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Volume 5, Issue 11

recovered from the lung of a harbour porpoise, and comparative analyses with spp. Open Access

Abstract

Strain M1325/93/1 (herein referred to by our laboratory identifier, GFKo1) of was isolated from the lung of a harbour porpoise in 1993. The genome sequence and antimicrobial resistance profile (genomic, phenotypic) of the strain were generated, with the genomic data compared with those from closely related bacteria. We demonstrate that the recently described chromosomally encoded AmpC β-lactamase is a core gene of , and suggest that new variants of this class of lactamase are encoded by other members of the genus . Although presence of is ubiquitous across the currently sequenced members of , we highlight that strain GFKo1 is sensitive to ampicillin and cephalosporins. These data suggest that may act as a useful genetic marker for identification of strains, but its presence may not correlate with expected phenotypic resistances. Further studies are required to determine the regulatory mechanisms of in .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AmpC , antimicrobial resistance , blaLAQ , Huaxiibacter , marine and veterinary microbiology
Funding
This study was supported by the:
  • Nottingham Trent University
    • Principle Award Recipient: NotApplicable
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-11-09
2024-05-03
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References

  1. Hoyles LSupplementary tables associated with Negus et al Figshare 2023 [View Article]
     [Google Scholar]
  2. Hoyles LGenbank PGAP-Annotated genome sequence Figshare 2023 [View Article]
     [Google Scholar]
  3. Hoyles LBakta annotations (Gbff format) for all Genomes Figshare 2023 [View Article]
     [Google Scholar]
  4. Hoyles LAlignment and Newick file used to generate figure 2 Figshare 2023 [View Article]
     [Google Scholar]
  5. Brady C, Cleenwerck I, Venter S, Coutinho T, De Vos P. Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 2013; 36:309–319 [View Article]
     [Google Scholar]
  6. Kämpfer P, Glaeser SP, Packroff G, Behringer K, Exner M et al. Lelliottia aquatilis sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2018; 68:2454–2461 [View Article] [PubMed]
     [Google Scholar]
  7. Yuk K-J, Kim Y-T, Huh C-S, Lee J-H. Lelliottia jeotgali sp. nov., isolated from a traditional Korean fermented clam. Int J Syst Evol Microbiol 2018; 68:1725–1731 [View Article] [PubMed]
     [Google Scholar]
  8. Lin J, Huang K, Huang JY, Xiong YR, Wei MM et al. Lelliottia steviae sp. nov. isolated from Stevia rebaudiana Bertoni. Arch Microbiol 2022; 204:475 [View Article]
     [Google Scholar]
  9. Wu W, Zong Z. Genome analysis-based reclassification of Lelliottia aquatilis as a later heterotypic synonym of Lelliottia jeotgali. Int J Syst Evol Microbiol 2019; 69:998–1000 [View Article] [PubMed]
     [Google Scholar]
  10. Guégan M, Tran Van V, Martin E, Minard G, Tran F-H et al. Who is eating fructose within the Aedes albopictus gut microbiota?. Environ Microbiol 2020; 22:1193–1206 [View Article] [PubMed]
     [Google Scholar]
  11. Wiktorczyk-Kapischke N, Skowron K, Kwiecińska-Piróg J, Białucha A, Wałecka-Zacharska E et al. Flies as a potential vector of selected alert pathogens in a hospital environment. Int J Environ Health Res 2022; 32:1868–1887 [View Article] [PubMed]
     [Google Scholar]
  12. Heinle CE, Junqueira ACM, Uchida A, Purbojati RW, Houghton JNI et al. Complete genome sequence of Lelliottia nimipressuralis type strain SGAir0187, isolated from tropical air collected in Singapore. Genome Announc 2018; 6:e00231-18 [View Article] [PubMed]
     [Google Scholar]
  13. Salgueiro V, Manageiro V, Bandarra NM, Reis L, Ferreira E et al. Bacterial diversity and antibiotic susceptibility of Sparus aurata from aquaculture. Microorganisms 2020; 8:1343 [View Article] [PubMed]
     [Google Scholar]
  14. Reitter C, Neuhaus K, Hügler M. Draft genome sequences of Enterobacter spp., Lelliottia spp., and Serratia spp., coliform bacteria from drinking water reservoirs and lakes. Microbiol Resour Announc 2021; 10:e0062221 [View Article] [PubMed]
     [Google Scholar]
  15. Leister C, Hügler M. Genome analysis of Enterobacter asburiae and Lelliottia spp. proliferating in oligotrophic drinking water reservoirs and lakes. Appl Environ Microbiol 2022; 88:e0047122 [View Article] [PubMed]
     [Google Scholar]
  16. Thakur P, Gauba P, Stewart FJ. Genomic characterization of Lelliottia amnigena PTJIIT1005, a nitrate tolerant strain isolated from water sample of Yamuna River, Delhi, India. Microbiol Resour Announc 2022; 11:e0022922 [View Article] [PubMed]
     [Google Scholar]
  17. Tran PN, Md Zoqratt MZH, Michalczyk A, Ackland ML. Genome sequence of Lelliottia sp. strain WAP21, isolated from soil in Canola fields in Victoria, Australia. Microbiol Resour Announc 2022; 11:e0101821 [View Article] [PubMed]
     [Google Scholar]
  18. Bilous S, Likhanov A, Boroday V, Marchuk Y, Zelena L et al. Antifungal activity and effect of plant-associated bacteria on phenolic synthesis of Quercus robur L. Plants 2023; 12:1352 [View Article] [PubMed]
     [Google Scholar]
  19. Suescun-Sepulveda JA, Rondón González F, Fuentes Lorenzo JL. Diversity of culturable bacteria of freshwater environments from an altitudinal gradient in the eastern Cordillera of Colombia. FEMS Microbiol Lett 2023; 370:fnad037 [View Article] [PubMed]
     [Google Scholar]
  20. Osei R, Yang C, Cui L, Ma T, Li Z et al. Isolation, identification, and pathogenicity of Lelliottia amnigena causing soft rot of potato tuber in China. Microb Pathog 2022; 164:105441 [View Article] [PubMed]
     [Google Scholar]
  21. Leal-Negredo A, Castelló-Abieta C, Leiva PS, Fernández J. Urinary tract infection by Lelliottia amnigena (Enterobacter amnigenus): an uncommon pathogen. Rev Esp Quimioter 2017; 30:483–484 [PubMed]
     [Google Scholar]
  22. Martín Guerra JM, Martín Asenjo M, Dueñas Gutiérrez CJ. Pyonephrosis by Lelliottia amnigena. Med Clin 2018; 151:419–420 [View Article]
     [Google Scholar]
  23. Choi H, Hwang M, Chatterjee P, Jinadatha C, Navarathna DH. Rare Lelliottia nimipressuralis from a wound infection case report using whole genome sequencing-based bacterial identification. Diagn Microbiol Infect Dis 2021; 101:115538 [View Article] [PubMed]
     [Google Scholar]
  24. Legese MH, Asrat D, Swedberg G, Hasan B, Mekasha A et al. Sepsis: emerging pathogens and antimicrobial resistance in Ethiopian referral hospitals. Antimicrob Resist Infect Control 2022; 11:83 [View Article] [PubMed]
     [Google Scholar]
  25. Li A, Yan C, Zhang L, Liu S, Feng C et al. Characterization and identification of a novel chromosomal class C β-lactamase, LAQ-1, and comparative genomic analysis of a multidrug resistance plasmid in Lelliottia amnigena P13. Front Microbiol 2022; 13:990736 [View Article] [PubMed]
     [Google Scholar]
  26. El Zowalaty ME, Falgenhauer L, Forsythe S, Helmy YA. Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa. J Glob Antimicrob Resist 2023; 33:231–237 [View Article] [PubMed]
     [Google Scholar]
  27. Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L et al. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. Microbiology 2022; 168: [View Article] [PubMed]
     [Google Scholar]
  28. Smith-Zaitlik T. Bioinformatic and Phenotypic Characterization of Bacteriophages Encoded within and Infecting Klebsiella Michiganensis [MRes] Nottingham Trent University; 2021
     [Google Scholar]
  29. Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. bioRxiv 20222022 [View Article]
     [Google Scholar]
  30. Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom 2021; 7:000685 [View Article] [PubMed]
     [Google Scholar]
  31. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012; 158:1005–1015 [View Article] [PubMed]
     [Google Scholar]
  32. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  33. Titus Brown C, Irber L. sourmash: a library for MinHash sketching of DNA. JOSS 2016; 1:27 [View Article]
     [Google Scholar]
  34. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  35. Redondo-Salvo S, Bartomeus-Peñalver R, Vielva L, Tagg KA, Webb HE et al. COPLA, a taxonomic classifier of plasmids. BMC Bioinformatics 2021; 22:390 [View Article] [PubMed]
     [Google Scholar]
  36. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
     [Google Scholar]
  37. Feldgarden M, Brover V, Fedorov B, Haft DH, Prasad AB et al. Curation of the AMRFinderPlus databases: applications, functionality and impact. Microb Genom 2022; 8:mgen000832 [View Article] [PubMed]
     [Google Scholar]
  38. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article] [PubMed]
     [Google Scholar]
  39. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article] [PubMed]
     [Google Scholar]
  40. Feng C-Q, Zhang Z-Y, Zhu X-J, Lin Y, Chen W et al. iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators. Bioinformatics 2019; 35:1469–1477 [View Article] [PubMed]
     [Google Scholar]
  41. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725–731 [View Article] [PubMed]
     [Google Scholar]
  42. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124 [View Article] [PubMed]
     [Google Scholar]
  43. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  44. Chen Y, Brook TC, Soe CZ, O’Neill I, Alcon-Giner C et al. Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors. Microb Genom 2020; 6:e000377 [View Article] [PubMed]
     [Google Scholar]
  45. Bollet C, Elkouby A, Pietri P, de Micco P. Isolation of Enterobacter amnigenus from a heart transplant recipient. Eur J Clin Microbiol Infect Dis 1991; 10:1071–1073 [View Article] [PubMed]
     [Google Scholar]
  46. Stock I, Wiedemann B. Natural antibiotic susceptibility of Enterobacter amnigenus, Enterobacter cancerogenus, Enterobacter gergoviae and Enterobacter sakazakii strains. Clin Microbiol Infect 2002; 8:564–578 [View Article] [PubMed]
     [Google Scholar]
  47. Murugaiyan J, Krueger K, Roesler U, Weinreich J, Schierack P. Assessment of species and antimicrobial resistance among Enterobacteriaceae isolated from mallard duck faeces. Environ Monit Assess 2015; 187:127 [View Article] [PubMed]
     [Google Scholar]
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Lelliottia amnigena recovered from the lung of a harbour porpoise, and comparative analyses with Lelliottia spp.
Access Microbiology 5, 000694.v3 (2023); https://doi.org/10.1099/acmi.0.000694.v3
/content/journal/acmi/10.1099/acmi.0.000694.v3
/content/journal/acmi/10.1099/acmi.0.000694.v3
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