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Volume 9, Issue 3

Global scenario of the RmtE pan-aminoglycoside-resistance mechanism: emergence of the gene in South America associated with a hospital-related IncL plasmid Open Access

Abstract

Antimicrobial resistance (AMR) mechanisms, especially those conferring resistance to critically important antibiotics, are a great concern for public health. 16S rRNA methyltransferases (16S-RMTases) abolish the effectiveness of most clinically used aminoglycosides, but some of them are considered sporadic, such as RmtE. The main goals of this work were the genomic analysis of bacteria producing 16S-RMTases from a ‘One Health’ perspective in Venezuela, and the study of the epidemiological and evolutionary scenario of RmtE variants and their related mobile genetic elements (MGEs) worldwide. A total of 21 samples were collected in 2014 from different animal and environmental sources in the Cumaná region (Venezuela). Highly aminoglycoside-resistant isolates were selected, identified and screened for 16S-RMTase genes. Illumina and Nanopore whole-genome sequencing data were combined to obtain hybrid assemblies and analyse their sequence type, resistome, plasmidome and pan-genome. Genomic collections of variants and their associated MGEs were generated to perform epidemiological and phylogenetic analyses. A single 16S-RMTase, the novel RmtE4, was identified in five isolates from wastewater samples of Cumaná. This variant possessed three amino acid modifications with respect to RmtE1–3 (Asn152Asp, Val216Ile and Lys267Ile), representing the most genetic distant among all known and novel variants described in this work, and the second most prevalent. variants were globally spread, and their geographical distribution was determined by the associated MGEs and the carrying bacterial species. Thus, was found to be confined to isolates from South America, where it was closely related to IS and an uncommon IncL plasmid related with hospital environments. This work uncovered the global scenario of RmtE and the existence of RmtE4, which could potentially emerge from South America. Surveillance and control measures should be developed based on these findings in order to prevent the dissemination of this AMR mechanism and preserve public health worldwide.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacterial genomics , gene evolution , pan-aminoglycoside resistance , plasmid epidemiology and RmtE 16S rRNA methyltransferase
Funding
This study was supported by the:
  • Comunidad de Madrid (Award REACT-EU)
    • Principle Award Recipient: NotApplicable
  • Ministerio de Economía y Competitividad (Award BES-2015-073164)
    • Principle Award Recipient: JoseF. Delgado-Blas
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-03-24
2024-04-26
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References

  1. Krause KM, Serio AW, Kane TR, Connolly LE. Aminoglycosides: an overview. Cold Spring Harb Perspect Med 2016; 6:a027029 [View Article]
     [Google Scholar]
  2. Davis BD. Mechanism of bactericidal action of aminoglycosides. Microbiol Rev 1987; 51:341–350 [View Article]
     [Google Scholar]
  3. Davis BD, Chen LL, Tai PC. Misread protein creates membrane channels: an essential step in the bactericidal action of aminoglycosides. Proc Natl Acad Sci USA 1986; 83:6164–6168 [View Article]
     [Google Scholar]
  4. Park SR, Park JW, Ban YH, Sohng JK, Yoon YJ. 2-Deoxystreptamine-containing aminoglycoside antibiotics: recent advances in the characterization and manipulation of their biosynthetic pathways. Nat Prod Rep 2013; 30:11–20 [View Article]
     [Google Scholar]
  5. WHO Critically Important Antimicrobials for Human Medicine, 6th Revision ( https://www.who.int/publications/i/item/9789241515528) Geneva: World Health Organization; 2019
     [Google Scholar]
  6. Ramirez MS, Tolmasky ME. Aminoglycoside modifying enzymes. Drug Resist Updat 2010; 13:151–171 [View Article] [PubMed]
     [Google Scholar]
  7. Shaeer KM, Zmarlicka MT, Chahine EB, Piccicacco N, Cho JC. Plazomicin: a next-generation aminoglycoside. Pharmacotherapy 2019; 39:77–93 [View Article]
     [Google Scholar]
  8. Beauclerk AA, Cundliffe E. Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides. J Mol Biol 1987; 193:661–671 [View Article] [PubMed]
     [Google Scholar]
  9. Wachino J, Arakawa Y. Exogenously acquired 16S rRNA methyltransferases found in aminoglycoside-resistant pathogenic Gram-negative bacteria: an update. Drug Resist Updat 2012; 15:133–148 [View Article] [PubMed]
     [Google Scholar]
  10. Wachino JI, Doi Y, Arakawa Y. Aminoglycoside resistance: updates with a focus on acquired 16S ribosomal RNA methyltransferases. Infect Dis Clin North Am 2020; 34:887–902 [View Article]
     [Google Scholar]
  11. Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y. Functional and structural characterization of acquired 16S rRNA methyltransferase NpmB1 conferring pan-aminoglycoside resistance. Antimicrob Agents Chemother 2021; 65:e0100921 [View Article]
     [Google Scholar]
  12. Davis MA, Baker KNK, Orfe LH, Shah DH, Besser TE et al. Discovery of a gene conferring multiple-aminoglycoside resistance in Escherichia coli. Antimicrob Agents Chemother 2010; 54:2666–2669 [View Article]
     [Google Scholar]
  13. Lee CS, Li JJ, Doi Y. Complete sequence of conjugative IncA/C plasmid encoding CMY-2 β-lactamase and RmtE 16S rRNA methyltransferase. Antimicrob Agents Chemother 2015; 59:4360–4361 [View Article] [PubMed]
     [Google Scholar]
  14. Li B, Pacey MP, Doi Y. Chromosomal 16S ribosomal RNA methyltransferase RmtE1 in Escherichia coli sequence type 448. Emerg Infect Dis 2017; 23:876–878 [View Article]
     [Google Scholar]
  15. Tada T, Hishinuma T, Watanabe S, Uchida H, Tohya M et al. Molecular characterization of multidrug-resistant Pseudomonas aeruginosa isolates in hospitals in Myanmar. Antimicrob Agents Chemother 2019; 63:e02397-18 [View Article]
     [Google Scholar]
  16. Oshiro S, Tada T, Watanabe S, Tohya M, Hishinuma T et al. Emergence and spread of carbapenem-resistant and aminoglycoside-panresistant Enterobacter cloacae complex isolates coproducing NDM-type metallo-β-lactamase and 16S rRNA methylase in Myanmar. mSphere 2020; 5:e00054-20 [View Article]
     [Google Scholar]
  17. Wangkheimayum J, Bhattacharjee M, Das BJ, Singha KM, Chanda DD et al. Expansion of acquired 16S rRNA methytransferases along with CTX-M-15, NDM and OXA-48 within three sequence types of Escherichia coli from northeast India. BMC Infect Dis 2020; 20:544 [View Article]
     [Google Scholar]
  18. Xia J, Sun J, Li L, Fang L-X, Deng H et al. First report of the IncI1/ST898 conjugative plasmid carrying rmtE2 16S rRNA methyltransferase gene in Escherichia coli. Antimicrob Agents Chemother 2015; 59:7921–7922 [View Article]
     [Google Scholar]
  19. Taylor E, Jauneikaite E, Sriskandan S, Woodford N, Hopkins KL. Novel 16S rRNA methyltransferase RmtE3 in Acinetobacter baumannii ST79. J Med Microbiol 2022; 71:001531 [View Article]
     [Google Scholar]
  20. Doi Y, Wachino JI, Arakawa Y. Aminoglycoside resistance: the emergence of acquired 16S ribosomal RNA methyltransferases. Infect Dis Clin North Am 2016; 30:523–537 [View Article]
     [Google Scholar]
  21. EUCAST Breakpoint Tables for Interpretation of MICs and Zone Diameters, version 9.0. Växjö: European Committee on Antimicrobial Susceptibility Testing; 2019 http://www.eucast.org/clinical_breakpoints/
  22. Bado I, Papa-Ezdra R, Delgado-Blas JF, Gaudio M, Gutiérrez C et al. Molecular characterization of carbapenem-resistant Acinetobacter baumannii in the intensive care unit of Uruguay’s university hospital identifies the first rmtC gene in the species. Microb Drug Resist 2018; 24:1012–1019 [View Article]
     [Google Scholar]
  23. Andrews S. FastQC: a Quality Control Analysis Tool for High Throughput Sequencing Data; 2019 https://github.com/s-andrews/FastQC
  24. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article]
     [Google Scholar]
  25. Wick R. Porechop; 2019 https://github.com/rrwick/Porechop
  26. 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 [View Article]
     [Google Scholar]
  27. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  28. Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 2015; 31:3350–3352 [View Article]
     [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  30. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  31. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
     [Google Scholar]
  33. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:R46 [View Article] [PubMed]
     [Google Scholar]
  34. Coordinators NR. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2018; 46:D8–D13 [View Article] [PubMed]
     [Google Scholar]
  35. J. Page A, Taylor B, A. Keane J. Multilocus sequence typing by blast from de novo assemblies against PubMLST. J Open Source Softw 2016; 8:118 [View Article]
     [Google Scholar]
  36. Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 2017; 3:e000131 [View Article] [PubMed]
     [Google Scholar]
  37. Seemann T. ABRicate; 2020 https://github.com/tseemann/abricate
  38. Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 2021; 12:4188 [View Article]
     [Google Scholar]
  39. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  40. 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]
     [Google Scholar]
  41. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  42. Rambaut A. FigTree; 2019 https://github.com/rambaut/figtree
  43. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012; 28:1647–1649 [View Article]
     [Google Scholar]
  44. Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2016; 2:e000093 [View Article] [PubMed]
     [Google Scholar]
  45. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [View Article]
     [Google Scholar]
  46. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  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]
     [Google Scholar]
  48. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [View Article]
     [Google Scholar]
  49. R Core Team R: a Language and Environment for Statistical Computing; 2019 https://www.r-project.org/
  50. RStudioTeam RStudio: Integrated Development Environment for R. RStudio; 2019 https://posit.co/
  51. Galili T. dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 2015; 31:3718–3720 [View Article] [PubMed]
     [Google Scholar]
  52. Yu G, Smith DK, Zhu H, Guan Y, Lam TTY. Ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017; 8:28–36
     [Google Scholar]
  53. Wickham H. The split-apply-combine strategy for data analysis. J Stat Soft 2011; 40:1 [View Article]
     [Google Scholar]
  54. Dowle M, Srinivasan A, Short T, Lianoglou S. Data.table: Extension of data.frame, R package version; 2019;1(8)
  55. Carattoli A, Seiffert SN, Schwendener S, Perreten V, Endimiani A. Differentiation of IncL and IncM plasmids associated with the spread of clinically relevant antimicrobial resistance. PLoS One 2015; 10:e0123063 [View Article]
     [Google Scholar]
  56. Blackwell GA, Doughty EL, Moran RA. Evolution and dissemination of L and M plasmid lineages carrying antibiotic resistance genes in diverse Gram-negative bacteria. Plasmid 2021; 113:102528 [View Article] [PubMed]
     [Google Scholar]
  57. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 2015; 43:e15 [View Article] [PubMed]
     [Google Scholar]
  58. Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM et al. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 2018; 34:292–293 [View Article] [PubMed]
     [Google Scholar]
  59. Grant JR, Stothard P. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008; 36:W181–W184 [View Article]
     [Google Scholar]
  60. Belbel Z, Chettibi H, Dekhil M, Ladjama A, Nedjai S et al. Outbreak of an armA methyltransferase-producing ST39 Klebsiella pneumoniae clone in a pediatric Algerian hospital. Microb Drug Resist 2014; 20:310–315 [View Article]
     [Google Scholar]
  61. Liu Y, Wan LG, Deng Q, Cao XW, Yu Y et al. First description of NDM-1-, KPC-2-, VIM-2- and IMP-4-producing Klebsiella pneumoniae strains in a single Chinese teaching hospital. Epidemiol Infect 2015; 143:376–384 [View Article]
     [Google Scholar]
  62. Gijón D, Curiao T, Baquero F, Coque TM, Cantón R. Fecal carriage of carbapenemase-producing Enterobacteriaceae: a hidden reservoir in hospitalized and nonhospitalized patients. J Clin Microbiol 2012; 50:1558–1563 [View Article]
     [Google Scholar]
  63. Ocampo AM, Chen L, Cienfuegos AV, Roncancio G, Chavda KD et al. A two-year surveillance in five Colombian tertiary care hospitals reveals high frequency of non-CG258 clones of carbapenem-resistant Klebsiella pneumoniae with distinct clinical characteristics. Antimicrob Agents Chemother 2016; 60:332–342 [View Article]
     [Google Scholar]
  64. Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol 2020; 18:344–359 [View Article]
     [Google Scholar]
  65. Doi Y, Wachino J, Arakawa Y. Nomenclature of plasmid-mediated 16S rRNA methylases responsible for panaminoglycoside resistance. Antimicrob Agents Chemother 2008; 52:2287–2288 [View Article] [PubMed]
     [Google Scholar]
  66. Martínez JL, Coque TM, Baquero F. What is a resistance gene? Ranking risk in resistomes. Nat Rev Microbiol 2015; 13:116–123 [View Article] [PubMed]
     [Google Scholar]
  67. Leon IM, Lawhon SD, Norman KN, Threadgill DS, Ohta N et al. Serotype diversity and antimicrobial resistance among Salmonella enterica isolates from patients at an equine referral hospital. Appl Environ Microbiol 2018; 84:e02829-17 [View Article]
     [Google Scholar]
  68. He T, Wang R, Liu D, Walsh TR, Zhang R et al. Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nat Microbiol 2019; 4:1450–1456 [View Article] [PubMed]
     [Google Scholar]
  69. He J, Sun L, Zhang L, Leptihn S, Yu Y et al. A SXT/R391 integrative and conjugative element carries two copies of the blandm-1gene in Proteus mirabilis. mSphere 2021; 6:e0058821
     [Google Scholar]
  70. Delgado-Blas JF, Valenzuela Agüi C, Marin Rodriguez E, Serna C, Montero N et al. Dissemination routes of carbapenem and pan-aminoglycoside resistance mechanisms in hospital and urban wastewater canalizations of Ghana. mSystems 2022; 7:e0101921 [View Article]
     [Google Scholar]
  71. Rojas LJ, Weinstock GM, De La Cadena E, Diaz L, Rios R et al. An analysis of the epidemic of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae: convergence of two evolutionary mechanisms creates the “Perfect Storm.”. J Infect Dis 2017; 217:82–92 [View Article]
     [Google Scholar]
  72. Weingarten RA, Johnson RC, Conlan S, Ramsburg AM, Dekker JP et al. Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio 2018; 9:e02011-17 [View Article]
     [Google Scholar]
  73. Pruden A, Vikesland PJ, Davis BC, de Roda Husman AM. Seizing the moment: now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments. Curr Opin Microbiol 2021; 64:91–99 [View Article] [PubMed]
     [Google Scholar]
  74. Roca I, Akova M, Baquero F, Carlet J, Cavaleri M et al. The global threat of antimicrobial resistance: science for intervention. New Microbes New Infect 2015; 6:22–29 [View Article] [PubMed]
     [Google Scholar]
  75. Sims N, Kasprzyk-Hordern B. Future perspectives of wastewater-based epidemiology: monitoring infectious disease spread and resistance to the community level. Environ Int 2020; 139:105689 [View Article]
     [Google Scholar]
  76. Zou H, Berglund B, Wang S, Zhou Z, Gu C et al. Emergence of blaNDM-1, blaNDM-5, blaKPC-2 and blaIMP-4 carrying plasmids in Raoultella spp. in the environment. Environ Pollut 2022; 306:119437 [View Article]
     [Google Scholar]
  77. Musoke D, Namata C, Lubega GB, Niyongabo F, Gonza J et al. The role of environmental health in preventing antimicrobial resistance in low- and middle-income countries. Environ Health Prev Med 2021; 26:100 [View Article]
     [Google Scholar]
  78. Sano D, Louise Wester A, Schmitt H, Amarasiri M, Kirby A et al. Updated research agenda for water, sanitation and antimicrobial resistance. J Water Health 2020; 18:858–866 [View Article] [PubMed]
     [Google Scholar]
  79. Christgen B, Yang Y, Ahammad SZ, Li B, Rodriquez DC et al. Metagenomics shows that low-energy anaerobic-aerobic treatment reactors reduce antibiotic resistance gene levels from domestic wastewater. Environ Sci Technol 2015; 49:2577–2584 [View Article]
     [Google Scholar]
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Global scenario of the RmtE pan-aminoglycoside-resistance mechanism: emergence of the rmtE4 gene in South America associated with a hospital-related IncL plasmid
M Gen 9, 000946 (2023); https://doi.org/10.1099/mgen.0.000946
/content/journal/mgen/10.1099/mgen.0.000946
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