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Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China.

ABSTRACT: Pulmonary diseases caused by nontuberculous mycobacteria (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the species using conventional and molecular methods, including multilocus PCR, rpoB and hsp65 PCR-PRA, hsp65, rpoB, and 16S-23S internal transcribed spacer region sequencing. The isolates were identified into 3 bacterium genera, including NTM, Gordonia bronchialis, and Nocardia farcinica, and, for the 488 NTM isolates, 27 species were identified. For all the 27 species of NTM which were found to cause pulmonary infections in humans, the most prevalent species was M. intracellulare, followed by M. avium and M. abscessus. And seven other species were for the first time identified in patients with TB in China. NTM species identification is very important for distinguishing between tuberculosis and NTM pulmonary diseases, and the species diversity drives the creation of diverse and integrated identification methods with higher accuracy and efficacy.

SUBMITTER: Liu H

PROVIDER: S-EPMC5110891 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China.

Liu Haican H Lian Lulu L Jiang Yi Y Huang Mingxiang M Tan Yunhong Y Zhao Xiuqin X Zhang Jingrui J Yu Qin Q Liu Jiao J Dong Haiyan H Lu Bing B Wu Yimou Y Wan Kanglin K

BioMed research international 20161102

Pulmonary diseases caused by nontuberculous <i>mycobacteria</i> (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the sp ...[more]

PMID: 27882322

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Project description:BackgroundNontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic evolution and diversity within mycobacteria is the presence of integrated viruses called prophages in the host genome. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhagesDB, an environmental mycobacteriophage database.MethodsProphages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhagesDB lettered clusters. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs.ResultsRapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM. We compared the abundance of bacterial virulence genes within prophage genomes from clinical isolates to mycobacteriophages from PhagesDB. Our data suggests that prophages from clinical mycobacteria are enriched for bacterial virulence genes relative to environmental mycobacteriophage from PhagesDB.ConclusionProphages are present in clinical NTM isolates. Prophages are more likely to be present in RGM compared to SGM genomes. The mechanism and selective advantage of this enrichment by growth rate remain unclear. In addition, the frequency of bacterial virulence genes in prophages from clinical NTM is enriched relative to the PhagesDB environmental proxy. This suggests prophages may act as a reservoir of genetic elements bacteria could use to thrive within a clinical environment.

Project description:BackgroundNontuberculous mycobacterial (NTM) lung infections are a major public health concern. Diagnosis of NTM-pulmonary disease (NTM-PD) is difficult because its clinical, microbiological, and radiological features resemble to those of pulmonary tuberculosis (TB), leading to misdiagnosis. Identification at the species level is essential for diagnosis and determination of therapy, which is currently not performed routinely in Indonesian laboratories.Methodology and principal findingsFrom January 2020 to May 2021, 94 NTM isolates were collected from three TB referral centers in Java Province. Species were identified using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). Tests were performed to determine antibiotic susceptibility, biofilm formation ability, sliding motility characteristics, and the ability to adhere to and invade pneumocytes. After identifying the species of all the isolates, we found nine groups of NTMs: M. fortuitum group 51% (48/94), M. abscessus 38.3% (36/94), M. intracellulare 3.1% (3/94), M. neoaurum 2.1% (2/94), M. chelonae 1.1% (1/94), M. gordonae 1.1% (1/94), M. szulgai 1.1% (1/94), M. mucogenicum 1.1% (1/94), and M. arupense 1.1% (1/94). Amikacin was the most effective antibiotic against M. fortuitum group and M. abscessus. The M. fortuitum group was significantly better at forming biofilms than M. abscessus, but both had the same sliding motility capability. The ability of the M. fortuitum group to adhere to and invade pneumocytes was better than that of M. abscessus, with the number isolates of the M. fortuitum group capable of superior adhesion and invasion to that of M. abscessus.Conclusions/significanceThis study shows that M. fortuitum group and M. abscessus were the most common NTM found in Java, Indonesia. The M. fortuitum group and M. abscessus were the most susceptible to amikacin; therefore, this was the empirical treatment of choice. The ability to form biofilms is directly proportional to the ability to adhere to and invade pneumocytes but not to the susceptibility profile or sliding motility characteristics.

Project description:RationaleNontuberculous mycobacteria (NTM) are a diverse group of environmental organisms that infrequently cause human disease. Understanding of the epidemiologic and clinical characteristics associated with NTM disease is needed to refine diagnostic and treatment strategies, particularly among the less commonly isolated species.ObjectivesTo improve knowledge of geographic variance of NTM species, to correlate detailed clinical information with isolation of specific NTM, and to examine the decision to treat and outcomes for specific NTM.MethodsMycobacterial cultures submitted to the University of Washington mycobacterial laboratory from 1998 to 2011 were examined. We report isolation frequency and demographic information from all samples with clinical variables. We also examined treatment decisions and outcomes in a subset of patients with Mycobacterium abscessus complex, Mycobacterium chelonae, Mycobacterium fortuitum, Mycobacterium gordonae, Mycobacterium kansasii, Mycobacterium lentiflavum, Mycobacterium porcinum, and Mycobacterium xenopi.ResultsCultures of NTM were available from 3,470 patients, 937 of whom had clinical data available. When we compared patients born within or outside Washington State, we found that the mycobacterial species frequency varied. Among 168 patients with one of the studied environmental mycobacteria, 72% had major comorbid conditions. Bronchiectasis was common among patients with pulmonary isolation of any NTM, including those with nonpathogenic M. gordonae. Although mortality was high (37%), few deaths were directly attributable to mycobacterial infection. Among 56 patients who met American Thoracic Society criteria for NTM lung disease, 22 were treated, and 19 of those had M. abscessus complex and M. kansasii. The treatment regimens used tended to follow published guidelines.ConclusionsIsolation of NTM varied by geographic region of origin and location within Washington State. Several clinical risk factors were specific to individual species. Comorbid conditions were common in patients with and without mycobacterial disease. Among patients with one of the studied organisms, there was a high mortality rate more frequently related to comorbid conditions than to mycobacterial disease.

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Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China.

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Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China.

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