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      Prevention of aerosol isolation of nontuberculous mycobacterium from the patient's bathroom

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          Abstract

          Recent clinical studies have revealed that reappearance of the same nontuberculous mycobacterium (NTM) infection is common after successful standard treatment [1, 2]. Using pulsed-field gel electrophoresis analysis, W allace et al. [1] found that ∼75% of Mycobacterium avium- intracellulare complex (MAC) isolates identified after successful treatment are the result of reinfection. According to a recent study conducted by K oh et al. [2] using repetitive sequence-based PCR analysis, all re-identified M.  abscessus subsp. abscessus isolates had a unique genotype. Therefore, patients with NTM are exposed to large amounts of microbes in their daily lives, particularly in cases of reinfection.

          Abstract

          Reinfection of nontuberculous mycobacterium pulmonary disease may be caused by identical and not different genotypes http://ow.ly/62cH30krdpa

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          TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing

          Tsuyoshi Sekizuka, Akifumi Yamashita, Yoshiro Murase … (2015)
          Whole-genome sequencing (WGS) with next-generation DNA sequencing (NGS) is an increasingly accessible and affordable method for genotyping hundreds of Mycobacterium tuberculosis (Mtb) isolates, leading to more effective epidemiological studies involving single nucleotide variations (SNVs) in core genomic sequences based on molecular evolution. We developed an all-in-one web-based tool for genotyping Mtb, referred to as the Total Genotyping Solution for TB (TGS-TB), to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface. This methodology is implemented with a KvarQ script to predict MTBC lineages/sublineages and potential antimicrobial resistance. Seven Mtb isolates (JP01 to JP07) in this study showing the same VNTR profile were accurately discriminated through median-joining network analysis using SNVs unique to those isolates. An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs. The results of in silico analyses using TGS-TB are consistent with those obtained using conventional molecular genotyping methods, suggesting that NGS short reads could provide multiple genotypes to discriminate multiple strains of Mtb, although longer NGS reads (≥300-mer) will be required for full genotyping on the TGS-TB web site. Most available short reads (~100-mer) can be utilized to discriminate the isolates based on the core genome phylogeny. TGS-TB provides a more accurate and discriminative strain typing for clinical and epidemiological investigations; NGS strain typing offers a total genotyping solution for Mtb outbreak and surveillance. TGS-TB web site: https://gph.niid.go.jp/tgs-tb/.
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            The recovery of Mycobacterium avium-intracellulare complex (MAC) from the residential bathrooms of patients with pulmonary MAC.

            Yukiko Nishiuchi, Ryoji Maekura, Seigo Kitada … (2007)
            The distribution of Mycobacterium avium-intracellulare complex (MAC) in residences was examined. MAC was only recovered from bathrooms but not from other sites of residences. The appearance ratio in the bathrooms of patients with pulmonary MAC was significantly higher than that in healthy volunteers' bathrooms (P=.01). For 2 patients, the genotypes of environmental isolates were identical to their respective clinical isolates.
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              Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial

              Adam Witney, Anna Bateson, Amina Jindani … (2017)
              Background RIFAQUIN was a tuberculosis chemotherapy trial in southern Africa including regimens with high-dose rifapentine with moxifloxacin. Here, the application of whole-genome sequencing (WGS) is evaluated within RIFAQUIN for identifying new infections in treated patients as either relapses or reinfections. WGS is further compared with mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) typing. This is the first report of WGS being used to evaluate new infections in a completed clinical trial for which all treatment and epidemiological data are available for analysis. Methods DNA from 36 paired samples of Mycobacterium tuberculosis cultured from patients before and after treatment was typed using 24-loci MIRU-VNTR, in silico spoligotyping and WGS. Following WGS, the sequences were mapped against the reference strain H37Rv, the single-nucleotide polymorphism (SNP) differences between pairs were identified, and a phylogenetic reconstruction was performed. Results WGS indicated that 32 of the paired samples had a very low number of SNP differences (0–5; likely relapses). One pair had an intermediate number of SNP differences, and was likely the result of a mixed infection with a pre-treatment minor genotype that was highly related to the post-treatment genotype; this was reclassified as a relapse, in contrast to the MIRU-VNTR result. The remaining three pairs had very high SNP differences (>750; likely reinfections). Conclusions WGS and MIRU-VNTR both similarly differentiated relapses and reinfections, but WGS provided significant extra information. The low proportion of reinfections seen suggests that in standard chemotherapy trials with up to 24 months of follow-up, typing the strains brings little benefit to an analysis of the trial outcome in terms of differentiating relapse and reinfection. However, there is a benefit to using WGS as compared to MIRU-VNTR in terms of the additional genotype information obtained, in particular for defining the presence of mixed infections and the potential to identify known and novel drug-resistance markers. Electronic supplementary material The online version of this article (doi:10.1186/s12916-017-0834-4) contains supplementary material, which is available to authorized users.
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                Author and article information

                Journal
                Journal ID (nlm-ta): ERJ Open Res
                Journal ID (iso-abbrev): ERJ Open Res
                Journal ID (publisher-id): ERJOR
                Journal ID (hwp): erjor
                Title: ERJ Open Research
                Publisher: European Respiratory Society
                ISSN (Electronic): 2312-0541
                Publication date Collection: July 2018
                Publication date (Electronic): 03 July 2018
                Volume: 4
                Issue: 3
                Electronic Location Identifier: 00150-2017
                Affiliations
                [1 ]Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
                [2 ]Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
                [3 ]Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
                [4 ]Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
                [5 ]Both authors contributed equally
                Author notes
                Kozo Morimoto, Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association, 3-1-24, Matsuyama, Kiyose, Tokyo, 204-8522 Japan. E-mail: morimotok@ 123456fukujuji.org
                Article
                Publisher ID: 00150-2017
                DOI: 10.1183/23120541.00150-2017
                PMC ID: 6028744
                PubMed ID: 29977902
                SO-VID: b52a09b2-449c-4402-ac27-28a65cdee59f
                Copyright © Copyright ©ERS 2018
                License:

                This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial Licence 4.0.

                History
                Date received : 21 November 2017
                Date accepted : 29 May 2018
                Funding
                Funded by: Japan Agency for Medical Research and Development http://doi.org/10.13039/100009619
                Categories
                Subject: Original Research Letter
                Subject: 4

                Data availability:

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