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Belman S, Pesonen H, Croucher NJ, Bentley SD, Corander J. Estimating between-country migration in pneumococcal populations. G3 (BETHESDA, MD.) 2024; 14:jkae058. [PMID: 38507601 PMCID: PMC11152062 DOI: 10.1093/g3journal/jkae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a globally distributed, human obligate opportunistic bacterial pathogen which, although often carried commensally, is also a significant cause of invasive disease. Apart from multi-drug resistant and virulent clones, the rate and direction of pneumococcal dissemination between different countries remains largely unknown. The ability for the pneumococcus to take a foothold in a country depends on existing population configuration, the extent of vaccine implementation, as well as human mobility since it is a human obligate bacterium. To shed light on its international movement, we used extensive genome data from the Global Pneumococcal Sequencing project and estimated migration parameters between multiple countries in Africa. Data on allele frequencies of polymorphisms at housekeeping-like loci for multiple different lineages circulating in the populations of South Africa, Malawi, Kenya, and The Gambia were used to calculate the fixation index (Fst) between countries. We then further used these summaries to fit migration coalescent models with the likelihood-free inference algorithms available in the ELFI software package. Synthetic datawere additionally used to validate the inference approach. Our results demonstrate country-pair specific migration patterns and heterogeneity in the extent of migration between different lineages. Our approach demonstrates that coalescent models can be effectively used for inferring migration rates for bacterial species and lineages provided sufficiently granular population genomics surveillance data. Further, it can demonstrate the connectivity of respiratory disease agents between countries to inform intervention policy in the longer term.
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Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Henri Pesonen
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, 0372, Norway
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London W12 0BZ, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, 0372, Norway
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Espoo, Helsinki, 02150, Finland
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2
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Kwun MJ, Ion AV, Oggioni MR, Bentley S, Croucher N. Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants of Streptococcus pneumoniae. Nucleic Acids Res 2023; 51:10375-10394. [PMID: 37757859 PMCID: PMC10602874 DOI: 10.1093/nar/gkad760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Despite enabling Streptococcus pneumoniae to acquire antibiotic resistance and evade vaccine-induced immunity, transformation occurs at variable rates across pneumococci. Phase variants of isolate RMV7, distinguished by altered methylation patterns driven by the translocating variable restriction-modification (tvr) locus, differed significantly in their transformation efficiencies and biofilm thicknesses. These differences were replicated when the corresponding tvr alleles were introduced into an RMV7 derivative lacking the locus. RNA-seq identified differential expression of the type 1 pilus, causing the variation in biofilm formation, and inhibition of competence induction in the less transformable variant, RMV7domi. This was partly attributable to RMV7domi's lower expression of ManLMN, which promoted competence induction through importing N-acetylglucosamine. This effect was potentiated by analogues of some proteobacterial competence regulatory machinery. Additionally, one of RMV7domi's phage-related chromosomal island was relatively active, which inhibited transformation by increasing expression of the stress response proteins ClpP and HrcA. However, HrcA increased competence induction in the other variant, with its effects depending on Ca2+ supplementation and heat shock. Hence the heterogeneity in transformation efficiency likely reflects the diverse signalling pathways by which it is affected. This regulatory complexity will modulate population-wide responses to synchronising quorum sensing signals to produce co-ordinated yet stochastic bet hedging behaviour.
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Affiliation(s)
- Min Jung Kwun
- MRC Centre for Global Infectious Disease Analysis, Sir Michael Uren Hub, White City Campus, Imperial College London, London W12 0BZ, UK
| | - Alexandru V Ion
- MRC Centre for Global Infectious Disease Analysis, Sir Michael Uren Hub, White City Campus, Imperial College London, London W12 0BZ, UK
| | - Marco R Oggioni
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Stephen D Bentley
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Sir Michael Uren Hub, White City Campus, Imperial College London, London W12 0BZ, UK
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3
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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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4
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Puzia W, Gawor J, Gromadka R, Żuchniewicz K, Wróbel-Pawelczyk I, Ronkiewicz P, Gołębiewska A, Hryniewicz W, Sadowy E, Skoczyńska A. Highly Resistant Serotype 19A Streptococcus pneumoniae of the GPSC1/CC320 Clone from Invasive Infections in Poland Prior to Antipneumococcal Vaccination of Children. Infect Dis Ther 2023; 12:2017-2037. [PMID: 37442903 PMCID: PMC10505132 DOI: 10.1007/s40121-023-00842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
INTRODUCTION The introduction of pneumococcal conjugate vaccines (PCV) into the national immunization programs (NIPs) has significantly reduced the number of pneumococcal infections. However, infections caused by isolates of non-vaccine serotypes (NVT) started spreading shortly thereafter and strains of NVT 19A have become the main cause of invasive pneumococcal disease burden worldwide. The aim of the study was to characterize serotype 19A invasive pneumococci of GPSC1/CC320 circulating in Poland before the introduction of PCV into the Polish NIP in 2017 and to compare them to isolates from other countries where PCVs were implemented much earlier than in Poland. METHODS All the GPSC1/CC320 isolates were analyzed by serotyping, susceptibility testing, and whole genome sequencing followed by analyses of resistome, virulome, and core genome multilocus sequence typing (cgMLST), including comparative analysis with isolates with publicly accessible genomic sequences (PubMLST). RESULTS During continuous surveillance the NRCBM collected 4237 invasive Streptococcus pneumoniae isolates between 1997 and 2016, including 200 isolates (4.7%) of serotype 19A. The most prevalent among 19A pneumococci were highly resistant representatives of Global Pneumococcal Sequence Cluster 1/Clonal Complex 320, GPSC1/CC320 (n = 97, 48.5%). Isolates of GPSC1/CC320 belonged to three sequence types (STs): ST320 (75.2%) ST4768 (23.7%), and ST15047 (1.0%), which all represented the 19A-III cps subtype and had complete loci for both PI-1 and PI-2 pili types. On the basis of the cgMLST analysis the majority of Polish GPSC1/CC320 isolates formed a group clearly distinct from pneumococci of this clone observed in other countries. CONCLUSION Before introduction of PCV in the Polish NIP we noticed an unexpected increase of serotype 19A in invasive pneumococcal infections, with the most common being representatives of highly drug-resistant GPSC1/CC320 clone, rarely identified in Europe both before and even after PCV introduction.
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Affiliation(s)
- Weronika Puzia
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Karolina Żuchniewicz
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106, Warsaw, Poland
| | - Izabela Wróbel-Pawelczyk
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Patrycja Ronkiewicz
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Agnieszka Gołębiewska
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Reference Centre for Bacterial Meningitis, National Medicines Institute, Chełmska 30/34 Str., 00-725, Warsaw, Poland.
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Kwun MJ, Ion AV, Cheng HC, D’Aeth JC, Dougan S, Oggioni MR, Goulding DA, Bentley SD, Croucher NJ. Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA. Genome Med 2022; 14:144. [PMID: 36539881 PMCID: PMC9764711 DOI: 10.1186/s13073-022-01147-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- Min Jung Kwun
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London, W12 0BZ UK
| | - Alexandru V. Ion
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London, W12 0BZ UK
| | - Hsueh-Chien Cheng
- grid.10306.340000 0004 0606 5382Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Joshua C. D’Aeth
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London, W12 0BZ UK
| | - Sam Dougan
- grid.10306.340000 0004 0606 5382Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Marco R. Oggioni
- grid.9918.90000 0004 1936 8411Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH UK ,grid.6292.f0000 0004 1757 1758Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - David A. Goulding
- grid.10306.340000 0004 0606 5382Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Stephen D. Bentley
- grid.10306.340000 0004 0606 5382Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Nicholas J. Croucher
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London, W12 0BZ UK
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6
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Marini S, Mora RA, Boucher C, Robertson Noyes N, Prosperi M. Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. Brief Bioinform 2022; 23:bbac020. [PMID: 35212354 PMCID: PMC8921637 DOI: 10.1093/bib/bbac020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 01/13/2023] Open
Abstract
Antimicrobial resistance (AMR) is a growing threat to public health and farming at large. In clinical and veterinary practice, timely characterization of the antibiotic susceptibility profile of bacterial infections is a crucial step in optimizing treatment. High-throughput sequencing is a promising option for clinical point-of-care and ecological surveillance, opening the opportunity to develop genotyping-based AMR determination as a possibly faster alternative to phenotypic testing. In the present work, we compare the performance of state-of-the-art methods for detection of AMR using high-throughput sequencing data from clinical settings. We consider five computational approaches based on alignment (AMRPlusPlus), deep learning (DeepARG), k-mer genomic signatures (KARGA, ResFinder) or hidden Markov models (Meta-MARC). We use an extensive collection of 585 isolates with available AMR resistance profiles determined by phenotypic tests across nine antibiotic classes. We show how the prediction landscape of AMR classifiers is highly heterogeneous, with balanced accuracy varying from 0.40 to 0.92. Although some algorithms-ResFinder, KARGA and AMRPlusPlus-exhibit overall better balanced accuracy than others, the high per-AMR-class variance and related findings suggest that: (1) all algorithms might be subject to sampling bias both in data repositories used for training and experimental/clinical settings; and (2) a portion of clinical samples might contain uncharacterized AMR genes that the algorithms-mostly trained on known AMR genes-fail to generalize upon. These results lead us to formulate practical advice for software configuration and application, and give suggestions for future study designs to further develop AMR prediction tools from proof-of-concept to bedside.
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Affiliation(s)
- Simone Marini
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Rodrigo A Mora
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA
| | - Noelle Robertson Noyes
- Department of Veterinary Population Medicine, University of Minnesota, Gainesville, FL, USA
| | - Mattia Prosperi
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
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Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C, Frost SDW, Corander J, Croucher NJ, Turner P, Bentley SD. Pneumococcal within-host diversity during colonization, transmission and treatment. Nat Microbiol 2022; 7:1791-1804. [PMID: 36216891 PMCID: PMC9613479 DOI: 10.1038/s41564-022-01238-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]
Abstract
Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child's life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.
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Affiliation(s)
- Gerry Tonkin-Hill
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway
| | - Clare Ling
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chrispin Chaguza
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.47100.320000000419368710Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Susannah J. Salter
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pattaraporn Hinfonthong
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Elissavet Nikolaou
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK ,grid.1058.c0000 0000 9442 535XInfection and Immunity, Murdoch Children’s Research Institute, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria Australia
| | - Natalie Tate
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Claudia Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Claire Chewapreecha
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.10223.320000 0004 1937 0490Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Simon D. W. Frost
- grid.419815.00000 0001 2181 3404Microsoft Research, Redmond, WA USA ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Nicholas J. Croucher
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Paul Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Stephen D. Bentley
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
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8
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Martín-Galiano AJ, García E. Streptococcus pneumoniae: a Plethora of Temperate Bacteriophages With a Role in Host Genome Rearrangement. Front Cell Infect Microbiol 2021; 11:775402. [PMID: 34869076 PMCID: PMC8637289 DOI: 10.3389/fcimb.2021.775402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/29/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria. They are the most abundant biological entity on Earth (current estimates suggest there to be perhaps 1031 particles) and are found nearly everywhere. Temperate phages can integrate into the chromosome of their host, and prophages have been found in abundance in sequenced bacterial genomes. Prophages may modulate the virulence of their host in different ways, e.g., by the secretion of phage-encoded toxins or by mediating bacterial infectivity. Some 70% of Streptococcus pneumoniae (the pneumococcus)—a frequent cause of otitis media, pneumonia, bacteremia and meningitis—isolates harbor one or more prophages. In the present study, over 4000 S. pneumoniae genomes were examined for the presence of prophages, and nearly 90% were found to contain at least one prophage, either defective (47%) or present in full (43%). More than 7000 complete putative integrases, either of the tyrosine (6243) or serine (957) families, and 1210 full-sized endolysins (among them 1180 enzymes corresponding to 318 amino acid-long N-acetylmuramoyl-L-alanine amidases [LytAPPH]) were found. Based on their integration site, 26 different pneumococcal prophage groups were documented. Prophages coding for tRNAs, putative virulence factors and different methyltransferases were also detected. The members of one group of diverse prophages (PPH090) were found to integrate into the 3’ end of the host lytASpn gene encoding the major S. pneumoniae autolysin without disrupting it. The great similarity of the lytASpnand lytAPPH genes (85–92% identity) allowed them to recombine, via an apparent integrase-independent mechanism, to produce different DNA rearrangements within the pneumococcal chromosome. This study provides a complete dataset that can be used to further analyze pneumococcal prophages, their evolutionary relationships, and their role in the pathogenesis of pneumococcal disease.
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Affiliation(s)
- Antonio J Martín-Galiano
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
| | - Ernesto García
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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9
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D'Aeth JC, van der Linden MPG, McGee L, de Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sá-Leão R, Ko KS, Hanage WP, Breiman RF, Beall B, Bentley SD, Croucher NJ. The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci. eLife 2021; 10:e67113. [PMID: 34259624 PMCID: PMC8321556 DOI: 10.7554/elife.67113] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
Multidrug-resistant Streptococcus pneumoniae 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 S. pneumoniae 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 Tn916-type and Tn1207.1-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 Tn1207.1-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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Affiliation(s)
- Joshua C D'Aeth
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Mark PG van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital RWTH AachenAachenGermany
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller UniversityNew YorkUnited States
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Jae-Hoon Song
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - Stephanie W Lo
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Rebecca A Gladstone
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory UniversityAtlantaUnited States
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Stephen D Bentley
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
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10
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Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. THE ISME JOURNAL 2021; 15:1523-1538. [PMID: 33408365 PMCID: PMC8115253 DOI: 10.1038/s41396-020-00867-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
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Affiliation(s)
- Gabrielle L Harrow
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Caroline Colijn
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK.
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11
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Lunde TM, Hjerde E, Al-Haroni M. Prevalence, diversity and transferability of the Tn 916-Tn 1545 family ICE in oral streptococci. J Oral Microbiol 2021; 13:1896874. [PMID: 33796228 PMCID: PMC7971310 DOI: 10.1080/20002297.2021.1896874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: The Tn916-Tn1545 family of Integrative Conjugative Elements (ICE) are mobile genetic elements (MGEs) that play a role in the spread of antibiotic resistance genes. The Tn916 harbors the tetracycline resistance gene tet(M) and it has been reported in various bacterial species. The increase in the levels of tetracycline resistance among oral streptococci is of great concern primarily due to the abundance of these species in the oral cavity and their ability to act as reservoirs for antibiotic resistance genes.Methods: In the current study, we screened 100 Norwegian clinical oral streptococcal isolates for the presence and diversity of the Tn916-Tn1545 family. In addition, we investigated the transferability the elements, and the associated transfer frequencies.Results: We observed that 21 isolates harboured the Tn916-Tn1545 family and that two of these elements were the novel Tn6815 and Tn6816. The most prevalent member of the Tn916 -Tn1545 family observed in the Norwegian clinical oral streptococcal isolates was the wild type Tn916.Conclusion: The detection of other members of this family of ICE and varying transfer frequencies suggests high versatility of the Tn916 element in oral streptococci in Norway.
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Affiliation(s)
- Tracy Munthali Lunde
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø
| | - Erik Hjerde
- bCenter for Bioinformatics, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø
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12
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Hanachi M, Kiran A, Cornick J, Harigua-Souiai E, Everett D, Benkahla A, Souiai O. Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13. Bioinform Biol Insights 2020; 14:1177932220962106. [PMID: 33088176 PMCID: PMC7545519 DOI: 10.1177/1177932220962106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Streptococcus pneumoniae serotype 1 is a common cause of global invasive pneumococcal disease. In New Caledonia, serotype 1 is the most prevalent serotype and led to two major outbreaks reported in the 2000s. The pneumococcal conjugate vaccine 13 (PCV13) was introduced into the vaccination routine, intending to prevent the expansion of serotype 1 in New Caledonia. Aiming to provide a baseline for monitoring the post-PCV13 changes, we performed a whole-genome sequence analysis on 67 serotype 1 isolates collected prior to the PCV13 introduction. To highlight the S. pneumoniae serotype 1 population structure, we performed a multilocus sequence typing (MLST) analysis revealing that NC serotype 1 consisted of 2 sequence types: ST3717 and the highly dominant ST306. Both sequence types harbored the same resistance genes to beta-lactams, macrolide, streptogramin B, fluoroquinolone, and lincosamide antibiotics. We have also identified 36 virulence genes that were ubiquitous to all the isolates. Among these virulence genes, the pneumolysin sequence presented an allelic profile associated with disease outbreaks and reduced hemolytic activity. Moreover, recombination hotspots were identified in 4 virulence genes and more notably in the cps locus (cps2L), potentially leading to capsular switching, a major mechanism of the emergence of nonvaccine types. In summary, this study represents the first overview of the genomic characteristics of S. pneumoniae serotype 1 in New Caledonia prior to the introduction of PCV13. This preliminary description represents a baseline to assess the impact of PCV13 on serotype 1 population structure and genomic diversity.
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Affiliation(s)
- Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Faculty of Science of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Anmol Kiran
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Departement of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology-LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Dean Everett
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Institut Supérieur des Technologies Médicales de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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13
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Spanelova P, Jakubu V, Malisova L, Musilek M, Kozakova J, Papagiannitsis CC, Bitar I, Hrabak J, Pantosti A, Del Grosso M, Zemlickova H. Whole genome sequencing of macrolide resistant Streptococcus pneumoniae serotype 19A sequence type 416. BMC Microbiol 2020; 20:224. [PMID: 32711478 PMCID: PMC7382794 DOI: 10.1186/s12866-020-01909-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/16/2020] [Indexed: 01/27/2023] Open
Abstract
Background The resistance of Streptococcus pneumoniae to macrolides is becoming an increasingly important issue and thus it is important to understand the genetics related to adaptation of this species to the widespread use of antibiotics in Europe. The 58 isolates of S. pneumoniae belonging to sequence type (ST) 416 and serotype 19A and to several different phenotypes originated from Italy, Portugal and Czech Republic were thus sequenced on Illumina MiSeq. The aim of the study was to describe genetical origine of isolates, investigate their macrolide resistance and suggest reasons for spread of ST416 in the Czech Republic. Results Investigation of genes associated with serotype determined serotype switch between 15B and 19A serotypes and core genome multilocus sequence typing (cgMLST) confirmed the origine of concerned isolates in Netherlands15B-37 clone. Inspected genomes proved variability of genes associated with the macrolide resistance even within closely genetically relative isolates. Conclusions Participation of 19A/ST416 on the spread of Netherlands15B-37 is accompanied by serotype switch between 19A and 15B serotypes and with acquisition of genes involved in macrolide resistance to the clone that was originally macrolide susceptible. There is evident tendency to interchanging and modifications of these and surrounding genes, that could lead to accelerate spreading of this sequence type in regions with high macrolide consumption.
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Affiliation(s)
- Petra Spanelova
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic.
| | - Vladislav Jakubu
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic.,Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - Lucia Malisova
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Martin Musilek
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Jana Kozakova
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | - Ibrahim Bitar
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czech Republic
| | - Jaroslav Hrabak
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czech Republic
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Del Grosso
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Helena Zemlickova
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic.,Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic.,Department of Laboratory Medicine, Third Faculty of Medicine, Charles University and Kralovske Vinohrady University Hospital, Prague, Czech Republic
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14
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Characterization of Bacteriophage Peptides of Pathogenic Streptococcus by LC-ESI-MS/MS: Bacteriophage Phylogenomics and Their Relationship to Their Host. Front Microbiol 2020; 11:1241. [PMID: 32582130 PMCID: PMC7296060 DOI: 10.3389/fmicb.2020.01241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023] Open
Abstract
The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2,546 non-redundant peptides belonging to 1,890 proteins were identified and analyzed. Among them, 65 phage-origin peptides were determined as specific Streptococcus spp. peptides. These peptides belong to proteins such as phage repressors, phage endopeptidases, structural phage proteins, and uncharacterized phage proteins. Studies involving bacteriophage phylogeny and the relationship between phages encoding the peptides determined and the bacteria they infect were also performed. The results show how specific peptides are present in closely related phages, and a link exists between bacteriophage phylogeny and the Streptococcus spp. they infect. Moreover, the phage peptide M∗ATNLGQAYVQIM∗PSAK is unique and specific for Streptococcus agalactiae. These results revealed that diagnostic peptides, among others, could be useful for the identification and characterization of mastitis-causing Streptococcus spp., particularly peptides that belong to specific functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Jose L. R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
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15
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Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. SCIENCE ADVANCES 2020; 6:eaaz6137. [PMID: 32671212 PMCID: PMC7314567 DOI: 10.1126/sciadv.aaz6137] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
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 Streptococcus pneumoniae. 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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Affiliation(s)
- Sonja Lehtinen
- Big Data Institute, University of Oxford, Oxford, UK
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Claire Chewapreecha
- Wellcome Sanger Institute, Hinxton, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - John Lees
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nicholas J. Croucher
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Rafał J. Mostowy
- Big Data Institute, University of Oxford, Oxford, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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16
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Gladstone RA, Lo SW, Goater R, Yeats C, Taylor B, Hadfield J, Lees JA, Croucher NJ, van Tonder AJ, Bentley LJ, Quah FX, Blaschke AJ, Pershing NL, Byington CL, Balaji V, Hryniewicz W, Sigauque B, Ravikumar K, Almeida SCG, Ochoa TJ, Ho PL, du Plessis M, Ndlangisa KM, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Pollard AJ, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, Metcalf BJ, Li Y, Beall BW, McGee L, Breiman RF, Aanensen DM, Bentley SD. Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. Microb Genom 2020; 6:e000357. [PMID: 32375991 PMCID: PMC7371119 DOI: 10.1099/mgen.0.000357] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
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 (tet, erm, cat) 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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Affiliation(s)
| | - Stephanie W. Lo
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Richard Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Corin Yeats
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Ben Taylor
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John A. Lees
- Faculty of Medicine, School of Public Health, Imperial College London, UK
| | | | - Andries J. van Tonder
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Leon J. Bentley
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Fu Xiang Quah
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Anne J. Blaschke
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Nicole L. Pershing
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | | | - Waleria Hryniewicz
- National Medicines Institute, Division of Clinical Microbiology and Infection Prevention, Warsaw, Poland
| | - Betuel Sigauque
- Fundação Manhiça / Centro de Investigação em Saúde da Manhiça (CISM), Maputo Mozambique, Instituto Nacional de Saúde, inistério de Saúde, Maputo, Mozambique
| | - K.L. Ravikumar
- Central Research Laboratory, Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Center, Bangalore, India
| | | | - Theresa J. Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Kedibone M. Ndlangisa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel
| | - Susan A. Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel
| | | | - Anne von Gottberg
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | | | - Yuan Li
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F. Breiman
- Rollins School Public Health, Emory University, GA, USA
- Emory Global Health Institute, Atlanta, GA, USA
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
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17
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McDougall S, Clausen L, Ha HJ, Gibson I, Bryan M, Hadjirin N, Lay E, Raisen C, Ba X, Restif O, Parkhill J, Holmes MA. Mechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases. Vet Microbiol 2020; 242:108592. [PMID: 32122596 DOI: 10.1016/j.vetmic.2020.108592] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 01/12/2020] [Accepted: 01/21/2020] [Indexed: 11/24/2022]
Abstract
A number of veterinary clinical pathology laboratories in New Zealand have been reporting emergence of increased minimum in inhibitory concentrations for β-lactams in the common clinical bovine mastitis pathogen Streptococcus uberis. The objective of this study was to determine the genetic basis of this increase in MIC for β-lactams amongst S. uberis. Illumina sequencing and determination of oxacillin MIC was performed on 265 clinical isolates. Published sequences of the five penicillin binding proteins pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x were used to identify, extract and align these sequences from the study isolates. Amino acid substitutions resulting from single nucleotide polymorphisms (SNP) within these genes were analysed for associations with elevated (≥ 0.5 mg/L) oxacillin MIC together with a genome wide association study. The population structure of the study isolates was approximated using a phylogenetic tree generated from an alignment of the core genome. A total of 53 % of isolates had MIC ≥ 0.5 mg/L for oxacillin. A total of 101 substitutions within the five pbp were identified, of which 11 were statistically associated with an MIC ≥ 0.5 mg/L. All 140 isolates which exhibited an increased β-lactam MIC had SNPs leading to pbp2x E381K and Q554E substitutions. The phylogenetic tree indicated that the genotype and phenotype associated with the increased MIC for oxacillin were present in several different lineages suggesting that acquisition of this increased β-lactam MIC had occurred in multiple geographically distinct regions. Reanalysis of the data from the intervention studies from which the isolates were originally drawn found a tendency for the pbp2x E381K substitution to be associated with lower cure rates. It is concluded that there is geographically and genetically widespread presence of pbp substitutions associated with reduced susceptibility to β-lactam antimicrobials. Additionally, presence of pbp substitutions tended to be associated with poorer cure rate outcomes following antimicrobial therapy for clinical mastitis.
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Affiliation(s)
| | | | - Hye-Jeong Ha
- Animal Health Laboratory, Ministry for Primary Industry, Upper Hutt, New Zealand
| | - Isobel Gibson
- New Zealand Veterinary Pathology, Hamilton, New Zealand
| | | | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Elizabeth Lay
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
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18
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Colijn C, Corander J, Croucher NJ. Designing ecologically optimized pneumococcal vaccines using population genomics. Nat Microbiol 2020; 5:473-485. [PMID: 32015499 PMCID: PMC7614922 DOI: 10.1038/s41564-019-0651-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a common nasopharyngeal commensal that can cause invasive pneumococcal disease (IPD). Each component of current protein-polysaccharide conjugate vaccines (PCVs) generally induces immunity specific to one of the approximately 100 pneumococcal serotypes, and typically eliminates it from carriage and IPD through herd immunity. Overall carriage rates remain stable owing to replacement by non-PCV serotypes. Consequently, the net change in IPD incidence is determined by the relative invasiveness of the pre- and post-PCV-carried pneumococcal populations. In the present study, we identified PCVs expected to minimize the post-vaccine IPD burden by applying Bayesian optimization to an ecological model of serotype replacement that integrated epidemiological and genomic data. We compared optimal formulations for reducing infant-only or population-wide IPD, and identified potential benefits to including non-conserved pneumococcal carrier proteins. Vaccines were also devised to minimize IPD resistant to antibiotic treatment, despite the ecological model assuming that resistance levels in the carried population would be preserved. We found that expanding infant-administered PCV valency is likely to result in diminishing returns, and that complementary pairs of infant- and adult-administered vaccines could be a superior strategy. PCV performance was highly dependent on the circulating pneumococcal population, further highlighting the advantages of a diversity of anti-pneumococcal vaccination strategies.
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Affiliation(s)
- Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
- Department of Mathematics, Imperial College London, London, UK.
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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19
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Functional and Structural Roles of the Major Facilitator Superfamily Bacterial Multidrug Efflux Pumps. Microorganisms 2020; 8:microorganisms8020266. [PMID: 32079127 PMCID: PMC7074785 DOI: 10.3390/microorganisms8020266] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogenic microorganisms that are multidrug-resistant can pose severe clinical and public health concerns. In particular, bacterial multidrug efflux transporters of the major facilitator superfamily constitute a notable group of drug resistance mechanisms primarily because multidrug-resistant pathogens can become refractory to antimicrobial agents, thus resulting in potentially untreatable bacterial infections. The major facilitator superfamily is composed of thousands of solute transporters that are related in terms of their phylogenetic relationships, primary amino acid sequences, two- and three-dimensional structures, modes of energization (passive and secondary active), and in their mechanisms of solute and ion translocation across the membrane. The major facilitator superfamily is also composed of numerous families and sub-families of homologous transporters that are conserved across all living taxa, from bacteria to humans. Members of this superfamily share several classes of highly conserved amino acid sequence motifs that play essential mechanistic roles during transport. The structural and functional importance of multidrug efflux pumps that belong to the major facilitator family and that are harbored by Gram-negative and -positive bacterial pathogens are considered here.
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20
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Whole-Genome-Sequence-Based Characterization of Extensively Drug-Resistant Acinetobacter baumannii Hospital Outbreak. mSphere 2020; 5:5/1/e00934-19. [PMID: 31941816 PMCID: PMC6968657 DOI: 10.1128/msphere.00934-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) has been implicated in hospital outbreaks worldwide. Here, we present a whole-genome-based investigation of an extensively drug-resistant CRAB outbreak rapidly spreading and causing high incidences of mortality at numerous wards of a large tertiary hospital in Lebanon. This is the first study of its kind in the region. Two circulating clones were identified using a combination of molecular typing approaches, short- and long-read sequencing and Bayesian transmission network analysis. One clone carried blaOXA-23 on Tn2006 (ST-1305, ST-195, and ST-218), and another carried blaOXA-72 on a pMAL-1 plasmid (ST-502 and ST-2059, a new ST). A pMAL-2 plasmid was circulating between the two clones. The approaches implemented in this study and the obtained findings facilitate the tracking of outbreak scenarios in Lebanon and the region at large. Carbapenem-resistant Acinetobacter baumannii (CRAB) is an important opportunistic pathogen linked to a variety of nosocomial infections and hospital outbreaks worldwide. This study aimed at investigating and characterizing a CRAB outbreak at a large tertiary hospital in Lebanon. A total of 41 isolates were collected and analyzed using pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing (WGS) was performed on all the isolates, and long-read PacBio sequencing was used to generate reference genomes. The multilocus sequence types (MLST), repertoire of resistance genes, and virulence factors were determined from the sequencing data. The plasmid content was analyzed both in silico and using the A. baumannii PCR-based replicon typing (AB-PBRT) method. Genome analysis initially revealed two clones, one carrying blaOXA-23 on Tn2006 (ST-1305, ST-195, and ST-218) and another carrying blaOXA-72 on pMAL-1 (ST-502 and ST-2059, a new ST), with the latter having two subclones, as revealed using the Bayesian transmission network. All isolates were extensively drug resistant (XDR). WGS analysis revealed the transmission pathways and demonstrated the diversity of CRAB isolates and mobile genetic elements in this health care setting. Outbreak detection using WGS and immediate implementation of infection control measures contribute to restraining the spread and decreasing mortality. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii (CRAB) has been implicated in hospital outbreaks worldwide. Here, we present a whole-genome-based investigation of an extensively drug-resistant CRAB outbreak rapidly spreading and causing high incidences of mortality at numerous wards of a large tertiary hospital in Lebanon. This is the first study of its kind in the region. Two circulating clones were identified using a combination of molecular typing approaches, short- and long-read sequencing and Bayesian transmission network analysis. One clone carried blaOXA-23 on Tn2006 (ST-1305, ST-195, and ST-218), and another carried blaOXA-72 on a pMAL-1 plasmid (ST-502 and ST-2059, a new ST). A pMAL-2 plasmid was circulating between the two clones. The approaches implemented in this study and the obtained findings facilitate the tracking of outbreak scenarios in Lebanon and the region at large.
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21
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Dewé TCM, D'Aeth JC, Croucher NJ. Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae. Microb Genom 2019; 5. [PMID: 31609685 PMCID: PMC6861860 DOI: 10.1099/mgen.0.000305] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Penicillin-non-susceptible Streptococcus pneumoniae (PNSP) were first detected in the 1960s, and are now common worldwide, predominantly through the international spread of a limited number of strains. Extant PNSP are characterized by mosaic pbp2x, pbp2b and pbp1a genes generated by interspecies recombinations, with the extent of these alterations determining the range and concentrations of β-lactams to which the genotype is non-susceptible. The complexity of the genetics underlying these phenotypes has been the subject of both molecular microbiology and genome-wide association and epistasis analyses. Such studies can aid our understanding of PNSP evolution and help improve the already highly-performing bioinformatic methods capable of identifying PNSP from genomic surveillance data.
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Affiliation(s)
- Tamsin C M Dewé
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Joshua C D'Aeth
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
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22
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Kwun MJ, Oggioni MR, Bentley SD, Fraser C, Croucher NJ. Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae. Genes (Basel) 2019; 10:genes10090707. [PMID: 31540216 PMCID: PMC6771155 DOI: 10.3390/genes10090707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 01/02/2023] Open
Abstract
A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the transformation machinery has been proposed to limit vertical transmission of chromosomally integrated MGEs. This work describes how these mechanisms can act in concert. Experimental data demonstrate RMS phase variation occurs at a sub-maximal rate. Simulations suggest this may be optimal if MGEs are sometimes vertically inherited, as it reduces the probability that an infected cell will switch between RMS variants while the MGE is invading the population, and thereby undermine the restriction barrier. Such vertically inherited MGEs can be deleted by transformation. The lack of between-strain transformation hotspots at known prophage att sites suggests transformation cannot remove an MGE from a strain in which it is fixed. However, simulations confirmed that transformation was nevertheless effective at preventing the spread of MGEs into a previously uninfected cell population, if a recombination barrier existed between co-colonising strains. Further simulations combining these effects of phase variable RMSs and transformation found they synergistically inhibited MGEs spreading, through limiting both vertical and horizontal transmission.
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Affiliation(s)
- Min Jung Kwun
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London W2 1PG, UK.
| | - Marco R Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
| | - Stephen D Bentley
- Pathogens and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK.
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London W2 1PG, UK.
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23
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Blanquart F, Lehtinen S, Lipsitch M, Fraser C. The evolution of antibiotic resistance in a structured host population. J R Soc Interface 2019; 15:rsif.2018.0040. [PMID: 29925579 PMCID: PMC6030642 DOI: 10.1098/rsif.2018.0040] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/29/2018] [Indexed: 11/12/2022] Open
Abstract
The evolution of antibiotic resistance in opportunistic pathogens such as Streptococcus pneumoniae, Escherichia coli or Staphylococcus aureus is a major public health problem, as infection with resistant strains leads to prolonged hospital stay and increased risk of death. Here, we develop a new model of the evolution of antibiotic resistance in a commensal bacterial population adapting to a heterogeneous host population composed of untreated and treated hosts, and structured in different host classes with different antibiotic use. Examples of host classes include age groups and geographic locations. Explicitly modelling the antibiotic treatment reveals that the emergence of a resistant strain is favoured by more frequent but shorter antibiotic courses, and by higher transmission rates. In addition, in a structured host population, localized transmission in host classes promotes both local adaptation of the bacterial population and the global maintenance of coexistence between sensitive and resistant strains. When transmission rates are heterogeneous across host classes, resistant strains evolve more readily in core groups of transmission. These findings have implications for the better management of antibiotic resistance: reducing the rate at which individuals receive antibiotics is more effective to reduce resistance than reducing the duration of treatment. Reducing the rate of treatment in a targeted class of the host population allows greater reduction in resistance, but determining which class to target is difficult in practice.
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Affiliation(s)
- François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France .,IAME, UMR 1137, INSERM, Université Paris Diderot, Site Xavier Bichat, Paris, France.,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sonja Lehtinen
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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24
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Jia H, Chen Y, Wang J, Xie X, Ruan Z. Emerging challenges of whole-genome-sequencing-powered epidemiological surveillance of globally distributed clonal groups of bacterial infections, giving Acinetobacter baumannii ST195 as an example. Int J Med Microbiol 2019; 309:151339. [PMID: 31451388 DOI: 10.1016/j.ijmm.2019.151339] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/05/2019] [Accepted: 08/18/2019] [Indexed: 10/26/2022] Open
Abstract
Whole-genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. However, it is still unexpectedly demanding to employ WGS for global epidemiological surveillance because of the high degree of similarity between the genomes of intercontinental isolates. The aim of this study was to utilize genomically derived bioinformatics analysis to identify globally distributed A. baumannii ST195 lineage and differentiation outbreaks to address this issue. The genomic sequences and their related epidemiological metadata of 2850 A. baumannii isolates were recruited from NCBI Genbank database. Assignment into sequence type (Oxford scheme) and lineage (global clone 2/CC92) were performed. A total of 91 ST195 A. baumannii isolates were subsequently classified to perform the bacterial source tracking analysis by implementing both core genome MLST (cgMLST) and core genome SNP (cgSNP) strategy that were integrated in our recently updated BacWGSTdb 2.0 server. Antibiotic resistance genes were identified using the ResFinder database. The ST195 A. baumannii isolates distributed widely in eight countries and harboured multiple antimicrobial resistance genes simultaneously. In most cases, the bacterial isolates recovered from geographically distant sources may present less genomic sequence similarity, i.e., the phylogenetic relationship between these ST195 isolates worldwide was roughly congruent with their country of isolation. However, a few isolates collected from distant geographic regions were revealed to possess smaller genetic distances (less than 8 loci or 20 SNPs) than the threshold without an observable epidemiological link. Our study highlights the emerging challenges entailed in the WGS-powered epidemiological surveillance of globally distributed clonal groups. Standardization is urgently required before WGS can be routinely applied to infectious diseases outbreak investigations.
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Affiliation(s)
- Huiqiong Jia
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Yan Chen
- Department of General Practice, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310018, China
| | - Jianfeng Wang
- Department of Respiratory Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310015, China
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
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25
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Baek JY, Kim SH, Kang CI, Chung DR, Peck KR, Ko KS, Song JH. Genome characterization of an extensively drug-resistant Streptococcus pneumoniae serotype 11A strain. Microbiol Immunol 2019; 63:206-212. [PMID: 31081554 DOI: 10.1111/1348-0421.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/18/2019] [Accepted: 05/01/2019] [Indexed: 11/27/2022]
Abstract
In this study, the whole genome sequences of two Streptococcus pneumoniae clinical isolates from South Korea were determined and compared. They were found to be the same serotype (11 A) and multilocus sequence typing analysis showed that they are single-locus variants (SLVs; ST8279 and ST166) of each other, differing at one allele (aroE). However, the ST8279 strain is extensively drug-resistant (XDR) whereas the ST166 strain is not. The genome of the XDR strain is very similar in structure to that of two previously reported genomes, AP200 (11 A:ST62) and 70585 (5:ST5803); however, some regions were inverted and there were some exogenous regions in the ST8279 strain. It was found that 6,502 single nucleotide polymorphisms are dispersed across the genome between the two serotype 11 A ST8279 and ST166 strains. Many of them are located in genes associated with antibiotic resistance. In addition, many amino acid differences were also identified in genes involved in DNA repair (mutL, uvrA and uvrC) and recombination (recU, recR and recA). On the basis of these results, it was inferred that the XDR strain did not evolve from its SLV via a single recombination event involving a large portion of the genome including the aroE gene. Rather, the strain likely evolved through many point mutations and recombination events involving small portions of the genome.
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Affiliation(s)
- Jin Yang Baek
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea
| | - So Hyun Kim
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Doo Ryeon Chung
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea.,Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kwan Soo Ko
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea.,Department of Molecular Cell Biology and Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Jae-Hoon Song
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea
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26
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Castillo JA, Agathos SN. A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum. BMC Evol Biol 2019; 19:123. [PMID: 31208326 PMCID: PMC6580516 DOI: 10.1186/s12862-019-1456-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Results Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’s D, θw and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. Conclusions We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses. Electronic supplementary material The online version of this article (10.1186/s12862-019-1456-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José A Castillo
- School of Biological Sciences and Engineering, Yachay Tech University, Hacienda San Jose s/n and Proyecto Yachay, Urcuquí, Ecuador.
| | - Spiros N Agathos
- School of Biological Sciences and Engineering, Yachay Tech University, Hacienda San Jose s/n and Proyecto Yachay, Urcuquí, Ecuador
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27
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Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine 2019; 43:338-346. [PMID: 31003929 PMCID: PMC6557916 DOI: 10.1016/j.ebiom.2019.04.021] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background. METHODS Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage. FINDINGS The combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction. Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R2 = 0.27 p < .0001). In 28/35 dominant-GPSCs, the country of isolation was a significant predictor (p < .05) of its antibiogram (mean misclassification error 0.28, SD ± 0.13). We detected increased invasiveness of six genetic backgrounds, when compared to other genetic backgrounds expressing the same serotype. Up to 1.6-fold changes in invasiveness odds ratio were observed. INTERPRETATION We define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing non-vaccine-serotypes in most GPSCs preclude the removal of these lineages by pneumococcal conjugate vaccines; leaving potential for serotype replacement. A subset of GPSCs have increased resistance, and/or serotype-independent invasiveness.
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Affiliation(s)
| | - Stephanie W Lo
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - John A Lees
- New York University School of Medicine, New York, NY, USA
| | | | | | - Jukka Corander
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK; Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
| | - Andrew J Page
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Pekka Marttinen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Espoo, Finland
| | - Leon J Bentley
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Theresa J Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pak Leung Ho
- Department of Microbiology, Carol Yu Centre for Infection, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, Blantyre, Malawi
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273 Banjul, the Gambia
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Susan A Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, South Africa; Department of Science and Technology, National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, South Africa
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, South Africa; Department of Science and Technology, National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, South Africa
| | | | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273 Banjul, the Gambia; Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, USA; Emory Global Health Institute, Atlanta, USA
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28
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Blanquart F. Evolutionary epidemiology models to predict the dynamics of antibiotic resistance. Evol Appl 2019; 12:365-383. [PMID: 30828361 PMCID: PMC6383707 DOI: 10.1111/eva.12753] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
The evolution of resistance to antibiotics is a major public health problem and an example of rapid adaptation under natural selection by antibiotics. The dynamics of antibiotic resistance within and between hosts can be understood in the light of mathematical models that describe the epidemiology and evolution of the bacterial population. "Between-host" models describe the spread of resistance in the host community, and in more specific settings such as hospitalized hosts (treated by antibiotics at a high rate), or farm animals. These models make predictions on the best strategies to limit the spread of resistance, such as reducing transmission or adapting the prescription of several antibiotics. Models can be fitted to epidemiological data in the context of intensive care units or hospitals to predict the impact of interventions on resistance. It has proven harder to explain the dynamics of resistance in the community at large, in particular because models often do not reproduce the observed coexistence of drug-sensitive and drug-resistant strains. "Within-host" models describe the evolution of resistance within the treated host. They show that the risk of resistance emergence is maximal at an intermediate antibiotic dose, and some models successfully explain experimental data. New models that include the complex host population structure, the interaction between resistance-determining loci and other loci, or integrating the within- and between-host levels will allow better interpretation of epidemiological and genomic data from common pathogens and better prediction of the evolution of resistance.
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Affiliation(s)
- François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERMPSL Research UniversityParisFrance
- IAME, UMR 1137, INSERMUniversité Paris DiderotParisFrance
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29
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Abudahab K, Prada JM, Yang Z, Bentley SD, Croucher NJ, Corander J, Aanensen DM. PANINI: Pangenome Neighbour Identification for Bacterial Populations. Microb Genom 2018; 5. [PMID: 30465642 PMCID: PMC6521588 DOI: 10.1099/mgen.0.000220] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce panini (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm. panini is browser-based and integrates with the Microreact platform for rapid online visualization and exploration of both core and accessory genome evolutionary signals, together with relevant epidemiological, geographical, temporal and other metadata. Several case studies with single- and multi-clone pneumococcal populations are presented to demonstrate the ability to identify biologically important signals from gene content data. panini is available at http://panini.pathogen.watch and code at http://gitlab.com/cgps/panini.
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Affiliation(s)
- Khalil Abudahab
- 1Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Joaquín M Prada
- 2School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Zhirong Yang
- 3Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Nicholas J Croucher
- 5Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jukka Corander
- 3Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, FI-00014 Helsinki, Finland.,6Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, N-0317 Oslo, Norway
| | - David M Aanensen
- 1Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.,7Big Data Institute, Li Ka Shing Centre for Health Informatics, University of Oxford, Oxford, UK
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30
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Molecular characterisation of multidrug-resistant pneumococcal clones colonising healthy children in Mérida, Venezuela. J Glob Antimicrob Resist 2018; 14:45-50. [DOI: 10.1016/j.jgar.2018.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 11/18/2022] Open
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31
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Žemličková H, Mališová L, Španělová P, Jakubů V, Kozáková J, Musílek M, Medvecký M. Molecular characterization of serogroup 19 Streptococcus pneumoniae in the Czech Republic in the post-vaccine era. J Med Microbiol 2018; 67:1003-1011. [PMID: 29856703 PMCID: PMC6152367 DOI: 10.1099/jmm.0.000765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 05/08/2018] [Indexed: 11/18/2022] Open
Abstract
Purpose. The aim of this study was to characterize serogroup 19 isolates resistant to macrolides and/or penicillin found among pneumococci recovered from cases of invasive and respiratory tract disease in the Czech Republic in 2014.Methods. Pneumococcal isolates of serotypes 19A (n=26) and 19F (n=10) that were non-susceptible to penicillin and/or macrolides and had been collected in 2014 were analysed using multi-locus sequence typing (MLST). Four isolates representing the major clones were subjected to whole-genome sequencing (WGS).Results. The penicillin-susceptible macrolide-resistant isolates of serotype 19A were mainly associated with sequence type (ST) 416 belonging to clonal complex (CC) 199, and the penicillin-resistant isolates were of serotype 19F belonging to ST1464 (CC 320). WGS revealed the presence of pilus 1, in association with pilus 2, in serotype19F isolates belonging to CC 320. Another adhesin, pneumococcal serine-rich protein (PsrP), was only present in serotype 19A isolates of ST416. Analysis of the penicillin-binding proteins (PBPs) of serotype 19F penicillin-resistant isolates (ST1464 and ST271) performed on PBP1a, 2b and 2x identified a large number of mutations in comparison to the reference strain, R6. Both isolates contained a unique PBP profile; however, they were highly similar to PBP sequences of the Taiwan19F-14 reference strain. The Pbp2b sequences of both 19F isolates showed the lowest similarity to those of the Taiwan19F-14 strain (91 % similarity), while they were also found to be distantly related to each other (94 % similarity).Conclusions. WGS revealed specific virulence factors in antibiotic-resistant pneumococcal clones that spread rapidly in the post-vaccine era in the Czech Republic.
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Affiliation(s)
- Helena Žemličková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - Lucia Mališová
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Petra Španělová
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Vladislav Jakubů
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Jana Kozáková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Martin Musílek
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
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32
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Cowley LA, Petersen FC, Junges R, Jimson D. Jimenez M, Morrison DA, Hanage WP. Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS Genet 2018; 14:e1007410. [PMID: 29897968 PMCID: PMC6016952 DOI: 10.1371/journal.pgen.1007410] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/25/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important in the adaptation and evolution of this pathogen. While competent pneumococci are able to scavenge DNA added to laboratory cultures, large-scale transfers of multiple kb are rare under these conditions. We used whole genome sequencing (WGS) to map transfers in recombinants arising from contact of competent cells with non-competent ‘target’ cells, using strains with known genomes, distinguished by a total of ~16,000 SNPs. Experiments designed to explore the effect of environment on large scale recombination events used saturating purified donor DNA, short-term cell assemblages on Millipore filters, and mature biofilm mixed cultures. WGS of 22 recombinants for each environment mapped all SNPs that were identical between the recombinant and the donor but not the recipient. The mean recombination event size was found to be significantly larger in cell-to-cell contact cultures (4051 bp in filter assemblage and 3938 bp in biofilm co-culture versus 1815 bp with saturating DNA). Up to 5.8% of the genome was transferred, through 20 recombination events, to a single recipient, with the largest single event incorporating 29,971 bp. We also found that some recombination events are clustered, that these clusters are more likely to occur in cell-to-cell contact environments, and that they cause significantly increased linkage of genes as far apart as 60,000 bp. We conclude that pneumococcal evolution through homologous recombination is more likely to occur on a larger scale in environments that permit cell-to-cell contact. Bacteria shuffle their genes far less often than humans do and genes or traits are more directly linked with the singular bacterial parent cell rather than the two parents that are involved in sexual reproduction. However, bacteria do occasionally have sex in the form of homologous recombination by taking up external DNA and incorporating it into their genomes. This happens far less regularly than sexual reproduction happens in human generations but is a known way that bacteria undergo ‘Horizontal gene transfer’. This means that genes can be acquired without being inherited. In this study we show that this form of horizontal gene transfer is more likely to happen in certain environments over others in Streptococcus pneumoniae. In particular, we show that this is more likely to happen in environments that closely mirror the nasopharynx which is the natural habitat of S. pneumoniae.
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Affiliation(s)
- Lauren A. Cowley
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States of America
- * E-mail:
| | | | - Roger Junges
- Department of Oral Biology, University of Oslo, Oslo, Norway
| | - Med Jimson D. Jimenez
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States of America
| | - Donald A. Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States of America
| | - William P. Hanage
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States of America
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33
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Blanquart F, Lehtinen S, Fraser C. An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae. Proc Biol Sci 2017; 284:rspb.2017.0679. [PMID: 28566489 PMCID: PMC5454275 DOI: 10.1098/rspb.2017.0679] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/02/2017] [Indexed: 11/12/2022] Open
Abstract
The frequency of resistance to antibiotics in Streptococcus pneumoniae has been stable over recent decades. For example, penicillin non-susceptibility in Europe has fluctuated between 12% and 16% without any major time trend. In spite of long-term stability, resistance fluctuates over short time scales, presumably in part due to seasonal fluctuations in antibiotic prescriptions. Here, we develop a model that describes the evolution of antibiotic resistance under selection by multiple antibiotics prescribed at seasonally changing rates. This model was inspired by, and fitted to, published data on monthly antibiotics prescriptions and frequency of resistance in two communities in Israel over 5 years. Seasonal fluctuations in antibiotic usage translate into small fluctuations of the frequency of resistance around the average value. We describe these dynamics using a perturbation approach that encapsulates all ecological and evolutionary forces into a generic model, whose parameters quantify a force stabilizing the frequency of resistance around the equilibrium and the sensitivity of the population to antibiotic selection. Fitting the model to the data revealed a strong stabilizing force, typically two to five times stronger than direct selection due to antibiotics. The strong stabilizing force explains that resistance fluctuates in phase with usage, as antibiotic selection alone would result in resistance fluctuating behind usage with a lag of three months when antibiotic use is seasonal. While most antibiotics selected for increased resistance, intriguingly, cephalosporins selected for decreased resistance to penicillins and macrolides, an effect consistent in the two communities. One extra monthly prescription of cephalosporins per 1000 children decreased the frequency of penicillin-resistant strains by 1.7%. This model emerges under minimal assumptions, quantifies the forces acting on resistance and explains up to 43% of the temporal variation in resistance.
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Affiliation(s)
- François Blanquart
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sonja Lehtinen
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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34
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Miller EL, Evans BA, Cornejo OE, Roberts IS, Rozen DE. Pherotype Polymorphism in Streptococcus pneumoniae Has No Obvious Effects on Population Structure and Recombination. Genome Biol Evol 2017; 9:2546-2559. [PMID: 28992304 PMCID: PMC5629823 DOI: 10.1093/gbe/evx188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2017] [Indexed: 12/30/2022] Open
Abstract
Natural transformation in the Gram-positive pathogen Streptococcus pneumoniae occurs when cells become "competent," a state that is induced in response to high extracellular concentrations of a secreted peptide signal called competence stimulating peptide (CSP) encoded by the comC locus. Two main CSP signal types (pherotypes) are known to dominate the pherotype diversity across strains. Using 4,089 fully sequenced pneumococcal genomes, we confirm that pneumococcal populations are highly genetically structured and that there is significant variation among diverged populations in pherotype frequencies; most carry only a single pherotype. Moreover, we find that the relative frequencies of the two dominant pherotypes significantly vary within a small range across geographical sites. It has been variously proposed that pherotypes either promote genetic exchange among cells expressing the same pherotype, or conversely that they promote recombination between strains bearing different pherotypes. We attempt to distinguish these hypotheses using a bioinformatics approach by estimating recombination frequencies within and between pherotypes across 4,089 full genomes. Despite underlying population structure, we observe extensive recombination between populations; additionally, we found significantly higher (although marginal) rates of genetic exchange between strains expressing different pherotypes than among isolates carrying the same pherotype. Our results indicate that pherotypes do not restrict, and may even slightly facilitate, recombination between strains; however, these marginal effects suggest the more likely possibility that the cause of CSP polymorphism lies outside of its effects on transformation. Our results suggest that the CSP balanced polymorphism does not causally underlie population differentiation. Therefore, when strains carrying different pherotypes encounter one another during cocolonization, genetic exchange can occur without restriction.
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Affiliation(s)
- Eric L. Miller
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom
- Institute of Biology, Leiden University, The Netherlands
| | - Benjamin A. Evans
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | | | - Ian S. Roberts
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom
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35
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Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination. Mol Biol Evol 2017; 34:2537-2554. [PMID: 28595308 PMCID: PMC5850285 DOI: 10.1093/molbev/msx173] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Diversity of the polysaccharide capsule in Streptococcus pneumoniae-main surface antigen and the target of the currently used pneumococcal vaccines-constitutes a major obstacle in eliminating pneumococcal disease. Such diversity is genetically encoded by almost 100 variants of the capsule biosynthesis locus, cps. However, the evolutionary dynamics of the capsule remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an evolutionary hotspot with elevated substitution and recombination rates. These rates were a consequence of relaxed purifying selection and positive, diversifying selection acting at this locus, supporting the hypothesis that the capsule has an increased potential to generate novel diversity compared with the rest of the genome. Diversifying selection was particularly evident in the region of wzd/wze genes, which are known to regulate capsule expression and hence the bacterium's ability to cause disease. Using a novel, capsule-centered approach, we analyzed the evolutionary history of 12 major serogroups. Such analysis revealed their complex diversification scenarios, which were principally driven by recombination with other serogroups and other streptococci. Patterns of recombinational exchanges between serogroups could not be explained by serotype frequency alone, thus pointing to nonrandom associations between co-colonizing serotypes. Finally, we discovered a previously unobserved mosaic serotype 39X, which was confirmed to carry a viable and structurally novel capsule. Adding to previous discoveries of other mosaic capsules in densely sampled collections, these results emphasize the strong adaptive potential of the bacterium by its ability to generate novel antigenic diversity by recombination.
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Affiliation(s)
- Rafał J. Mostowy
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicola De Maio
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Institute for Emerging Infections, Oxford Martin School, Oxford, United Kingdom
| | - Claire Chewapreecha
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Susannah J. Salter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Turner
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - David M. Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D. Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Nuffield Department of Medicine, Li Ka Shing Centre for Health Information and Discovery, Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom
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36
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Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P. Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations. Mol Biol Evol 2017; 34:1167-1182. [PMID: 28199698 PMCID: PMC5400400 DOI: 10.1093/molbev/msx066] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared with state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analyzing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/~pemartti/fastGEAR/ (last accessed February 6, 2017).
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Affiliation(s)
- Rafal Mostowy
- Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, United Kingdom
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, United Kingdom
| | - Cheryl P Andam
- Department of Epidemiology, Harvard TH Chan School of Public Health, Center for Communicable Disease Dynamics, Boston, MA
| | - Jukka Corander
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland.,Department of Biostatistics, University of Oslo, Oslo, Norway
| | - William P Hanage
- Department of Epidemiology, Harvard TH Chan School of Public Health, Center for Communicable Disease Dynamics, Boston, MA
| | - Pekka Marttinen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland
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37
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Lees JA, Croucher NJ, Goldblatt D, Nosten F, Parkhill J, Turner C, Turner P, Bentley SD. Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLife 2017; 6:e26255. [PMID: 28742023 PMCID: PMC5576492 DOI: 10.7554/elife.26255] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/21/2017] [Indexed: 01/04/2023] Open
Abstract
Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.
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Affiliation(s)
- John A Lees
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Nicholas J Croucher
- Department of Infectious Disease EpidemiologySt. Mary’s Campus, Imperial College LondonLondonUnited Kingdom
| | - David Goldblatt
- Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Julian Parkhill
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Stephen D Bentley
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
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38
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Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM, Parkhill J, Bentley SD, Aurell E, Corander J. Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PLoS Genet 2017; 13:e1006508. [PMID: 28207813 PMCID: PMC5312804 DOI: 10.1371/journal.pgen.1006508] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/24/2016] [Indexed: 12/05/2022] Open
Abstract
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus). For pneumococcus we identified 5,199 putative epistatic interactions between 1,936 sites. Over three-quarters of the links were between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of which are critical in determining non-susceptibility to beta-lactam antibiotics. A network-based analysis found these genes were also coupled to that encoding dihydrofolate reductase, changes to which underlie trimethoprim resistance. Distinct from these antibiotic resistance genes, a large network component of 384 protein coding sequences encompassed many genes critical in basic cellular functions, while another distinct component included genes associated with virulence. The group A Streptococcus (GAS) data set population represents a clonal population with relatively little genetic variation and a high level of linkage disequilibrium across the genome. Despite this, we were able to pinpoint two RNA pseudouridine synthases, which were each strongly linked to a separate set of loci across the chromosome, representing biologically plausible targets of co-selection. The population genomic analysis method applied here identifies statistically significantly co-evolving locus pairs, potentially arising from fitness selection interdependence reflecting underlying protein-protein interactions, or genes whose product activities contribute to the same phenotype. This discovery approach greatly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for targeted experimental work. Epistatic interactions between polymorphisms in DNA are recognized as important drivers of evolution in numerous organisms. Study of epistasis in bacteria has been hampered by the lack of densely sampled population genomic data, suitable statistical models and inference algorithms sufficiently powered for extremely high-dimensional parameter spaces. We introduce the first model-based method for genome-wide epistasis analysis and use two of the largest available bacterial population genome data sets on Streptococcus pneumoniae (the pneumococcus) and Streptococcus pyogenes (group A Streptococcus) to demonstrate its potential for biological discovery. Our approach reveals interacting networks of resistance, virulence and core machinery genes in the pneumococcus, which highlights putative candidates for novel drug targets. We also discover a number of plausible targets of co-selection in S. pyogenes linked to RNA pseudouridine synthases. Our method significantly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for targeted experimental work.
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Affiliation(s)
- Marcin J Skwark
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Santeri Puranen
- Department of Computer Science, Aalto University, Espoo, Finland
| | | | - Maiju Pesonen
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Ying Ying Xu
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon R Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Stephen B Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, United States of America
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, United States of America.,Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Erik Aurell
- Department of Computational Biology, KTH-Royal Institute of Technology, Stockholm, Sweden.,Departments of Applied Physics and Computer Science, Aalto University, Espoo, Finland.,Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Jukka Corander
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.,Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,Department of Biostatistics, University of Oslo, Oslo, Norway.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening. Proc Natl Acad Sci U S A 2017; 114:E357-E366. [PMID: 28053228 DOI: 10.1073/pnas.1613937114] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Characterizing the immune response to pneumococcal proteins is critical in understanding this bacterium's epidemiology and vaccinology. Probing a custom-designed proteome microarray with sera from 35 healthy US adults revealed a continuous distribution of IgG affinities for 2,190 potential antigens from the species-wide pangenome. Reproducibly elevated IgG binding was elicited by 208 "antibody binding targets" (ABTs), which included 109 variants of the diverse pneumococcal surface proteins A and C (PspA and PspC) and zinc metalloprotease A and B (ZmpA and ZmpB) proteins. Functional analysis found ABTs were enriched in motifs for secretion and cell surface association, with extensive representation of cell wall synthesis machinery, adhesins, transporter solute-binding proteins, and degradative enzymes. ABTs were associated with stronger evidence for evolving under positive selection, although this varied between functional categories, as did rates of diversification through recombination. Particularly rapid variation was observed at some immunogenic accessory loci, including a phage protein and a phase-variable glycosyltransferase ubiquitous among the diverse set of genomic islands encoding the serine-rich PsrP glycoprotein. Nevertheless, many antigens were conserved in the core genome, and strains' antigenic profiles were generally stable. No strong evidence was found for any epistasis between antigens driving population dynamics, or redundancy between functionally similar accessory ABTs, or age stratification of antigen profiles. These results highlight the paradox of why substantial variation is observed in only a subset of epitopes. This result may indicate only some interactions between immunoglobulins and ABTs clear pneumococcal colonization or that acquired immunity to pneumococci is an accumulation of individually weak responses to ABTs evolving under different levels of functional constraint.
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Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD. Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infect Dis 2016; 16:649. [PMID: 27821148 PMCID: PMC5100261 DOI: 10.1186/s12879-016-1987-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/30/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. METHODS We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. RESULTS Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1's rarity in carriage and consequently its lower recombination rates. CONCLUSIONS The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates.
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Affiliation(s)
- Chrispin Chaguza
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Jennifer E. Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Simon R. Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Cheryl P. Andam
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Massachusetts, MA 02115 USA
| | - Laura Bricio-Moreno
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - Feyruz Yalcin
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Sani Ousmane
- Unité de Biologie, Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Shanil Govindpersad
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Madikay Senghore
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
| | - Chinelo Ebruke
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Mignon Du Plessis
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Anmol M. Kiran
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia GA 30329 USA
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Bill and Melinda Gates Foundation, Seattle, WA 98109 USA
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Jean-Marc Collard
- Unité de Biologie, Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Martin Antonio
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert S. Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - William P. Hanage
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Massachusetts, MA 02115 USA
| | - Dean B. Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Stephen D. Bentley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
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Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013. J Clin Microbiol 2016; 54:1326-34. [PMID: 26962082 PMCID: PMC4844715 DOI: 10.1128/jcm.00055-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/25/2016] [Indexed: 12/25/2022] Open
Abstract
Serotype 1 is an important cause of invasive pneumococcal disease in South Africa and has declined following the introduction of the 13-valent pneumococcal conjugate vaccine in 2011. We genetically characterized 912 invasive serotype 1 isolates from 1989 to 2013. Simpson's diversity index (D) and recombination ratios were calculated. Factors associated with sequence types (STs) were assessed. Clonal complex 217 represented 96% (872/912) of the sampled isolates. Following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), ST diversity increased in children <5 years (D, 0.39 to 0.63, P = 0.002) and individuals >14 years (D, 0.35 to 0.54, P < 0.001): ST-217 declined proportionately in children <5 years (153/203 [75%] versus 21/37 [57%], P = 0.027) and individuals >14 years (242/305 [79%] versus 96/148 [65%], P = 0.001), whereas ST-9067 increased (4/684 [0.6%] versus 24/228 [11%], P < 0.001). Three subclades were identified within ST-217: ST-217C1 (353/382 [92%]), ST-217C2 (15/382 [4%]), and ST-217C3 (14/382 [4%]). ST-217C2, ST-217C3, and single-locus variant (SLV) ST-8314 (20/912 [2%]) were associated with nonsusceptibility to chloramphenicol, tetracycline, and co-trimoxazole. ST-8314 (20/912 [2%]) was also associated with increased nonsusceptibility to penicillin (P < 0.001). ST-217C3 and newly reported ST-9067 had higher recombination ratios than those of ST-217C1 (4.344 versus 0.091, P < 0.001; and 0.086 versus 0.013, P < 0.001, respectively). Increases in genetic diversity were noted post-PCV13, and lineages associated with antimicrobial nonsusceptibility were identified.
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42
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Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser C. Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict. PLoS Biol 2016; 14:e1002394. [PMID: 26934590 PMCID: PMC4774983 DOI: 10.1371/journal.pbio.1002394] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/29/2016] [Indexed: 01/21/2023] Open
Abstract
Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated.
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Affiliation(s)
- Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Rafal Mostowy
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Christopher Wymant
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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Lapierre M, Blin C, Lambert A, Achaz G, Rocha EPC. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography. Mol Biol Evol 2016; 33:1711-25. [PMID: 26931140 PMCID: PMC4915353 DOI: 10.1093/molbev/msw048] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present.
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Affiliation(s)
- Marguerite Lapierre
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Camille Blin
- Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, Paris Cedex05, France Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
| | - Amaury Lambert
- Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France UPMC Univ Paris 06, Laboratoire de Probabilités et Modèles Aléatoires (LPMA), CNRS UMR 7599, Paris, France
| | - Guillaume Achaz
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
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Coordinated Bacteriocin Expression and Competence in Streptococcus pneumoniae Contributes to Genetic Adaptation through Neighbor Predation. PLoS Pathog 2016; 12:e1005413. [PMID: 26840124 PMCID: PMC4739721 DOI: 10.1371/journal.ppat.1005413] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/04/2016] [Indexed: 02/03/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) has remained a persistent cause of invasive and mucosal disease in humans despite the widespread use of antibiotics and vaccines. The resilience of this organism is due to its capacity for adaptation through the uptake and incorporation of new genetic material from the surrounding microbial community. DNA uptake and recombination is controlled by a tightly regulated quorum sensing system that is triggered by the extracellular accumulation of competence stimulating peptide (CSP). In this study, we demonstrate that CSP can stimulate the production of a diverse array of blp bacteriocins. This cross stimulation occurs through increased production and secretion of the bacteriocin pheromone, BlpC, and requires a functional competence regulatory system. We show that a highly conserved motif in the promoter of the operon encoding BlpC and its transporter mediates the upregulation by CSP. The accumulation of BlpC following CSP stimulation results in augmented activation of the entire blp locus. Using biofilm-grown organisms as a model for competition and genetic exchange on the mucosal surface, we demonstrate that DNA exchange is enhanced by bacteriocin secretion suggesting that co-stimulation of bacteriocins with competence provides an adaptive advantage. The blp and com regulatory pathways are believed to have diverged and specialized in a remote ancestor of pneumococcus. Despite this, the two systems have maintained a regulatory connection that promotes competition and adaptation by targeting for lysis a wide array of potential competitors while simultaneously providing the means for incorporation of their DNA.
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Bentley SD, Parkhill J. Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 2015; 282:20150488. [PMID: 26702036 PMCID: PMC4707741 DOI: 10.1098/rspb.2015.0488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens.
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Affiliation(s)
- Stephen D Bentley
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Park YD, Williamson PR. Masking the Pathogen: Evolutionary Strategies of Fungi and Their Bacterial Counterparts. J Fungi (Basel) 2015; 1:397-421. [PMID: 29376918 PMCID: PMC5753132 DOI: 10.3390/jof1030397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 11/21/2022] Open
Abstract
Pathogens reduce immune recognition of their cell surfaces using a variety of inert structural polysaccharides. For example, capsular polysaccharides play critical roles in microbial survival strategies. Capsules are widely distributed among bacterial species, but relatively rare in eukaryotic microorganisms, where they have evolved considerable complexity in structure and regulation and are exemplified by that of the HIV/AIDS-related fungus Cryptococcus neoformans. Endemic fungi that affect normal hosts such as Histoplasma capsulatum and Blastomyces dermatitidis have also evolved protective polysaccharide coverings in the form of immunologically inert α-(1,3)-glucan polysaccharides to protect their more immunogenic β-(1,3)-glucan-containing cell walls. In this review we provide a comparative update on bacterial and fungal capsular structures and immunogenic properties as well as the polysaccharide masking strategies of endemic fungal pathogens.
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Affiliation(s)
- Yoon-Dong Park
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Building 10, Rm 11N222, MSC 1888, Bethesda, MD 20892, USA.
| | - Peter R Williamson
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Building 10, Rm 11N222, MSC 1888, Bethesda, MD 20892, USA.
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47
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Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. Sci Data 2015; 2:150058. [PMID: 26528397 PMCID: PMC4622223 DOI: 10.1038/sdata.2015.58] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/28/2015] [Indexed: 11/08/2022] Open
Abstract
Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency of asymptomatic carriage, through altering the bacterial population structure. These changes can be studied in detail through using genome sequencing to characterise systematically-sampled collections of carried S. pneumoniae. This dataset consists of 616 annotated draft genomes of isolates collected from children during routine visits to primary care physicians in Massachusetts between 2001, shortly after the seven valent polysaccharide conjugate vaccine was introduced, and 2007. Also made available are a core genome alignment and phylogeny describing the overall population structure, clusters of orthologous protein sequences, software for inferring serotype from Illumina reads, and whole genome alignments for the analysis of closely-related sets of pneumococci. These data can be used to study both bacterial evolution and the epidemiology of a pathogen population under selection from vaccine-induced immunity.
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Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System. mBio 2015; 6:e00173. [PMID: 26081630 PMCID: PMC4471560 DOI: 10.1128/mbio.00173-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The human pathogen Streptococcus pneumoniae (pneumococcus) exhibits a high degree of genomic diversity and plasticity. Isolates with high genomic similarity are grouped into lineages that undergo homologous recombination at variable rates. PMEN1 is a pandemic, multidrug-resistant lineage. Heterologous gene exchange between PMEN1 and non-PMEN1 isolates is directional, with extensive gene transfer from PMEN1 strains and only modest transfer into PMEN1 strains. Restriction-modification (R-M) systems can restrict horizontal gene transfer, yet most pneumococcal strains code for either the DpnI or DpnII R-M system and neither limits homologous recombination. Our comparative genomic analysis revealed that PMEN1 isolates code for DpnIII, a third R-M system syntenic to the other Dpn systems. Characterization of DpnIII demonstrated that the endonuclease cleaves unmethylated double-stranded DNA at the tetramer sequence 5′ GATC 3′, and the cognate methylase is a C5 cytosine-specific DNA methylase. We show that DpnIII decreases the frequency of recombination under in vitro conditions, such that the number of transformants is lower for strains transformed with unmethylated DNA than in those transformed with cognately methylated DNA. Furthermore, we have identified two PMEN1 isolates where the DpnIII endonuclease is disrupted, and phylogenetic work by Croucher and colleagues suggests that these strains have accumulated genomic differences at a higher rate than other PMEN1 strains. We propose that the R-M locus is a major determinant of genetic acquisition; the resident R-M system governs the extent of genome plasticity. Pneumococcus is one of the most important community-acquired bacterial pathogens. Pneumococcal strains can develop resistance to antibiotics and to serotype vaccines by acquiring genes from other strains or species. Thus, genomic plasticity is associated with strain adaptability and pneumococcal success. PMEN1 is a widespread and multidrug-resistant highly pathogenic pneumococcal lineage, which has evolved over the past century and displays a relatively stable genome. In this study, we characterize DpnIII, a restriction-modification (R-M) system that limits recombination. DpnIII is encountered in the PMEN1 lineage, where it replaces other R-M systems that do not decrease plasticity. Our hypothesis is that this genomic region, where different pneumococcal lineages code for variable R-M systems, plays a role in the fine-tuning of the extent of genomic plasticity. It is possible that well-adapted lineages such as PMEN1 have a mechanism to increase genomic stability, rather than foster genomic plasticity.
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Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci. J Clin Microbiol 2015; 53:2271-85. [PMID: 25972423 PMCID: PMC4473186 DOI: 10.1128/jcm.00744-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/06/2015] [Indexed: 02/02/2023] Open
Abstract
The pneumococcus is a leading pathogen infecting children and adults. Safe, effective vaccines exist, and they work by inducing antibodies to the polysaccharide capsule (unique for each serotype) that surrounds the cell; however, current vaccines are limited by the fact that only a few of the nearly 100 antigenically distinct serotypes are included in the formulations. Within the serotypes, serogroup 6 pneumococci are a frequent cause of serious disease and common colonizers of the nasopharynx in children. Serotype 6E was first reported in 2004 but was thought to be rare; however, we and others have detected serotype 6E among recent pneumococcal collections. Therefore, we analyzed a diverse data set of ∼1,000 serogroup 6 genomes, assessed the prevalence and distribution of serotype 6E, analyzed the genetic diversity among serogroup 6 pneumococci, and investigated whether pneumococcal conjugate vaccine-induced serotype 6A and 6B antibodies mediate the killing of serotype 6E pneumococci. We found that 43% of all genomes were of serotype 6E, and they were recovered worldwide from healthy children and patients of all ages with pneumococcal disease. Four genetic lineages, three of which were multidrug resistant, described ∼90% of the serotype 6E pneumococci. Serological assays demonstrated that vaccine-induced serotype 6B antibodies were able to elicit killing of serotype 6E pneumococci. We also revealed three major genetic clusters of serotype 6A capsular sequences, discovered a new hybrid 6C/6E serotype, and identified 44 examples of serotype switching. Therefore, while vaccines appear to offer protection against serotype 6E, genetic variants may reduce vaccine efficacy in the longer term because of the emergence of serotypes that can evade vaccine-induced immunity.
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Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP. Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet 2015; 11:e1005095. [PMID: 25826208 PMCID: PMC4380333 DOI: 10.1371/journal.pgen.1005095] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 02/23/2015] [Indexed: 11/19/2022] Open
Abstract
Streptococcus pneumoniae isolates typically express one of over 90 immunologically distinguishable polysaccharide capsules (serotypes), which can be classified into “serogroups” based on cross-reactivity with certain antibodies. Pneumococci can alter their serotype through recombinations affecting the capsule polysaccharide synthesis (cps) locus. Twenty such “serotype switching” events were fully characterised using a collection of 616 whole genome sequences from systematic surveys of pneumococcal carriage. Eleven of these were within-serogroup switches, representing a highly significant (p < 0.0001) enrichment based on the observed serotype distribution. Whereas the recombinations resulting in between-serogroup switches all spanned the entire cps locus, some of those that caused within-serogroup switches did not. However, higher rates of within-serogroup switching could not be fully explained by either more frequent, shorter recombinations, nor by genetic linkage to genes involved in β–lactam resistance. This suggested the observed pattern was a consequence of selection for preserving serogroup. Phenotyping of strains constructed to express different serotypes in common genetic backgrounds was used to test whether genotypes were physiologically adapted to particular serogroups. These data were consistent with epistatic interactions between the cps locus and the rest of the genome that were specific to serotype, but not serogroup, meaning they were unlikely to account for the observed distribution of capsule types. Exclusion of these genetic and physiological hypotheses suggested future work should focus on alternative mechanisms, such as host immunity spanning multiple serotypes within the same serogroup, which might explain the observed pattern. Streptococcus pneumoniae is a major respiratory pathogen responsible for a high burden of morbidity and mortality worldwide. Current anti-pneumococcal vaccines target the bacterium’s polysaccharide capsule, of which at least 95 different variants (‘serotypes’) are known, which are classified into ‘serogroups’. Bacteria can change their serotype through genetic recombination, termed ‘switching’, which can allow strains to evade vaccine-induced immunity. By combining epidemiological data with whole genome sequencing, this work finds a robust and unexpected pattern of serotype switching in a sample of bacteria collected following the introduction of routine anti-pneumococcal vaccination: switching was much more likely to exchange one serotype for another within the same serogroup than expected by chance. Several hypotheses are presented and tested to explain this pattern, including limitations of genetic recombination, interactions between the genes that determine serotype and the rest of the genome, and the constraints imposed by bacterial metabolism. This provides novel information on the evolution of S. pneumoniae, particularly regarding how the bacterium might diversify as newer vaccines are introduced.
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Affiliation(s)
- Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| | - Lisa Kagedan
- Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Claudette M. Thompson
- Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jonathan A. Finkelstein
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
- Division of General Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
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