Identification of nontuberculous mycobacteria isolated from hospital water by sequence analysis of the hsp65 and 16S rRNA genes

Maleki, M; Kafil, Hossein Samadi; Harzandi, Naser; Moaddab, Seyyed Reza

doi:10.2166/wh.2017.046

Cited by 17 publications

(12 citation statements)

References 40 publications

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“…However, considering the diversity in species composition and largely unknown epidemiology of NTM in China, diagnosis using anti-GPL IgA needs to be investigated in the future. The molecular identification including genes (rpoB, hsp65, 16S rRNA and ITS region) sequencing rely on a large number of the strains, and should be performed based on a positive culture [22][23][24] . LPA and GeneXpert assays (detecting MTB/RIF) could differentiate MTB and NTM with considerable specificity and sensitivity in a broad range of sample sources, but it has not been applied commonly in primary hospitals because of requiring special equipment 25 .…”

Section: Discussionmentioning

confidence: 99%

Retrospective analysis of patients with non-tuberculous mycobacteria from a primary hospital in Southeast China

Sun

et al. 2020

Sci Rep

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to achieve a comprehensive understanding of the characteristics of patients with non-tuberculous mycobacteria (NTM), patients with NTM between January 2016 and June 2019 were recruited from a primary hospital. NTM were identified based on the MBP64 protein assay. The clinical records and laboratory assay results were retrospectively reviewed. A total of 204 patients with NTM were included in the final analysis. The patients with multiple isolations were more likely accompanied with chronic obstructive pulmonary disease (copD) (p = 0.029) and arthritis (p = 0.049), but showed a lower percentage of positive t-spot results (p = 0.022). In addition, patients with multiple isolations showed a higher rate of positive acid-fast staining results and their symptom duration was more likely longer than 30 days (p = 0.019). Patients with a positive response in T-spot assay showed a higher proportion of nodular manifestation on computed tomography (ct) than those with a negative response. compared with male patients with ntM, female patients showed lower rates of positive acid-fast staining results (p = 0.03), but were more likely accompanied with COPD (p < 0.0001). The positive acid-fast staining results were closely associated with pulmonary cavities and tuberculosis antibody. patients with different NTM isolation frequencies were closely associated with coexisting diseases and examination results.

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Section: Discussionmentioning

confidence: 99%

Retrospective analysis of patients with non-tuberculous mycobacteria from a primary hospital in Southeast China

Sun

et al. 2020

Sci Rep

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“…If the mass spectrometry identifications at the species and genus levels were inconsistent with the results of 16S rDNA sequencing, then the mass spectrometry results were considered incorrect. The 16S rRNA genes of all bacteria were sequenced, along with dnaJ , sodA , tuf , or ropB for Gram-positive cocci [ 30 , 31 ]; ropB , gyrB , recA , or cpn60 for Gram-negative bacteria [ 30 , 32 ]; and ropB , gyrB , SecA1 , or hsp65 for Gram-positive bacilli [ 30 , 33 ]. For yeasts, the internal transcribed spacer located between the nuclear 18S and 26S rRNA genes was sequenced [ 30 ].…”

Section: Methodsmentioning

confidence: 99%

Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates

Yuan

et al. 2020

BMC Microbiol

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Background To evaluate the accuracy and performance of the Autof MS1000 mass spectrometer in bacteria and yeast identification, 2342 isolates were obtained from microbial cultures of clinical specimens (e.g. blood, cerebrospinal fluid, respiratory tract samples, lumbar puncture fluid, wound samples, stool, and urine) collected in 2019 in Henan Provincial People’s Hospital. Repetitive strains from the same patient were excluded. We tested the Autof MS1000 and Bruker Biotyper mass spectrometry systems and the classical biochemical identification system VITEK 2/API 20C AUX. Inconsistencies in strain identification among the three systems were identified by 16S rDNA and gene sequencing. Results At the species level, the Autof MS1000 and Bruker Biotyper systems had isolate identification accuracies of 98.9 and 98.5%, respectively. At the genus level, the Autof MS1000 and Bruker Biotyper systems were 99.7 and 99.4% accurate, respectively. The instruments did not significantly differ in identification accuracy at either taxonomic level. The frequencies of unreliable identification were 1.1% (26/2342) for the Autof MS1000 and 1.5% (34/2342) for the Bruker Biotyper. In vitro experiments demonstrated that the coincidence rate of the Autof MS1000 mass spectrometer in the identification of five types of bacteria was > 93%, the identification error rate was < 3%, and the no identification rate was 0. This indicates that the Autof MS1000 system is acceptable for identification. Conclusions The Autof MS1000 mass spectrometer can be utilised to identify clinical isolates. However, an upgradation of the database is recommended to correctly identify rare strains.

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“…If the mass spectrometry identi cations at the species and genus levels were inconsistent with the results of 16S rDNA sequencing, then the mass spectrometry results were considered incorrect. The 16S rRNA genes of all bacteria were sequenced, along with dnaJ, sodA, tuf, or ropB for Gram-positive cocci [30,31]; ropB, gyrB, recA, or cpn60 for Gram-negative bacteria [30,32]; and ropB, gyrB, SecA1, or hsp65 for Gram-positive bacilli [30,33]. For yeasts, the internal transcribed spacer located between the nuclear 18S and 26S rRNA genes was sequenced [30].…”

Section: Sequencingmentioning

confidence: 99%

Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates

Zhang

Yuan

et al. 2020

Preprint

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Background: To evaluate the accuracy and performance of the Autof MS1000 mass spectrometer in bacteria and yeast identification, 2,342 isolates were obtained from microbial cultures of clinical specimens (e.g. blood, cerebrospinal fluid, respiratory tract samples, lumbar puncture fluid, wound samples, stool, and urine) collected in 2019 in Henan Provincial People’s Hospital. Repetitive strains from the same patient were excluded. We tested the Autof MS1000 and Bruker Biotyper mass spectrometry systems and the classical biochemical identification system VITEK 2/API 20C AUX. Inconsistencies in strain identification among the three systems were identified by 16S rDNA and gene sequencing.Results: At the species level, the Autof MS1000 and Bruker Biotyper systems had isolate identification accuracies of 98.9% and 98.5%, respectively. At the genus level, the Autof MS1000 and Bruker Biotyper systems were 99.7% and 99.4% accurate, respectively. The instruments did not significantly differ in identification accuracy at either taxonomic level. The frequencies of unreliable identification were 1.1% (26/2,342) for the Autof MS1000 and 1.5% (34/2,342) for the Bruker Biotyper. In vitro experiments demonstrated that the coincidence rate of the Autof MS1000 mass spectrometer in the identification of five types of bacteria was >93%, the identification error rate was <3%, and the no identification rate was 0. This indicates that the Autof MS1000 system is acceptable for identification.Conclusions: The Autof MS1000 mass spectrometer can be utilised to identify clinical isolates. However, an upgradation of the database is recommended to correctly identify rare strains.

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Identification of nontuberculous mycobacteria isolated from hospital water by sequence analysis of the hsp65 and 16S rRNA genes

Cited by 17 publications

References 40 publications

Retrospective analysis of patients with non-tuberculous mycobacteria from a primary hospital in Southeast China

Retrospective analysis of patients with non-tuberculous mycobacteria from a primary hospital in Southeast China

Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates

Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates

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