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Volume 7, Issue 11

Genomic investigation of a suspected outbreak in a neonatal care unit in sub-Saharan Africa Open Access

Abstract

A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infections, and a suspected outbreak of multi-drug-resistant was investigated using genomic characterisation. All bloodstream infections (BSIs) from patients in the neonatal ward (=62), and a subset of BSI isolates (=38) from other paediatric wards in the hospital, collected over a 4 year period were studied. After whole genome sequencing, the strain sequence types (STs), plasmid types, virulence and resistance genes were identified. One ST340 clone, part of clonal complex 258 (CC258) and an ST that drives hospital outbreaks worldwide, harbouring numerous resistance genes and plasmids, was implicated as the likely cause of the outbreak. This study contributes molecular information necessary for tracking and characterizing this important hospital pathogen in sub-Saharan Africa.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , genome sequencing , hospital outbreak , Klebsiella pneumoniae , neonatal infection and sub-Saharan Africa
Funding
This study was supported by the:
  • Wellcome Trust (Award 206545)
    • Principle Award Recipient: AmyK Cain
  • University of Liverpool (Award RDF160301AC12)
    • Principle Award Recipient: AmyK Cain
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2021-11-18
2024-05-02
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References

  1. Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev 2017; 41:252–275 [View Article]
     [Google Scholar]
  2. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 2015; 112:E3574–81 [View Article] [PubMed]
     [Google Scholar]
  3. Stapleton PJM, Murphy M, McCallion N, Brennan M, Cunney R. Outbreaks of extended spectrum beta-lactamase-producing Enterobacteriaceae in neonatal intensive care units: a systematic review. Arch Dis Child Fetal Neonatal Ed 2016; 101:F72–8 [View Article] [PubMed]
     [Google Scholar]
  4. Zheng B, Dai Y, Liu Y, Shi W, Dai E. Molecular epidemiology and risk factors of carbapenem-resistant Klebsiella pneumoniae infections in Eastern China. Front Microbiol 2017; 8:1–11 [View Article]
     [Google Scholar]
  5. Wyres KL, Gorrie C, Edwards DJ, Wertheim HFL, Hsu LY. Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal group 258. Genome Biol Evol 2015; 7:1267–1279 [View Article] [PubMed]
     [Google Scholar]
  6. Musicha P, Cornick JE, Bar-Zeev N, French N, Masesa C. Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998-2016): a surveillance study. Lancet Infect Dis 2017; 17:1042–1052 [View Article] [PubMed]
     [Google Scholar]
  7. Davis MPA, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. Kraken: A set of tools for quality control and analysis of high-throughput sequence data. Methods 2013; 63:41–49 [View Article]
     [Google Scholar]
  8. Diancourt L, Passet V, Verhoef J, Grimont PAD, Brisse S. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 2005; 43:4178–4182 [View Article]
     [Google Scholar]
  9. Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014; 6:11 [View Article]
     [Google Scholar]
  10. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 2005; 63:219–228 [View Article] [PubMed]
     [Google Scholar]
  11. 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: [View Article] [PubMed]
     [Google Scholar]
  12. Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom 2016; 2:e000102 [View Article] [PubMed]
     [Google Scholar]
  13. Wick RR, Heinz E, Holt KE, Wyres KL. Kaptive web: User-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes. J Clin Microbiol 2018; 56:e00197 [View Article] [PubMed]
     [Google Scholar]
  14. Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 2021; 12:4188 [View Article] [PubMed]
     [Google Scholar]
  15. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Tolentino FM, Bueno MFC, Franscisco GR, Barcelos DD de P, Lobo SM et al. Endemicity of the high-risk clone Klebsiella pneumoniae ST340 coproducing QnrB, CTX-M-15, and KPC-2 in a Brazilian hospital. Microbial Drug Resistance 201925528–537 [View Article]
     [Google Scholar]
  18. Netikul T, Kiratisin P. Genetic characterization of carbapenem-resistant Enterobacteriaceae and the spread of carbapenem-resistant Klebsiella pneumonia ST340 at a university hospital in thailand. PLoS One 2015; 10:e0139116 [View Article] [PubMed]
     [Google Scholar]
  19. Kumwenda GP, Sugawara Y, Abe R, Akeda Y, Kasambara W et al. First Identification and genomic characterization of multidrug-resistant carbapenemase-producing Enterobacteriaceae clinical isolates in Malawi, Africa. J Med Microbiol 2019; 68:1707–1715 [View Article] [PubMed]
     [Google Scholar]
  20. Henson SP, Boinett CJ, Ellington MJ, Kagia N, Mwarumba S. Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya. Int J Med Microbiol 2017; 307:422–429 [View Article] [PubMed]
     [Google Scholar]
  21. Moradigaravand D, Martin V, Peacock SJ, Parkhill J. Evolution and epidemiology of multidrug-resistant Klebsiella pneumoniae in the United Kingdom and Ireland. mBio 2017; 8:e01976 [View Article] [PubMed]
     [Google Scholar]
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Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa
M Gen 7, 000703 (2021); https://doi.org/10.1099/mgen.0.000703
/content/journal/mgen/10.1099/mgen.0.000703
/content/journal/mgen/10.1099/mgen.0.000703
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