Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates

The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study

Background

IMP carbapenemases confer extensive drug resistance and are increasingly noted worldwide. Despite this, little is known regarding the global epidemiology of IMP carbapenemases.

Methods

We comprehensively identified bla IMP genes in all publicly available bacterial genomes, then systematically analysed the distribution of variants across species, lineages, plasmids and mobile elements, examining patterns over time, across geographic regions and by source. Structural analysis of IMP variants was performed.

Findings

4,556 bla IMP -containing genomes were identified from 1996-2023, including 52 bla IMP variants across 93 bacterial species. Key variants ( bla IMP-1 , bla IMP-4 , bla IMP-7 , bla IMP-8 and bla IMP-13 ) achieved global endemicity, while bla IMP-26 and bla IMP-27 were regionally endemic in Southeast Asia and North America, respectively. bla IMP dissemination was driven by horizontal gene transfer, facilitating inter-species spread. Proliferation of multidrug-resistant Enterobacter hormaechei , Pseudomonas aeruginosa and Klebsiella pneumoniae lineages led to local outbreaks. Dereplication removed 3,175/4,556 (69.9%) genomes, indicating that most bla IMP -containing genomes were highly related. bla IMP variants were associated with mobile genetic element combinations including class 1 integrons and insertion sequences (99.7%), aiding mobilisation into ≥52 plasmid clusters, predominantly IncHI2A, IncN, IncL/M and IncC. Genomes of environmental and animal origin accounted for 10.0% and 1.1% of the dataset, respectively. Evidence of cross-source transmission was limited, with most spillover occurring between genomes of human and environmental origin. Structural analysis revealed a conserved carbapenemase structure (mean lDDT 0.977), with convergent missense mutations at seven catalytically relevant sites.

Interpretation

Global analysis enabled us to historically reconstruct the emergence and variant-specific epidemiologies of bla IMP carbapenemase genes. Intersecting mobile elements enabled bla IMP genes to spread across multiple plasmids and bacterial genera, facilitating global and multi-source spread within a One Health framework. Additionally, convergent evolutionary patterns indicate that IMP variants may continue evolving, potentially evading novel beta-lactam antimicrobial agents.

Funding

NHMRC EL1 (APP1176324) to N.M.; NHMRC PF (APP1117940) to A.Y.P.; NIH/NIAID R01AI175414 to A.G-S.

Research in context panel

Evidence before this study: Despite being a major cause of carbapenem resistance in Gram negative infections, little is known about the global epidemiology of IMP carbapenemases. IMP carbapenemases are metallo-beta-lactamases that were first identified in 1991 and have evolved into 96 different IMP variants. On May 21 2025, we searched all published reports available in PubMed using the terms "'IMP' and 'carbapenemase' genomics NOT (Review[Publication Type]) NOT (Case Reports[Publication Type]) NOT PCR" with no language restrictions and no publication date restrictions. We identified 223 articles, 62 and 121 of which reported single species or a single study centre/country, respectively. Only 6 articles employed genomics to examine multi-species and multi-geographical isolates, though this was in the context of carbapenem resistance more broadly rather than IMP carbapenemases specifically. The most relevant study included 38 globally distributed genomes across four species and tracked seven blaIMP variants across mobile genetic elements.Added value of this study: To our knowledge, this global characterisation provides the most comprehensive account of bla IMP carbapenemase gene epidemiology. To analyse the global distribution and diversity of bla IMP genes, we compiled all available public genome data resulting in a dataset of 4,646 genomes. This has allowed us to identify local, regional and international spread of bla IMP variants and determine the contributions of clonal expansion, plasmid proliferation and co-localised mobile genetic elements. We demonstrated that key bla IMP variants display global (IMP-1, IMP-4, IMP-7, IMP-8 and IMP-13) and regional (IMP-26 within Southeast Asia and IMP-27 within North America) endemicity and that these patterns have been previously unacknowledged, reframing the previous understanding that IMP carbapenemases were largely confined to the Asia-Pacific region. Our observation of convergent evolutionary patterns raise concern that IMP variants may continue to evolve, potentially evading new β-lactam antimicrobials. This analysis has revealed the under-recognised contribution IMP carbapenemases make to global carbapenem resistance. Implications of all the available evidence: These findings provide the first comprehensive atlas of bla IMP carbapenemase gene dissemination and underscore the silent global spread of IMP carbapenemases. We note the critical need for enhanced surveillance systems, particularly in low- and middle-income countries, that can detect complex plasmid-mediated and mobile genetic element-associated spread, as we noted with bla IMP carbapenemase genes. Moreover, our analyses show that systematic sampling across human, animal, and environmental reservoirs is crucial to address the One Health dimensions of emerging antimicrobial resistance threats. The study provides a framework for future interventions aimed at tracking and stopping the spread of IMP carbapenemases and calls for co-ordinated, real-time public health responses to this growing challenge.

Pneumococcal serotypes and their association with death risk in invasive pneumococcal disease: a systematic review and meta-analysis

Background

Streptococcus pneumoniae and its infections are a global public health concern. Invasive pneumococcal disease accounts for significant mortality in the aged and immunocompromised. Over 100 unique capsular serotypes have been identified, with 80-90% of invasive disease attributable to about 23 serotypes. Pneumococcal serotype influences invasiveness, virulence, carriage, and IPD outcome. Case fatality rates among different pneumococcal serotypes in IPD have been inconsistently reported, prompting the need for a comprehensive meta-analysis. We hypothesized that specific pneumococcal serotypes would be associated with higher case fatality rates and that non-vaccine serotypes may exhibit increased mortality risks over time.

Methods

We conducted a systematic review and meta-analysis of serotype-specific risk of death due to invasive pneumococcal disease (IPD) in the last decade. We calculated the risk ratio (RR) and 95% confidence interval (CI) for each serotype compared with serotype 14 in each study. Pooled risk ratios were computed using random effects size model analysis. We also conducted heterogeneity testing and meta-regression sub-analysis.

Results

In total, 45 eligible studies were included, and 16 were selected for meta-analysis. Study distribution showed a global disparity, with Europe as the major data source. Serotype 31 had the highest case fatality rate (31.4%), indicating a concerning mortality risk associated with this serotype, particularly in immunocompromised patients. Overall, IPD patients with serotypes 3, 6A, 11A, 15A, 19F, and 31 were more likely to die. In contrast, serotypes 1, 5, 7F, and 8 IPD isolates recorded a reduced risk ratio compared to serotype 14. Subgroup analysis showed that vaccine serotypes were associated with a greater risk of death than non-vaccine serotypes, but there were no significant differences in risk estimates between population groups.

Conclusion

The study confirms the stable role of pneumococcal serotype in determining the clinical outcomes of invasive pneumococcal disease. Our findings underscore the importance of serotype-specific surveillance in IPD and call for the reconsideration of current pneumococcal vaccine formulations to address high-risk non-vaccine serotypes. Efforts to build research capacity, especially in low-resource regions such as Africa and South America, are highly recommended.

Integrated population clustering and genomic epidemiology with PopPIPE

Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due to their variable gene content and order, reference-free methods offer more sensitive detection of genetic differences, especially among closely related samples found in outbreaks. However, across longer genetic distances, frequent recombination can make calculation and interpretation of these differences more challenging, requiring significant bioinformatic expertise and manual intervention during the analysis process. Here, we present a Population analysis PIPEline (PopPIPE) which combines rapid reference-free genome analysis methods to analyse bacterial genomes across these two scales, splitting whole populations into subclusters and detecting plausible transmission events within closely related clusters. We use k-mer sketching to split populations into strains, followed by split k-mer analysis and recombination removal to create alignments and subclusters within these strains. We first show that this approach creates high-quality subclusters on a population-wide dataset of Streptococcus pneumoniae. When applied to nosocomial vancomycin-resistant Enterococcus faecium samples, PopPIPE finds transmission clusters that are more epidemiologically plausible than core genome or multilocus sequence typing (MLST) approaches. Our pipeline is rapid and reproducible, creates interactive visualizations and can easily be reconfigured and re-run on new datasets. Therefore, PopPIPE provides a user-friendly pipeline for analyses spanning species-wide clustering to outbreak investigations.

Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia

Background and aims. Despite the introduction of pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae still remains an important cause of morbidity and mortality, especially among children under 5 years in sub-Saharan Africa. We sought to determine the distribution of serotypes, lineages and antimicrobial resistance of S. pneumoniae from carriage and disease among children presenting to health facilities, 5-6 years after the introduction of PCV10 in Ethiopia.Methods. Whole-genome sequencing (WGS) was performed on 103 S. pneumoniae (86 from nasopharyngeal swabs, 4 from blood and 13 from middle ear discharge) isolated from children aged <15 years at 3 healthcare facilities in Addis Ababa, Ethiopia, from September 2016 to August 2017. Using the WGS data, serotypes were predicted, isolates were assigned to clonal complexes, global pneumococcal sequence clusters (GPSCs) were inferred and screening for alleles and mutations that confer resistance to antibiotics was performed using multiple bioinformatic pipelines.Results. The 103 S. pneumoniae isolates were assigned to 38 serotypes (including nontypeable) and 46 different GPSCs. The most common serotype was serotype 19A. Common GPSCs were GPSC1 [14.6% (15/103), sequence type (ST) 320, serotype 19A], GPSC268 [8.7% (9/103), ST 6882 and novel STs; serotypes 16F, 11A and 35A] and GPSC10 [8.7% (9/103), STs 2013, 230 and 8804; serotype 19A]. The four invasive isolates were serotype 19A (n=2) and serotype 33C (n=2). Resistance to penicillin (>0.06 µg ml-1, CLSI meningitis cutoff) was predicted in 57% (59/103) of the isolates, and 43% (25/58) penicillin-binding protein allele combinations were predicted to be associated with penicillin resistance. Resistance mutations in folA (I100L) and/or folP (indel between fifty-sixth and sixty-seventh aa) were identified among 66% (68/103) of the isolates, whilst tetracycline (tetM) and macrolide (ermB and mefA) resistance genes were found in 46.6% (48/103), 20.4% (21/103) and 20.4% (21/103) of the isolates, respectively. Multidrug resistance (MDR) (≥3 antibiotic classes) was observed in 31.1% (32/103) of the isolates. GPSC1 and GPSC10 accounted for 46.8% (15/32) and 18.7% (6/32) of the overall MDR.Conclusion. Five to 6 years after the introduction of PCV10 in Ethiopia, the S. pneumoniae obtained from carriage and disease among paediatric patients showed diverse serotype and pneumococcal lineages. The most common serotype identified was 19A, expressed by the MDR lineages GPSC1 and GPSC10, which is not covered by PCV10 but is included in PCV13. Continued assessment of the impact of PCV on the population structure of S. pneumoniae in Ethiopia is warranted during and after PCV13 introduction.

Re-evaluation of boundaries of Streptococcus mitis and Streptococcus oralis and demonstration of multiple later synonyms of Streptococcus mitis, Streptococcus oralis and Streptococcus thalassemiae: description of Streptococcus mitis subsp. carlssonii subsp. nov. and emended description of Streptococcus mitis

The commensal species Streptococcus mitis and Streptococcus oralis are genetically diverse to a degree that challenges traditional definitions of species. This causes automatic identification based on DNA sequences or cellular extract profiles problematic. Based on an initial analysis of 266 genomes, we subjected a subset of 100 representative genomes to detailed phylogenetic, pairwise distance and gene pattern analyses. S. mitis and S. oralis constitute a continuum of clones that are genetically unique. To recognize most isolates as separate species is biologically and practically meaningless. We recommend bending the proposed similarity borders to accommodate the biological reality. Accordingly, we conclude that Streptococcus toyakuensis, Streptococcus chosunensis, Streptococcus gwangjuensis, Streptococcus humanilactis and Streptococcus hohhotensis are later heterotypic synonyms of S. mitis. Type strains of effectively but not validly published 'Streptococcus shenyangsis', 'Streptococcus symci' and 'Streptococcus vulneris' belong in S. mitis. Streptococcus parapneumoniae and Streptococcus nakanonensis are later synonyms of Streptococcus thalassemiae. Streptococcus downii is a later synonym of Streptococcus oralis subsp. dentisani, and the type of 'Streptococcus halitosis' belongs in Streptococcus oralis subsp. tigurinus. The genome sequence of the type of the recently proposed 'Streptococcus bouchesdurhonensis' is based on a mixed culture. Phylogenetic results and the pattern of presence/absence of accessory genes support the distinction of two subspecies of S. mitis, i.e. Sreptococcus mitis subsp. mitis subsp. nov. (type strain is NCTC 12261T) and Sreptococcus mitis subsp. carlssonii subsp. nov. (type strain is SK608=CCUG 55085T=LMG 33510T). The special population structure of the Streptococcus mitis-pneumoniae-pseudopneumoniae-thalassemiae complex renders automated classification of isolates based on average nucleotide identity or digital DNA-DNA hybridization values problematic. As an alternative, for initial taxonomic assignment, we present a whole-genome phylogeny-based method that enables phylogenetic comparison of new isolates in the context of a set of 117 well-characterized reference strains assigned to the Mitis/Sanguinis group.

Prediction of antimicrobial susceptibility of pneumococci based on whole-genome sequencing data: a direct comparison of two genomic tools to conventional antimicrobial susceptibility testing

Determination of antimicrobial resistance (AMR) in pneumococcal isolates is important for surveillance purposes and in a clinical context. Antimicrobial susceptibility testing (AST) of pneumococci is complicated by the need for exact minimal inhibitory concentrations (MICs) of beta-lactam antibiotics. Two next-generation sequencing (NGS) analysis tools have implemented the prediction of AMR in their analysis workflow, including the prediction of MICs: Pathogenwatch (https://pathogen.watch/) and AREScloud (OpGen). The performance of these tools in comparison to phenotypic AST following EUCAST guidelines is unknown. A total of 538 Streptococcus pneumoniae isolates were used to compare both tools with phenotypic AST for penicillin, amoxicillin, cefotaxime/ceftriaxone, erythromycin, trimethoprim-sulfamethoxazole, and tetracycline. Disk diffusion was performed for all isolates, and broth microdilution was performed for isolates with reduced beta-lactam susceptibility. Demultiplexed FASTQ files from Illumina sequencing, covering the whole genome of pneumococci, were used as input for the NGS tools. Categorical agreement (CA), major error (ME), and very major error (VME) rates were calculated. For beta-lactam antibiotics, CA was high (>94%) associated with none or only one ME and VME (<1%). For erythromycin and tetracycline, CA was >93% for predictions by AREScloud, while for Pathogenwatch, this ranged around 88%. For trimethoprim-sulfamethoxazole, CA was for both tools <86%. High VME rates were observed for erythromycin and tetracycline, higher for Pathogenwatch (53.6% and 47.0%, respectively) compared to AREScloud (14.3% and 19.1%, respectively). Both tools performed excellently despite the complexity of predicting beta-lactam resistance in pneumococci. Further optimization and validation are needed for non-beta-lactams since high (very) major error rates were observed.

Arginine Regulates the Mucoid Phenotype of Hypervirulent Klebsiella pneumoniae

Hypervirulent Klebsiella pneumoniae is associated with severe community-acquired infections. Hypervirulent K. pneumoniae colonies typically exhibit a mucoid phenotype. K. pneumoniae mucoidy is influenced by a complex combination of environmental factors and genetic mechanisms. Mucoidy results from altered capsular polysaccharide chain length, yet the specific environmental cues regulating this phenotype and their impact on pathogenesis remain unclear. This study demonstrates that casamino acids enhance the mucoidy phenotype but do not affect total capsular polysaccharide levels. Through targeted screening of each amino acid present in casamino acids, we identified that arginine is necessary and sufficient to stimulate the mucoid phenotype without altering capsule abundance. Furthermore, arginine activates the rmpADC promoter, increasing rmpD transcript levels, which in turn modulates capsular polysaccharide chain length and diversity. The arginine regulator, ArgR, plays a pivotal role in this regulatory cascade since deleting argR decreases mucoidy and increases capsular polysaccharide chain length diversity. Additionally, the ∆argR mutant displays increased macrophage association and has a substantial competitive defect in the lungs of mice, suggesting a link between arginine-dependent gene regulation, immune evasion and in vivo fitness. We discovered that arginine-dependent regulation of mucoidy is conserved in four additional hypervirulent K. pneumoniae isolates likely via a conserved ARG binding box present in rmp promoters. Our findings support a model in which arginine activates ArgR and increases mucoidy in hypervirulent K. pneumoniae. As a result, it is possible that arginine-dependent regulation of mucoidy allows hypervirulent K. pneumoniae to adapt the cell surface across different niches. This study underscores the significance of arginine as a regulatory signal in bacterial virulence.

A genome-based survey of invasive pneumococci in Norway over four decades reveals lineage-specific responses to vaccination

BACKGROUND

Streptococcus pneumoniae is a major cause of mortality globally. The introduction of pneumococcal conjugate vaccines (PCVs) has reduced the incidence of the targeted serotypes significantly, but expansion of non-targeted serotypes, serotype replacement, and incomplete vaccine-targeting contribute to pneumococcal disease in the vaccine era. Here, we characterize the changing population genetic landscape of S. pneumoniae in Norway over a 41-year period (1982-2022).

METHODS

Since 2018, all cases of invasive pneumococcal disease have undergone whole-genome sequencing (WGS) at the Norwegian Institute of Public Health. In order to characterize the changing population over time, historical isolates were re-cultured and sequenced, resulting in a historical WGS dataset. Isolates were assigned to global pneumococcal sequence clusters (GPSCs) using PathogenWatch and assigned to serotypes using in silico (SeroBA) and in vitro methods (Quellung reaction). Temporal phylogenetic analyses were performed on GPSCs of particular interest.

RESULTS

The availability of WGS data allowed us to study capsular variation at the level of individual lineages. We detect highly divergent fates for different GPSCs following the introduction of PCVs. For two out of eight major GPSCs, we identified multiple instances of serotype switching from vaccine types to non-vaccine types. Dating analyses suggest that most instances of serotype switching predated the introduction of PCVs, but expansion occurred after their introduction. Furthermore, selection for penicillin non-susceptibility was not a driving force for the changing serotype distribution within the GPSCs over time.

CONCLUSIONS

PCVs have been major shapers of the Norwegian disease-causing pneumococcal population, both at the level of serotype distributions and the underlying lineage dynamics. Overall, the introduction of PCVs has reduced the incidence of invasive disease. However, some GPSCs initially dominated by vaccine types escaped the effect of vaccination through expansion of non-vaccine serotypes. Close monitoring of circulating lineages and serotypes will be key for ensuring optimal vaccination coverage going forward.

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 Streptococcus pneumoniae genomes to compare four clustering methods: gene-by-gene seven-locus 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 utilize cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods shows 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, standardized and stable nomenclature is important as the number of genomes available expands. Furthermore, the research community should transition away from seven-locus MLST, whilst 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 standardized within the research.

Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations

Evaluation of the apportionment of genetic diversity of human bacterial commensals within and between human populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among human populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oro-nasopharyngeal healthy-carriage Streptococcus mitis and Streptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119 S. mitis genomes showed higher within- and among-host variation than 810 S. pneumoniae genomes in European, East Asian and African populations. Summary statistics of the site-frequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher ancestral bacterial population effective size (Ne) in S. mitis, whose genomic variation has been maintained close to mutation-drift equilibrium across (at least many) generations, whereas S. pneumoniae has been expanding from a smaller ancestral bacterial population. Strikingly, both species show limited differentiation among human populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem), we argue that large Ne have led to similar differentiation patterns, even if m is very low for S. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to large Ne.

Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data

Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. Streptococcus pneumoniae (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of S. pneumoniae. While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country.This article contains data hosted by Microreact.

Characterization of the resistome and predominant genetic lineages of Gram-positive bacteria causing keratitis

Bacterial keratitis is a vision-threatening infection mainly caused by Gram-positive bacteria (GPB). Antimicrobial therapy is commonly empirical using broad-spectrum agents with efficacy increasingly compromised by the emergence of antimicrobial resistance. We used a combination of phenotypic tests and genome sequencing to identify the predominant lineages of GPB causing keratitis and to characterize their antimicrobial resistance patterns. A total of 161 isolates, including Staphylococcus aureus (n = 86), coagulase-negative staphylococci (CoNS; n = 34), Streptococcus spp. (n = 34), and Enterococcus faecalis (n = 7), were included. The population of S. aureus isolates consisted mainly of clonal complex 5 (CC5) (30.2%). Similarly, the population of Staphylococcus epidermidis was homogenous with most of them belonging to CC2 (78.3%). Conversely, the genetic population of Streptococcus pneumoniae was highly diverse. Resistance to first-line antibiotics was common among staphylococci, especially among CC5 S. aureus. Methicillin-resistant S. aureus was commonly resistant to fluoroquinolones and azithromycin (78.6%) and tobramycin (57%). One-third of the CoNS were resistant to fluoroquinolones and 53% to azithromycin. Macrolide resistance was commonly caused by erm genes in S. aureus, mphC and msrA in CoNS, and mefA and msr(D) in streptococci. Aminoglycoside resistance in staphylococci was mainly associated with genes commonly found in mobile genetic elements and that encode for nucleotidyltransferases like ant(4')-Ib and ant(9)-Ia. Fluroquinolone-resistant staphylococci carried from 1 to 4 quinolone resistance-determining region mutations, mainly in the gyrA and parC genes. We found that GPB causing keratitis are associated with strains commonly resistant to first-line topical therapies, especially staphylococcal isolates that are frequently multidrug-resistant and associated with major hospital-adapted epidemic lineages.

Application of Pathogen Genomics to Outbreak Investigation

Outbreaks are a risk to public health particularly when pathogenic, hypervirulent, and/or multidrug-resistant organisms (MDROs) are involved. In a hospital setting, vulnerable populations such as the immunosuppressed, intensive care patients, and neonates are most at risk. Rapid and accurate outbreak detection is essential to implement effective interventions in clinical areas to control and stop further transmission. Advances in the field of whole genome sequencing (WGS) have resulted in lowered costs, increased capacity, and improved reproducibility of results. WGS now has the potential to revolutionize the investigation and management of outbreaks replacing conventional genotyping and other discrimination systems. Here, we outline specific procedures and protocols to implement WGS into investigation of outbreaks in healthcare settings.

Comparative genomic analysis of two ST320 Streptococcus pneumoniae isolates, representing serotypes 19A and 19F

BACKGROUND

Streptococcus pneumoniae (pneumococcus) represents an important human pathogen, responsible for respiratory and invasive infections in the community. The efficacy of polysaccharide conjugate vaccines formulated against pneumococci is reduced by the phenomenon of serotype replacement in population of this pathogen. The aim of the current study was to obtain and compare complete genomic sequences of two pneumococcal isolates, both belonging to ST320 but differing by the serotype.

RESULTS

Here, we report genomic sequences of two isolates of important human pathogen, S. pneumoniae. Genomic sequencing resulted in complete sequences of chromosomes of both isolates, 2,069,241 bp and 2,103,144 bp in size, and confirmed the presence of cps loci specific for serotypes 19A and 19F. The comparative analysis of these genomes revealed several instances of recombination, which involved not only S. pneumoniae but also presumably other streptococci as donors.

CONCLUSIONS

We report the complete genomic sequences of two S. pneumoniae isolates of ST320 and serotypes 19A and 19F. The detailed comparative analysis of these genomes revealed the history of several recombination events, clustered in the region including the cps locus.

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.

Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA

BACKGROUND

The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 immunologically distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally disseminated strain, GPSC12 (clonal complex 180).

METHODS

A genomic epidemiology study combined previous surveillance datasets of serotype 3 pneumococci to analyse the population structure, dynamics, and differences in rates of diversification within GPSC12 during the period of PCV introductions. Transcriptomic analyses, whole genome sequencing, mutagenesis, and electron microscopy were used to characterise the phenotypic impact of loci hypothesised to affect this strain's evolution.

RESULTS

GPSC12 was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage ϕOXC141. Prior to the introduction of PCV13, this clade's composition shifted towards a ϕOXC141-negative subpopulation in a systematically sampled UK collection. In the post-PCV13 era, more rapidly recombining non-Clade I isolates, also ϕOXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the ~100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage ϕOXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in ~30% of all pneumococci and was particularly common in the unusually clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR experiments using a genetically tractable pneumococcus demonstrated the altered csRNA3 was more effective at inhibiting production of the competence-stimulating peptide pheromone. This resulted in a reduction in the induction of competence for transformation.

CONCLUSION

This interference with the quorum sensing needed to induce competence reduces the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.

Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing

Invasive pneumococcal disease remains one of the leading causes of morbidity and mortality worldwide. In Russia, 13- valent pneumococcal conjugate vaccine (PCV13) was introduced into the childhood immunization programme nationwide in 2014. As part of the Global Pneumococcal Sequencing Project (GPS), we used genome data to characterize 179 pneumococcal isolates collected from Russia in 2011–2018 to investigate the circulating pneumococcal strains using a standardized genomic definition of pneumococcal lineages (global pneumococcal sequence clusters, GPSCs), prevalent serotypes and antimicrobial resistance profiles.

We observed high serotype and lineage diversity among the 179 isolates recovered from cerebrospinal fluid (n=77), nasopharyngeal swabs (n=99) and other non-sterile site swabs (n=3). Overall, 60 GPSCs were identified, including 48 clonal complexes (CCs) and 14 singletons, and expressed 42 serotypes (including non-typable). Among PCV13 serotypes, 19F, 6B and 23F were the top three serotypes while 11A, 15B/C and 8 were the top three among non-PCV13 serotypes in the collection. Two lineages (GPSC6 and GPSC47) expressed both PCV13 and non-PCV13 serotypes that caused invasive disease, and were penicillin- and multidrug-resistant (MDR), highlighting their potential to adapt and continue to cause infections under vaccine and antibiotic selective pressure. PCV13 serotypes comprised 92 % (11/12) of the CSF isolates from the children aged below 5 years; however, the prevalence of PCV13 serotype isolates dropped to 53 % (31/58) among the nasopharyngeal isolates. Our analysis showed that 59 % (105/179) of the isolates were predicted to be non-susceptible to at least one class of antibiotics and 26 % (46/179) were MDR. Four MDR lineages (GPSC1, GPSC6, GPSC10 and GPSC47) accounted for 65 % (30/46) of the MDR isolates and expressed PCV13 serotypes (93 %, 28/30).

This study provides evidence of high genetic and serotype diversity contributed by a mix of globally spreading and regionally circulating lineages in Russia. The observations suggest that the PCV13 vaccine could be important in reducing both invasive disease and antimicrobial resistance. We also identify potential lineages (GPSC6 and GPSC47) that may evade the vaccine.

Pneumococcal genetic variability in age-dependent bacterial carriage

The characteristics of pneumococcal carriage vary between infants and adults. Host immune factors have been shown to contribute to these age-specific differences, but the role of pathogen sequence variation is currently less well-known. Identification of age-associated pathogen genetic factors could leadto improved vaccine formulations. We therefore performed genome sequencing in a large carriage cohort of children and adults and combined this with data from an existing age-stratified carriage study. We compiled a dictionary of pathogen genetic variation, including serotype, strain, sequence elements, single-nucleotide polymorphisms (SNPs), and clusters of orthologous genes (COGs) for each cohort - all of which were used in a genome-wide association with host age. Age-dependent colonization showed weak evidence of being heritable in the first cohort (h2 = 0.10, 95% CI 0.00-0.69) and stronger evidence in the second cohort (h2 = 0.56, 95% CI 0.23-0.87). We found that serotypes and genetic background (strain) explained a proportion of the heritability in the first cohort (h2serotype = 0.07, 95% CI 0.04-0.14 and h2GPSC = 0.06, 95% CI 0.03-0.13) and the second cohort (h2serotype = 0.11, 95% CI 0.05-0.21 and h2GPSC = 0.20, 95% CI 0.12-0.31). In a meta-analysis of these cohorts, we found one candidate association (p=1.2 × 10-9) upstream of an accessory Sec-dependent serine-rich glycoprotein adhesin. Overall, while we did find a small effect of pathogen genome variation on pneumococcal carriage between child and adult hosts, this was variable between populations and does not appear to be caused by strong effects of individual genes. This supports proposals for adaptive future vaccination strategies that are primarily targeted at dominant circulating serotypes and tailored to the composition of the pathogen populations.

Current Methods for Recombination Detection in Bacteria

The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of software. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic approaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.

Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization

Streptococcus pneumoniae is a major human pathogen responsible for over 317000 deaths in children <5 years of age with the burden of the disease being highest in low- and middle-income countries including South Africa. Following the introduction of the 7-valent and 13-valent pneumococcal conjugate vaccine (PCV) in South Africa in 2009 and 2011, respectively, a decrease in both invasive pneumococcal infections and asymptomatic carriage of vaccine-type pneumococci were reported. In this study, we described the changing epidemiology of the pneumococcal carriage population in South Africa, by sequencing the genomes of 1825 isolates collected between 2009 and 2013. Using these genomic data, we reported the changes in serotypes, Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance before and after the introduction of PCV13. The pneumococcal carriage population in South Africa has a high level of diversity, comprising of 126 GPSCs and 49 serotypes. Of the ten most prevalent GPSCs detected, six were predominantly found in Africa (GPSC22, GPSC21, GPSC17, GPSC33, GPSC34 and GPSC52). We found a significant decrease in PCV7 serotypes (19F, 6B, 23F and 14) and an increase in non-vaccine serotypes (NVT) (16F, 34, 35B and 11A) among children <2 years of age. The increase in NVTs was driven by pneumococcal lineages GPSC33, GPSC34, GPSC5 and GPSC22. Overall, a decrease in antibiotic resistance for 11 antimicrobials was detected in the PCV13 era. Further, we reported a higher resistance prevalence among vaccine types (VTs), as compared to NVTs; however, an increase in penicillin resistance among NVT was observed between the PCV7 and PCV13 eras. The carriage isolates from South Africa predominantly belonged to pneumococcal lineages, which are endemic to Africa. While the introduction of PCV resulted in an overall reduction of resistance in pneumococcal carriage isolates, an increase in penicillin resistance among NVTs was detected in children aged between 3 and 5 years, driven by the expansion of penicillin-resistant clones associated with NVTs in the PCV13 era.

Population structure of ocular Streptococcus pneumoniae is highly diverse and formed by lineages that escape current vaccines

Streptococcus pneumoniae is a leading cause of ocular infections including serious and sight-threatening conditions. The use of pneumococcal conjugate vaccines (PCV) has substantially reduced the incidence of pneumonia and invasive pneumococcal diseases, but has had limited impact on ocular infections. Additionally, widespread vaccine use has resulted in ongoing selective pressure and serotype replacement in carriage and disease. To gain insight into the population structure of pneumococcal isolates causing ocular infections in a post-PCV-13 time period, we investigated the genomic epidemiology of ocular S. pneumoniae isolates (n=45) collected at Massachusetts Eye and Ear between 2014 and 2017. By performing a series of molecular typing methods from draft genomes, we found that the population structure of ocular S. pneumoniae is highly diverse with 27 sequence types (grouped into 18 clonal complexes) and 17 serotypes being identified. Distribution of these lineages diverged according to the site of isolation, with conjunctivitis being commonly caused by isolates grouped in the Epidemic Conjunctivitis Cluster-ECC (60 %), and ST448 (53.3 %) being most frequently identified. Conversely, S. pneumoniae keratitis cases were caused by a highly diverse population of isolates grouping within 15 different clonal complexes. Serotyping inference demonstrated that 95.5 % of the isolates were non-PCV-13 vaccine types. Most of the conjunctivitis isolates (80 %) were unencapsulated, with the remaining belonging to serotypes 15B, 3 and 23B. On the other hand, S. pneumoniae causing keratitis were predominantly encapsulated (95.2 %) with 13 different serotypes identified, mostly being non-vaccine types. Carriage of macrolide resistance genes was common in our ocular S. pneumoniae population (42.2 %), and usually associated with the mefA +msrD genotype (n=15). These genes were located in the Macrolide Efflux Genetic Assembly cassette and were associated with low-level in vitro resistance to 14- and 15-membered macrolides. Less frequently, macrolide-resistant isolates carried an ermB gene (n=4), which was co-located with the tetM gene in a Tn-916-like transposon. Our study demonstrates that the population structure of ocular S. pneumoniae is highly diverse, mainly composed by isolates that escape the PCV-13 vaccine, with patterns of tissue/niche segregation, adaptation and specialization. These findings suggest that the population structure of ocular pneumococcus may be shaped by multiple factors including PCV-13 selective pressure, microbial-related and niche-specific host-associated features.

International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

BACKGROUND

Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them.

METHODS

Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating.

RESULTS

Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017.

CONCLUSION

The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

Effect of pneumococcal conjugate vaccine availability on Streptococcus pneumoniae infections and genetic recombination in Zhejiang, China from 2009 to 2019

Pneumococcal pneumonia is one of the main reasons for child death worldwide. Pneumococcal conjugate vaccines (PCVs) are considered the most effective strategy for pneumococcal disease (PD) prevention, but how a pause in PCV vaccination affects the prevalence of PD or the genetic evolution of Streptococcus pneumoniae genetic evolution is unknown. Based on the unique PCV introduction timeline (vaccine unavailable during April 2015-April 2017) in China, we aimed to evaluate the effect of interrupted PCV availability on PD and pneumococcal genome variation. Pneumococcal isolates (n = 386) were collected retrospectively from eight sites in Zhejiang, China from 2009 to 2019 in which 184 pathogenic (isolates from sterile and infection sites) strains were identified. An interrupted time series analysis was conducted to estimate changes in PD and the recombination frequency of whole genome-sequenced strains was estimated via SNP calling. We found that both PD and pneumococcal genome variation were affected by interrupted PCV availability. The proportion (∼70%) of vaccine-type pneumococcal LRTI (VT-LRTI) in all LRTI cases decreased to ∼30% in the later PCV7 period and rebounded to ∼70% in children once PCV7 became unavailable in April 2015 (p = 0.0007). The major clone CC271 strains showed slowed (p = 0.0293) recombination frequency (decreased from 2.82 ± 1.16–0.72 ± 0.21) upon PCV removal. Our study illustrated for the first time that VT-LRTI fluctuated upon interrupted vaccine availability in China and causing a decreased of recombination frequency of vaccine types. Promoting a nationwide continuous vaccination programme and strengthening S. pneumoniae molecular epidemiology surveillance are essential for PD prevention.

Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis

Streptococcus consists of ecologically diverse species, some of which are important pathogens of humans and animals. We sought to quantify and compare the frequencies and characteristics of within-species recombination in the pan-genomes of Streptococcus agalactiae, Streptococcus pyogenes and Streptococcus suis. We used 1081, 1813 and 1204 publicly available genome sequences of each species, respectively. Based on their core genomes, S. agalactiae had the highest relative rate of recombination to mutation (11.5743) compared to S. pyogenes (1.03) and S. suis (0.57). The proportion of the species pan-genome that have had a history of recombination was 12.85%, 24.18% and 20.50% of the pan-genomes of each species, respectively. The composition of recombining genes varied among the three species, and some of the most frequently recombining genes are implicated in adhesion, colonization, oxidative stress response and biofilm formation. For each species, a total of 22.75%, 29.28% and 18.75% of the recombining genes were associated with prophages. The cargo genes of integrative conjugative elements and integrative and mobilizable elements contained genes associated with antimicrobial resistance and virulence. Homologous recombination and mobilizable pan-genomes enable the creation of novel combinations of genes and sequence variants, and the potential for high-risk clones to emerge.

Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil

In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children’s immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008–2009): n=232, post-PCV10 (2012–2013): n=234;<5 years old: n=310, ≥5 years old: n=156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin (P=0.0123) and cotrimoxazole (P<0.0001) resistance and an increase in tetracycline (P=0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l⁻¹); cotrimoxazole (folA and/or folP alterations), macrolide (mef and/or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.

Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina

Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998-1999 (pre-PCV), before the introduction of PCV13 2010-2011 (PCV7) and after the introduction of PCV13 2012-2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50 % of the isolates. Resistance to penicillin was 34.9 %, cefotaxime 10.6 %, meropenem 4.9 %, cotrimoxazole 45 %, erythromycin 21.5 %, tetracycline 15.4 % and chloramphenicol 0.4 %. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9 %) were non-susceptible to at least one antibiotic and 235(13.7 %) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococcal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0 % in pre-PCV to 3.2 % in the PCV13 period. Our analysis showed that 66.1 % (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9 % (49/413) were multidrug resistant. We found an agreement of 100 % when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4 % of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.

Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach

Globally, India has a high burden of pneumococcal disease, and pneumococcal conjugate vaccine (PCV) has been rolled out in different phases across the country since May 2017 in the national infant immunization programme (NIP). To provide a baseline for assessing the impact of the vaccine on circulating pneumococci in India, genetic characterization of pneumococcal isolates detected prior to introduction of PCV would be helpful. Here we present a population genomic study of 480 Streptococcus pneumoniae isolates collected across India and from all age groups before vaccine introduction (2009–2017), including 294 isolates from pneumococcal disease and 186 collected through nasopharyngeal surveys. Population genetic structure, serotype and antimicrobial susceptibility profile were characterized and predicted from whole-genome sequencing data. Our findings revealed high levels of genetic diversity represented by 110 Global Pneumococcal Sequence Clusters (GPSCs) and 54 serotypes. Serotype 19F and GPSC1 (CC320) was the most common serotype and pneumococcal lineage, respectively. Coverage of PCV13 (Pfizer) and 10-valent Pneumosil (Serum Institute of India) serotypes in age groups of ≤2 and 3–5 years were 63–75 % and 60–69 %, respectively. Coverage of PPV23 (Merck) serotypes in age groups of ≥50 years was 62 % (98/158). Among the top five lineages causing disease, GPSC10 (CC230), which ranked second, is the only lineage that expressed both PCV13 (serotypes 3, 6A, 14, 19A and 19F) and non-PCV13 (7B, 13, 10A, 11A, 13, 15B/C, 22F, 24F) serotypes. It exhibited multidrug resistance and was the largest contributor (17 %, 18/103) of NVTs in the disease-causing population. Overall, 42 % (202/480) of isolates were penicillin-resistant (minimum inhibitory concentration ≥0.12 µg ml⁻¹) and 45 % (217/480) were multidrug-resistant. Nine GPSCs (GPSC1, 6, 9, 10, 13, 16, 43, 91, 376) were penicillin-resistant and among them six were multidrug-resistant. Pneumococci expressing PCV13 serotypes had a higher prevalence of antibiotic resistance. Sequencing of pneumococcal genomes has significantly improved our understanding of the biology of these bacteria. This study, describing the pneumococcal disease and carriage epidemiology pre-PCV introduction, demonstrates that 60–75 % of pneumococcal serotypes in children ≤5 years are covered by PCV13 and Pneumosil. Vaccination against pneumococci is very likely to reduce antibiotic resistance. A multidrug-resistant pneumococcal lineage, GPSC10 (CC230), is a high-risk clone that could mediate serotype replacement.

Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics

Vaccines are powerful agents in infectious disease prevention but often designed to protect against some strains that are most likely to spread and cause diseases. Most vaccines do not succeed in eradicating the pathogen and thus allow the potential emergence of vaccine evading strains. As with most evolutionary processes, being able to capture all variations across the entire genome gives us the best chance of monitoring and understanding the processes of vaccine evasion. Genomics is being widely adopted as the optimum approach for pathogen surveillance with the potential for early and precise identification of high-risk strains. Given sufficient longitudinal data, genomics also has the potential to forecast the emergence of such strains enabling immediate or pre-emptive intervention. In this review, we consider the strengths and challenges for pathogen genomic surveillance using the experience of the Global Pneumococcal Sequencing (GPS) project as an early example. We highlight the multifaceted nature of genome data and recent advances in genome-based tools to extract useful information relevant to inform vaccine strategies and treatment options. We conclude with future perspectives for genomic pathogen surveillance.

Molecular characterization and epidemiology of Streptococcus pneumoniae serotype 8 in Denmark

Background

Streptococcus pneumoniae serotype 8 incidence has increased in Denmark after the introduction of pneumococcal conjugated vaccines (PCV). The mechanism behind the serotype 8 replacement is not well understood. In this study, we aimed to present epidemiological data on invasive pneumococcal disease (IPD) and molecular characterization of 96 serotype 8 clinical isolates.

Methods

IPD data from 1999 to 2019 were used to calculate the incidence and age distribution. Whole-genome sequencing (WGS) analysis was performed on 96 isolates (6.8% of the total serotype 8 IPD isolates in the period) to characterize the isolates with respect to pneumococcal lineage traits, a range of genes with potential species discrimination, presence of colonization and virulence factors, and molecular resistance pattern.

Results

The serotype 8 IPD incidence increased significantly (P < 0.05) for the age groups above 15 years after the introduction of PCV13, primarily affecting the elderly (65+). All isolates were phenotypically susceptible to penicillin, erythromycin and clindamycin.

Molecular characterization revealed seven different MLST profiles with ST53 as the most prevalent lineage (87.5%) among the analyzed serotype 8 isolates. The genes covering the cell-surface proteins: lytA, rspB, pspA, psaA & Xisco and the pneumococcal toxin pneumolysin = ply were present in all isolates, while genes for the membrane transporter proteins: piaA/piaB/piaC; the capsular genes: cpsA (wzg) & psrP; the metallo-binding proteins zmpB & zmpC; and the neuroamidase proteins: nanA/nanB were variably present. Surprisingly, the putative transcriptional regulator gene SP2020 was not present in all isolates (98%). Susceptibility to penicillin, erythromycin and clindamycin was molecularly confirmed.

Conclusion

The observed serotype 8 replacement was not significantly reflected with a change in the MLST profile or changes in antibiotic resistance- or virulence determinants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06103-w.

Genome-Wide Analysis of the Temporal Genetic Changes in Streptococcus pneumoniae Isolates of Genotype ST320 and Serotype 19A from South Korea

Since the introduction of the pneumococcal conjugate vaccine, an increase in the incidence of Streptococcus pneumoniae serotype 19A and sequence type 320 (19A-ST320) isolates have been observed worldwide including in South Korea. We conducted a genome-wide analysis to investigate the temporal genetic changes in 26 penicillin-non-susceptible 19A-ST320 pneumococcal isolates from a hospital in South Korea over a period of 17 years (1999; 2004 to 2015). Although the strains were isolated from a single hospital and showed the same genotype and serotype, a whole-genome sequencing (WGS) analysis revealed that the S. pneumoniae isolates showed more extensive genetic variations compared with a reference isolate obtained in 1999. A phylogenetic analysis based on single nucleotide polymorphisms (SNPs) showed that the pneumococcal isolates from South Korea were not grouped together into limited clusters among the 19A-ST320 isolates from several continents. It was predicted that recombination events occurred in 11 isolates; larger numbers of SNPs were found within recombination blocks compared with point mutations identified in five isolates. WGS data indicated that S. pneumoniae 19A-ST320 isolates might have been introduced into South Korea from various other countries. In addition, it was revealed that recombination may play a great role in the evolution of pneumococci even in very limited places and periods.

Sugar-Coated Killer: Serotype 3 Pneumococcal Disease

Capsular polysaccharide (CPS), which surrounds the bacteria, is one of the most significant and multifaceted contributors to Streptococcus pneumoniae virulence. Capsule prevents entrapment in mucus during colonization, traps water to protect against desiccation, can serve as an energy reserve, and protects the bacterium against complement-mediated opsonization and immune cell phagocytosis. To date, 100 biochemically and serologically distinct capsule types have been identified for S. pneumoniae; 20 to 30 of which have well-defined propensity to cause opportunistic human infection. Among these, serotype 3 is perhaps the most problematic as serotype 3 infections are characterized as having severe clinical manifestations including empyema, bacteremia, cardiotoxicity, and meningitis; consequently, with a fatality rate of 30%-47%. Moreover, serotype 3 resists antibody-mediated clearance despite its inclusion in the current 13-valent conjugate vaccine formulation. This review covers the role of capsule in pneumococcal pathogenesis and the importance of serotype 3 on human disease. We discuss how serotype 3 capsule synthesis and presentation on the bacterial surface is distinct from other serotypes, the biochemical and physiological properties of this capsule type that facilitate its ability to cause disease, and why existing vaccines are unable to confer protection. We conclude with discussion of the clonal properties of serotype 3 and how these have changed since introduction of the 13-valent vaccine in 2000.

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo .

Interest of bacterial pangenome analyses in clinical microbiology

Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.