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Pallen MJ. Formation of prokaryote names from personal names: a review of current practice and a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38226641 DOI: 10.1099/ijsem.0.006233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
The practice of naming elements from the natural world after notable individuals stretches back to ancient times. This practice of creating eponyms-terms derived from personal names-has been carried forward into prokaryotic nomenclature, where the International Code of Nomenclature of Prokaryotes (ICNP) sets guidelines for creating scientific names from personal names. However, these guidelines can be seen as culturally biased, disjointed and, on occasion, misguided. Here, with the goal of modernizing these recommendations to render them more user-friendly, coherent and inclusive, I review current practice in the light of precedents and key linguistic and cultural principles, while questioning the applicability of the first-name/last-name paradigm for many cultural traditions. Procedural challenges include romanization of the personal name (including handling of diacritics), creation of a short and agreeable latinized stem, assignment of the stem to a declension and addition of suffixes or compound word components to create genus names or species epithets, customizing the approach for names and stems that end in a vowel. I review the pros and cons of stem augmentation, which involves addition of an extra 'i' to the original stem. Next, I formulate a coherent workflow, which I incorporate into a Python script to enable computer-based automation of name creation. Rather than following the ICNP in limiting discussion to a few dozen mainly European names, I examine how these principles work out when applied to the tens of thousands of last names under which scientists publish in the PubMed database, focusing on edge cases where conventional approaches fail, particularly very short and very long names. Drawing on these explorations and analyses, I propose emendations to the advice currently presented in the ICNP to usher in a modern, consistent, pragmatic and globally inclusive approach to the creation of prokaryotic eponyms.
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Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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Pallen MJ. Use of connecting vowels after stems ending in the same vowel: a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73. [PMID: 38054495 DOI: 10.1099/ijsem.0.006191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) provides guidance on the formation of names from compound words. This includes recommendations on the use of connecting vowels, which are meant to make names easier to pronounce. However, deployment of a connecting vowel when the preceding word element ends in the same vowel can make a name harder to spell or say, bringing us into conflict with the recommendations that we should avoid names that are disagreeable and difficult to pronounce. Given that there are many precedents where connecting vowels are not used in this context, particularly in names formed from the term 'alkali', I hereby propose an emendation to the ICNP to drop the connecting vowel when the preceding word element ends in the same vowel.
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Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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3
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Pallen MJ. Request for an Opinion on the standing and retention of Firmicutes as a phylum name. Int J Syst Evol Microbiol 2023; 73. [PMID: 37409558 DOI: 10.1099/ijsem.0.005933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
Oren and Garrity recently published 42 new prokaryotic phylum names, including Bacillota, which they describe as a synonym of the effectively published name Firmacutes and its orthographic correction Firmicutes. However, the name Firmacutes was listed as a division in the Approved Lists of Bacterial Names, which suggests that it should be treated as having been validly published. Recent emendations to rules require that a named phylum now requires a named type genus and a phylum name is formed by the addition of the suffix -ota to the stem of the name of the designated type genus. However, there are strong practical arguments for retaining the name Firmicutes, notwithstanding the uncertainty over whether the name already has standing. This matter is referred to the Judicial Commission, asking for an opinion on the standing and retention of the name Firmicutes.
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Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
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Gilroy R, Adam ME, Kumar B, Pallen MJ. An initial genomic blueprint of the healthy human oesophageal microbiome. Access Microbiol 2023; 5:acmi000558.v3. [PMID: 37424544 PMCID: PMC10323806 DOI: 10.1099/acmi.0.000558.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
Background The oesophageal microbiome is thought to contribute to the pathogenesis of oesophageal cancer. However, investigations using culture and molecular barcodes have provided only a low-resolution view of this important microbial community. We therefore explored the potential of culturomics and metagenomic binning to generate a catalogue of reference genomes from the healthy human oesophageal microbiome, alongside a comparison set from saliva. Results Twenty-two distinct colonial morphotypes from healthy oesophageal samples were genome-sequenced. These fell into twelve species clusters, eleven of which represented previously defined species. Two isolates belonged to a novel species, which we have named Rothia gullae. We performed metagenomic binning of reads generated from UK samples from this study alongside reads generated from Australian samples in a recent study. Metagenomic binning generated 136 medium or high-quality metagenome-assembled genomes (MAGs). MAGs were assigned to 56 species clusters, eight representing novel Candidatus species, which we have named Ca. Granulicatella gullae, Ca. Streptococcus gullae, Ca. Nanosynbacter quadramensis, Ca. Nanosynbacter gullae, Ca. Nanosynbacter colneyensis, Ca. Nanosynbacter norwichensis, Ca. Nanosynococcus oralis and Ca. Haemophilus gullae. Five of these novel species belong to the recently described phylum Patescibacteria . Although members of the Patescibacteria are known to inhabit the oral cavity, this is the first report of their presence in the oesophagus. Eighteen of the metagenomic species were, until recently, identified only by hard-to-remember alphanumeric placeholder designations. Here we illustrate the utility of a set of recently published arbitrary Latinate species names in providing user-friendly taxonomic labels for microbiome analyses.Our non-redundant species catalogue contained 63 species derived from cultured isolates or MAGs. Mapping revealed that these species account for around half of the sequences in the oesophageal and saliva metagenomes. Although no species was present in all oesophageal samples, 60 species occurred in at least one oesophageal metagenome from either study, with 50 identified in both cohorts. Conclusions Recovery of genomes and discovery of new species represents an important step forward in our understanding of the oesophageal microbiome. The genes and genomes that we have released into the public domain will provide a base line for future comparative, mechanistic and intervention studies.
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Affiliation(s)
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mina E. Adam
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Bhaskar Kumar
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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Pallen MJ, Rodriguez-R LM, Alikhan NF. Corrigendum: Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database. Int J Syst Evol Microbiol 2023; 73. [PMID: 37171866 DOI: 10.1099/ijsem.0.005885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Affiliation(s)
- Mark J Pallen
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Luis M Rodriguez-R
- Department of Microbiology, University of Innsbruck, Innsbruck, Tyrol, Austria
- Digital Science Center, University of Innsbruck, Innsbruck, Tyrol, Austria
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Pallen MJ, Rodriguez-R LM, Alikhan NF. Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database. Int J Syst Evol Microbiol 2022; 72. [PMID: 36125864 DOI: 10.1099/ijsem.0.005482] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.
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Affiliation(s)
- Mark J Pallen
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK.,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Luis M Rodriguez-R
- Department of Microbiology, University of Innsbruck, Innsbruck, Tyrol, Austria.,Digital Science Center, University of Innsbruck, Innsbruck, Tyrol, Austria
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Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ. Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity. PeerJ 2022; 10:e13084. [PMID: 35345588 PMCID: PMC8957277 DOI: 10.7717/peerj.13084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
Background The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. Results We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes. Conclusions Our metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.
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Affiliation(s)
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Joy Leng
- School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Anuradha Ravi
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Aharon Oren
- The Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dave Baker
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | | | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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Thomson NM, Gilroy R, Getino M, Foster-Nyarko E, van Vliet AH, La Ragione RM, Pallen MJ. Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens. PeerJ 2022; 10:e12935. [PMID: 35251780 PMCID: PMC8896058 DOI: 10.7717/peerj.12935] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/23/2022] [Indexed: 01/11/2023] Open
Abstract
The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.
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Affiliation(s)
| | - Rachel Gilroy
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Infection Biology, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
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Abstract
Escherichia coli has a rich history as biology's ‘rock star’, driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance—including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Corresponding author: Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom. E-mail:
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
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Callanan J, Stockdale SR, Adriaenssens EM, Kuhn JH, Rumnieks J, Pallen MJ, Shkoporov AN, Draper LA, Ross RP, Hill C. Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses. Microb Genom 2021; 7:000686. [PMID: 34747690 PMCID: PMC8743537 DOI: 10.1099/mgen.0.000686] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 11/18/2022] Open
Abstract
The vast majority of described prokaryotic viruses have double-stranded or single-stranded DNA or double-stranded RNA genomes. Until 2020, a mere four prokaryotic single-stranded, positive-sense RNA viruses have been classified in two genera (Riboviria; Lenarviricota; Allassoviricetes; Leviviridae). Several recent metagenomic and metatranscriptomic studies revealed a vastly greater diversity of these viruses in prokaryotic soil communities than ever anticipated. Phylogenetic analysis of these newly discovered viruses prompted the reorganization of class Allassoviricetes, now renamed Leviviricetes, to include two orders, Norzivirales and Timlovirales, and a total of six families, 428 genera and 882 species. Here we outline the new taxonomy of Leviviricetes, approved and ratified in 2021 by the International Committee on Taxonomy of Viruses, and describe open-access hidden Markov models to accommodate the anticipated identification and future classification of hundreds, if not thousands, of additional class members into this new taxonomic framework.
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Affiliation(s)
- Julie Callanan
- APC Microbiome Ireland, University College Cork, Cork, Co. Cork, T12 YT20, Ireland
| | - Stephen R. Stockdale
- APC Microbiome Ireland, University College Cork, Cork, Co. Cork, T12 YT20, Ireland
| | | | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Centre, Rātsupītes 1, Riga, LV-1067, Latvia
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Andrey N. Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Co. Cork, T12 YT20, Ireland
| | - Lorraine A. Draper
- APC Microbiome Ireland, University College Cork, Cork, Co. Cork, T12 YT20, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Co. Cork, T12 YT20, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Co. Cork, T12 YT20, Ireland
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Stubberfield E, Sheldon J, Card RM, AbuOun M, Rogers J, Williamson S, Kay GL, Pallen MJ, Anjum MF. Whole-Genome Sequencing of Brachyspira hyodysenteriae Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials. Front Microbiol 2021; 12:713233. [PMID: 34531838 PMCID: PMC8439570 DOI: 10.3389/fmicb.2021.713233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022] Open
Abstract
Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 B. hyodysenteriae archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published. Multi-locus sequence typing (MLST) showed a diverse population with 32 sequence types (STs) among the 115 APHA isolates, 25 of them identified only in England; while also confirming that the dominant European clonal complexes, CC8 and CC52, were common in the United Kingdom. A core-genome SNP tree typically clustered the isolates by ST, with isolates from some STs detected only within a specific region in England, although others were more widespread, suggesting transmission between different regions. Also, some STs were more conserved in their core genome than others, despite these isolates being from different holdings, regions and years. Minimum inhibitory concentrations to commonly used antimicrobials (Tiamulin, Valnemulin, Doxycycline, Lincomycin, Tylosin, Tylvalosin) were determined for 82 of the genome-sequenced isolates; genomic analysis revealed mutations generally correlated well with the corresponding resistance phenotype. There was a major swine dysentery intervention program in 2009–2010, and antimicrobial survival curves showed a significant reduction in sensitivity to tiamulin and valnemulin in isolates collected in and after 2010, compared to earlier isolates. This correlated with a significant increase in post-2009 isolates harboring the pleuromutilin resistance gene tva(A), which if present, may facilitate higher levels of resistance. The reduction in susceptibility of Brachyspira from diagnostic submissions to pleuromutilins, emphasizes the need for prudent treatment, control and eradication strategies.
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Affiliation(s)
- Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jonathan Sheldon
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Roderick M Card
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jon Rogers
- Animal and Plant Health Agency, Bury St Edmunds, United Kingdom
| | | | - Gemma L Kay
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich, United Kingdom.,Norwich Medical School, University of East Anglia, Norwich, United Kingdom.,School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom.,School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
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12
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Abstract
The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.
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Affiliation(s)
- Mark J Pallen
- University of East Anglia, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
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13
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Konings F, Perkins MD, Kuhn JH, Pallen MJ, Alm EJ, Archer BN, Barakat A, Bedford T, Bhiman JN, Caly L, Carter LL, Cullinane A, de Oliveira T, Druce J, El Masry I, Evans R, Gao GF, Gorbalenya AE, Hamblion E, Herring BL, Hodcroft E, Holmes EC, Kakkar M, Khare S, Koopmans MPG, Korber B, Leite J, MacCannell D, Marklewitz M, Maurer-Stroh S, Rico JAM, Munster VJ, Neher R, Munnink BO, Pavlin BI, Peiris M, Poon L, Pybus O, Rambaut A, Resende P, Subissi L, Thiel V, Tong S, van der Werf S, von Gottberg A, Ziebuhr J, Van Kerkhove MD. SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nat Microbiol 2021; 6:821-823. [PMID: 34108654 DOI: 10.1038/s41564-021-00932-w] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Mark J Pallen
- Quadram Institute Bioscience, University of East Anglia, Norwich, UK
| | - Erik J Alm
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | | | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jinal N Bhiman
- National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne, Victoria, Australia
| | | | - Anne Cullinane
- Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | | | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne, Victoria, Australia
| | - Ihab El Masry
- Emergency Centre for Transboundary Animal Disease, Food and Agriculture Organization of the United Nations (FAO), Cairo, Egypt
| | - Roger Evans
- World Health Organization, Geneva, Switzerland
| | - George F Gao
- Chinese Center for Disease Control and Prevention, Beijing, P.R. China
| | - Alexander E Gorbalenya
- Leiden University Medical Center, Leiden, The Netherlands.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Edward C Holmes
- The University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Duncan MacCannell
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Sebastian Maurer-Stroh
- The Global Initiative on Sharing All Influenza Data (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Vincent J Munster
- Virus Ecology Unit, National Institute of Allergy and Infectious Diseases, Rockville, MA, USA
| | - Richard Neher
- Biozentrum, University of Basel, Switzerland Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | | | | | - Leo Poon
- The University of Hong Kong, Hong Kong, China
| | | | - Andrew Rambaut
- Institute for Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Paola Resende
- Laboratory of Respiratory Viruses and Measles (LVRS), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | | | - Volker Thiel
- University of Bern, Bern, Switzerland.,Institute of Virology and Immunology, Mittelhäusern, Switzerland
| | - Suxiang Tong
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Anne von Gottberg
- National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
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14
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Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan NF, Baker D, Gharbi K, Hall N, Watson M, Adriaenssens EM, Foster-Nyarko E, Jarju S, Secka A, Antonio M, Oren A, Chaudhuri RR, La Ragione R, Hildebrand F, Pallen MJ. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ 2021; 9:e10941. [PMID: 33868800 PMCID: PMC8035907 DOI: 10.7717/peerj.10941] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. RESULTS We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. CONCLUSIONS Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.
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Affiliation(s)
| | | | - Maria Getino
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Isabella Pursley
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Daniel L. Horton
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | | | - Dave Baker
- Quadram Institute Bioscience, Norwich, UK
| | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Arss Secka
- West Africa Livestock Innovation Centre, Banjul, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roy R. Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, UK
- University of East Anglia, Norwich, UK
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15
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Glendinning L, Stewart RD, Pallen MJ, Watson KA, Watson M. Author Correction: Assembly of hundreds of novel bacterial genomes from the chicken caecum. Genome Biol 2021; 22:60. [PMID: 33579307 PMCID: PMC7879605 DOI: 10.1186/s13059-021-02284-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Laura Glendinning
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK.
| | - Robert D Stewart
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK
| | - Mark J Pallen
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Kellie A Watson
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK
| | - Mick Watson
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK
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16
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Foster-Nyarko E, Alikhan NF, Ikumapayi UN, Sarwar G, Okoi C, Tientcheu PEM, Defernez M, O'Grady J, Antonio M, Pallen MJ. Genomic diversity of Escherichia coli from healthy children in rural Gambia. PeerJ 2021; 9:e10572. [PMID: 33505796 PMCID: PMC7796664 DOI: 10.7717/peerj.10572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/23/2020] [Indexed: 01/21/2023] Open
Abstract
Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative E. coli, and 53% of the isolates encode resistance to three or more classes of antimicrobials. Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity compared to independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom.,Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Usman N Ikumapayi
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Golam Sarwar
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Marianne Defernez
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom.,School of Veterinary Medicine, University of Surrey, Surrey, United Kingdom
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17
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Thomson NM, Pallen MJ. Restoration of wild-type motility to flagellin-knockout Escherichia coli by varying promoter, copy number and induction strength in plasmid-based expression of flagellin. Curr Res Biotechnol 2021; 2:45-52. [PMID: 33381753 PMCID: PMC7758877 DOI: 10.1016/j.crbiot.2020.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Flagellin is the major constituent of the flagellar filament and faithful restoration of wild-type motility to flagellin mutants may be beneficial for studies of flagellar biology and biotechnological exploitation of the flagellar system. However, gene complementation studies often fail to report whether true wild-type motility was restored by expressing flagellin from a plasmid. Therefore, we explored the restoration of motility by flagellin expressed from a variety of combinations of promoter, plasmid copy number and induction strength. Motility was only partially (~50%) restored using the tightly regulated rhamnose promoter due to weak flagellin gene expression, but wild-type motility was regained with the T5 promoter, which, although leaky, allowed titration of induction strength. The endogenous E. coli flagellin promoter also restored wild-type motility. However, flagellin gene transcription levels increased 3.1–27.9-fold when wild-type motility was restored, indicating disturbances in the flagellar regulatory mechanisms. Motility was little affected by plasmid copy number when dependent on inducible promoters. However, plasmid copy number was important when expression was controlled by the native E. coli flagellin promoter. Motility was poorly correlated with flagellin transcription levels, but strongly correlated with the amount of flagellin associated with the flagellar filament, suggesting that excess monomers are either not exported or not assembled into filaments. This study provides a useful reference for further studies of flagellar function and a simple blueprint for similar studies with other proteins. Restoration of motility to flagellin-knockout E. coli depends on choice of promoter. Plasmid copy number is important when using the natural flagellin promoter. For inducible promoters, induction strength is more important than copy number. Large increase in flagellin transcription but not flagella-associated protein. Plasmid-based expression interrupts flagellin expression control mechanisms.
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Affiliation(s)
- Nicholas M Thomson
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
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18
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Pallen MJ, Telatin A, Oren A. The Next Million Names for Archaea and Bacteria. Trends Microbiol 2020; 29:289-298. [PMID: 33288384 DOI: 10.1016/j.tim.2020.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 01/12/2023]
Abstract
Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.
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Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK; School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK; University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Aharon Oren
- The Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
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19
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Abstract
Background Gene doctoring is an efficient recombination-based genetic engineering approach to mutagenesis of the bacterial chromosome that combines the λ-Red recombination system with a suicide donor plasmid that is cleaved in vivo to generate linear DNA fragments suitable for recombination. The use of a suicide donor plasmid makes Gene Doctoring more efficient than other recombineering technologies. However, generation of donor plasmids typically requires multiple cloning and screening steps. Results We constructed a simplified acceptor plasmid, called pDOC-GG, for the assembly of multiple DNA fragments precisely and simultaneously to form a donor plasmid using Golden Gate assembly. Successful constructs can easily be identified through blue-white screening. We demonstrated proof of principle by inserting a gene for green fluorescent protein into the chromosome of Escherichia coli. We also provided related genetic parts to assist in the construction of mutagenesis cassettes with a tetracycline-selectable marker. Conclusions Our plasmid greatly simplifies the construction of Gene Doctoring donor plasmids and allows for the assembly of complex, multi-part insertion or deletion cassettes with a free choice of target sites and selection markers. The tools we developed are applicable to gene editing for a wide variety of purposes in Enterobacteriaceae and potentially in other diverse bacterial families.
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Affiliation(s)
- Nicholas M Thomson
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Chuanzhen Zhang
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TU, UK. .,School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, Surrey, GU2 7AL, UK.
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20
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Foster-Nyarko E, Alikhan NF, Ravi A, Thilliez G, Thomson NM, Baker D, Kay G, Cramer JD, O’Grady J, Antonio M, Pallen MJ. Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia. Microb Genom 2020; 6:mgen000428. [PMID: 32924917 PMCID: PMC7643976 DOI: 10.1099/mgen.0.000428] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 08/13/2020] [Indexed: 01/27/2023] Open
Abstract
Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2 - characterized by strains that cause human extraintestinal infections - and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes - indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
| | | | - Anuradha Ravi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | - Gaëtan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | | | - David Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | - Gemma Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | | | - Justin O’Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | - Martin Antonio
- Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
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21
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Foster-Nyarko E, Alikhan NF, Ravi A, Thomson N, Jarju S, Secka A, Antonio M, J. Pallen M. Gambian poultry isolates from hyperendemic group of AMR Escherichia coli strains in sub-Saharan Africa. Access Microbiol 2020. [DOI: 10.1099/acmi.ac2020.po0824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from ten chickens and nine guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (four of them novel), of which ST155 was the most common (22/68, 32%). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64%) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates sit within a tight genomic cluster (100 alleles difference) of strains from poultry and livestock in sub-Saharan Africa (the Gambia, Uganda and Kenya). Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.
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Affiliation(s)
| | | | - Anuradha Ravi
- Quadram Institute Bioscience,Norwich Research Park,Norwich
| | | | - Sheikh Jarju
- Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine,Atlantic Boulevard Road,Fajara
| | - Arss Secka
- West Africa Livestock Innovation Centre,Banjul,Gambia
| | - Martin Antonio
- Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine,Atlantic Boulevard Road,Fajara
| | - Mark J. Pallen
- Quadram Institute Bioscience,Norwich Research Park,Norwich
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22
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Hildebrand F, Pallen MJ, Bork P. Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology. Gut 2020; 69:1358-1359. [PMID: 31203204 PMCID: PMC7306977 DOI: 10.1136/gutjnl-2019-319045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/30/2019] [Indexed: 12/08/2022]
Affiliation(s)
- Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK,Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mark J Pallen
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
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23
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Glendinning L, Stewart RD, Pallen MJ, Watson KA, Watson M. Assembly of hundreds of novel bacterial genomes from the chicken caecum. Genome Biol 2020; 21:34. [PMID: 32051016 PMCID: PMC7014784 DOI: 10.1186/s13059-020-1947-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/27/2020] [Indexed: 11/22/2022] Open
Abstract
Background Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. Results We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. Conclusions This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.
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Affiliation(s)
- Laura Glendinning
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK.
| | - Robert D Stewart
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK
| | - Mark J Pallen
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Kellie A Watson
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK
| | - Mick Watson
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK
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24
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Senghore M, Diarra B, Gehre F, Otu J, Worwui A, Muhammad AK, Kwambana-Adams B, Kay GL, Sanogo M, Baya B, Orsega S, Doumbia S, Diallo S, de Jong BC, Pallen MJ, Antonio M. Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali. Sci Rep 2020; 10:327. [PMID: 31941887 PMCID: PMC6962199 DOI: 10.1038/s41598-019-56001-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/30/2019] [Indexed: 11/10/2022] Open
Abstract
In recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Whole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. Among the 76 patients, 61(80.3%) new cases and 15(19.7%) retreatment cases, 12 (16%) were infected by MDR-TB. The dominant lineage was the Euro-American lineage, Lineage 4. Within Lineage 4, the Cameroon genotype was the most prevalent genotype (n = 20, 26%), followed by the Ghana genotype (n = 16, 21%). A sub-clade of the Cameroon genotype, which emerged ~22 years ago was likely to be involved in community transmission. A sub-clade of the Ghana genotype that arose approximately 30 years ago was an important cause of MDR-TB in Bamako. The Ghana genotype isolates appeared more likely to be MDR than other genotypes after controlling for treatment history. We identified a clade of four related Beijing isolates that included one MDR-TB isolate. It is a major concern to find the Cameroon and Ghana genotypes involved in community transmission and MDR-TB respectively. The presence of the Beijing genotype in Bamako remains worrying, given its high transmissibility and virulence.
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Affiliation(s)
- Madikay Senghore
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Florian Gehre
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Jacob Otu
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Abdul Khalie Muhammad
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Brenda Kwambana-Adams
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Gemma L Kay
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Moumine Sanogo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Susan Orsega
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Souleymane Diallo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Mark J Pallen
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia.
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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25
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Ravi A, Halstead FD, Bamford A, Casey A, Thomson NM, van Schaik W, Snelson C, Goulden R, Foster-Nyarko E, Savva GM, Whitehouse T, Pallen MJ, Oppenheim BA. Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients. Microb Genom 2019; 5. [PMID: 31526447 PMCID: PMC6807385 DOI: 10.1099/mgen.0.000293] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson’s index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii. In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.
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Affiliation(s)
- Anuradha Ravi
- Quadram Institute Bioscience and University of East Anglia, Norwich, NR4 7UA, UK
| | - Fenella D Halstead
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, B15 2GW, UK
| | - Amy Bamford
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, B15 2GW, UK
| | - Anna Casey
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, B15 2GW, UK
| | - Nicholas M Thomson
- Quadram Institute Bioscience and University of East Anglia, Norwich, NR4 7UA, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Catherine Snelson
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK
| | | | | | - George M Savva
- Quadram Institute Bioscience and University of East Anglia, Norwich, NR4 7UA, UK
| | - Tony Whitehouse
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK.,Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK
| | - Mark J Pallen
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK.,Quadram Institute Bioscience and University of East Anglia, Norwich, NR4 7UA, UK.,School of Veterinary Medicine, University of Surrey, Daphne Jackson Rd, Guildford GU2 7AL, UK
| | - Beryl A Oppenheim
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, B15 2GW, UK
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26
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Ravi A, Ereqat S, Al-Jawabreh A, Abdeen Z, Abu Shamma O, Hall H, Pallen MJ, Nasereddin A. Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus. PLoS Negl Trop Dis 2019; 13:e0006805. [PMID: 30640905 PMCID: PMC6347332 DOI: 10.1371/journal.pntd.0006805] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/25/2019] [Accepted: 11/29/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Across the world, ticks act as vectors of human and animal pathogens. Ticks rely on bacterial endosymbionts, which often share close and complex evolutionary links with tick-borne pathogens. As the prevalence, diversity and virulence potential of tick-borne agents remain poorly understood, there is a pressing need for microbial surveillance of ticks as potential disease vectors. METHODOLOGY/PRINCIPAL FINDINGS We developed a two-stage protocol that includes 16S-amplicon screening of pooled samples of hard ticks collected from dogs, sheep and camels in Palestine, followed by shotgun metagenomics on individual ticks to detect and characterise tick-borne pathogens and endosymbionts. Two ticks isolated from sheep yielded an abundance of reads from the genus Rickettsia, which were assembled into draft genomes. One of the resulting genomes was highly similar to Rickettsia massiliae strain MTU5. Analysis of signature genes showed that the other represents the first genome sequence of the potential pathogen Candidatus Rickettsia barbariae. Ticks from a dog and a sheep yielded draft genome sequences of Coxiella strains. A sheep tick yielded sequences from the sheep pathogen Anaplasma ovis, while Hyalomma ticks from camels yielded sequences belonging to Francisella-like endosymbionts. From the metagenome of a dog tick from Jericho, we generated a genome sequence of a canine parvovirus. SIGNIFICANCE Here, we have shown how a cost-effective two-stage protocol can be used to detect and characterise tick-borne pathogens and endosymbionts. In recovering genome sequences from an unexpected pathogen (canine parvovirus) and a previously unsequenced pathogen (Candidatus Rickettsia barbariae), we demonstrate the open-ended nature of metagenomics. We also provide evidence that ticks can carry canine parvovirus, raising the possibility that ticks might contribute to the spread of this troublesome virus.
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Affiliation(s)
- Anuradha Ravi
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Suheir Ereqat
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Deis, East Jerusalem, Palestine
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University Abu Deis, East Jerusalem, Palestine and Al-Quds Public Health Society, Abu Deis, East Jerusalem, Palestine
| | - Amer Al-Jawabreh
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University Abu Deis, East Jerusalem, Palestine and Al-Quds Public Health Society, Abu Deis, East Jerusalem, Palestine
- Faculty of Allied Medical Sciences, Arab American University Palestine, Jenin, Palestine
| | - Ziad Abdeen
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University Abu Deis, East Jerusalem, Palestine and Al-Quds Public Health Society, Abu Deis, East Jerusalem, Palestine
| | - Omar Abu Shamma
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University Abu Deis, East Jerusalem, Palestine and Al-Quds Public Health Society, Abu Deis, East Jerusalem, Palestine
| | - Holly Hall
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Mark J. Pallen
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - Abedelmajeed Nasereddin
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University Abu Deis, East Jerusalem, Palestine and Al-Quds Public Health Society, Abu Deis, East Jerusalem, Palestine
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27
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Yasir M, Icke C, Abdelwahab R, Haycocks JR, Godfrey RE, Sazinas P, Pallen MJ, Henderson IR, Busby SJW, Browning DF. Organization and architecture of AggR-dependent promoters from enteroaggregative Escherichia coli. Mol Microbiol 2018; 111:534-551. [PMID: 30485564 PMCID: PMC6392122 DOI: 10.1111/mmi.14172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 11/27/2022]
Abstract
Enteroaggregative Escherichia coli (EAEC), is a diarrhoeagenic human pathogen commonly isolated from patients in both developing and industrialized countries. Pathogenic EAEC strains possess many virulence determinants, which are thought to be involved in causing disease, though, the exact mechanism by which EAEC causes diarrhoea is unclear. Typical EAEC strains possess the transcriptional regulator, AggR, which controls the expression of many virulence determinants, including the attachment adherence fimbriae (AAF) that are necessary for adherence to human gut epithelial cells. Here, using RNA‐sequencing, we have investigated the AggR regulon from EAEC strain 042 and show that AggR regulates the transcription of genes on both the bacterial chromosome and the large virulence plasmid, pAA2. Due to the importance of fimbriae, we focused on the two AAF/II fimbrial gene clusters in EAEC 042 (afaB‐aafCB and aafDA) and identified the promoter elements and AggR‐binding sites required for fimbrial expression. In addition, we examined the organization of the fimbrial operon promoters from other important EAEC strains to understand the rules of AggR‐dependent activation. Finally, we generated a series of semi‐synthetic promoters to define the minimal sequence required for AggR‐mediated activation and show that the correct positioning of a single AggR‐binding site is sufficient to confer AggR‐dependence.
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Affiliation(s)
- Muhammad Yasir
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA, UK
| | - Christopher Icke
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Radwa Abdelwahab
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.,Faculty of Medicine, Assiut University, Assiut, Egypt
| | - James R Haycocks
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rita E Godfrey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pavelas Sazinas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen J W Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Douglas F Browning
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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28
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Thomson NM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ. Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria. PLoS One 2018; 13:e0206544. [PMID: 30462661 PMCID: PMC6248924 DOI: 10.1371/journal.pone.0206544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/15/2018] [Indexed: 01/04/2023] Open
Abstract
Flagella, the primary means of motility in bacteria, are helical filaments that function as microscopic propellers composed of thousands of copies of the protein flagellin. Here, we show that many bacteria encode “giant” flagellins, greater than a thousand amino acids in length, and that two species that encode giant flagellins, the marine γ-proteobacteria Bermanella marisrubri and Oleibacter marinus, produce monopolar flagellar filaments considerably thicker than filaments composed of shorter flagellin monomers. We confirm that the flagellum from B. marisrubri is built from its giant flagellin. Phylogenetic analysis reveals that the mechanism of evolution of giant flagellins has followed a stepwise process involving an internal domain duplication followed by insertion of an additional novel insert. This work illustrates how “the” bacterial flagellum should not be seen as a single, idealised structure, but as a continuum of evolved machines adapted to a range of niches.
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Affiliation(s)
| | - Josie L. Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Mark J. Pallen
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
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29
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Senghore M, Otu J, Witney A, Gehre F, Doughty EL, Kay GL, Butcher P, Salako K, Kehinde A, Onyejepu N, Idigbe E, Corrah T, de Jong B, Pallen MJ, Antonio M. Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria. PLoS One 2017; 12:e0184510. [PMID: 28926571 PMCID: PMC5604961 DOI: 10.1371/journal.pone.0184510] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/27/2017] [Indexed: 11/18/2022] Open
Abstract
Nigeria has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole-genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from two tertiary referral centers in Southwest Nigeria. In line with previous molecular epidemiology studies, most isolates of Mycobacterium tuberculosis from this dataset belonged to the Cameroon clade within the Euro-American lineage. Phylogenetic analysis showed this clade was undergoing clonal expansion in this region, and suggests that it was involved in community transmission of sensitive and multidrug-resistant tuberculosis. Five patients enrolled for retreatment were infected with pre-extensively drug resistant (pre-XDR) due to fluoroquinolone resistance in isolates from the Cameroon clade. In all five cases resistance was conferred through a mutation in the gyrA gene. In some patients, genomic changes occurred in bacterial isolates during the course of treatment that potentially led to decreased drug susceptibility. We conclude that inter-patient transmission of resistant isolates, principally from the Cameroon clade, contributes to the spread of MDR-TB in this setting, underscoring the urgent need to curb the spread of multi-drug resistance in this region.
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MESH Headings
- Adolescent
- Adult
- Antitubercular Agents/pharmacology
- Bacterial Proteins/genetics
- Cameroon/epidemiology
- Child
- Child, Preschool
- DNA Gyrase/genetics
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Female
- Genome, Bacterial
- Humans
- Infant
- Infant, Newborn
- Male
- Mutation
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Nigeria/epidemiology
- Phylogeny
- Sequence Analysis, DNA
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/microbiology
- Young Adult
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Affiliation(s)
- Madikay Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Jacob Otu
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Adam Witney
- Institute of Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Emma L. Doughty
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Gemma L. Kay
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Phillip Butcher
- Institute of Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Kayode Salako
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria
| | - Aderemi Kehinde
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria
| | - Nneka Onyejepu
- National Tuberculosis Reference Laboratory, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Emmanuel Idigbe
- National Tuberculosis Reference Laboratory, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Tumani Corrah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | | | - Mark J. Pallen
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
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30
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Card RM, Cawthraw SA, Nunez-Garcia J, Ellis RJ, Kay G, Pallen MJ, Woodward MJ, Anjum MF. An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli. mBio 2017; 8:e00777-17. [PMID: 28720731 PMCID: PMC5516254 DOI: 10.1128/mbio.00777-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/06/2017] [Indexed: 01/28/2023] Open
Abstract
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies.IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections. Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between commensals and pathogens. Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to commensal Escherichia coli occurs at a high rate, even in the absence of antibiotic administration. Our work demonstrates that the in vitro gut model provides a powerful screening tool that can be used to assess and refine interventions that mitigate the spread of antibiotic resistance in the gut before undertaking animal studies.
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Affiliation(s)
- Roderick M Card
- Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Shaun A Cawthraw
- Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Javier Nunez-Garcia
- Central Sequencing Unit, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Richard J Ellis
- Central Sequencing Unit, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Gemma Kay
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Martin J Woodward
- Food and Nutritional Sciences Department, University of Reading, Whiteknights, Reading, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
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31
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Abstract
The advent of next-generation sequencing has enabled in-depth analysis to study the composition and function of the gut microbiota in a culture-independent manner. Consequently, this has led to rapid interest in understanding the pathogenesis and progression of chronic liver disease in relation to perturbations of the gut microbiota. Animal models and human studies have demonstrated its crucial role in contributing to disease mechanisms in alcoholic and non-alcoholic liver disease and more recently in primary sclerosing cholangitis. There is increasing evidence to suggest that the gut microbiota and its components influence the development and modulation of chronic liver damage through direct communication via the portal system, metabolite production, alterations in gut barrier integrity, liver/gut immune axis and bile acid metabolism. The impact of microbiota-directed therapies for liver disease is still in its infancy. Better understanding of its role in disease mechanisms will lead to a more targeted approach in modulation of gut microbiota to influence both progression and complications of liver disease. This review discusses the current evidence for the gut microbiota-liver axis and its role in the development, progression and treatment of liver disease.
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Affiliation(s)
- Mark J Pallen
- University Hospital Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
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32
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Guy CS, Tichauer E, Kay GL, Phillips DJ, Bailey TL, Harrison J, Furze CM, Millard AD, Gibson MI, Pallen MJ, Fullam E. Identification of the anti-mycobacterial functional properties of piperidinol derivatives. Br J Pharmacol 2017; 174:2183-2193. [PMID: 28195652 PMCID: PMC5481654 DOI: 10.1111/bph.13744] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/06/2017] [Accepted: 02/10/2017] [Indexed: 11/26/2022] Open
Abstract
Background and Purpose Tuberculosis (TB) remains a major global health threat and is now the leading cause of death from a single infectious agent worldwide. The current TB drug regimen is inadequate, and new anti‐tubercular agents are urgently required to be able to successfully combat the increasing prevalence of drug‐resistant TB. The purpose of this study was to investigate a piperidinol compound derivative that is highly active against the Mycobacterium tuberculosis bacillus. Experimental Approach The antibacterial properties of the piperidinol compound and its corresponding bis‐Mannich base analogue were evaluated against M. smegmatis and Gram‐negative organisms. Cytotoxicity studies were undertaken in order to determine the selectivity index for these compounds. Spontaneous resistant mutants of M. smegmatis were generated against the piperidinol and corresponding bis‐Mannich base lead derivatives and whole genome sequencing employed to determine the genetic modifications that lead to selection pressure in the presence of these compounds. Key Results The piperidinol and the bis‐Mannich base analogue were found to be selective for mycobacteria and rapidly kill this organism with a cytotoxicity selectivity index for mycobacteria of >30‐fold. Whole genome sequencing of M. smegmatis strains resistant to the lead compounds led to the identification of a number of single nucleotide polymorphisms indicating multiple targets. Conclusion and Implications Our results indicate that the piperidinol moiety represents an attractive compound class in the pursuit of novel anti‐tubercular agents. Linked Articles This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro‐organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc
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Affiliation(s)
- Collette S Guy
- School of Life Sciences, University of Warwick, Coventry, UK.,Department of Chemistry, University of Warwick, Coventry, UK
| | - Esther Tichauer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Gemma L Kay
- Medical School, University of Warwick, Coventry, UK
| | | | - Trisha L Bailey
- Department of Chemistry, University of Warwick, Coventry, UK
| | - James Harrison
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry, UK.,Medical School, University of Warwick, Coventry, UK
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33
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Unnikrishnan M, Constantinidou C, Palmer T, Pallen MJ. The Enigmatic Esx Proteins: Looking Beyond Mycobacteria. Trends Microbiol 2017; 25:192-204. [DOI: 10.1016/j.tim.2016.11.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/20/2016] [Accepted: 11/04/2016] [Indexed: 01/17/2023]
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34
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Gehre F, Otu J, Kendall L, Forson A, Kwara A, Kudzawu S, Kehinde AO, Adebiyi O, Salako K, Baldeh I, Jallow A, Jallow M, Dagnra A, Dissé K, Kadanga EA, Idigbe EO, Onubogu C, Onyejepu N, Gaye-Diallo A, Ba-Diallo A, Rabna P, Mane M, Sanogo M, Diarra B, Dezemon Z, Sanou A, Senghore M, Kwambana-Adams BA, Demba E, Faal-Jawara T, Kumar S, Tientcheu LD, Jallow A, Ceesay S, Adetifa I, Jaye A, Pallen MJ, D'Alessandro U, Kampmann B, Adegbola RA, Mboup S, Corrah T, de Jong BC, Antonio M. The emerging threat of pre-extensively drug-resistant tuberculosis in West Africa: preparing for large-scale tuberculosis research and drug resistance surveillance. BMC Med 2016; 14:160. [PMID: 27806714 PMCID: PMC5094099 DOI: 10.1186/s12916-016-0704-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/28/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (TB) is a global public health problem. Adequate management requires baseline drug-resistance prevalence data. In West Africa, due to a poor laboratory infrastructure and inadequate capacity, such data are scarce. Therefore, the true extent of drug-resistant TB was hitherto undetermined. In 2008, a new research network, the West African Network of Excellence for Tuberculosis, AIDS and Malaria (WANETAM), was founded, comprising nine study sites from eight West African countries (Burkina Faso, The Gambia, Ghana, Guinea-Bissau, Mali, Nigeria, Senegal and Togo). The goal was to establish Good Clinical Laboratory Practice (GCLP) principles and build capacity in standardised smear microscopy and mycobacterial culture across partnering laboratories to generate the first comprehensive West African drug-resistance data. METHODS Following GCLP and laboratory training sessions, TB isolates were collected at sentinel referral sites between 2009-2013 and tested for first- and second-line drug resistance. RESULTS From the analysis of 974 isolates, an unexpectedly high prevalence of multi-drug-resistant (MDR) strains was found in new (6 %) and retreatment patients (35 %) across all sentinel sites, with the highest prevalence amongst retreatment patients in Bamako, Mali (59 %) and the two Nigerian sites in Ibadan and Lagos (39 % and 66 %). In Lagos, MDR is already spreading actively amongst 32 % of new patients. Pre-extensively drug-resistant (pre-XDR) isolates are present in all sites, with Ghana showing the highest proportion (35 % of MDR). In Ghana and Togo, pre-XDR isolates are circulating amongst new patients. CONCLUSIONS West African drug-resistance prevalence poses a previously underestimated, yet serious public health threat, and our estimates obtained differ significantly from previous World Health Organisation (WHO) estimates. Therefore, our data are reshaping current concepts and are essential in informing WHO and public health strategists to implement urgently needed surveillance and control interventions in West Africa.
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Affiliation(s)
- Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Jacob Otu
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Lindsay Kendall
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Audrey Forson
- University of Ghana Medical School, Accra, Ghana.,Korle-Bu Teaching Hospital, Accra, Ghana
| | - Awewura Kwara
- Warren Alpert Medical School of Brown University, Providence, RI, USA.,The Miriam Hospital, Providence, RI, USA
| | | | - Aderemi O Kehinde
- College of Medicine, University of Ibadan, Ibadan, Nigeria.,University College Hospital, Ibadan, Oyo, 23402, Nigeria
| | | | - Kayode Salako
- University College Hospital, Ibadan, Oyo, 23402, Nigeria
| | - Ignatius Baldeh
- National Public Health Laboratory Services, Banjul, The Gambia
| | - Aisha Jallow
- National Public Health Laboratory Services, Banjul, The Gambia
| | - Mamadou Jallow
- National Public Health Laboratory Services, Banjul, The Gambia
| | - Anoumou Dagnra
- Laboratoire National de Reference Mycobacteria, Lome, Togo
| | - Kodjo Dissé
- Laboratoire National de Reference Mycobacteria, Lome, Togo
| | | | | | | | | | | | - Awa Ba-Diallo
- Laboratoire Bactériologie Virologie Aristide Le Dantec Sénégal, Dakar, Senegal
| | - Paulo Rabna
- National Institute of Public Health, Bissau, Guinea-Bissau
| | - Morto Mane
- National Institute of Public Health, Bissau, Guinea-Bissau
| | - Moumine Sanogo
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bassirou Diarra
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Zingue Dezemon
- Centre Muraz and the National TB Program, Ouagadougou, Burkina Faso
| | - Adama Sanou
- Centre Muraz and the National TB Program, Ouagadougou, Burkina Faso
| | - Madikay Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Brenda A Kwambana-Adams
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Edward Demba
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Tutty Faal-Jawara
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Samrat Kumar
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Leopold D Tientcheu
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Adama Jallow
- National Tuberculosis/Leprosy Control Program, Banjul, The Gambia
| | - Samba Ceesay
- Health Services, Ministry of Health and Social Welfare, Banjul, The Gambia
| | - Ifedayo Adetifa
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Disease Control and Elimination, Medical Research Council Unit, Serrekunda, The Gambia
| | - Assan Jaye
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Umberto D'Alessandro
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Disease Control and Elimination, Medical Research Council Unit, Serrekunda, The Gambia.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Department of Paediatrics, Imperial College London, London, UK
| | | | - Souleymane Mboup
- Laboratoire Bactériologie Virologie Aristide Le Dantec Sénégal, Dakar, Senegal
| | - Tumani Corrah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | | | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia. .,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK. .,Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
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Kwambana-Adams BA, Asiedu-Bekoe F, Sarkodie B, Afreh OK, Kuma GK, Owusu-Okyere G, Foster-Nyarko E, Ohene SA, Okot C, Worwui AK, Okoi C, Senghore M, Otu JK, Ebruke C, Bannerman R, Amponsa-Achiano K, Opare D, Kay G, Letsa T, Kaluwa O, Appiah-Denkyira E, Bampoe V, Zaman SMA, Pallen MJ, D'Alessandro U, Mwenda JM, Antonio M. An outbreak of pneumococcal meningitis among older children (≥5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana. BMC Infect Dis 2016; 16:575. [PMID: 27756235 PMCID: PMC5070171 DOI: 10.1186/s12879-016-1914-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND An outbreak of pneumococcal meningitis among non-infant children and adults occurred in the Brong-Ahafo region of Ghana between December 2015 and April 2016 despite the recent nationwide implementation of a vaccination programme for infants with the 13-valent pneumococcal conjugate vaccine (PCV13). METHODS Cerebrospinal fluid (CSF) specimens were collected from patients with suspected meningitis in the Brong-Ahafo region. CSF specimens were subjected to Gram staining, culture and rapid antigen testing. Quantitative PCR was performed to identify pneumococcus, meningococcus and Haemophilus influenzae. Latex agglutination and molecular serotyping were performed on samples. Antibiogram and whole genome sequencing were performed on pneumococcal isolates. RESULTS Eight hundred eighty six patients were reported with suspected meningitis in the Brong-Ahafo region during the period of the outbreak. In the epicenter district, the prevalence was as high as 363 suspected cases per 100,000 people. Over 95 % of suspected cases occurred in non-infant children and adults, with a median age of 20 years. Bacterial meningitis was confirmed in just under a quarter of CSF specimens tested. Pneumococcus, meningococcus and Group B Streptococcus accounted for 77 %, 22 % and 1 % of confirmed cases respectively. The vast majority of serotyped pneumococci (80 %) belonged to serotype 1. Most of the pneumococcal isolates tested were susceptible to a broad range of antibiotics, with the exception of two pneumococcal serotype 1 strains that were resistant to both penicillin and trimethoprim-sulfamethoxazole. All sequenced pneumococcal serotype 1 strains belong to Sequence Type (ST) 303 in the hypervirulent ST217 clonal complex. CONCLUSION The occurrence of a pneumococcal serotype 1 meningitis outbreak three years after the introduction of PCV13 is alarming and calls for strengthening of meningitis surveillance and a re-evaluation of the current vaccination programme in high risk countries.
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Affiliation(s)
- Brenda Anna Kwambana-Adams
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | | | | | | | | | | | - Ebenezer Foster-Nyarko
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | | | | | - Archibald Kwame Worwui
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Catherine Okoi
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Madikay Senghore
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Jacob Kweku Otu
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Chinelo Ebruke
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Richard Bannerman
- Brong Ahafo Regional Health Directorate, Sunyani, Brong Ahafo, Ghana
| | | | - David Opare
- National Public Health Reference Laboratory, Ghana Health Service, Accra, Ghana
| | - Gemma Kay
- Microbiology and Infection Unit, Warwick Medical School, Warwick, UK
| | - Timothy Letsa
- Brong Ahafo Regional Health Directorate, Sunyani, Brong Ahafo, Ghana
| | | | | | | | - Syed M A Zaman
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, Warwick, UK
| | - Umberto D'Alessandro
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.,London School of Hygiene and Tropical Medicine, London, UK.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Jason M Mwenda
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | - Martin Antonio
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia. .,Microbiology and Infection Unit, Warwick Medical School, Warwick, UK. .,London School of Hygiene and Tropical Medicine, London, UK.
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Connor TR, Loman NJ, Thompson S, Smith A, Southgate J, Poplawski R, Bull MJ, Richardson E, Ismail M, Thompson SE, Kitchen C, Guest M, Bakke M, Sheppard SK, Pallen MJ. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microb Genom 2016; 2:e000086. [PMID: 28785418 PMCID: PMC5537631 DOI: 10.1099/mgen.0.000086] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/21/2016] [Indexed: 12/14/2022] Open
Abstract
The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.
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Affiliation(s)
- Thomas R. Connor
- Cardiff University School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 2AX, UK
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Simon Thompson
- IT Services (Research Computing), University of Birmingham, Birmingham B15 2TT, UK
| | - Andy Smith
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Joel Southgate
- Cardiff University School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 2AX, UK
| | - Radoslaw Poplawski
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
- IT Services (Research Computing), University of Birmingham, Birmingham B15 2TT, UK
| | - Matthew J. Bull
- Cardiff University School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 2AX, UK
| | - Emily Richardson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Matthew Ismail
- Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK
| | | | | | - Martyn Guest
- Advanced Research Computing@Cardiff (ARCCA), Cardiff University, UK
| | - Marius Bakke
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Mark J. Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
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Abstract
Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever‐growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale‐up to the million‐microbial‐genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user‐friendly outputs. The “internet of things” will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd‐sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand‐held sequencers will be analysed on mobile devices. Open‐source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty‐first century, microbial sequence space will remain the final frontier!
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Affiliation(s)
- Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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38
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Bianucci R, Loynes RD, Sutherland ML, Lallo R, Kay GL, Froesch P, Pallen MJ, Charlier P, Nerlich AG. Forensic Analysis Reveals Acute Decompensation of Chronic Heart Failure in a 3500-Year-Old Egyptian Dignitary. J Forensic Sci 2016; 61:1378-81. [DOI: 10.1111/1556-4029.13138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/19/2015] [Accepted: 01/02/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Raffaella Bianucci
- Legal Medicine Section; Department of Public Health and Paediatric Sciences; University of Turin; Corso Galileo Galilei 22, 10126 Turin Italy
- UMR 7268; Laboratoire d'Anthropologie bio-culturelle; Droit, Etique & Santé (Adés); Faculté de Médecine de Marseille; Bd Pierre Dramard, BAT A CS, 80011 13444 Marseilles- Cedex 15- France
| | - Robert D. Loynes
- KNH Centre for Biomedical Egyptology; University of Manchester; 3.5 Stopford Building, Oxford Road Manchester, M13 9PT U.K
| | | | - Rudy Lallo
- Clinica Pinna Pintor; Via Amerigo Vespucci 61 10129 Turin Italy
| | - Gemma L. Kay
- Microbiology and Infection Unit; Warwick Medical School; University of Warwick; Medical School Building Coventry, West Midlands CV4 United Kingdom
| | - Philippe Froesch
- Section of Medical and Forensic Anthropology (UVSQ & Paris 5 University EA 4569); 2 Avenue de la source de la Bièvre, Montigny-le-Bretonneux 78180 France
| | - Mark J. Pallen
- Microbiology and Infection Unit; Warwick Medical School; University of Warwick; Medical School Building Coventry, West Midlands CV4 United Kingdom
| | - Philippe Charlier
- Section of Medical and Forensic Anthropology (UVSQ & Paris 5 University EA 4569); 2 Avenue de la source de la Bièvre, Montigny-le-Bretonneux 78180 France
| | - Andreas G. Nerlich
- Institute of Pathology; Klinikum München-Bogenhausen; Englschalkinger Str. 77 81925 Munich Germany
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Abstract
Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond.
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Affiliation(s)
- Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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Hänsch S, Cilli E, Catalano G, Gruppioni G, Bianucci R, Stenseth NC, Bramanti B, Pallen MJ. The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis. BMC Res Notes 2015; 8:535. [PMID: 26438258 PMCID: PMC4593223 DOI: 10.1186/s13104-015-1525-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/24/2015] [Indexed: 11/30/2022] Open
Abstract
Here we present evidence to show that the pla gene, previously thought to be specific to Yersinia pestis, occurs in some strains of Citrobacter koseri and Escherichia coli. This means that detection of this gene on its own can no longer be taken as evidence of detection of Y. pestis.
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Affiliation(s)
- Stephanie Hänsch
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna Campus, Bologna, Italy.
| | - Giulio Catalano
- Department of Cultural Heritage, University of Bologna, Ravenna Campus, Bologna, Italy.
| | - Giorgio Gruppioni
- Department of Cultural Heritage, University of Bologna, Ravenna Campus, Bologna, Italy.
| | - Raffaella Bianucci
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
| | - Nils C Stenseth
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
| | - Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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Webber MA, Whitehead RN, Mount M, Loman NJ, Pallen MJ, Piddock LJV. Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure. J Antimicrob Chemother 2015; 70:2241-8. [PMID: 25953808 PMCID: PMC4500774 DOI: 10.1093/jac/dkv109] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/01/2015] [Indexed: 11/30/2022] Open
Abstract
Objectives Biocides are widely used to prevent infection. We aimed to determine whether exposure of Salmonella to various biocides could act as a driver of antibiotic resistance. Methods Salmonella enterica serovar Typhimurium was exposed to four biocides with differing modes of action. Antibiotic-resistant mutants were selected during exposure to all biocides and characterized phenotypically and genotypically to identify mechanisms of resistance. Results All biocides tested selected MDR mutants with decreased antibiotic susceptibility; these occurred randomly throughout the experiments. Mutations that resulted in de-repression of the multidrug efflux pump AcrAB-TolC were seen in MDR mutants. A novel mutation in rpoA was also selected and contributed to the MDR phenotype. Other mutants were highly resistant to both quinolone antibiotics and the biocide triclosan. Conclusions This study shows that exposure of bacteria to biocides can select for antibiotic-resistant mutants and this is mediated by clinically relevant mechanisms of resistance prevalent in human pathogens.
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Affiliation(s)
- Mark A Webber
- Antimicrobials Research Group, School of Immunity and Infection and Institute for Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Rebekah N Whitehead
- Antimicrobials Research Group, School of Immunity and Infection and Institute for Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Manuella Mount
- Antimicrobials Research Group, School of Immunity and Infection and Institute for Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Nick J Loman
- School of Bioscience and Institute for Microbiology & Infection, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark J Pallen
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Laura J V Piddock
- Antimicrobials Research Group, School of Immunity and Infection and Institute for Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Kay GL, Sergeant MJ, Zhou Z, Chan JZM, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat Commun 2015; 6:6717. [PMID: 25848958 PMCID: PMC4396363 DOI: 10.1038/ncomms7717] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/18/2015] [Indexed: 01/05/2023] Open
Abstract
Tuberculosis (TB) was once a major killer in Europe, but it is unclear how the strains and patterns of infection at ‘peak TB' relate to what we see today. Here we describe 14 genome sequences of M. tuberculosis, representing 12 distinct genotypes, obtained from human remains from eighteenth-century Hungary using metagenomics. All our historic genotypes belong to M. tuberculosis Lineage 4. Bayesian phylogenetic dating, based on samples with well-documented dates, places the most recent common ancestor of this lineage in the late Roman period. We find that most bodies yielded more than one M. tuberculosis genotype and we document an intimate epidemiological link between infections in two long-dead individuals. Our results suggest that metagenomic approaches usefully inform detection and characterization of historical and contemporary infections. Tuberculosis was once a major killer in Europe. Here the authors use metagenomics to obtain genomic sequences of Mycobacterium tuberculosis from human remains from eighteenth-century Hungary, revealing mixed infections within individuals as well as presence of the same strain in two individuals.
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Affiliation(s)
- Gemma L Kay
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Martin J Sergeant
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Zhemin Zhou
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jacqueline Z-M Chan
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Andrew Millard
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Mark Spigelman
- 1] Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 9112102, Israel [2] Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark Achtman
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Helen D Donoghue
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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Quick J, Cumley N, Wearn CM, Niebel M, Constantinidou C, Thomas CM, Pallen MJ, Moiemen NS, Bamford A, Oppenheim B, Loman NJ. Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing. BMJ Open 2014; 4:e006278. [PMID: 25371418 PMCID: PMC4225241 DOI: 10.1136/bmjopen-2014-006278] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Pseudomonas aeruginosa is a common nosocomial pathogen responsible for significant morbidity and mortality internationally. Patients may become colonised or infected with P. aeruginosa after exposure to contaminated sources within the hospital environment. The aim of this study was to determine whether whole-genome sequencing (WGS) can be used to determine the source in a cohort of burns patients at high risk of P. aeruginosa acquisition. STUDY DESIGN An observational prospective cohort study. SETTING Burns care ward and critical care ward in the UK. PARTICIPANTS Patients with >7% total burns by surface area were recruited into the study. METHODS All patients were screened for P. aeruginosa on admission and samples taken from their immediate environment, including water. Screening patients who subsequently developed a positive P. aeruginosa microbiology result were subject to enhanced environmental surveillance. All isolates of P. aeruginosa were genome sequenced. Sequence analysis looked at similarity and relatedness between isolates. RESULTS WGS for 141 P. aeruginosa isolates were obtained from patients, hospital water and the ward environment. Phylogenetic analysis revealed eight distinct clades, with a single clade representing the majority of environmental isolates in the burns unit. Isolates from three patients had identical genotypes compared with water isolates from the same room. There was clear clustering of water isolates by room and outlet, allowing the source of acquisitions to be unambiguously identified. Whole-genome shotgun sequencing of biofilm DNA extracted from a thermostatic mixer valve revealed this was the source of a P. aeruginosa subpopulation previously detected in water. In the remaining two cases there was no clear link to the hospital environment. CONCLUSIONS This study reveals that WGS can be used for source tracking of P. aeruginosa in a hospital setting, and that acquisitions can be traced to a specific source within a hospital ward.
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Affiliation(s)
- Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK
| | - Nicola Cumley
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK
| | - Christopher M Wearn
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK
- Healing Foundation Centre for Burns Research, University Hospital Birmingham Foundation Trust, Birmingham, UK
| | - Marc Niebel
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK
| | | | - Chris M Thomas
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark J Pallen
- Division of Microbiology and Immunology, University of Warwick, Warwick, UK
| | - Naiem S Moiemen
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK
- Healing Foundation Centre for Burns Research, University Hospital Birmingham Foundation Trust, Birmingham, UK
| | - Amy Bamford
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK
- Healing Foundation Centre for Burns Research, University Hospital Birmingham Foundation Trust, Birmingham, UK
| | - Beryl Oppenheim
- NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ 2014; 2:e585. [PMID: 25279265 PMCID: PMC4179564 DOI: 10.7717/peerj.585] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/28/2014] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of "modern" M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence-based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplification steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.
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Affiliation(s)
- Emma L Doughty
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick , Coventry , United Kingdom
| | - Martin J Sergeant
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick , Coventry , United Kingdom
| | | | - Martin Antonio
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick , Coventry , United Kingdom ; Medical Research Council Unit , Fajara , The Gambia
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick , Coventry , United Kingdom
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Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, Pallen MJ. Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS One 2014; 9:e91941. [PMID: 24657972 PMCID: PMC3962364 DOI: 10.1371/journal.pone.0091941] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 02/18/2014] [Indexed: 11/18/2022] Open
Abstract
Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.
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Affiliation(s)
- Martin J. Sergeant
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Chrystala Constantinidou
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | | | - Charles W. Penn
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Mark J. Pallen
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Bingle LEH, Constantinidou C, Shaw RK, Islam MS, Patel M, Snyder LAS, Lee DJ, Penn CW, Busby SJW, Pallen MJ. Microarray analysis of the Ler regulon in enteropathogenic and enterohaemorrhagic Escherichia coli strains. PLoS One 2014; 9:e80160. [PMID: 24454682 PMCID: PMC3891560 DOI: 10.1371/journal.pone.0080160] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/09/2013] [Indexed: 11/18/2022] Open
Abstract
The type III protein secretion system is an important pathogenicity factor of enteropathogenic and enterohaemorrhagic Escherichia coli pathotypes. The genes encoding this apparatus are located on a pathogenicity island (the locus of enterocyte effacement) and are transcriptionally activated by the master regulator Ler. In each pathotype Ler is also known to regulate genes located elsewhere on the chromosome, but the full extent of the Ler regulon is unclear, especially for enteropathogenic E. coli. The Ler regulon was defined for two strains of E. coli: E2348/69 (enteropathogenic) and EDL933 (enterohaemorrhagic) in mid and late log phases of growth by DNA microarray analysis of the transcriptomes of wild-type and ler mutant versions of each strain. In both strains the Ler regulon is focused on the locus of enterocyte effacement - all major transcriptional units of which are activated by Ler, with the sole exception of the LEE1 operon during mid-log phase growth in E2348/69. However, the Ler regulon does extend more widely and also includes unlinked pathogenicity genes: in E2348/69 more than 50 genes outside of this locus were regulated, including a number of known or potential pathogenicity determinants; in EDL933 only 4 extra-LEE genes, again including known pathogenicity factors, were activated. In E2348/69, where the Ler regulon is clearly growth phase dependent, a number of genes including the plasmid-encoded regulator operon perABC, were found to be negatively regulated by Ler. Negative regulation by Ler of PerC, itself a positive regulator of the ler promoter, suggests a negative feedback loop involving these proteins.
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Affiliation(s)
- Lewis E. H. Bingle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Robert K. Shaw
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Md. Shahidul Islam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Mala Patel
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Lori A. S. Snyder
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - David J. Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Charles W. Penn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Stephen J. W. Busby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Mark J. Pallen
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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Snyder LA, Loman NJ, Faraj LA, Levi K, Weinstock G, Boswell TC, Pallen MJ, Ala'Aldeen DA. Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing. ACTA ACUST UNITED AC 2013; 18. [PMID: 24176582 DOI: 10.2807/1560-7917.es2013.18.42.20611] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Although previous bacterial typing methods have been informative about potential relatedness of isolates collected during outbreaks, next-generation sequencing has emerged as a powerful tool to not only look at similarity between isolates, but also put differences into biological context. In this study, we have investigated the whole genome sequence of five Pseudomonas aeruginosa isolates collected during a persistent six-year outbreak at Nottingham University Hospitals National Health Service (NHS) Trust – City Campus, United Kingdom. Sequencing, using both Roche 454 and Illumina, reveals that most of these isolates are closely related. Some regions of difference are noted between this cluster of isolates and previously published genome sequences. These include regions containing prophages and prophage remnants such as the serotype-converting bacteriophage D3 and the cytotoxin-converting phage phi CTX. Additionally, single nucleotide polymorphisms (SNPs) between the genomic sequence data reveal key single base differences that have accumulated during the course of this outbreak, giving insight into the evolution of the outbreak strain. Differentiating SNPs were found within a wide variety of genes, including lasR, nrdG, tadZ, and algB. These have been generated at a rate estimated to be one SNP every four to five months. In conclusion, we demonstrate that the single base resolution of whole genome sequencing is a powerful tool in analysis of outbreak isolates that can not only show strain similarity, but also evolution over time and potential adaptation through gene sequence changes.
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Affiliation(s)
- L A Snyder
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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Chan JZM, Sergeant MJ, Lee OYC, Minnikin DE, Besra GS, Pap I, Spigelman M, Donoghue HD, Pallen MJ. Metagenomic analysis of tuberculosis in a mummy. N Engl J Med 2013; 369:289-90. [PMID: 23863071 DOI: 10.1056/nejmc1302295] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Loman NJ, Gladstone RA, Constantinidou C, Tocheva AS, Jefferies JMC, Faust SN, O’Connor L, Chan J, Pallen MJ, Clarke SC. Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine. PLoS One 2013; 8:e64731. [PMID: 23724086 PMCID: PMC3665553 DOI: 10.1371/journal.pone.0064731] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/17/2013] [Indexed: 12/29/2022] Open
Abstract
Streptococcus pneumoniae causes invasive infections, primarily at the extremes of life. A seven-valent conjugate vaccine (PCV7) is used to protect against invasive pneumococcal disease in children. Within three years of PCV7 introduction, we observed a fourfold increase in serotype 6C carriage, predominantly due to a single clone. We determined the whole-genome sequences of nineteen S. pneumoniae serotype 6C isolates, from both carriage (n = 15) and disease (n = 4) states, to investigate the emergence of serotype 6C in our population, focusing on a single multi-locus sequence type (MLST) clonal complex 395 (CC395). A phylogenetic network was constructed to identify different lineages, followed by analysis of variability in gene sets and sequences. Serotype 6C isolates from this single geographical site fell into four broad phylogenetically distinct lineages. Variation was seen in the 6C capsular locus and in sequences of genes encoding surface proteins. The largest clonal complex was characterised by the presence of lantibiotic synthesis locus. In our population, the 6C capsular locus has been introduced into multiple lineages by independent capsular switching events. However, rapid clonal expansion has occurred within a single MLST clonal complex. Worryingly, plasticity exists within current and potential vaccine-associated loci, a consideration for future vaccine use, target selection and design.
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Affiliation(s)
- Nicholas J. Loman
- Centre for Systems Biology, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rebecca A. Gladstone
- Molecular Microbiology Group, Sir Henry Wellcome Laboratories, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Chrystala Constantinidou
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Anna S. Tocheva
- Molecular Microbiology Group, Sir Henry Wellcome Laboratories, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Johanna M. C. Jefferies
- Molecular Microbiology Group, Sir Henry Wellcome Laboratories, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Southampton NIHR, Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom
| | - Saul N. Faust
- Molecular Microbiology Group, Sir Henry Wellcome Laboratories, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- NIHR, Wellcome Trust Clinical Research Facility, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom
- Southampton NIHR, Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom
| | - Leigh O’Connor
- Centre for Systems Biology, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Jacqueline Chan
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Mark J. Pallen
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- * E-mail:
| | - Stuart C. Clarke
- Molecular Microbiology Group, Sir Henry Wellcome Laboratories, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Health Protection Agency, Southampton, United Kingdom
- Southampton NIHR, Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom
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Abstract
Outbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identification and characterization of outbreaks, focusing on the application of whole-genome sequencing (WGS) to outbreaks of bacterial infection. We describe traditional epidemiological analysis and show how WGS can be informative at multiple steps in outbreak investigation, as evidenced by many recent studies. We conclude that high-throughput sequencing approaches can make a significant contribution to the investigation of outbreaks of bacterial infection and that the integration of WGS with epidemiological investigation, diagnostic assays and antimicrobial susceptibility testing will precipitate radical changes in clinical microbiology and infectious disease epidemiology in the near future. However, several challenges remain before WGS can be routinely used in outbreak investigation and clinical practice.
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Affiliation(s)
| | - Timothy M Walker
- Nuffield Department of Clinical Medicine, University of Oxford, OX3 7LJ, UK
| | - Mark J Pallen
- Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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