1
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Gupta S. Darwin review: the evolution of virulence in human pathogens. Proc Biol Sci 2024; 291:20232043. [PMID: 38320607 PMCID: PMC10846939 DOI: 10.1098/rspb.2023.2043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
By definition, all pathogens cause some level of harm to their hosts. If this harm occurs while the pathogen is transmitting, it can negatively affect the pathogen's fitness by shortening the duration over which transmission can occur. However, many of the factors that increase virulence (i.e. harm to host) also promote transmission, driving the pathogen population towards an optimal state of intermediate virulence. A wider spectrum of virulence may be maintained among pathogen populations which are structured into multiple discrete strains though direct resource and immune-mediated competition. These various evolutionary outcomes, and the effects of medical and public health interventions, are best understood within a framework that recognizes the complex relationship between transmission and virulence in the context of the antigenic diversity of the pathogen population.
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Affiliation(s)
- Sunetra Gupta
- Department of Biology, University of Oxford, Oxford, UK
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2
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Rafiqullah IM, Varghese R, Hellmann KT, Velmurugan A, Neeravi A, Kumar Daniel JL, Vidal JE, Kompithra RZ, Verghese VP, Veeraraghavan B, Robinson DA. Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India. Microb Genom 2024; 10:001191. [PMID: 38315173 PMCID: PMC10926699 DOI: 10.1099/mgen.0.001191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Streptococcus pneumoniae is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected characteristics were determined for 402 invasive isolates collected from children <5 years of age during routine surveillance from 1991 to 2020. Overall, the prevalence and diversity of vaccine type (VT) and non-vaccine type (NVT) isolates did not significantly change post-uptake of PCV. Individually, serotype 1 and global pneumococcal sequence cluster (GPSC or strain lineage) 2 significantly decreased, whereas serotypes 6B, 9V and 19A and GPSCs 1, 6, 10 and 23 significantly increased in proportion post-uptake of PCV. Resistance determinants to penicillin, erythromycin, co-trimoxazole, fluoroquinolones and tetracycline, and multidrug resistance significantly increased in proportion post-uptake of PCV and especially among VT isolates. Co-trimoxazole resistance determinants were common pre- and post-uptake of PCV (85 and 93 %, respectively) and experienced the highest rates of recombination in the genome. Accessory gene frequencies were seen to be changing by small amounts across the frequency spectrum specifically among VT isolates, with the largest changes linked to antimicrobial resistance determinants. In summary, these results indicate that as of 2020 this pneumococcal population was not yet approaching a PCV-induced equilibrium and they highlight changes related to antimicrobial resistance. Augmenting PCV coverage and prudent use of antimicrobials are needed to counter invasive pneumococcal disease in this region.
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Affiliation(s)
- Iftekhar M. Rafiqullah
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - K. Taylor Hellmann
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Aravind Velmurugan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | | | - Jorge E. Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rajeev Z. Kompithra
- Department of Child Health, Christian Medical College and Hospital, Vellore, India
| | - Valsan P. Verghese
- Department of Child Health, Christian Medical College and Hospital, Vellore, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
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3
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Lourenço J, McNaughton AL, Pley C, Obolski U, Gupta S, Matthews PC. Polymorphisms predicting phylogeny in hepatitis B virus. Virus Evol 2022; 9:veac116. [PMID: 36628296 PMCID: PMC9825179 DOI: 10.1093/ve/veac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/30/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B viruses (HBVs) are compact viruses with circular genomes of ∼3.2 kb in length. Four genes (HBx, Core, Surface, and Polymerase) generating seven products are encoded on overlapping reading frames. Ten HBV genotypes have been characterised (A-J), which may account for differences in transmission, outcomes of infection, and treatment response. However, HBV genotyping is rarely undertaken, and sequencing remains inaccessible in many settings. We set out to assess which amino acid (aa) sites in the HBV genome are most informative for determining genotype, using a machine learning approach based on random forest algorithms (RFA). We downloaded 5,496 genome-length HBV sequences from a public database, excluding recombinant sequences, regions with conserved indels, and genotypes I and J. Each gene was separately translated into aa, and the proteins concatenated into a single sequence (length 1,614 aa). Using RFA, we searched for aa sites predictive of genotype and assessed covariation among the sites with a mutual information-based method. We were able to discriminate confidently between genotypes A-H using ten aa sites. Half of these sites (5/10) sites were identified in Polymerase (Pol), of which 4/5 were in the spacer domain and one in reverse transcriptase. A further 4/10 sites were located in Surface protein and a single site in HBx. There were no informative sites in Core. Properties of the aa were generally not conserved between genotypes at informative sites. Among the highest co-varying pairs of sites, there were fifty-five pairs that included one of these 'top ten' sites. Overall, we have shown that RFA analysis is a powerful tool for identifying aa sites that predict the HBV lineage, with an unexpectedly high number of such sites in the spacer domain, which has conventionally been viewed as unimportant for structure or function. Our results improve ease of genotype prediction from limited regions of HBV sequences and may have future applications in understanding HBV evolution.
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Affiliation(s)
| | | | - Caitlin Pley
- Guy’s and St Thomas’ NHS Foundation Trust, Westminster Bridge Rd, London SE1 7EH, UK
| | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv 6997801, Israel,Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
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4
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Lourenço J, Daon Y, Gori A, Obolski U. Pneumococcal Competition Modulates Antibiotic Resistance in the Pre-Vaccination Era: A Modelling Study. Vaccines (Basel) 2021; 9:265. [PMID: 33809706 PMCID: PMC8002235 DOI: 10.3390/vaccines9030265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 11/30/2022] Open
Abstract
The ongoing emergence of antibiotic resistant strains and high frequencies of antibiotic resistance of Streptococcus pneumoniae poses a major public health challenge. How and which ecological and evolutionary mechanisms maintain the coexistence of antibiotic resistant and susceptible strains remains largely an open question. We developed an individual-based, stochastic model expanding on a previous pneumococci modelling framework. We explore how between- and within-host mechanisms of competition can sustain observed levels of resistance to antibiotics in the pre-vaccination era. Our framework considers that within-host competition for co-colonization between resistant and susceptible strains can arise via pre-existing immunity (immunological competition) or intrinsic fitness differences due to resistance costs (ecological competition). We find that beyond stochasticity, population structure or movement, competition at the within-host level can explain observed resistance frequencies. We compare our simulation results to pneumococcal antibiotic resistance data in the European region using approximate Bayesian computation. Our results demonstrate that ecological competition for co-colonization can explain the variation in co-existence of resistant and susceptible pneumococci observed in the pre-vaccination era. Furthermore, we show that within-host pneumococcal competition can facilitate the maintenance of resistance in the pre-vaccination era. Accounting for these competition-related components of pneumococcal dynamics can improve our understanding of drivers for the emergence and maintenance of antibiotic resistance in pneumococci.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Yair Daon
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel;
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK;
| | - Uri Obolski
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel;
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Azarian T, Martinez PP, Arnold BJ, Qiu X, Grant LR, Corander J, Fraser C, Croucher NJ, Hammitt LL, Reid R, Santosham M, Weatherholtz RC, Bentley SD, O’Brien KL, Lipsitch M, Hanage WP. Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biol 2020; 18:e3000878. [PMID: 33091022 PMCID: PMC7580979 DOI: 10.1371/journal.pbio.3000878] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022] Open
Abstract
Predicting how pathogen populations will change over time is challenging. Such has been the case with Streptococcus pneumoniae, an important human pathogen, and the pneumococcal conjugate vaccines (PCVs), which target only a fraction of the strains in the population. Here, we use the frequencies of accessory genes to predict changes in the pneumococcal population after vaccination, hypothesizing that these frequencies reflect negative frequency-dependent selection (NFDS) on the gene products. We find that the standardized predicted fitness of a strain, estimated by an NFDS-based model at the time the vaccine is introduced, enables us to predict whether the strain increases or decreases in prevalence following vaccination. Further, we are able to forecast the equilibrium post-vaccine population composition and assess the invasion capacity of emerging lineages. Overall, we provide a method for predicting the impact of an intervention on pneumococcal populations with potential application to other bacterial pathogens in which NFDS is a driving force.
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Affiliation(s)
- Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Pamela P. Martinez
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Brian J. Arnold
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Lindsay R. Grant
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jukka Corander
- Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Infection Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas J. Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Laura L. Hammitt
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Raymond Reid
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Mathuram Santosham
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Robert C. Weatherholtz
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Stephen D. Bentley
- Infection Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | | | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
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6
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Buelow E, Rico A, Gaschet M, Lourenço J, Kennedy SP, Wiest L, Ploy MC, Dagot C. Hospital discharges in urban sanitation systems: Long-term monitoring of wastewater resistome and microbiota in relationship to their eco-exposome. WATER RESEARCH X 2020; 7:100045. [PMID: 32072151 PMCID: PMC7013138 DOI: 10.1016/j.wroa.2020.100045] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/03/2020] [Accepted: 01/26/2020] [Indexed: 05/05/2023]
Abstract
Wastewaters (WW) are important sources for the dissemination of antimicrobial resistance (AMR) into the environment. Hospital WW (HWW) contain higher loads of micro-pollutants and AMR markers than urban WW (UWW). Little is known about the long-term dynamics of H and U WW and the impact of their joined treatment on the general burden of AMR. Here, we characterized the resistome, microbiota and eco-exposome signature of 126 H and U WW samples treated separately for three years, and then mixed, over one year. Multi-variate analysis and machine learning revealed a robust signature for each WW with no significant variation over time before mixing, and once mixed, both WW closely resembled Urban signatures. We demonstrated a significant impact of pharmaceuticals and surfactants on the resistome and microbiota of H and U WW. Our results present considerable targets for AMR related risk assessment of WW.
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Affiliation(s)
- Elena Buelow
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
- Corresponding author. UMR Inserm 1092, Agents Anti-Microbiens, CBRS, 1 rue du Pr Bernard Descottes, 87000, Limoges, France.
| | - Andreu Rico
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Madrid, Spain
| | - Margaux Gaschet
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - Sean P. Kennedy
- Biomics Pole, CITECH, Institut Pasteur, Paris, 75015, France
| | - Laure Wiest
- Univ Lyon, CNRS, Université Claude Bernard Lyon, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100, Villeurbanne, France
| | - Marie-Cecile Ploy
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
| | - Christophe Dagot
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
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7
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Chen Q, Wu G, Chen H, Li H, Li S, Zhang C, Pang X, Wang L, Zhao L, Shen J. Quantification of Human Oral and Fecal Streptococcus parasanguinis by Use of Quantitative Real-Time PCR Targeting the groEL Gene. Front Microbiol 2020; 10:2910. [PMID: 31921079 PMCID: PMC6933288 DOI: 10.3389/fmicb.2019.02910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/03/2019] [Indexed: 11/13/2022] Open
Abstract
Two pairs of species-specific PCR primers targeting the housekeeping groEL gene, Spa146f-Spa525r and Spa93f-Spa525r, were designed to quantify human oral and fecal Streptococcus parasanguinis. Blast analysis against reference sequences of NCBI nucleotide collection database and the Chaperonin Sequence Database showed the forward primers Spa146f and Spa93f 100% matched only with S. parasanguinis, and the in silico Simulated PCR algorithm showed both primer pairs hit only S. parasanguinis groEL gene in Chaperonin Sequence Database. The two primer pairs were respectively used to perform PCR with saliva DNA of each of 6 human subjects, and the amplicons of individual PCR reactions were cloned. The phylogenetic analysis showed cloned sequences were all affiliated to S. parasanguinis, which further validates the specificity of two primer pairs, and that individual subjects harbored multiple genotypes of S. parasanguinis in saliva. By spiking S. parasanguinis into human fecal samples, we found the quantification limit of quantitative real-time PCR (qPCR) assays for both primer pairs was 5-6 log10 groEL copies/g feces. Human fecal S. parasanguinis amounts quantified with qPCR using each of the two primer pairs correlated well with those determined with metagenomic sequencing. qPCR with either primer pair showed periodontitis patients had significantly lower level of saliva S. parasanguinis than healthy people. In both feces and saliva, the S. parasanguinis abundances quantified with two primer pairs exhibited strong and significant correlation. Our results show that the two S. parasanguinis-specific primer pairs can be used to quantify and profile human saliva and fecal S. parasanguinis.
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Affiliation(s)
- Qiurong Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyan Pang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linghua Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Shen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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8
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Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nat Commun 2019; 10:2176. [PMID: 31092817 PMCID: PMC6520353 DOI: 10.1038/s41467-019-09976-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.
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Affiliation(s)
- John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Bart Ferwerda
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Philip H C Kremer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicole E Wheeler
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- The Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Mercedes Valls Serón
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | | | - Hester J Bootsma
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Alienke J Wijmega-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Elisabeth A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Anne L Wyllie
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Aeilko H Zwinderman
- Amsterdam UMC, University of Amsterdam, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Zitta B Harboe
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, DK-2300, Denmark
| | - Lene F Lundbo
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Lisette C P G M de Groot
- Department of Human Nutrition, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Natasja M van Schoor
- Amsterdam UMC, VU University, Department of Epidemiology and Biostatistics, Amsterdam Public Health, Van der Boechorststraat 7, Amsterdam, 1007 MB, The Netherlands
| | - Nathalie van der Velde
- Amsterdam UMC, University of Amsterdam, Department of Internal Medicine, Geriatrics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Centre Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Lars H Ängquist
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospitals, The Capital Region, Copenhagen, DK-2000, Denmark
| | - Thorkild I A Sørensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Copenhagen, DK-2200, Denmark
- The Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-1014, Denmark
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Odense, DK-5000, Denmark
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Tara C Mills
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Mignon du Plessis
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Susan Nzenze
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
| | - Julian Parkhill
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Shabir Madhi
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Anne von Gottberg
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Arie van der Ende
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Infection and Immunity, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC/RIVM, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Matthijs C Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Jeffrey C Barrett
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Genomics Plc, East Road, Cambridge, CB1 1BH, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
| | - Diederik van de Beek
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
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9
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Identifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data. Sci Rep 2019; 9:4049. [PMID: 30858412 PMCID: PMC6411942 DOI: 10.1038/s41598-019-40346-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 02/04/2019] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pneumoniae, a normal commensal of the upper respiratory tract, is a major public health concern, responsible for substantial global morbidity and mortality due to pneumonia, meningitis and sepsis. Why some pneumococci invade the bloodstream or CSF (so-called invasive pneumococcal disease; IPD) is uncertain. In this study we identify genes associated with IPD. We transform whole genome sequence (WGS) data into a sequence typing scheme, while avoiding the caveat of using an arbitrary genome as a reference by substituting it with a constructed pangenome. We then employ a random forest machine-learning algorithm on the transformed data, and find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of the genes we identified as associated with IPD, we find 23 genes previously shown to be directly relevant to IPD, as well as 18 uncharacterized genes. We suggest that these uncharacterized genes identified by us are also likely to be relevant for IPD.
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10
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Reverse immunodynamics: a new method for identifying targets of protective immunity. Sci Rep 2019; 9:2164. [PMID: 30770839 PMCID: PMC6377634 DOI: 10.1038/s41598-018-37288-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Despite a dramatic increase in our ability to catalogue variation among pathogen genomes, we have made far fewer advances in using this information to identify targets of protective immunity. Epidemiological models predict that strong immune selection can cause antigenic variants to structure into genetically discordant sets of antigenic types (e.g. serotypes). A corollary of this theory is that targets of immunity may be identified by searching for non-overlapping associations of amino acids among co-circulating antigenic variants. We propose a novel population genetics methodology that combines such predictions with phylogenetic analyses to identify genetic loci (epitopes) under strong immune selection. We apply this concept to the AMA-1 protein of the malaria parasite Plasmodium falciparum and find evidence of epitopes among certain regions of low variability which could render them ideal vaccine candidates. The proposed method can be applied to a myriad of multi-strain pathogens for which vast amounts of genetic data has been collected in recent years.
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11
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Hiller NL, Sá-Leão R. Puzzling Over the Pneumococcal Pangenome. Front Microbiol 2018; 9:2580. [PMID: 30425695 PMCID: PMC6218428 DOI: 10.3389/fmicb.2018.02580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/09/2018] [Indexed: 12/11/2022] Open
Abstract
The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.
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Affiliation(s)
- N. Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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12
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Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124. [PMID: 30345391 PMCID: PMC6192448 DOI: 10.12688/wellcomeopenres.14826.1] [Citation(s) in RCA: 1477] [Impact Index Per Article: 246.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2018] [Indexed: 12/29/2022] Open
Abstract
The
PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera. Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes. Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications. The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation. Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes. There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question. In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.
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Affiliation(s)
- Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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13
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Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O’Brien KL, Hanage WP, Lipsitch M. The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS Pathog 2018; 14:e1006966. [PMID: 29617440 PMCID: PMC5902063 DOI: 10.1371/journal.ppat.1006966] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/16/2018] [Accepted: 03/09/2018] [Indexed: 11/18/2022] Open
Abstract
In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998-2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998-2000) than the preceding period (2006-2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines.
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Affiliation(s)
- Taj Azarian
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University; Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Lindsay R. Grant
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; United States of America
| | - Brian J. Arnold
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University; Cambridge, Massachusetts, United States of America
| | - Laura L. Hammitt
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; United States of America
| | - Raymond Reid
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; United States of America
| | - Mathuram Santosham
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; United States of America
| | - Robert Weatherholtz
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; United States of America
| | - Novalene Goklish
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; United States of America
| | - Claudette M. Thompson
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University; Cambridge, Massachusetts, United States of America
| | | | - Katherine L. O’Brien
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; United States of America
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University; Cambridge, Massachusetts, United States of America
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University; Cambridge, Massachusetts, United States of America
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14
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Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2018; 115:3102-3107. [PMID: 29511100 DOI: 10.1073/pnas.1718712115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The bacterial pathogen Streptococcus pneumoniae is a major public health concern, being responsible for more than 1.5 million deaths annually through pneumonia, meningitis, and septicemia. Available vaccines target only a subset of serotypes, so vaccination is often accompanied by a rise in the frequency of nonvaccine serotypes. Epidemiological studies suggest that such a change in serotype frequencies is often coupled with an increase of antibiotic resistance among nonvaccine serotypes. Building on previous multilocus models for bacterial pathogen population structure, we have developed a theoretical framework incorporating variation of serotype and antibiotic resistance to examine how their associations may be affected by vaccination. Using this framework, we find that vaccination can result in a rapid increase in the frequency of preexisting resistant variants of nonvaccine serotypes due to the removal of competition from vaccine serotypes.
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15
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Ashby B, Watkins E, Lourenço J, Gupta S, Foster KR. Competing species leave many potential niches unfilled. Nat Ecol Evol 2017; 1:1495-1501. [PMID: 28983517 PMCID: PMC5624504 DOI: 10.1038/s41559-017-0295-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Abstract
A cornerstone of biology is that coexisting species evolve to occupy separate ecological niches. Classical theory predicts that interspecific competition should lead to all potential niches being occupied, yet observational data suggest that many niches are unfilled. Here we show that theory can be reconciled with observational data by reconceptualising competition in the Hutchinsonian niche space to distinguish between substitutable and non-substitutable resources. When resources are substitutable (e.g. seeds of different size), the components of competition along the niche axes combine multiplicatively, leading to a densely packed niche space. However, when resources are non-substitutable (e.g. seeds and nest sites), we show that the components of competition combine additively. Disruptive selection therefore limits niche overlap between non-substitutable niche axes, leaving most potential niches unfilled. A key corollary is that increasing the number of niche axes may greatly increase the number of potential niches but does not necessarily increase diversity. We discuss observational data that are consistent with our model and consider implications for systems with invasive species. Our work reinforces the power of competition to drive major ecological patterns: while niche space informs on species that might exist, only a small and potentially arbitrary subset will coexist in sympatry.
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Affiliation(s)
- Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, BA2 7AY, UK
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eleanor Watkins
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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