Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

Rahman, Syed Asad; Singh, Yadvir; Kohli, Sandeep; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.; Hasnain, Seyed E.

doi:10.1128/mbio.02020-14

Cited by 57 publications

(41 citation statements)

References 50 publications

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“…Notably, the most abundant population recovered in the metagenomes (average Ϯ SD relative abundance among samples, 66.7% Ϯ 8.21% of the total) represented a close relative of M. rhodesiae and M. tusciae. These two mycobacterial species are considered potential opportunistic pathogens, since they have been identified as the causative agent of pulmonary and disseminated infections in immunocompromised individuals (10,(64)(65)(66) (Fig. 2).…”

Section: Resultsmentioning

confidence: 99%

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

Soto-Girón

Rodriguez-R

Luo

et al. 2016

Appl Environ Microbiol

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e Although the source of drinking water (DW) used in hospitals is commonly disinfected, biofilms forming on water pipelines are a refuge for bacteria, including possible pathogens that survive different disinfection strategies. These biofilm communities are only beginning to be explored by culture-independent techniques that circumvent the limitations of conventional monitoring efforts. Hence, theories regarding the frequency of opportunistic pathogens in DW biofilms and how biofilm members withstand high doses of disinfectants and/or chlorine residuals in the water supply remain speculative. The aim of this study was to characterize the composition of microbial communities growing on five hospital shower hoses using both 16S rRNA gene sequencing of bacterial isolates and whole-genome shotgun metagenome sequencing. The resulting data revealed a Mycobacterium-like population, closely related to Mycobacterium rhodesiae and Mycobacterium tusciae, to be the predominant taxon in all five samples, and its nearly complete draft genome sequence was recovered. In contrast, the fraction recovered by culture was mostly affiliated with Proteobacteria, including members of the genera Sphingomonas, Blastomonas, and Porphyrobacter. The biofilm community harbored genes related to disinfectant tolerance (2.34% of the total annotated proteins) and a lower abundance of virulence determinants related to colonization and evasion of the host immune system. Additionally, genes potentially conferring resistance to ␤-lactam, aminoglycoside, amphenicol, and quinolone antibiotics were detected. Collectively, our results underscore the need to understand the microbiome of DW biofilms using metagenomic approaches. This information might lead to more robust management practices that minimize the risks associated with exposure to opportunistic pathogens in hospitals.

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Section: Resultsmentioning

confidence: 99%

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

Soto-Girón

Rodriguez-R

Luo

et al. 2016

Appl Environ Microbiol

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“…Furthermore, comparative genomics analysis across Bacillus strains revealed the significance of mobile genetic elements in imparting virulence to bacterial strains [83]. Genomic analyses between pathogenic and nonpathogenic Mycobacterium tuberculosis strains revealed new set of pathways in pathogenic strains in contrast to avirulent strains [84]. Most significant finding of this study was discovery of alternate metabolic pathways which shed light into their mechanisms of pathogenesis thus providing a base for developing diagnostic markers against tuberculosis [84].…”

Section: Application Of (Meta)genomics In Clinical Microbiologymentioning

confidence: 81%

“…Genomic analyses between pathogenic and nonpathogenic Mycobacterium tuberculosis strains revealed new set of pathways in pathogenic strains in contrast to avirulent strains [84]. Most significant finding of this study was discovery of alternate metabolic pathways which shed light into their mechanisms of pathogenesis thus providing a base for developing diagnostic markers against tuberculosis [84]. Comparative genomics has provided significant information regarding credible virulence determining factors that can be further targeted for vaccine development.…”

Section: Application Of (Meta)genomics In Clinical Microbiologymentioning

confidence: 84%

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

Sharma

Lal

2016

Indian J Microbiol

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Advancement in the next generation sequencing technologies has led to evolution of the field of genomics and metagenomics in a slim duration with nominal cost at precipitous higher rate. While metagenomics and genomics can be separately used to reveal the culture-independent and culture-based microbial evolution, respectively, (meta)genomics together can be used to demonstrate results at population level revealing in-depth complex community interactions for specific ecotypes. The field of metagenomics which started with answering ''who is out there?'' based on 16S rRNA gene has evolved immensely with the precise organismal reconstruction at species/strain level from the deeply covered metagenome data outweighing the need to isolate bacteria of which 99% are de facto non-cultivable. In this review we have underlined the appeal of metagenomic-derived genomes in providing insights into the evolutionary patterns, growth dynamics, genome/gene-specific sweeps, and durability of environmental pressures. We have demonstrated the use of culturebased genomics and environmental shotgun metagenome data together to elucidate environment specific genome modulations via metagenomic recruitments in terms of gene loss/gain, accessory and core-genome extent. We further illustrated the benefit of (meta)genomics in the understanding of infectious diseases by deducing the relationship between human microbiota and clinical microbiology. This review summarizes the technological advances in the (meta)genomic strategies using the genome and metagenome datasets together to increase the resolution of microbial population studies.

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“…The nomenclature and classification of mycobacteria has remained unchanged for most of its known history (33). Species are generally grouped into three major categories based on propensity for human infection: obligate pathogens (e.g., Mycobacterium leprae, Mycobacterium tuberculosis, Mycobacterium marinum, and Mycobacterium ulcerans), facultative or opportunistic pathogens (e.g., M. avium, Mycobacterium intracellulare, M. abscessus, and Mycobacterium kansasii), and strictly commensal or saprophytic bacilli (e.g., Mycobacterium smegmatis, Mycobacterium vanbaalenii, and Mycobacterium thermoresistibile) (34). There are more than 170 recognized species of mycobacteria, with more being added on a regular basis (35).…”

Section: The Diverse Lives Of Nontuberculous Mycobacteriamentioning

confidence: 99%

The Many Lives of Nontuberculous Mycobacteria

Claeys

Robinson

2018

J Bacteriol

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Nontuberculous mycobacteria (NTM) include species that colonize human epithelia, as well as species that are ubiquitous in soil and aquatic environments. NTM that primarily inhabit soil and aquatic environments include the complex (MAC, and ) and the complex (MABSC, subspecies, , and), and can be free-living, biofilm-associated, or amoeba-associated. Although NTM are rarely pathogenic in immunocompetent individuals, those who are immunocompromised - due to either an inherited or acquired immunodeficiency - are highly susceptible to NTM infection (NTMI). Several characteristics such as biofilm formation and the ability of select NTM species to form distinct colony morphotypes all may play a role in pathogenesis not observed in the related, well-characterized pathogen The recognition of different morphotypes of NTM has been established and characterized since the 1950s, but the mechanisms that underlie colony phenotype change and subsequent differences in pathogenicity are just beginning to be explored. Advances in genomic analysis have led to progress in identifying genes important to the pathogenesis and persistence of MAC disease as well as illuminating genetic aspects of different colony morphotypes. Here we review recent literature regarding NTM ecology and transmission, as well as the factors which regulate colony morphotype and pathogenicity.

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Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

Cited by 57 publications

References 50 publications

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

The Many Lives of Nontuberculous Mycobacteria

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