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Weinert LA, Tucker AWD. Lessons from birth to decline of pig-adapted Salmonella. Nat Food 2024:10.1038/s43016-024-00986-z. [PMID: 38730272 DOI: 10.1038/s43016-024-00986-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Affiliation(s)
- Lucy A Weinert
- Department of Vet Medicine, University of Cambridge, Cambridge, UK.
| | - A W Dan Tucker
- Department of Vet Medicine, University of Cambridge, Cambridge, UK
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Murray GGR, Hossain ASMM, Miller EL, Bruchmann S, Balmer AJ, Matuszewska M, Herbert J, Hadjirin NF, Mugabi R, Li G, Ferrando ML, Fernandes de Oliveira IM, Nguyen T, Yen PLK, Phuc HD, Zaw Moe A, Su Wai T, Gottschalk M, Aragon V, Valentin-Weigand P, Heegaard PMH, Vrieling M, Thein Maw M, Thidar Myint H, Tun Win Y, Thi Hoa N, Bentley SD, Clavijo MJ, Wells JM, Tucker AW, Weinert LA. The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs. Proc Natl Acad Sci U S A 2023; 120:e2307773120. [PMID: 37963246 PMCID: PMC10666105 DOI: 10.1073/pnas.2307773120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023] Open
Abstract
The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.
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Affiliation(s)
- Gemma G. R. Murray
- Department of Genetics, Evolution and Environment, University College London, LondonWC1E 6BT, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | | | - Eric L. Miller
- Department of Biology, Haverford College, Haverford, PA19041
| | - Sebastian Bruchmann
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Andrew J. Balmer
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Department of Medicine, University of Cambridge, CambridgeCB2 2QQ, United Kingdom
| | - Josephine Herbert
- Centre for Enzyme Innovation, University of Portsmouth, PortsmouthPO1 2DD, United Kingdom
| | - Nazreen F. Hadjirin
- Nuffield Department of Population Health, University of Oxford, OxfordOX3 7LF, United Kingdom
| | - Robert Mugabi
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Ganwu Li
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Maria Laura Ferrando
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | | | - Thanh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phung L. K. Yen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Aung Zaw Moe
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Thiri Su Wai
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, QuébecJ2S 2M2, Canada
| | - Virginia Aragon
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Barcelona08193, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona08193, Spain
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover30559, Germany
| | - Peter M. H. Heegaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Manouk Vrieling
- Wageningen Bioveterinary Research, 8221 RALelystad, The Netherlands
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | | | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7LG, United Kingdom
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, CambridgeCB10 1RQ, United Kingdom
| | - Maria J. Clavijo
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Jerry M. Wells
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
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Matuszewska M, Dabrowska A, Murray GGR, Kett SM, Vick AJA, Banister SC, Pantoja Munoz L, Cunningham P, Welch JJ, Holmes MA, Weinert LA. Absence of Staphylococcus aureus in Wild Populations of Fish Supports a Spillover Hypothesis. Microbiol Spectr 2023; 11:e0485822. [PMID: 37341608 PMCID: PMC10434045 DOI: 10.1128/spectrum.04858-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Staphylococcus aureus is a human commensal and opportunistic pathogen that also infects other animals. In humans and livestock, where S. aureus is most studied, strains are specialized for different host species. Recent studies have also found S. aureus in diverse wild animals. However, it remains unclear whether these isolates are also specialized for their hosts or whether their presence is due to repeated spillovers from source populations. This study focuses on S. aureus in fish, testing the spillover hypothesis in two ways. First, we examined 12 S. aureus isolates obtained from the internal and external organs of a farmed fish. While all isolates were from clonal complex 45, genomic diversity indicates repeated acquisition. The presence of a φSa3 prophage containing human immune evasion genes suggests that the source was originally human. Second, we tested for S. aureus in wild fish that were isolated from likely sources. In particular, we sampled 123 brown trout and their environment at 16 sites in the remote Scottish Highlands with variable levels of exposure to humans, birds, and livestock. This screen found no S. aureus infection in any of the wild populations or their environment. Together, these results support that the presence of S. aureus in fish and aquaculture is due to spillover from humans rather than specialization. Given the trends of increasing fish consumption, a better understanding of the dynamics of S. aureus spillover in aquaculture will mitigate future risks to fish and human health. IMPORTANCE Staphylococcus aureus is a human and livestock commensal but also an important pathogen responsible for high human mortality rates and economic losses in farming. Recent studies show that S. aureus is common in wild animals, including fish. However, we do not know whether these animals are part of the normal host range of S. aureus or whether infection is due to repeated spillover events from true S. aureus hosts. Answering this question has implications for public health and conservation. We find support for the spillover hypothesis by combining genome sequencing of S. aureus isolates from farmed fish and screens for S. aureus in isolated wild populations. The results imply that fish are unlikely to be a source of novel emergent S. aureus strains but highlight the prominence of the spillover of antibiotic-resistant bacteria from humans and livestock. This may affect both future fish disease potential and the risk of human food poisoning.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alicja Dabrowska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Gemma G. R. Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, London
| | - Steve M. Kett
- Department of Natural Sciences, Middlesex University London, London, United Kingdom
| | - Andy J. A. Vick
- RAL Space (UKRI-STFC), Harwell Campus, Didcot, Oxfordshire, United Kingdom
| | - Sofie C. Banister
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Peter Cunningham
- Wester Ross Fisheries Trust, Harbour Centre, Gairloch, Wester Ross, United Kingdom
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Walsh SK, Imrie RM, Matuszewska M, Paterson GK, Weinert LA, Hadfield JD, Buckling A, Longdon B. The host phylogeny determines viral infectivity and replication across Staphylococcus host species. PLoS Pathog 2023; 19:e1011433. [PMID: 37289828 PMCID: PMC10284401 DOI: 10.1371/journal.ppat.1011433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 06/21/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023] Open
Abstract
Virus host shifts, where a virus transmits to and infects a novel host species, are a major source of emerging infectious disease. Genetic similarity between eukaryotic host species has been shown to be an important determinant of the outcome of virus host shifts, but it is unclear if this is the case for prokaryotes where anti-virus defences can be transmitted by horizontal gene transfer and evolve rapidly. Here, we measure the susceptibility of 64 strains of Staphylococcaceae bacteria (48 strains of Staphylococcus aureus and 16 non-S. aureus species spanning 2 genera) to the bacteriophage ISP, which is currently under investigation for use in phage therapy. Using three methods-plaque assays, optical density (OD) assays, and quantitative (q)PCR-we find that the host phylogeny explains a large proportion of the variation in susceptibility to ISP across the host panel. These patterns were consistent in models of only S. aureus strains and models with a single representative from each Staphylococcaceae species, suggesting that these phylogenetic effects are conserved both within and among host species. We find positive correlations between susceptibility assessed using OD and qPCR and variable correlations between plaque assays and either OD or qPCR, suggesting that plaque assays alone may be inadequate to assess host range. Furthermore, we demonstrate that the phylogenetic relationships between bacterial hosts can generally be used to predict the susceptibility of bacterial strains to phage infection when the susceptibility of closely related hosts is known, although this approach produced large prediction errors in multiple strains where phylogeny was uninformative. Together, our results demonstrate the ability of bacterial host evolutionary relatedness to explain differences in susceptibility to phage infection, with implications for the development of ISP both as a phage therapy treatment and as an experimental system for the study of virus host shifts.
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Affiliation(s)
- Sarah K. Walsh
- Centre for Ecology and Conservation; Faculty of Environment, Science, and Economy; Biosciences; University of Exeter; Cornwall; United Kingdom
- Environment and Sustainability Institute; University of Exeter; Cornwall; United Kingdom
| | - Ryan M. Imrie
- Centre for Ecology and Conservation; Faculty of Environment, Science, and Economy; Biosciences; University of Exeter; Cornwall; United Kingdom
| | - Marta Matuszewska
- Department of Medicine; University of Cambridge; Cambridge; United Kingdom
| | - Gavin K. Paterson
- Royal (Dick) School of Veterinary Studies and the Roslin Institute; University of Edinburgh;Edinburgh; United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine; University of Cambridge; Cambridge; United Kingdom
| | - Jarrod D. Hadfield
- Institute of Evolutionary Biology; The University of Edinburgh; Edinburgh; United Kingdom
| | - Angus Buckling
- Centre for Ecology and Conservation; Faculty of Environment, Science, and Economy; Biosciences; University of Exeter; Cornwall; United Kingdom
- Environment and Sustainability Institute; University of Exeter; Cornwall; United Kingdom
| | - Ben Longdon
- Centre for Ecology and Conservation; Faculty of Environment, Science, and Economy; Biosciences; University of Exeter; Cornwall; United Kingdom
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Nahar N, Tram G, Jen FEC, Phillips ZN, Weinert LA, Bossé JT, Jabbari JS, Gouil Q, Du MRM, Ritchie ME, Bowden R, Langford PR, Tucker AW, Jennings MP, Turni C, Blackall PJ, Atack JM. Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions. Nucleic Acids Res 2023; 51:3240-3260. [PMID: 36840716 PMCID: PMC10123105 DOI: 10.1093/nar/gkad091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/26/2023] Open
Abstract
Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic losses to the swine industry. Many host-adapted bacterial pathogens encode systems known as phasevarions (phase-variable regulons). Phasevarions result from variable expression of cytoplasmic DNA methyltransferases. Variable expression results in genome-wide methylation differences within a bacterial population, leading to altered expression of multiple genes via epigenetic mechanisms. Our examination of a diverse population of A. pleuropneumoniae strains determined that Type I and Type III DNA methyltransferases with the hallmarks of phase variation were present in this species. We demonstrate that phase variation is occurring in these methyltransferases, and show associations between particular Type III methyltransferase alleles and serovar. Using Pacific BioSciences Single-Molecule, Real-Time (SMRT) sequencing and Oxford Nanopore sequencing, we demonstrate the presence of the first ever characterised phase-variable, cytosine-specific Type III DNA methyltransferase. Phase variation of distinct Type III DNA methyltransferase in A. pleuropneumoniae results in the regulation of distinct phasevarions, and in multiple phenotypic differences relevant to pathobiology. Our characterisation of these newly described phasevarions in A. pleuropneumoniae will aid in the selection of stably expressed antigens, and direct and inform development of a rationally designed subunit vaccine against this major veterinary pathogen.
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Affiliation(s)
- Nusrat Nahar
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Greg Tram
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Freda E-C Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Zachary N Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Janine T Bossé
- Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Jafar S Jabbari
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Mei R M Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Rory Bowden
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.,School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
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Ba X, Matuszewska M, Kalmar L, Fan J, Zou G, Corander D, Raisen CL, Li S, Li L, Weinert LA, Tucker AW, Grant AJ, Zhou R, Holmes MA. High-Throughput Mutagenesis Reveals a Role for Antimicrobial Resistance- and Virulence-Associated Mobile Genetic Elements in Staphylococcus aureus Host Adaptation. Microbiol Spectr 2023; 11:e0421322. [PMID: 36815781 PMCID: PMC10101091 DOI: 10.1128/spectrum.04213-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex 398 (CC398) is the dominant livestock-associated (LA) MRSA lineage in European livestock and an increasing cause of difficult-to-treat human disease. LA-CC398 MRSA evolved from a diverse human-associated methicillin-sensitive population, and this transition from humans to livestock was associated with three mobile genetic elements (MGEs). In this study, we apply transposon-directed insertion site sequencing (TraDIS), a high-throughput transposon mutagenesis approach, to investigate genetic signatures that contribute to LA-CC398 causing disease in humans. We identified 26 genes associated with LA-CC398 survival in human blood and 47 genes in porcine blood. We carried out phylogenetic reconstruction on 1,180 CC398 isolates to investigate the genetic context of all identified genes. We found that all genes associated with survival in human blood were part of the CC398 core genome, while 2/47 genes essential for survival in porcine blood were located on MGEs. Gene SAPIG0966 was located on the previously identified Tn916 transposon carrying a tetracycline resistance gene, which has been shown to be stably inherited within LA-CC398. Gene SAPIG1525 was carried on a phage element, which in part, matched phiSa2wa_st1, a previously identified bacteriophage carrying the Panton-Valentine leucocidin (PVL) virulence factor. Gene deletion mutants constructed in two LA-CC398 strains confirmed that the SAPIG0966 carrying Tn916 and SAPIG1525 were important for CC398 survival in porcine blood. Our study shows that MGEs that carry antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for host adaptation. IMPORTANCE CC398 is the dominant type of methicillin-resistant Staphylococcus aureus (MRSA) in European livestock and a growing cause of human infections. Previous studies have suggested MRSA CC398 evolved from human-associated methicillin-sensitive Staphylococcus aureus and is capable of rapidly readapting to human hosts while maintaining antibiotic resistance. Using high-throughput transposon mutagenesis, our study identified 26 and 47 genes important for MRSA CC398 survival in human and porcine blood, respectively. Two of the genes important for MRSA CC398 survival in porcine blood were located on mobile genetic elements (MGEs) carrying resistance or virulence genes. Our study shows that these MGEs carrying antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for blood infection and host adaptation.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jingyan Fan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
| | - Geng Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
| | - Desirée Corander
- Department of Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Claire L. Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
- Cooperative Innovation Centre of Sustainable Pig Production, Wuhan, China
- International Research Centre for Animal Diseases (MOST), Wuhan, China
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew J. Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University College of Veterinary Medicine, Wuhan, China
- Cooperative Innovation Centre of Sustainable Pig Production, Wuhan, China
- International Research Centre for Animal Diseases (MOST), Wuhan, China
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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7
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Matuszewska M, Murray GGR, Ba X, Wood R, Holmes MA, Weinert LA. Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA. eLife 2022; 11:74819. [PMID: 35762208 PMCID: PMC9239682 DOI: 10.7554/elife.74819] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/23/2022] [Indexed: 01/11/2023] Open
Abstract
Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised. Antibiotic-resistant infections are a growing threat to human health. In 2019, these hard-to-treat infections resulted in 4.95 million deaths making them the third leading cause of death that year. Excessive use of antibiotics in humans is likely driving the emergence of drug-resistant bacteria. But there is a concern that use of antibiotics on livestock farms is also contributing. A type of bacteria traced back to livestock is a growing cause of human infections that do not respond to treatment with the antibiotic methicillin in Europe. It is called livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA). Bacteria can share genes that make them drug resistant or more deadly. These genes are often carried on mobile genetic elements that promote their movement from one bacterial cell to another. The most common type of LA-MRSA in Europe is clonal-complex 398 (CC398). It has two mobile genetic elements carrying antibiotic-resistance genes, but generally lacks a mobile genetic element that helps the bacterium escape the human immune system. Learning more about how LA-MRSA acquired these genetic changes may help scientists develop better strategies to protect the public. Matuszewska, Murray et al. analyzed the genomes of more than 1,000 samples of CC398 collected from humans, pigs and 13 other animal species in 28 countries over 27 years. They used this data to reconstruct the bacteria’s evolutionary history. Matuszewska, Murray et al. show that two mobile elements containing antibiotic resistance genes in CC398 were gained decades ago. One is more than 50 years old and was likely acquired around the time antibiotic use in livestock became common. While most CC398 in livestock do not have a mobile element that helps LA-MRSA evade the human immune system, they often gain it when they infect humans. This leads to highly drug-resistant human MRSA infections. The results of this study suggest that LA-MRSA is a serious threat to human health. The resistance of this bacterium has persisted for decades, spreading across different livestock species and different countries. These drug-resistant bacteria in livestock readily infect humans. Current efforts to reduce antibiotic use in farms may take decades to mitigate these risks. Additionally, the ban on zinc-oxide use on livestock in the European Union (coming into force June 2022) may not help reduce LA-MRSA, because the genes conferring resistance to bacteria and zinc treatment are not always linked.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rhiannon Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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8
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Murray GGR, Balmer AJ, Herbert J, Hadjirin NF, Kemp CL, Matuszewska M, Bruchmann S, Hossain ASMM, Gottschalk M, Tucker AW, Miller E, Weinert LA. Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen. PLoS Genet 2021; 17:e1009864. [PMID: 34748531 PMCID: PMC8601623 DOI: 10.1371/journal.pgen.1009864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/18/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study, we investigate two factors that are predicted to influence the mutation rate: ecology and genome size. We conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact that ecology can have on the adaptive potential of bacterial pathogens.
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Affiliation(s)
- Gemma G. R. Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Andrew J. Balmer
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Josephine Herbert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nazreen F. Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Caroline L. Kemp
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sebastian Bruchmann
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, Montréal, Canada
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eric Miller
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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9
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Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW(D, Hoa NT, Welch JJ, Weinert LA. Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biol 2021; 19:191. [PMID: 34493269 PMCID: PMC8422772 DOI: 10.1186/s12915-021-01094-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. RESULTS We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. CONCLUSIONS We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.
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Affiliation(s)
- Nazreen F. Hadjirin
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eric L. Miller
- grid.256868.70000 0001 2215 7365Microbial Ecology and Evolution Laboratory, Haverford College, Haverford, USA
| | - Gemma G. R. Murray
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Phung L. K. Yen
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thomas M. Wileman
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Juan Hernandez-Garcia
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Susanna M. Williamson
- grid.13689.350000 0004 0426 1697Department for Environment, Food and Rural Affairs (Defra), London, UK
| | - Julian Parkhill
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J. Maskell
- grid.1008.90000 0001 2179 088XChancellery, University of Melbourne, Melbourne, Australia
| | - Rui Zhou
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Nahuel Fittipaldi
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - Marcelo Gottschalk
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - A. W. ( Dan) Tucker
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ngo Thi Hoa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - John J. Welch
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, UK
| | - Lucy A. Weinert
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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10
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Murray GGR, Charlesworth J, Miller EL, Casey MJ, Lloyd CT, Gottschalk M, Tucker AW(D, Welch JJ, Weinert LA. Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence. Mol Biol Evol 2021; 38:1570-1579. [PMID: 33313861 PMCID: PMC8042751 DOI: 10.1093/molbev/msaa323] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.
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Affiliation(s)
- Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jane Charlesworth
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Eric L Miller
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Haverford College, Haverford, PA, USA
| | - Michael J Casey
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- School of Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Catrin T Lloyd
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, Montréal, QC, Canada
| | | | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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11
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Hau SJ, Luan SL, Loving CL, Nicholson TL, Wang J, Peters SE, Seilly D, Weinert LA, Langford PR, Rycroft AN, Wren BW, Maskell DJ, Tucker AW, Brockmeier SL. Evaluation of the recombinant proteins RlpB and VacJ as a vaccine for protection against Glaesserella parasuis in pigs. BMC Vet Res 2020; 16:167. [PMID: 32460764 PMCID: PMC7252510 DOI: 10.1186/s12917-020-02377-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/14/2020] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Glaesserella parasuis, the causative agent of Glӓsser's disease, is widespread in swine globally resulting in significant economic losses to the swine industry. Prevention of Glӓsser's disease in pigs has been plagued with an inability to design broadly protective vaccines, as many bacterin based platforms generate serovar or strain specific immunity. Subunit vaccines are of interest to provide protective immunity to multiple strains of G. parasuis. Selected proteins for subunit vaccination should be widespread, highly conserved, and surface exposed. RESULTS Two candidate proteins for subunit vaccination (RlpB and VacJ) against G. parasuis were identified using random mutagenesis and an in vitro organ culture system. Pigs were vaccinated with recombinant RlpB and VacJ, outer membrane proteins with important contributions to cellular function and viability. Though high antibody titers to the recombinant proteins and increased interferon-γ producing cells were found in subunit vaccinated animals, the pigs were not protected from developing systemic disease. CONCLUSIONS It appears there may be insufficient RlpB and VacJ exposed on the bacterial surface for antibody to bind, preventing high RlpB and VacJ specific antibody titers from protecting animals from G. parasuis. Additionally, this work confirms the importance of utilizing the natural host species when assessing the efficacy of vaccine candidates.
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Affiliation(s)
- Samantha J Hau
- USDA, ARS, National Animal Disease Center, 1920 Dayton Ave, Ames, IA, 50010, USA
| | - Shi-Lu Luan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Crystal L Loving
- USDA, ARS, National Animal Disease Center, 1920 Dayton Ave, Ames, IA, 50010, USA
| | - Tracy L Nicholson
- USDA, ARS, National Animal Disease Center, 1920 Dayton Ave, Ames, IA, 50010, USA
| | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - David Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Paul R Langford
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, St. Mary's Campus, London, UK
| | | | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,Current address: The University of Melbourne, Level 9, Raymond Priestley Building, Melbourne, Victoria, 3010, Australia
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Susan L Brockmeier
- USDA, ARS, National Animal Disease Center, 1920 Dayton Ave, Ames, IA, 50010, USA.
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12
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Segura M, Aragon V, Brockmeier SL, Gebhart C, de Greeff A, Kerdsin A, O’Dea MA, Okura M, Saléry M, Schultsz C, Valentin-Weigand P, Weinert LA, Wells JM, Gottschalk M. Update on Streptococcus suis Research and Prevention in the Era of Antimicrobial Restriction: 4th International Workshop on S. suis. Pathogens 2020; 9:pathogens9050374. [PMID: 32422856 PMCID: PMC7281350 DOI: 10.3390/pathogens9050374] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022] Open
Abstract
Streptococcus suis is a swine pathogen and a zoonotic agent afflicting people in close contact with infected pigs or pork meat. Sporadic cases of human infections have been reported worldwide. In addition, S. suis outbreaks emerged in Asia, making this bacterium a primary health concern in this part of the globe. In pigs, S. suis disease results in decreased performance and increased mortality, which have a significant economic impact on swine production worldwide. Facing the new regulations in preventive use of antimicrobials in livestock and lack of effective vaccines, control of S. suis infections is worrisome. Increasing and sharing of knowledge on this pathogen is of utmost importance. As such, the pathogenesis and epidemiology of the infection, antimicrobial resistance, progress on diagnosis, prevention, and control were among the topics discussed during the 4th International Workshop on Streptococcus suis (held in Montreal, Canada, June 2019). This review gathers together recent findings on this important pathogen from lectures performed by lead researchers from several countries including Australia, Canada, France, Germany, Japan, Spain, Thailand, The Netherlands, UK, and USA. Finally, policies and recommendations for the manufacture, quality control, and use of inactivated autogenous vaccines are addressed to advance this important field in veterinary medicine.
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Affiliation(s)
- Mariela Segura
- Research Group on Infectious Diseases in Production Animals and Swine and Poultry Infectious Diseases Research Centre, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC J2S 2M2, Canada
- Correspondence: (M.S.); (M.G.); Tel.: +1-450-773-8521 (ext. 0080) (M.S.); +1-450-773-8521 (ext. 8374) (M.G.)
| | - Virginia Aragon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | | | - Connie Gebhart
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA;
| | - Astrid de Greeff
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands;
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand;
| | - Mark A O’Dea
- Antimicrobial Resistance and Infectious Disease Laboratory, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia;
| | - Masatoshi Okura
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan;
| | - Mariette Saléry
- French Agency for Veterinary Medicinal Products-French Agency for food, Environmental and Occupational Health Safety (Anses-ANMV), 35302 Fougères, France;
| | - Constance Schultsz
- Department of Global Health-Amsterdam Institute for Global Health and Development and Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, 1105 BP Amsterdam, The Netherlands;
| | | | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK;
| | - Jerry M. Wells
- Host-Microbe Interactomics Group, Department Animal Sciences, Wageningen University and Research, 6709 PG Wageningen, The Netherlands;
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Marcelo Gottschalk
- Research Group on Infectious Diseases in Production Animals and Swine and Poultry Infectious Diseases Research Centre, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC J2S 2M2, Canada
- Correspondence: (M.S.); (M.G.); Tel.: +1-450-773-8521 (ext. 0080) (M.S.); +1-450-773-8521 (ext. 8374) (M.G.)
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13
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Matuszewska M, Murray GGR, Harrison EM, Holmes MA, Weinert LA. The Evolutionary Genomics of Host Specificity in Staphylococcus aureus. Trends Microbiol 2020; 28:465-477. [PMID: 31948727 DOI: 10.1016/j.tim.2019.12.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/18/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022]
Abstract
Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and epidemiological studies show that S. aureus has jumped between host species many times over its evolutionary history. These jumps have involved the dynamic gain and loss of host-specific adaptive genes, usually located on mobile genetic elements. The same functional elements are often consistently gained in jumps into a particular species. Further sampling of diverse animal species is likely to uncover an even broader host range and greater genetic diversity of S. aureus than is already known, and understanding S. aureus host specificity in these hosts will mitigate the risks of emergent human and livestock strains.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Ewan M Harrison
- Wellcome Sanger Institute, University of Cambridge, Cambridge, CB10 1SA, UK; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK; Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
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14
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Abstract
Bacterial endosymbionts are very common in terrestrial arthropods, but infection levels vary widely among populations. Experiments and within-species comparisons suggest that environmental temperature might be important in explaining this variation. To investigate the importance of temperature, at broad geographical and taxonomic scales, we extended a global database of terrestrial arthropods screened for Wolbachia and Cardinium. Our final dataset contained data from more than 117 000 arthropods (over 2500 species) screened for Wolbachia and more than 18 000 arthropods (over 800 species) screened for Cardinium, including samples from 137 different countries, with mean temperatures varying from -6.5 to 29.2°C. In insects and relatives, Cardinium infection showed a clear and consistent tendency to increase with temperature. For Wolbachia, a tendency to increase with temperature in temperate climates is counteracted by reduced prevalence in the tropics, resulting in a weak negative trend overall. We discuss the implications of these results for natural and introduced symbionts in regions affected by climate change.
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Affiliation(s)
- J Charlesworth
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - L A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - E V Araujo
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - J J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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15
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Abstract
Our understanding of the ecological and evolutionary context of novel infections is largely based on viral diseases, even though bacterial pathogens may display key differences in the processes underlying their emergence. For instance, host-shift speciation, in which the jump of a pathogen into a novel host species is followed by the specialization on that host and the loss of infectivity of previous host(s), is commonly observed in viruses, but less often in bacteria. Here, we suggest that the extent to which pathogens evolve host generalism or specialism following a jump into a novel host will depend on their level of adaptation to dealing with different environments, their rates of molecular evolution and their ability to recombine. We then explore these hypotheses using a formal model and show that the high levels of phenotypic plasticity, low rates of evolution and the ability to recombine typical of bacterial pathogens should reduce their propensity to specialize on novel hosts. Novel bacterial infections may therefore be more likely to result in transient spillovers or increased host ranges than in host shifts. Finally, consistent with our predictions, we show that, in two unusual cases of contemporary bacterial host shifts, the bacterial pathogens both have small genomes and rapid rates of substitution. Further tests are required across a greater number of emerging pathogens to assess the validity of our hypotheses. This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
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Affiliation(s)
- Camille Bonneaud
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Bram Kuijper
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
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16
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Atack JM, Weinert LA, Tucker AW, Husna AU, Wileman TM, F. Hadjirin N, Hoa NT, Parkhill J, Maskell DJ, Blackall PJ, Jennings MP. Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution. Nucleic Acids Res 2018; 46:11466-11476. [PMID: 30304532 PMCID: PMC6265453 DOI: 10.1093/nar/gky913] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 10/06/2018] [Indexed: 12/22/2022] Open
Abstract
Streptococcus suis is a major pathogen of swine, responsible for a number of chronic and acute infections, and is also emerging as a major zoonotic pathogen, particularly in South-East Asia. Our study of a diverse population of S. suis shows that this organism contains both Type I and Type III phase-variable methyltransferases. In all previous examples, phase-variation of methyltransferases results in genome wide methylation differences, and results in differential regulation of multiple genes, a system known as the phasevarion (phase-variable regulon). We hypothesized that each variant in the Type I and Type III systems encoded a methyltransferase with a unique specificity, and could therefore control a distinct phasevarion, either by recombination-driven shuffling between different specificities (Type I) or by biphasic on-off switching via simple sequence repeats (Type III). Here, we present the identification of the target specificities for each Type III allelic variant from S. suis using single-molecule, real-time methylome analysis. We demonstrate phase-variation is occurring in both Type I and Type III methyltransferases, and show a distinct association between methyltransferase type and presence, and population clades. In addition, we show that the phase-variable Type I methyltransferase was likely acquired at the origin of a highly virulent zoonotic sub-population.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Asma U Husna
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Thomas M Wileman
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Nazreen F. Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Ngo T Hoa
- Oxford University Clinical Research Unit (OUCRU), 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | | | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
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17
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Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat Ecol Evol 2018; 2:1468-1478. [PMID: 30038246 PMCID: PMC7610605 DOI: 10.1038/s41559-018-0617-0] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/25/2018] [Indexed: 01/15/2023]
Abstract
The capacity for some pathogens to jump into different host-species populations is a major threat to public health and food security. Staphylococcus aureus is a multi-host bacterial pathogen responsible for important human and livestock diseases. Here, using a population-genomic approach, we identify humans as a major hub for ancient and recent S. aureus host-switching events linked to the emergence of endemic livestock strains, and cows as the main animal reservoir for the emergence of human epidemic clones. Such host-species transitions are associated with horizontal acquisition of genetic elements from host-specific gene pools conferring traits required for survival in the new host-niche. Importantly, genes associated with antimicrobial resistance are unevenly distributed among human and animal hosts, reflecting distinct antibiotic usage practices in medicine and agriculture. In addition to gene acquisition, genetic diversification has occurred in pathways associated with nutrient acquisition, implying metabolic remodelling after a host switch in response to distinct nutrient availability. For example, S. aureus from dairy cattle exhibit enhanced utilization of lactose-a major source of carbohydrate in bovine milk. Overall, our findings highlight the influence of human activities on the multi-host ecology of a major bacterial pathogen, underpinned by horizontal gene transfer and core genome diversification.
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Affiliation(s)
- Emily J Richardson
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Rodrigo Bacigalupe
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Samantha Lycett
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Manouk Vrieling
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital and The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Menzies School of Health Research, Darwin, Australia
| | - Adebayo Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Willem van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Hinxton, UK.,Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | | | - Jukka Corander
- Wellcome Trust Sanger Institute, Hinxton, UK.,Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - J Ross Fitzgerald
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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18
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Bigot D, Dalmon A, Roy B, Hou C, Germain M, Romary M, Deng S, Diao Q, Weinert LA, Cook JM, Herniou EA, Gayral P. The discovery of Halictivirus resolves the Sinaivirus phylogeny. J Gen Virol 2017; 98:2864-2875. [DOI: 10.1099/jgv.0.000957] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Anne Dalmon
- INRA UR 406 Abeilles et environnement, Centre de recherche Provence-Alpes-Côte d'Azur, Site Agroparc, Domaine St Paul 228, Route de l'aérodrome CS40509 84914 Avignon, France
| | - Bronwen Roy
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Michèle Germain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Manon Romary
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Shuai Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Lucy A. Weinert
- Institut des Sciences de l'Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
- Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - James M. Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
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19
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Abstract
Bacteria that cause serious disease often have smaller genomes, and fewer genes, than their nonpathogenic, or less pathogenic relatives. Here, we review evidence for the generality of this association, and summarise the various reasons why the association might hold. We focus on the population genetic processes that might lead to reductive genome evolution, and show how several of these could be connected to pathogenicity. We find some evidence for most of the processes having acted in bacterial pathogens, including several different modes of genome reduction acting in the same lineage. We argue that predictable processes of genome evolution might not reflect any common underlying process.
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Affiliation(s)
- Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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20
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Hernandez-Garcia J, Wang J, Restif O, Holmes MA, Mather AE, Weinert LA, Wileman TM, Thomson JR, Langford PR, Wren BW, Rycroft A, Maskell DJ, Tucker AW. Patterns of antimicrobial resistance in Streptococcus suis isolates from pigs with or without streptococcal disease in England between 2009 and 2014. Vet Microbiol 2017; 207:117-124. [PMID: 28757010 PMCID: PMC5548070 DOI: 10.1016/j.vetmic.2017.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 12/25/2022]
Abstract
Antimicrobial resistance in Streptococcus suis, a global zoonotic pathogen of pigs, has been mostly studied only in diseased animals using surveys that have not evaluated changes over time. We compared patterns of resistance between S. suis isolates from clinical cases of disease (CC) and non-clinical case (NCC) pigs in England, collected over two discrete periods, 2009-2011 and 2013-2014. Minimum inhibitory concentrations (MIC) of 17 antimicrobials (nine classes) were determined on 405 S. suis isolates categorised by sampling period and disease association to assess changes in resistance over time and association with disease. First, isolates were characterized as resistant or susceptible using published clinical breakpoints. Second, epidemiological cut-offs (ECOFF) were derived from MIC values, and isolates classified as wild type (WT) below the ECOFF and non-wild type (NWT) above the ECOFF. Finally, isolate subsets were analysed for shifts in MIC distribution. NCC isolates were more resistant than CC isolates to cephalosporins, penams, pleuromutilins, potentiated sulphonamides and tetracyclines in both study periods. Resistance levels among CC isolates increased in 2013-2014 relative to 2009-2011 for antimicrobials including aminoglycosides, cephalosporins, fluoroquinolones, pleuromutilins, potentiated sulphonamides and tetracyclines. The prevalence of isolates categorised as NWT for five or more classes of antimicrobials was greater among NCC than CC isolates for both time periods, and increased with time. This study used standardised methods to identify significant shifts in antimicrobial resistance phenotypes of S. suis isolated from pigs in England, not only over time but also between isolates from known clinical cases or disease-free pigs.
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Affiliation(s)
- Juan Hernandez-Garcia
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Thomas M Wileman
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Jill R Thomson
- SAC Consulting: Veterinary Services, Bush State, Penicuik, EH26 0QE, Scotland, UK.
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, W2 1 PG, UK.
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Andrew Rycroft
- The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire, AL9 7TA, UK.
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
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21
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Willemse N, Howell KJ, Weinert LA, Heuvelink A, Pannekoek Y, Wagenaar JA, Smith HE, van der Ende A, Schultsz C. An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis. Sci Rep 2016; 6:28984. [PMID: 27381348 PMCID: PMC4933891 DOI: 10.1038/srep28984] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/13/2016] [Indexed: 01/03/2023] Open
Abstract
Streptococcus suis is a zoonotic swine pathogen and a major public health concern in Asia, where it emerged as an important cause of bacterial meningitis in adults. While associated with food-borne transmission in Asia, zoonotic S. suis infections are mainly occupational hazards elsewhere. To identify genomic differences that can explain zoonotic potential, we compared whole genomes of 98 S. suis isolates from human patients and pigs with invasive disease in the Netherlands, and validated our observations with 18 complete and publicly available sequences. Zoonotic isolates have smaller genomes than non-zoonotic isolates, but contain more virulence factors. We identified a zoonotic S. suis clone that diverged from a non-zoonotic clone by means of gene loss, a capsule switch, and acquisition of a two-component signalling system in the late 19th century, when foreign pig breeds were introduced. Our results indicate that zoonotic potential of S. suis results from gene loss, recombination and horizontal gene transfer events.
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Affiliation(s)
- N Willemse
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.,Department of Global Health-Amsterdam Institute for Global Health and Development, Academic Medical Center, University of Amsterdam, 1105 BM Amsterdam, The Netherlands
| | - K J Howell
- Department of Paediatrics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - L A Weinert
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - A Heuvelink
- GD Animal Health, 7400 AA Deventer, The Netherlands
| | - Y Pannekoek
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands.,Central Veterinary Institute part of Wageningen UR, 8221 RA Lelystad, The Netherlands
| | - H E Smith
- Central Veterinary Institute part of Wageningen UR, 8221 RA Lelystad, The Netherlands
| | - A van der Ende
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.,National Reference Laboratory of Bacterial Meningitis, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - C Schultsz
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.,Department of Global Health-Amsterdam Institute for Global Health and Development, Academic Medical Center, University of Amsterdam, 1105 BM Amsterdam, The Netherlands.,Oxford University Clinical Research Unit, Centre for Tropical Medicine, District 5, Ho Chi Minh City, Vietnam
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22
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Abstract
Intracellular endosymbiotic bacteria are found in many terrestrial arthropods and have a profound influence on host biology. A basic question about these symbionts is why they infect the hosts that they do, but estimating symbiont incidence (the proportion of potential host species that are actually infected) is complicated by dynamic or low prevalence infections. We develop a maximum-likelihood approach to estimating incidence, and testing hypotheses about its variation. We apply our method to a database of screens for bacterial symbionts, containing more than 3600 distinct arthropod species and more than 150 000 individual arthropods. After accounting for sampling bias, we estimate that 52% (CIs: 48-57) of arthropod species are infected with Wolbachia, 24% (CIs: 20-42) with Rickettsia and 13% (CIs: 13-55) with Cardinium. We then show that these differences stem from the significantly reduced incidence of Rickettsia and Cardinium in most hexapod orders, which might be explained by evolutionary differences in the arthropod immune response. Finally, we test the prediction that symbiont incidence should be higher in speciose host clades. But while some groups do show a trend for more infection in species-rich families, the correlations are generally weak and inconsistent. These results argue against a major role for parasitic symbionts in driving arthropod diversification.
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Affiliation(s)
- Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Eli V Araujo-Jnr
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK
| | - Muhammad Z Ahmed
- University of Florida, Institute of Food and Agricultural Sciences, Tropical Research and Education Center, 18905 SW 280th Street, Homestead, FL 33031, USA
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK
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23
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Dedeine F, Weinert LA, Bigot D, Josse T, Ballenghien M, Cahais V, Galtier N, Gayral P. Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PLoS One 2015; 10:e0145596. [PMID: 26698123 PMCID: PMC4689415 DOI: 10.1371/journal.pone.0145596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 12/07/2015] [Indexed: 01/24/2023] Open
Abstract
Termites are eusocial insects related to cockroaches that feed on lignocellulose. These insects are key species in ecosystems since they recycle a large amount of nutrients but also are pests, exerting major economic impacts. Knowledge on the molecular pathways underlying reproduction, caste differentiation or lignocellulose digestion would largely benefit from additional transcriptomic data. This study focused on transcriptomes of secondary reproductive females (nymphoid neotenics). Thirteen transcriptomes were used: 10 of Reticulitermes flavipes and R. grassei sequenced from a previous study, and two transcriptomes of R. lucifugus sequenced for the present study. After transcriptome assembly and read mapping, we examined interspecific variations of genes expressed by termites or gut microorganisms. A total of 18,323 orthologous gene clusters were detected. Functional annotation and taxonomic assignment were performed on a total of 41,287 predicted contigs in the three termite species. Between the termite species studied, functional categories of genes were comparable. Gene ontology (GO) terms analysis allowed the discovery of 9 cellulases and a total of 79 contigs potentially involved in 11 enzymatic activities used in wood metabolism. Altogether, results of this study illustrate the strong potential for the use of comparative interspecific transcriptomes, representing a complete resource for future studies including differentially expressed genes between castes or SNP analysis for population genetics.
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Affiliation(s)
- Franck Dedeine
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Lucy A. Weinert
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Marion Ballenghien
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Vincent Cahais
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
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24
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Murray GGR, Weinert LA, Rhule EL, Welch JJ. The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution? Syst Biol 2015; 65:265-79. [PMID: 26559010 PMCID: PMC4748751 DOI: 10.1093/sysbio/syv084] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/04/2015] [Indexed: 11/14/2022] Open
Abstract
Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives.
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Affiliation(s)
- Gemma G R Murray
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emma L Rhule
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
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25
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Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MTG, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ. Whole genome investigation of a divergent clade of the pathogen Streptococcus suis. Front Microbiol 2015; 6:1191. [PMID: 26583006 PMCID: PMC4631834 DOI: 10.3389/fmicb.2015.01191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/12/2015] [Indexed: 11/23/2022] Open
Abstract
Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here, we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN, and cpn60) did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70), of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further, sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.
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Affiliation(s)
- Abiyad Baig
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Kate J Howell
- Department of Paediatrics, University of Cambridge Cambridge, UK
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield Sheffield, UK
| | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | | | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Cambridge, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London London, UK
| | | | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine London, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
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26
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Bossé JT, Li Y, Atherton TG, Walker S, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Holden MTG, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR. Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae. Vet Microbiol 2015; 178:279-82. [PMID: 26049592 PMCID: PMC4503812 DOI: 10.1016/j.vetmic.2015.05.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 12/02/2022]
Abstract
First complete sequence of a floR plasmid from Actinobacillus pleuropneumoniae Extended similarity to floR plasmids in other Pasteurellaceae species Conjugal transfer between between species confirmed
The complete nucleotide sequence of a 7.7 kb mobilisable plasmid (pM3446F), isolated from a florfenicol resistant isolate of Actinobacillus pleuropneumoniae, showed extended similarity to plasmids found in other members of the Pasteurellaceae containing the floR gene as well as replication and mobilisation genes. Mobilisation into other Pasteurellaceae species confirmed that this plasmid can be transferred horizontally.
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Affiliation(s)
- Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, W2 1PG, UK.
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, W2 1PG, UK
| | - Tom G Atherton
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, W2 1PG, UK
| | - Stephanie Walker
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, W2 1PG, UK
| | - Susanna M Williamson
- Animal and Plant Health Agency (APHA) Bury St Edmunds, Rougham Hill, Bury St Edmunds, Suffolk, IP33 2RX, UK
| | - Jon Rogers
- Animal and Plant Health Agency (APHA) Bury St Edmunds, Rougham Hill, Bury St Edmunds, Suffolk, IP33 2RX, UK
| | - Roy R Chaudhuri
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Matthew T G Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Andrew N Rycroft
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, W2 1PG, UK.
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27
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Bossé JT, Li Y, Walker S, Atherton T, Fernandez Crespo R, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Oshota O, Holden MTG, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR. Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae. J Antimicrob Chemother 2015; 70:2217-22. [PMID: 25957382 PMCID: PMC4500777 DOI: 10.1093/jac/dkv121] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/05/2015] [Indexed: 11/30/2022] Open
Abstract
Objectives The objective of this study was to determine the distribution and genetic basis of trimethoprim resistance in Actinobacillus pleuropneumoniae isolates from pigs in England. Methods Clinical isolates collected between 1998 and 2011 were tested for resistance to trimethoprim and sulphonamide. The genetic basis of trimethoprim resistance was determined by shotgun WGS analysis and the subsequent isolation and sequencing of plasmids. Results A total of 16 (out of 106) A. pleuropneumoniae isolates were resistant to both trimethoprim (MIC >32 mg/L) and sulfisoxazole (MIC ≥256 mg/L), and a further 32 were resistant only to sulfisoxazole (MIC ≥256 mg/L). Genome sequence data for the trimethoprim-resistant isolates revealed the presence of the dfrA14 dihydrofolate reductase gene. The distribution of plasmid sequences in multiple contigs suggested the presence of two distinct dfrA14-containing plasmids in different isolates, which was confirmed by plasmid isolation and sequencing. Both plasmids encoded mobilization genes, the sulphonamide resistance gene sul2, as well as dfrA14 inserted into strA, a streptomycin-resistance-associated gene, although the gene order differed between the two plasmids. One of the plasmids further encoded the strB streptomycin-resistance-associated gene. Conclusions This is the first description of mobilizable plasmids conferring trimethoprim resistance in A. pleuropneumoniae and, to our knowledge, the first report of dfrA14 in any member of the Pasteurellaceae. The identification of dfrA14 conferring trimethoprim resistance in A. pleuropneumoniae isolates will facilitate PCR screens for resistance to this important antimicrobial.
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Affiliation(s)
- Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Stephanie Walker
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Tom Atherton
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Roberto Fernandez Crespo
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Susanna M Williamson
- Animal and Plant Health Agency (APHA) Bury St Edmunds, Rougham Hill, Bury St Edmunds, Suffolk IP33 2RX, UK
| | - Jon Rogers
- Animal and Plant Health Agency (APHA) Bury St Edmunds, Rougham Hill, Bury St Edmunds, Suffolk IP33 2RX, UK
| | - Roy R Chaudhuri
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Olusegun Oshota
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Matt T G Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Andrew N Rycroft
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire AL9 7TA, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London W2 1PG, UK
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Weinert LA, Depledge DP, Kundu S, Gershon AA, Nichols RA, Balloux F, Welch JJ, Breuer J. Rates of vaccine evolution show strong effects of latency: implications for varicella zoster virus epidemiology. Mol Biol Evol 2015; 32:1020-8. [PMID: 25568346 PMCID: PMC4379407 DOI: 10.1093/molbev/msu406] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Varicella-zoster virus (VZV) causes chickenpox and shingles, and is found in human populations worldwide. The lack of temporal signal in the diversity of VZV makes substitution rate estimates unreliable, which is a barrier to understanding the context of its global spread. Here, we estimate rates of evolution by studying live attenuated vaccines, which evolved in 22 vaccinated patients for known periods of time, sometimes, but not always undergoing latency. We show that the attenuated virus evolves rapidly (∼ 10(-6) substitutions/site/day), but that rates decrease dramatically when the virus undergoes latency. These data are best explained by a model in which viral populations evolve for around 13 days before becoming latent, but then undergo no replication during latency. This implies that rates of viral evolution will depend strongly on transmission patterns. Nevertheless, we show that implausibly long latency periods are required to date the most recent common ancestor of extant VZV to an "out-of-Africa" migration with humans, as has been previously suggested.
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Affiliation(s)
- Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom Department of Genetics, Evolution and Environment, UCL, London, United Kingdom
| | - Daniel P Depledge
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, UCL, London, United Kingdom
| | - Samit Kundu
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, UCL, London, United Kingdom
| | - Anne A Gershon
- Division of Infectious Disease, Columbia University Medical Centre, New York, USA
| | - Richard A Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Francois Balloux
- Department of Genetics, Evolution and Environment, UCL, London, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, UCL, London, United Kingdom
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Howell KJ, Weinert LA, Chaudhuri RR, Luan SL, Peters SE, Corander J, Harris D, Angen Ø, Aragon V, Bensaid A, Williamson SM, Parkhill J, Langford PR, Rycroft AN, Wren BW, Holden MTG, Tucker AW, Maskell DJ. The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis. BMC Genomics 2014; 15:1179. [PMID: 25539682 PMCID: PMC4532294 DOI: 10.1186/1471-2164-15-1179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/12/2014] [Indexed: 01/06/2023] Open
Abstract
Background Haemophilus parasuis is the etiologic agent of Glässer’s disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between genetics and disease outcome has been only partially established. In particular, there is weak correlation between serovar and disease phenotype. We sequenced the genomes of 212 isolates of H. parasuis and have used this to describe the pan-genome and to correlate this with clinical and carrier status, as well as with serotype. Results Recombination and population structure analyses identified five groups with very high rates of recombination, separated into two clades of H. parasuis with no signs of recombination between them. We used genome-wide association methods including discriminant analysis of principal components (DAPC) and generalised linear modelling (glm) to look for genetic determinants of this population partition, serovar and pathogenicity. We were able to identify genes from the accessory genome that were significantly associated with phenotypes such as potential serovar specific genes including capsule genes, and 48 putative virulence factors that were significantly different between the clinical and non-clinical isolates. We also show that the presence of many previously suggested virulence factors is not an appropriate marker of virulence. Conclusions These genes will inform the generation of new molecular diagnostics and vaccines, and refinement of existing typing schemes and show the importance of the accessory genome of a diverse species when investigating the relationship between genotypes and phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1179) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kate J Howell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Shi-Lu Luan
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, 00100, Finland.
| | - David Harris
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Øystein Angen
- Norwegian Veterinary Institute, N-0106, Oslo, Norway.
| | - Virginia Aragon
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, and, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain.
| | - Albert Bensaid
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, and, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain.
| | - Susanna M Williamson
- Animal Health and Veterinary Laboratories Agency (AHVLA), Rougham Hill, Bury St Edmunds, Suffolk, IP33 2RX, UK.
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Paul R Langford
- Department of Medicine, Section of Paediatrics, Imperial College London, St. Mary's Campus, London, W2 1PG, UK.
| | - Andrew N Rycroft
- The Royal Veterinary College, Hawkshead Campus, Hatfield, AL9 7TA, Hertfordshire, UK.
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Matthew T G Holden
- School of Medicine, University of St. Andrews, St Andrews, KY16 9TF, UK.
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
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Rieux A, Eriksson A, Li M, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares A, Manica A, Balloux F. Improved calibration of the human mitochondrial clock using ancient genomes. Mol Biol Evol 2014; 31:2780-92. [PMID: 25100861 PMCID: PMC4166928 DOI: 10.1093/molbev/msu222] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 ancient and modern human complete mitochondrial DNA genomes, among which 146 were generated for the purpose of this study and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same data set, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.
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Affiliation(s)
- Adrien Rieux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Sobkowiak
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Lucy A Weinert
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Vera Warmuth
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Andres Ruiz-Linares
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - François Balloux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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Abstract
Uncovering the ecological determinants of parasite host range is a central goal of comparative parasitology and infectious disease ecology. But while parasites are often distributed nonrandomly across the host phylogeny, such patterns are difficult to interpret without a genealogy for the parasite samples and without knowing what sorts of ecological dynamics might lead to what sorts of nonrandomness. We investigated inferences from comparative data, using presence/absence records from protozoan parasites of the New World monkeys. We first demonstrate several distinct types of phylogenetic signal in these data, showing, for example, that parasite species are clustered on the host tree and that closely related host species harbor similar numbers of parasite species. We then show that all of these patterns can be generated by a single, simple dynamical model, in which parasite host range changes more rapidly than host speciation/extinction and parasites preferentially colonize uninfected host species that are closely related to their existing hosts. Fitting this model to data, we then estimate its parameters. Finally, we caution that quite different ecological processes can lead to similar signatures but show how phylogenetic variation in host susceptibility can be distinguished from a tendency for parasites to colonize closely related hosts. Our new process-based analyses, which estimate meaningful parameters, should be useful for inferring the determinants of parasite host range and transmission success.
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Affiliation(s)
- David Waxman
- Centre for Computational Systems Biology, Fudan University, Shanghai 200433, People's Republic of China
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32
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Brisse S, Brehony C, Conceição T, Cubero M, Glasner C, Le Gouil M, Renvoisé A, Sheppard S, Weinert LA. Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference. Res Microbiol 2014; 165:140-53. [PMID: 24486597 PMCID: PMC7126388 DOI: 10.1016/j.resmic.2014.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sylvain Brisse
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France; CNRS, UMR3525, Paris, France.
| | - Carina Brehony
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Teresa Conceição
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Meritxell Cubero
- Microbiology Department, Hospital Universitari de Bellvitge-University of Barcelona-IDIBELL, Barcelona, Spain; CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Corinna Glasner
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Meriadeg Le Gouil
- Institut Pasteur, Environment and Infectious Risks unit, Paris, France
| | - Aurélie Renvoisé
- AP-HP, Hôpital Pitié-Salpêtrière, Bactériologie-Hygiène, F-75013, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, U1135, Centre for Immunology and Microbial Infections, team 13, F-75013, Paris, France; INSERM, U1135, Centre for Immunology and Microbial Infections, team 13, F-75013, Paris, France
| | | | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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33
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Chrostek E, Marialva MSP, Esteves SS, Weinert LA, Martinez J, Jiggins FM, Teixeira L. Wolbachia variants induce differential protection to viruses in Drosophila melanogaster: a phenotypic and phylogenomic analysis. PLoS Genet 2013; 9:e1003896. [PMID: 24348259 PMCID: PMC3861217 DOI: 10.1371/journal.pgen.1003896] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/06/2013] [Indexed: 12/22/2022] Open
Abstract
Wolbachia are intracellular bacterial symbionts that are able to protect various insect hosts from viral infections. This tripartite interaction was initially described in Drosophila melanogaster carrying wMel, its natural Wolbachia strain. wMel has been shown to be genetically polymorphic and there has been a recent change in variant frequencies in natural populations. We have compared the antiviral protection conferred by different wMel variants, their titres and influence on host longevity, in a genetically identical D. melanogaster host. The phenotypes cluster the variants into two groups--wMelCS-like and wMel-like. wMelCS-like variants give stronger protection against Drosophila C virus and Flock House virus, reach higher titres and often shorten the host lifespan. We have sequenced and assembled the genomes of these Wolbachia, and shown that the two phenotypic groups are two monophyletic groups. We have also analysed a virulent and over-replicating variant, wMelPop, which protects D. melanogaster even better than the closely related wMelCS. We have found that a ~21 kb region of the genome, encoding eight genes, is amplified seven times in wMelPop and may be the cause of its phenotypes. Our results indicate that the more protective wMelCS-like variants, which sometimes have a cost, were replaced by the less protective but more benign wMel-like variants. This has resulted in a recent reduction in virus resistance in D. melanogaster in natural populations worldwide. Our work helps to understand the natural variation in wMel and its evolutionary dynamics, and inform the use of Wolbachia in arthropod-borne disease control.
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Affiliation(s)
- Ewa Chrostek
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Julien Martinez
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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34
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Spoor LE, McAdam PR, Weinert LA, Rambaut A, Hasman H, Aarestrup FM, Kearns AM, Larsen AR, Skov RL, Fitzgerald JR. Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus. mBio 2013; 4:e00356-13. [PMID: 23943757 PMCID: PMC3747577 DOI: 10.1128/mbio.00356-13%0a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 06/14/2013] [Indexed: 11/19/2023] Open
Abstract
UNLABELLED The importance of livestock as a source of bacterial pathogens with the potential for epidemic spread in human populations is unclear. In recent years, there has been a global increase in community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections of healthy humans, but an understanding of the different evolutionary origins of CA-MRSA clones and the basis for their recent expansion is lacking. Here, using a high-resolution phylogenetic approach, we report the discovery of two emergent clones of human epidemic CA-MRSA which resulted from independent livestock-to-human host jumps by the major bovine S. aureus complex, CC97. Of note, one of the new clones was isolated from human infections on four continents, demonstrating its global dissemination since the host jump occurred over 40 years ago. The emergence of both human S. aureus clones coincided with the independent acquisition of mobile genetic elements encoding antimicrobial resistance and human-specific mediators of immune evasion, consistent with an important role for these genetic events in the capacity to survive and transmit among human populations. In conclusion, we provide evidence that livestock represent a reservoir for the emergence of new human-pathogenic S. aureus clones with the capacity for pandemic spread. These findings have major public health implications highlighting the importance of surveillance for early identification of emergent clones and improved transmission control measures at the human-livestock interface. IMPORTANCE Animals are the major source of new pathogens affecting humans. However, the potential for pathogenic bacteria that originally were found in animals to switch hosts and become widely established in human populations is not clear. Here, we report the discovery of emergent clones of methicillin-resistant Staphylococcus aureus (MRSA) that originated in livestock and switched to humans, followed by host-adaptive evolution and epidemic spread in global human populations. Our findings demonstrate that livestock can act as a reservoir for the emergence of new human bacterial clones with potential for pandemic spread, highlighting the potential role of surveillance and biosecurity measures in the agricultural setting for preventing the emergence of new human pathogens.
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Affiliation(s)
- Laura E. Spoor
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Paul R. McAdam
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Lucy A. Weinert
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Henrik Hasman
- National Food Institute, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Angela M. Kearns
- Microbiology Services, Colindale, Health Protection Agency, London, United Kingdom
| | - Anders R. Larsen
- Department of Antimicrobial Surveillance and Research, Statens Serum Institute, Copenhagen, Denmark
| | - Robert L. Skov
- Department of Antimicrobial Surveillance and Research, Statens Serum Institute, Copenhagen, Denmark
| | - J. Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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35
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Luan SL, Chaudhuri RR, Peters SE, Mayho M, Weinert LA, Crowther SA, Wang J, Langford PR, Rycroft A, Wren BW, Tucker AW, Maskell DJ. Generation of a Tn5 transposon library in Haemophilus parasuis and analysis by transposon-directed insertion-site sequencing (TraDIS). Vet Microbiol 2013; 166:558-66. [PMID: 23928120 DOI: 10.1016/j.vetmic.2013.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Haemophilus parasuis is an important respiratory tract pathogen of swine and the etiological agent of Glässer's disease. The molecular pathogenesis of H. parasuis is not well studied, mainly due to the lack of efficient tools for genetic manipulation of this bacterium. In this study we describe a Tn5-based random mutagenesis method for use in H. parasuis. A novel chloramphenicol-resistant Tn5 transposome was electroporated into the virulent H. parasuis serovar 5 strain 29755. High transposition efficiency of Tn5, up to 10(4) transformants/μg of transposon DNA, was obtained by modification of the Tn5 DNA in the H. parasuis strain HS071 and establishment of optimal electrotransformation conditions, and a library of approximately 10,500 mutants was constructed. Analysis of the library using transposon-directed insertion-site sequencing (TraDIS) revealed that the insertion of Tn5 was evenly distributed throughout the genome. 10,001 individual mutants were identified, with 1561 genes being disrupted (69.4% of the genome). This newly-developed, efficient mutagenesis approach will be a powerful tool for genetic manipulation of H. parasuis in order to study its physiology and pathogenesis.
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Affiliation(s)
- Shi-Lu Luan
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
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36
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Holden MTG, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlicková H, Coombs G, Kearns AM, Hill RLR, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramírez S, Feil EJ, Hudson LO, Enright MC, Balloux F, Aanensen DM, Spratt BG, Fitzgerald JR, Parkhill J, Achtman M, Bentley SD, Nübel U. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res 2013; 23:653-64. [PMID: 23299977 PMCID: PMC3613582 DOI: 10.1101/gr.147710.112] [Citation(s) in RCA: 334] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with health care. The most rapidly spreading and tenacious health-care-associated clone in Europe currently is EMRSA-15, which was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 subclone in the English Midlands during the mid-1980s appears to have played a key role in triggering pandemic spread, and occurred shortly after the first clinical trials of this drug. Genome-based coalescence analysis estimated that the population of this subclone over the last 20 yr has grown four times faster than its progenitor. Using comparative genomic analysis we identified the molecular genetic basis of 99.8% of the antimicrobial resistance phenotypes of the isolates, highlighting the potential of pathogen genome sequencing as a diagnostic tool. We document the genetic changes associated with adaptation to the hospital environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens.
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Affiliation(s)
- Matthew T G Holden
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB19 1SA, United Kingdom
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Weinert LA, Welch JJ, Suchard MA, Lemey P, Rambaut A, Fitzgerald JR. Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication. Biol Lett 2012; 8:829-32. [PMID: 22628096 DOI: 10.1098/rsbl.2012.0290] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Host species switches by bacterial pathogens leading to new endemic infections are important evolutionary events that are difficult to reconstruct over the long term. We investigated the host switching of Staphylococcus aureus over a long evolutionary timeframe by developing Bayesian phylogenetic methods to account for uncertainty about past host associations and using estimates of evolutionary rates from serially sampled whole-genome data. Results suggest multiple jumps back and forth between human and bovids with the first switch from humans to bovids taking place around 5500 BP, coinciding with the expansion of cattle domestication throughout the Old World. The first switch to poultry is estimated at around 275 BP, long after domestication but still preceding large-scale commercial farming. These results are consistent with a central role for anthropogenic change in the emergence of new endemic diseases.
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Farrer RA, Weinert LA, Bielby J, Garner TWJ, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, Anderson L, Pond SLK, Shahar-Golan R, Henk DA, Fisher MC. Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc Natl Acad Sci U S A 2011; 108:18732-6. [PMID: 22065772 PMCID: PMC3219125 DOI: 10.1073/pnas.1111915108] [Citation(s) in RCA: 298] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Batrachochytrium dendrobatidis (Bd) is a globally ubiquitous fungal infection that has emerged to become a primary driver of amphibian biodiversity loss. Despite widespread effort to understand the emergence of this panzootic, the origins of the infection, its patterns of global spread, and principle mode of evolution remain largely unknown. Using comparative population genomics, we discovered three deeply diverged lineages of Bd associated with amphibians. Two of these lineages were found in multiple continents and are associated with known introductions by the amphibian trade. We found that isolates belonging to one clade, the global panzootic lineage (BdGPL) have emerged across at least five continents during the 20th century and are associated with the onset of epizootics in North America, Central America, the Caribbean, Australia, and Europe. The two newly identified divergent lineages, Cape lineage (BdCAPE) and Swiss lineage (BdCH), were found to differ in morphological traits when compared against one another and BdGPL, and we show that BdGPL is hypervirulent. BdGPL uniquely bears the hallmarks of genomic recombination, manifested as extensive intergenomic phylogenetic conflict and patchily distributed heterozygosity. We postulate that contact between previously genetically isolated allopatric populations of Bd may have allowed recombination to occur, resulting in the generation, spread, and invasion of the hypervirulent BdGPL leading to contemporary disease-driven losses in amphibian biodiversity.
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Affiliation(s)
- Rhys A Farrer
- Department Infectious Disease Epidemiology, Imperial College, London W2 1PG, United Kingdom.
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Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Romero IG, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 2011; 334:94-8. [PMID: 21940856 PMCID: PMC3991479 DOI: 10.1126/science.1211177] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
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Affiliation(s)
- Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
| | - Xiaosen Guo
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Wang
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kirk E. Lohmueller
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Line Skotte
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stinus Lindgreen
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mait Metspalu
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Thibaut Jombart
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Toomas Kivisild
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Weiwei Zhai
- Beijing Institute of Genomics, Chinese Academy of Sciences, No. 7 Beitucheng West Road, Chaoyang District, Beijing 100029, China
| | - Anders Eriksson
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Silvana Tridico
- Ancient DNA Lab, School of Biological Sciences and Biotechnology, Murdoch University, Western Australia 6150, Australia
| | - Ene Metspalu
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Kasper Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - María C. Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - J. Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Undergraduate Program on Genomic Sciences, National Autonomous University of Mexico, Avenida Universidad s/n Chamilpa 62210, Cuernavaca, Morelos, Mexico
| | - Craig Muller
- Goldfields Land and Sea Council Aboriginal Corporation, 14 Throssell Street, Kalgoorlie, Western Australia 6430, Australia
| | - Joe Dortch
- Archaeology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Agata Wesolowska
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Monika Karmin
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Lucy A. Weinert
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Bo Wang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Li
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuaishuai Tai
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Fei Xiao
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0374, Japan
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, 3000 Bern 9, Switzerland
| | - Aashish R. Jha
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Université de Toulouse (Paul Sabatier)–CNRS UMR 5288, 31073 Toulouse Cedex 3, France
| | - Peter de Knijff
- Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Andrea B Migliano
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
- Department of Anthropology, University College London, London WC1E 6BT, UK
| | | | - Karsten Kristiansen
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland 4111, Australia
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Peter Forster
- Murray Edwards College, University of Cambridge, Cambridge CB3 0DF, UK
- Institute for Forensic Genetics, D-48161 Münster, Germany
| | | | - Olaf Nehlich
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Bunce
- Ancient DNA Lab, School of Biological Sciences and Biotechnology, Murdoch University, Western Australia 6150, Australia
| | - Michael Richards
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anders Krogh
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Marta M. Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Francois Balloux
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Richard Villems
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
- Estonian Academy of Sciences, 6 Kohtu Street, 10130 Tallinn, Estonia
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jun Wang
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
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Guinane CM, Ben Zakour NL, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay JA, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penadés JR, Fitzgerald JR. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biol Evol 2010; 2:454-66. [PMID: 20624747 PMCID: PMC2997551 DOI: 10.1093/gbe/evq031] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Phenotypic biotyping has traditionally been used to differentiate bacteria occupying distinct ecological niches such as host species. For example, the capacity of Staphylococcus aureus from sheep to coagulate ruminant plasma, reported over 60 years ago, led to the description of small ruminant and bovine S. aureus ecovars. The great majority of small ruminant isolates are represented by a single, widespread clonal complex (CC133) of S. aureus, but its evolutionary origin and the molecular basis for its host tropism remain unknown. Here, we provide evidence that the CC133 clone evolved as the result of a human to ruminant host jump followed by adaptive genome diversification. Comparative whole-genome sequencing revealed molecular evidence for host adaptation including gene decay and diversification of proteins involved in host–pathogen interactions. Importantly, several novel mobile genetic elements encoding virulence proteins with attenuated or enhanced activity in ruminants were widely distributed in CC133 isolates, suggesting a key role in its host-specific interactions. To investigate this further, we examined the activity of a novel staphylococcal pathogenicity island (SaPIov2) found in the great majority of CC133 isolates which encodes a variant of the chromosomally encoded von Willebrand-binding protein (vWbpSov2), previously demonstrated to have coagulase activity for human plasma. Remarkably, we discovered that SaPIov2 confers the ability to coagulate ruminant plasma suggesting an important role in ruminant disease pathogenesis and revealing the origin of a defining phenotype of the classical S. aureus biotyping scheme. Taken together, these data provide broad new insights into the origin and molecular basis of S. aureus ruminant host specificity.
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Affiliation(s)
- Caitriona M Guinane
- The Roslin Institute and Centre for Infectious Diseases, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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Abstract
Rickettsia are endosymbionts of arthropods, some of which are vectored to vertebrates where they cause disease. Recently, it has been found that some Rickettsia strains harbour conjugative plasmids and others encode some conjugative machinery within the bacterial genome. We investigated the distribution of these conjugation genes in a phylogenetically diverse collection of Rickettsia isolated from arthropods. We found that these genes are common throughout the genus and, in stark contrast to other genes in the genome, conjugation genes are frequently horizontally transmitted between strains. There is no evidence to suggest that these genes are preferentially transferred between phylogenetically related strains, which is surprising given that closely related strains infect similar host species. In addition to detecting patterns of horizontal transmission between diverse Rickettsia species, these findings have implications for the evolution of pathogenicity, the evolution of Rickettsia genomes and the genetic manipulation of intracellular bacteria.
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Affiliation(s)
- Lucy A Weinert
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
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Abstract
Background Rickettsia are intracellular symbionts of eukaryotes that are best known for infecting and causing serious diseases in humans and other mammals. All known vertebrate-associated Rickettsia are vectored by arthropods as part of their life-cycle, and many other Rickettsia are found exclusively in arthropods with no known secondary host. However, little is known about the biology of these latter strains. Here, we have identified 20 new strains of Rickettsia from arthropods, and constructed a multi-gene phylogeny of the entire genus which includes these new strains. Results We show that Rickettsia are primarily arthropod-associated bacteria, and identify several novel groups within the genus. Rickettsia do not co-speciate with their hosts but host shifts most often occur between related arthropods. Rickettsia have evolved adaptations including transmission through vertebrates and killing males in some arthropod hosts. We uncovered one case of horizontal gene transfer among Rickettsia, where a strain is a chimera from two distantly related groups, but multi-gene analysis indicates that different parts of the genome tend to share the same phylogeny. Conclusion Approximately 150 million years ago, Rickettsia split into two main clades, one of which primarily infects arthropods, and the other infects a diverse range of protists, other eukaryotes and arthropods. There was then a rapid radiation about 50 million years ago, which coincided with the evolution of life history adaptations in a few branches of the phylogeny. Even though Rickettsia are thought to be primarily transmitted vertically, host associations are short lived with frequent switching to new host lineages. Recombination throughout the genus is generally uncommon, although there is evidence of horizontal gene transfer. A better understanding of the evolution of Rickettsia will help in the future to elucidate the mechanisms of pathogenicity, transmission and virulence.
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Affiliation(s)
- Lucy A Weinert
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK.
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Weinert LA, Tinsley MC, Temperley M, Jiggins FM. Are we underestimating the diversity and incidence of insect bacterial symbionts? A case study in ladybird beetles. Biol Lett 2008; 3:678-81. [PMID: 17878145 PMCID: PMC2111056 DOI: 10.1098/rsbl.2007.0373] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Vertically transmitted bacterial symbionts are common in arthropods. However, estimates of their incidence and diversity are based on studies that test for a single bacterial genus and often only include small samples of each host species. Focussing on ladybird beetles, we collected large samples from 21 species and tested them for four different bacterial symbionts. Over half the species were infected, and there were often multiple symbionts in the same population. In most cases, more females than males were infected, suggesting that the symbionts may be sex ratio distorters. Many of these infections would have been missed in previous studies as they only infect a small proportion of the population. Furthermore, 11 out of the 17 symbionts discovered by us were either in the genus Rickettsia or Spiroplasma, which are rarely sampled. Our results suggest that the true incidence and diversity of bacterial symbionts in insects may be far greater than previously thought.
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Affiliation(s)
- Lucy A Weinert
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
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