1887

Abstract

The outer core locus (OCL) that includes genes for the synthesis of the variable outer core region of the lipooligosaccharide (LOS) is one of the key epidemiological markers used for tracing the spread of , a bacterial pathogen of global concern. In this study, we screened 12 476 publicly available genome assemblies for novel OCL sequences, detecting six new OCL types that were designated OCL17–OCL22. These were compiled with previously characterized OCL sequences to create an updated version of the OCL reference database, providing a total of 22 OCL reference sequences for use with the bioinformatics tool . Use of this database against the 12 476 downloaded assemblies found OCL1 to be the most common locus, present in 73.6 % of sequenced genomes assigned by with a match confidence score of good or above. OCL1 was most common amongst isolates belonging to sequence types (STs) ST1, ST2, ST3 and ST78, all of which are over-represented clonal lineages. The highest level of diversity in OCL types was found in ST2, with eight different OCLs identified. The updated OCL reference database is available for download from GitHub (https://github.com/klebgenomics/Kaptive; under version ), and has been integrated for use on Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods for strain identification, classification and surveillance.

Funding
This study was supported by the:
  • Australian Research Council (Award DE180101563)
    • Principle Award Recipient: JohannaJ Kenyon
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.001042
2023-06-13
2024-10-03
Loading full text...

Full text loading...

/deliver/fulltext/mgen/9/6/mgen001042.html?itemId=/content/journal/mgen/10.1099/mgen.0.001042&mimeType=html&fmt=ahah

References

  1. Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 2022; 399:629–655 [View Article]
    [Google Scholar]
  2. Ayobami O, Willrich N, Harder T, Okeke IN, Eckmanns T et al. The incidence and prevalence of hospital-acquired (carbapenem-resistant) Acinetobacter baumannii in Europe, Eastern Mediterranean and Africa: a systematic review and meta-analysis. Emerg Microbes Infect 2019; 8:1747–1759 [View Article] [PubMed]
    [Google Scholar]
  3. Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis 2018; 18:318–327 [View Article] [PubMed]
    [Google Scholar]
  4. Hamidian M, Nigro SJ. Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii. Microb Genom 2019; 5:e000306 [View Article] [PubMed]
    [Google Scholar]
  5. Gaiarsa S, Batisti Biffignandi G, Esposito EP, Castelli M, Jolley KA et al. Comparative analysis of the two Acinetobacter baumannii multilocus sequence typing (MLST) schemes. Front Microbiol 2019; 10:930 [View Article] [PubMed]
    [Google Scholar]
  6. Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM et al. New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. mBio 2014; 5:e00963-13 [View Article] [PubMed]
    [Google Scholar]
  7. Hamidian M, Hawkey J, Wick R, Holt KE, Hall RM. Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1. Microb Genom 2019; 5:e000242 [View Article] [PubMed]
    [Google Scholar]
  8. Holt K, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ et al. Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1. Microb Genom 2016; 2:e000052 [View Article] [PubMed]
    [Google Scholar]
  9. Koong J, Johnson C, Rafei R, Hamze M, Myers GSA et al. Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1. Microb Genom 2021; 7:000705 [View Article] [PubMed]
    [Google Scholar]
  10. Iovleva A, Mustapha MM, Griffith MP, Komarow L, Luterbach C et al. Carbapenem-resistant Acinetobacter baumannii in U.S. hospitals: diversification of circulating lineages and antimicrobial resistance. mBio 2022; 13:e0275921 [View Article] [PubMed]
    [Google Scholar]
  11. Kenyon JJ, Hall RM. Variation in the complex carbohydrate biosynthesis loci of Acinetobacter baumannii genomes. PLoS One 2013; 8:e62160 [View Article] [PubMed]
    [Google Scholar]
  12. Wyres KL, Cahill SM, Holt KE, Hall RM, Kenyon JJ. Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Microb Genom 2020; 6:e000339 [View Article] [PubMed]
    [Google Scholar]
  13. Cahill SM, Hall RM, Kenyon JJ. An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus. Microb Genom 2022; 8:mgen000878 [View Article] [PubMed]
    [Google Scholar]
  14. Kenyon JJ, Nigro SJ, Hall RM. Variation in the OC locus of Acinetobacter baumannii genomes predicts extensive structural diversity in the lipooligosaccharide. PLoS One 2014; 9:e107833 [View Article] [PubMed]
    [Google Scholar]
  15. Kenyon JJ, Holt KE, Pickard D, Dougan G, Hall RM. Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides. Res Microbiol 2014; 165:472–475 [View Article] [PubMed]
    [Google Scholar]
  16. Talyansky Y, Nielsen TB, Yan J, Carlino-Macdonald U, Di Venanzio G et al. Capsule carbohydrate structure determines virulence in Acinetobacter baumannii. PLoS Pathog 2021; 17:e1009291 [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. Meumann EM, Anstey NM, Currie BJ, Piera KA, Kenyon JJ et al. Genomic epidemiology of severe community-onset Acinetobacter baumannii infection. Microb Genom 2019; 5:e000258 [View Article] [PubMed]
    [Google Scholar]
  19. Kenyon JJ, Hall RM. Updated analysis of the surface carbohydrate gene clusters in a diverse panel of Acinetobacter baumannii isolates. Antimicrob Agents Chemother 2022; 66:e0180721 [View Article] [PubMed]
    [Google Scholar]
  20. Lam MMC, Wick RR, Judd LM, Holt KE, Wyres KL. Kaptive 2.0: updated capsule and LPS locus typing for the Klebsiella pneumoniae species complex. Microb Genom 2022; 8:000800 [View Article] [PubMed]
    [Google Scholar]
  21. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [View Article] [PubMed]
    [Google Scholar]
  22. Potter SC, Luciani A, Eddy SR, Park Y, Lopez R et al. HMMER web server: 2018 update. Nucleic Acids Res 2018; 46:W200–W204 [View Article] [PubMed]
    [Google Scholar]
  23. Fregolino E, Fugazza G, Galano E, Gargiulo V, Landini P et al. Complete lipooligosaccharide structure of the clinical isolate Acinetobacter baumannii, strain SMAL. Eur J Org Chem 2010; 2010:1345–1352 [View Article]
    [Google Scholar]
  24. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Wickham H. ggplot2 Cham: Springer; 2016 [View Article]
    [Google Scholar]
  27. 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:e00197-18 [View Article] [PubMed]
    [Google Scholar]
  28. Galac MR, Snesrud E, Lebreton F, Stam J, Julius M et al. A diverse panel of clinical Acinetobacter baumannii for research and development. Antimicrob Agents Chemother 2020; 64:e00840-20 [View Article] [PubMed]
    [Google Scholar]
  29. Sahl JW, Del Franco M, Pournaras S, Colman RE, Karah N et al. Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage. Sci Rep 2015; 5:15188 [View Article] [PubMed]
    [Google Scholar]
  30. Adams MD, Wright MS, Karichu JK, Venepally P, Fouts DE et al. Rapid replacement of Acinetobacter baumannii strains accompanied by changes in lipooligosaccharide loci and resistance gene repertoire. mBio 2019; 10:e00356-19 [View Article] [PubMed]
    [Google Scholar]
  31. Iwashkiw JA, Seper A, Weber BS, Scott NE, Vinogradov E et al. Identification of a general O-linked protein glycosylation system in Acinetobacter baumannii and its role in virulence and biofilm formation. PLoS Pathog 2012; 8:e1002758 [View Article] [PubMed]
    [Google Scholar]
  32. Harding CM, Nasr MA, Kinsella RL, Scott NE, Foster LJ et al. Acinetobacter strains carry two functional oligosaccharyltransferases, one devoted exclusively to type IV pilin, and the other one dedicated to O-glycosylation of multiple proteins. Mol Microbiol 2015; 96:1023–1041 [View Article] [PubMed]
    [Google Scholar]
  33. Douraghi M, Kenyon JJ, Aris P, Asadian M, Ghourchian S et al. Accumulation of antibiotic resistance genes in carbapenem-resistant Acinetobacter baumannii isolates belonging to lineage 2, global clone 1, from outbreaks in 2012–2013 at a Tehran burns hospital. mSphere 2020; 5:e00164-20 [View Article] [PubMed]
    [Google Scholar]
  34. Hua X, Zhang L, He J, Leptihn S, Yu Y. Population biology and epidemiological studies of Acinetobacter baumannii in the era of whole genome sequencing: is the Oxford scheme still appropriate?. Front Microbiol 2020; 11:775 [View Article] [PubMed]
    [Google Scholar]
  35. Loraine J, Heinz E, Soontarach R, Blackwell GA, Stabler RA et al. Genomic and phenotypic analyses of Acinetobacter baumannii isolates from three tertiary care hospitals in Thailand. Front Microbiol 2020; 11:548 [View Article] [PubMed]
    [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.001042
Loading
/content/journal/mgen/10.1099/mgen.0.001042
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Supplementary material 2

PDF
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