Skip to content
1887

Microbial Genomics logo Microbial Genomics

Volume 10, Issue 12

Global genomic epidemiology of carbapenemase-associated integrons Open Access

Abstract

Antimicrobial resistance (AMR) gene cassettes comprise an AMR gene flanked by short recombination sites ( and  or and ). Integrons are genetic elements able to capture, excise and shuffle these cassettes, providing ‘adaptation on demand’, and can be found on both chromosomes and plasmids. Understanding the patterns of integron diversity may help to understand the epidemiology of AMR genes. As a case study, we examined the clinical resistance gene , an integron-associated class A carbapenemase first reported in Greece in 2004 and since observed worldwide, which to our knowledge has not been the subject of a previous global analysis. Using a dataset comprising all de-duplicated NCBI contigs containing (=104), we developed a pangenome graph-based workflow to characterize and cluster the diversity of -associated integrons. We demonstrate that -associated integrons on plasmids are different to those on chromosomes. Chromosomal integrons were almost all identified in ST235, with a consistent gene cassette content and order. We observed instances where insertion sequence IS disrupted sites, which might immobilize the gene cassettes and explain the conserved integron structure despite the presence of integrase promoters, which would typically facilitate capture or excision and rearrangement. The plasmid-associated integrons were more diverse in their gene cassette content and order, which could be an indication of greater integrase activity and ‘shuffling’ of integrons on plasmids.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): beta-lactamase , GES , mobile genetic elements and Pseudomonas aeruginosa
Funding
This study was supported by the:
  • Wellcome Trust (Award 220422/Z/20/Z)
    • Principal Award Recipient: LiamP. Shaw
  • Medical Research Foundation (Award MRF-145-0004-TPG-AVISO)
    • Principal Award Recipient: WilliamMatlock
  • NIHR HPRU in Healthcare-Associated Infections and Antimicrobial Resistance (Award HPRU-2012–10041 and NIHR200915)
    • Principal Award Recipient: WilliamMatlock
© 2024 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.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.001312
2024-12-04
2025-12-12

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/mgen/10/12/mgen001312.html?itemId=/content/journal/mgen/10.1099/mgen.0.001312&mimeType=html&fmt=ahah

References

  1. Baquero F, Martínez JL, F Lanza V, Rodríguez-Beltrán J, Galán JC et al. Evolutionary pathways and trajectories in antibiotic resistance. Clin Microbiol Rev 2021; 34:e0005019 [View Article] [PubMed]
     [Google Scholar]
  2. Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A et al. Nested Russian doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC. Antimicrob Agents Chemother 2016; 60:3767–3778 [View Article] [PubMed]
     [Google Scholar]
  3. Partridge SR, Tsafnat G, Coiera E, Iredell JR. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 2009; 33:757–784 [View Article] [PubMed]
     [Google Scholar]
  4. Nunes-Düby SE, Kwon HJ, Tirumalai RS, Ellenberger T, Landy A. Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 1998; 26:391–406 [View Article] [PubMed]
     [Google Scholar]
  5. Messier N, Roy PH. Integron integrases possess a unique additional domain necessary for activity. J Bacteriol 2001; 183:6699–6706 [View Article] [PubMed]
     [Google Scholar]
  6. Demarre G, Frumerie C, Gopaul DN, Mazel D. Identification of key structural determinants of the IntI1 integron integrase that influence attC x attI1 recombination efficiency. Nucleic Acids Res 2007; 35:6475–6489 [View Article] [PubMed]
     [Google Scholar]
  7. Jové T, Da Re S, Denis F, Mazel D, Ploy M-C. Inverse correlation between promoter strength and excision activity in class 1 integrons. PLoS Genet 2010; 6:e1000793 [View Article] [PubMed]
     [Google Scholar]
  8. Escudero JA, Loot C, Nivina A, Mazel D. The integron: adaptation on demand. Microbiol Spectr 2015; 3:MDNA3–0019 [View Article] [PubMed]
     [Google Scholar]
  9. Kaushik M, Kumar S, Kapoor RK, Virdi JS, Gulati P. Integrons in Enterobacteriaceae: diversity, distribution and epidemiology. Int J Antimicrob Agents 2018; 51:167–176 [View Article] [PubMed]
     [Google Scholar]
  10. Gillings M, Boucher Y, Labbate M, Holmes A, Krishnan S et al. The evolution of class 1 integrons and the rise of antibiotic resistance. J Bacteriol 2008; 190:5095–5100 [View Article] [PubMed]
     [Google Scholar]
  11. Ghaly TM, Chow L, Asher AJ, Waldron LS, Gillings MR. Evolution of class 1 integrons: mobilization and dispersal via food-borne bacteria. PLoS One 2017; 12:e0179169 [View Article] [PubMed]
     [Google Scholar]
  12. Deng Y, Bao X, Ji L, Chen L, Liu J et al. Resistance integrons: class 1, 2 and 3 integrons. Ann Clin Microbiol Antimicrob 2015; 14:45 [View Article] [PubMed]
     [Google Scholar]
  13. Gillings MR. Class 1 integrons as invasive species. Curr Opin Microbiol 2017; 38:10–15 [View Article] [PubMed]
     [Google Scholar]
  14. Moura A, Soares M, Pereira C, Leitão N, Henriques I et al. INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 2009; 25:1096–1098 [View Article] [PubMed]
     [Google Scholar]
  15. Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM et al. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J 2015; 9:1269–1279 [View Article] [PubMed]
     [Google Scholar]
  16. Ross K, Varani AM, Snesrud E, Huang H, Alvarenga DO et al. TnCentral: a prokaryotic transposable element database and web portal for transposon analysis. mBio 2021; 12: [View Article]
     [Google Scholar]
  17. Sheppard AE, Stoesser N, German-Mesner I, Vegesana K, Sarah Walker A et al. TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data. Microb Genom 2018; 4: [View Article]
     [Google Scholar]
  18. Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP et al. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 2021; 76:101–109 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Arredondo-Alonso S, Gladstone RA, Pöntinen AK, Gama JA, Schürch AC et al. Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR Genom Bioinform 2023; 5:lqad066 [View Article] [PubMed]
     [Google Scholar]
  21. Redondo-Salvo S, Bartomeus-Peñalver R, Vielva L, Tagg KA, Webb HE et al. COPLA, a taxonomic classifier of plasmids. BMC Bioinform 2021; 22:390 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  24. Ghaly TM, Penesyan A, Pritchard A, Qi Q, Rajabal V et al. Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities. Microb Genom 2022; 8:000788 [View Article] [PubMed]
     [Google Scholar]
  25. Buongermino Pereira M, Österlund T, Eriksson KM, Backhaus T, Axelson-Fisk M et al. A comprehensive survey of integron-associated genes present in metagenomes. BMC Genom 2020; 21:495 [View Article] [PubMed]
     [Google Scholar]
  26. Abramova A, Karkman A, Bengtsson-Palme J. Metagenomic assemblies tend to break around antibiotic resistance genes. BMC Genomics959 2024; 25 [View Article]
     [Google Scholar]
  27. Zhang AN, Li L-G, Ma L, Gillings MR, Tiedje JM et al. Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection. Microbiome 2018; 6: [View Article]
     [Google Scholar]
  28. Mazel D. Integrons: agents of bacterial evolution. Nat Rev Microbiol 2006; 4:608–620 [View Article] [PubMed]
     [Google Scholar]
  29. Boucher Y, Labbate M, Koenig JE, Stokes HW. Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol 2007; 15:301–309 [View Article] [PubMed]
     [Google Scholar]
  30. Cambray G, Sanchez-Alberola N, Campoy S, Guerin É, Da Re S et al. Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons. Mob DNA 2011; 2:6 [View Article] [PubMed]
     [Google Scholar]
  31. Ghaly TM, Tetu SG, Gillings MR. Predicting the taxonomic and environmental sources of integron gene cassettes using structural and sequence homology of attC sites. Commun Biol 2021; 4:946 [View Article] [PubMed]
     [Google Scholar]
  32. Macesic N, Hawkey J, Vezina B, Wisniewski JA, Cottingham H et al. Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer. Nat Commun 2023; 14:4764 [View Article] [PubMed]
     [Google Scholar]
  33. Yang D-D, Rusch LM, Widney KA, Morgenthaler AB, Copley SD. Synonymous edits in the Escherichia coli genome have substantial and condition-dependent effects on fitness. Proc Natl Acad Sci U S A 2024; 121:e2316834121 [View Article] [PubMed]
     [Google Scholar]
  34. Zwart MP, Schenk MF, Hwang S, Koopmanschap B, de Lange N et al. Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase. Heredity 2018; 121:406–421 [View Article] [PubMed]
     [Google Scholar]
  35. Ballard A, Bieniek S, Carlini DB. The fitness consequences of synonymous mutations in Escherichia coli: experimental evidence for a pleiotropic effect of translational selection. Gene 2019; 694:111–120 [View Article] [PubMed]
     [Google Scholar]
  36. Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 2018; 27:135–145 [View Article] [PubMed]
     [Google Scholar]
  37. Naas T, Oueslati S, Bonnin RA, Dabos ML, Zavala A et al. Beta-lactamase database (BLDB) - structure and function. J Enzyme Inhib Med Chem 2017; 32:917–919 [View Article] [PubMed]
     [Google Scholar]
  38. Sayers EW, Bolton EE, Brister JR, Canese K, Chan J et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2022; 50:D20–D26 [View Article] [PubMed]
     [Google Scholar]
  39. Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J et al. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021; 11:12728 [View Article] [PubMed]
     [Google Scholar]
  40. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinform 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  41. Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S et al. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biol 2019; 20:232 [View Article] [PubMed]
     [Google Scholar]
  42. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009; 25:1422–1423 [View Article] [PubMed]
     [Google Scholar]
  43. Kans J. Entrez direct: E-utilities on the UNIX command line. Entrez Programming Utilities Help; 2014
  44. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  45. Néron B, Littner E, Haudiquet M, Perrin A, Cury J et al. IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella. Microorganisms 2022; 10:700 [View Article] [PubMed]
     [Google Scholar]
  46. Seeman T. Abricate, Github; 2015 https://github.com/tseemann/abricate
  47. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–D36 [View Article] [PubMed]
     [Google Scholar]
  48. Noll N, Molari M, Shaw LP, Neher RA. PanGraph: scalable bacterial pan-genome graph construction. Microb Genom 2023; 9:mgen001034 [View Article] [PubMed]
     [Google Scholar]
  49. Chen Y, Ye W, Zhang Y, Xu Y. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res 2015; 43:7762–7768 [View Article] [PubMed]
     [Google Scholar]
  50. Seemann T. mlst, Github; 2017 https://github.com/tseemann/mlst
  51. Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom 2018; 4:e000206 [View Article] [PubMed]
     [Google Scholar]
  52. Seeman T. snp-dists, Github; 2021 https://github.com/tseemann/snp-dists
  53. Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom 2016; 2:e000056 [View Article] [PubMed]
     [Google Scholar]
  54. Wickham H. Ggplot2: Elegant Graphics for Data Analysis Springer-Verlag New York. ISBN 978-3-319-24277-4; 2016 [View Article]
     [Google Scholar]
  55. Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 2015; 31:3350–3352 [View Article] [PubMed]
     [Google Scholar]
  56. Acman M, Wang R, van Dorp L, Shaw LP, Wang Q et al. Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM. Nat Commun 2022; 13:1131 [View Article] [PubMed]
     [Google Scholar]
  57. Poirel L, Le Thomas I, Naas T, Karim A, Nordmann P. Biochemical sequence analyses of GES-1, a novel class A extended-spectrum beta-lactamase, and the class 1 integron In52 from Klebsiella pneumoniae. Antimicrob Agents Chemother 2000; 44:622–632 [View Article] [PubMed]
     [Google Scholar]
  58. Poirel L, Carrër A, Pitout JD, Nordmann P. Integron mobilization unit as a source of mobility of antibiotic resistance genes. Antimicrob Agents Chemother 2009; 53:2492–2498 [View Article]
     [Google Scholar]
  59. Kanayama A, Kawahara R, Yamagishi T, Goto K, Kobaru Y et al. Successful control of an outbreak of GES-5 extended-spectrum β-lactamase-producing Pseudomonas aeruginosa in a long-term care facility in Japan. J Hosp Infect 2016; 93:35–41 [View Article] [PubMed]
     [Google Scholar]
  60. Jeong SH, Bae IK, Kim D, Hong SG, Song JS et al. First outbreak of Klebsiella pneumoniae clinical isolates producing GES-5 and SHV-12 extended-spectrum beta-lactamases in Korea. Antimicrob Agents Chemother 2005; 49:4809–4810 [View Article] [PubMed]
     [Google Scholar]
  61. Ellington MJ, Davies F, Jauneikaite E, Hopkins KL, Turton JF et al. A multispecies cluster of GES-5 carbapenemase-producing enterobacterales linked by a geographically disseminated plasmid. Clin Infect Dis 2020; 71:2553–2560 [View Article] [PubMed]
     [Google Scholar]
  62. Chudejova K, Rotova V, Skalova A, Medvecky M, Adamkova V et al. Emergence of sequence type 252 Enterobacter cloacae producing GES-5 carbapenemase in a Czech hospital. Diagn Microbiol Infect Dis 2018; 90:148–150 [View Article] [PubMed]
     [Google Scholar]
  63. Doumith M, Alhassinah S, Alswaji A, Alzayer M, Alrashidi E et al. Genomic characterization of carbapenem-non-susceptible Pseudomonas aeruginosa clinical isolates from Saudi Arabia revealed a global dissemination of GES-5-producing ST235 and VIM-2-producing ST233 sub-lineages. Front Microbiol 2021; 12:765113 [View Article] [PubMed]
     [Google Scholar]
  64. Pablo-Marcos D, Siller M, Agüero J, Álvarez-Justel A, García-Fernández S et al. Are GES carbapenemases underdiagnosed? An allelic discrimination assay for their accurate detection and differentiation. J Microbiol Methods 2023; 207:106694 [View Article] [PubMed]
     [Google Scholar]
  65. Gonzalez C, Volland H, Oueslati S, Niol L, Legrand C et al. Evaluation of a new rapid immunochromatographic assay for the detection of GES-producing Gram-negative bacteria. J Antimicrob Chemother 2023; 78:1282–1287 [View Article] [PubMed]
     [Google Scholar]
  66. Matlock W, Lipworth S, Constantinides B, Peto TEA, Walker AS et al. Flanker: a tool for comparative genomics of gene flanking regions. Microb Genom 2021; 7:000634 [View Article] [PubMed]
     [Google Scholar]
  67. Tetu SG, Holmes AJ. A family of insertion sequences that impacts integrons by specific targeting of gene cassette recombination sites, the IS1111-attC Group. J Bacteriol 2008; 190:4959–4970 [View Article] [PubMed]
     [Google Scholar]
  68. Post V, Hall RM. Insertion sequences in the IS1111 family that target the attC recombination sites of integron-associated gene cassettes. FEMS Microbiol Lett 2009; 290:182–187 [View Article] [PubMed]
     [Google Scholar]
  69. Collis CM, Hall RM. Expression of antibiotic resistance genes in the integrated cassettes of integrons. Antimicrob Agents Chemother 1995; 39:155–162 [View Article] [PubMed]
     [Google Scholar]
  70. Souque C, Escudero JA, MacLean RC. Integron activity accelerates the evolution of antibiotic resistance. eLife 2021; 10:e62474 [View Article] [PubMed]
     [Google Scholar]
  71. Gillings MR, Holley MP, Stokes HW, Holmes AJ. Integrons in Xanthomonas: a source of species genome diversity. Proc Natl Acad Sci U S A 2005; 102:4419–4424 [View Article] [PubMed]
     [Google Scholar]
  72. Baharoglu Z, Bikard D, Mazel D. Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation. PLoS Genet 2010; 6:e1001165 [View Article] [PubMed]
     [Google Scholar]
  73. Roy Chowdhury P, Scott M, Worden P, Huntington P, Hudson B et al. Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa. Open Biol 2016; 6:150175 [View Article] [PubMed]
     [Google Scholar]
  74. Vourli S, Giakkoupi P, Miriagou V, Tzelepi E, Vatopoulos AC et al. Novel GES/IBC extended-spectrum beta-lactamase variants with carbapenemase activity in clinical enterobacteria. FEMS Microbiol Lett 2004; 234:209–213 [View Article] [PubMed]
     [Google Scholar]
  75. Gillings MR. Integrons: past, present, and future. Microbiol Mol Biol Rev 2014; 78:257–277 [View Article] [PubMed]
     [Google Scholar]
  76. Papagiannitsis CC, Tzouvelekis LS, Tzelepi E, Miriagou V. attI1-located small open reading frames ORF-17 and ORF-11 in a class 1 integron affect expression of a gene cassette possessing a canonical shine-dalgarno sequence. Antimicrob Agents Chemother 2017; 61:e02070-16 [View Article] [PubMed]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.001312
Loading
Global genomic epidemiology of blaGES-5 carbapenemase-associated integrons
M Gen 10, 001312 (2024); https://doi.org/10.1099/mgen.0.001312
/content/journal/mgen/10.1099/mgen.0.001312
/content/journal/mgen/10.1099/mgen.0.001312
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error