Biology subjects

McGee, L.

Publications and source records attributed to McGee, L..

12 recordsLinked to original sources

bioRxiv2026

The global evolutionary dynamics of natural capsule switching in a human-restricted bacterial pathogen

Exchange of genetic loci encoding extracellular capsular polysaccharides in bacteria can change capsular antigens or serotype, which, in turn, can lead to evasion of vaccines targeting the capsule. However, the evolutionary dynamics and drivers of bacterial capsule switching remain poorly understood. Here, we investigate the evolutionary dynamics and correlates of capsule switching in bacteria, using the human-restricted bacterial pathogen Streptococcus pneumoniae as an example, using 10,558 genetically and geographically diverse whole-genome sequences. Our phylogenomic and ancestral state reconstruction analysis revealed that the propensity for capsule switching varies by capsule type and genetic background. We found capsule switches only between ~4% of all possible capsule-type pairs, varying by specific pairs and switching direction. We also found associations between capsule switching patterns and genetic and ecological factors, including nasopharyngeal carriage duration, capsule biosynthesis locus size, and capsule thickness. Furthermore, the genetic similarity of the replacing and replaced capsule loci was primarily associated with the frequency of switching between specific capsule type pairs. Although a few specific non-capsule genomic loci were associated with the propensity for capsule switching across distinct lineages, the collective effect of the genetic background appears to influence capsule switching more strongly. These findings shed light on how bacterial capsule types and lineages undergo capsule switching influenced by genetic and ecological factors, informing our understanding of the emergence of novel capsule-genotype combinations that may impact the design of capsule-targeting glycoconjugate vaccines.

microbiology↗

bioRxiv2026

Scalable single-cell isoform profiling with sequencing-by-expansion

Single-cell RNA sequencing has transformed our understanding of cellular systems, yet the reliance on short-read sequencing restricts analysis to gene-level quantification and obscures the immense biological diversity generated by alternative splicing. While long-read sequencing technologies can capture full-length RNA and resolve transcript isoforms, current platforms remain constrained by throughput and high per-base costs, rendering them impractical for modern million-cell applications. To address this critical limitation, we developed and optimized sequencing-by-expansion (SBX) chemistry for high-throughput single-cell RNA isoform profiling. Integrated within the AXELIOS 1 sequencing platform, SBX employs a unique biochemical conversion process that transforms complementary DNA into expanded surrogate high signal-to-noise polymers called Xpandomers which are sequenced via translocation through a dense nanopore array yielding over 9.5 billion reads in a two-hour run. To leverage this unique data type for long-read single-cell RNA isoform sequencing, we developed the Consensus UMI Deduplication using Longest Length (CUDLL) algorithm, which computationally consolidates variable-length raw SBX reads into single, high-fidelity consensus reads, elevating sequence accuracy to 99.83% and maximizing per transcript read length. We demonstrate that this consensus approach successfully captures the vast isoform diversity of single-cell libraries and enables the accurate measure of differential isoform expression across distinct cell types in peripheral blood mononuclear cells. Furthermore, SBX coupled with CUDLL efficiently resolves T-cell and B-cell receptor clonotypes directly from whole-transcriptome libraries without the need for VDJ-specific target enrichment. Ultimately, this work establishes SBX and the AXELIOS 1 as a transformative platform for high-scale single-cell isoform sequencing.

genetics↗

bioRxiv2026

Global population structure and phase variation of serotype 12F Streptococcus pneumoniae following the introduction of pneumococcal conjugate vaccine

BackgroundAfter the global deployment of pneumococcal conjugate vaccines (PCVs), serotype 12F has become the predominant serotype responsible for invasive pneumococcal disease (IPD) worldwide. As PCVs that include serotype 12F are gradually introduced, we aim to characterise the global population structure and genetic diversity of the 12F capsule locus using whole-genome sequencing. Capsule variants with vaccine evasion potential were further investigated by functional experiments. MethodsA global collection of pneumococcal serotype 12F genomes (n=806) from 37 countries across six continents were included in this study. To characterise the serotype 12F population, Global Pneumococcal Sequence Cluster (GPSC), in silico serotype, and antimicrobial resistance profile were inferred from whole-genome data for each isolate. The capsule biosynthesis (cps) locus was analysed for gene content variations that could alter polysaccharide capsule production or structure, thereby influencing recognition by vaccine-induced antibodies. These isolates were further investigated by assessing their capsule production using immunofluorescence assays and its susceptibility to vaccine-elicited antibody killing by opsonophagocytosis assays. FindingsThe global increase in serotype 12F was driven by both distinct pneumococcal lineages across different continents, and a globally-disseminated and multidrug-resistant lineage GPSC26. We identified six capsule variants in nine isolates that had disruptive mutations in cps genes including wze, wcil, wciJ and fnlA. Most (6/9) of the disruptive mutations were a result of strand-slippage mutations. A convergent strand-slippage mutation disrupting the glycosyltransferase gene wciJ was identified in four isolates from distinct lineages and countries. Despite the truncation, three of four isolates with available Quellung typing results still identified them as 12F, indicating the production of the capsule. We then created a genetically engineered lab strain with wciJ knockout and complemented with wciJ containing the strand-slipppage mutation. The knockout strain did not produce any capsule. In contrast, the lab strain with wciJ containing the strand-slippage mutation produced a mixed population of encapsulated and non-encapsulated pneumococci, even within the same chain of pneumococcal cells. This observation indicated encapsulated subpopulation possesses a functional WciJ and rapidly reversible strand-slippage mutation during replication. Opsonophagocytosis assays indicated that the clinical 12F strain with strand-slippage mutation in wciJ exhibited reduced susceptibility to vaccine-elicited serum killing, compared to a genetically closely related 12F clinical strain with an intact wciJ. However, substantial inter-individual antisera variation limits definitive interpretation. InterpretationOur work revealed the global rise of serotype 12F pneumococci has been driven by both regional-specific lineages, and a globally-disseminated and multidrug-resistant lineage GPSC26. We demonstrated that strand-slippage mutation is one of the major drivers of serotype 12F capsule variants and represents a novel mechanism enabling reversible on-off switching of capsule production. The ability to switch off capsule expression in a subpopulation may enable evasion of antibody-mediated killing but increase susceptibility to innate immune clearance. FundingBill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.

genomics↗

bioRxiv2025

SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae

The unprecedented number of Streptococcus pneumoniae (the pneumococcus) genomes sequenced in recent years has accelerated the discovery of novel serotypes and highlighted the genetic diversity both between and within each serotype. A novel serotype should demonstrate a distinct cps locus, capsular structure, and serological profile. In only the past four years, nine new serotypes have been identified. Accurate and timely serotyping of pneumococcal isolates is key to understanding its global distribution, evolution, and the response of the bacterial population to vaccination. However, current bioinformatics serotyping tools are infrequently updated, and struggle to accommodate the rapid discovery of new serotypes in a timely manner. To address these limitations, we built a comprehensive and curated library (SeroBAnk) encompassing all known pneumococcal serotypes; this resource is presented as an atlas on a dedicated publicly accessible webpage (https://www.pneumogen.net/gps/#/serobank). Building upon this resource, we developed SeroBA(v2.0), a tool with an easy-to-update database that can accurately identify 102 of 107 known pneumococcal serotypes (except for serotypes 24B, 24C, 24F, 7D and 6H) and 18 genetic subtypes within serotypes 6A, 6B, 11A, 19A, 19F and 33F. We validated SeroBA(v2.0) on 26,306 genomes from the Global Pneumococcal Sequencing project, reference isolates and simulated reads derived from the reference genetic sequences of capsular polysaccharide biosynthetic (cps) locus and showed that SeroBA(v2.0) can reliably detect the nine recently discovered serotypes. Additionally, we show that in silico serotypes inferred by SeroBA(v2.0) had high concordance with phenotypic serotypes determined by either Quellung or latex agglutination at the serotype level (88.9%; 15,945/17,933), and at the serogroup level (91.9%; 16,480/17,933). Finally, we propose a community-contribution based approach to ensure that SeroBA(v2.0) is maintained and updated as novel serotypes continue to be discovered. The global community can submit putative novel serotypes through our public repository on GitHub (https://github.com/GlobalPneumoSeq/seroba/issues). The submitted putative novel serotypes will be curated based on the genetic sequence of cps region, capsular structure and serological profile by people of relevant expertise in the field. SeroBA(v2.0) can be accessed at https://github.com/GlobalPneumoSeq/seroba. Data summaryGenome sequences are available in the European Nucleotide Archive (ENA) and are also available alongside metadata on the Monocle Database available at https://data.monocle.sanger.ac.uk/. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact StatementThe polysaccharide capsule has been an effective vaccine antigen against diseases caused by Streptococcus pneumoniae (the pneumococcus). The pneumococcal conjugate vaccine has been estimated to have halved pneumococcal-related childhood mortality over 15 years (2000-2015). We collated the genetic locus and capsular structure of each known capsule type (serotype), alongside with pneumococcal vaccine formulation and licensure history, into a single webpage (SeroBAnk), providing a valuable resource for basic research and vaccine development. With increasing use of whole genome sequencing in clinical and public health laboratories, we also provided a fast and accurate bioinformatics tool, SeroBA(v2.0), to identify 102 pneumococcal serotypes, alongside a proposed system to expand SeroBA(v2.0) to include new serotypes as they are discovered, ensuring that the tool remains valuable to the global research community in the long-term.

bioinformatics↗

bioRxiv2025

Sequencing by Expansion (SBX) -- a novel, high-throughput single-molecule sequencing technology

Remarkable advances in high-throughput sequencing have enabled major biological discoveries and clinical applications, but achieving wider distribution and use depends critically on further improvements in scale and cost reduction. Nanopore sequencing has long held the promise for such progress, but has had limited market penetration. This is because efficient and accurate nanopore sequencing of nucleic acids has been challenged by fundamental signal-to-noise limitations resulting from the poor spatial resolution and molecular distinction of nucleobases. Here, we describe Sequencing by Expansion (SBX), a single-molecule sequencing technology that overcomes these limitations by using a biochemical conversion process to encode the sequence of a target nucleic acid molecule into an Xpandomer, a highly measurable surrogate polymer. Expanding over 50 times longer than the parent DNA templates, Xpandomers are engineered with high signal-to-noise reporter codes to enable facile, high-accuracy nanopore sequencing. We demonstrate the performance of SBX and present the specialized molecular structures, chemistries, enzymes and methods that enable it. The innovative molecular and systems engineering in SBX create a transformative technology to address the needs of existing and emerging sequencing applications.

genomics↗

bioRxiv2024

A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline

Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomic information captured from whole-genome sequencing to enhance pathogen surveillance. However, there is a growing need for developing user-friendly tools to effectively analyse the increasing volume of data. To meet this need, we have developed a genomic analysis pipeline, GPS Pipeline, which is portable and scalable to analyse genomes of Streptococcus pneumoniae, a major bacterial pathogen that is estimated to cause 317,000 child deaths worldwide every year. The GPS Pipeline is based on Nextflow and containerisation technology, and designed to enable researchers generating public health relevant output, including in silico serotypes, pneumococcal lineages (i.e. GPSCs), multilocus sequence types, and antimicrobial susceptibilities against 20 commonly used antibiotics,with minimal software setup requirements and bioinformatic expertise, in order to analyse genomic data at scale with ease. The GPS Pipeline provides a streamlined workflow that improves responsiveness in genomic surveillance on pneumococci. Data SummaryThe GPS Pipeline is available on GitHub at github.com/GlobalPneumoSeq/gps-pipeline. Published data from the GPS Database is available on Monocle Data Viewer at data.monocle.sanger.ac.uk and associated sequence read files are searchable and downloadable in the European Nucleotide Archive at ebi.ac.uk/ena via their ERR accession numbers. Impact StatementThe GPS Pipeline advances global genomic surveillance of Streptococcus pneumoniae by providing a scalable, portable, and user-friendly tool for analysing whole-genome sequencing data. Leveraging Nextflow and containerisation technology, it minimises bioinformatics expertise requirements and infrastructure needs, making it particularly valuable in low- and middle-income countries where pneumococcal disease burden is high. This pipeline ensures reproducibility and stability across platforms, facilitating rapid and accurate pneumococci genomic analysis. By streamlining data processing, the GPS Pipeline enhances pathogen surveillance, generates evidence to support vaccine strategy development, and empowers researchers worldwide, ultimately contributing to improved public health outcomes.

genomics↗

bioRxiv2024

Comparison of gene-by-gene and genome-wide short nucleotide sequence based approaches to define the global population structure of Streptococcus pneumoniae

Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods are currently used to cluster together closely- related genomes, potentially leading to inconsistency between studies. Here, we use a global dataset of 26,306 S. pneumoniae genomes to compare four clustering methods: gene-by- gene seven-locus multi-locus sequencing typing (MLST), core genome MLST (cgMLST)- based hierarchical clustering (HierCC) assignments, Life Identification Number (LIN) barcoding, and k-mer-based PopPUNK clustering (known as GPSCs in this species). We compare the clustering results with phylogenetic and pan-genome analyses to assess their relationship with genome diversity and evolution, as we would expect a good clustering method to form a single monophyletic cluster that has high within-cluster similarity of genomic content. We show that the four methods are generally able to accurately reflect the population structure based on these metrics, and that the methods were broadly consistent with each other. We investigated further to study the discrepancies in clusters. The greatest concordance was seen between LIN barcoding and HierCC (Adjusted Mutual Information Score = 0.950), which was expected given that both methods utilise cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods show that the selection of a core genome schema can introduce inconsistencies between studies. GPSC and HierCC assignments were also highly concordant (AMI = 0.946), showing that k-mer based methods which use the whole genome and do not require the careful selection of a core genome schema are just as effective at representing the population structure. Additionally, where there were differences in clustering between these methods, this could be explained by differences in the accessory genome that were not identified in cgMLST. We conclude that for S. pneumoniae, standardised and stable nomenclature is important as the number of genomes available expands. Furthermore, the research community should transition away from seven- locus MLST, and cgMLST, GPSC, and LIN assignments should be used more widely. However, to allow for easy comparison between studies and to make previous literature relevant, the reporting of multiple clustering names should be standardised within research. Data summaryGenome sequences are deposited in the European Nucleotide Archive (ENA); accession numbers. Metadata of the pneumococcal isolates in this study have been submitted as a supplementary file and are also available on the Monocle Database available at https://data.monocle.sanger.ac.uk/. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact StatementUsing a global dataset of S. pneumoniae genomes allows us to thoroughly observe and analyse discrepancies between different clustering methods. Whilst all methods in this study are used to cluster S. pneumoniae genomes, no study has yet thoroughly compared the clustering results and discrepancies. This work summarises the strengths and weaknesses of the different methods and highlights the need for consistency between studies.

genomics↗

bioRxiv2024

Phototactic preference and its genetic basis in the planulae of the colonial hydrozoan Hydractinia symbiolongicarpus

BackgroundMarine organisms with sessile adults commonly possess motile larval stages that make settlement decisions based on integrating environmental sensory cues. Phototaxis, the movement toward or away from light, is a common behavioral characteristic of aquatic and marine metazoan larvae, and of algae, protists, and fungi. In cnidarians, behavioral genomic investigations of motile planulae larvae have been conducted in anthozoans (corals and sea anemones) and scyphozoans (true jellyfish), but such studies are presently lacking in hydrozoans. Here, we examined the behavioral genomics of phototaxis in planulae of the hydrozoan Hydractinia symbiolongicarpus. ResultsA behavioral phototaxis study of day 3 planulae indicated preferential phototaxis to green (523 nm) and blue (470 nm) wavelengths of light, but not red (625 nm) wavelengths. A developmental transcriptome study where planula larvae were collected from four developmental time points for RNA-seq revealed that many genes critical to the physiology and development of ciliary photosensory systems are dynamically expressed in planula development and correspond to the expression of phototactic behavior. Microscopical investigations using immunohistochemistry and in situ hybridization demonstrated that several transcripts with predicted function in photoreceptors, including cnidops class opsin, CNG ion channel, and CRX-like transcription factor, localize to ciliated bipolar sensory neurons of the aboral sensory neural plexus, which is associated with the direction of phototaxis and the site of settlement. ConclusionsThe phototactic preference displayed by planulae is consistent with the shallow sandy marine habitats they experience in nature. Our genomic investigations add further evidence of similarities between cnidops-mediated photoreceptors of hydrozoans and other cnidarians and ciliary photoreceptors as found in the eyes of humans and other bilaterians, suggesting aspects of their shared evolutionary history.

evolutionary biology↗

bioRxiv2023

Evidence of virulence and antimicrobial resistance in Streptococcus pneumoniae serotype 16F lineages

IntroductionDue to the emergence of non-vaccine serotypes in vaccinated populations, Streptococcus pneumoniae remains a major global health challenge despite advances in vaccine development. Serotype 16F is among the predominant non-vaccine serotypes identified among vaccinated infants in South Africa (SA). AimTo characterise lineages and antimicrobial resistance in 16F isolates obtained from South Africa and placed the local findings in a global context. MethodologyWe analysed 10923 S. pneumoniae carriage isolates obtained from infants recruited as part of a broader SA birth cohort. We inferred serotype, resistance profile for penicillin, chloramphenicol, cotrimoxazole, erythromycin and tetracycline, and Global Pneumococcal Sequence Clusters (GPSCs) from genomic data. To ensure global representation, we also included S. pneumoniae carriage and disease isolates from the Global Pneumococcal Sequencing (GPS) project database (n=19,607, collected from 49 countries across five continents, years covered (1995 - 2018), accessed on 17th March 2022). ResultsNine percent (934/10923) of isolates obtained from infants in the Drakenstein community in SA and 2% (419/19607) of genomes in the GPS dataset were serotype 16F. Serotype 16F isolates were from 28 different lineages of S. pneumoniae, with GPSC33 and GPSC46 having the highest proportion of serotype 16F isolates at 26% (346/1353) and 53% (716/1353), respectively. Serotype 16F isolates were identified globally, however, most isolates were collected from Africa. GPSC33 was associated with carriage [OR (95% CI) 0.24 (0.09 - 0.66); p=0.003], while GPSC46 was associated with disease [OR (95% CI) 19.9 (2.56 - 906.50); p=0.0004]. 10% (37/346) and 15% (53/346) of isolates within GPSC33 had genes associated with resistance to penicillin and co-trimoxazole, respectively, and 18% (128/716) of isolates within GPSC46 had genes associated with resistance to co-trimoxazole. Resistant isolates formed genetic clusters which may suggest emerging resistant lineages. DiscussionSerotype 16F lineages are common in Southern Africa. Some of these lineages are associated with disease, and resistance to penicillin and cotrimoxazole. We recommend continuous genomic surveillance to determine long term impact of serotype 16F lineages on vaccine efficacy and antimicrobial therapy globally. Investing in vaccine strategies that offer protection over a wide range of serotypes/lineages remains essential. DATA SUMMARYThe sequencing reads for the genomes analysed have been deposited in the European Nucleotide Archive and the accession numbers for each isolate are listed in Supplementary Table1. Phylogenetic tree of serotype 16F pneumococcal genomes and associated metadata are available for download and visualisation on the Microreact website: Phylogenies of seotype 16F, GPSC33 and GPSC46 are available on the Microreact serotype-16F, GPSC33 and GPSC46, respectively. IMPACT STATEMENTThis study shows that serotype 16F lineages are predominant in Southern Africa and are associated with disease and antimicrobial resistance. Although serotype 16F has been included in the newer formulation of the upcoming vaccine formulations of PCV21 and IVT-25, continuous surveillance to determine long term impact of serotype 16F lineages on vaccines and antimicrobial therapy remains essential.

genomics↗

bioRxiv2021

The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci

AbstractThe evolutionary histories of the antibiotic-resistant Streptococcus pneumoniae lineages PMEN3 and PMEN9 were reconstructed using global collections of genomes. In PMEN3, one resistant clade spread worldwide, and underwent 25 serotype switches, enabling evasion of vaccine-induced immunity. In PMEN9, only 9 switches were detected, and multiple resistant lineages emerged independently and circulated locally. In Germany, PMEN9s expansion correlated significantly with the macrolide:penicillin consumption ratio. These isolates were penicillin sensitive but macrolide resistant, through a homologous recombination that integrated Tn1207.1 into a competence gene, preventing further diversification via transformation. Analysis of a species-wide dataset found 183 acquisitions of macrolide resistance, and multiple gains of the tetracycline-resistant transposon Tn916, through homologous recombination, often originating in other streptococcal species. Consequently, antibiotic selection preserves atypical recom- bination events that cause sequence divergence and structural variation throughout the S. pneumoniae chromosome. These events reveal the genetic exchanges between species normally counter-selected until perturbed by clinical interventions.

genomics↗

bioRxiv2019

A novel mosaic tetracycline resistance gene tet(S/M) detected in a multidrug-resistant pneumococcal CC230 lineage that underwent capsular switching in South Africa

SynopsisO_ST_ABSObjectiveC_ST_ABSWe reported a novel tetracycline-resistant gene in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions.\n\nMethodsWe whole genome sequenced 12,254 pneumococcal isolates from twenty-nine countries on an Illumina HiSeq Sequencer. Serotypes, sequence types and antibiotic resistance were inferred from genomes. Phylogeny was built based on single-nucleotide variants. Temporal changes of spread were reconstructed using a birth-death model.\n\nResultsWe identified tet(S/M) in 131 pneumococcal isolates, 97 (74%) caused invasive pneumococcal diseases among young children (59% HIV-positive, where HIV status was available) in South Africa. A majority of tet(S/M)-positive isolates (129/131) belong to clonal complex (CC)230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sub-lineage that exhibited multidrug-resistance. Using the genomic data and a birth-death model, we detected an unrecognised outbreak of this sub-lineage in South Africa between 2000 and 2004 with an expected secondary infections (R) of ~2.5. R declined to ~1.0 in 2005 and <1.0 in 2012. The declining epidemic coincided and could be related to the nationwide implementation of anti-retroviral treatment (ART) for HIV-infected individuals in 2004 and PCVs in late 2000s. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sub-lineage.\n\nConclusionsThe prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognised outbreak of CC230 in South Africa prior to ART and PCVs. However, capsular switching in this multidrug-resistant sub-lineage highlighted its potential to continue to cause disease in the post-PCV13 era.

microbiology↗

bioRxiv2018

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

Streptococcus pneumoniae serotype 3 remains a significant cause of morbidity and mortality worldwide, despite inclusion in the 13-valent pneumococcal conjugate vaccine (PCV13). Serotype 3 increased in carriage since the implementation of PCV13 in the United States, while invasive disease rates remain unchanged. We investigated the persistence of serotype 3 in carriage and disease, through genomic analyses of a global sample of 301 serotype 3 isolates of the Netherlands3-31 (PMEN31) clone CC180, combined with associated patient data and PCV utilization among countries of isolate collection. We assessed phenotypic variation between dominant clades in capsule charge (zeta potential), capsular polysaccharide shedding, and susceptibility to opsonophagocytic killing, which have previously been associated with carriage duration, invasiveness, and vaccine escape. We identify a recent shift in the CC180 population attributed to a lineage termed Clade II, which was estimated by Bayesian coalescent analysis to have first appeared in 1968 [95% HPD: 1939-1989] and increased in prevalence and effective population size thereafter. Clade II isolates are divergent from the pre-PCV13 serotype 3 population in non-capsular antigenic composition, competence, and antibiotic susceptibility, the last resulting from the acquisition of a Tn916-like conjugative transposon. Differences in recombination rates among clades correlated with variations in the ATP-binding subunit of Clp protease as well as amino acid substitutions in the comCDE operon. Opsonophagocytic killing assays elucidated the low observed efficacy of PCV13 against serotype 3. Variation in PCV13 use among sampled countries was not independently correlated with the CC180 population shift; therefore, genotypic and phenotypic differences in protein antigens and, in particular, antibiotic resistance may have contributed to the increase of Clade II. Our analysis emphasizes the need for routine, representative sampling of isolates from disperse geographic regions, including historically under-sampled areas. We also highlight the value of genomics in resolving antigenic and epidemiological variations within a serotype, which may have implications for future vaccine development.\n\nAuthor SummaryStreptococcus pneumoniae is a leading cause of bacterial pneumoniae, meningitis, and otitis media. Despite inclusion in the most recent pneumococcal conjugate vaccine, PCV13, serotype 3 remains epidemiologically important globally. We investigated the persistence of serotype 3 using whole-genome sequencing data form 301 isolates collected among 24 countries from 1993-2014. Through phylogenetic analysis, we identified three distinct lineages within a single clonal complex, CC180, and found one has recently emerged and grown in prevalence. We then compared genomic difference among lineages as well as variations in pneumococcal vaccine use among sampled countries. We found that the recently emerged lineage, termed Clade II, has a higher prevalence of antibiotic resistance compared to other lineages, diverse surface protein antigens, and a higher rate of recombination, a process by which bacteria can uptake and incorporate genetic material from its surroundings. Differences in vaccine use among sampled countries did not appear to be associated with the emergence of Clade II. We highlight the need to routine, representative sampling of bacterial isolates from diverse geographic areas and show the utility of genomic data in resolving epidemiological differences within a pathogen population.

evolutionary biology↗