Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae

Cornick, Jennifer; Chaguza, Chrispin; Harris, Simon R.; Yalcin, Feyruz; Senghore, Madikay; Kiran, Anmol; Govindpershad, Shanil; Ousmane, Sani; Plessis, Mignon du; Pluschke, Gerd; Ebruke, Chinelo; McGee, Lesley; Sigaùque, Beutel; Collard, Jean-Marc; Antonio, Martín; Gottberg, Anne von; French, Neil; Klugman, Keith P.; Heyderman, Robert S.; Bentley, Stephen D.; Everett, Dean

doi:10.1099/mgen.0.000027

Cited by 31 publications

(56 citation statements)

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“…We observed the distribution of genetic recombination events consistent with previous studies [15,50,58]. The mean sizes of the recombination events varied significantly (p < 0.0001) between the SCs and the mean sizes ranged from 4650 bp to 75156 bp ( Table 1).…”

Section: Genetic Recombination In the St217 Sequence Clusterssupporting

confidence: 89%

“…The rarity of serotype 1 isolates in carriage has led to the hypothesis it has a lower rate of recombination due to limited opportunities for genetic exchange during carriage [14]. A recent report has identified the presence of genetic recombination in a global serotype 1 population [15].…”

Section: Introductionmentioning

confidence: 99%

“…European and American isolates clustered into clades A and C respectively, whilst clade B associated with African isolates. Recently, using a whole genome phylogeny, we have reported an additional clade named clade D, which consisted of isolates from Asia [15].…”

Section: Introductionmentioning

confidence: 99%

“…We have previously described the global population structure of multiple serotype 1 STs [15]. In the present study, we collected 226 ST217 serotype 1 isolates from multiple African and Asian countries to gain further insights into the biology of the clone.…”

Section: Introductionmentioning

confidence: 99%

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Understanding Pneumococcal Serotype 1 Biology Through Population Genomic Analysis

Chaguza¹

2016

Preprint

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Background: Pneumococcus 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. Methods: We 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. Results: Population 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. Conclusions: The 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.

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Section: Genetic Recombination In the St217 Sequence Clusterssupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Understanding Pneumococcal Serotype 1 Biology Through Population Genomic Analysis

Chaguza¹

2016

Preprint

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“…In this study, we also obtained 3.3% and 70.5% of intermediate and full resistance to tetracycline, indicating circulation in carriage of tetracycline resistant isolates among children aged 0 to 2 year old. High level of resistance to tetracycline (84%) was already observed in clinical isolates of serotype1 SPN from Niger in which, tet (M) gene coding for resistance to tetracycline was found [26]. Though progressively being abandoned for its toxicity (National treatment guidelines) since 2012, we tested the sensitivity of isolates to chloramphenicol and found that 24/211 (11.4%) were fully resistant to this antibiotic.…”

Section: Discussionmentioning

confidence: 89%

Serotype Distribution and Antimicrobial Sensitivity Profile of Streptococcus pneumoniae Carried in Healthy Toddlers before PCV13 Introduction in Niamey, Niger

et al. 2017

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BackgroundTo mitigate the burden of pneumococcal infections in Niger, a 13-valent pneumococcal vaccine, PCV13, was introduced for routine child vaccination in July 2014. In order to provide pre-vaccine baseline data and allow appreciation of changes on carriage due to vaccination, we analyzed retrospectively pneumococcal isolates obtained from healthy, 0 to 2 year old children prior to the vaccine introduction.MethodsFrom June 5, 2007, to May 26, 2008, 1200 nasopharyngeal swabs were collected from healthy 0 to 2 year old children and analyzed by standard microbiological methods. Serotyping was done by SM-PCR and the data were analyzed with R version 2.15.0 (2012-03-30).ResultsStreptococcus pneumoniae was detected in 654/1200 children (54.5%) among whom 339 (51.8%) were males. The ages of the study subjects varied from few days to 26 months (mean = 7.1, median = 6, 95% CI [6.8–7.4]). Out of 654 frozen isolates, 377 (54.8%) were able to be re-grown and analyzed. In total, 32 different serogroups/serotypes were detected of which, the most prevalent were 6/(6A/6B/6C/6D) (15.6%), 23F (10.6%), 19F (9.3%), 14 (9%), 19A (5.6%), 23B (4.0%), 25F/38 (3.7%), 18/(18A/18B/18C/18F) (2.9%) and PCR non-typeable (16.4%). Eleven serogroups/serotypes accounting for 57.3% (216/377) were of PCV13 types. Of the 211/377 (56%) isolates tested for drug sensitivity, 23/211 (10.9%), 24/211 (11.4%), 9/211(4.3%) and 148/210 (70.5%) were respectively resistance to oxacillin, chloramphenicol, erythromycin and tetracycline. Thirteen of the oxacillin resistant isolates were additionally multidrug-resistant. No resistance was however detected to gentamycin500μg and to fluoroquinolones (ø Norfloxacin5μg <7mm). Age > 3 months and presence in family of more than one sibling aged < 6 years were significant risk factors for carriage.ConclusionA global rate of 54.5% pneumococcal carriage was detected in this study. The introduced PCV13 vaccine should cover 57.3% (216/377) of circulating serogroups/serotypes, among which were those resistant to antibiotics. Age > 3 months and presence in family of children aged < 6 years were significant factors for pneumococcal carriage. The present data should help understanding post vaccine introduction changes in pneumococcal carriage and infections for better action.

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Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes

Collins

Didelot

2016

Methods in Molecular Biology

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Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.

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Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae

Cited by 31 publications

References 46 publications

Understanding Pneumococcal Serotype 1 Biology Through Population Genomic Analysis

Understanding Pneumococcal Serotype 1 Biology Through Population Genomic Analysis

Serotype Distribution and Antimicrobial Sensitivity Profile of Streptococcus pneumoniae Carried in Healthy Toddlers before PCV13 Introduction in Niamey, Niger

Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes

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