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Invasive Non-typhoidal Salmonella Infections in Asia
Nguyen Phu Huong Lan, Tu Le Thi Phuong, Hien Nguyen Huu, Le Thuy, Alison E Mather, Se Eun Park, Florian Marks, Guy E Thwaites, Nguyen Van Vinh Chau, Corinne N Thompson, Stephen Baker
Feb 19, 2019
Invasive non-typhoidal Salmonella (iNTS) infections are now a well-described cause of morbidity and mortality in children and HIV-infected adults in sub-Saharan Africa. In contrast, the epidemiology and clinical manifestations...
Adult Aged Anti-Infective Agents Ceftriaxone Drug Therapy Combination Female Fluoroquinolones HIV Infections Hospitals Humans Logistic Models Male Middle Aged Multilocus Sequence Typing Multivariate Analysis Retrospective Studies Salmonella Infections Salmonella enterica Serogroup Sex Factors Trimethoprim Sulfamethoxazole Drug Combination Typhoid Fever Vietnam
Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes.
Kathy E Raven, Catherine Ludden, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Nicholas M Brown, Julian Parkhill, Sharon J Peacock
Apr 15, 2019
We examined whether genomic surveillance of Escherichia coli in wastewater could capture the dominant E. coli lineages associated with bloodstream infection and livestock in the East of England, together with the...
Escherichia coli Genomic Surveillance resistance Wastewater Animals Cross-Sectional Studies England Environmental Monitoring Escherichia coli Escherichia coli Infections Escherichia coli Proteins Genes Bacterial Genomics Hospitals Humans Interspersed Repetitive Sequences Livestock Multilocus Sequence Typing Phylogeny Public Health Wastewater Water Purification beta-Lactamases
Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato
In order to understand the population structure and dynamics of bacterial microorganisms, typing systems that accurately reflect the phylogenetic and evolutionary relationship of the agents are required. Over the past 15 years...
Genomic analysis of European bovine Staphylococcus aureus from clinical versus subclinical mastitis.
Jurriaan Hoekstra, Aldert L Zomer, Victor PMG Rutten, Lindert Benedictus, Arjan Stegeman, Mirlin P Spaninks, Torben W Bennedsgaard, Andrew Biggs, Sarne De Vliegher, Demetrio Herrera Mateo, Reglindis Huber-Schlenstedt, Jørgen Katholm, Péter Kovács, Volker Krömker, Guillaume Lequeux, Paolo Moroni, Luís Pinho, Sebastian Smulski, Karlien Supré, Jantijn M Swinkels, Mark A Holmes, Theo JGM Lam, Gerrit Koop
Jan 08, 2021
Intramammary infections (IMI) with Staphylococcus aureus are a common cause of bovine mastitis and can result in both clinical (CM) or subclinical mastitis (SCM). Although bacterial isolates of S. aureus differ in their...
Animals Anti-Bacterial Agents Bacterial Typing Techniques Cattle Clonal Evolution Drug Resistance Bacterial Europe Female Genes Bacterial genetic variation Genome-Wide Association Study Genomics Genotype Mastitis Bovine Multilocus Sequence Typing Phylogeny Staphylococcus aureus Virulence Virulence Factors
Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory.
Kathy E Raven, Beth Blane, Danielle Leek, Carol Churcher, Paula Kokko-Gonzales, Dhamayanthi Pugazhendhi, Louise Fraser, Jason Betley, Julian Parkhill, Sharon J Peacock
Mar 26, 2019
There is growing evidence for the value of bacterial whole-genome sequencing in hospital outbreak investigations. Our aim was to develop methods that support efficient and accurate low-throughput clinical sequencing of...
Increasing incidence of group B streptococcus neonatal infections in the Netherlands is associated with clonal expansion of CC17 and CC23.
Dorota Jamrozy, Merijn W Bijlsma, Marcus C de Goffau, Diederik van de Beek, Taco W Kuijpers, Julian Parkhill, Arie van der Ende, Stephen D Bentley
Aug 03, 2020
Group B streptococcus (GBS) is the leading cause of neonatal invasive disease worldwide. In the Netherlands incidence of the disease increased despite implementation of preventive guidelines. We describe a genomic analysis of...
Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam.
Jeremy N Day, Seet Qihui, Lam Tuan Thanh, Phan Hai Trieu, Anh Duong Van, Nha Hoang Thu, Tran Thi Hong Chau, Nguyen PH Lan, Nguyen Van Vinh Chau, Philip M Ashton, Guy E Thwaites, Maciej F Boni, Marcel Wolbers, Niranjan Nagarajan, Patrick BO Tan, Stephen Baker
Apr 10, 2019
The vast burden of cryptococcal meningitis occurs in immunosuppressed patients, driven by HIV, and is caused by Cryptococcus neoformans var. grubii. We previously reported cryptococcal meningitis in Vietnam arising atypically in...
Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks.
Ewan M Harrison, Catherine Ludden, Hayley J Brodrick, Beth Blane, Gráinne Brennan, Dearbháile Morris, Francesc Coll, Sandra Reuter, Nicholas M Brown, Mark A Holmes, Brian O'Connell, Julian Parkhill, M Estee Török, Martin Cormican, Sharon J Peacock
Dec 16, 2016
long-term care facilities MRSA molecular epidemiology nursing home Staphylococcus aureus transmission whole-genome sequencing Adult Aged Aged 80 and over Cross Infection DNA Bacterial Female Health Facility Environment High-Throughput Nucleotide Sequencing Humans infection control Long-Term Care Male Methicillin-Resistant Staphylococcus aureus Middle Aged Multilocus Sequence Typing Prospective Studies Staphylococcal Infections United Kingdom
Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest.
Ferry Hagen, Paulo C Ceresini, Itzhack Polacheck, Hansong Ma, Filip Van Nieuwerburgh, Toni Gabaldón, Sarah Kagan, E Rhiannon Pursall, Hans L Hoogveld, Leo JJ van Iersel, Gunnar W Klau, Steven M Kelk, Leen Stougie, Karen H Bartlett, Kerstin Voelz, Leszek P Pryszcz, Elizabeth Castañeda, Marcia Lazera, Wieland Meyer, Dieter Deforce, Jacques F Meis, Robin C May, Corné HW Klaassen, Teun Boekhout
Oct 22, 2019
Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy...
Animals Brazil British Columbia Cells Cultured Cryptococcosis Cryptococcus gattii Disease Outbreaks Genes Fungal Humans Likelihood Functions MACROPHAGES Mice Mice Inbred BALB C Molecular Sequence Data Multilocus Sequence Typing Mycological Typing Techniques Northwestern United States Phylogeny Polymorphism Restriction Fragment Length Trees Tropical Climate Virulence
The speciation and hybridization history of the genus Salmonella.
Alexis Criscuolo, Sylvie Issenhuth-Jeanjean, Xavier Didelot, Kaisa Thorell, James Hale, Julian Parkhill, Nicholas R Thomson, François-Xavier Weill, Daniel Falush, Sylvain Brisse
Sep 06, 2019
Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella, an...
Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand.
Chandler Roe, Adam J Vazquez, Paul D Phillips, Chris J Allender, Richard A Bowen, Roxanne D Nottingham, Adina Doyle, Gumphol Wongsuwan, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Sharon Peacock, Paul Keim, Apichai Tuanyok, David M Wagner, Jason W Sahl
Mar 13, 2022
Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although the global genomic diversity of clinical B. pseudomallei isolates has been...
Divergent evolution of Corynebacterium diphtheriae in India
Naveen Kumar Devanga Ragupathi, Dhiviya Prabaa Muthuirulandi Sethuvel, Dhivya Murugan, Ranjini Ranjan, Vikas Gautam, Prashanth Gupta, Jaichand Johnson, Naresh Chand Sharma, Ankur Mutreja, Pradeep Haldar, Arun Kumar, Pankaj Bhatnagar, Lucky Sangal, Balaji Veeraraghavan
Jan 28, 2022
Diphtheria is caused by a toxigenic bacterium Corynebacterium diphtheria which is being an emerging pathogen in India. Since diphtheria morbidity and mortality continues to be high in the country, the present study aimed to...
Are commercial providers a viable option for clinical bacterial sequencing?
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine...
MRSA clinical application whole-genome sequencing Contract Services DNA Bacterial Disease Outbreaks Genome Bacterial Humans Methicillin-Resistant Staphylococcus aureus Multilocus Sequence Typing Polymorphism Single Nucleotide Sequence Analysis DNA Staphylococcal Infections United Kingdom whole genome sequencing
Evidence of land-sea transfer of the zoonotic pathogen <i>Campylobacter</i> to a wildlife marine sentinel species
Johanna L Baily, Guillaume Méric, Sion Bayliss, Geoffrey Foster, Simon E Moss, Eleanor Watson, Ben Pascoe, Jane Mikhail, Romain Pizzi, Robert J Goldstone, David G E Smith, Kim Willoughby, Ailsa J Hall, Samuel K Sheppard, Mark P Dagleish
Jan 06, 2015
Environmental pollution often accompanies the expansion and urbanization of human populations where sewage and wastewaters commonly have an impact on the marine environments. Here, we explored the potential for faecal...
Animals Bacterial Typing Techniques Campylobacter Campylobacter Infections DNA Bacterial Environmental Monitoring Models Genetic Multilocus Sequence Typing Phylogeny Scotland Seals Earless Sequence Analysis DNA Zoonoses /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being name=SDG 3 - Good Health and Well-being /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water
Helicobacter pylori's historical journey through Siberia and the Americas.
Yoshan Moodley, Andrea Brunelli, Silvia Ghirotto, Andrey Klyubin, Ayas S Maady, William Tyne, Zilia Y Muñoz-Ramirez, Zhemin Zhou, Andrea Manica, Bodo Linz, Mark Achtman
Nov 09, 2021
The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human...
A shared population of epidemic methicillin-resistant Staphylococcus aureus 15 circulates in humans and companion animals.
Ewan M Harrison, Lucy A Weinert, Matthew TG Holden, John J Welch, Katherine Wilson, Fiona JE Morgan, Simon R Harris, Anette Loeffler, Amanda K Boag, Sharon J Peacock, Gavin K Paterson, Andrew S Waller, Julian Parkhill, Mark A Holmes
Jul 15, 2014
Adaptation Biological Animal Diseases Animals Drug Resistance Bacterial evolution Molecular Genome Bacterial Genome-Wide Association Study Humans Methicillin-Resistant Staphylococcus aureus Multilocus Sequence Typing Phylogeny Polymorphism Single Nucleotide Staphylococcal Infections Virulence Factors
One hypervirulent clone, sequence type 283, accounts for a large proportion of invasive Streptococcus agalactiae isolated from humans and diseased tilapia in Southeast Asia.
Timothy Barkham, Ruth N Zadoks, Mohammad Noor Amal Azmai, Stephen Baker, Vu Thi Ngoc Bich, Victoria Chalker, Man Ling Chau, David Dance, Rama Narayana Deepak, H Rogier van Doorn, Ramona A Gutierrez, Mark A Holmes, Lan Nguyen Phu Huong, Tse Hsien Koh, Elisabete Martins, Kurosh Mehershahi, Paul Newton, Lee Ching Ng, Nguyen Ngoc Phuoc, Ornuma Sangwichian, Pongpun Sawatwong, Uraiwan Surin, Thean Yen Tan, Wen Ying Tang, Nguyen Vu Thuy, Paul Turner, Manivanh Vongsouvath, Defeng Zhang, Toni Whistler, Swaine L Chen
Jul 09, 2019
BACKGROUND: In 2015, Singapore had the first and only reported foodborne outbreak of invasive disease caused by the group B Streptococcus (GBS; Streptococcus agalactiae). Disease, predominantly septic arthritis and meningitis...
Adolescent Adult Aged Aged 80 and over Animals Asia Southeastern Child Child Preschool Female Fish Diseases Foodborne Diseases Genotype Humans Infant Infant Newborn Male Middle Aged molecular epidemiology Multilocus Sequence Typing Phylogeny Pregnancy Streptococcal Infections Streptococcus Agalactiae Tilapia whole genome sequencing Young Adult
Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales.
Alison E Mather, Becki Lawson, Elizabeth de Pinna, Paul Wigley, Julian Parkhill, Nicholas R Thomson, Andrew J Page, Mark A Holmes, Gavin K Paterson
Oct 25, 2016
Animals Animals Wild Bacteriophage Typing Bird Diseases Cats Disease Reservoirs Drug Resistance Bacterial England Genome Bacterial Genomics Humans Multilocus Sequence Typing Phylogeny Plasmids Polymorphism Single Nucleotide Salmonella Infections Salmonella Infections Animal Salmonella typhimurium Serogroup Serotyping Sparrows Virulence Wales
Genomic landscape of extended-spectrum β-lactamase resistance in $\textit{Escherichia coli}$ from an urban African setting
P Musicha, NA Feasey, AK Cain, T Kallonen, C Chaguza, C Peno, M Khonga, S Thompson, KJ Gray, AE Mather, RS Heyderman, DB Everett, NR Thomson, CL Msefula
Apr 25, 2017
Adolescent Adult Child Child Preschool Chloramphenicol Drug Resistance Multiple Bacterial Escherichia coli Escherichia coli Infections Female Genes Bacterial genetic variation Genomics Humans Malawi Male Microbial Sensitivity Tests Multilocus Sequence Typing Phylogeny Urban Population Young Adult beta-Lactam Resistance beta-Lactamases
Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato
In order to understand the population structure and dynamics of bacterial microorganisms, typing systems that accurately reflect the phylogenetic and evolutionary relationship of the agents are required. Over the past 15 years...
Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.
Danesh Moradigaravand, Theodore Gouliouris, Catherine Ludden, Sandra Reuter, Dorota Jamrozy, Beth Blane, Plamena Naydenova, Kim Judge, Sani H Aliyu, Nazreen F Hadjirin, Mark A Holmes, Estée Török, Nicholas M Brown, Julian Parkhill, Sharon Peacock
May 22, 2018
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is...
Clostridium difficile One Health genomic epidemiology wastewater treatment plants Bayes Theorem Clostridioides difficile Cross-Sectional Studies DNA Bacterial Diarrhea England Genome Bacterial Genomics Humans Multilocus Sequence Typing Retrospective Studies Sequence Analysis DNA Waste Management Wastewater
Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England
Evidence of land-sea transfer of the zoonotic pathogen <i>Campylobacter</i> to a wildlife marine sentinel species
Johanna L Baily, Guillaume Méric, Sion Bayliss, Geoffrey Foster, Simon E Moss, Eleanor Watson, Ben Pascoe, Jane Mikhail, Romain Pizzi, Robert J Goldstone, David G E Smith, Kim Willoughby, Ailsa J Hall, Samuel K Sheppard, Mark P Dagleish
Jan 06, 2015
Environmental pollution often accompanies the expansion and urbanization of human populations where sewage and wastewaters commonly have an impact on the marine environments. Here, we explored the potential for faecal...
Animals Bacterial Typing Techniques Campylobacter Campylobacter Infections DNA Bacterial Environmental Monitoring Models Genetic Multilocus Sequence Typing Phylogeny Scotland Seals Earless Sequence Analysis DNA Zoonoses /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being name=SDG 3 - Good Health and Well-being /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water
Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks.
Nicholas M Brown, Beth Blane, Kathy E Raven, Narender Kumar, Danielle Leek, Eugene Bragin, Paul A Rhodes, David A Enoch, Rachel Thaxter, Julian Parkhill, Sharon J Peacock
Aug 30, 2019
Genomic surveillance that combines bacterial sequencing and epidemiological information will become the gold standard for outbreak detection, but its clinical translation is hampered by the lack of automated interpretation...
Staphylococcus aureus Bioinformatics microbiology whole-genome sequencing Anti-Bacterial Agents Automation Laboratory Bacterial Typing Techniques Computational Biology Disease Outbreaks England Genome Bacterial Humans Methicillin Methicillin-Resistant Staphylococcus aureus Multilocus Sequence Typing Pilot Projects Prospective Studies Sequence Analysis DNA Staphylococcal Infections whole genome sequencing
Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.
Andrew J Page, Nishadi De Silva, Martin Hunt, Michael A Quail, Julian Parkhill, Simon R Harris, Thomas D Otto, Jacqueline A Keane
Sep 06, 2019
The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in large-scale microbial analysis. Though mapping approaches can be used to find differences relative to the reference, many bacteria are...
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