1887

Abstract

Serotyping of is a critical tool in the surveillance of the pathogen and in the development and evaluation of vaccines. Whole-genome DNA sequencing and analysis is becoming increasingly common and is an effective method for pneumococcal serotype identification of pure isolates. However, because of the complexities of the pneumococcal capsular loci, current analysis software requires samples to be pure (or nearly pure) and only contain a single pneumococcal serotype. We introduce a new software tool called SeroCall, which can identify and quantitate the serotypes present in samples, even when several serotypes are present. The sample preparation, library preparation and sequencing follow standard laboratory protocols. The software runs as fast as or faster than existing identification tools on typical computing servers and is freely available under an open source licence at https://github.com/knightjimr/serocall. Using samples with known concentrations of different serotypes as well as blinded samples, we were able to accurately quantify the abundance of different serotypes of pneumococcus in mixed cultures, with 100 % accuracy for detecting the major serotype and up to 86 % accuracy for detecting minor serotypes. We were also able to track changes in serotype frequency over time in an experimental setting. This approach could be applied in both epidemiological field studies of pneumococcal colonization and experimental laboratory studies, and could provide a cheaper and more efficient method for serotyping than alternative approaches.

Funding
This study was supported by the:
  • DanielM Weinberger , National Institute of Allergy and Infectious Diseases , (Award R01AI123208)
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000494
2020-12-23
2021-02-26
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/1/mgen000494.html?itemId=/content/journal/mgen/10.1099/mgen.0.000494&mimeType=html&fmt=ahah

References

  1. Bogaert D, De Groot R, Hermans PWM. Streptococcus pneumoniae colonisation: the key to pneumococcal disease. Lancet Infect Dis 2004; 4:144–154 [CrossRef][PubMed]
    [Google Scholar]
  2. Auranen K, Rinta-Kokko H, Goldblatt D, Nohynek H, O'Brien KL et al. Colonisation endpoints in Streptococcus pneumoniae vaccine trials. Vaccine 2013; 32:153–158 [CrossRef][PubMed]
    [Google Scholar]
  3. Weinberger DM, Bruden DT, Grant LR, Lipsitch M, O'Brien KL et al. Using pneumococcal carriage data to monitor postvaccination changes in invasive disease. Am J Epidemiol 2013; 178:1488–1495 [CrossRef][PubMed]
    [Google Scholar]
  4. Nzenze SA, Madhi SA, Shiri T, Klugman KP, de Gouveia L et al. Imputing the direct and indirect effectiveness of childhood pneumococcal conjugate vaccine against invasive pneumococcal disease by surveying temporal changes in nasopharyngeal pneumococcal colonization. Am J Epidemiol 2017; 186:435–444 [CrossRef][PubMed]
    [Google Scholar]
  5. Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M et al. Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 2013; 32:165–179 [CrossRef][PubMed]
    [Google Scholar]
  6. Pimenta FC, Roundtree A, Soysal A, Bakir M, du Plessis M et al. Sequential triplex real-time PCR assay for detecting 21 pneumococcal capsular serotypes that account for a high global disease burden. J Clin Microbiol 2013; 51:647–652 [CrossRef][PubMed]
    [Google Scholar]
  7. Pai R, Gertz RE, Beall B. Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates. J Clin Microbiol 2006; 44:124–131 [CrossRef][PubMed]
    [Google Scholar]
  8. Centers for Disease Control and Prevention 2020; Resources and protocols. https://www.cdc.gov/streplab/pneumococcus/resources.html
  9. Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP et al. Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ 2016; 4:e2477 [CrossRef][PubMed]
    [Google Scholar]
  10. Epping L, van Tonder AJ, Gladstone RA, Bentley SD, Page AJ. The Global Pneumococcal Sequencing Consortium SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microb Genom 2018; 4:
    [Google Scholar]
  11. Newton R, Hinds J, Wernisch L. Empirical Bayesian models for analysing molecular serotyping microarrays. BMC Bioinformatics 2011; 12:88 [CrossRef][PubMed]
    [Google Scholar]
  12. Satzke C, Dunne EM, Porter BD, Klugman KP, Mulholland EK et al. The PneuCarriage project: a multi-centre comparative study to identify the best serotyping methods for examining pneumococcal carriage in vaccine evaluation studies. PLoS Med 2015; 12:e1001903 [CrossRef][PubMed]
    [Google Scholar]
  13. Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM et al. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One 2015; 10:e0128036 [CrossRef][PubMed]
    [Google Scholar]
  14. Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E. Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clin Microbiol Infect 2018; 24:335–341 [CrossRef][PubMed]
    [Google Scholar]
  15. Saha S, Modak JK, Naziat H, Al-Emran HM, Chowdury M et al. Detection of co-colonization with Streptococcus pneumoniae by algorithmic use of conventional and molecular methods. Vaccine 2015; 33:713–718 [CrossRef][PubMed]
    [Google Scholar]
  16. Carvalho MdaG, Pimenta FC, Moura I, Roundtree A, Gertz RE et al. Non-pneumococcal mitis-group streptococci confound detection of pneumococcal capsular serotype-specific loci in upper respiratory tract. PeerJ 2013; 1:e97 [CrossRef]
    [Google Scholar]
  17. Costello M, Fleharty M, Abreu J, Farjoun Y, Ferriera S et al. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms. BMC Genomics 2018; 19:332 [CrossRef]
    [Google Scholar]
  18. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013; 1303.3997v1 [q-bio.GN]:
    [Google Scholar]
  19. van Selm S, van Cann LM, Kolkman MAB, van der Zeijst BAM, van Putten JPM. Genetic basis for the structural difference between Streptococcus pneumoniae serotype 15b and 15C capsular polysaccharides. Infect Immun 2003; 71:6192–6198 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000494
Loading
/content/journal/mgen/10.1099/mgen.0.000494
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited this month Most Cited RSS feed

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