1887

Abstract

Blood stream invasion by is the commonest cause of bacteremia in the UK and elsewhere with an attributable mortality of about 15–20 %; antibiotic resistance to multiple agents is common in this microbe and is associated with worse outcomes. Genes conferring antimicrobial resistance, and their frequent location on horizontally transferred genetic elements is well-recognised, but the origin of these determinants, and their ability to be maintained and spread within clinically-relevant bacterial populations is unclear. Here, we set out to examine the distribution of antimicrobial resistance genes in chromosomes and plasmids of 16 bloodstream isolates of from patients within Scotland, and how these genes are maintained and spread. Using a combination of short and long-read whole genome sequencing methods, we were able to assemble complete sequences of 44 plasmids, with 16 Inc group F and 20 col plasmids; antibiotic resistance genes located almost exclusively within the F group. genes had re-arranged in some strains into the chromosome alone (five strains), while others contained plasmid copies alone (two strains). Integrons containing multiple antibiotic genes were widespread in plasmids, notably many with a gene encoding resistance to trimethoprim, thus linking trimethoprim resistance to the other antibiotic resistance genes within the plasmids. This will allow even narrow spectrum antibiotics such as trimethoprim to act as a selective agent for plasmids containing antibiotic resistance genes mediating much broader resistance, including C. To our knowledge, this is the first analysis to provide complete sequence data of chromosomes and plasmids in a collection of pathogenic human bloodstream isolates of . Our findings reveal the interplay between plasmids and integrative and conjugative elements in the maintenance and spread of antibiotic resistance genes within pathogenic .

Funding
This study was supported by the:
  • Matthew T G Holden , Chief Scientist Office, Scottish Government Health and Social Care Directorate , (Award 67365/1)
  • Thomas J Evans , Chief Scientist Office, Scottish Government Health and Social Care Directorate , (Award 67365/1)
  • Alistair Leanord , Chief Scientist Office, Scottish Government Health and Social Care Directorate , (Award 67365/1)
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000353
2020-03-11
2020-06-02
Loading full text...

Full text loading...

/deliver/fulltext/mgen/6/4/mgen000353.html?itemId=/content/journal/mgen/10.1099/mgen.0.000353&mimeType=html&fmt=ahah

References

  1. Blair JMA, Webber MA, Baylay AJ, Ogbolu DO, Piddock LJV. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol 2015; 13:42–51 [CrossRef]
    [Google Scholar]
  2. Spellberg B, Guidos R, Gilbert D, Bradley J, Boucher HW et al. The epidemic of antibiotic-resistant infections: a call to action for the medical community from the infectious diseases Society of America. Clin Infect Dis 2008; 46:155–164 [CrossRef]
    [Google Scholar]
  3. U.S. Centers for Disease Control and Prevention Antibiotic resistance threats in the United States 2013; 2013
  4. Cassini A, Högberg LD, Plachouras D, Quattrocchi A, Hoxha A et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European economic area in 2015: a population-level modelling analysis. Lancet Infect Dis 2019; 19:56–66 [CrossRef]
    [Google Scholar]
  5. O’Neill J. Antimicrobial resistance: tackling a crisis for the health and wealth of nations; 2014
  6. Laupland KB. Incidence of bloodstream infection: a review of population-based studies. Clin Microbiol Infect 2013; 19:492–500 [CrossRef]
    [Google Scholar]
  7. Abernethy J, Guy R, Sheridan EA, Hopkins S, Kiernan M et al. Epidemiology of Escherichia coli bacteraemia in England: results of an enhanced sentinel surveillance programme. J Hosp Infect 2017; 95:365–375 [CrossRef]
    [Google Scholar]
  8. Russo TA, Johnson JR. Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem. Microbes Infect 2003; 5:449–456 [CrossRef]
    [Google Scholar]
  9. Health Protection Scotland Healthcare associated infections. 2017; 2017
  10. Public Health England English surveillance programme for antimicrobial utilisation and resistance (ESPAUR) report; 2018
  11. European Centre for Disease Prevention and Control Surveillance of antimicrobial resistance in Europe – annual report of the European antimicrobial resistance surveillance network (EARS-Net) 2017; 2018
  12. McDanel J, Schweizer M, Crabb V, Nelson R, Samore M et al. Incidence of extended-spectrum β-Lactamase (ESBL)-Producing Escherichia coli and Klebsiella infections in the United States: a systematic literature review. Infect Control Hosp Epidemiol 2017; 38:1209–1215 [CrossRef]
    [Google Scholar]
  13. Public Health England Thirty-day all-cause fatality subsequent to MRSA, MSSA and Gram-negative bacteraemia and C. difficile infection: 2017 to 20182019.
  14. Laupland KB, Gregson DB, Church DL, Ross T, Pitout JDD. Incidence, risk factors and outcomes of Escherichia coli bloodstream infections in a large Canadian region. Clin Microbiol Infect 2008; 14:1041–1047 [CrossRef]
    [Google Scholar]
  15. Vihta K-D, Stoesser N, Llewelyn MJ, Quan TP, Davies T et al. Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998-2016: a study of electronic health records. Lancet Infect Dis 2018; 18:1138–1149 [CrossRef]
    [Google Scholar]
  16. Anunnatsiri S, Towiwat P, Chaimanee P. Risk factors and clinical outcomes of extended spectrum beta-lactamase (ESBL)-producing Escherichia coli septicemia at Srinagarind University Hospital, Thailand. Southeast Asian J Trop Med Public Health 2012; 43:1169–1177
    [Google Scholar]
  17. Rodríguez-Baño J, Navarro MD, Romero L, Muniain MA, de Cueto M et al. Bacteremia due to extended-spectrum beta -lactamase-producing Escherichia coli in the CTX-M era: a new clinical challenge. Clin Infect Dis 2006; 43:1407–1414 [CrossRef]
    [Google Scholar]
  18. Ur Rahman S, Ali T, Ali I, Khan NA, Han B et al. The growing genetic and functional diversity of extended spectrum beta-lactamases. Biomed Res Int 2018; 2018:951971814 [CrossRef]
    [Google Scholar]
  19. Cantón R, González-Alba JM, Galán JC. Ctx-M enzymes: origin and diffusion. Front Microbiol 2012; 3:110 [CrossRef]
    [Google Scholar]
  20. Bevan ER, Jones AM, Hawkey PM. Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype. J Antimicrob Chemother 2017; 72:2145–2155 [CrossRef]
    [Google Scholar]
  21. Nicolas-Chanoine M-H, Bertrand X, Madec J-Y. Escherichia coli ST131, an intriguing clonal group. Clin Microbiol Rev 2014; 27:543–574 [CrossRef]
    [Google Scholar]
  22. Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S et al. Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins. Microb Genom 2018; 4: 06 08 2018 [CrossRef]
    [Google Scholar]
  23. Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EPC, de la Cruz F. Mobility of plasmids. Microbiol Mol Biol Rev 2010; 74:434–452 [CrossRef]
    [Google Scholar]
  24. San Millan A, MacLean RC. Fitness costs of plasmids: a limit to plasmid transmission. Microbiol Spectr 2017; 5: [CrossRef]
    [Google Scholar]
  25. Page R, Peti W. Toxin-antitoxin systems in bacterial growth arrest and persistence. Nat Chem Biol 2016; 12:208–214 [CrossRef]
    [Google Scholar]
  26. Durão P, Balbontín R, Gordo I. Evolutionary mechanisms shaping the maintenance of antibiotic resistance. Trends Microbiol 2018; 26:677–691 [CrossRef]
    [Google Scholar]
  27. Hülter N, Ilhan J, Wein T, Kadibalban AS, Hammerschmidt K et al. An evolutionary perspective on plasmid lifestyle modes. Curr Opin Microbiol 2017; 38:74–80 [CrossRef]
    [Google Scholar]
  28. Manges AR. Escherichia coli and urinary tract infections: the role of poultry-meat. Clin Microbiol Infect 2016; 22:122–129 [CrossRef]
    [Google Scholar]
  29. Enne VI, Livermore DM, Stephens P, Hall LM. Persistence of sulphonamide resistance in Escherichia coli in the UK despite national prescribing restriction. Lancet 2001; 357:1325–1328 [CrossRef]
    [Google Scholar]
  30. Silva RF, Mendonça SCM, Carvalho LM, Reis AM, Gordo I et al. Pervasive sign epistasis between conjugative plasmids and drug-resistance chromosomal mutations. PLoS Genet 2011; 7:e1002181 [CrossRef]
    [Google Scholar]
  31. Goswami C, Fox S, Holden M, Connor M, Leanord A et al. Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections. Microb Genom 2018; 4: 22 06 2018 [CrossRef]
    [Google Scholar]
  32. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef]
    [Google Scholar]
  33. 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 [CrossRef]
    [Google Scholar]
  34. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [CrossRef]
    [Google Scholar]
  35. Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ et al. SRST2: rapid genomic surveillance for public health and hospital microbiology Labs. Genome Med 2014; 6:90 [CrossRef]
    [Google Scholar]
  36. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014; 58:212–220 [CrossRef]
    [Google Scholar]
  37. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli . J Clin Microbiol 2014; 52:1501–1510 [CrossRef]
    [Google Scholar]
  38. 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 [CrossRef]
    [Google Scholar]
  39. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012; 28:464–469 [CrossRef]
    [Google Scholar]
  40. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [CrossRef]
    [Google Scholar]
  41. Cury J, Jové T, Touchon M, Néron B, Rocha EP. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res 2016; 44:4539–4550 [CrossRef]
    [Google Scholar]
  42. Koboldt DC, Larson DE, Wilson RK. Using VarScan 2 for germline variant calling and somatic mutation detection. Curr Protoc Bioinformatics 2013; 44:11–17 [CrossRef]
    [Google Scholar]
  43. 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 [CrossRef]
    [Google Scholar]
  44. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef]
    [Google Scholar]
  45. Johnson TJ, Danzeisen JL, Youmans B, Case K, Llop K et al. Separate F-type plasmids have shaped the evolution of the H30 subclone of Escherichia coli sequence type 131. mSphere 2016; 1: 29 06 2016 [CrossRef]
    [Google Scholar]
  46. Suzuki H, Sota M, Brown CJ, Top EM. Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. Nucleic Acids Res 2008; 36:e147 [CrossRef]
    [Google Scholar]
  47. 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]
  48. Bergquist PL, Saadi S, Maas WK. Distribution of basic replicons having homology with RepFIA, RepFIB, and RepFIC among IncF group plasmids. Plasmid 1986; 15:19–34 [CrossRef]
    [Google Scholar]
  49. Sengupta M, Austin S. Prevalence and significance of plasmid maintenance functions in the virulence plasmids of pathogenic bacteria. Infect Immun 2011; 79:2502–2509 [CrossRef]
    [Google Scholar]
  50. Escudero JA, Loot C, Nivina A, Mazel D. The integron: adaptation on demand. Microbiol Spectr 2015; 3:MDNA3-0019-2014 [CrossRef]
    [Google Scholar]
  51. Cambray G, Guerout A-M, Mazel D. Integrons. Annu Rev Genet 2010; 44:141–166 [CrossRef]
    [Google Scholar]
  52. Boucher Y, Labbate M, Koenig JE, Stokes HW. Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol 2007; 15:301–309 [CrossRef]
    [Google Scholar]
  53. Paulsen IT, Littlejohn TG, Rådström P, Sundström L, Sköld O et al. The 3' conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants. Antimicrob Agents Chemother 1993; 37:761–768 [CrossRef]
    [Google Scholar]
  54. Labar AS, Millman JS, Ruebush E, Opintan JA, Bishar RA et al. Regional dissemination of a trimethoprim-resistance gene cassette via a successful transposable element. PLoS One 2012; 7:e38142 [CrossRef]
    [Google Scholar]
  55. Adrian PV, Thomson CJ, Klugman KP, Amyes SG. New gene cassettes for trimethoprim resistance, dfr13, and Streptomycin-spectinomycin resistance, aadA4, inserted on a class 1 integron. Antimicrob Agents Chemother 2000; 44:355–361 [CrossRef]
    [Google Scholar]
  56. Woodford N, Carattoli A, Karisik E, Underwood A, Ellington MJ et al. Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom. All Belonging to the International O25:H4-ST131 Clone 2009; 53:4472–4482
    [Google Scholar]
  57. Solberg OD, Ajiboye RM, Riley LW. Origin of class 1 and 2 integrons and gene cassettes in a population-based sample of uropathogenic Escherichia coli . J Clin Microbiol 2006; 44:1347–1351 [CrossRef]
    [Google Scholar]
  58. Sundin GW, Bender CL. Dissemination of the strA-strB streptomycin-resistance genes among commensal and pathogenic bacteria from humans, animals, and plants. Mol Ecol 1996; 5:133–143 [CrossRef]
    [Google Scholar]
  59. Boyd ES, Barkay T. The mercury resistance operon: from an origin in a geothermal environment to an efficient detoxification machine. Front Microbiol 2012; 3: [CrossRef]
    [Google Scholar]
  60. Skurnik D, Ruimy R, Ready D, Ruppe E, Bernède-Bauduin C et al. Is exposure to mercury a driving force for the carriage of antibiotic resistance genes?. J Med Microbiol 2010; 59:804–807 [CrossRef]
    [Google Scholar]
  61. Reith ME, Singh RK, Curtis B, Boyd JM, Bouevitch A et al. The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics 2008; 9:427 [CrossRef]
    [Google Scholar]
  62. He S, Chandler M, Varani AM, Hickman AB, Dekker JP et al. Mechanisms of evolution in High-Consequence drug resistance plasmids. mBio 2016; 7:e01987–01916 [CrossRef]
    [Google Scholar]
  63. He S, Hickman AB, Varani AM, Siguier P, Chandler M et al. Insertion sequence IS26 reorganizes plasmids in clinically isolated multidrug-resistant bacteria by replicative transposition. mBio 2015; 6:e00762 [CrossRef]
    [Google Scholar]
  64. Harmer CJ, Moran RA, Hall RM. Movement of IS26-associated antibiotic resistance genes occurs via a translocatable unit that includes a single IS26 and preferentially inserts adjacent to another IS26. mBio 2014; 5:e01801–01814 [CrossRef]
    [Google Scholar]
  65. Livermore DM, Day M, Cleary P, Hopkins KL, Toleman MA et al. Oxa-1 β-lactamase and non-susceptibility to penicillin/β-lactamase inhibitor combinations among ESBL-producing Escherichia coli. J Antimicrob Chemother 2019; 74:326–333 [CrossRef]
    [Google Scholar]
  66. Bergstrom CT, Lipsitch M, Levin BR. Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 2000; 155:1505–1519
    [Google Scholar]
  67. Porse A, Schønning K, Munck C, Sommer MOA. Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts. Mol Biol Evol 2016; 33:2860–2873 [CrossRef]
    [Google Scholar]
  68. Lawrence JG, Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997; 44:383–397 [CrossRef]
    [Google Scholar]
  69. Carroll AC, Wong A. Plasmid persistence: costs, benefits, and the plasmid paradox. Can J Microbiol 2018; 64:293–304 [CrossRef]
    [Google Scholar]
  70. Argudín MA, Hoefer A, Butaye P. Heavy metal resistance in bacteria from animals. Res Vet Sci 2019; 122:132–147 [CrossRef]
    [Google Scholar]
  71. Hobman JL, Crossman LC. Bacterial antimicrobial metal ion resistance. J Med Microbiol 2015; 64:471–497 [CrossRef]
    [Google Scholar]
  72. MacLean RC, San Millan A. Microbial evolution: towards resolving the plasmid paradox. Curr Biol 2015; 25:R764–R767 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000353
Loading
/content/journal/mgen/10.1099/mgen.0.000353
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited this month 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