Complete Genome Sequence of Mycobacterium avium subsp.
            <i>hominissuis</i>
            Strain H87 Isolated from an Indoor Water Sample

Zhao, Xueyan; Epperson, L. Elaine; Hasan, Nabeeh A.; Honda, Jennifer R.; Chan, Edward D.; Strong, Michael; Walter, Nicholas D.; Davidson, Rebecca M.

doi:10.1128/genomea.00189-17

Cited by 16 publications

(12 citation statements)

References 11 publications

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“…We observed that the isolates from patient 9 were closely related to Mav 104, whereas isolates from patient 4 and 13 were closely related to Mav strain subsp. hominissuis H87 (26) (Fig. 1b).…”

Section: Resultsmentioning

confidence: 99%

Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium

Kannan

Lai

Haug

et al. 2018

Preprint

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2Mycobacterium avium (Mav) complex (MAC) are characterized as non-tuberculosis 2 3 3 2 form of single nucleotide polymorphisms (SNPs), suggesting that Mav accumulates mutations at 3 3 high rates during persistent infections. Infection of murine macrophages and mice with sequential 3 4 isolates from patients showed a tendency towards increased persistence and down-regulation of 3 5 inflammatory cytokines by host-adapted Mav strains. The study revealed rapid genetic evolution 3 6 of Mav in chronically infected patients accompanied with change in virulence properties of the 3 7 sequential mycobacterial isolates. 3 8 IMPORTANCE 3 9 MAC are a group of opportunistic pathogens, consisting of Mav and M. intracellulare species. 4 0 Mav is found ubiquitously in the environment. In Mav infected individuals, Mav has been known 4 1 to persist for long periods of time, and anti-mycobacterial drugs are unable to effectively clear the 4 2infection. The continued presence of the bacteria, could be attributed to either a single persistent 4 3 strain or reinfection with the same or different strain. We examined sequential isolates collected 4 4 3 over time from Mav infected individuals and observed that most patients carried the same strain 4 5 overtime and were not re infected. We observed high rates of mutation within the serial isolates, 4 6

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Section: Resultsmentioning

confidence: 99%

Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium

Kannan

Lai

Haug

et al. 2018

Preprint

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“…Lineage 3 contained the highest number of CF-RDP isolates (n=29) along with a laboratory strain with low virulence in mouse models (strain 100) 38 and a clinical pulmonary isolate from Germany (strain MAH-P-0913) 26 . Interestingly, lineage 3 also included strain H87 39 , which was isolated from a water source in Colorado and exhibits the ability to infect and survive within freeliving amoebae 40 . Lineage 4 is composed of isolates from patients and dust samples collected in Germany 26 and six CF-RDP patient isolates.…”

Section: Mycobacterium Aviummentioning

confidence: 99%

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients

Epperson

et al. 2019

Preprint

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Nontuberculous mycobacteria (NTM) pose a threat to individuals with cystic fibrosis (CF) due to an increased prevalence of pulmonary infections, innate drug resistance of the bacteria, and potential transmission between CF patients. To explore the genetic diversity of NTM isolated from CF patients within the United States (US) and to identify potential transmission events, we sequenced and analyzed the genomes of 341 NTM isolates from 191 CF patients as part of a nationwide surveillance study. The most abundant species in the isolate cohort were Mycobacterium abscessus (59.5%), followed by species in the Mycobacterium avium complex (37.5%). Phylogenomic analyses of the three M. abscessus subspecies revealed that more than half of CF patients had isolates in one of four dominant clones, including two dominant clones of M. abscessus subspecies abscessus and two dominant clones of M. abscessus subspecies massiliense. M. avium isolates from US CF patients, however, do not have dominant clones and are phylogenetically diverse. Longitudinal NTM isolates were compared to determine genome-wide single nucleotide polymorphisms (SNPs) that occur within patients over time. This information was used to compare between and within-patient SNP distributions, to quantitatively define SNP thresholds suggestive of transmission, and calculate a posterior probability of recent transmission given the SNP distance between two isolates from different patients. Out of 114 patients with M. abscessus subspecies, ten clusters of highly similar isolates from 26 patients were identified. Among the 26 patients in the M. abscessus clusters, 12 attended the same CF care centers. No highly similar isolate clusters were observed in M. avium. Our study reveals the contrasting genomic diversity and epidemiology of two major NTM taxa and the potential for between-patient exposure and cross-transmission of these emerging pathogens.

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“…These species were selected because they represent the two most common NTM species of clinical signi cance (29). All complete genomes were isolated from clinical sources, with the exception of an M. avium isolate from a hospital water source (30). Our decision to look at complete genomes was driven by the desire to examine bacteriophage trends between species regardless of assembly status (complete vs. draft genome).…”

Section: Methods Bacterial Genome Assembly and Isolate Datasetsmentioning

confidence: 99%

Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

Glickman

Kammlade

Hasan

et al. 2020

Preprint

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Background Nontuberculous 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. Methods Prophages 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. Results Rapidly 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. Conclusion Prophages 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.

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Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain H87 Isolated from an Indoor Water Sample

Cited by 16 publications

References 11 publications

Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium

Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients

Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

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Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain H87 Isolated from an Indoor Water Sample

Cited by 16 publications

References 11 publications

Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium

Genetic variation/evolution and differential host responses resulting from in-patient adaptation ofMycobacterium avium

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients

­­­Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

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Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria