Diverse Molecular Genotypes ofMycobacterium tuberculosisComplex Isolates Circulating in the Free State, South Africa

Tuberculosis is a serious public health concern especially in Africa and Asia. Studies describing strain diversity are lacking in the Free State region of South Africa. The aim of the study was to describe the diversity ofMycobacterium tuberculosis(M. tuberculosis) strain families in the Free State province of South Africa. A total of 86M. tuberculosisisolates were genotyped using spoligotyping. A 12-locus mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTRs) typing was used to further characterize the resulting spoligotyping clusters. SITVITWEB identified 49 different patterns with allocation to six lineages including Latin-American-Mediterranean (LAM) (18 isolates), T (14 isolates), Beijing (five isolates), S (six isolates), Haarlem (one isolate), and X (five isolates), while 37 (43.0%) orphans were identified. Eight clusters included 37 isolates with identical spoligotypes (2 to 13/cluster). MIRU-VNTR typing further differentiated three spoligotyping clusters: SIT1/Beijing/MIT17, SIT33/LAM3/MIT213, and confirmed one SIT34/S/MIT311. In addition, SpolDB3/RIM assignment of the orphan strains resulted in a further 10 LAM and 13 T families. In total, LAM (28 isolates) and T (27 isolates) cause 63% of the individual cases of MTB in our study. The Free State has a highly diverse TB population with LAM being predominant. Further studies with inclusion of multidrug-resistant strains with larger sample size are warranted.

Download Full-text

Investigation of Salmonella Enteritidis outbreaks in South Africa using multi-locus variable-number tandem-repeats analysis, 2013-2015

BMC Infectious Diseases ◽

10.1186/s12879-017-2751-8 ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 14

Author(s):

Munyadziwa Muvhali ◽

Anthony Marius Smith ◽

Andronica Moipone Rakgantso ◽

Karen Helena Keddy

Keyword(s):

South Africa ◽

Salmonella Enteritidis ◽

Tandem Repeats ◽

Variable Number ◽

Variable Number Tandem Repeats

Download Full-text

Population structure of drug-resistant Mycobacterium tuberculosis in Central Asia

BMC Infectious Diseases ◽

10.1186/s12879-019-4480-7 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Anna Engström ◽

Uladzimir Antonenka ◽

Abdylat Kadyrov ◽

Gulmira Kalmambetova ◽

Katharina Kranzer ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Population Structure ◽

Central Asia ◽

Tandem Repeats ◽

Relative Size ◽

Multidrug Resistant ◽

Variable Number ◽

Health Concern ◽

Drug Resistant ◽

Recent Emergence

Abstract Background Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan. Methods The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed. Results The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94–32 (n = 145) and 100–32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes. Conclusions Beijing clusters 94–32 and 100–32 are the dominant MTB genotypes in Central Asia. The relative size of 100–32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.

Download Full-text

Reverse zoonotic tuberculosis transmission from an emerging Uganda I strain between pastoralists and cattle in South-Eastern Nigeria

BMC Veterinary Research ◽

10.1186/s12917-019-2185-1 ◽

2019 ◽

Vol 15 (1) ◽

Cited By ~ 6

Author(s):

Hezekiah Kehinde Adesokan ◽

Victor Oluwatoyin Akinseye ◽

Elizabeth Maria Streicher ◽

Paul Van Helden ◽

Rob Mark Warren ◽

...

Keyword(s):

Public Health ◽

Mycobacterium Bovis ◽

Latin American ◽

Disease Burden ◽

Tandem Repeats ◽

Variable Number ◽

Molecular Tools ◽

Tuberculosis Transmission ◽

Public Health Challenge ◽

Variable Number Tandem Repeats

Abstract Background Tuberculosis remains a major public health challenge globally with increasing risks for inter-transmission between pastoralists and cattle in Nigeria. This study was aimed at using molecular tools to establish zoonotic transmission of tuberculosis between pastoralists and their cattle in Ebonyi State, Nigeria. Sputum (n = 149) and milk (n = 144) samples from pastoralists and cattle, respectively were screened on the assumption of subclinical infections considering unguarded human-livestock interactions. Isolates obtained were analysed using deletion typing, spoligotyping and 24-Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats (MIRU-VNTR). Results Fifty-four MTC were confirmed by deletion typing and were differentiated accordingly (M. tuberculosis: pastoralists =42, cattle = 2; M. bovis: pastoralists =1; M. africanum: pastoralists =9). Spoligotyping indicated 59.2% Uganda I/SIT46 (pastoralists =28; cattle = 1), 16.3% Latin American Mediterranean/SIT61 (pastoralists =8), 2.0% T/SIT53 (pastoralists =1) strains of M. tuberculosis and new strains of M. bovis and M. africanum. The 24-MIRU-VNTR of selected predominant cluster isolates shared by cattle and pastoralists (Uganda I/SIT46: pastoralists =9; cattle = 1) showed the same number of copies at each of the repetitive loci. Conclusions Mycobacterium bovis was confirmed in humans and a reverse zoonotic tuberculosis transmission from an emerging Uganda I M. tuberculosis strain between pastoralists and cattle in Nigeria evidenced by MIRU-VNTR. Using molecular tools will help mitigate disease burden through informed epidemiological insights.

Download Full-text

Dysglycemia is associated with Mycobacterium tuberculosis lineages in tuberculosis patients of North Lima - Peru

10.1101/2020.11.18.388124 ◽

2020 ◽

Author(s):

Kattya Lopez ◽

María B. Arriaga ◽

Juan G. Aliaga ◽

Nadia N. Barreda ◽

Oswaldo M. Sanabria ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Pulmonary Tuberculosis ◽

Latin American ◽

Tandem Repeats ◽

Scientific Evidence ◽

Variable Number ◽

Health Care Facilities ◽

Variable Number Tandem Repeats ◽

Epidemiological Characteristics

AbstractThis study was performed to investigate the role of dysglycemia on the genetic diversity of Mycobacterium tuberculosis (MTB) among pulmonary tuberculosis (TB) patients to build scientific evidence about the possible mechanisms of TB transmission. MTB isolates obtained of patients affected by pulmonary tuberculosis from health care facilities of North Lima - Peru, were analyzed using whole genome sequencing and 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem repeats (MIRU-VNTR). Subsequently, clinical and epidemiological characteristics were associated with clustering, lineages and comorbid conditions. The analysis carried out 112 pulmonary TB patients from various health centers in North Lima, 17 (15%) had diabetes mellitus (DM) and 33 (29%) had pre-diabetes (PDM). Latin American-Mediterranean, Haarlem and Beijing were the most frequent MTB lineages found in those patients. Previous TB (adjusted odds ratio [aOR]=3.65; 95%CI: 1.32-17.81), age (aOR=1.12; 95%CI: 1.03-1.45) and Beijing lineage (aOR=3.53; 95%CI: 1.08-13.2) were associated with TB-DM comorbidity. Alcoholism (aOR=2.92; 95%CI: 1.10-8.28), age (aOR=1.05; 95%CI: 1.03-1.12) and Haarlem lineage (aOR=2.54; 95%CI: 1.04-6.51) were associated with TB-PDM comorbidity. Beijing and Haarlem lineages were independently associated with TB-DM and TB-PDM comorbidities, respectively. Although these findings may be surprising, we must be cautious to suggest that dysglycemia could be associated with a highly clustering and predisposition of MTB lineages related to a serious impact on the severity of TB disease, which requires further research.

Download Full-text

Dysglycemia is associated with Mycobacterium tuberculosis lineages in tuberculosis patients of North Lima—Peru

PLoS ONE ◽

10.1371/journal.pone.0243184 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0243184

Author(s):

Kattya Lopez ◽

María B. Arriaga ◽

Juan G. Aliaga ◽

Nadia N. Barreda ◽

Oswaldo M. Sanabria ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Pulmonary Tuberculosis ◽

Latin American ◽

Tandem Repeats ◽

Scientific Evidence ◽

Variable Number ◽

Health Care Facilities ◽

Variable Number Tandem Repeats ◽

Epidemiological Characteristics

This study was performed to investigate the role of dysglycemia on the genetic diversity of Mycobacterium tuberculosis (MTB) among pulmonary tuberculosis (TB) patients to build scientific evidence about the possible mechanisms of TB transmission. MTB isolates obtained of patients affected by pulmonary tuberculosis from health care facilities of North Lima—Peru, were analyzed using whole genome sequencing and 24-locus mycobacterial interspersed repetitive-unit -variable-number tandem repeats (MIRU-VNTR). Subsequently, clinical and epidemiological characteristics were associated with clustering, lineages and comorbid conditions. The analysis carried out 112 pulmonary TB patients from various health centers in North Lima, 17 (15%) had diabetes mellitus (DM) and 33 (29%) had pre-diabetes (PDM). Latin American-Mediterranean, Haarlem and Beijing were the most frequent MTB lineages found in those patients. Previous TB (adjusted odds ratio [aOR] = 3.65; 95%CI: 1.32–17.81), age (aOR = 1.12; 95%CI: 1.03–1.45) and Beijing lineage (aOR = 3.53; 95%CI: 1.08–13.2) were associated with TB-DM comorbidity. Alcoholism (aOR = 2.92; 95%CI: 1.10–8.28), age (aOR = 1.05; 95%CI: 1.03–1.12) and Haarlem lineage (aOR = 2.54; 95%CI: 1.04–6.51) were associated with TB-PDM comorbidity. Beijing and Haarlem lineages were independently associated with TB-DM and TB-PDM comorbidities, respectively. Although these findings may be surprising, we must be cautious to suggest that dysglycemia could be associated with a highly clustering and predisposition of MTB lineages related to a serious impact on the severity of TB disease, which requires further research.

Download Full-text

Molecular characteristics of Brucella melitensis isolates from humans in Qinghai Province, China

Infectious Diseases of Poverty ◽

10.1186/s40249-021-00829-0 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Zhi-Jun Zhao ◽

Ji-Quan Li ◽

Li Ma ◽

Hong-Mei Xue ◽

Xu-Xin Yang ◽

...

Keyword(s):

Tandem Repeats ◽

Brucella Melitensis ◽

Draft Genome ◽

Geographic Origin ◽

Variable Number ◽

Human Brucellosis ◽

Molecular Characteristics ◽

Whole Genome ◽

Qinghai Province ◽

Variable Number Tandem Repeats

Abstract Background The prevalence of human brucellosis in Qinghai Province of China has been increasing rapidly, with confirmed cases distributed across 31 counties. However, the epidemiology of brucellosis transmission has not been fully elucidated. To characterize the infecting strains isolated from humans, multiple-locus variable-number tandem repeats analysis (MLVA) and whole-genome single-nucleotide polymorphism (SNP)-based approaches were employed. Methods Strains were isolated from two males blood cultures that were confirmed Brucella melitensis positive following biotyping and MLVA. Genomic DNA was extracted from these two strains, and whole-genome sequencing was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. Results The two Brucella isolates were identified as B. melitensis biovar 3 (QH2019001 and QH2019005) following conventional biotyping and were found to have differences in their variable number tandem repeats (VNTRs) using MLVA-16. Phylogenetic examination assigned the 96 strains to five genotype groups, with QH2019001 and QH2019005 assigned to the same group, but different subgroups. Moreover, the QH2019005 strain was assigned to a new subgenotype, IIj, within genotype II. These findings were then combined to determine the geographic origin of the two Brucella strains. Conclusions Utilizing a whole-genome SNP-based approach enabled differences between the two B. melitensis strains to be more clearly resolved, and facilitated the elucidation of their different evolutionary histories. This approach also revealed that QH2019005 is a member of a new subgenotype (IIj) with an ancient origin in the eastern Mediterranean Sea.

Download Full-text

Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽

10.1093/genetics/155.3.1313 ◽

2000 ◽

Vol 155 (3) ◽

pp. 1313-1320 ◽

Cited By ~ 2

Author(s):

John S Taylor ◽

Felix Breden

Keyword(s):

Tandem Repeat ◽

Poecilia Reticulata ◽

Tandem Repeats ◽

Phylogenetic Reconstruction ◽

Variable Number ◽

Repeat Motif ◽

Raw Material ◽

Direct Repeats ◽

Mt Dna ◽

Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

Download Full-text