Use of Short Tandem Repeat Sequences to Study Mycobacterium leprae in Leprosy Patients in Malawi and India

Molecular typing has provided an important tool for studies of many pathogens. Such methods could be particularly useful in studies of leprosy, given the many outstanding questions about the pathogenesis and epidemiology of this disease. The approach is particularly difficult with leprosy, however, because of the genetic homogeneity of M. leprae and our inability to culture it. This paper describes molecular epidemiological studies carried out on leprosy patients in Malawi and in India, using short tandem repeat sequences (STRS) as markers of M. leprae strains. It reveals evidence for continuous changes in these markers within individual patients over time, and for selection of different STRS-defined strains between different tissues (skin and nerve) in the same patient. Comparisons between patients collected under different circumstances reveal the uses and limitations of the approach—STRS analysis may in some circumstances provide a means to trace short transmission chains, but it does not provide a robust tool for distinguishing between relapse and reinfection. This encourages further work to identify genetic markers with different stability characteristics for incorporation into epidemiological studies of leprosy

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

Reductive evolution and massive pseudogene formation have shaped the 3.31-Mb genome of Mycobacterium leprae, an unculturable obligate pathogen that causes leprosy in humans. The complete genome sequence of M. leprae strain Br4923 from Brazil was obtained by conventional methods (6 x coverage), and Illumina resequencing technology was used to obtain the sequences of strains Thai53 (38 x coverage) and NHDP63 (46 x coverage) from Thailand and the United States, respectively. Whole-genome comparisons with the previously sequenced TN strain from India revealed that the four strains share 99.995% sequence identity and differ only in 215 polymorphic sites, mainly SNPs, and by 5 pseudogenes. Sixteen interrelated SNP subtypes were defined by genotyping both extant and extinct strains of M. leprae from around the world. The 16 SNP subtypes showed a strong geographical association that reflects the migration patterns of early humans and trade routes, with the Silk Road linking Europe to China having contributed to the spread of leprosy

Multiple displacement amplification as an adjunct to PCR-based detection of Staphylococcus aureus in synovial fluid

<p>Abstract</p> <p>Background</p> <p>Detection of bacterial nucleic acids in synovial fluid following total joint arthroplasty with suspected infection can be difficult; among other technical challenges, inhibitors in the specimens require extensive sample preparation and can diminish assay sensitivity even using polymerase chain reaction (PCR)-based methods. To address this problem a simple protocol for prior use of multiple displacement amplification (MDA) as an adjunct to PCR was established and tested on both purified <it>S. aureus </it>DNA as well as on clinical samples known to contain <it>S. aureus </it>nucleic acids.</p> <p>Findings</p> <p>A single round of MDA on purified nucleic acids resulted in a > 300 thousand-fold increase in template DNA on subsequent quantitative PCR (qPCR) analysis. MDA use on clinical samples resulted in at least a 100-fold increase in sensitivity on subsequent qPCR and required no sample preparation other than a simple alkali/heat lysis step. Mixed samples of <it>S. aureus </it>DNA with a 10³- 10⁴-fold excess of human genomic DNA still allowed for MDA amplification of the minor bacterial component to the threshold of detectability.</p> <p>Conclusion</p> <p>MDA is a promising technique that may serve to significantly enhance the sensitivity of molecular assays in cases of suspected joint infection while simultaneously reducing the specimen handling required.</p

Desafios na era pós genômica para o desenvolvimento de testes laboratoriais para o diagnóstico da hanseníase Challenges in the post genomic era for the development of tests for leprosy diagnosis

O diagnóstico da hanseníase se baseia em manifestações clínicas e não existe teste laboratorial para diagnosticar casos assintomáticos ou para prever progressão da doença entre indivíduos expostos. Novas análises genômicas comparativas in silico e ferramentas de biologia molecular têm sido empregadas para revelar proteínas exclusivas do Mycobacterium leprae que apresentem potencial aplicação diagnóstica. A hanseníase tuberculóide paucibacilar (PB) apresenta baixo nível de anticorpos e forte resposta imune celular (RIC) tipo Th1/interferon gamma (IFN-&#947;). A doença lepromatosa multibacilar (MB) apresenta sorologia positiva e fraca RIC. Portanto, testes laboratoriais para diagnosticar hanseníase PB e MB devem contemplar testes de RIC e sorologia. Proteínas recombinantes do Mycobacterium leprae sorologicamente reativas podem ser incorporadas ao antígeno PGLI para melhorar o diagnóstico sorológico de pacientes MB. Proteínas recombinantes e peptídeos sintéticos do Mycobacterium leprae têm sido testados em ensaios de RIC/IFN-&#947; para diagnosticar casos PB. Sorologia anti-PGLI modificada incorporando novos antígenos do Mycobacterium leprae e ensaios baseados na RIC/produção de IFN-&#947; devem permitir a detecção precoce de casos MB e PB em países endêmicos.<br>Leprosy diagnosis is based mainly on clinical manifestations and no laboratory test is available to diagnose asymptomatic disease or to predict disease progression among exposed individuals. Novel comparative genomic in silico analyses and molecular biology tools have discovered unique Mycobacterium leprae proteins with potential diagnostic application. Tuberculoid paucibacillary leprosy (PB) shows low antibodies titers and strong Th1 type/ IFN-&#947; specific cell mediated immunity (CMI), while lepromatous multibacillary patients (MB) show high antibody titers and low CMI. Therefore, laboratory tests for PB and MB leprosy diagnosis will require CMI and antibody based assays. Serologically reactive recombinant Mycobacterium leprae proteins were identified and may be used in conjunction with PGL-I to improve MB patient diagnosis. Mycobacterium leprae recombinant proteins and synthetic peptides have been tested for CMI-interferon gamma based assays for PB diagnosis. Modified PGL-I serology incorporating new Mycobacterium leprae antigens and CMI tests based on IFN-&#947; &#947; production may permit the detection of leprosy PB and MB forms in endemic countries

Genotyping of Mycobacterium leprae present on Ziehl-Neelsen-stained microscopic slides and in skin biopsy samples from leprosy patients in different geographic regions of Brazil

We analysed 16 variable number tandem repeats (VNTR) and three single-nucleotide polymorphisms (SNP) in Mycobacterium leprae present on 115 Ziehl-Neelsen (Z-N)-stained slides and in 51 skin biopsy samples derived from leprosy patients from Ceará (n = 23), Pernambuco (n = 41), Rio de Janeiro (n = 22) and Rondônia (RO) (n = 78). All skin biopsies yielded SNP-based genotypes, while 48 of the samples (94.1%) yielded complete VNTR genotypes. We evaluated two procedures for extracting M. leprae DNA from Z-N-stained slides: the first including Chelex and the other combining proteinase and sodium dodecyl sulfate. Of the 76 samples processed using the first procedure, 30.2% were positive for 16 or 15 VNTRs, whereas of the 39 samples processed using the second procedure, 28.2% yielded genotypes defined by at least 10 VNTRs. Combined VNTR and SNP analysis revealed large variability in genotypes, but a high prevalence of SNP genotype 4 in the Northeast Region of Brazil. Our observation of two samples from RO with an identical genotype and seven groups with similar genotypes, including four derived from residents of the same state or region, suggest a tendency to form groups according to the origin of the isolates. This study demonstrates the existence of geographically related M. leprae genotypes and that Z-N-stained slides are an alternative source for M. leprae genotyping