Field Evaluation of Culture plus Latex Sweep Serotyping for Detection of Multiple Pneumococcal Serotype Colonisation in Infants and Young Children

Turner, Paul; Turner, Claudia; Jankhot, Auscharee; Phakaudom, Kawalee; Nosten, François

doi:10.1371/journal.pone.0067933

Cited by 21 publications

(21 citation statements)

References 27 publications

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“…Pneumococcus was found in 79% (1258/1595) of the nasopharyngeal specimens by culture. Vaccine serotypes were detected in 30% (383/1258) of the pneumococcus positive specimens by the sweep latex agglutination serotyping method 19 . Pneumococcal carriage among Group 1 infants in the first 12 months of life was 79%(95CI: 76–83), comparable to Group 2 75%(95% CI: 71–79), p = 0.28 and Group 3 82%(95% CI: 79–85), p = 0.29.…”

Section: Resultsmentioning

confidence: 99%

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Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology

Kwambana-Adams

Hanson

Worwui

et al. 2017

Sci Rep

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There is growing concern that interventions that alter microbial ecology can adversely affect health. We characterised the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal carriage and the bacterial component of the nasopharyngeal microbiome during infancy. Newborns were recruited into three groups as follows: Group1 (n = 33) was the control group and comprised infants who received PCV7 after 6 months and came from unvaccinated communities. Group 2 (n = 30) came from unvaccinated communities and Group 3 (n = 39) came from vaccinated communities. Both group 2 and 3 received PCV7 at 2, 3 and 4 months. Culture and 16 S rRNA gene sequencing were performed on nasopharyngeal specimens collected at regular intervals from infants. Nasopharyngeal carriage of PCV7 serotypes in Group 1 was significantly higher than in Group 2 and 3 (p < 0.01). However, pneumococcal carriage remained comparable due to an expansion of non-vaccine serotypes in Groups 2 and 3. Determination of phylogenetic dis(similarities) showed that the bacterial community structures were comparable across groups. A mixed effects model showed no difference in community richness (p = 0.15) and Shannon α-diversity (p = 0.48) across the groups. Immediate replacement of pneumococcal vaccine serotypes with non-vaccine serotypes may mitigate the impact of PCV7 on nasopharyngeal bacterial community structure and ecology.

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Section: Resultsmentioning

confidence: 99%

“…However, it is important to note that the culture-based detection of pneumococci employed in this study has lower sensitivity than molecular methods 31 , 32 . Molecular pneumococcal detection and serotyping tools have the added benefit of enhancing multiple serotype detection and providing quantitative data 19 , 32 , 33 .…”

Section: Discussionmentioning

confidence: 99%

Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology

Kwambana-Adams

Hanson

Worwui

et al. 2017

Sci Rep

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“…Ascertainment of carriage episode duration using epidemiological modelling We first estimated carriage duration from longitudinal swab data available for the study population. For 598 unvaccinated children a complete set of 24 swabs taken over a two year period were available, an extension on the previous study (11,20) . We only considered swabs from infants in the study, as mothers did not have sufficient sampling resolution relative to their average length of carriage to determine carriage duration.…”

Section: Resultsmentioning

confidence: 99%

“…In the 'routine' cohort, 364 infants were swabbed monthly from birth, 24 times in total. All swabs were cultured and serotyped using the latex sweep method (20) . In the 'immunology' cohort 234 infants were swabbed on the same time schedule, but cultured and serotyped following the World Health Organisation (WHO) method (11) .…”

Section: Sample Collectionmentioning

confidence: 99%

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

Lees

Croucher

Goldblatt

et al. 2017

Preprint

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Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, and the duration of carriage is an important consideration in modelling transmission dynamics and vaccine response. Existing studies of carriage duration variability are based at the serotype level only, and do not probe variation within lineages or fully quantify interactions with other environmental factors.Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data. By combining these results with whole genome sequence data we estimate that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas host traits accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). For the locus effects, a genome-wide association study identified 16 loci which may have an effect on carriage duration independent of serotype. Hits at a genome-wide level of significance were to prophage sequences, suggesting infection by such viruses substantially affects carriage duration. These results show that both serotype and non-serotype specific effects alter carriage duration in infants and young children and are more important than other environmental factors such as host genetics. This has implications for models of pneumococcal competition and antibiotic resistance, and leads the way for the analysis of heritability of complex bacterial traits. Significance statementOther than serotype, the genetic determinants of pneumococcal carriage duration are unknown. In this study we used longitudinal sampling to measure the duration of carriage in infants, and searched for any associated variation in the pan-genome. While we found that the pathogen genome explains most of the variability in duration, serotype did not fully account for this. Recent theoretical work has proposed the existence of alleles which alter carriage duration to explain the puzzle of continued coexistence of antibiotic-resistant and sensitive strains. Here we have shown that these alleles do exist in a natural population, and also identified candidates for the loci which fulfil this role. Together these findings have implications for future modelling of pneumococcal epidemiology and resistance.

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“…Multiple carriage of pneumococcal strains has been investigated with modified culture methods including conventional Quellung typing of at least five colonies [ 18 ], or latex agglutination of a sweep of colonies from a plate culture [ 19 , 20 ]. Other methods isolate DNA directly from the NP sample, or after an additional enrichment step, and utilize different platforms such as multiplex PCR approaches [ 21 – 23 ], a microarray platform [ 19 ] or a MassTag PCR assay [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Single-Plex Quantitative Assays for the Detection and Quantification of Most Pneumococcal Serotypes

et al. 2015

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Streptococcus pneumoniae globally kills more children than any other infectious disease every year. A prerequisite for pneumococcal disease and transmission is colonization of the nasopharynx. While the introduction of pneumococcal conjugate vaccines has reduced the burden of pneumococcal disease, understanding the impact of vaccination on nasopharyngeal colonization has been hampered by the lack of sensitive quantitative methods for the detection of >90 known S. pneumoniae serotypes. In this work, we developed 27 new quantitative (q)PCR reactions and optimized 26 for a total of 53 qPCR reactions targeting pneumococcal serotypes or serogroups, including all vaccine types. Reactions proved to be target-specific with a limit of detection of 2 genome equivalents per reaction. Given the number of probes required for these assays and their unknown shelf-life, the stability of cryopreserved reagents was evaluated. Our studies demonstrate that two-year cryopreserved probes had similar limit of detection as freshly-diluted probes. Moreover, efficiency and limit of detection of 1-month cryopreserved, ready-to-use, qPCR reaction mixtures were similar to those of freshly prepared mixtures. Using these reactions, our proof-of-concept studies utilizing nasopharyngeal samples (N=30) collected from young children detected samples containing ≥2 serotypes/serogroups. Samples colonized by multiple serotypes/serogroups always had a serotype that contributes at least 50% of the pneumococcal load. In addition, a molecular approach called S6-q(PCR)2 was developed and proven to individually detect and quantify epidemiologically-important serogroup 6 strains including 6A, 6B, 6C and 6D. This technology will be useful for epidemiological studies, diagnostic platforms and to study the pneumobiome.

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Field Evaluation of Culture plus Latex Sweep Serotyping for Detection of Multiple Pneumococcal Serotype Colonisation in Infants and Young Children

Cited by 21 publications

References 27 publications

Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology

Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

Single-Plex Quantitative Assays for the Detection and Quantification of Most Pneumococcal Serotypes

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