Genome Sequences of Sp. Elmwood and Accompanying Phage, Isolated from a Public Swimming Pool in Nebraska

Overview

Journal Microbiol Resour Announc

Publisher American Society for Microbiology

Specialty Microbiology

Date 2024 Sep 30

PMID 39345178

Authors

Daniela Hernandez-Velazquez

Madelynn K Vasquez

Rana Petre

John A Kyndt

Affiliations

Soon will be listed here.

Abstract

Genome sequencing of a non-tuberculosis species, isolated from a public pool, shows that the genome contains several genes for antibiotic resistance and anti-phage defense, which are absent from other related . Metagenomic binning also provided the genome of the accompanying phage, which is distinct from other mycobacterial phages.

References

. Diagnosis and treatment of disease caused by nontuberculous mycobacteria. This official statement of the American Thoracic Society was approved by the Board of Directors, March 1997. Medical Section of the American Lung Association. Am J Respir Crit Care Med. 1997; 156(2 Pt 2):S1-25. DOI: 10.1164/ajrccm.156.2.atsstatement. View

Wentworth A, Drage L, Wengenack N, Wilson J, Lohse C . Increased incidence of cutaneous nontuberculous mycobacterial infection, 1980 to 2009: a population-based study. Mayo Clin Proc. 2012; 88(1):38-45. PMC: 3690780. DOI: 10.1016/j.mayocp.2012.06.029. View

Parrello B, Butler R, Chlenski P, Pusch G, Overbeek R . Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC. PLoS One. 2021; 16(4):e0250092. PMC: 8049274. DOI: 10.1371/journal.pone.0250092. View

Letunic I, Bork P . Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019; 47(W1):W256-W259. PMC: 6602468. DOI: 10.1093/nar/gkz239. View

LeRoux M, Laub M . Toxin-Antitoxin Systems as Phage Defense Elements. Annu Rev Microbiol. 2022; 76:21-43. DOI: 10.1146/annurev-micro-020722-013730. View

Nurk S, Meleshko D, Korobeynikov A, Pevzner P . metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017; 27(5):824-834. PMC: 5411777. DOI: 10.1101/gr.213959.116. View

Johnson M, ODell J . Nontuberculous mycobacterial pulmonary infections. J Thorac Dis. 2014; 6(3):210-20. PMC: 3949190. DOI: 10.3978/j.issn.2072-1439.2013.12.24. View

Richter M, Rossello-Mora R, Glockner F, Peplies J . JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics. 2015; 32(6):929-31. PMC: 5939971. DOI: 10.1093/bioinformatics/btv681. View

Ondov B, Treangen T, Melsted P, Mallonee A, Bergman N, Koren S . Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016; 17(1):132. PMC: 4915045. DOI: 10.1186/s13059-016-0997-x. View

10.

Bhattacharya J, Mohandas S, Goldman D . Nontuberculous Mycobacterial Infections in Children. Pediatr Rev. 2019; 40(4):179-190. DOI: 10.1542/pir.2018-0131. View

11.

Wattam A, Davis J, Assaf R, Boisvert S, Brettin T, Bun C . Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2016; 45(D1):D535-D542. PMC: 5210524. DOI: 10.1093/nar/gkw1017. View

12.

Falkinham 3rd J . Surrounded by mycobacteria: nontuberculous mycobacteria in the human environment. J Appl Microbiol. 2009; 107(2):356-67. DOI: 10.1111/j.1365-2672.2009.04161.x. View

13.

Overbeek R, Begley T, Butler R, Choudhuri J, Chuang H, Cohoon M . The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005; 33(17):5691-702. PMC: 1251668. DOI: 10.1093/nar/gki866. View

14.

Gygli S, Borrell S, Trauner A, Gagneux S . Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives. FEMS Microbiol Rev. 2017; 41(3):354-373. DOI: 10.1093/femsre/fux011. View

15.

Meier-Kolthoff J, Goker M . TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019; 10(1):2182. PMC: 6522516. DOI: 10.1038/s41467-019-10210-3. View

16.

Stamatakis A, Hoover P, Rougemont J . A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008; 57(5):758-71. DOI: 10.1080/10635150802429642. View

17.

Overbeek R, Olson R, Pusch G, Olsen G, Davis J, Disz T . The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2013; 42(Database issue):D206-14. PMC: 3965101. DOI: 10.1093/nar/gkt1226. View

18.

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki E, Zaslavsky L . NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016; 44(14):6614-24. PMC: 5001611. DOI: 10.1093/nar/gkw569. View

19.

Davis J, Gerdes S, Olsen G, Olson R, Pusch G, Shukla M . PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. Front Microbiol. 2016; 7:118. PMC: 4744870. DOI: 10.3389/fmicb.2016.00118. View

20.

Leoni E, Legnani P, Mucci M, Pirani R . Prevalence of mycobacteria in a swimming pool environment. J Appl Microbiol. 1999; 87(5):683-8. DOI: 10.1046/j.1365-2672.1999.00909.x. View