Genetic diversity of human isolates of Mycobacterium bovis assessed by spoligotyping and Variable Number Tandem Repeat genotyping

Lari, Nicoletta; Bimbi, Nicola; Rindi, Laura; Tortoli, Enrico; Garzelli, Carlo

doi:10.1016/j.meegid.2010.09.004

Cited by 23 publications

(17 citation statements)

References 27 publications

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“…2). Revisiting a recently published MST employed to study M. bovis strains, we found that there were about 250,000 possible alternative solutions (Table 1) with the standard equidistant distance matrix utilized by Lari et al (13). By simply using an arithmetic distance matrix optimal for VNTRs, the number of alternative trees could be reduced to about 7,000.…”

Section: Discussionmentioning

confidence: 89%

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Inadequacies of Minimum Spanning Trees in Molecular Epidemiology

Salipante

Hall

2011

J Clin Microbiol

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Minimum spanning trees (MSTs) are frequently used in molecular epidemiology research to estimate relationships among individual strains or isolates. Nevertheless, there are significant caveats to MST algorithms that have been largely ignored in molecular epidemiology studies and that have the potential to confound or alter the interpretation of the results of those analyses. Specifically, (i) presenting a single, arbitrarily selected MST illustrates only one of potentially many equally optimal solutions, and (ii) statistical metrics are not used to assess the credibility of MST estimations. Here, we survey published MSTs previously used to infer microbial population structure in order to determine the effect of these factors. We propose a technique to estimate the number of alternative MSTs for a data set and find that multiple MSTs exist for each case in our survey. By implementing a bootstrapping metric to evaluate the reliability of alternative MST solutions, we discover that they encompass a wide range of credibility values. On the basis of these observations, we conclude that current approaches to studying population structure using MSTs are inadequate. We instead propose a systematic approach to MST estimation that bases analyses on the optimal computation of an input distance matrix, provides information about the number and configurations of alternative MSTs, and allows identification of the most credible MST or MSTs by using a bootstrapping metric. It is our hope this algorithm will become the new "gold standard" approach for analyzing MSTs for molecular epidemiology so that this generally useful computational approach can be used informatively and to its full potential.Although a classic problem of academic mathematics (10), minimum spanning trees (MSTs) have become an increasingly common tool for molecular epidemiology research. With a set of pairwise distances that describe the degree of dissimilarity among individuals, an MST represents a set of edges (connections) that link together nodes (individuals) by the shortest possible distance. In molecular epidemiology, this path is interpreted as the most likely chain of pathogen transmission. Given that MSTs are calculated from simple arithmetic distance matrices, they are particularly useful for examining relationships of organisms over short time scales, such as disease outbreaks or the short-range transmission of pathogens within communities, where not enough genetic diversity has accrued to permit the use of more mathematically sophisticated algorithms for inferring population structure, such as phylogenetic analysis (20) or model-based clustering algorithms (7).Despite their popularity, there are serious problems in applying MSTs to molecular epidemiology that are almost invariably overlooked. (i) Although a single MST is reported by virtually all algorithms, there are frequently multiple, equally optimal solutions to the MST problem. In any data set, there can exist several equally parsimonious paths if two or more edges have the same lengths. In ...

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Section: Discussionmentioning

confidence: 89%

“…We therefore considered data from a survey of prior publications (1,3,11,13,16,17,19,(22)(23)(24) where MSTs had been used to draw inferences about population structure from various data, including spoligotypes, VNTRs, DNA sequences, and multilocus sequence types (MLST).…”

Section: Resultsmentioning

confidence: 99%

Inadequacies of Minimum Spanning Trees in Molecular Epidemiology

Salipante

Hall

2011

J Clin Microbiol

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“…However, in some geographical settings, this cost-effective high-throughput technique does not offer adequate discrimination (2,3,4) and is thus complemented with mycobacterial interspersed repetitive-unit-variablenumber tandem-repeat (MIRU-VNTR) typing (5,6). The MIRU-VNTR technique has been evaluated in many countries using different sets of makers (2,4,(7)(8)(9)(10)(11)(12)(13)(14)(15).…”

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confidence: 99%

Splitting of a Prevalent Mycobacterium bovis Spoligotype by Variable-Number Tandem-Repeat Typing Reveals High Heterogeneity in an Evolving Clonal Group

et al. 2013

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Bovine tuberculosis (Mycobacterium bovis) remains a concern in Spain; although herd prevalence has been considerably reduced since the systematic implementation of the national eradication program in the 1990s, infection still affected 1.33% of herds in 2011 (per the Ministry of the Environment and Rural and Marine Affairs). In consideration of the economic and public health implications of this zoonosis, tracing the source of infection by genotyping has become a key element within the program. The most widely used technique to type M. bovis isolates is direct variable repeat (DVR) spoligotyping (1). However, in some geographical settings, this cost-effective high-throughput technique does not offer adequate discrimination (2, 3, 4) and is thus complemented with mycobacterial interspersed repetitive-unit-variablenumber tandem-repeat (MIRU-VNTR) typing (5, 6). The MIRU-VNTR technique has been evaluated in many countries using different sets of makers (2, 4, 7-15).In recent surveys in the Iberian Peninsula, SB0121 was found to be the most frequent spoligotype of M. bovis (26.3% in Portugal [16] and 27.9% in Spain [17]). These studies showed that high levels of discrimination could be achieved by spoligotyping (discriminatory index [D] ϭ 0.89 and 0.87 in Portugal and Spain, respectively), although subsequent studies from Portugal found that discrimination actually increased with MIRU-VNTR typing (12,13).In this study, we used nine MIRU-VNTR markers to type a panel of randomly selected Spanish M. bovis isolates with the spoligotype SB0121. The allelic diversity and overall discriminatory power of the technique were evaluated, using several different formats. Additionally, MIRU-VNTR was applied to all the infected animals from farms infected with M. bovis SB0121 to evaluate if heterogeneity was underdetected. MATERIALS AND METHODSMycobacterial strains. The study was carried out in M. bovis isolates with spoligotype SB0121 that were sampled from across Spain between 1997 and 2010. To evaluate the discriminatory power of MIRU-VNTR, we used a panel (n ϭ 115) (see Table S1 in the supplemental material) comprising 111 isolates selected randomly from 3,863 M. bovis SB0121 isolates from the Spanish strain collection at the VISAVET Health Surveillance Centre affecting animals plus four additionally selected M. bovis isolates from less frequently affected species. The isolates originated from cattle (Bos taurus) (n ϭ 98), goats (Capra aegagrus hircus) (n ϭ 2), wild boars (Sus scrofa) (n ϭ 7), red deer (Cervus elaphus) (n ϭ 2), fallow deer (Dama dama) (n ϭ 2), badgers (Meles meles) (n ϭ 2 [18]), and domestic pigs (Sus scrofa domestica) (n ϭ 2).To evaluate potential heterogeneity within the farms infected by M. bovis SB0121, we randomly selected 15 farms from 1,342 cattle farms from which isolates were included in the strain collection to design a second panel that comprised all the SB0121 isolates obtained from infected animals from these farms (total n ϭ 176; number of isolates per farm, 2 to 31).

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“…Generally, these preclinical studies are performed with historic laboratory-adapted M. tuberculosis strains such as H37Rv (ATCC 25618 and 27294) (22,29) or Erdman (ATCC 35801) (9). M. tuberculosis is a member of the M. tuberculosis complex, and genetic diversity has recently been linked to clinical, pathogenic, and immunologic heterogeneity in disease progression and outcomes (5,12,30). Strains are currently being classified into six major phylogenic clades: East African, East Asian, Euro-American, Indo-Oceanic, and two West African (M. africanum) types (13,14).…”

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confidence: 99%

Importance of Confirming Data on the In Vivo Efficacy of Novel Antibacterial Drug Regimens against Various Strains of Mycobacterium tuberculosis

Groote

Gruppo

Woolhiser

et al. 2012

Antimicrob Agents Chemother

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In preclinical testing of antituberculosis drugs, laboratory-adapted strains of Mycobacterium tuberculosis are usually used both for in vitro and in vivo studies. However, it is unknown whether the heterogeneity of M. tuberculosis stocks used by various laboratories can result in different outcomes in tests of antituberculosis drug regimens in animal infection models. In head-to-head studies, we investigated whether bactericidal efficacy results in BALB/c mice infected by inhalation with the laboratory-adapted strains H37Rv and Erdman differ from each other and from those obtained with clinical tuberculosis strains. Treatment of mice consisted of dual and triple drug combinations of isoniazid (H), rifampin (R), and pyrazinamide (Z). The results showed that not all strains gave the same in vivo efficacy results for the drug combinations tested. Moreover, the ranking of HRZ and RZ efficacy results was not the same for the two H37Rv strains evaluated. The magnitude of this strain difference also varied between experiments, emphasizing the risk of drawing firm conclusions for human trials based on single animal studies. The results also confirmed that the antagonism seen within the standard HRZ regimen by some investigators appears to be an M. tuberculosis strainspecific phenomenon. In conclusion, the specific identity of M. tuberculosis strain used was found to be an important variable that can change the apparent outcome of in vivo efficacy studies in mice. We highly recommend confirmation of efficacy results in late preclinical testing against a different M. tuberculosis strain than the one used in the initial mouse efficacy study, thereby increasing confidence to advance potent drug regimens to clinical trials.

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Genetic diversity of human isolates of Mycobacterium bovis assessed by spoligotyping and Variable Number Tandem Repeat genotyping

Cited by 23 publications

References 27 publications

Inadequacies of Minimum Spanning Trees in Molecular Epidemiology

Inadequacies of Minimum Spanning Trees in Molecular Epidemiology

Splitting of a Prevalent Mycobacterium bovis Spoligotype by Variable-Number Tandem-Repeat Typing Reveals High Heterogeneity in an Evolving Clonal Group

Importance of Confirming Data on the In Vivo Efficacy of Novel Antibacterial Drug Regimens against Various Strains of Mycobacterium tuberculosis

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