Genomic Analysis Distinguishes
            <i>Mycobacterium africanum</i>

Mostowy, Serge; Onipede, Anthony; Gagneux, Sébastien; Niemann, Stefan; Kremer, Kristin; Desmond, Edward; Kato‐Maeda, Midori; Behr, Marcel A.

doi:10.1128/jcm.42.8.3594-3599.2004

Cited by 91 publications

(94 citation statements)

References 44 publications

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“…In various mycobacterial species, LSPs represent robust and accurate markers for mapping of chromosomal imbalances. In M. tuberculosis (15,32,58), Mycobacterium africanum (40), M. bovis (39), the vaccine strain M. bovis BCG (6,19), and in other mycobacteria (18,35,42,43,48), most known LSPs have been identified using microarray technologies. Previous identification of RDs in a collection of M. ulcerans patient isolates originating from different regions worldwide where BU is endemic suggested that a whole-genome microarray might lead to the identification of LSPs also at a regional level (47).…”

Section: Discussionmentioning

confidence: 99%

Lack of Insertional-Deletional Polymorphism in a Collection of Mycobacterium ulcerans Isolates from Ghanaian Buruli Ulcer Patients

et al. 2009

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Mycobacterium ulcerans causes the devastating infectious skin disease Buruli ulcer and has a monomorphic population structure. The resolution of conventional genetic fingerprinting methods is therefore not sufficient for microepidemiological studies aiming to characterize transmission pathways. In a previous comparative genomic hybridization analysis with a microarray covering part of the M. ulcerans genome, we have found extensive insertional-deletional sequence polymorphisms among M. ulcerans isolates of diverse geographic origins that allowed us to distinguish between strains coming from different continents. Since large numbers of insertion sequences are spread over the genome of African M. ulcerans strains, we reasoned that these may drive large sequence polymorphisms in otherwise clonal local mycobacterial populations. In this study, we used a printed DNA microarray covering the whole genome of the Ghanaian M. ulcerans reference strain Agy99 for comparative genomic hybridization. The assay identified multiple regions of difference when DNA of a Japanese M. ulcerans strain was analyzed. In contrast, not a single insertional-deletional genomic variation was found within a panel of disease isolates coming from an area of Ghana where Buruli ulcer is endemic. These results indicate that, despite the expectations deduced from other mycobacterial pathogens, only analyses of single nucleotide polymorphisms will have the potential to differentiate local populations of M. ulcerans.

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Section: Discussionmentioning

confidence: 99%

Lack of Insertional-Deletional Polymorphism in a Collection of Mycobacterium ulcerans Isolates from Ghanaian Buruli Ulcer Patients

et al. 2009

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“…In the previous study the species were determined on the basis of a combination of biochemical testing and DNA typing (36). However, identification of mycobacterial strains has since improved by the use of chromosomal deletions (10,28,44,48), SNPs (28), and sequencing of the 16S rRNA gene DNA (8,33 (11,44,45). The latter designation was established after revision of the interpretative guidelines used for analysis of genetic data (44).…”

Section: Methodsmentioning

confidence: 99%

“…However, identification of mycobacterial strains has since improved by the use of chromosomal deletions (10,28,44,48), SNPs (28), and sequencing of the 16S rRNA gene DNA (8,33 (11,44,45). The latter designation was established after revision of the interpretative guidelines used for analysis of genetic data (44). The M. tuberculosis strains from this collection represent at least 17 genotype families or subfamilies, as determined by previous studies (35,36) and a large spoligotype database described by Filliol et al (17,18).…”

Section: Methodsmentioning

confidence: 99%

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Discriminatory Power and Reproducibility of Novel DNA Typing Methods forMycobacterium tuberculosisComplex Strains

et al. 2005

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In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. (J. Clin. Microbiol. 37:2607-2618, 1999). This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.

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“…M. africanum type II (lack of spacer 40) is isolated predominantly in Uganda (15), and although we obtained six spoligotypes lacking spacer 40, all of ours were aerophilic on Lebek media, which is not the case for M. africanum. Indeed, recent genomic analysis could not differentiate M. africanum subtype II from modern M. tuberculosis, casting doubt on whether subtype II should be considered separately from M. tuberculosis (14). In total, spoligotyping identified 13 strains with the Cameroon family spoligotype (lacking spacers 23 to 25).…”

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Molecular Characterization and Drug Resistance Testing of Mycobacterium tuberculosis Isolates from Chad

et al. 2006

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The molecular characterizations of the first 40 Mycobacterium tuberculosis isolates from Chad revealed a high proportion of isolates of the Cameroon family (33%), of which one isolate showed a monodrug resistance. In total, 9/33 (27%) isolates were resistant to isoniazid. The implications of these findings are discussed.In Chad, the annual incidence rate of pulmonary tuberculosis was estimated at 60 to 120 of 100,000 in 1990 (12) but increased to 370 of 100,000 in 2000 (19), making Chad a highincidence country. The recommended WHO treatment strategy for patients with open and extrapulmonary tuberculosis is directly observed chemotherapy, which has been adopted in most African countries, including Chad, where its coverage was 25% in 2003 (20). An increase in drug resistance due to noncompliance during treatment is feared; however, the lack of baseline data on drug resistance from these countries makes monitoring difficult.Drug resistance testing, molecular characterization, and fingerprinting of Mycobacterium tuberculosis complex members have become common practices in most mycobacterial laboratories. A variety of molecular genetic typing tools for M. tuberculosis complex isolates have been developed (18), with the most widely used, IS6110 restriction fragment length polymorphism typing, as the gold standard. More recently, spoligotyping (8) has shown advantages over IS6110 typing. It is more cost-effective, easier to perform, and possible to compare results between laboratories.The outcome of the drug resistance tests and molecular characterization by spoligotyping of the first M. tuberculosis isolates from Chad are presented and implications for treatment control discussed.Between March and July 2001 and February and October 2002, a total of 357 sputum and 282 urine samples were collected from tuberculosis patients at the National Reference Hospital (HGRNT) in the Chadian capital, NЈDjaména, and at four rural health centers that were 50 to 200 kilometers away from NЈDjaména. All specimens (sputum and urine) were decontaminated (9) and inoculated onto two Löwenstein-Jensen slants, one containing 0.75% glycerol and the other containing 0.6% sodium pyruvate. In addition, liquid Middlebrook 7H9 medium containing oleic acid-albumin-dextrose-catalase and polymyxin-amphotericin B-nalidixic acid-trimethoprim-azlocillin was used. The inoculated media were incubated at 37°C without CO 2 for 8 weeks. Smears were made from the sediment and were stained by the Ziehl-Neelsen method (9). Growth of mycobacteria was confirmed by smear. Acid-fast-bacillus-positive colonies were subcultured on three Löwenstein-Jensen slants and a Middlebrook 7H10 agar plate. Three biochemical tests (nitrate, niacin, and 68°C catalase) (9) were used to identify M. tuberculosis complex (MTC) from nontuberculous mycobacteria. The Lebek method was used as an additional phenotypic test to distinguish between MTC members (7), and in addition the standard method for molecular identification of MTC isolates, real-time PCR (10), was performed. Genotyping ...

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Genomic Analysis Distinguishes Mycobacterium africanum

Cited by 91 publications

References 44 publications

Lack of Insertional-Deletional Polymorphism in a Collection of Mycobacterium ulcerans Isolates from Ghanaian Buruli Ulcer Patients

Lack of Insertional-Deletional Polymorphism in a Collection of Mycobacterium ulcerans Isolates from Ghanaian Buruli Ulcer Patients

Discriminatory Power and Reproducibility of Novel DNA Typing Methods forMycobacterium tuberculosisComplex Strains

Molecular Characterization and Drug Resistance Testing of Mycobacterium tuberculosis Isolates from Chad

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