Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi

Journal of Antimicrobial Chemotherapy

Volumn 73, Issue 2, 2018, Pages 365-372

  Day, Martin R ^a   Doumith, Michel ^a   Do Nascimento, Vivienne ^a   Nair, Satheesh ^a   Ashton, Philip M ^a   Jenkins, Claire ^a   Dallman, Timothy J ^a   Stevens, Flora J ^a   Freedman, Joanne ^a   Hopkins, Katie L ^a   Woodford, Neil ^a   De Pinna, Elizabeth M ^a   Godbole, Gauri ^a  

^a PUBLIC HEALTH ENGLAND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; BACTERIAL GENE; DRUG EFFECT; FEMALE; GENETICS; GENOTYPE; HUMAN; ISOLATION AND PURIFICATION; MALE; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MUTATION; PARATYPHOID FEVER; SALMONELLA ENTERICA SEROVAR PARATYPHI A; SALMONELLA ENTERICA SEROVAR TYPHI; TYPHOID FEVER; WHOLE GENOME SEQUENCING;

ANTI-BACTERIAL AGENTS; DRUG RESISTANCE, BACTERIAL; FEMALE; GENES, BACTERIAL; GENOTYPE; HUMANS; MALE; MICROBIAL SENSITIVITY TESTS; MUTATION; PARATYPHOID FEVER; SALMONELLA PARATYPHI A; SALMONELLA TYPHI; TYPHOID FEVER; WHOLE GENOME SEQUENCING;

EID: 85044460032     PISSN: 03057453     EISSN: 14602091     Source Type: Journal    
DOI: 10.1093/jac/dkx379     Document Type: Article

References (42)

1. Connor BA, Schwartz E. Typhoid and paratyphoid fever in travellers. Lancet Infect Dis 2005; 5: 623-8.
2. Buckle GC, Walker CL, Black RE. Typhoid fever and paratyphoid fever: systematic review to estimate global morbidity and mortality for 2010. J Glob Health 2012; 2: 10401.
3. Wain J, Hendriksen RS, Mikoleit ML et al. Typhoid fever. Lancet 2015; 385: 1136-45.
4. Bhan MK, Bahl R, Bhatnagar S. Typhoid and paratyphoid fever. Lancet 2005; 366: 749-62.
5. Mirza SH, Beeching NJ, Hart CA. Multi-drug resistant typhoid: a global problem. JMedMicrobiol 1996; 44: 317-9.
6. Wain J, Hoa NT, Chinh NT et al. Quinolone-resistant Salmonella typhi in Viet Nam: molecular basis of resistance and clinical response to treatment. Clin Infect Dis 1997; 25: 1404-10.
7. Threlfall EJ, Ward LR, Skinner JA et al. Ciprofloxacin-resistant Salmonella typhi and treatment failure. Lancet 1999; 353: 1590-1.
8. Threlfall EJ, Fisher IS, Berghold C et al. Trends in antimicrobial drug resistance in Salmonella enterica serotypes Typhi and Paratyphi A isolated in Europe, 1999-2001. Int J Antimicrob Agents 2003; 22: 487-91.
9. HPA. Pilot of Enhanced Surveillance of Enteric Fever in England, Wales, and Northern Ireland, 1May 2006 to 30 April 2007. London: HPA, 2008.
10. Saha SK, Talukder SY, Islam M et al. A highly ceftriaxone-resistant Salmonella typhi in Bangladesh. Pediatr Infect Dis J 1999; 18: 387.
11. Hassing RJ, Goessens WH, van Pelt W et al. Salmonella subtypes with increased MICs for azithromycin in travelers returned to The Netherlands. Emerg Infect Dis 2014; 20: 705-8.
12. Ashton PM, Nair S, Peters TM et al. Identification of Salmonella for public health surveillance usingwhole genomesequencing. PeerJ 2016; 4: e1752.
13. McDermott PF, Tyson GH, Kabera C et al. Whole genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella. Antimicrob Agents Chemother 2016; 60: 5515-20.
14. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. NatMethods 2012; 9: 357-9.
15. Day M, Doumith M, Jenkins C, D et al. Antimicrobial resistance in Shiga toxin-producing Escherichia coli serogroups O157 and O26 isolated from human cases of diarrhoeal disease in England, 2015. J AntimicrobChemother 2017; 72: 145-52.
16. Sadouki Z, DayMR, DoumithMet al. Comparison of phenotypic andWGSderived antimicrobial resistance profiles of Shigella sonnei isolated from cases of diarrhoeal disease in England and Wales, 2015. J Antimicrob Chemother 2017; 72: 2496-502.
17. Tewolde R, Dallman T, Schaefer U et al. MOST: a modified MLST typing tool based on short read sequencing. PeerJ 2016; 4: e2308.
18. Achtman M, Wain J, Weill FX et al. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathog 2012; 8: e1002776.
19. Magiorakos A-P, Srinivasan A, Carey RB et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 2012; 18: 268-81.
20. Stoesser N, Batty EM, Eyre DW et al. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 2013; 68: 2234-44.
21. Zankari E, Hasman H, Kaas RS et al. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. JAntimicrobChemother 2013; 68: 771-7.
22. Tyson GH, McDermott PF, Li C et al.WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother 2015; 70: 2763-9.
23. DoumithM, Godbole G, Ashton P et al. Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales. J Antimicrob Chemother 2016; 71: 2300-5.
24. Wong VK, Baker S, Pickard DJ et al. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies interand intracontinental transmission events. Nat Genet 2015; 47: 632-9.
25. Cooke FJ, Wain J. The emergence of antibiotic resistance in typhoid fever. Travel Med Infect Dis 2004; 2: 67-74.
26. Sood S, Kapil A, Das B et al. Re-emergence of chloramphenicol-sensitive Salmonella typhi. Lancet 1999; 353: 1241-2.
27. Rahman M, Ahmad A, Shoma S. Decline in epidemic of multidrug resistant Salmonella typhi is not associated with increased incidence of antibiotic-susceptible strain in Bangladesh. Epidemiol Infect 2002; 129: 29-34.
28. Clark TW, Daneshvar C, PareekMet al. Enteric fever in a UK regional infectious diseases unit: a 10 year retrospective review. J Infect 2010; 60: 91-8.
29. Kariuki S, Revathi G, Muyodi J et al. Characterization ofmultidrug resistant typhoid outbreaks in Kenya. JClinMicrobiol 2004; 42: 1477-82.
30. Renuka K, Kapil A, Kabra SK et al. Reduced susceptibility to ciprofloxacin and gyrA gene mutation in North Indian strains of Salmonella enterica serotype Typhi and serotype Paratyphi A. Microb Drug Resist 2004; 10: 146-53.
31. Parry CM. The treatment of multidrug-resistant and nalidixic acidresistant typhoid fever in Viet Nam. Trans R Soc Trop Med Hyg 2004; 98: 413-22.
32. Brown JC, Shanahan PM, Jesudason MV et al. Mutations responsible for reduced susceptibility to 4-quinolones in clinical isolates of multi-resistant Salmonella typhi in India.JAntimicrobChemother 1996; 37: 891-900.
33. Walker RA, Skinner JA, Ward LR et al. LightCycler gyrA mutation assay (GAMA) identifies heterogeneity in GyrA in Salmonella enterica serotypes Typhi and Paratyphi A with decreased susceptibility to ciprofloxacin. Int J Antimicrob Agents 2003; 226: 622-5.
34. Ling JM, Chan EW, Lam AW et al. Mutations in topoisomerase genes of fluoroquinolone-resistant salmonellae in Hong Kong. Antimicrob Agents Chemother 2003; 47: 3567-73.
35. Nüesch-Inderbinen M, Abgottspon H, Sägesser G et al. Antimicrobial susceptibility of travel-related Salmonella enterica serovar Typhi isolates detected in Switzerland (2002-2013) and molecular characterization of quinolone resistant isolates. BMC Infect Dis 2015; 15: 212.
36. Menezes GA, Harish BN, Khan MA et al. Antimicrobial resistance trends in blood culture positive Salmonella Typhi isolates from Pondicherry, India, 2005-2009. ClinMicrobiol Infect 2012; 18: 239-45.
37. Humphries RM, Fang FC, Aarestrup FM et al. In vitro susceptibility testing of fluoroquinolone activity against Salmonella: recent changes to CLSI standards. Clin Infect Dis 2012; 55: 1107-13.
38. Gupta R, Gaind R, Singh LC et al. Detection of mutations in gyrB using denaturing high performance liquid chromatography (DHPLC) among Salmonella enterica serovar Typhi and Paratyphi A. Trans R Soc Trop Med Hyg 2016; 110: 684-9.
39. Skov R, Matuschek E, Sjölund-KarlssonMet al. Development of a pefloxacin disk diffusion method for detection of fluoroquinolone-resistant Salmonella enterica. JClinMicrobiol 2015; 53: 3411-7.
40. Ellington MJ, Ekelund O, Aarestrup FM et al. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect 2017; 23: 2-22.
41. Holt KE, Parkhill J, Mazzoni CJ et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008; 40: 987-93.
42. Pham Thanh D, Karkey A, Dongol S et al. A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure. Elife 2016; 5: e14003.