666
Views
0
CrossRef citations to date
0
Altmetric
Research article

Uncovering the hidden threat: The widespread presence of chromosome-borne accessory genetic elements and novel antibiotic resistance genetic environments in Aeromonas

, , , , , , , , & show all
Article: 2271688 | Received 25 Jul 2023, Accepted 11 Oct 2023, Published online: 27 Oct 2023

References

  • Fernandez-Bravo A, Figueras MJ. An update on the genus Aeromonas: taxonomy, epidemiology, and pathogenicity. Microorganisms. 2020;8(1):129. doi: 10.3390/microorganisms8010129
  • Pessoa RBG, de Oliveira WF, Correia M, et al. Aeromonas and human health disorders: clinical approaches. Front Microbiol. 2022;13:868890. doi: 10.3389/fmicb.2022.868890
  • Song Y, Wang LF, Zhou K, et al. Epidemiological characteristics, virulence potential, antimicrobial resistance profiles, and phylogenetic analysis of Aeromonas caviae isolated from extra-intestinal infections. Front Cell Infect Microbiol. 2023;13:1084352. doi: 10.3389/fcimb.2023.1084352
  • Puah SM, Khor WC, Aung KT, et al. Aeromonas dhakensis: clinical isolates with high carbapenem resistance. Pathogens. 2022;11(8):833. doi: 10.3390/pathogens11080833
  • Xu Z, Shen W, Zhang R, et al. Clonal dissemination of Aeromonas hydrophila with binary carriage of bla (KPC-2)-bearing plasmids in a Chinese Hospital. Front Microbiol. 2022;13:918561. doi: 10.3389/fmicb.2022.918561
  • Wu Y, Dong N, Cai C, et al. Aeromonas spp. From hospital sewage act as a reservoir of genes resistant to last-line antibiotics. Drug Resist Updat. 2023;67:100925. doi: 10.1016/j.drup.2023.100925
  • Gonzalez-Avila LU, Loyola-Cruz MA, Hernandez-Cortez C, et al. Colistin resistance in Aeromonas spp. Int J Mol Sci. 2021;22(11):5974. doi: 10.3390/ijms22115974
  • Piotrowska M, Popowska M. Insight into the mobilome of Aeromonas strains. Front Microbiol. 2015;6:494. doi: 10.3389/fmicb.2015.00494
  • Partridge SR, Kwong SM, Firth N, et al. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev. 2018;31(4). doi: 10.1128/CMR.00088-17
  • Wang P, Jiang X, Mu K, et al. DANMEL: a manually curated reference database for analyzing mobile genetic elements associated with bacterial drug resistance. mLife. 2022;1(4):460–16. doi: 10.1002/mlf2.12046
  • Guedon G, Libante V, Coluzzi C, et al. The obscure world of integrative and mobilizable elements, highly widespread elements that Pirate bacterial conjugative systems. genes (Basel). Genes. 2017;8(11):337. doi: 10.3390/genes8110337
  • Michaelis C, Grohmann E. Horizontal gene transfer of antibiotic resistance genes in biofilms. Antibiotics. 2023;12(2):328. doi: 10.3390/antibiotics12020328
  • Bello-Lopez JM, Cabrero-Martinez OA, Ibanez-Cervantes G, et al. Horizontal gene transfer and its association with antibiotic resistance in the genus Aeromonas spp. Microorganisms. 2019;7(9):363. doi: 10.3390/microorganisms7090363
  • Urban-Chmiel R, Marek A, Stepien-Pysniak D, et al. Antibiotic resistance in bacteria—A review. Antibiotics. 2022;11(8):1079. doi: 10.3390/antibiotics11081079
  • Tang L, Huang J, She J, et al. Co-occurrence of the bla KPC-2 and mcr-3.3 gene in Aeromonas caviae SCAc2001 isolated from patients with diarrheal disease. Infect Drug Resist. 2020;13:1527–1536. doi: 10.2147/IDR.S245553
  • Messaoudi A, Belguith H, Ben Hamida J. Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase. Theor Biol Med Model. 2013;10(1):22. doi: 10.1186/1742-4682-10-22
  • Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009;106(45):19126–19131. doi: 10.1073/pnas.0906412106
  • CLSI, Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated or fastidious bacteria. 3rd. ( CLSI guideline M45). Clinical and Laboratory Standards Institute: Wayne, PA: 2016.
  • Fu J, Zhang J, Yang L, et al. Precision methylome and in vivo methylation kinetics characterization of Klebsiella pneumoniae. Int J Genomics Proteomics. 2022;20(2):418–434. doi: 10.1016/j.gpb.2021.04.002
  • Li C, Jiang X, Yang T, et al. Genomic epidemiology of carbapenemase-producing Klebsiella pneumoniae in china. Genomics Proteomics Bioinf. 2022;20(6):1154–1167. doi: 10.1016/j.gpb.2022.02.005
  • Hackl T, Hedrich R, Schultz J, et al. Proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics. 2014;30(21):3004–3011. doi: 10.1093/bioinformatics/btu392
  • De Coster W, D’Hert S, Schultz DT, et al. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15):2666–2669. doi: 10.1093/bioinformatics/bty149
  • Delcher AL, Salzberg SL, Phillippy AM. Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics. 2003;(1). Chapter 10:Unit 10 13. doi: 10.1002/0471250953.bi1003s00
  • Minh BQ, Schmidt HA, Chernomor O, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic Era. Mol Biol Evol. 2020;37(5):1530–1534. doi: 10.1093/molbev/msaa015
  • Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W293–W296. doi: 10.1093/nar/gkab301
  • Brettin T, Davis JJ, Disz T, et al. Rasttk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5(1):8365. doi: 10.1038/srep08365
  • Boratyn GM, Camacho C, Cooper PS, et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013;41(Web Server issue):W29–33. doi: 10.1093/nar/gkt282
  • Alcock BP, Raphenya AR, Lau TTY, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48(D1):D517–D525. doi: 10.1093/nar/gkz935
  • Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–2644. doi: 10.1093/jac/dks261
  • Siguier P, Perochon J, Lestrade L, et al. Isfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34(Database issue):D32–36. doi: 10.1093/nar/gkj014
  • Moura A, Soares M, Pereira C, et al. INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics. 2009;25(8):1096–1098. doi: 10.1093/bioinformatics/btp105
  • Roberts AP, Chandler M, Courvalin P, et al. Revised nomenclature for transposable genetic elements. Plasmid. 2008;60(3):167–173. doi: 10.1016/j.plasmid.2008.08.001
  • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinf. 2004;5(1):113. doi: 10.1186/1471-2105-5-113
  • Shi Y, Tian Z, Leclercq SO, et al. Genetic characterization and potential molecular dissemination mechanism of tet(31) gene in Aeromonas caviae from an oxytetracycline wastewater treatment system. J Environ Sci. 2019;76:259–266. doi: 10.1016/j.jes.2018.05.008
  • Luo X, Mu K, Zhao Y, et al. Emergence of bla NDM- 1-Carrying Aeromonas caviae K433 isolated from patient with community-acquired pneumonia. Front Microbiol. 2022;13:825389. doi: 10.3389/fmicb.2022.825389
  • Lim SR, Lee DH, Park SY, et al. Wild nutria (Myocastor coypus) is a potential reservoir of carbapenem-resistant and zoonotic Aeromonas spp. In Korea. Microorganisms. 2019;7(8):224. doi: 10.3390/microorganisms7080224
  • Liu L, Li N, Zhang D, et al. Complete genome sequence of the highly virulent Aeromonas schubertii strain WL1483, isolated from Diseased Snakehead Fish (Channa argus) in China. Genome Announc. 2016;4(1). doi: 10.1128/genomeA.01567-15
  • Weingarten RA, Johnson RC, Conlan S, et al. Genomic analysis of Hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. MBio. 2018;9(1). doi: 10.1128/mBio.02011-17
  • Roh HJ, Kim BS, Kim A, et al. Whole-genome analysis of multi-drug-resistant Aeromonas veronii isolated from diseased discus (symphysodon discus) imported to Korea. J Fish Dis. 2019;42(1):147–153. doi: 10.1111/jfd.12908
  • Sekizuka T, Inamine Y, Segawa T, et al. Potential KPC-2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan. Environ Microbiol Rep. 2019;11(4):589–597. doi: 10.1111/1758-2229.12772
  • Hughes HY, Conlan SP, Lau AF, et al. Detection and Whole-genome sequencing of carbapenemase-producing Aeromonas hydrophila isolates from routine perirectal surveillance culture. J Clin Microbiol. 2016;54(4):1167–1170. doi: 10.1128/JCM.03229-15
  • Pfeiffer F, Zamora-Lagos MA, Blettinger M, et al. The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains. BMC Genomics. 2018;19(1):20. doi: 10.1186/s12864-017-4301-6
  • Partridge SR, Tsafnat G, Coiera E, et al. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev. 2009;33(4):757–784. doi: 10.1111/j.1574-6976.2009.00175.x
  • Partridge SR. Analysis of antibiotic resistance regions in Gram-negative bacteria. FEMS Microbiol Rev. 2011;35(5):820–855. doi: 10.1111/j.1574-6976.2011.00277.x
  • Nicolas E, Lambin M, Dandoy D, et al. The Tn3-family of replicative transposons. Microbiol Spectr. 2015;3(4). doi: 10.1128/microbiolspec.MDNA3-0060-2014
  • Stokes HW, Elbourne LD, Hall RM. Tn1403, a multiple-antibiotic resistance transposon made up of three distinct transposons. Antimicrob Agents Chemother. 2007;51(5):1827–1829. doi: 10.1128/AAC.01279-06
  • L’Abee-Lund TM, Sorum H. Functional Tn5393-like transposon in the R plasmid pRAS2 from the fish pathogen Aeromonas salmonicida subspecies salmonicida isolated in Norway. Appl Environ Microbiol. 2000;66(12):5533–5535. doi: 10.1128/AEM.66.12.5533-5535.2000
  • Peters JE, Fricker AD, Kapili BJ, et al. Heteromeric transposase elements: generators of genomic islands across diverse bacteria. Mol Microbiol. 2014;93(6):1084–1092. doi: 10.1111/mmi.12740
  • Peters JE. Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond. Mol Microbiol. 2019;112(6):1635–1644. doi: 10.1111/mmi.14383
  • Hernando-Amado S, Coque TM, Baquero F, et al. Defining and combating antibiotic resistance from one health and Global health perspectives. Nat Microbiol. 2019;4(9):1432–1442. doi: 10.1038/s41564-019-0503-9