1887

Abstract

are Gram-negative bacteria belonging to the sub-phyla , commonly associated with soils, animal feeds and water. Some members of the have been implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the whole-genome sequence of LC510, an species isolated from deep within a pristine location of the Lechuguilla Cave. Pairwise nucleotide comparison to three type strains within the genus assigned LC510 as an isolate. Scanning of the LC510 genome identified two genes coding for b-lactamase resistance, despite the fact that LC510 was isolated from a portion of the cave not previously visited by humans and protected from anthropogenic input. The ability to produce acyl-homoserine lactone (AHL) signal in culture medium, an observation that is consistent with the identification of the luxI and luxR homologues in its genome, suggests that cell-to-cell communication remains important in an isolated cave ecosystem.

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2020-01-20
2020-02-28
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References

  1. Pawlowski AC, Wang W, Koteva K, Barton HA, McArthur AG et al. A diverse intrinsic antibiotic resistome from a cave bacterium. Nat Commun 2016;7: 13803 [CrossRef]
    [Google Scholar]
  2. Peterson E, Kaur P. Antibiotic resistance mechanisms in bacteria: relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front Microbiol 2018;9: [CrossRef]
    [Google Scholar]
  3. Bhullar K, Waglechner N, Pawlowski A, Koteva K, Banks ED et al. Antibiotic resistance is prevalent in an isolated cave microbiome. PLoS One 2012;7: e34953 [CrossRef]
    [Google Scholar]
  4. Gan HM, Wengert PC, Barton HA, Hudson AO, Savka MA. Draft Genome Sequences of Five Proteobacteria Isolated from Lechuguilla Cave, New Mexico, USA, and Insights into Taxonomy and Quorum Sensing. Microbiol Resour Announc 2019;8: e00913– 00919 [CrossRef]
    [Google Scholar]
  5. Gan HY, Gan HM, Tarasco AM, Busairi NI, Barton HA et al. Whole-Genome sequences of five oligotrophic bacteria isolated from deep within Lechuguilla cave, new Mexico. Genome Announc 2014;2: e01133– 14 [CrossRef]
    [Google Scholar]
  6. Cho G-S, Li B, Rostalsky A, Fiedler G, Rösch N et al. Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany. Front Microbiol 2018;9: 536 [CrossRef]
    [Google Scholar]
  7. Gonzalez C, Garcia A, Urrea R, del Solar E, Bello H et al. A combination of ampicillin and sulbactam: effect on aerobic and anaerobic gram-negative bacteria. Revista medica de Chile 1990;118: 548– 554
    [Google Scholar]
  8. Grandjean F, Tan MH, Gan HM, Lee YP, Kawai T et al. Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern hemisphere freshwater crayfish. Zool Scr 2017;46: 718– 728 [CrossRef]
    [Google Scholar]
  9. Tan MH, Gan HM, Schultz MB, Austin CM, MitoPhAST ACM. MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Mol Phylogenet Evol 2015;85: 180– 188 [CrossRef]
    [Google Scholar]
  10. Martins RF, Fickel J, Le M, van Nguyen T, Nguyen HM et al. Phylogeography of red muntjacs reveals three distinct mitochondrial lineages. BMC Evol Biol 2017;17: 34 [CrossRef]
    [Google Scholar]
  11. Dhanoa A, Hassan SS, Ngim CF, Lau CF, Chan TS et al. Impact of dengue virus (DENV) co-infection on clinical manifestations, disease severity and laboratory parameters. BMC Infect Dis 2016;16: 406 [CrossRef]
    [Google Scholar]
  12. Gan HY, Gan HM, Savka MA, Triassi AJ, Wheatley MS et al. Whole-genome sequences of 13 endophytic bacteria isolated from shrub willow (Salix) grown in Geneva, New York. Genome Announc 2014;2: e00288– 14 [CrossRef]
    [Google Scholar]
  13. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014;30: 2114– 2120 [CrossRef]
    [Google Scholar]
  14. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017;13: e1005595 [CrossRef]
    [Google Scholar]
  15. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32: 929– 931 [CrossRef]
    [Google Scholar]
  16. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30: 2068– 2069 [CrossRef]
    [Google Scholar]
  17. Kleinheinz KA, Joensen KG, Larsen MV. Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences. Bacteriophage 2014;4: e27943 [CrossRef]
    [Google Scholar]
  18. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010;5: e9490 [CrossRef]
    [Google Scholar]
  19. Lowe N, Gan HM, Chakravartty V, Scott R, Szegedi ErnÅ‘ et al. Quorum-sensing signal production by Agrobacterium vitis strains and their tumor-inducing and tartrate-catabolic plasmids. FEMS Microbiol Lett 2009;296: 102– 109 [CrossRef]
    [Google Scholar]
  20. Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 2010;11: 431 [CrossRef]
    [Google Scholar]
  21. Gan HM, Gan HY, Ahmad NH, Aziz NA, Hudson AO. et al. Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family. Front Cell Infect Microbiol 2015;4: 188 [CrossRef]
    [Google Scholar]
  22. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011;27: 1009– 1010 [CrossRef]
    [Google Scholar]
  23. Périchon B, Goussard S, Walewski V, Krizova L, Cerqueira G et al. Identification of 50 Class D β-Lactamases and 65 Acinetobacter-Derived Cephalosporinases in Acinetobacter spp. Antimicrob Agents Chemother 2014;58: 936– 949 [CrossRef]
    [Google Scholar]
  24. Lopes BS, Amyes SGB. Role of ISAba1 and ISAba125 in governing the expression of blaADC in clinically relevant Acinetobacter baumannii strains resistant to cephalosporins. J Med Microbiol 2012;61: 1103– 1108 [CrossRef]
    [Google Scholar]
  25. Yamamoto M, Nagao M, Matsumura Y, Hotta G, Matsushima A et al. Regional dissemination of Acinetobacter species harbouring metallo-β-lactamase genes in Japan. Clinical Microbiology and Infection 2013;19: 729– 736 [CrossRef]
    [Google Scholar]
  26. Kamolvit W, Derrington P, Paterson DL, Sidjabat HE. A case of IMP-4-, OXA-421-, OXA-96-, and CARB-2-producing Acinetobacter pittii sequence type 119 in Australia. J Clin Microbiol 2015;53: 727– 730 [CrossRef]
    [Google Scholar]
  27. Clemmer KM, Bonomo RA, Rather PN. Genetic analysis of surface motility in Acinetobacter baumannii. Microbiology 2011;157: 2534– 2544 [CrossRef]
    [Google Scholar]
  28. Marx CJ. Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Res Notes 2008;1: 1 [CrossRef]
    [Google Scholar]
  29. Gan HM, Ibrahim Z, Shahir S, Yahya A. Identification of genes involved in the 4-aminobenzenesulfonate degradation pathway of Hydrogenophaga sp. PBC via transposon mutagenesis. FEMS Microbiol Lett 2011;318: 108– 114 [CrossRef]
    [Google Scholar]
  30. Gao R, Krysciak D, Petersen K, Utpatel C, Knapp A et al. Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain. Appl Environ Microbiol 2015;81: 7993– 8007 [CrossRef]
    [Google Scholar]
  31. Evans BA, Amyes SGB. Oxa β-lactamases. Clin Microbiol Rev 2014;27: 241– 263 [CrossRef]
    [Google Scholar]
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