When compared with hsp65 gene sequencing and MIRU-VNTR for Mycobacterium avium , rep-PCR provided results that agreed with these less discriminatory genotyping methods but provided a higher level of discrimination for situations such as outbreak investigations. We also evaluated the kit for its ability to identify closely related rapidly growing NTM. While rep-PCR was informative in some cases, a much larger library of isolates would be necessary to truly evaluate it as an identification tool. Overall, rep-PCR was able to provide improved reproducibility over RAPD and a discriminatory genotyping method for the isolates evaluated in this study.


Subject(s)
Bacterial Typing Techniques/standards , Nontuberculous Mycobacteria/genetics , Polymerase Chain Reaction , Random Amplified Polymorphic DNA Technique , Cluster Analysis , Genotype , Nontuberculous Mycobacteria/classification , Reproducibility of Results
14.
J Biol Chem ; 285(4): 2227-31, 2010 Jan 22.
Article in English | MEDLINE | ID: mdl-19948723

ABSTRACT

Vitamin D signaling through its nuclear vitamin D receptor has emerged as a key regulator of innate immunity in humans. Here we show that hormonal vitamin D, 1,25-dihydroxyvitamin D(3), robustly stimulates expression of pattern recognition receptor NOD2/CARD15/IBD1 gene and protein in primary human monocytic and epithelial cells. The vitamin D receptor signals through distal enhancers in the NOD2 gene, whose function was validated by chromatin immunoprecipitation and chromatin conformation capture assays. A key downstream signaling consequence of NOD2 activation by agonist muramyl dipeptide is stimulation of NF-kappaB transcription factor function, which induces expression of the gene encoding antimicrobial peptide defensin beta2 (DEFB2/HBD2). Pretreatment with 1,25-dihydroxyvitamin D(3) synergistically induced NF-kappaB function and expression of genes encoding DEFB2/HBD2 and antimicrobial peptide cathelicidin in the presence of muramyl dipeptide. Importantly, this synergistic response was also seen in macrophages from a donor wild type for NOD2 but was absent in macrophages from patients with Crohn disease homozygous for non-functional NOD2 variants. These studies provide strong molecular links between vitamin D deficiency and the genetics of Crohn disease, a chronic incurable inflammatory bowel condition, as Crohn's pathogenesis is associated with attenuated NOD2 or DEFB2/HBD2 function.


Subject(s)
Calcitriol/pharmacology , Crohn Disease , Nod2 Signaling Adaptor Protein/genetics , Vitamin D Deficiency , beta-Defensins/genetics , Acetylmuramyl-Alanyl-Isoglutamine/pharmacology , Adjuvants, Immunologic/pharmacology , Calcitriol/metabolism , Crohn Disease/genetics , Crohn Disease/immunology , Crohn Disease/metabolism , Drug Synergism , Epithelial Cells/immunology , Humans , Macrophages/immunology , Macrophages/metabolism , Monocytes/immunology , Monocytes/metabolism , NF-kappa B/metabolism , Signal Transduction/immunology , Transcriptional Activation/immunology , Vitamin D Deficiency/genetics , Vitamin D Deficiency/immunology , Vitamin D Deficiency/metabolism
15.
J Clin Microbiol ; 49(12): 4112-6, 2011 Dec.
Article in English | MEDLINE | ID: mdl-21998413

ABSTRACT

The purpose of this study was to establish a standardized protocol for second-line antimicrobial susceptibility testing of Mycobacterium tuberculosis using the Bactec MGIT 960 system in Canadian laboratories. Four Canadian public health laboratories compared the susceptibility testing results of 9 second-line antimicrobials between the Bactec 460 and Bactec MGIT 960 systems. Based on the data generated, we have established that the Bactec MGIT 960 system provides results comparable to those obtained with the previous Bactec 460 method. The critical concentrations established for the testing of the antimicrobials used are as follows: amikacin, 1 µg/ml; capreomycin, 2.5 µg/ml; ethionamide, 5 µg/ml; kanamycin, 2.5 µg/ml; linezolid, 1 µg/ml; moxifloxacin, 0.25 µg/ml; ofloxacin, 2 µg/ml; p-aminosalicylic acid, 4 µg/ml; rifabutin, 0.5 µg/ml.


Subject(s)
Antitubercular Agents/pharmacology , Microbial Sensitivity Tests/methods , Microbial Sensitivity Tests/standards , Mycobacterium tuberculosis/drug effects , Canada , Humans
16.
Biomed Res Int ; 2021: 5553173, 2021.
Article in English | MEDLINE | ID: mdl-34258267

ABSTRACT

Real-time genome monitoring of the SARS-CoV-2 pandemic outbreak is of utmost importance for designing diagnostic tools, guiding antiviral treatment and vaccination strategies. In this study, we present an accurate method for temporal and geographical comparison of mutational events based on GISAID database genome sequencing. Among 42523 SARS-CoV-2 genomes analyzed, we found 23202 variants compared to the reference genome. The Ti/Tv (transition/transversion) ratio was used to filter out possible false-positive errors. Transition mutations generally occurred more frequently than transversions. Our clustering analysis revealed remarkable hotspot mutation patterns for SARS-CoV-2. Mutations were clustered based on how their frequencies changed over time according to each geographical location. We observed some clusters showing a clear variation in mutation frequency and continuously evolving in the world. However, many mutations appeared in specific periods without a clear pattern over time. Various important nonsynonymous mutations were observed, mainly in Oceania and Asia. More than half of these mutations were observed only once. Four hotspot mutations were found in all geographical locations at least once: T265I (NSP2), P314L (NSP12), D614G (S), and Q57H (ORF3a). The current analysis of SARS-CoV-2 genomes provides valuable information on the geographical and temporal mutational evolution of SARS-CoV-2.


Subject(s)
COVID-19 , Databases, Nucleic Acid , Evolution, Molecular , Genome, Viral , Mutation , Pandemics , Phylogeny , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/genetics , Humans
17.
Open Forum Infect Dis ; 6(4): ofz088, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30949534

ABSTRACT

Mycobacterium africanum is an important cause of human tuberculosis and is found almost exclusively in West Africa. We identified a cluster of patients in Montreal, Canada, with M africanum disease that share identical genotypic signatures by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and a putative epidemiological link, thus providing evidence of possible local transmission of M africanum in Montreal over a 10-year period.

18.
Int J Mycobacteriol ; 8(3): 273-280, 2019.
Article in English | MEDLINE | ID: mdl-31512604

ABSTRACT

Background: Mycobacterium abscessus is a rapid growing nontuberculous mycobacteria (NTM) and a clinically significant pathogen capable of causing variable infections in humans that are difficult to treat and may require months of therapy/surgical interventions. Like other NTMs, M. abscessus can be associated with outbreaks leading to complex investigations and treatment of affected cases. Typing schemes for bacterial pathogens provide numerous applications; including identifying chain of transmission and tracking genomic evolution, are lacking or limited for many NTMs including M. abscessus. Methods: We extended the existing scheme from PubMLST using whole-genome data for M. abscessus by extracting data for 15 genetic regions within the M. abscessus genome. A total of 168 whole genomes and 11 gene sequences were used to build this scheme (MAB-multilocus sequence typing [MLST]). Results: All seven genes from the PubMLST scheme, namely argH, cya, gnd, murC, pta, purH, and rpoB, were expanded by 10, 14, 13, 10, 13, 10, and 9 alleles, respectively. Another eight novel genes were added including hsp 65, erm(41), arr, rrs, rrl, gyrA, gyrB, and recA with 16, 16, 25, 7, 32, 35, 29, and 15 alleles, respectively, with 85 unique sequence types identified among all isolates. Conclusion: MAB-MLST can provide identification of M. abscessus complex to the subspecies level based on three genes and can provide antimicrobial resistance susceptibility prediction based on results from seven genes. MAB-MLST generated a total of 85 STs, resulting in subtyping of 90 additional isolates that could not be genotyped using PubMLST and yielding results comparable to whole-genome sequencing (WGS). Implementation of a Galaxy-based data analysis tool, MAB-MLST, that simplifies the WGS data and yet maintains a high discriminatory index that can aid in deciphering an outbreak has vast applicability for routine diagnostics.


Subject(s)
Multilocus Sequence Typing , Mycobacterium abscessus/classification , Whole Genome Sequencing , Bacterial Proteins/genetics , Bacterial Typing Techniques , DNA, Bacterial , Drug Resistance, Multiple, Bacterial/genetics , Genome, Bacterial , Genotype , Mycobacterium Infections, Nontuberculous/microbiology , Mycobacterium abscessus/genetics , Phylogeny , Sequence Analysis, DNA
19.
J Leukoc Biol ; 82(6): 1437-45, 2007 Dec.
Article in English | MEDLINE | ID: mdl-18040083

ABSTRACT

Phagosomes containing M. tuberculosis and M. bovis BCG interact normally with early endosomes but fail to fuse with late endosomes and lysosomes. Whereas many early events of mycobacterial phagosomes have been elucidated, the exact mechanism of the inhibition of fusion with lysosomes is still unclear. Several Rab GTPase proteins were shown to be involved in membrane fusion and vesicular transport. In particular, Rab7 associates with the phagosomal membrane and regulates the fusion between late endosomes and lysosomes. This function of Rab7 was shown to be mediated in epithelial cell models by the Rab7 effector RILP (Rab7-interacting lysosomal protein). However, the relevance of Rab7-RILP interaction to phagosome biogenesis in macrophage infected with mycobacteria is still unknown. In this study, cotransfection of RAW 264.7 cells with Rab7 and RILP revealed that Rab7-RILP interaction occurs in macrophages ingesting latex beads. Thereafter, this cell system model was used to demonstrate that infection with live but not killed M. bovis BCG inhibited RILP recruitment despite Rab7 acquisition by the phagosome. Further investigation using immobilized RILP to pull down active Rab7 (GTP-bound form) from macrophage lysates demonstrated that inactive Rab7 (GDP-bound form) predominates in cells infected with live BCG. In addition, cell-free system experiments demonstrated that BCG culture supernatant contains a factor that catalyzes the GTP/GDP switch on recombinant Rab7 molecules. Such a factor was shown to diffuse beyond BCG phagosomes and target other Rab7-positive compartments. These findings suggest that live mycobacteria express within the macrophage a Rab7 deactivating factor leading to abortion of RILP-mediated fusion with lysosomes.


Subject(s)
Carrier Proteins/metabolism , Mycobacterium bovis/physiology , Phagosomes/metabolism , Phagosomes/microbiology , rab GTP-Binding Proteins/metabolism , Animals , Diffusion , Macrophages/cytology , Macrophages/microbiology , Mice , Mice, Inbred C57BL , Microbial Viability , Protein Binding , rab7 GTP-Binding Proteins
20.
Retin Cases Brief Rep ; 12(4): 326-330, 2018.
Article in English | MEDLINE | ID: mdl-27893591

ABSTRACT

BACKGROUND: Intravesical Bacillus Calmette-Guérin (BCG) instillation has become one of the mainstays of adjunctive therapy in the treatment of superficial bladder cancer. Ophthalmologic complications are rare, but few cases are reported in the literature. METHODS: Retrospective observational case report. RESULTS: The authors report a case of unilateral Mycobacterium bovis BCG endophthalmitis after intravesical BCG instillations. Despite appropriate systemic antituberculous and corticosteroid therapy, the patient almost completely lost sight in the affected eye. This is the fourth case in the literature of proven M. bovis endophthalmitis suggesting a direct choroidal mycobacterial infection and not only a hypersensitivity immunologic reaction as previously suggested. CONCLUSION: This case highlights the direct choroidal mycobacterial infection of the disease after BCG instillations for bladder cancer and failure of treatment despite culture-proven drug sensitivity, thus suggesting the need to revaluate adequate treatment to avoid loss of vision.


Subject(s)
BCG Vaccine/adverse effects , Endophthalmitis/microbiology , Eye Infections, Bacterial/microbiology , Immunotherapy/adverse effects , Mycobacterium Infections/microbiology , Administration, Intravesical , Aged, 80 and over , Endophthalmitis/etiology , Humans , Male , Mycobacterium bovis , Retrospective Studies
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