Seasonality and outbreak of a predominant Streptococcus pneumoniae serotype 1 clone from The Gambia: Expansion of ST217 hypervirulent clonal complex in West Africa

Antonio, Martín; Hakeem, Ishrat; Awine, Timothy; Secka, Ousman; Sankareh, Kawsu; Nsekpong, David; Lahai, George; Akisanya, Abiodun; Egere, Uzochukwu; Enwere, Godwin; Zaman, Syed M A; Hill, Philip C.; Corrah, Tumani; Cutts, Felicity; Greenwood, Brian; Adegbola, Richard A.

doi:10.1186/1471-2180-8-198

Cited by 57 publications

(71 citation statements)

References 16 publications

(37 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interestingly, the observed higher resistance to tetracycline was much higher than to chloramphenicol in the West African lineage despite the presence of only Tn 5253 element which carries resistance conferring genes for both antibiotics [76]. This observation was consistent with previous study from the Gambia, which also reported such a discrepancy using in vitro phenotypic data [77]. Because resistance to both antibiotics was due to the presence of only the Tn 5253 element, this suggested that the chloramphenicol resistant isolates contained a deletion of the chloramphenicol resistance encoding loci.…”

Section: Discussionsupporting

confidence: 88%

“…This further suggests that the deletion of the chloramphenicol resistance encoding loci was restricted to the West African isolates. These findings explain why ST217 isolates from West Africa are more susceptible to chloramphenicol than tetracycline as previously reported [77]. …”

Section: Discussionsupporting

confidence: 79%

“…This further suggests that the deletion was not recent and if it was recent it would imply that the defective Tn 5253 has spread at a high rate possibly as a consequence of selection in West Africa. During the sampling period, chloramphenicol was widely used in The Gambia [77] and possibly other West African countries while its use decreased in Southern African countries such as Malawi where all the resistant isolates harbored an intact Tn 5253 element. This may suggest that the observed widespread loss of chloramphenicol resistance mechanism in West African isolates may not be a consequence of low chloramphenicol usage.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Understanding pneumococcal serotype 1 biology through population genomic analysis

et al. 2016

Self Cite

View full text Add to dashboard Cite

BackgroundPneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries.MethodsWe analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes.ResultsPopulation structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1’s rarity in carriage and consequently its lower recombination rates.ConclusionsThe high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-016-1987-z) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionsupporting

confidence: 88%

Section: Discussionsupporting

confidence: 79%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Understanding pneumococcal serotype 1 biology through population genomic analysis

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Of note, 88.3% (95% CI 43.2, 99.6) and 98.6% (95% CI 70.6, 100.0) of serotypes causing nonbacteremic pneumonia and noninvasive disease were included in the available PCV10 and PCV13, respectively (Appendix Figure 1). Serotypes 1 and 5, which are the most commonly identified serotypes in previous studies in Africa 46–49 and in more recent outbreaks, 50,51 accounted for 12.8% (95% CI 4.9, 24.0) of meningitis, 10.2% (95% 5.7, 15.6) of IPD, and 6.1% (95% CI 0.0, 71.2) of nonbacteremic pneumonia/noninvasive cases, respectively.…”

Section: Resultsmentioning

confidence: 75%

Childhood pneumococcal disease in Africa – A systematic review and meta-analysis of incidence, serotype distribution, and antimicrobial susceptibility

Tam

Thielen

Obaro

et al. 2017

Vaccine

View full text Add to dashboard Cite

Background Determining the incidence, disease-associated serotypes and antimicrobial susceptibility of invasive pneumococcal disease (IPD) among children in Africa is essential in order to monitor the impact of these infections prior to widespread introduction of the pneumococcal conjugate vaccine (PCV). Methods To provide updated estimates of the incidence, serotype distribution, and antimicrobial susceptibility profile of Streptococcus pneumoniae causing disease in Africa, we performed a systematic review of articles published from 2000–2015 using Ovid Medline and Embase. We included prospective and surveillance studies that applied predefined diagnostic criteria. Meta-analysis for all pooled analyses was based on random-effects models. Results We included 38 studies consisting of 386,880 participants in 21 countries over a total of 350,613 person-years. The pooled incidence of IPD was 62.6 (95% CI 16.9, 226.5) per 100,000 person-years, including meningitis which had a pooled incidence of 24.7 (95% CI 11.9, 51.6) per 100,000 person-years. The pooled prevalence of penicillin susceptibility was 78.1% (95% CI 61.9, 89.2). Cumulatively, PCV10 and PCV13 included 66.9% (95% CI 55.9, 76.7) and 80.6% (95% CI 66.3, 90.5) of IPD serotypes, respectively. Conclusions Our study provides an integrated and robust summary of incidence data, serotype distribution and antimicrobial susceptibility for S. pneumoniae in children ≤5 years of age in Africa prior to widespread introduction of PCV on the continent. The heterogeneity of studies and wide range of incidence rates across the continent indicate that surveillance efforts should be intensified in all regions of Africa to improve the integrity of epidemiologic data, vaccine impact and cost benefit. Although the incidence of IPD in young children in Africa is substantial, currently available conjugate vaccines are estimated to cover the majority of invasive disease-causing pneumococcal serotypes. These data provide a reliable baseline from which to monitor the impact of the broad introduction of PCV.

show abstract

“…Genetically, the lineage occurring in Bangladesh is distinct from the historic strain D39 isolated in the early 1900 s.The meningitis-causing feature of the serotype-2 pneumococcal lineage reported here is unusual or even unparalleled for a pneumococcus in having such a high odds for causing meningitis. In studies of meningitis from Africa, compared to serotype-1, serotype 2 did not account for a prominent proportion of meningitis cases [18], [19], [20]. It raises the question of whether a variant with specific central nervous system tropism has recently evolved within the clonal complex CC74 in Bangladesh which differentiates it from the members of the same lineage observed in West Africa [11].…”

Section: Discussionmentioning

confidence: 99%

Streptococcus pneumoniae Serotype-2 Childhood Meningitis in Bangladesh: A Newly Recognized Pneumococcal Infection Threat

et al. 2012

View full text Add to dashboard Cite

Background Streptococcus pneumonia e is a leading cause of meningitis in countries where pneumococcal conjugate vaccines (PCV) targeting commonly occurring serotypes are not routinely used. However, effectiveness of PCV would be jeopardized by emergence of invasive pneumococcal diseases (IPD) caused by serotypes which are not included in PCV. Systematic hospital based surveillance in Bangladesh was established and progressively improved to determine the pathogens causing childhood sepsis and meningitis. This also provided the foundation for determining the spectrum of serotypes causing IPD. This article reports an unprecedented upsurge of serotype 2, an uncommon pneumococcal serotype, without any known intervention. Methods and Findings Cases with suspected IPD had blood or cerebrospinal fluid (CSF) collected from the beginning of 2001 till 2009. Pneumococcal serotypes were determined by capsular swelling of isolates or PCR of culture-negative CSF specimens. Multicenter national surveillance, expanded from 2004, identified 45,437 patients with suspected bacteremia who were blood cultured and 10,618 suspected meningitis cases who had a lumber puncture. Pneumococcus accounted for 230 culture positive cases of meningitis in children <5 years. Serotype-2 was the leading cause of pneumococcal meningitis, accounting for 20.4% (45/221; 95% CI 15%–26%) of cases. Ninety eight percent (45/46) of these serotype-2 strains were isolated from meningitis cases, yielding the highest serotype-specific odds ratio for meningitis (29.6; 95% CI 3.4–256.3). The serotype-2 strains had three closely related pulsed field gel electrophoresis types. Conclusions S. pneumoniae serotype-2 was found to possess an unusually high potential for causing meningitis and was the leading serotype-specific cause of childhood meningitis in Bangladesh over the past decade. Persisting disease occurrence or progressive spread would represent a major potential infection threat since serotype-2 is not included in PCVs currently licensed or under development.

show abstract

Seasonality and outbreak of a predominant Streptococcus pneumoniae serotype 1 clone from The Gambia: Expansion of ST217 hypervirulent clonal complex in West Africa

Cited by 57 publications

References 16 publications

Understanding pneumococcal serotype 1 biology through population genomic analysis

Understanding pneumococcal serotype 1 biology through population genomic analysis

Childhood pneumococcal disease in Africa – A systematic review and meta-analysis of incidence, serotype distribution, and antimicrobial susceptibility

Streptococcus pneumoniae Serotype-2 Childhood Meningitis in Bangladesh: A Newly Recognized Pneumococcal Infection Threat

Contact Info

Product

Resources

About