1887

Abstract

Ceftriaxone is the drug of choice for typhoid fever and the emergence of resistant Typhi raises major concerns for treatment. There are an increasing number of sporadic reports of ceftriaxone-resistant . Typhi and limiting the risk of treatment failure in the patient and outbreaks in the community must be prioritized. This study describes the use of whole genome sequencing to guide outbreak identification and case management.

An isolate of ceftriaxone-resistant . Typhi from the blood of a child taken in 2000 at the Popular Diagnostic Center, Dhaka, Bangladesh was subjected to whole genome sequencing, using an Illumina NextSeq 500 and analysis using Geneious software.

Comparison with other ceftriaxone-resistant . Typhi revealed an isolate from the Democratic Republic of the Congo in 2015 as the closest relative but no evidence of an outbreak. A plasmid belonging to incompatibility group I1 (IncI1-ST31) which included (ceftriaxone resistance) associated with was identified. High similarity (90 %) was seen with pS115, an IncI1 plasmid from . Enteritidis, and with pESBL-EA11, an incI1 plasmid from (99 %) showing that Typhi has access to ceftriaxone resistance through the acquisition of common plasmids.

The transmission of ceftriaxone resistance from to Typhi is of concern because of clinical resistance to ceftriaxone, the main stay of typhoid treatment. Whole genome sequencing, albeit several years after the isolation, demonstrated the success of containment but clinical trials with alternative agents are urgently required.

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2018-05-01
2024-04-18
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References

  1. Kothari A, Pruthi A, Chugh TD. The burden of enteric fever. J Infect Dev Ctries 2008; 2:253–259[PubMed] [Crossref]
    [Google Scholar]
  2. Reddy S, Rangaiah J, Addiman S, Wareham D, Wilson P et al. Epidemiology, antibiotic resistance trends and the cost of enteric fever in East London, 2005-2010. Travel Med Infect Dis 2011; 9:206–212 [View Article][PubMed]
    [Google Scholar]
  3. Wain J, Hendriksen RS, Mikoleit ML, Keddy KH, Ochiai RL. Typhoid fever. Lancet 2015; 385:1136–1145 [View Article][PubMed]
    [Google Scholar]
  4. Feigin V. GBD 2015 Mortality and Causes of Death Collaborators Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015: a systematic analysis for the Global Burden of Disease Study 2015. Lancet 2016; 388:1459–1544 [View Article][PubMed]
    [Google Scholar]
  5. Maurice J. A first step in bringing typhoid fever out of the closet. Lancet 2012; 379:699–700 [View Article][PubMed]
    [Google Scholar]
  6. Obaro SK, Iroh Tam PY, Mintz ED. The unrecognized burden of typhoid fever. Expert Rev Vaccines 2017; 16:249–260 [View Article][PubMed]
    [Google Scholar]
  7. Wain J, Kidgell C. The emergence of multidrug resistance to antimicrobial agents for the treatment of typhoid fever. Trans R Soc Trop Med Hyg 2004; 98:423–430 [View Article][PubMed]
    [Google Scholar]
  8. Raffatellu M, Wilson RP, Winter SE, Bäumler AJ. Clinical pathogenesis of typhoid fever. J Infect Dev Ctries 2008; 2:260–266[PubMed]
    [Google Scholar]
  9. Wain J, Diep TS, Ho VA, Walsh AM, Nguyen TT et al. Quantitation of bacteria in blood of typhoid fever patients and relationship between counts and clinical features, transmissibility, and antibiotic resistance. J Clin Microbiol 1998; 36:1683–1687[PubMed]
    [Google Scholar]
  10. Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S et al. Evolutionary history of Salmonella Typhi. Science 2006; 314:1301–1304 [View Article][PubMed]
    [Google Scholar]
  11. Feasey NA, Gaskell K, Wong V, Msefula C, Selemani G et al. Rapid emergence of multidrug resistant, H58-lineage Salmonella Typhi in Blantyre, Malawi. PLoS Negl Trop Dis 2015; 9:e0003748 [View Article][PubMed]
    [Google Scholar]
  12. Murgia M, Rubino S, Wain J, Gaind R, Paglietti B. A novel broadly applicable PCR-RFLP method for rapid identification and subtyping of H58 Salmonella Typhi. J Microbiol Methods 2016; 127:219–223 [View Article][PubMed]
    [Google Scholar]
  13. Holt KE, Phan MD, Baker S, Duy PT, Nga TV et al. Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid. PLoS Negl Trop Dis 2011; 5:e1245 [View Article][PubMed]
    [Google Scholar]
  14. Crump JA, Sjölund-Karlsson M, Gordon MA, Parry CM. Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clin Microbiol Rev 2015; 28:901–937 [View Article][PubMed]
    [Google Scholar]
  15. Saha SK, Saha S, Ruhulamin M, Hanif M, Islam M. Decreasing trend of multiresistant Salmonella Typhi in Bangladesh. J Antimicrob Chemother 1997; 39:554–556 [View Article][PubMed]
    [Google Scholar]
  16. Saha SK, Darmstadt GL, Baqui AH, Crook DW, Islam MN et al. Molecular basis of resistance displayed by highly ciprofloxacin-resistant Salmonella enterica serovar Typhi in Bangladesh. J Clin Microbiol 2006; 44:3811–3813 [View Article][PubMed]
    [Google Scholar]
  17. Engberg J, Aarestrup FM, Taylor DE, Gerner-Smidt P, Nachamkin I. Quinolone and macrolide resistance in Campylobacter jejuni and C. coli: resistance mechanisms and trends in human isolates. Emerg Infect Dis 2001; 7:24–34 [View Article][PubMed]
    [Google Scholar]
  18. Hasanuzzaman M, Malaker R, Islam M, Baqui AH, Darmstadt GL et al. Detection of macrolide resistance genes in culture-negative specimens from Bangladeshi children with invasive pneumococcal diseases. J Glob Antimicrob Resist 2017; 8:131–134 [View Article][PubMed]
    [Google Scholar]
  19. Ovetchkine P, Rieder MJ. Canadian Paediatric Society, Drug Therapy and Hazardous Substances Committee Azithromycin use in paediatrics: a practical overview. Paediatr Child Health 2013; 18:311–313[PubMed] [Crossref]
    [Google Scholar]
  20. Cantón R, Coque TM. The CTX-M beta-lactamase pandemic. Curr Opin Microbiol 2006; 9:466–475 [View Article][PubMed]
    [Google Scholar]
  21. Morita M, Takai N, Terajima J, Watanabe H, Kurokawa M et al. Plasmid-mediated resistance to cephalosporins in Salmonella enterica serovar Typhi. Antimicrob Agents Chemother 2010; 54:3991–3992 [View Article][PubMed]
    [Google Scholar]
  22. Saha SK, Talukder SY, Islam M, Saha S. A highly ceftriaxone-resistant Salmonella Typhi in Bangladesh. Pediatr Infect Dis J 1999; 18:387 [View Article][PubMed]
    [Google Scholar]
  23. Ahmed D, Hoque A, Mazumder R, Nahar K, Islam N et al. Salmonella enterica serovar Typhi strain producing extended-spectrum β-lactamases in Dhaka, Bangladesh. J Med Microbiol 2012; 61:1032–1033 [View Article][PubMed]
    [Google Scholar]
  24. Akinyemi KO, Iwalokun BA, Alafe OO, Mudashiru SA, Fakorede C. blaCTX-MI group extended spectrum beta lactamase-producing Salmonella Typhi from hospitalized patients in Lagos, Nigeria. Infect Drug Resist 2015; 8:99 [View Article][PubMed]
    [Google Scholar]
  25. Pfeifer Y, Matten J, Rabsch W. Salmonella enterica serovar Typhi with CTX-M beta-lactamase, Germany. Emerg Infect Dis 2009; 15:1533–1535 [View Article][PubMed]
    [Google Scholar]
  26. Rodrigues C, Kapil A, Sharma A, Devanga Ragupathi NK, Inbanathan FY et al. Whole-genome shotgun sequencing of cephalosporin-resistant Salmonella enterica serovar Typhi. Genome Announc 2017; 5:e01639-16 [View Article][PubMed]
    [Google Scholar]
  27. Veeraraghavan B, Anandan S, Muthuirulandi Sethuvel DP, Puratchiveeran N, Walia K et al. Molecular characterization of intermediate susceptible typhoidal Salmonella to ciprofloxacin, and its impact. Mol Diagn Ther 2016; 20:213–219 [View Article][PubMed]
    [Google Scholar]
  28. The Clinical and Laboratory Standards Institute Performance Standards for Antimicrobial Susceptibility Testing, 26th ed. CLSI Supplement M100S Wayne, PA: CLSI; 2016
    [Google Scholar]
  29. Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 2016; 44:W3–W10 [View Article][PubMed]
    [Google Scholar]
  30. Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Kaiser BL et al. Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol 2015; 53:1685–1692 [View Article][PubMed]
    [Google Scholar]
  31. Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VP et al. The Salmonella in silico typing resource (SISTR): an open Web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS One 2016; 11:e0147101 [View Article][PubMed]
    [Google Scholar]
  32. 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]
  33. 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][PubMed]
    [Google Scholar]
  34. 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]
  35. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12:402 [View Article][PubMed]
    [Google Scholar]
  36. Phoba MF, Barbé B, Lunguya O, Masendu L, Lulengwa D et al. Salmonella enterica serovar Typhi producing CTX-M-15 extended spectrum β-lactamase in the Democratic Republic of the Congo. Clin Infect Dis 2017cix342
    [Google Scholar]
  37. Ahmed SA, Awosika J, Baldwin C, Bishop-Lilly KA, Biswas B et al. Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2. PLoS One 2012; 7:e48228 [View Article][PubMed]
    [Google Scholar]
  38. Smet A, van Nieuwerburgh F, Vandekerckhove TT, Martel A, Deforce D et al. Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences. PLoS One 2010; 5:e11202 [View Article][PubMed]
    [Google Scholar]
  39. Rotimi VO, Jamal W, Pal T, Sovenned A, Albert MJ. Emergence of CTX-M-15 type extended-spectrum beta-lactamase-producing Salmonella spp. in Kuwait and the United Arab Emirates. J Med Microbiol 2008; 57:881–886 [View Article][PubMed]
    [Google Scholar]
  40. Lartigue MF, Poirel L, Aubert D, Nordmann P. In vitro analysis of ISEcp1B-mediated mobilization of naturally occurring beta-lactamase gene blaCTX-M of Kluyvera ascorbata. Antimicrob Agents Chemother 2006; 50:1282–1286 [View Article][PubMed]
    [Google Scholar]
  41. Poirel L, Decousser JW, Nordmann P. Insertion sequence ISEcp1B is involved in expression and mobilization of a blaCTX-M β-lactamase gene. Antimicrob Agents Chemother 2003; 47:2938–2945 [View Article][PubMed]
    [Google Scholar]
  42. Butler T, Rumans L, Arnold K. Response of typhoid fever caused by chloramphenicol-susceptible and chloramphenicol-resistant strains of Salmonella Typhi to treatment with trimethoprim-sulfamethoxazole. Rev Infect Dis 1982; 4:551–561 [View Article][PubMed]
    [Google Scholar]
  43. Phan MD, Wain J. IncHI plasmids, a dynamic link between resistance and pathogenicity. J Infect Dev Ctries 2008; 2:272–278[PubMed]
    [Google Scholar]
  44. García-Fernández A, Chiaretto G, Bertini A, Villa L, Fortini D et al. Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum beta-lactamases in Escherichia coli and Salmonella of human and animal origin. J Antimicrob Chemother 2008; 61:1229–1233 [View Article][PubMed]
    [Google Scholar]
  45. Johnson TJ, Wannemuehler YM, Johnson SJ, Logue CM, White DG et al. Plasmid replicon typing of commensal and pathogenic Escherichia coli isolates. Appl Environ Microbiol 2007; 73:1976–1983 [View Article][PubMed]
    [Google Scholar]
  46. Reddy EA, Shaw AV, Crump JA. Community-acquired bloodstream infections in Africa: a systematic review and meta-analysis. Lancet Infect Dis 2010; 10:417–432 [View Article][PubMed]
    [Google Scholar]
  47. Hopkins KL, Liebana E, Villa L, Batchelor M, Threlfall EJ et al. Replicon typing of plasmids carrying CTX-M or CMY beta-lactamases circulating among Salmonella and Escherichia coli isolates. Antimicrob Agents Chemother 2006; 50:3203–3206 [View Article][PubMed]
    [Google Scholar]
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