1887

Abstract

serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase () and DNA topoisomerase IV (), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.

Keyword(s): Kentucky , MDR , phylogenomics , Salmonella , SGI and ST198
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000269
2019-05-20
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/mgen/5/7/mgen000269.html?itemId=/content/journal/mgen/10.1099/mgen.0.000269&mimeType=html&fmt=ahah

References

  1. WHO Antimicrobial Resistance: Global Report onSurveillance 2014
    [Google Scholar]
  2. Weill FX, Bertrand S, Guesnier F, Baucheron S, Cloeckaert A et al. Ciprofloxacin-resistant Salmonella Kentucky in travelers. Emerg Infect Dis 2006; 12:1611–1612 [View Article]
    [Google Scholar]
  3. Le Hello S, Hendriksen RS, Doublet B, Fisher I, Nielsen EM et al. International spread of an epidemic population of Salmonella enterica serotype Kentucky ST198 resistant to ciprofloxacin. J Infect Dis 2011; 204:675–684 [View Article]
    [Google Scholar]
  4. Le Hello S, Harrois D, Bouchrif B, Sontag L, Elhani D et al. Highly drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a microbiological study. Lancet Infect Dis 2013; 13:672–679 [View Article]
    [Google Scholar]
  5. Le Hello S, Bekhit A, Granier SA, Barua H, Beutlich J et al. The global establishment of a highly-fluoroquinolone resistant Salmonella enterica serotype Kentucky ST198 strain. Front Microbiol 2013; 4:395 [View Article]
    [Google Scholar]
  6. Westrell T, Monnet DL, Gossner C, Heuer O, Takkinen J. Drug-resistant Salmonella enterica serotype Kentucky in Europe. Lancet Infect Dis 2014; 14:270–271 [View Article]
    [Google Scholar]
  7. Haley BJ, Kim SW, Pettengill J, Luo Y, Karns JS et al. Genomic and evolutionary analysis of two Salmonella enterica serovar Kentucky sequence types isolated from bovine and poultry sources in North America. PLoS One 2016; 11:e0161225
    [Google Scholar]
  8. Le Hello S, Weill FX, Guibert V, Praud K, Cloeckaert A et al. Early strains of multidrug-resistant Salmonella enterica serovar Kentucky sequence type 198 from Southeast Asia harbor Salmonella genomic island 1-J variants with a novel insertion sequence. Antimicrob Agents Chemother 2012; 56:5096–5102 [View Article]
    [Google Scholar]
  9. Boyd D, Peters GA, Cloeckaert A, Boumedine KS, Chaslus-Dancla E et al. Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona. J Bacteriol 2001; 183:5725–5732 [View Article]
    [Google Scholar]
  10. Boyd D, Cloeckaert A, Chaslus-Dancla E, Mulvey MR. Characterization of variant Salmonella genomic island 1 multidrug resistance regions from serovars Typhimurium DT104 and Agona. Antimicrob Agents Chemother 2002; 46:1714–1722 [View Article]
    [Google Scholar]
  11. Siebor E, Neuwirth C. Emergence of Salmonella genomic island 1 (SGI1) among Proteus mirabilis clinical isolates in Dijon, France. J Antimicrob Chemother 2013; 68:1750–1756 [View Article]
    [Google Scholar]
  12. Hamidian M, Holt KE, Hall RM. Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate. J Antimicrob Chemother 2015; 70:2519–2523
    [Google Scholar]
  13. Doublet B, Boyd D, Mulvey MR, Cloeckaert A. The Salmonella genomic island 1 is an integrative mobilizable element. Mol Microbiol 2005; 55:1911–1924 [View Article]
    [Google Scholar]
  14. Carraro N, Matteau D, Luo P, Rodrigue S, Burrus V. The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination. PLoS Genet 2014; 10:e1004714 [View Article]
    [Google Scholar]
  15. Douard G, Praud K, Cloeckaert A, Doublet B. The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family. PLoS ONE 2010; 5:e15302 [View Article]
    [Google Scholar]
  16. Hall RM. Salmonella genomic islands and antibiotic resistance in Salmonella enterica . Future Microbiol 2010; 5:1525–1538 [View Article]
    [Google Scholar]
  17. Siebor E, Neuwirth C. Proteus genomic island 1 (PGI1), a new resistance genomic island from two Proteus mirabilis French clinical isolates. J Antimicrob Chemother 2014; 69:3216–3220
    [Google Scholar]
  18. Soliman AM, Shimamoto T, Nariya H, Shimamoto T. Emergence of Salmonella Genomic Island 1 Variant SGI1-W in a Clinical Isolate of Providencia stuartii from Egypt. Antimicrob Agents Chemother 2018; 63:01793–18
    [Google Scholar]
  19. Levings RS, Djordjevic SP, Hall RM. SGI2, a relative of Salmonella genomic island SGI1 with an independent origin. Antimicrob Agents Chemother 2008; 52:2529–2537 [View Article]
    [Google Scholar]
  20. Doublet B, Praud K, Weill FX, Cloeckaert A. Association of IS26-composite transposons and complex In4-type integrons generates novel multidrug resistance loci in Salmonella genomic island 1. J Antimicrob Chemother 2009; 63:282–289 [View Article]
    [Google Scholar]
  21. Doublet B, Praud K, Bertrand S, Collard JM, Weill FX et al. Novel insertion sequence- and transposon-mediated genetic rearrangements in genomic island SGI1 of Salmonella enterica serovar Kentucky. Antimicrob Agents Chemother 2008; 52:3745–3754 [View Article]
    [Google Scholar]
  22. Levings RS, Partridge SR, Djordjevic SP, Hall RM. SGI1-K, a variant of the SGI1 genomic island carrying a mercury resistance region, in Salmonella enterica serovar Kentucky. Antimicrob Agents Chemother 2007; 51:317–323 [View Article]
    [Google Scholar]
  23. Baucheron S, Le Hello S, Doublet B, Giraud E, Weill FX et al. ramR mutations affecting fluoroquinolone susceptibility in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198. Front Microbiol 2013; 4:213 [View Article]
    [Google Scholar]
  24. Kuijpers LMF, Le Hello S, Fawal N, Fabre L, Tourdjman M et al. Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013–2015. Microb Genom 2016; 2:e000092
    [Google Scholar]
  25. Allard MW, Strain E, Melka D, Bunning K, Musser SM. Practical value of food pathogen traceability through building a whole-genome sequencing network and database. J Clin Microbiol 2016; 54:1975–1983 [View Article]
    [Google Scholar]
  26. Timme RE, Rand H, Sanchez Leon M, Hoffmann M, Strain E et al. GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015. Microb Genom 2018; 4:289 [View Article]
    [Google Scholar]
  27. Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ et al. SRST2: rapid genomic surveillance for public health and hospital microbiology Labs. Genome Med 2014; 6:90 [View Article]
    [Google Scholar]
  28. Blanchard TG, Czinn SJ, Correa P, Nakazawa T, Keelan M et al. Genome sequences of 65 Helicobacter pylori strains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis. Pathog Dis 2013; 68:39–43
    [Google Scholar]
  29. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article]
    [Google Scholar]
  30. Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M et al. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 2011; 12:356
    [Google Scholar]
  31. Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008; 40:987–993 [View Article]
    [Google Scholar]
  32. Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet 2012; 44:1056–1059 [View Article]
    [Google Scholar]
  33. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article]
    [Google Scholar]
  34. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article]
    [Google Scholar]
  35. 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
    [Google Scholar]
  36. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH et al. beast 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2014; 10:e1003537 [View Article]
    [Google Scholar]
  37. Rambaut A, Suchard MA, Xie D, Drummond AJ. Tracer v1.6 2014 http://beast.bio.ed.ac.uk
  38. Drummond AJ, Rambaut A. beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007; 7:214 [View Article]
    [Google Scholar]
  39. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article]
    [Google Scholar]
  40. United Nations Statistics Division Composition of macro geographical (continental) regions, geographical sub-regions, and selected economic and other groupings; 2013 https://unstats.un.org/unsd/methodology/m49/
  41. Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 2006; 7:88 [View Article]
    [Google Scholar]
  42. Revell LJ. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 2012; 3:217–223 [View Article]
    [Google Scholar]
  43. Hannon Lab FastXToolkit 2010 http://hannonlab.cshl.edu/fastx_toolkit/
  44. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article]
    [Google Scholar]
  45. 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 [View Article]
    [Google Scholar]
  46. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011; 27:578–579 [View Article]
    [Google Scholar]
  47. Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol 2012; 13:R56 [View Article]
    [Google Scholar]
  48. Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 2009; 25:1968–1969 [View Article]
    [Google Scholar]
  49. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
    [Google Scholar]
  50. 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 [View Article]
    [Google Scholar]
  51. 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]
    [Google Scholar]
  52. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. blast+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article]
    [Google Scholar]
  53. Chen L, Zheng D, Liu B, Yang J, Jin Q. VFDB 2016: hierarchical and refined dataset for big data analysis–10 years on. Nucleic Acids Res 2016; 44:D694–D697 [View Article]
    [Google Scholar]
  54. Arndt D, Marcu A, Liang Y, Wishart DS. PHAST, PHASTER and PHASTEST: tools for finding prophage in bacterial genomes. Brief Bioinform 2017
    [Google Scholar]
  55. Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H et al. ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 2015; 16:667 [View Article]
    [Google Scholar]
  56. 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]
  57. 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]
  58. Hancock SJ, Phan MD, Peters KM, Forde BM, Chong TM et al. Identification of IncA/C plasmid replication and maintenance genes and development of a plasmid multilocus sequence typing scheme. Antimicrob Agents Chemother 2017; 61:e01740–16
    [Google Scholar]
  59. Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica . PLoS One 2014; 9:e87991 [View Article]
    [Google Scholar]
  60. Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM et al. Intra-continental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.. Nat Genet 2012; 44:1215–1221
    [Google Scholar]
  61. Zhou Z, McCann A, Litrup E, Murphy R, Cormican M. Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona. PLoS Genet 2013; 9:e1003471 [View Article]
    [Google Scholar]
  62. Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ et al. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet 2015; 47:632–639 [View Article]
    [Google Scholar]
  63. Zhou Z, McCann A, Weill FX, Blin C, Nair S et al. Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proc Natl Acad Sci USA 2014; 111:12199–12204 [View Article]
    [Google Scholar]
  64. Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J et al. Genome-scale rates of evolutionary change in bacteria. Microb Genom 2016; 2:e000094 [View Article]
    [Google Scholar]
  65. Villa L, Guerra B, Schmoger S, Fischer J, Helmuth R et al. IncA/C plasmid carrying bla(NDM-1), bla(CMY-16), and fosA3 in a Salmonella enterica serovar Corvallis strain isolated from a migratory wild bird in Germany. Antimicrob Agents Chemother 2015; 59:6597–6600 [View Article]
    [Google Scholar]
  66. Mollet B, Iida S, Shepherd J, Arber W. Nucleotide sequence of IS26, a new prokaryotic mobile genetic element. Nucleic Acids Res 1983; 11:6319–6330 [View Article]
    [Google Scholar]
  67. 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 [View Article]
    [Google Scholar]
  68. Cuypers WL, Jacobs J, Wong V, Klemm EJ, Deborggraeve S et al. Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Microb Genom 2018; 4:
    [Google Scholar]
  69. Shah DH, Paul NC, Sischo WC, Crespo R, Guard J. Population dynamics and antimicrobial resistance of the mostprevalent poultry-associated Salmonella serotypes. Poultry Sci 2017; 96:687–702
    [Google Scholar]
  70. Baker S, Duy PT, Nga TV, Dung TT, Phat VV et al. Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure. Elife 2013; 2:e01229 [View Article]
    [Google Scholar]
  71. Webber MA, Ricci V, Whitehead R, Patel M, Fookes M et al. Clinically relevant mutant DNA gyrase alters supercoiling, changes the transcriptome, and confers multidrug resistance. MBio 2013; 4:e00273–13 [View Article]
    [Google Scholar]
  72. Harmer CJ, Hamidian M, Ambrose SJ, Hall RM. Destabilization of IncA and IncC plasmids by SGI1 and SGI2 type Salmonella genomic islands. Plasmid 2016; 87–88:51–57 [View Article]
    [Google Scholar]
  73. Huguet KT, Gonnet M, Doublet B, Cloeckaert A. A toxin antitoxin system promotes the maintenance of the IncA/C-mobilizable Salmonella genomic island 1. Sci Rep 2016; 6:32285 [View Article]
    [Google Scholar]
  74. Hammarlöf DL, Kröger C, Owen SV, Canals R, Lacharme-Lora L et al. Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella . Proc Natl Acad Sci USA 2018; 115:E2614–E2623
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000269
Loading
/content/journal/mgen/10.1099/mgen.0.000269
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 1

EXCEL
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