Simultaneous Sequence Analysis of the 16S rRNA and
            <i>rpoB</i>
            Genes by Use of RipSeq Software To Identify
            <i>Mycobacterium</i>
            Species

Mycobacteria play an important role in human and animal health fields. We here examine the place of non tuberculous mycobacteria (NTM) infections in the veterinary context. Relevant aspects of a reference laboratory experience and a literature review are presented in this article. Importance is given both to productivity and to economic losses due to misdiagnosis with bovine tuberculosis and paratuberculosis. The impact NTM may have is relative to geographical location, ecology, husbandry, extent of surveillance programs and bovine tuberculosis and paratuberculosis prevalence. The role of the most relevant NTM in animal disease is summarized with a special focus on Mycobacterium avium subsp. paratuberculosis, given its role as causative agent of paratuberculosis, a disease with huge economic consequences for ruminant livestock.

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“…A combined use of the sequences of 16S rRNA and rpoB gene increases the level of 435 isolates' differentiation (Simmon et al, 2010). 436…”

Section: Environment and Ecology Of Ntm 169mentioning

confidence: 99%

Non-tuberculous mycobacterial infections of veterinary relevance

Biet

Boschiroli

2014

Research in Veterinary Science

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“…Delayed identification of RGM species may lead to inappropriate antimicrobial therapy . In our case, we first identified the pathogen simply as an RGM, and it took several weeks for identifying as M. wolinskyi .…”

Section: Discussionmentioning

confidence: 88%

Mycobacterium wolinskyi Infection Confirmed by rpoB Gene Sequencing

Jeong

Seo

Kim

et al. 2012

Clinical Laboratory Analysis

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Identification of rapidly growing mycobacteria (RGM) is problematic because there are many taxonomic changes. 16S rRNA gene is commonly used to identify Mycobacterium species, but alternative gene targets have been introduced for more accurate identification. We report a rare case of a prosthetic knee infection due to Mycobacterium wolinskyi. The isolate was not identified by 16S rRNA gene sequencing alone and substantially confirmed by rpoB gene sequencing. The identification was delayed because our laboratory did not routinely identify RGM to the species level. Simultaneous sequencing of both 16S rRNA and rpoB genes will allow rapid and accurate identification of M. wolinskyi isolates.

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“…However, the general utility of rpoB sequencing for identification of NTM isolates received at a Mycobacterium reference laboratory remained unclear. Two studies on the usefulness of rpoB sequencing for identification reported a slightly lower percentage of isolates identified to species level: 84% in the study by Simmon et al of 139 human clinical isolates (16) and 80% in the study by Higgins et al of 386 animal isolates (15).…”

Section: Discussionmentioning

confidence: 99%

“…(8,9). However, Simmon et al also noted a lack of interspecies variability for these four species (16). The general problem is that in mycobacteriology, no cutoffs for separate species based on any genetic targets have been set and agreed upon (7).…”

Section: Discussionmentioning

confidence: 99%

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Utility of rpoB Gene Sequencing for Identification of Nontuberculous Mycobacteria in the Netherlands

2014

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bIn the Netherlands, clinical isolation of nontuberculous mycobacteria (NTM) has increased over the past decade. Proper identification of isolates is important, as NTM species differ strongly in clinical relevance. Most of the currently applied identification methods cannot distinguish between all different Mycobacterium species and complexes within species. rpoB gene sequencing exhibits a promising level of discrimination among rapidly and slowly growing mycobacteria, including the Mycobacterium avium complex. In this study, we prospectively compared rpoB gene sequencing with our routine algorithm of reverse line blot identification combined with partial 16S rRNA gene sequencing of 455 NTM isolates. rpoB gene sequencing identified 403 isolates to species level as 45 different known species and identified 44 isolates to complex level, and eight isolates remained unidentifiable to species level. In contrast, our reference reverse line blot assay with adjunctive 16S rRNA gene sequencing identified 390 isolates to species level (30 distinct species) and identified 56 isolates to complex level, and nine isolates remained unidentified. The higher discriminatory power of rpoB gene sequencing results largely from the distinction of separate species within complexes and subspecies. Also, Mycobacterium gordonae, Mycobacterium kansasii, and Mycobacterium interjectum were separated into multiple groupings with relatively low sequence similarity (98 to 94%), suggesting that these are complexes of closely related species. We conclude that rpoB gene sequencing is a more discriminative identification technique than the combination of reverse line blot and 16S rRNA gene sequencing and could introduce a major improvement in clinical care of NTM disease and the research on the epidemiology and clinical relevance of NTM.

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Simultaneous Sequence Analysis of the 16S rRNA and rpoB Genes by Use of RipSeq Software To Identify Mycobacterium Species

Cited by 18 publications

References 20 publications

Non-tuberculous mycobacterial infections of veterinary relevance

Non-tuberculous mycobacterial infections of veterinary relevance

Mycobacterium wolinskyi Infection Confirmed by rpoB Gene Sequencing

Utility of rpoB Gene Sequencing for Identification of Nontuberculous Mycobacteria in the Netherlands

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