Genomic and antigenic diversity of colonizing isolates mirrors that of invasive isolates in Blantyre, Malawi Open Access

Abstract

Members of the species complex, particularly subsp. are antimicrobial resistance (AMR) associated pathogens of global importance, and polyvalent vaccines targeting O-antigens are in development. Whole-genome sequencing has provided insight into O-antigen distribution in the species complex as well as population structure and virulence determinants, but genomes from sub-Saharan Africa are underrepresented in global sequencing efforts. We therefore carried out a genomic analysis of extended-spectrum beta-lactamase (ESBL)-producing species complex isolates colonizing adults in Blantyre, Malawi. We placed these isolates in a global genomic context, and compared colonizing to invasive isolates from the main public hospital in Blantyre. In total, 203 isolates from stool and rectal swabs from adults were whole-genome sequenced and compared to a publicly available multicounty collection and previously sequenced Malawian and Kenyan isolates from blood or sterile sites. We inferred phylogenetic relationships and analysed the diversity of genetic loci linked to AMR, virulence, capsule and LPS O-antigen (O-types). We find that the diversity of Malawian subsp. isolates represents the species’ population structure, but shows distinct local signatures concerning clonal expansions. Siderophore and hypermucoidy genes were more frequent in invasive versus colonizing isolates (present in 13 % vs 1 %) but still generally lacking in most invasive isolates. O-antigen population structure and distribution was similar in invasive and colonizing isolates, with O4 more common (14%) than in previously published studies (2–5 %). We conclude that host factors, pathogen opportunity or alternate virulence loci not linked to invasive disease elsewhere are likely to be the major determinants of invasive disease in Malawi. Distinct ST and O-type distributions in Malawi highlight the need to sample locations where the burden of invasive disease is greatest to robustly define secular trends in diversity to assist in the development of a useful vaccine. Colonizing and invasive isolates in Blantyre are similar, hence O-typing of colonizing isolates may be a rapid and cost-effective approach to describe global diversity and guide vaccine development.

Funding
This study was supported by the:
  • Wellcome Trust (Award 109105z/15/a)
    • Principle Award Recipient: JosephM Lewis
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000778
2022-03-18
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/mgen/8/3/mgen000778.html?itemId=/content/journal/mgen/10.1099/mgen.0.000778&mimeType=html&fmt=ahah

References

  1. Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR et al. Gastrointestinal carriage is a major reservoir of Klebsiella pneumoniae Infection in intensive care patients. Clin Infect Dis 2017; 65:208–215 [View Article] [PubMed]
    [Google Scholar]
  2. Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae . Nat Rev Microbiol 2020; 18:344–359 [View Article] [PubMed]
    [Google Scholar]
  3. Okomo U, Akpalu ENK, Le Doare K, Roca A, Cousens S et al. Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in sub-Saharan Africa: a systematic review and meta-analysis in line with the STROBE-NI reporting guidelines. Lancet Infect Dis 2019; 19:1219–1234 [View Article] [PubMed]
    [Google Scholar]
  4. World Health Organisation Prioritization of Pathogens to Guide Discovery, Research and Development of New Antibiotics for Drug-Resistant Bacterial Infections, Including Tuberculosis Geneva: 2017
    [Google Scholar]
  5. Lester R, Haigh K, Wood A, MacPherson EE, Maheswaran H et al. Sustained reduction in third-generation cephalosporin usage in adult inpatients following introduction of an antimicrobial Stewardship Program in a Large, Urban Hospital in Malawi. Clin Infect Dis 2020; 71:e478–e486 [View Article] [PubMed]
    [Google Scholar]
  6. Labi A-K, Obeng-Nkrumah N, Dayie NTKD, Egyir B, Sampane-Donkor E et al. Antimicrobial use in hospitalized patients: a multicentre point prevalence survey across seven hospitals in Ghana. JAC Antimicrob Resist 2021; 3:dlab087 [View Article] [PubMed]
    [Google Scholar]
  7. Horumpende PG, Mshana SE, Mouw EF, Mmbaga BT, Chilongola JO et al. Point prevalence survey of antimicrobial use in three hospitals in North-Eastern Tanzania. Antimicrob Resist Infect Control 2020; 9:149 [View Article] [PubMed]
    [Google Scholar]
  8. Musicha P, Cornick JE, Bar-Zeev N, French N, Masesa C et al. 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]
  9. Sands K, Carvalho MJ, Portal E, Thomson K, Dyer C et al. Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries. Nat Microbiol 2021; 6:512–523 [View Article] [PubMed]
    [Google Scholar]
  10. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA et al. 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]
  11. Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microb Genom 2018; 4: [View Article] [PubMed]
    [Google Scholar]
  12. Walker KA, Miner TA, Palacios M, Trzilova D, Frederick DR et al. A Klebsiella pneumoniae regulatory mutant has reduced capsule expression but retains hypermucoviscosity. mBio 2019; 10:e00089-19 [View Article] [PubMed]
    [Google Scholar]
  13. Wyres KL, Nguyen TNT, Lam MMC, Judd LM, van Vinh Chau N et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med 2020; 12:11 [View Article] [PubMed]
    [Google Scholar]
  14. Russo TA, Marr CM. Hypervirulent Klebsiella pneumoniae . Clin Microbiol Rev 2019; 32:e00001-19 [View Article] [PubMed]
    [Google Scholar]
  15. Choi M, Tennant SM, Simon R, Cross AS. Progress towards the development of Klebsiella vaccines. Expert Rev Vaccines 2019; 18:681–691 [View Article] [PubMed]
    [Google Scholar]
  16. Follador R, Heinz E, Wyres KL, Ellington MJ, Kowarik M et al. The diversity of Klebsiella pneumoniae surface polysaccharides. Microb Genom 2016; 2:e000073 [View Article] [PubMed]
    [Google Scholar]
  17. Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R et al. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom 2016; 2:e000102 [View Article] [PubMed]
    [Google Scholar]
  18. Choi M, Hegerle N, Nkeze J, Sen S, Jamindar S et al. The diversity of lipopolysaccharide (O) and capsular polysaccharide (K) antigens of invasive Klebsiella pneumoniae in a multi-country collection. Front Microbiol 2020; 11:1249 [View Article]
    [Google Scholar]
  19. Long SW, Olsen RJ, Eagar TN, Beres SB, Zhao P et al. Population genomic analysis of 1,777 extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307. mBio 2017; 8:e00489-17 [View Article]
    [Google Scholar]
  20. David S, Reuter S, Harris SR, Glasner C, Feltwell T et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nat Microbiol 2019; 4:1919–1929 [View Article] [PubMed]
    [Google Scholar]
  21. Lewis J, Mphasa M, Banda R, Beale MA, Heinz E et al. n.d Dynamics of gut mucosal colonisation with extended spectrum beta-lactamase producing Enterobacterales in malawi. medRxiv [View Article]
    [Google Scholar]
  22. Malawi National Statistical Office 2018 Malawi Population and Housing Census Main Report. Zomba 2019 http://www.nsomalawi.mw/
    [Google Scholar]
  23. World Health Organisation Consolidated Guidelines On the Use of Antiretroviral Drugs for Treating and Preventing HIV Infection: Recommendations for a Public Health Approach. Second Edition Geneva: 2016
    [Google Scholar]
  24. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:R46 [View Article] [PubMed]
    [Google Scholar]
  25. 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] [PubMed]
    [Google Scholar]
  26. Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb Genom 2016; 2:e000083 [View Article] [PubMed]
    [Google Scholar]
  27. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
    [Google Scholar]
  28. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  30. 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] [PubMed]
    [Google Scholar]
  31. Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom 2016; 2:e000056 [View Article] [PubMed]
    [Google Scholar]
  32. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  33. Yu G, Smith DK, Zhu H, Guan Y, Lam T-Y. GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017; 8:28–36
    [Google Scholar]
  34. Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL et al. 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]
  35. Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 2017; 3:e000131 [View Article] [PubMed]
    [Google Scholar]
  36. Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019; 47:D687–D692 [View Article] [PubMed]
    [Google Scholar]
  37. 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] [PubMed]
    [Google Scholar]
  38. 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 [View Article] [PubMed]
    [Google Scholar]
  39. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
    [Google Scholar]
  40. Cornick J, Musicha P, Peno C, Saeger E, Toh PI et al. Genomic investigation of a suspected multi-drug resistant Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa. bioRxiv 20202020.08.06.236117
    [Google Scholar]
  41. Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK et al. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. J Antimicrob Chemother 2019; 74:1223–1232 [View Article] [PubMed]
    [Google Scholar]
  42. Henson SP, Boinett CJ, Ellington MJ, Kagia N, Mwarumba S et al. 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]
  43. Lewis J. joelewis101/blantyreESBL: v1.0.0 Zenodo: 2021 https://joelewis101.github.io/blantyreESBL/
  44. Ellington MJ, Heinz E, Wailan AM, Dorman MJ, de Goffau M et al. Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center. Genome Biol 2019; 20:184 [View Article] [PubMed]
    [Google Scholar]
  45. Heinz E, Ejaz H, Bartholdson Scott J, Wang N, Gujaran S et al. Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1. Sci Rep 2019; 9:2392 [View Article] [PubMed]
    [Google Scholar]
  46. Heinz E, Brindle R, Morgan-McCalla A, Peters K, Thomson NR. Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors. Microb Genom 2019; 5: [View Article] [PubMed]
    [Google Scholar]
  47. Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes | Journal of Clinical Microbiology. n.d https://jcm.asm.org/content/56/6/e00197-18 accessed 16 March 2021
  48. Strahilevitz J, Jacoby GA, Hooper DC, Robicsek A. Plasmid-mediated quinolone resistance: a multifaceted threat. Clin Microbiol Rev 2009; 22:664–689 [View Article] [PubMed]
    [Google Scholar]
  49. Andrade LN, Novais Â, Stegani LMM, Ferreira JC, Rodrigues C et al. Virulence genes, capsular and plasmid types of multidrug-resistant CTX-M(-2, -8, -15) and KPC-2-producing Klebsiella pneumoniae isolates from four major hospitals in Brazil. Diagn Microbiol Infect Dis 2018; 91:164–168 [View Article] [PubMed]
    [Google Scholar]
  50. Lewis JM, Lester R, Mphasa M, Banda R, Edwards T et al. Emergence of carbapenemase-producing Enterobacteriaceae in Malawi. J Glob Antimicrob Resist 2020; 20:225–227 [View Article] [PubMed]
    [Google Scholar]
  51. 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]
  52. Lipworth S, Vihta K-D, Chau KK, Kavanagh J, Davies T et al. Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae Serotype surveillance informs vaccine development for invasive infections. Clin Infect Dis 2021; 73:2276–2282 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000778
Loading
/content/journal/mgen/10.1099/mgen.0.000778
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Supplementary material 2

PDF

Most cited Most Cited RSS feed