1
|
Subedi A, Iruegas-Bocardo F, Luo L, Minsavage GV, Roberts PD, Jones JB, Goss EM. Amylase-associated genetic pattern in Xanthomonas euvesicatoria on pepper. Appl Environ Microbiol 2024:e0131324. [PMID: 39291986 DOI: 10.1128/aem.01313-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024] Open
Abstract
Bacterial leaf spot of pepper (BSP), primarily caused by Xanthomonas euvesicatoria (Xe), poses a significant challenge to pepper production worldwide. Despite its impact, the genetic diversity of this pathogen remains underexplored, which limits our understanding of its population structure. To bridge this knowledge gap, we conducted a comprehensive analysis using 103 Xe strains isolated from pepper in southwest Florida to characterize genomic and type III effector (T3E) variation in this population. Phylogenetic analysis of core genomes revealed a major distinct genetic lineage associated with amylolytic activity. This amylolytic lineage was represented in Xe strains globally. Molecular clock analysis dated the emergence of amylolytic strains in Xe to around 1972. Notably, non-amylolytic strains possessed a single base pair frameshift deletion in the ⍺-amylase gene yet retained a conserved C-terminus. GUS assay revealed the expression of two open reading frames in non-amylolytic strains, one at the N-terminus and another that starts 136 base pairs upstream of the ⍺-amylase gene. Analysis of T3Es in the Florida Xe population identified variation in 12 effectors, including two classes of mutations in avrBs2 that prevent AvrBs2 from triggering a hypersensitive response in Bs2-resistant pepper plants. Knowledge of T3E variation could be used for effector-targeted disease management. This study revealed previously undescribed population structure in this economically important pathogen.IMPORTANCEBacterial leaf spot (BSP), a significant threat to pepper production globally, is primarily caused by Xanthomonas euvesicatoria (Xe). Limited genomic data has hindered detailed studies on its population diversity. This study analyzed the whole-genome sequences of 103 Xe strains from peppers in southwest Florida, along with additional global strains, to explore the pathogen's diversity. The study revealed two major distinct genetic groups based on their amylolytic activity, the ability to break down starch, with non-amylolytic strains having a mutation in the ⍺-amylase gene. Additionally, two classes of mutations in the avrBs2 gene were found, leading to susceptibility in pepper plants with the Bs2 resistance gene, a commercially available resistance gene for BSP. These findings highlight the need to forecast the emergence of such strains, identify genetic factors for innovative disease management, and understand how this pathogen evolves and spreads.
Collapse
Affiliation(s)
- Aastha Subedi
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | | | - Laixin Luo
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Pamela D Roberts
- Southwest Florida Research & Education Center, University of Florida, Immokalee, Florida, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
2
|
Chase-Topping M, Dallman TJ, Allison L, Lupolova N, Matthews L, Mitchell S, Banks CJ, Prentice J, Brown H, Tongue S, Henry M, Evans J, Gunn G, Hoyle D, McNeilly TN, Fitzgerald S, Smith-Palmer A, Shaaban S, Holmes A, Hanson M, Woolhouse M, Didelot X, Jenkins C, Gally DL. Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health. Microb Genom 2023; 9:001090. [PMID: 37672388 PMCID: PMC10569735 DOI: 10.1099/mgen.0.001090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3-33.7; P<0.001] and humans [OR 2.2 (1.5-3.2); P<0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27-33.3); P=0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9-1161); P<0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (P<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.
Collapse
Affiliation(s)
- Margo Chase-Topping
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Timothy J. Dallman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - Lesley Allison
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Nadejda Lupolova
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Louise Matthews
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sonia Mitchell
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Christopher J. Banks
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Jamie Prentice
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sue Tongue
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Madeleine Henry
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - George Gunn
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Deborah Hoyle
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | - Stephen Fitzgerald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | | | - Sharif Shaaban
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Anne Holmes
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mary Hanson
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3DL, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick CV4 7AL, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - David L. Gally
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| |
Collapse
|
3
|
Pereira AG, Kohlsdorf T. Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways. Genet Mol Biol 2023; 46:e20220384. [PMID: 37486083 PMCID: PMC10364090 DOI: 10.1590/1678-4685-gmb-2022-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/25/2023] Open
Abstract
Repeated phenotypes, often referred to as 'homoplasies' in cladistic analyses, may evolve through changes in developmental processes. Genetic bases of recurrent evolution gained attention and have been studied in the past years using approaches that combine modern analytical phylogenetic tools with the stunning assemblage of new information on developmental mechanisms. In this review, we evaluated the topic under an integrated perspective, revisiting the classical definitions of convergence and parallelism and detailing comparative methods used to evaluate evolution of repeated phenotypes, which include phylogenetic inference, estimates of evolutionary rates and reconstruction of ancestral states. We provide examples to illustrate how a given methodological approach can be used to identify evolutionary patterns and evaluate developmental mechanisms associated with the intermittent expression of a given trait along the phylogeny. Finally, we address why repeated trait loss challenges strict definitions of convergence and parallelism, discussing how changes in developmental pathways might explain the high frequency of repeated trait loss in specific lineages.
Collapse
Affiliation(s)
- Anieli Guirro Pereira
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
| | - Tiana Kohlsdorf
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
| |
Collapse
|
4
|
Ashton PM, Cha J, Anscombe C, Thuong NTT, Thwaites GE, Walker TM. Distribution and origins of Mycobacterium tuberculosis L4 in Southeast Asia. Microb Genom 2023; 9:mgen000955. [PMID: 36729036 PMCID: PMC9997747 DOI: 10.1099/mgen.0.000955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Molecular and genomic studies have revealed that Mycobacterium tuberculosis Lineage 4 (L4, Euro-American lineage) emerged in Europe before becoming distributed around the globe by trade routes, colonial migration and other historical connections. Although L4 accounts for tens or hundreds of thousands of tuberculosis (TB) cases in multiple Southeast Asian countries, phylogeographical studies have either focused on a single country or just included Southeast Asia as part of a global analysis. Therefore, we interrogated public genomic data to investigate the historical patterns underlying the distribution of L4 in Southeast Asia and surrounding countries. We downloaded 6037 genomes associated with 29 published studies, focusing on global analyses of L4 and Asian studies of M. tuberculosis. We identified 2256 L4 genomes including 968 from Asia. We show that 81 % of L4 in Thailand, 51 % of L4 in Vietnam and 9 % of L4 in Indonesia belong to sub-lineages of L4 that are rarely seen outside East and Southeast Asia (L4.2.2, L4.4.2 and L4.5). These sub-lineages have spread between East and Southeast Asian countries, with no recent European ancestor. Although there is considerable uncertainty about the exact direction and order of intra-Asian M. tuberculosis dispersal, due to differing sampling frames between countries, our analysis suggests that China may be the intermediate location between Europe and Southeast Asia for two of the three predominantly East and Southeast Asian L4 sub-lineages (L4.2.2 and L4.5). This new perspective on L4 in Southeast Asia raises the possibility of investigating host population-specific evolution and highlights the need for more structured sampling from Southeast Asian countries to provide more certainty of the historical and current routes of dispersal.
Collapse
Affiliation(s)
- Philip M. Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jaeyoon Cha
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Catherine Anscombe
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nguyen T. T. Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
5
|
Didelot X. Phylogenetic Analysis of Bacterial Pathogen Genomes. Methods Mol Biol 2023; 2674:87-99. [PMID: 37258962 DOI: 10.1007/978-1-0716-3243-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The development of high-throughput sequencing technology has led to a significant reduction in the time and cost of sequencing whole genomes of bacterial pathogens. Studies can sequence and compare hundreds or even thousands of genomes within a given bacterial population. A phylogenetic tree is the most frequently used method of depicting the relationships between these bacterial pathogen genomes. However, the presence of homologous recombination in most bacterial pathogen species can invalidate the application of standard phylogenetic tools. Here we describe a method to produce phylogenetic analyses that accounts for the disruptive effect of recombination. This allows users to investigate the recombination events that have occurred, as well as to produce more meaningful phylogenetic analyses which recover the clonal genealogy representing the clonal relationships between genomes.
Collapse
Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK.
| |
Collapse
|
6
|
Didelot X, Parkhill J. A scalable analytical approach from bacterial genomes to epidemiology. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210246. [PMID: 35989600 PMCID: PMC9393561 DOI: 10.1098/rstb.2021.0246] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/17/2022] [Indexed: 12/21/2022] Open
Abstract
Recent years have seen a remarkable increase in the practicality of sequencing whole genomes from large numbers of bacterial isolates. The availability of this data has huge potential to deliver new insights into the evolution and epidemiology of bacterial pathogens, but the scalability of the analytical methodology has been lagging behind that of the sequencing technology. Here we present a step-by-step approach for such large-scale genomic epidemiology analyses, from bacterial genomes to epidemiological interpretations. A central component of this approach is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. The construction of dated phylogenies from bacterial genomic data needs to account for the disruptive effect of recombination on phylogenetic relationships, and we describe how this can be achieved. Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which genomes are available. A key feature of this approach is computational scalability and in particular the ability to process hundreds or thousands of genomes within a matter of hours. This is a clear advantage of the step-by-step approach described here. We discuss other advantages and disadvantages of the approach, as well as potential improvements and avenues for future research. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
Collapse
Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| |
Collapse
|
7
|
Guillier L, Palma F, Fritsch L. Taking account of genomics in quantitative microbial risk assessment: what methods? what issues? Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
8
|
Sévellec Y, Ascencio E, Douarre PE, Félix B, Gal L, Garmyn D, Guillier L, Piveteau P, Roussel S. Listeria monocytogenes: Investigation of Fitness in Soil Does Not Support the Relevance of Ecotypes. Front Microbiol 2022; 13:917588. [PMID: 35770178 PMCID: PMC9234652 DOI: 10.3389/fmicb.2022.917588] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm, little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR < 2%), phenotype 2 “moderate survivors” (2% < SR < 5%) and phenotype 3 “good survivors” (SR > 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness.
Collapse
Affiliation(s)
- Yann Sévellec
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Eliette Ascencio
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Pierre-Emmanuel Douarre
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Benjamin Félix
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
| | - Laurent Gal
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Dominique Garmyn
- Agroecologie, AgroSup Dijon, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Laurent Guillier
- Risk Assessment Department, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), University of Paris-Est, Maisons-Alfort, France
| | | | - Sophie Roussel
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Maisons-Alfort, France
- *Correspondence: Sophie Roussel,
| |
Collapse
|
9
|
Helekal D, Ledda A, Volz E, Wyllie D, Didelot X. Bayesian inference of clonal expansions in a dated phylogeny. Syst Biol 2021; 71:1073-1087. [PMID: 34893904 PMCID: PMC9366454 DOI: 10.1093/sysbio/syab095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial population genetics models often assume that all lineages are constrained by the same population size dynamics over time. However, many neutral and selective events can invalidate this assumption and can contribute to the clonal expansion of a specific lineage relative to the rest of the population. Such differential phylodynamic properties between lineages result in asymmetries and imbalances in phylogenetic trees that are sometimes described informally but which are difficult to analyze formally. To this end, we developed a model of how clonal expansions occur and affect the branching patterns of a phylogeny. We show how the parameters of this model can be inferred from a given dated phylogeny using Bayesian statistics, which allows us to assess the probability that one or more clonal expansion events occurred. For each putative clonal expansion event, we estimate its date of emergence and subsequent phylodynamic trajectory, including its long-term evolutionary potential which is important to determine how much effort should be placed on specific control measures. We demonstrate the applicability of our methodology on simulated and real data sets. Inference under our clonal expansion model can reveal important features in the evolution and epidemiology of infectious disease pathogens. [Clonal expansion; genomic epidemiology; microbial population genomics; phylodynamics.]
Collapse
Affiliation(s)
- David Helekal
- Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick, United Kingdom
| | - Alice Ledda
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, United Kingdom
| | - Erik Volz
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
| | - David Wyllie
- Field Service, East of England, National Infection Service, Public Health England, Cambridge, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, United Kingdom
| |
Collapse
|
10
|
Smith DA, Fernandez-Antunez C, Magri A, Bowden R, Chaturvedi N, Fellay J, McLauchlan J, Foster GR, Irving WL, Simmonds P, Pedergnana V, Ramirez S, Bukh J, Barnes E, Ansari MA. Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure. Nat Commun 2021; 12:6105. [PMID: 34671027 PMCID: PMC8528821 DOI: 10.1038/s41467-021-25649-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment.
Collapse
Affiliation(s)
- David A Smith
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Magri
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Graham R Foster
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - William L Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
| |
Collapse
|
11
|
Arning N, Sheppard SK, Bayliss S, Clifton DA, Wilson DJ. Machine learning to predict the source of campylobacteriosis using whole genome data. PLoS Genet 2021; 17:e1009436. [PMID: 34662334 PMCID: PMC8553134 DOI: 10.1371/journal.pgen.1009436] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 10/28/2021] [Accepted: 08/26/2021] [Indexed: 11/18/2022] Open
Abstract
Campylobacteriosis is among the world's most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using the classifier we named aiSource. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.
Collapse
Affiliation(s)
- Nicolas Arning
- Big Data institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
- * E-mail:
| | - Samuel K. Sheppard
- The Milner Centre of Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Sion Bayliss
- The Milner Centre of Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - David A. Clifton
- Department of Engineering Science, University of Oxford, Oxford, UK; Oxford-Suzhou Centre for Advanced Research, Suzhou, China
| | - Daniel J. Wilson
- Big Data institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, United Kingdom
| |
Collapse
|
12
|
Mokaya J, Vasylyeva TI, Barnes E, Ansari MA, Pybus OG, Matthews PC. Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations. J Viral Hepat 2021; 28:1110-1120. [PMID: 33893696 PMCID: PMC8581767 DOI: 10.1111/jvh.13525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Vaccination and anti-viral therapy with nucleos(t)ide analogues (NAs) are key approaches to reducing the morbidity, mortality and transmission of hepatitis B virus (HBV) infection. However, the efficacy of these interventions may be reduced by the emergence of drug resistance-associated mutations (RAMs) and/or vaccine escape mutations (VEMs). We have assimilated data on the global prevalence and distribution of HBV RAMs/VEMs from publicly available data and explored the evolution of these mutations. We analysed sequences downloaded from the HBV Database and calculated prevalence of 41 RAMs and 38 VEMs catalogued from published studies. We generated maximum likelihood phylogenetic trees and used treeBreaker to investigate the distribution and estimated the age of selected mutations across tree branches. RAM M204I/V had the highest prevalence, occurring in 3.8% (109/2838) of all HBV sequences in our data set, and a significantly higher rate in genotype C at 5.4% (60/1102, p = 0.0007). VEMs had an overall prevalence of 1.3% (37/2837) and had the highest prevalence in genotype C and in Asia at 2.2% (24/1102; p = 0.002) and 1.6% (34/2109; p = 0.009), respectively. Phylogenetic analysis suggested that RAM/VEMs can arise independently of treatment/vaccine exposure. In conclusion, HBV RAMs/VEMs have been found globally and across genotypes, with the highest prevalence observed in genotype C. Screening for genotype and for resistance-associated mutations may help to improve stratified patient treatment. As NAs and HBV vaccines are increasingly being deployed for HBV prevention and treatment, monitoring for resistance and advocating for better treatment regimens for HBV remains essential.
Collapse
Affiliation(s)
| | - Tetyana I. Vasylyeva
- Division of Infectious Diseases & Global Public HealthDepartment of MedicineUniversity of CaliforniaSan DiegoCAUSA
| | - Eleanor Barnes
- Nuffield Department of MedicineOxfordUK
- Department of HepatologyOxford University Hospitals NHS Foundation TrustJohn Radcliffe HospitalOxfordUK
- National Institutes of Health Research Health Informatics CollaborativeNIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUK
| | - M. Azim Ansari
- Nuffield Department of MedicineOxfordUK
- Wellcome Centre for Human GeneticsOxfordUK
| | | | - Philippa C. Matthews
- Nuffield Department of MedicineOxfordUK
- National Institutes of Health Research Health Informatics CollaborativeNIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUK
- Department of Infectious Diseases and MicrobiologyOxford University Hospitals NHS Foundation TrustJohn Radcliffe HospitalOxfordUK
| |
Collapse
|
13
|
Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M. An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. Mol Biol Evol 2021; 38:108-127. [PMID: 32781465 PMCID: PMC7783168 DOI: 10.1093/molbev/msaa191] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
Collapse
Affiliation(s)
- Heiner Kuhl
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany.,Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Gerhard Nikolaus
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Stefan T Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| |
Collapse
|
14
|
Abstract
Genome-wide association studies in bacteria have great potential to deliver a better understanding of the genetic basis of many biologically important phenotypes, including antibiotic resistance, pathogenicity, and host adaptation. Such studies need however to account for the specificities of bacterial genomics, especially in terms of population structure, homologous recombination, and genomic plasticity. A powerful way to tackle this challenge is to use a phylogenetic approach, which is based on long-standing methodology for the evolutionary analysis of bacterial genomic data. Here we present both the theoretical and practical aspects involved in the use of phylogenetic methods for bacterial genome-wide association studies.
Collapse
Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK.
| |
Collapse
|
15
|
Crouse WL, Kelada SNP, Valdar W. Inferring the Allelic Series at QTL in Multiparental Populations. Genetics 2020; 216:957-983. [PMID: 33082282 PMCID: PMC7768242 DOI: 10.1534/genetics.120.303393] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
Multiparental populations (MPPs) are experimental populations in which the genome of every individual is a mosaic of known founder haplotypes. These populations are useful for detecting quantitative trait loci (QTL) because tests of association can leverage inferred founder haplotype descent. It is difficult, however, to determine how haplotypes at a locus group into distinct functional alleles, termed the allelic series. The allelic series is important because it provides information about the number of causal variants at a QTL and their combined effects. In this study, we introduce a fully Bayesian model selection framework for inferring the allelic series. This framework accounts for sources of uncertainty found in typical MPPs, including the number and composition of functional alleles. Our prior distribution for the allelic series is based on the Chinese restaurant process, a relative of the Dirichlet process, and we leverage its connection to the coalescent to introduce additional prior information about haplotype relatedness via a phylogenetic tree. We evaluate our approach via simulation and apply it to QTL from two MPPs: the Collaborative Cross (CC) and the Drosophila Synthetic Population Resource (DSPR). We find that, although posterior inference of the exact allelic series is often uncertain, we are able to distinguish biallelic QTL from more complex multiallelic cases. Additionally, our allele-based approach improves haplotype effect estimation when the true number of functional alleles is small. Our method, Tree-Based Inference of Multiallelism via Bayesian Regression (TIMBR), provides new insight into the genetic architecture of QTL in MPPs.
Collapse
Affiliation(s)
- Wesley L Crouse
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Samir N P Kelada
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599
| | - William Valdar
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| |
Collapse
|
16
|
Abstract
Tree-like structures are abundant in the empirical sciences as they can summarize high-dimensional data and show latent structure among many samples in a single framework. Prominent examples include phylogenetic trees or hierarchical clustering derived from genetic data. Currently, users employ ad hoc methods to test for association between a given tree and a response variable, which reduces reproducibility and robustness. In this paper, we introduce treeSeg, a simple to use and widely applicable methodology with high power for testing between all levels of hierarchy for a given tree and the response while accounting for the overall false positive rate. Our method allows for precise uncertainty quantification and therefore, increases interpretability and reproducibility of such studies across many fields of science. Tree structures, showing hierarchical relationships and the latent structures between samples, are ubiquitous in genomic and biomedical sciences. A common question in many studies is whether there is an association between a response variable measured on each sample and the latent group structure represented by some given tree. Currently, this is addressed on an ad hoc basis, usually requiring the user to decide on an appropriate number of clusters to prune out of the tree to be tested against the response variable. Here, we present a statistical method with statistical guarantees that tests for association between the response variable and a fixed tree structure across all levels of the tree hierarchy with high power while accounting for the overall false positive error rate. This enhances the robustness and reproducibility of such findings.
Collapse
|
17
|
Ansari MA, Aranday-Cortes E, Ip CL, da Silva Filipe A, Lau SH, Bamford C, Bonsall D, Trebes A, Piazza P, Sreenu V, Cowton VM, Hudson E, Bowden R, Patel AH, Foster GR, Irving WL, Agarwal K, Thomson EC, Simmonds P, Klenerman P, Holmes C, Barnes E, Spencer CC, McLauchlan J, Pedergnana V. Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. eLife 2019; 8:42463. [PMID: 31478835 PMCID: PMC6721795 DOI: 10.7554/elife.42463] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is a highly variable pathogen that frequently establishes chronic infection. This genetic variability is affected by the adaptive immune response but the contribution of other host factors is unclear. Here, we examined the role played by interferon lambda-4 (IFN-λ4) on HCV diversity; IFN-λ4 plays a crucial role in spontaneous clearance or establishment of chronicity following acute infection. We performed viral genome-wide association studies using human and viral data from 485 patients of white ancestry infected with HCV genotype 3a. We demonstrate that combinations of host genetic variants, which determine IFN-λ4 protein production and activity, influence amino acid variation across the viral polyprotein - not restricted to specific viral proteins or HLA restricted epitopes - and modulate viral load. We also observed an association with viral di-nucleotide proportions. These results support a direct role for IFN-λ4 in exerting selective pressure across the viral genome, possibly by a novel mechanism.
Collapse
Affiliation(s)
- M Azim Ansari
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elihu Aranday-Cortes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Camilla Lc Ip
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Siu Hin Lau
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Connor Bamford
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - David Bonsall
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Amy Trebes
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Vattipally Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | | | - Emma Hudson
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Graham R Foster
- Blizard Institute, Queen Mary University, London, United Kingdom
| | - William L Irving
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Kosh Agarwal
- Institute of Liver Studies, King's College Hospital, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Holmes
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Ca Spencer
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vincent Pedergnana
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom.,Laboratoire MIVEGEC (UMR CNRS 5290, IRD, UM), Montpellier, France
| |
Collapse
|
18
|
The impact of antimicrobials on gonococcal evolution. Nat Microbiol 2019; 4:1941-1950. [PMID: 31358980 PMCID: PMC6817357 DOI: 10.1038/s41564-019-0501-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 05/30/2019] [Indexed: 12/19/2022]
Abstract
The sexually transmitted pathogen Neisseria gonorrhoeae
is regarded as being on the way to becoming an untreatable superbug. Despite its
clinical importance, little is known about its emergence and evolution, and how
this corresponds with the introduction of antimicrobials. We present a
genome-based phylogeographic analysis of 419 gonococcal isolates from across the
globe. Results indicate that modern gonococci originated in Europe or Africa,
possibly as late as the 16th century and subsequently disseminated
globally. We provide evidence that the modern gonococcal population has been
shaped by antimicrobial treatment of sexually transmitted and other infections,
leading to the emergence of two major lineages with different evolutionary
strategies. The well-described multi-resistant lineage is associated with high
rates of homologous recombination and infection in high-risk sexual networks. A
second, multi-susceptible lineage is more associated with heterosexual networks,
with potential implications for infection control.
Collapse
|
19
|
Fritsch L, Felten A, Palma F, Mariet JF, Radomski N, Mistou MY, Augustin JC, Guillier L. Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions. Int J Food Microbiol 2018; 291:181-188. [PMID: 30530095 DOI: 10.1016/j.ijfoodmicro.2018.11.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 10/09/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
Intraspecific variability of the behavior of most foodborne pathogens is well described and taken into account in Quantitative Microbial Risk Assessment (QMRA), but factors (strain origin, serotype, …) explaining these differences are scarce or contradictory between studies. Nowadays, Whole Genome Sequencing (WGS) offers new opportunities to explain intraspecific variability of food pathogens, based on various recently published bioinformatics tools. The objective of this study is to get a better insight into different existing bioinformatics approaches to associate bacterial phenotype(s) and genotype(s). Therefore, a dataset of 51 L. monocytogenes strains, isolated from multiple sources (i.e. different food matrices and environments) and belonging to 17 clonal complexes (CC), were selected to represent large population diversity. Furthermore, the phenotypic variability of growth at low temperature was determined (i.e. qualitative phenotype), and the whole genomes of selected strains were sequenced. The almost exhaustive gene content, as well as the core genome SNPs based phylogenetic reconstruction, were derived from the whole sequenced genomes. A Bayesian inference method was applied to identify the branches on which the phenotype distribution evolves within sub-lineages. Two different Genome Wide Association Studies (i.e. gene- and SNP-based GWAS) were independently performed in order to link genetic mutations to the phenotype of interest. The genomic analyses presented in this study were successfully applied on the selected dataset. The Bayesian phylogenetic approach emphasized an association with "slow" growth ability at 2 °C of the lineage I, as well as CC9 of the lineage II. Moreover, both gene- and SNP-GWAS approaches displayed significant statistical associations with the tested phenotype. A list of 114 significantly associated genes, including genes already known to be involved in the cold adaption mechanism of L. monocytogenes and genes associated to mobile genetic elements (MGE), resulted from the gene-GWAS. On the other hand, a group of 184 highly associated SNPs were highlighted by SNP-GWAS, including SNPs detected in genes which were already likely involved in cold adaption; hypothetical proteins; and intergenic regions where for example promotors and regulators can be located. The successful application of combined bioinformatics approaches associating WGS-genotypes and specific phenotypes, could contribute to improve prediction of microbial behaviors in food. The implementation of this information in hazard identification and exposure assessment processes will open new possibilities to feed QMRA-models.
Collapse
Affiliation(s)
- Lena Fritsch
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Arnaud Felten
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Federica Palma
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Jean-François Mariet
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Nicolas Radomski
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Michel-Yves Mistou
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France
| | - Jean-Christophe Augustin
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France; Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort F-94704, France
| | - Laurent Guillier
- French Agency for Food, Environmental and Occupational Health & Safety (Anses), Laboratory for Food Safety, Université Paris-Est, Maisons-Alfort F-94701, France.
| |
Collapse
|
20
|
Ghosh PN, Fisher MC, Bates KA. Diagnosing Emerging Fungal Threats: A One Health Perspective. Front Genet 2018; 9:376. [PMID: 30254662 PMCID: PMC6141620 DOI: 10.3389/fgene.2018.00376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 11/17/2022] Open
Abstract
Emerging fungal pathogens are a growing threat to global health, ecosystems, food security, and the world economy. Over the last century, environmental change and globalized transport, twinned with the increasing application of antifungal chemical drugs have led to increases in outbreaks of fungal diseases with sometimes catastrophic effects. In order to tackle contemporary epidemics and predemic threats, there is a pressing need for a unified approach in identification and monitoring of fungal pathogens. In this paper, we discuss current high throughput technologies, as well as new platforms capable of combining diverse data types to inform practical epidemiological strategies with a focus on emerging fungal pathogens of wildlife.
Collapse
Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Kieran A. Bates
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| |
Collapse
|
21
|
Harris SR, Cole MJ, Spiteri G, Sánchez-Busó L, Golparian D, Jacobsson S, Goater R, Abudahab K, Yeats CA, Bercot B, Borrego MJ, Crowley B, Stefanelli P, Tripodo F, Abad R, Aanensen DM, Unemo M. Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey. THE LANCET. INFECTIOUS DISEASES 2018; 18:758-768. [PMID: 29776807 PMCID: PMC6010626 DOI: 10.1016/s1473-3099(18)30225-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/22/2018] [Accepted: 03/20/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction with linked epidemiological and phenotypic data, to describe the gonococcal population in 20 European countries. We aimed to detail changes in phenotypic antimicrobial resistance levels (and the reasons for these changes) and strain distribution (with a focus on antimicrobial resistance strains in risk groups), and to predict antimicrobial resistance from WGS data. METHODS We carried out an observational study, in which we sequenced isolates taken from patients with gonorrhoea from the European Gonococcal Antimicrobial Surveillance Programme in 20 countries from September to November, 2013. We also developed a web platform that we used for automated antimicrobial resistance prediction, molecular typing (N gonorrhoeae multi-antigen sequence typing [NG-MAST] and multilocus sequence typing), and phylogenetic clustering in conjunction with epidemiological and phenotypic data. FINDINGS The multidrug-resistant NG-MAST genogroup G1407 was predominant and accounted for the most cephalosporin resistance, but the prevalence of this genogroup decreased from 248 (23%) of 1066 isolates in a previous study from 2009-10 to 174 (17%) of 1054 isolates in this survey in 2013. This genogroup previously showed an association with men who have sex with men, but changed to an association with heterosexual people (odds ratio=4·29). WGS provided substantially improved resolution and accuracy over NG-MAST and multilocus sequence typing, predicted antimicrobial resistance relatively well, and identified discrepant isolates, mixed infections or contaminants, and multidrug-resistant clades linked to risk groups. INTERPRETATION To our knowledge, we provide the first use of joint analysis of WGS and epidemiological data in an international programme for regional surveillance of sexually transmitted infections. WGS provided enhanced understanding of the distribution of antimicrobial resistance clones, including replacement with clones that were more susceptible to antimicrobials, in several risk groups nationally and regionally. We provide a framework for genomic surveillance of gonococci through standardised sampling, use of WGS, and a shared information architecture for interpretation and dissemination by use of open access software. FUNDING The European Centre for Disease Prevention and Control, The Centre for Genomic Pathogen Surveillance, Örebro University Hospital, and Wellcome.
Collapse
Affiliation(s)
- Simon R Harris
- Infection Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Michelle J Cole
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | | | | | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, Örebro, Sweden
| | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, Örebro, Sweden
| | - Richard Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Hinxton, UK
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Hinxton, UK
| | - Corin A Yeats
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Hinxton, UK
| | - Beatrice Bercot
- Assistance Publique Hôpitaux de Paris, St Louis Hospital, Paris, France
| | | | | | | | - Francesco Tripodo
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Hinxton, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, Örebro, Sweden.
| |
Collapse
|
22
|
Resistant gonorrhoea: east meets west. THE LANCET. INFECTIOUS DISEASES 2018; 18:702-703. [PMID: 29776806 DOI: 10.1016/s1473-3099(18)30276-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 11/21/2022]
|
23
|
A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination. PLoS Comput Biol 2018; 14:e1005958. [PMID: 29401456 PMCID: PMC5814097 DOI: 10.1371/journal.pcbi.1005958] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 02/15/2018] [Accepted: 12/30/2017] [Indexed: 11/28/2022] Open
Abstract
Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, microbial GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS. Measurable differences often exist within a microbial population, with important ecological or epidemiological consequences. Examples include differences in growth rates, host range, transmissibility, antimicrobial resistance, virulence, etc. Understanding the genetic factors involved in these phenotypic properties is a crucial aim in microbial genomics. A fundamental approach for doing so is to perform a Genome-Wide Association Study (GWAS), where genomes are compared to search for genetic markers systematically correlated with the property of interest. If this strategy were implemented naively in microbes, it could lead to spurious results due to the confounding effects of population structure and recombination. Here we present treeWAS, a new phylogenetic method to perform microbial GWAS that avoids these pitfalls. We show, using simulated datasets, that treeWAS is able to distinguish between genetic markers that are truly associated with the property of interest and those that are not. Furthermore, we demonstrate that treeWAS offers advantages in both sensitivity and specificity over alternative cluster-based and dimension-reduction techniques. We also showcase treeWAS in two applications to real datasets from N. meningitidis. We have developed an easy-to-use implementation of treeWAS in the R environment, which should be useful to a wide range of researchers in microbial genomics.
Collapse
|
24
|
Iraola G, Forster SC, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR, Vidal A, Lévesque S, Yamazaki W, Balzan C, Vargas A, Piccirillo A, Chaban B, Hill JE, Betancor L, Collado L, Truyers I, Midwinter AC, Dagi HT, Mégraud F, Calleros L, Pérez R, Naya H, Lawley TD. Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nat Commun 2017; 8:1367. [PMID: 29118316 PMCID: PMC5678084 DOI: 10.1038/s41467-017-01449-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/15/2017] [Indexed: 12/31/2022] Open
Abstract
Campylobacter fetus is a venereal pathogen of cattle and sheep, and an opportunistic human pathogen. It is often assumed that C. fetus infection occurs in humans as a zoonosis through food chain transmission. Here we show that mammalian C. fetus consists of distinct evolutionary lineages, primarily associated with either human or bovine hosts. We use whole-genome phylogenetics on 182 strains from 17 countries to provide evidence that C. fetus may have originated in humans around 10,500 years ago and may have "jumped" into cattle during the livestock domestication period. We detect C. fetus genomes in 8% of healthy human fecal metagenomes, where the human-associated lineages are the dominant type (78%). Thus, our work suggests that C. fetus is an unappreciated human intestinal pathobiont likely spread by human to human transmission. This genome-based evolutionary framework will facilitate C. fetus epidemiology research and the development of improved molecular diagnostics and prevention schemes for this neglected pathogen.
Collapse
Affiliation(s)
- Gregorio Iraola
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay. .,Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay. .,Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK
| | - Philippe Lehours
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3.,Départment de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, QC, Canada, H3T 1J4
| | - Francisco J García-Peña
- Departamento de Bacteriología, Laboratorio Central de Veterinaria de Algete (MAGRAMA), 28110, Algete, Spain
| | - Fernando Paolicchi
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Claudia Morsella
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743, Jena, Germany
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Ana Vidal
- Animal and Plant Health Association (APHA), Addlestone, KT15 3NB, UK
| | - Simon Lévesque
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3
| | - Wataru Yamazaki
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Claudia Balzan
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Agueda Vargas
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, 35122, Italy
| | - Bonnie Chaban
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatchewan, SK, Canada, S7N 5A2
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, 11600, Uruguay
| | - Luis Collado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5090000, Valdivia, Chile
| | - Isabelle Truyers
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Anne C Midwinter
- EpiLab, Infectious Disease Research Centre, Massey University, Palmerston North, 4442, New Zealand
| | - Hatice T Dagi
- Department of Microbiology, Faculty of Medicine, Selçuk University, Selçuklu, 42250, Turkey
| | - Francis Mégraud
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay.,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, 12900, Montevideo, Uruguay
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
| |
Collapse
|
25
|
A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains. Sci Rep 2016; 6:37811. [PMID: 27892531 PMCID: PMC5124939 DOI: 10.1038/srep37811] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/02/2016] [Indexed: 01/04/2023] Open
Abstract
Carbapenems are a class of last-resort antibiotics; thus, the increase in bacterial carbapenem-resistance is a serious public health threat. Acinetobacter baumannii is one of the microorganisms that can acquire carbapenem-resistance; it causes severe nosocomial infection, and is notoriously difficult to control in hospitals. Recently, a machine-learning approach was first used to analyze the genome sequences of hundreds of susceptible and resistant A. baumannii strains, including those carrying commonly acquired resistant mechanisms, to build a classifier that can predict strain resistance. A complementary approach is to explore novel genetic elements that could be associated with the antimicrobial resistance of strains, independent of known mechanisms. Therefore, we carefully selected A. baumannii strains, spanning various genotypes, from public genome databases, and conducted the first genome-wide association study (GWAS) of carbapenem resistance. We employed a recently developed method, capable of identifying any kind of genetic variation and accounting for bacterial population structure, and evaluated its effectiveness. Our study identified a surface adhesin gene that had been horizontally transferred to an ancestral branch of A. baumannii, as well as a specific region of that gene that appeared to accumulate multiple individual variations across the different branches of carbapenem-resistant A. baumannii strains.
Collapse
|