Recent Advances in Diagnostic Microbiology

Bravo, Lulette Tricia C.; Procop, Gary W.

doi:10.1053/j.seminhematol.2009.03.009

Cited by 18 publications

(5 citation statements)

References 69 publications

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“…WGS can provide comprehensive genetic information including all possible genomic targets, as well as additional valuable information on drug resistance, virulence determinants, and genome evolution. As ongoing technological developments are rapidly decreasing costs, WGS has the potential to become the ultimate tool for diagnostics and pathogen typing, and to dramatically amplify the impact of molecular diagnostics on clinical microbiology [15]. Although the potential of WGS-based Mtb genotyping has started to be explored [12],[13],[16], its precise potential for accurately tracing particular outbreak clones has remained largely undefined.…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

et al. 2013

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Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

et al. 2013

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“…Les laboratoires de microbiologie possèdent tous les outils nécessaires pour faire un diagnostic souvent très rapide et précis (identification d'espèce) de la grande majorité des maladies infectieuses et pour déterminer la sensibilité des agents pathogènes aux différents traitements anti-infectieux [43,44]…”

Section: La Place Prépondérante Des Laboratoires De Microbiologie Danunclassified

Quelle place et quel avenir pour l’anatomo-cyto-pathologie des maladies infectieuses et tropicales en France ?

Hofman

2014

Annales de Pathologie

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The management of tissues and cellular samples by the pathologists in the infectious and tropical diseases pathology field in 2014 needs a strong knowledge of both morphological and molecular domains which includes the good control: (i) of the taxonomy of infectious and tropical diseases pathology leading to the pathogens identification and (ii) of the ancillary methods which can be used in fixed samples in order to detect or better identify these pathogens. There is a recent paradox in France concerning the frequency of infectious diseases to be diagnosed in pathology laboratories and the progressive loss of pathologist's expertise in this domain. Different reasons could explain this statement including the omnipresence of the tumour lesions to be managed in a pathology laboratory as well as the recent constraints associated with the different biomarkers that are mandatory to be detected by immunohistochemistry and/or by molecular biology. Even if the microbiologists play a pivotal role for identifying the different pathogens as well as for the assessment of their sensitivity to the anti-microbial drugs, a large number of infectious diseases can be diagnosed only on fixed tissue and/or cells by the pathologists. The purpose of this review is to describe the current and future issues of infectious and tropical diseases diagnoses in pathology laboratories, in particular in France.

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“…This limitation may be overcome by next generation whole genome sequencing (WGS) for genome-based epidemiology [ 16 ]. WGS is becoming the ultimate tool for diagnosing and typing pathogens, and has amplified the impact of molecular diagnostics on clinical microbiology [ 17 ]. The potential of WGS-based MTBC genotyping has started to be explored [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer

et al. 2015

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BackgroundAlthough Mycobacterium tuberculosis isolates are consisted of several different lineages and the epidemiology analyses are usually assessed relative to a particular reference genome, M. tuberculosis H37Rv, which might introduce some biased results. Those analyses are essentially based genome sequence information of M. tuberculosis and could be performed in sillico in theory, with whole genome sequence (WGS) data available in the databases and obtained by next generation sequencers (NGSs). As an approach to establish higher resolution methods for such analyses, whole genome sequences of the M. tuberculosis complexes (MTBCs) strains available on databases were aligned to construct virtual reference genome sequences called the consensus sequence (CS), and evaluated its feasibility in in sillico epidemiological analyses.ResultsThe consensus sequence (CS) was successfully constructed and utilized to perform phylogenetic analysis, evaluation of read mapping efficacy, which is crucial for detecting single nucleotide polymorphisms (SNPs), and various MTBC typing methods virtually including spoligotyping, VNTR, Long sequence polymorphism and Beijing typing. SNPs detected based on CS, in comparison with H37Rv, were utilized in concatemer-based phylogenetic analysis to determine their reliability relative to a phylogenetic tree based on whole genome alignment as the gold standard. Statistical comparison of phylogenic trees based on CS with that of H37Rv indicated the former showed always better results that that of later. SNP detection and concatenation with CS was advantageous because the frequency of crucial SNPs distinguishing among strain lineages was higher than those of H37Rv. The number of SNPs detected was lower with the consensus than with the H37Rv sequence, resulting in a significant reduction in computational time. Performance of each virtual typing was satisfactory and accorded with those published when those are available.ConclusionsThese results indicated that virtual CS constructed from genome sequence data is an ideal approach as a reference for MTBC studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1368-9) contains supplementary material, which is available to authorized users.

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Recent Advances in Diagnostic Microbiology

Cited by 18 publications

References 69 publications

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

Quelle place et quel avenir pour l’anatomo-cyto-pathologie des maladies infectieuses et tropicales en France ?

Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer

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