Publications by authors named "Stephen D Bentley"

224 Publications

RCandy: an R package for visualising homologous recombinations in bacterial genomes.

Bioinformatics 2021 Dec 2. Epub 2021 Dec 2.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.

Motivation: Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, which increases genomic sequence diversity and can facilitate adaptation. Several methods and tools have been developed to detect genomic regions recently affected by recombination. Exploration and visualisation of such recombination events can reveal valuable biological insights, but it remains challenging. Here, we present RCandy, a platform-independent R package for rapid, simple, and flexible visualisation of recombination events in bacterial genomes.

Availability: RCandy is an R package freely available for use under the MIT license. It is platform-independent and has been tested on Windows, Linux, and MacOSX. The source code comes together with a detailed vignette available on GitHub at https://github.com/ChrispinChaguza/RCandy.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btab814DOI Listing
December 2021

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

Microb Genom 2021 10;7(10)

National Reference Laboratory for Meningitis and Pneumococcal Infections, Institute Adolfo Lutz, São Paulo, 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 isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008-2009): =232, post-PCV10 (2012-2013): =234;<5 years old: =310, ≥5 years old: =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 (=0.0123) and cotrimoxazole (<0.0001) resistance and an increase in tetracycline (=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); cotrimoxazole (A and/or P alterations), macrolide ( and/or ) and tetracycline (M, O or SM) 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.
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http://dx.doi.org/10.1099/mgen.0.000635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8627213PMC
October 2021

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

Microb Genom 2021 09;7(9)

Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.

Invasive disease caused by (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 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.
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http://dx.doi.org/10.1099/mgen.0.000636DOI Listing
September 2021

serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from .

Microb Genom 2021 09;7(9)

NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK.

is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus , the rates and effects of HGT between and its close relatives involving the penicillin binding protein () genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in genes using a global collection of whole-genome sequences of , and . With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired fragments. was a more frequent pneumococcal donor of fragments and a source of higher nucleotide diversity when compared with . Pneumococci that acquired fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as .
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http://dx.doi.org/10.1099/mgen.0.000622DOI Listing
September 2021

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

Microb Genom 2021 09;7(9)

Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India.

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 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) 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.
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http://dx.doi.org/10.1099/mgen.0.000645DOI Listing
September 2021

Patterns of within-host genetic diversity in SARS-CoV-2.

Elife 2021 08 13;10. Epub 2021 Aug 13.

Public Health England, Cambridge, United Kingdom.

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.
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http://dx.doi.org/10.7554/eLife.66857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8363274PMC
August 2021

Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.

Microb Genom 2021 07;7(7)

WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.

Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 . isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (=6) in the post-PCV introduction period compared to 21.9 % (=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.
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http://dx.doi.org/10.1099/mgen.0.000506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8477402PMC
July 2021

The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci.

Elife 2021 07 14;10. Epub 2021 Jul 14.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.

Multidrug-resistant emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn-type and Tn-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome.
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http://dx.doi.org/10.7554/eLife.67113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8321556PMC
July 2021

The effect of recombination on the evolution of a population of .

Genome Res 2021 Jun 9. Epub 2021 Jun 9.

Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom.

(the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal genomes is limited by the rarity of large-scale genomic population studies and lack of in-depth investigation of the genomic events associated with routine pathogen transmission. Here, we fill this knowledge gap by a detailed analysis of 2839 meningococcal genomes obtained through a carriage study of over 50,000 samples collected systematically in Burkina Faso, West Africa, before, during, and after the serogroup A vaccine rollout, 2009-2012. Our findings indicate that the meningococcal genome is highly dynamic, with highly recombinant loci and frequent gene sharing across deeply separated lineages in a structured population. Furthermore, our findings illustrate how population structure can correlate with genome flexibility, as some lineages in Burkina Faso are orders of magnitude more recombinant than others. We also examine the effect of selection on the population, in particular how it is correlated with recombination. We find that recombination principally acts to prevent the accumulation of deleterious mutations, although we do also find an example of recombination acting to speed the adaptation of a gene. In general, we show the importance of recombination in the evolution of a geographically expansive population with deep population structure in a short timescale. This has important consequences for our ability to both foresee the outcomes of vaccination programs and, using surveillance data, predict when lineages of the meningococcus are likely to become a public health concern.
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http://dx.doi.org/10.1101/gr.264465.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8256868PMC
June 2021

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

Genome Med 2021 05 17;13(1):84. Epub 2021 May 17.

Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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.
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http://dx.doi.org/10.1186/s13073-021-00901-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130287PMC
May 2021

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.

Nat Commun 2021 03 9;12(1):1523. Epub 2021 Mar 9.

Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.

Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.
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http://dx.doi.org/10.1038/s41467-021-21749-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7943827PMC
March 2021

Pneumococcal Colonization and Virulence Factors Identified Via Experimental Evolution in Infection Models.

Mol Biol Evol 2021 05;38(6):2209-2226

Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.

Streptococcus pneumoniae is a commensal of the human nasopharynx and a major cause of respiratory and invasive disease. We examined adaptation and evolution of pneumococcus, within nasopharynx and lungs, in an experimental system where the selective pressures associated with transmission were removed. This was achieved by serial passage of pneumococci, separately, in mouse models of nasopharyngeal carriage or pneumonia. Passaged pneumococci became more effective colonizers of the respiratory tract and we observed several examples of potential parallel evolution. The cell wall-modifying glycosyltransferase LafA was under strong selection during lung passage, whereas the surface expressed pneumococcal vaccine antigen gene pvaA and the glycerol-3-phosphate dehydrogenase gene gpsA were frequent targets of mutation in nasopharynx-passaged pneumococci. These mutations were not identified in pneumococci that were separately evolved by serial passage on laboratory agar. We focused on gpsA, in which the same single nucleotide polymorphism arose in two independently evolved nasopharynx-passaged lineages. We describe a new role for this gene in nasopharyngeal carriage and show that the identified single nucleotide change confers resistance to oxidative stress and enhanced nasopharyngeal colonization potential. We demonstrate that polymorphisms in gpsA arise and are retained during human colonization. These findings highlight how within-host environmental conditions can determine trajectories of bacterial evolution. Relative invasiveness or attack rate of pneumococcal lineages may be defined by genes that make niche-specific contributions to bacterial fitness. Experimental evolution in animal infection models is a powerful tool to investigate the relative roles played by pathogen virulence and colonization factors within different host niches.
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http://dx.doi.org/10.1093/molbev/msab018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136498PMC
May 2021

Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life.

Front Pediatr 2020 8;8:587730. Epub 2021 Jan 8.

Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia.

(the pneumococcus) carriage precedes invasive disease and influences population-wide strain dynamics, but limited data exist on temporal carriage patterns of serotypes due to the prohibitive costs of longitudinal studies. Here, we report carriage prevalence, clearance and acquisition rates of pneumococcal serotypes sampled from newborn infants bi-weekly from weeks 1 to 27, and then bi-monthly from weeks 35 to 52 in the Gambia. We used sweep latex agglutination and whole genome sequencing to serotype the isolates. We show rapid pneumococcal acquisition with nearly 31% of the infants colonized by the end of first week after birth and quickly exceeding 95% after 2 months. Co-colonization with multiple serotypes was consistently observed in over 40% of the infants at each sampling point during the first year of life. Overall, the mean acquisition time and carriage duration regardless of serotype was 38 and 24 days, respectively, but varied considerably between serotypes comparable to observations from other regions. Our data will inform disease prevention and control measures including providing baseline data for parameterising infectious disease mathematical models including those assessing the impact of clinical interventions such as pneumococcal conjugate vaccines.
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http://dx.doi.org/10.3389/fped.2020.587730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820366PMC
January 2021

Genetic Variation in Does Not Influence Disease Severity in Meningococcal Meningitis.

Front Med (Lausanne) 2020 11;7:594769. Epub 2020 Nov 11.

Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands.

causes sepsis and meningitis in humans. It has been suggested that pathogen genetic variation determines variance in disease severity. Here we report results of a genome-wide association study of 486 genomes from meningococcal meningitis patients and their association with disease severity. Of 369 meningococcal meningitis patients for whom clinical data was available, 44 (12%) had unfavorable outcome and 24 (7%) died. To increase power, thrombocyte count was used as proxy marker for disease severity. Bacterial genetic variants were called as k-mers, SNPs, insertions and deletions and clusters of orthologous genes (COGs). Population-level meningococcal genetic variation did not explain variance in disease severity (unfavorable outcome or thrombocyte count) in this cohort (h = 0.0%; 95% confidence interval: 0.0-0.9). Genetic variants in the bacterial gene represented the top signal associated with thrombocyte count (-value = 9.96e-07) but this did not reach statistical significance. We did not find an association between previously published variants in , and genes and unfavorable outcome or thrombocyte count. A power analysis based on simulated phenotypes based on real genetic data from 880 genomes showed that we would be able to detect a continuous phenotype with h > = 0.5 with the population size available in this study. This rules out a major contribution of pathogen genetic variation to disease severity in meningococcal meningitis, and shows that much larger sample sizes are required to find specific low-effect genetic variants modulating disease outcome in meningococcal meningitis.
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http://dx.doi.org/10.3389/fmed.2020.594769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7686797PMC
November 2020

A Nationwide Outbreak of Invasive Pneumococcal Disease in Israel Caused by Streptococcus Pneumoniae Serotype 2.

Clin Infect Dis 2020 Nov 17. Epub 2020 Nov 17.

Government Central Laboratories, Ministry of Health, Jerusalem, Israel.

Background: Invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae serotype 2 (Sp2) is infrequent. Large scale outbreaks have not been reported following pneumococcal conjugate vaccine (PCV) implementation. We describe a Sp2 IPD outbreak in Israel, in the 13-valent PCV (PCV13) era, with focus on Sp2 population structure and evolutionary dynamics.

Methods: The data derived from a population-based, nationwide active surveillance of IPD since 2009. 7-valent PCV (PCV7)/PCV13 vaccines were introduced in July 2009 and November 2010, respectively. Sp2 isolates were tested for antimicrobial susceptibility, Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis.

Results: Overall, 170 Sp2 IPD cases were identified during 2009-2019; Sp2 increased in 2015 and caused 6% of IPD during 2015-2019, a 7-fold increase compared with 2009-2014.The outbreak was caused by a previously unreported molecular type (ST-13578), initially observed in Israel in 2014. This clone caused 88% of Sp2 during 2015-2019. ST-13578 is a single-locus variant of ST-1504, previously reported globally, including in Israel. WGS analysis confirmed clonality among the ST-13578 population. Single-nucleotide polymorphisms-dense regions support a hypothesis that the ST-13578 outbreak clone evolved from ST-1504 by recombination.All tested strains were penicillin-susceptible (MIC <0.06 μg/mL). The ST-13578 clone was identified almost exclusively (99%) in the Jewish population and was mainly distributed in 3/7 Israeli districts. The outbreak is still ongoing, although declining since 2017.Conclusions: To the best of our knowledge, this is the first widespread Sp2 outbreak since PCV13 introduction worldwide, caused by the emerging ST-13578 clone.
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http://dx.doi.org/10.1093/cid/ciaa1720DOI Listing
November 2020

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.

PLoS Biol 2020 10 22;18(10):e3000878. Epub 2020 Oct 22.

Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America.

Predicting how pathogen populations will change over time is challenging. Such has been the case with Streptococcus pneumoniae, an important human pathogen, and the pneumococcal conjugate vaccines (PCVs), which target only a fraction of the strains in the population. Here, we use the frequencies of accessory genes to predict changes in the pneumococcal population after vaccination, hypothesizing that these frequencies reflect negative frequency-dependent selection (NFDS) on the gene products. We find that the standardized predicted fitness of a strain, estimated by an NFDS-based model at the time the vaccine is introduced, enables us to predict whether the strain increases or decreases in prevalence following vaccination. Further, we are able to forecast the equilibrium post-vaccine population composition and assess the invasion capacity of emerging lineages. Overall, we provide a method for predicting the impact of an intervention on pneumococcal populations with potential application to other bacterial pathogens in which NFDS is a driving force.
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http://dx.doi.org/10.1371/journal.pbio.3000878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7580979PMC
October 2020

Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism.

Commun Biol 2020 10 8;3(1):559. Epub 2020 Oct 8.

Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.

Hyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation in serotype 1 strains modulates tropism into cerebrospinal fluid to cause central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal serotype 1 isolates collected from CNS and non-CNS human samples. By controlling for host age, geography, and strain population structure, we identify genome-wide statistically significant genotype-phenotype associations in surface-exposed choline-binding (P = 5.00 × 10) and helicase proteins (P = 1.32 × 10) important for invasion, immune evasion and pneumococcal tropism to CNS. The small effect sizes and negligible heritability indicated that causation of CNS infection requires multiple genetic and other factors reflecting a complex and polygenic aetiology. Our findings suggest that certain pathogen genetic variation modulate pneumococcal survival and tropism to CNS tissue, and therefore, virulence for meningitis.
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http://dx.doi.org/10.1038/s42003-020-01290-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545184PMC
October 2020

Diversification in immunogenicity genes caused by selective pressures in invasive meningococci.

Microb Genom 2020 09 10;6(9). Epub 2020 Aug 10.

Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscienc, Amsterdam, The Netherlands.

We studied population genomics of 486 isolates causing meningitis in the Netherlands during the period 1979-2003 and 2006-2013 using whole-genome sequencing to evaluate the impact of a hyperendemic period of serogroup B invasive disease. The majority of serogroup B isolates belonged to ST-41/44 (41 %) and ST-32 complex (16 %). Comparing the time periods, before and after the decline of serogroup B invasive disease, there was a decrease of ST-41/44 complex sequences (=0.002). We observed the expansion of a sub-lineage within ST-41/44 complex sequences being associated with isolation from the 1979-2003 time period (=0.014). Isolates belonging to this sub-lineage expansion within ST-41/44 complex were marked by four antigen allele variants. Presence of these allele variants was associated with isolation from the 1979-2003 time period after correction for multiple testing (Wald test, =0.0043 for FetA 1-5; =0.0035 for FHbp 14; =0.012 for PorA 7-2.4 and =0.0031 for NHBA two peptide allele). These sequences were associated with 4CMenB vaccine coverage (Fisher's exact test, <0.001). Outside of the sub-lineage expansion, isolates with markedly lower levels of predicted vaccine coverage clustered in phylogenetic groups showing a trend towards isolation in the 2006-2013 time period (=0.08). In conclusion, we show the emergence and decline of a sub-lineage expansion within ST-41/44 complex isolates concurrent with a hyperendemic period in meningococcal meningitis. The expansion was marked by specific antigen peptide allele combinations. We observed preliminary evidence for decreasing 4CMenB vaccine coverage in the post-hyperendemic period.
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http://dx.doi.org/10.1099/mgen.0.000422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643973PMC
September 2020

Mass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx.

Clin Microbiol Infect 2021 Jun 1;27(6):864-870. Epub 2020 Aug 1.

London School of Hygiene & Tropical Medicine, Keppel Street, London, UK. Electronic address:

Objective: Mass drug administration (MDA) with azithromycin for trachoma elimination reduces nasopharyngeal carriage of Streptococcus pneumoniae in the short term. We evaluated S. pneumoniae carried in the nasopharynx before and after a round of azithromycin MDA to determine whether MDA was associated with changes in pneumococcal population structure and resistance.

Methods: We analysed 514 pneumococcal whole genomes randomly selected from nasopharyngeal samples collected in two Gambian villages that received three annual rounds of MDA for trachoma elimination. The 514 samples represented 293 participants, of which 75% were children aged 0-9 years, isolated during three cross-sectional surveys (CSSs) conducted before the third round of MDA (CSS-1) and at 1 (CSS-2) and 6 (CSS-3) months after MDA. Bayesian Analysis of Population Structure (BAPS) was used to cluster related isolates by capturing variation in the core genome. Serotype and multilocus sequence type were inferred from the genotype. Antimicrobial resistance determinants were identified from assemblies, including known macrolide resistance genes.

Results: Twenty-seven BAPS clusters were assigned. These consisted of 81 sequence types (STs). Two BAPS clusters not observed in CSS-1 (n = 109) or CSS-2 (n = 69), increased in frequency in CSS-3 (n = 126); BAPS20 (8.73%, p 0.016) and BAPS22 (7.14%, p 0.032) but were not associated with antimicrobial resistance. Macrolide resistance within BAPS17 increased after treatment (CSS-1 n = 0/6, CSS-2/3 n = 5/5, p 0.002) and was carried on a mobile transposable element that also conferred resistance to tetracycline.

Discussion: Limited changes in pneumococcal population structure were observed after the third round of MDA, suggesting treatment had little effect on the circulating lineages. An increase in macrolide resistance within one BAPS highlights the need for antimicrobial resistance surveillance in treated villages.
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http://dx.doi.org/10.1016/j.cmi.2020.07.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8203556PMC
June 2021

Producing polished prokaryotic pangenomes with the Panaroo pipeline.

Genome Biol 2020 07 22;21(1):180. Epub 2020 Jul 22.

Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.

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 .
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http://dx.doi.org/10.1186/s13059-020-02090-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376924PMC
July 2020

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in .

Sci Adv 2020 May 20;6(21):eaaz6137. Epub 2020 May 20.

Big Data Institute, University of Oxford, Oxford, UK.

The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move between genetic lineages is an open question, which we address in the context of antibiotic resistance in . We analyze microbiological, genomic, and epidemiological data from the largest-to-date sequenced pneumococcal carriage study in 955 infants from a refugee camp on the Thailand-Myanmar border. Using a unified framework, we simultaneously test prior hypotheses on rates of HGT and a key evolutionary covariate (duration of carriage) as determinants of resistance frequencies. We conclude that in this setting, there is little evidence of HGT playing a major role in determining resistance frequencies. Instead, observed resistance frequencies are best explained as the outcome of selection acting on a pool of variants, irrespective of the rate at which resistance determinants move between genetic lineages.
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http://dx.doi.org/10.1126/sciadv.aaz6137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314567PMC
May 2020

Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.

Nat Commun 2020 07 10;11(1):3442. Epub 2020 Jul 10.

Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.

Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting. We show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed over longer timescales in S. pneumoniae and other bacteria drives high within-host pneumococcal genetic diversity. Highly divergent co-existing strain variants emerge during colonisation episodes through real-time intra-host homologous recombination while the rest are co-transmitted or acquired independently during multiple colonisation episodes. Genic and intergenic parallel evolution occur particularly in antibiotic resistance, immune evasion and epithelial adhesion genes. Our findings suggest that within-host microevolution is rapid and adaptive during natural colonisation.
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http://dx.doi.org/10.1038/s41467-020-17327-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351774PMC
July 2020

The global meningitis genome partnership.

J Infect 2020 10 29;81(4):510-520. Epub 2020 Jun 29.

Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK.

Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1935), Sa (9026); The Wellcome Sanger Institute: Nm (13,711), Sp (> 24,000), Sa (6200), Hi (1738); and BMGAP: Nm (8785), Hi (2030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data.
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http://dx.doi.org/10.1016/j.jinf.2020.06.064DOI Listing
October 2020

Persistent and emerging pneumococcal carriage serotypes in a rural Gambian community after ten years of pneumococcal conjugate vaccine pressure.

Clin Infect Dis 2020 Jun 25. Epub 2020 Jun 25.

Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at London School Hygiene and Tropical Medicine, Fajara The Gambia.

Background: The continuing impact of pneumococcal conjugate vaccines (PCVs) in regions with high pneumococcal transmission is threatened by the persistence of vaccine serotypes (VT) and the emergence of non-vaccine serotypes (NVT).

Methods: In 2016, we conducted a cross-sectional carriage survey (CSS5) in a community where PCV7 was first introduced in 2006 during a cluster randomised trial conducted before nationwide introduction of PCV7 (2009) and PCV13 (2011). We estimated the prevalence of PCV13 VT and NVT by age and compared these to earlier surveys before (CSS0), during (CSS1-3), and after the trial but before PCV13 (CSS4). Genomic analysis was conducted for the non-typeable pneumococci.

Results: The prevalence of PCV13 VT carriage decreased during the 10 years between CSS0 and CSS5 across all age groups (67·6% to 13·5%, p<0.001; 59·8% to 14·4%, p<0.001; 43·1% to 17·9%, p<0.001; and 24·0% to 5·1%, p<0.001 in <2, 2-4, 5-14 and ≥15 years respectively). However, there was no difference between CSS4 and CSS5 in children ≥2 years and adults (children < 2 years, no data). The prevalence of PCV13 NVT increased between CSS0 and CSS5 for children <2 years but decreased in older children and adults.In CSS5, serotypes 3, 6A and 19F were the most common VT and non-typeable isolates, the most common NVT. Among non-typeable isolates, 73·0% lost the ability to express a capsule. Of these, 70·8% were from a VT background.

Conclusions: The decrease in PCV13 VT that has occurred since the introduction of PCV13 appears to have plateaued. Significant carriage of these serotypes remains in all age groups.
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http://dx.doi.org/10.1093/cid/ciaa856DOI Listing
June 2020

Increasing incidence of group B streptococcus neonatal infections in the Netherlands is associated with clonal expansion of CC17 and CC23.

Sci Rep 2020 06 12;10(1):9539. Epub 2020 Jun 12.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

Group B streptococcus (GBS) is the leading cause of neonatal invasive disease worldwide. In the Netherlands incidence of the disease increased despite implementation of preventive guidelines. We describe a genomic analysis of 1345 GBS isolates from neonatal (age 0-89 days) invasive infections in the Netherlands reported between 1987 and 2016. Most isolates clustered into one of five major lineages: CC17 (39%), CC19 (25%), CC23 (18%), CC10 (9%) and CC1 (7%). There was a significant rise in the number of infections due to isolates from CC17 and CC23. Phylogenetic clustering analysis revealed that this was caused by expansion of specific sub-lineages, designated CC17-A1, CC17-A2 and CC23-A1. Dating of phylogenetic trees estimated that these clones diverged in the 1960s/1970s, representing historical rather than recently emerged clones. For CC17-A1 the expansion correlated with acquisition of a new phage, carrying gene encoding a putative cell-surface protein. Representatives of CC17-A1, CC17-A2 and CC23-A1 clones were identified in datasets from other countries demonstrating their global distribution.
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http://dx.doi.org/10.1038/s41598-020-66214-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293262PMC
June 2020

Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages.

Environ Microbiol 2020 12 23;22(12):5058-5072. Epub 2020 Jun 23.

Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.

Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.
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http://dx.doi.org/10.1111/1462-2920.15111DOI Listing
December 2020

A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large Fragment from an Oral Streptococcus.

mBio 2020 05 19;11(3). Epub 2020 May 19.

Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA

(pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes. Herein, we report a new and the 100th capsule type, named serotype 10D, by determining its unique chemical structure and biosynthetic roles of all capsule synthesis locus () genes. The name 10D reflects its serologic cross-reaction with serotype 10A and appearance of cross-opsonic antibodies in response to immunization with 10A polysaccharide in a 23-valent pneumococcal vaccine. Genetic analysis showed that 10D has three large regions syntenic to and highly homologous with loci from serotype 6C, serotype 39, and an oral streptococcus strain ( SK145). The 10D region syntenic to SK145 is about 6 kb and has a short gene fragment of α at the 5' end. The presence of this nonfunctional α fragment provides compelling evidence for a recent interspecies genetic transfer from oral streptococcus to pneumococcus. Since oral streptococci have a large repertoire of loci, widespread PCV usage could facilitate the appearance of novel serotypes through interspecies recombination. The polysaccharide capsule is essential for the pathogenicity of pneumococcus, which is responsible for millions of deaths worldwide each year. Currently available pneumococcal vaccines are designed to elicit antibodies to the capsule polysaccharides of the pneumococcal isolates commonly causing diseases, and the antibodies provide protection only against the pneumococcus expressing the vaccine-targeted capsules. Since pneumococci can produce different capsule polysaccharides and therefore reduce vaccine effectiveness, it is important to track the appearance of novel pneumococcal capsule types and how these new capsules are created. Herein, we describe a new and the 100th pneumococcal capsule type with unique chemical and serological properties. The capsule type was named 10D for its serologic similarity to 10A. Genetic studies provide strong evidence that pneumococcus created 10D capsule polysaccharide by capturing a large genetic fragment from an oral streptococcus. Such interspecies genetic exchanges could greatly increase diversity of pneumococcal capsules and complicate serotype shifts.
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http://dx.doi.org/10.1128/mBio.00937-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240158PMC
May 2020

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

Microb Genom 2020 05 29;6(5). Epub 2020 Apr 29.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK.

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (, , ) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.
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http://dx.doi.org/10.1099/mgen.0.000357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371119PMC
May 2020

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928-2013): antimicrobial use/misuse selects for resistance and drives evolution.

BMC Genomics 2020 Feb 3;21(1):116. Epub 2020 Feb 3.

WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, SE-710 85, Örebro, Sweden.

Background: Multidrug-resistant Neisseria gonorrhoeae strains are prevalent, threatening gonorrhoea treatment globally, and understanding of emergence, evolution, and spread of antimicrobial resistance (AMR) in gonococci remains limited. We describe the genomic evolution of gonococci and their AMR, related to the introduction of antimicrobial therapies, examining isolates from 1928 (preantibiotic era) to 2013 in Denmark. This is, to our knowledge, the oldest gonococcal collection globally.

Methods: Lyophilised isolates were revived and examined using Etest (18 antimicrobials) and whole-genome sequencing (WGS). Quality-assured genome sequences were obtained for 191 viable and 40 non-viable isolates and analysed with multiple phylogenomic approaches.

Results: Gonococcal AMR, including an accumulation of multiple AMR determinants, started to emerge particularly in the 1950s-1970s. By the twenty-first century, resistance to most antimicrobials was common. Despite that some AMR determinants affect many physiological functions and fitness, AMR determinants were mainly selected by the use/misuse of gonorrhoea therapeutic antimicrobials. Most AMR developed in strains belonging to one multidrug-resistant (MDR) clade with close to three times higher genomic mutation rate. Modern N. gonorrhoeae was inferred to have emerged in the late-1500s and its genome became increasingly conserved over time.

Conclusions: WGS of gonococci from 1928 to 2013 showed that no AMR determinants, except penB, were in detectable frequency before the introduction of gonorrhoea therapeutic antimicrobials. The modern gonococcus is substantially younger than previously hypothesized and has been evolving into a more clonal species, driven by the use/misuse of antimicrobials. The MDR gonococcal clade should be further investigated for early detection of strains with predispositions to develop and maintain MDR and for initiation of public health interventions.
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http://dx.doi.org/10.1186/s12864-020-6511-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6998845PMC
February 2020
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