Evaluating methods for identifying and quantifying Streptococcus pneumoniae co-colonisation using next-generation sequencing data

Hackman, Jada, Hibberd, Martin, Swarthout, Todd, Hinds, Jason, Ashall, James, Sheppard, Carmen, Tonkin-Hill, Gerry, Gould, Kate, Brown, Comfort, Msefula, Jacquline, Mataya, Andrew, Toizumi, Michiko, Yoshida, Lay-Myint, French, Neil, Heyderman, Robert, Flasche, Stefan, Kwambana, Brenda and Hue, Stephane (2024) 'Evaluating methods for identifying and quantifying Streptococcus pneumoniae co-colonisation using next-generation sequencing data'. Microbiology Spectrum. (In Press)

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Abstract

Detection of multiple pneumococcal serotype carriage can enhance monitoring of pneumococcal vaccine impact, particularly among high-burden childhood populations. We assessed methods for identifying co-carriage of pneumococcal serotypes from whole-genome sequences.
24 nasopharyngeal samples were collected during community carriage surveillance from healthy children in Blantyre, Malawi which were then serotyped by microarray. Pneumococcal DNA from culture plate sweeps were sequenced using Illumina MiSeq and genomic serotyping was carried out using SeroCall and PneumoKITy. Their sensitivity was calculated in reference to the microarray data. Local maxima in the SNP density distributions were assessed for their correspondence to the relative abundance of serotypes.
Across the 24 individuals, microarray detected 77 non-unique serotypes, of which 42 occurred at high relative abundance (>10%) (per individual, median, 3; range, 1 - 6 serotypes). The average sequencing depth was 57X (range: 21X - 88X). The sensitivity of SeroCall for identifying high abundance serotypes was 98% (95% CI, 0.87-1.00), 20% (0.08-0.36) for low abundance (<10%), and 62% (0.50-0.72) overall.
PneumoKITy’s sensitivity was 86% (0.72-0.95), 20% (0.06-0.32), and 56% (0.42-0.65), respectively. Local maxima in the SNP frequency distribution were highly correlated with the relative abundance of high-abundance serotypes. Six samples were resequenced and the pooled runs had an average 4-fold increase in sequencing depth. This allowed genomic serotyping of two of the previously undetectable
seven low-abundance serotypes.
Genomic serotyping is highly sensitive for the detection of high-abundance serotypes in samples with co-carriage. Serotype associated reads may be identified through SNP frequency and increased read depth can increase sensitivity for low-abundance serotype detection.

Item Type:	Article
Subjects:	QU Biochemistry > Genetics > QU 550 Genetic techniques. PCR. Chromosome mapping WC Communicable Diseases > WC 20 Research (General) WC Communicable Diseases > Infection. Bacterial Infections > Bacterial Infections > WC 210 Streptococcal infections (General or not elsewhere classified)
Faculty: Department:	Clinical Sciences & International Health > Clinical Sciences Department
Digital Object Identifer (DOI):	Temp_DOI_4
Depositing User:	Lynn Roberts-Maloney
Date Deposited:	18 Jul 2024 08:13
Last Modified:	01 Aug 2024 15:24
URI:	https://archive.lstmed.ac.uk/id/eprint/24949

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