Mycobacterium tuberculosis isolates belonging to katG gyrA group 2 are associated with clustered cases of tuberculosis in Italian patients

Prevalence and Characterization of Heterogeneous Variable-Number Tandem-Repeat Clusters Comprising Drug-Susceptible and/or Variable Resistant Mycobacterium tuberculosis Complex Isolates in the Netherlands from 2004 to 2016

The variable-number tandem-repeat (VNTR) typing method is used to study tuberculosis (TB) transmission. Clustering of Mycobacterium tuberculosis isolates with identical VNTR patterns is assumed to reflect recent transmission. Hence, clusters are thought to be homogeneous regarding antibiotic resistance. In practice, however, heterogeneous clusters are also identified. This study investigates the prevalence and characteristics of heterogeneous VNTR clusters and assesses whether isolates in these clusters remain clustered when subjected to whole-genome sequencing (WGS). In the period from 2004 to 2016, 9,072 isolates were included. Demographic and epidemiological linkage data were obtained from the Netherlands Tuberculosis Register. VNTR clusters were defined as homogeneous when isolates shared identical resistance profiles or as heterogeneous if both susceptible and (variable) resistant isolates were found. Multivariate logistic regression analysis was performed to identify factors associated with heterogeneous clustering. Isolates from 2016 were subjected to WGS, and a genetic distance of 12 single nucleotide polymorphisms (SNPs) was used as the cutoff for WGS clustering. In total, 4,661/9,072 (51%) isolates were clustered into 985 different VNTR clusters, of which 217 (22%) were heterogeneous. Patient characteristics associated with heterogeneous clustering were non-Dutch ethnicity (odds ratio [OR], 1.46 [95% confidence interval {CI}, 1.22 to 1.75]), asylum seeker (OR, 1.51 [95% CI, 1.24 to 1.85]), extrapulmonary TB (OR, 1.26 [95% CI, 1.09 to 1.46]), previous TB diagnosis (OR, 1.38 [95% CI, 1.04 to 1.82]), and not being a contact of a TB patient (OR, 1.35 [95% CI, 1.08 to 1.69]). With WGS, 34% of heterogeneous and 78% of homogeneous isolates from 2016 remained clustered. Heterogeneous VNTR clusters are common but seem to be explained by a substantial degree of false clustering by VNTR typing compared to WGS.

Current trends of Mycobacterium tuberculosis molecular epidemiology in Saudi Arabia and associated demographical factors

Data are scarce on demographical factors related to the population structure of Mycobacterium tuberculosis in Saudi Arabia. A study was conducted on 902 clinical isolates to explore current trends in the phylogeography and associated demographical factors of tuberculosis by using spoligotyping and 24 loci based MIRU-VNTR typing. Young male patients (aged 16-29 and 30-44) were predominant in this cohort. The phylogenetic diversity among M. tuberculosis isolates was found high, as almost all known genetic lineages were identified. Delhi/CAS (26.4%), EAI (13.7%) and Haarlem (11.3%) were the most common lineages observed, particularly among the low age groups (16-29 and 30-44 years), whereas elderly patients (>60 years) showed a predominance in the lineages S, Ghana, TUR and Uganda-I. A statistically significant association was observed between gender of the patients and lineages of EAI (p value 0.026) and LAM (p value 0.005). Overall, molecular strain cluster rate was 34.4% with an elevated rate among patients aged below 15 years (43.1%), while cases among the elderly (>60 years) showed the lowest degree of clustering (12.5%). The largest level of clustering was noticed among cases caused by strains of the lineages Haarlem (59.8%), Beijing (55.8%) and LAM (42.8%). The current population structure of M. tuberculosis in Saudi Arabia is highly diverse with significant associations to demography, transmission dynamics and origin of the patients. The difference in genotype distributions among low and high aged patients reflects the ongoing change in the strain population structure in the country.

Epidemiologic characterization of culture positive Mycobacterium tuberculosis patients by katG-gyrA principal genetic grouping

Molecular typing techniques make it possible to genetically characterize Mycobacterium tuberculosis isolates. Public health strategies to control the spread of tuberculosis are enhanced by the use of molecular data to study tuberculosis transmission dynamics within populations. This study compared epidemiological and clinical characteristics of three M. tuberculosis groups based on polymorphisms at katG codon 463 and gyrA codon 95 in 1893 culture-positive patients by a retrospective nested case-comparison design. Study participants, diagnosed from 1995 to 2001 in the Houston, Texas metropolitan area, were >/= 18 years old, 70% male, 66% U.S.-born, 40% Black, 29% Hispanic, 19% White, and 12% Asian/Pacific Islander. The prevalence of each principal genetic group (GG) was 30% (GG1), 52% (GG2), and 18% (GG3). Multiple logistic regression analysis showed that GG1 participants were more likely to be Asian, male, and have a history of homelessness, as compared with participants with either GG2 or GG3 isolates. GG2 participants were more likely to be Hispanic, have streptomycin-resistant isolates, and be infected with HIV than either GG1 or GG3 participants. GG3 participants were more likely to be Black or Hispanic, report illicit drug use, and live in a congregative facility at the time of diagnosis, than GG1 or GG2 participants. Ethnicity and sociodemographic findings were significant, prompting additional research into social networks, genetic susceptibility, immunology, and virulence factors.

Association between Mycobacterium tuberculosis Beijing/W lineage strain infection and extrathoracic tuberculosis: Insights from epidemiologic and clinical characterization of the three principal genetic groups of M. tuberculosis clinical isolates

Clinical strains of Mycobacterium tuberculosis can be divided into three principal genetic groups based on the single-nucleotide polymorphisms at the katG gene codon 463 and the gyrA gene codon 95. One subgroup of genetic group 1, the Beijing/W lineage, has been widely studied because of its worldwide distribution and association with outbreaks. In order to increase our understanding of the clinical and epidemiological relevance of the genetic grouping of M. tuberculosis clinical strains and the Beijing/W lineage, we investigated the genetic grouping of 679 clinical isolates of M. tuberculosis, representing 96.3% of culture-confirmed tuberculosis cases diagnosed in Arkansas between January 1996 and December 2000 using PCR and DNA sequencing. We assessed the associations of infections by different genetic groups of M. tuberculosis strains and infection by the Beijing/W lineage strains with the clinical and epidemiological characteristics of the patients using chi-square tests and multivariate logistic regression analysis. Of the 679 study isolates, 676 fell into one of the three principal genetic groups, with 63 (9.3%) in group 1, 438 (64.8%) in group 2, and 175 (25.9%) in group 3. After adjusting for potential confounding of age, gender, race/ethnicity, human immunodeficiency virus serostatus, and plcD genotype in a multivariate logistic regression model, patients infected by the Beijing/W lineage isolates were nearly three times as likely as patients infected with the non-Beijing/W lineage isolates to have an extrathoracic involvement (odds ratio [95% confidence interval], 2.85 [1.33, 6.12]). Thus, the Beijing/W lineage strains may have some special biological features that facilitate the development of extrathoracic tuberculosis.

Identification of a Haarlem genotype-specific single nucleotide polymorphism in the mgtC virulence gene of Mycobacterium tuberculosis

MgtC is a virulence factor common to several intracellular pathogens, including Mycobacterium tuberculosis, that might have been acquired through horizontal gene transfer. In the present study, we investigated the polymorphism of mgtC in clinical isolates representative of the main epidemic groups of M. tuberculosis. MgtC appears to have a low polymorphism rate in M. tuberculosis that consists exclusively of nonsynonymous mutations. We identified a single nucleotide polymorphism (SNP) at mgtC codon 182 (mgtC182) specifically associated with the Haarlem genotype. A simple PCR assay, called the "on/off switch assay," using phosphorothioate-modified primers and Pfu polymerase allowed us to distinguish Haarlem from non-Haarlem strains based on the mgtC182 SNP. The amino acid change (H182R) associated with the mgtC182 SNP in Haarlem strains does not appear to procure a selective advantage. Our results offer a simple and rapid tool to distinguish between Haarlem and non-Haarlem strains. In addition, the on/off switch assay, which allows the detection of SNPs on chromosomal DNA and M. tuberculosis cultures, provides a novel approach for the screening of known SNPs in M. tuberculosis.

Genetic diversity, determined on the basis of katG463 and gyrA95 polymorphisms, Spoligotyping, and IS6110 typing, of Mycobacterium tuberculosis complex isolates from Italy

Mycobacterium tuberculosis complex isolates (n = 248) collected during a 1-year period in Tuscany, Italy, were genotyped for the katG463 and gyrA95 polymorphisms and by standard spacer oligonucleotide typing (spoligotyping) and IS6110 restriction fragment length polymorphism (RFLP) assays. Most of the isolates (n = 212; 85.5%) belonged to genotypic groups 2 and 3, which included most isolates from Italian-born patients. The remaining isolates were genotypic group 1 organisms, which were prevalent among foreign-born patients (29 of 36; 80.6%). Spoligotype analysis detected 116 unique patterns and 34 clusters including 166 isolates. The combination of spoligotyping and IS6110 RFLP analyses yielded 28 distinct clusters including 65 identical isolates (26.2%)--22 clusters with 2 isolates, 4 clusters with 3 isolates, 1 cluster with 4 isolates, and 1 cluster with 5 isolates--thus proving a low transmission rate in the community. Predominant spoligotypes representing 50% of clustered isolates were found in six clusters that included widespread type ST53 (clade T1) with 29 isolates (11.7% of total isolates); types ST50 and ST47 (Haarlem family) with 18 isolates (7.3%) and 8 isolates (3.2%), respectively; type ST42 (Latino-American and Mediterranean clade) with 13 isolates (5.2%); new type ST1737 (named "Tuscany") with 8 isolates (3.2%); and type ST1 (W-Beijing family) with 7 isolates (2.8%). Other spoligotype families, such as the Mycobacterium africanum, East African-Indian (EAI2/Manila), and central Asia 1 (CAS1/Delhi) families (all including organisms of genotypic group 1) and the Cameroun family (genotypic group 2), were detected especially among immigrant patients. The occurrence of genotypes originally found in distant geographic areas with a high prevalence of tuberculosis may represent a hallmark for changes in the dynamics of transmission of tuberculosis in the region in the near future.

Mycobacterium tuberculosis molecular evolution in western Mediterranean Islands of Sicily and Sardinia

In this study, a total of 204 Mycobacterium tuberculosis DNAs from Sicily (n = 144) and Sardinia (n = 60) were studied by three genotyping methods. Results were analyzed both within and across islands, to define the phylogeographical specificities of the genotypes, look for their diversity and infer a molecular evolutionary scenario. A strong link between geography and tuberculosis genotypes was observed in Sardinia. The results were also matched against a world-wide genetic diversity database to compare the population structure of the tubercle bacilli in the islands. Eight common genotypes between Sicily, Sardinia and continental Italy were found which underlines the influences of the Italian mainland on the population structure on the islands and vice versa. A unified evolutionary scenario of M. tuberculosis evolution was built using numerical taxonomy and maximum parsimony (MP) methods. The finding of multiple families of M. tuberculosis strains (S, T, LAM, Haarlem), their presumed links with the major genetic groups (MGG) of M. tuberculosis complex, supports the view of independent introduction of several ancestral genotypes in Sicily and in Sardinia. We conclude that the two PCR-based genotyping combination (spoligotyping-VNTR) is an excellent tool to reconstruct M. tuberculosis phylogeny, that may be used to construct global and local evolutionary scenarios of the M. tuberculosis complex. The results obtained are paradigmatic of the complex interplay that exists between epidemic dynamics and evolutionary genetics of M. tuberculosis.

Detection of Mycobacterium tuberculosis genotypic groups by a duplex real-time PCR targeting the katG and gyrA genes

A duplex real-time PCR assay was developed for the assignment of Mycobacterium tuberculosis isolates to the three genotypic groups based on the katG463/gyrA95 polymorphism. The assay was as sensitive and specific as nucleotide sequencing and proved also able to detect unambiguously the isolate genotype in clinical specimens.