DOCSLIB.ORG

Field Pathogenomics Reveals the Emergence of a Diverse Wheat Yellow Rust Population

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Field Pathogenomics Reveals the Emergence of a Diverse Wheat Yellow Rust Population Hubbard et al. Genome Biology (2015) 16:23 DOI 10.1186/s13059-015-0590-8 RESEARCH Open Access Field pathogenomics reveals the emergence of a diverse wheat yellow rust population Amelia Hubbard1, Clare M Lewis2, Kentaro Yoshida3, Ricardo H Ramirez-Gonzalez4, Claude de Vallavieille-Pope5, Jane Thomas1, Sophien Kamoun3, Rosemary Bayles1, Cristobal Uauy1,2* and Diane GO Saunders2,3,4* Abstract Background: Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. Results: To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. Conclusions: Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens. Background mechanisms and diagnostic tools are needed to rapidly re- Emerging and re-emerging diseases of humans, animals spond to these emerging threats. With recent advances in and plants pose a significant hazard to public health and DNA and RNA sequencing, bacteriologists and virologists food security. These threats can arise from newly discov- are capitalizing on these technological advances by inte- ered pathogens, such as the Middle East respiratory syn- grating high-resolution genotypic data into pathogen drome (MERS) coronavirus in humans [1], or novel host surveillance activities [6]. However, the application of adaptation, as in zoonotic influenza [2]. Recent disease genomics to emerging filamentous plant pathogens has outbreaks in plants have been associated with expan- lagged. Filamentous plant pathogens tend to have large sions of pathogen geographic distribution and increased genomes and are often obligate parasites that cannot be virulence of known pathogens, such as in the European axenically cultured in the laboratory. The time-consuming outbreak of ash dieback [3] and wheat stem rust across and tedious protocols required to maintain these pathogens Africa and the Middle East [4]. Independent of the host on their hosts have impeded the translation of genomic organism, the scale and frequency of emerging diseases technologies into surveillance and diagnostics methods. have increased with the globalization and industrialization Traditional diagnostic tools for pathogens have been of food production systems [5]. Improved surveillance based on targeted cultures, PCR-based approaches and/ or phenotypic evaluation of disease response in specific * Correspondence: [email protected]; [email protected] plant genotypes [7]. These methods detect only known 1National Institute of Agricultural Botany, Cambridge CB3 0LE, UK pathogenic agents, can introduce bias, and can fail to 2 John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK recognize novel variants or races due to their narrow Full list of author information is available at the end of the article © 2015 Hubbard et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Hubbard et al. Genome Biology (2015) 16:23 Page 2 of 15 scope [8]. However, next-generation sequencing tech- system [21]. The signatures of adaptation and gene ex- nologies can circumvent these limitations to provide a pression patterns of pathogen isolates with distinct rich source of data for the development of surveillance virulence profiles can provide a powerful means of and diagnostic tools. The high resolution of these ap- identifying specific avirulence/virulence proteins that proaches also enables exploration of the genetic deter- can be used to track pathotypes at a national and inter- minants underpinning pathogenicity. Whole-genome national level. Furthermore, publication of these draft sequencing has emerged as a preferred technology, espe- reference genomes also provides an opportunity to cially for viruses with relatively small genomes (approxi- characterize pathogen populations at a considerably mately 50 kb on average) [9], although this methodology higher resolution and on a much wider scale through is less tractable in pathogens with large genomes such as re-sequencing of PST isolates. filamentous plant pathogens, which have genomes that In this study, we developed a robust and rapid ‘field range from 19 to 280 Mb [10]. Alternatively, RNA sequen- pathogenomics’ strategy, using transcriptome sequencing cing (RNA-seq), which focuses solely on the expressed of PST-infected wheat leaves to gain insight into the fraction of the genome, reduces the sequence space of the population structure of an emerging pathogen. Our ana- sample and provides relevant transcriptome data for both lysis uncovered a dramatic shift in the PST population the pathogen and host in situ [11]. in the UK and supports the hypothesis that recent intro- Despite modern agricultural practices, diseases of the duction of a diverse set of exotic PST lineages may have major food crops cause up to 15% pre-harvest yield loss displaced the previous PST populations. Our field patho- [12]. Among these crops, wheat is a critical staple pro- genomics approach circumvents the difficulties associated viding 20% of the calories and over 25% of the protein with less-tractable filamentous plant pathogens and can consumed by humans [13]. One of the major fungal dis- be applied to other emerging populations of pathogens. eases of wheat is yellow (stripe) rust caused by the obligate fungus Puccinia striiformis Westend. f. sp. tritici Eriks Results (PST) [14]. This disease is widespread across the major Genotyping pathogens and their hosts using RNA-seq of wheat-producing areas of the world and can cause signifi- field-collected infected leaves cant reductions in both grain quality and yield in suscep- To characterize the genotypic diversity of PST at the tible cultivars [15]. In the past decade, new PST races field level, we collected 219 samples of wheat and triti- have emerged that are capable of adapting to warmer tem- cale infected with PST from 17 different counties across peratures, have expanded virulence profiles, and are more the UK in the spring and summer of 2013 (Figure 1a; aggressive than previously characterized races [16]. More Table S1 in Additional file 1). From these, we selected recently, a series of PST races have arisen in Europe and 35 PST-infected wheat samples from wheat varieties that overcome many of the major resistance genes in European spanned the resistance spectrum, and 4 PST-infected germplasm [17]. For instance, in 2011 a race group col- triticale samples (Table S1 in Additional file 1). Total lectively called ‘Warrior’ (based on the virulence of one of RNA was extracted from each sample and subjected to the initial variants of this group to the UK wheat variety RNA-seq analysis (Figure 1a). After filtering, an average Warrior) emerged as a serious threat to wheat production. of 37% (standard deviation 12.7%) reads aligned to the However, the origin of this new race and its relationship PST-130 reference genome [18], indicating that fungal with previously characterized races remain unclear. transcripts account for a high percentage of the transcripts An important first step towards the development of in PST-infected plant tissue (Table S2 in Additional file 1). more effective surveillance and diagnostic tools is the To address whether each sample comprised a single availability of a draft reference genome and annotation. PST genotype without considerable bias in allele- Cantu et al. [18] published a first draft sequence of PST specific expression, we calculated the distribution of isolate 130 (PST-130) with 22,185 annotated protein- read counts for biallelic single nucleotide polymor- coding sequences across the 64.8 Mb assembly. More phisms (SNPs), determined from alignment to the recently, Zheng et al. [19] published a 110 Mb draft PST-130 genome. As a dikaryon,
Load more

Recommended publications
  • The Pathogenomics and Evolution of Anthrax-Like Bacillus Cereus Isolates and Plasmids
    The Pathogenomics and Evolution of Anthrax-like Bacillus cereus Isolates and Plasmids A white paper proposal submitted by: Geraldine A. Van der Auwera, Ph.D. Harvard Medical School Michael Feldgarden, Ph.D. Genomic Sequencing Center for Infectious Diseases The Broad Institute of MIT and Harvard 1 Executive summary A key member of the Bacillus cereus group, Bacillus anthracis is defined by phenotypic and molecular characteristics that are conferred by two large plasmids, pXO1 and pXO2. However the very concept of B. anthracis as a distinct species has been called into question by recent discoveries of “intermediate” isolates identified as B. cereus and B. thuringiensis but possessing features similar to those of B. anthracis, including large plasmids that share a common backbone with pXO1 and/or pXO2. Many of these “intermediate” isolates possess potential or demonstrated lethal pathogenic properties and are sometimes called “anthrax-like”, even though they do not meet the strict definition of anthrax-causing B. anthracis. We recently showed that pXO1- and pXO2- like plasmids are widely prevalent in environmental isolates of the B. cereus group. Because B. anthracis-like isolates do not possess all the molecular hallmarks of typical B. anthracis, there is a significant risk that they would escape being flagged as dangerous. Consequently, accidental infection by naturally occurring pathotypes which are not immediately recognized as life-threatening could present a serious health concern. Such cases have already been reported, some with a fatal outcome. The second risk posed by these B. anthracis-like isolates could be the intentional use as “stealth anthrax” bioweapon, either in natural form or with genetic modifications that would require only minimal skills and facilities to produce.
    [Show full text]
  • 14S802 - Strain Specific Pathogenicity of Staphylococcus Aureus Final Report
    14S802 - Strain Specific Pathogenicity of Staphylococcus aureus Final Report This project was funded under the Department of Agriculture, Food and the Marine Competitive Funding Programme. SUMMARY Mastitis is a costly endemic disease for the dairy industry. It is primarily caused by bacterial infection and is the most common reason for antibiotic use in dairy cows in Ireland. Staphylococcus aureus is the most common mastitis pathogen in Ireland and the S. aureus strains that cause mastitis belong to specific bovine-adapted lineages. Current selection for mastitis-resistance is based on the host immune response, as determined by somatic cell count (SCC). However, the ability of S. aureus to evade and subvert the host immune response is well known, including the ability to internalise and survive within host cells. This project tested the hypothesis that bovine intramammary infection with different S. aureus strains results in differential activation of the host immune response. Supporting this hypothesis, significant differences between S. aureus lineages in their ability to internalise within bovine mammary epithelial cells were found with some strains internalising at higher levels than others. It was also found that some strains induced higher expression of cytokines and chemokines responsible for attracting immune cells and these strains induced mammary epithelial cells to produce factors that attracted somatic cells, while other strains did not. Differences in disease presentation in vivo in cows infected with different strains were also observed, indicating strain-specific virulence. Significantly higher somatic cell count and anti- Staphylococcus IgG and significantly lower milk yield were observed in response to infection with a more virulent strain.
    [Show full text]
  • The Role of Genomics in the Identification, Prediction, and Prevention of Biological Threats
    Perspective The Role of Genomics in the Identification, Prediction, and Prevention of Biological Threats W. Florian Fricke, David A. Rasko, Jacques Ravel* Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, Maryland, United States of America Since the publication in 1995 of the first Biodefense Funding for of programs, the genome sequences of over complete genome sequence of a free-living Genomic Research 90,000 influenza viruses were rapidly organism, the bacterium Haemophilus influ- generated and are now deposited in enzae [1], more than 1,000 genomes of Since the anthrax letter attacks of 2001, GenBank (http://www.ncbi.nlm.nih.gov/ species from all three domains of life— when letters containing anthrax spores genomes/FLU/aboutdatabase.html). Be- Bacteria, Archaea, and Eukarya—have were mailed to several news media offices cause of the availability of large sequencing been completed and a staggering 4,300 and two Democratic senators in the capacity and the large amount of informa- are in progress (not including an even United States, killing five people and tion, the response to the 2009 H1N1 larger number of viral genome projects) infecting 17 others, funding agencies in influenza pandemic was rapid and efficient (GOLD, Genomes Online Database v. the US and other countries have priori- (Box 2): Genomics information was gener- 2.0; http://www.genomesonline.org/gold. tized research projects on organisms that ated within days and validated diagnostic cgi, as of August 2009). Whole-genome might potentially challenge our security tools were approved within weeks [5,6]. A shotgun sequencing remains the standard and economy should they be used as global response was made possible through in biomedical, biotechnological, environ- biological weapons.
    [Show full text]
  • Microbes and Metagenomics in Human Health an Overview of Recent Publications Featuring Illumina® Technology TABLE of CONTENTS
    Microbes and Metagenomics in Human Health An overview of recent publications featuring Illumina® technology TABLE OF CONTENTS 4 Introduction 5 Human Microbiome Gut Microbiome Gut Microbiome and Disease Inflammatory Bowel Disease (IBD) Metabolic Diseases: Diabetes and Obesity Obesity Oral Microbiome Other Human Biomes 25 Viromes and Human Health Viral Populations Viral Zoonotic Reservoirs DNA Viruses RNA Viruses Human Viral Pathogens Phages Virus Vaccine Development 44 Microbial Pathogenesis Important Microorganisms in Human Health Antimicrobial Resistance Bacterial Vaccines 54 Microbial Populations Amplicon Sequencing 16S: Ribosomal RNA Metagenome Sequencing: Whole-Genome Shotgun Metagenomics Eukaryotes Single-Cell Sequencing (SCS) Plasmidome Transcriptome Sequencing 63 Glossary of Terms 64 Bibliography This document highlights recent publications that demonstrate the use of Illumina technologies in immunology research. To learn more about the platforms and assays cited, visit www.illumina.com. An overview of recent publications featuring Illumina technology 3 INTRODUCTION The study of microbes in human health traditionally focused on identifying and 1. Roca I., Akova M., Baquero F., Carlet J., treating pathogens in patients, usually with antibiotics. The rise of antibiotic Cavaleri M., et al. (2015) The global threat of resistance and an increasingly dense—and mobile—global population is forcing a antimicrobial resistance: science for interven- tion. New Microbes New Infect 6: 22-29 1, 2, 3 change in that paradigm. Improvements in high-throughput sequencing, also 2. Shallcross L. J., Howard S. J., Fowler T. and called next-generation sequencing (NGS), allow a holistic approach to managing Davies S. C. (2015) Tackling the threat of anti- microbial resistance: from policy to sustainable microbes in human health.
    [Show full text]
  • Molecular Complexity of Successive Bacterial Epidemics Deconvoluted by Comparative Pathogenomics
    Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics Stephen B. Beresa,b, Ronan K. Carrolla,b, Patrick R. Sheaa,b, Izabela Sitkiewicza,b, Juan Carlos Martinez-Gutierreza,b, Donald E. Lowc, Allison McGeerd, Barbara M. Willeyd, Karen Greend, Gregory J. Tyrrelld, Thomas D. Goldmanf, Michael Feldgardeng, Bruce W. Birreng, Yuriy Fofanovh, John Boosi, William D. Wheatoni, Christiane Honischf, and James M. Mussera,b,1 aCenter for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and bDepartment of Pathology, The Methodist Hospital, Houston, TX 77030; cOntario Agency for Health Protection and Promotion, and University of Toronto, Toronto, ON M5G 1X5, Canada; dDepartment of Microbiology, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; eDepartment of Laboratory medicine and Pathology, University of Alberta, Edmonton, AB T6G 2J2, Canada; fSequenom, Inc., San Diego, CA 92121; gBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142; hDepartment of Computer Science and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204; and iRTI International, Research Triangle Park, NC 27709 Edited* by Charles R. Cantor, Sequenom Inc., San Diego, CA, and approved December 14, 2009 (received for review September 30, 2009) Understanding the fine-structure molecular architecture of bacterial century that GAS has the capacity to cause epidemics charac- epidemics has been a long-sought goal of infectious disease research. terized by rapid increase in disease frequency and severity. For We used short-read-length DNA sequencing coupled with mass example, Weech (6) described an epidemic of septic scarlet fever spectroscopy analysis of SNPs to study the molecular pathogenomics in Yunnanfu, China, that killed 50,000 people, fully 25% of the of three successive epidemics of invasive infections involving 344 population of the province.
    [Show full text]
  • Microbial Risk Assessment Guideline
    EPA/100/J-12/001 USDA/FSIS/2012-001 MICROBIAL RISK ASSESSMENT GUIDELINE PATHOGENIC MICROORGANISMS WITH FOCUS ON FOOD AND WATER Prepared by the Interagency Microbiological Risk Assessment Guideline Workgroup July 2012 Microbial Risk Assessment Guideline Page ii DISCLAIMER This guideline document represents the current thinking of the workgroup on the topics addressed. It is not a regulation and does not confer any rights for or on any person and does not operate to bind USDA, EPA, any other federal agency, or the public. Further, this guideline is not intended to replace existing guidelines that are in use by agencies. The decision to apply methods and approaches in this guideline, either totally or in part, is left to the discretion of the individual department or agency. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. Environmental Protection Agency (EPA) (2012). Microbial Risk Assessment Guideline: Pathogenic Microorganisms with Focus on Food and Water. EPA/100/J-12/001 Microbial Risk Assessment Guideline Page iii TABLE OF CONTENTS Disclaimer .......................................................................................................................... ii Interagency Workgroup Members ................................................................................ vii Preface ............................................................................................................................. viii Abbreviations ..................................................................................................................
    [Show full text]
  • Comparative Pathogenomics of Aeromonas Veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone
    microorganisms Article Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone Yogandree Ramsamy 1,2,3,* , Koleka P. Mlisana 2, Daniel G. Amoako 3 , Akebe Luther King Abia 3 , Mushal Allam 4 , Arshad Ismail 4 , Ravesh Singh 1,2 and Sabiha Y. Essack 3 1 Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; [email protected] 2 National Health Laboratory Service, Durban 4001, South Africa; [email protected] 3 Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; [email protected] (D.G.A.); [email protected] (A.L.K.A.); [email protected] (S.Y.E.) 4 Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa; [email protected] (M.A.); [email protected] (A.I.) * Correspondence: [email protected] Received: 9 November 2020; Accepted: 15 December 2020; Published: 16 December 2020 Abstract: The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (blaCPHA3 and blaOXA-12) and belonged to a novel sequence type, ST657 (a satellite clone).
    [Show full text]
  • Genomic Diversity of Escherichia Coli Isolates from Non-Human Primates in the Gambia
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.29.971309; this version posted March 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia 2 Ebenezer Foster-Nyarko1,2, Nabil-Fareed Alikhan1, Anuradha Ravi1, Gaëtan Thilliez1, 3 Nicholas Thomson1, David Baker1, Gemma Kay1, Jennifer D. Cramer3, Justin O’Grady1, 4 Martin Antonio2,4, Mark J. Pallen1,5† 5 6 1 Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom 7 2 Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical 8 Medicine, Atlantic Boulevard Road, Fajara, The Gambia 9 3 American Public University System, Charles Town, WV, USA 10 4 Microbiology and Infection Unit, Warwick Medical School, University of Warwick, 11 Coventry, United Kingdom 12 5 School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom. 13 14 †Correspondence: Professor Mark Pallen, Quadram Institute Bioscience, Norwich Research 15 Park, Norwich, Norfolk, United Kingdom 16 Email: [email protected] 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.29.971309; this version posted March 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • Pangenome Analysis Reveals Genetic Isolation in Campylobacter Hyointestinalis Subspecies Adapted to Different Mammalian Hosts
    www.nature.com/scientificreports OPEN Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to diferent mammalian hosts Daniela Costa 1,2, Simon Lévesque3, Nitin Kumar4, Pablo Fresia1,5, Ignacio Ferrés 1, Trevor D. Lawley4 & Gregorio Iraola 1,4,6* Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. hyointestinalis subsp. lawsonii which is predominantly recovered from pigs, and C. hyointestinalis subsp. hyointestinalis which can be found in a much wider range of mammalian hosts. Despite C. hyointestinalis being reported as an emerging pathogen, its evolutionary and host-associated diversifcation patterns are still vastly unexplored. For this reason, we generated whole-genome sequences of 13 C. hyointestinalis subsp. hyointestinalis strains and performed a comprehensive comparative analysis including publicly available C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii genomes, to gain insight into the genomic variation of these diferentially-adapted subspecies. Both subspecies are distinct phylogenetic lineages which present an apparent barrier to homologous recombination, suggesting genetic isolation. This is further supported by accessory gene patterns that recapitulate the core genome phylogeny. Additionally, C. hyointestinalis subsp. hyointestinalis presents a bigger and more diverse accessory genome, which probably refects its capacity to colonize diferent mammalian hosts unlike C. hyointestinalis subsp. lawsonii that is presumably host-restricted. This greater plasticity in the accessory genome of C. hyointestinalis subsp. hyointestinalis correlates to a higher incidence of genome-wide recombination events, that may be the underlying mechanism driving its diversifcation. Concordantly, both subspecies present distinct patterns of gene families involved in genome plasticity and DNA repair like CRISPR-associated proteins and restriction-modifcation systems.
    [Show full text]
  • Snapshot Study of Whole Genome Sequences of Escherichia Coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy
    antibiotics Article Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy Elisa Massella 1, Cameron J. Reid 2, Max L. Cummins 2, Kay Anantanawat 2, Tiziana Zingali 2, Andrea Serraino 1 , Silvia Piva 1, Federica Giacometti 1 and Steven P. Djordjevic 2,* 1 Department of Veterinary Medical Sciences, University of Bologna, 40126 Bologna, Italy; [email protected] (E.M.); [email protected] (A.S.); [email protected] (S.P.); [email protected] (F.G.) 2 The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; [email protected] (C.J.R.); [email protected] (M.L.C.); [email protected] (K.A.); [email protected] (T.Z.) * Correspondence: [email protected] Received: 15 September 2020; Accepted: 5 November 2020; Published: 6 November 2020 Abstract: Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, blaCTX-M1,15,55, blaCMY-2, gyrA/parC/parE, ampC and pmrB).
    [Show full text]
  • Pathogenomic Characterisation of a Novel, Layer-Associated Avian
    Pathogenomic characterisation of a novel, layer‐associated Avian Pathogenic Escherichia coli Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Charlotte Rose Collingwood July 2016 Author’s Declaration I declare that the work in this dissertation was carried out in accordance with the University’s Regulations and Code of Practice for Research. Except where indicated, the work is my own. Work done in collaboration, or with the assistance of others, is indicated as such. Any views expressed in the dissertation are those of the author. Signed: Date: i Acknowledgements Firstly I would like to thank my supervisor, Paul Wigley, for his help, support, guidance and most importantly encouragement during my studies. Your expertise, good humour, and kindness have been unparalleled. I’ve also learnt more about certain (obscure?) musical genres than I could have imagined. I’d also like to thank Craig Winstanley, in particular in enabling me to get the 3770 genome sequenced. Without your timely input, this particular chapter would be considerably briefer. I would also like to thank many people in the labs at Leahurst and in the Ronald Ross building for their help and friendship during my studies. Whether experiments went wrong or right; there was always someone there to commiserate or congratulate. There are too many to name individually, but special thanks go to Georgina Crayford, Elli Wright and Camilla Brena, you have helped more than you could know. On a practical note, I would like to thank Roy Chaudhuri for his expertise in genomics and phylogenetics, Mark Stevens for the kind gift of the χ7122 isolate, and Tim Wallis at Ridgeway Biologicals for sharing the SPS‐associated isolates used in this project.
    [Show full text]
  • The Perfect Condition for the Rising of Superbugs: Person-To-Person Contact and Antibiotic Use Are the Key Factors Responsible F
    antibiotics Article The Perfect Condition for the Rising of Superbugs: Person-to-Person Contact and Antibiotic Use Are the Key Factors Responsible for the Positive Correlation between Antibiotic Resistance Gene Diversity and Virulence Gene Diversity in Human Metagenomes Célia P. F. Domingues 1,2,† , João S. Rebelo 1,† , Joël Pothier 3 , Francisca Monteiro 1 , Teresa Nogueira 1,2,*,‡ and Francisco Dionisio 1,* 1 cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; [email protected] (C.P.F.D.); [email protected] (J.S.R.); [email protected] (F.M.) 2 INIAV—National Institute for Agrarian and Veterinary Research, Bacteriology and Mycology Laboratory, 2780-157 Oeiras, Portugal 3 Atelier de Bioinformatique, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, Muséum National d’Histoire Naturelle, CP 50, 45 rue Buffon, F-75005 Paris, France; [email protected] * Correspondence: [email protected] (T.N.); [email protected] (F.D.) Citation: Domingues, C.P.F.; Rebelo, † These authors have contributed equally to this work. J.S.; Pothier, J.; Monteiro, F.; Nogueira, ‡ The Institution is Located in Oeiras, and the Author’s Office is in 4485-655 Vairão, Portugal. T.; Dionisio, F. The Perfect Condition for the Rising of Superbugs: Abstract: Human metagenomes with a high diversity of virulence genes tend to have a high diversity Person-to-Person Contact and of antibiotic-resistance genes and vice-versa. To understand this positive correlation, we simulated Antibiotic Use Are the Key Factors the transfer of these genes and bacterial pathogens in a community of interacting people that take Responsible for the Positive antibiotics when infected by pathogens.
    [Show full text]