MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria

Weniger, Thomas; Krawczyk, Justina; Supply, Philip; Niemann, Stefan; Harmsen, Dag

doi:10.1093/nar/gkq351

Cited by 287 publications

(258 citation statements)

References 24 publications

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“…For the first step, we investigated the population structure and classified all strains in major phylogenetic lineages of the MTBC through combined analysis of IS6110 DNA fingerprint, 24-loci MIRU-VNTR, and spoligotyping patterns ( Fig. 1) using a reference strain collection and the tools available at the MIRU-VNTRplus webpage (http://www.miru-vntrplus .org) (18).…”

Section: Resultsmentioning

confidence: 99%

Evaluation of Mycobacterium tuberculosis Typing Methods in a 4-Year Study in Schleswig-Holstein, Northern Germany

et al. 2011

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In order to evaluate the discriminatory power of different methods for genotyping of Mycobacterium tuberculosis complex (MTBC) isolates, we compared the performance of (i) IS6110 DNA fingerprint typing, (ii) spoligotyping, and (iii) 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing in a long-term study on the epidemiology of tuberculosis (TB) in Schleswig-Holstein, the northernmost federal state of Germany. In total, we analyzed 277 MTBC isolates collected from patients between the years 2006 and 2010. The collection comprised a broad spectrum of 13 different genotypes, among which strains of the Haarlem genotype (31%) were most prominent, followed by strains belonging to the Delhi and Beijing lineages (7% and 6%, respectively). On the basis of IS6110 restriction fragment length polymorphism (RFLP) and spoligotyping analyses, 211 isolates had unique patterns (76%) and 66 isolates (24%) were in 20 clusters. MIRU-VNTR combined with spoligotyping analyses revealed 202 isolates with unique patterns (73%) and 75 isolates in 18 clusters (27%). Overall, there was 93.1% concordance between the typing results obtained; 198 strains were identified as unique, and 60 isolates were clustered by both typing combinations (including all 31 isolates with confirmed epidemiological links). Of the remaining 19 isolates with discrepant results, 15 were falsely clustered by MIRU-VNTR (six Beijing genotype strains) and four were clustered by IS6110 RFLP (low IS6110 copy number) only. In conclusion, in the study population investigated, a minority of isolates, especially of the Beijing genotype, clustered by standard 24-loci MIRU-VNTR and without an obvious epidemiological link may require second-line typing by IS6110 RFLP or hypervariable MIRU-VNTR loci.

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Section: Resultsmentioning

confidence: 99%

Evaluation of Mycobacterium tuberculosis Typing Methods in a 4-Year Study in Schleswig-Holstein, Northern Germany

et al. 2011

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“…The seven unique M. pinnipedii VNTR profiles were analyzed using the MIRU-VNTRplus webbased application (Alix-Beguec et al 2008;Weniger et al 2010;). Clustering analysis used a distance matrix generated using the most conservative coefficient-a categorical distance-and the dendrogram was constructed with the unweighted pair-group method with arithmetic mean.…”

Section: Statistical Methods For Dendrogrammentioning

confidence: 99%

The Seal Tuberculosis Agent, Mycobacterium Pinnipedii, Infects Domestic Cattle in New Zealand: Epidemiologic Factors and Dna Strain Typing

Loeffler¹,

Lisle

Neill³

et al. 2014

Journal of Wildlife Diseases

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ABSTRACT:The fur seal (Arctocephalus forsteri), which is abundant in coastal areas of New Zealand, harbors several zoonotic pathogens, including Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis complex. We describe the microbiology and epidemiology of seven cases of M. pinnipedii infection in beef cattle (Bos primigenius) in coastal areas of New Zealand in 1991-2011. Epidemiologic factors were analyzed on six case farms and a telephone survey of 55 neighboring farms. A DNA-strain typing, using analysis of variable number tandem repeats and the direct repeats (VNTR/DR) of those isolates, was used to compare them to M. bovis isolates commonly found in New Zealand cattle and wildlife. In all cases of M. pinnipedii in cattle, only one animal in the herd was found to be infected. In six of seven cases, the lesions were in the thoracic lymph nodes, indicating a likely aerosol pathway. The lack of multiple cases within a herd suggests that cow-to-cow transmission is uncommon, if it occurs at all. There was no significant difference between case and control farms in distance to sea, herd size, herd type, or farming practice. The odds ratio for access to the beach for cattle on the Chatham Islands was significantly higher than it was for farms on the mainland coastal areas (odds ratio [OR]53.6, 95% CI51.1-11.4) Likewise, the odds ratio for acquiring tuberculosis was increased when farmers had seen seals on the property (OR5 9, 95% CI51.4-56.1 ). In all case farms, cattle had access to seals by beach grazing areas or waterways connecting directly with the ocean. The VNTR/DR typing of the isolates showed some variation in the M. pinnipedii isolates, with only two being identical; all isolates were easily distinguishable from M. bovis isolates.

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“…Cluster analysis of the MLVA typing data was done using the MLVA plus online tools software (www.miru-vntrplus. org/) [24]. Double locus variation was the maximum locus difference within a CC [25].…”

Section: Identification Of Carbapenemase and Integron Genesmentioning

confidence: 99%

Significant spread of extensively drug-resistant Acinetobacter baumannii genotypes of clonal complex 92 among intensive care unit patients in a university hospital in southern Iran

Saffari

Monsen

Karmostaji

et al. 2017

Journal of Medical Microbiology

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MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria

Cited by 287 publications

References 24 publications

Evaluation of Mycobacterium tuberculosis Typing Methods in a 4-Year Study in Schleswig-Holstein, Northern Germany

Evaluation of Mycobacterium tuberculosis Typing Methods in a 4-Year Study in Schleswig-Holstein, Northern Germany

The Seal Tuberculosis Agent, Mycobacterium Pinnipedii, Infects Domestic Cattle in New Zealand: Epidemiologic Factors and Dna Strain Typing

Significant spread of extensively drug-resistant Acinetobacter baumannii genotypes of clonal complex 92 among intensive care unit patients in a university hospital in southern Iran

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