Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data

Publication: Lancet Microbe

Francesc Coll, Theodore Gouliouris, Beth Blane, Corin A Yeats, Kathy E Raven, Catherine Ludden, Fahad A Khokhar, Hayley J Wilson, Leah W Roberts, Ewan M Harrison, Carolyne S Horner, Le Thi Hoi, Nguyen Thi Hoa, Nguyen Vu Trung, Nicholas M Brown, Prof Mark A Holmes, Prof Julian Parkhill, P Mili Estee Török, Prof Sharon J Peacock,

11 January 2024

Summary

A team of scientists at the Cambridge University Hospitals NHS Foundation Trust, University of Cambridge, Wellcome Sanger Institute and the London School of Hygiene and Tropical Medicine have gone a step forward by establishing the agreement between culture-based laboratory methods and genome sequencing for antibiotic resistance determination in Enterococcus faecium, one of the top 10 bacterial pathogens with the highest mortality burden globally. The team curated a set of over 200 genetic markers that most accurately predict resistance to 12 different, clinically relevant antibiotics in a collection of over 4,000 E. faecium strains. For key antibiotics such as ampicillin, ciprofloxacin, vancomycin and linezolid, the team reported very high diagnostic accuracy, and improved accuracy for the detection of resistance to other antibiotics compared to previous state-of-the-art predictive methods. In addition, the authors implemented the antibiotic resistance predictions on Pathogenwatch

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Impact of penicillin allergy labels on surgical site infections in a large UK cohort of gastrointestinal surgery patients

Publication: JAC-Antimicrobial Resistance

Nick K Jones, Brian Tom, Constantinos Simillis, John Bennet, Stavros Gourgiotis, Jo Griffin, Helen Blaza, Shuaib Nasser, Stephen Baker, Theodore Gouliouris

16 February 2024

Summary

Being labelled as allergic to penicillin has been associated with an increase in the risk of infection after surgery in a number of studies in USA, Canada and France. This is thought to be due to the use of inferior antibiotic regimens for preventing infection at the time of surgery. We studied a large cohort of patients that had undergone gastrointestinal surgery at Addenbrooke’s Hospital to see if this observation could be generalised to a UK population, where the range of preventative antibiotic regimens in routine use differs significantly. We found no evidence of association between penicillin allergy labels and likelihood of surgical site infection in this cohort, suggesting significant international variation in the impact of penicillin allergy labels on patients.

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Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae

Publication: Nature Communications

Robert C. Will, Thandavarayan Ramamurthy, Naresh Chand Sharma, Balaji Veeraraghavan, Lucky Sangal, Pradeep Haldar, Agila Kumari Pragasam, Karthick Vasudevan, Dhirendra Kumar, Bhabatosh Das, Eva Heinz, Vyacheslav Melnikov, Stephen Baker, Vartul Sangal, Gordon Dougan & Ankur Mutreja

8 March 2021


Summary

Diphtheria is a highly contagious infection that can affect the nose and throat, and sometimes the skin.

In a study published in Nature Communications,  an international team of researchers analysed the genomes of 61 bacteria isolated from patients and combining these with 441 publicly available genomes. They used this information to assess the presence of antimicrobial resistance (AMR) genes and assess toxin variation. Read the full story.

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Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

Publication: The Lancet Infectious Diseases

Luke W Meredith, William L Hamilton, Ben Warne, Charlotte J Houldcroft, Myra Hosmillo, Aminu S Jahun, Martin D Curran, Surendra Parmar, Laura G Caller, Sarah L Caddy, Fahad A Khokhar, Anna Yakovleva, Grant Hall, Theresa Feltwell, Sally Forrest, Sushmita Sridhar, Michael P Weekes, Prof Stephen Baker, Nicholas Brown, Elinor Moore, Ashley Popay, Iain Roddick, Mark Reacher, Theodore Gouliouris, Prof Sharon J Peacock, Prof Gordon Dougan, M Estée Török, Prof Ian Goodfellow.

14 July 2020


Summary:

Cambridge researchers have shown how rapid genome sequencing of virus samples and enhanced testing of hospital staff can help to identify clusters of healthcare-associated COVID-19 infections. Read the full news article.

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Ventilator-associated pneumonia in critically ill patients with COVID-19

Publication: Critical Care

Mailis Maes, Ellen Higginson, Joana Pereira-Dias, Martin D. Curran, Surendra Parmar, Fahad Khokhar, Delphine Cuchet-Lourenço, Janine Lux, Sapna Sharma-Hajela, Benjamin Ravenhill, Islam Hamed, Laura Heales, Razeen Mahroof, Amelia Solderholm, Sally Forrest, Sushmita Sridhar, Nicholas M. Brown, Stephen Baker, Vilas Navapurkar, Gordon Dougan, Josefin Bartholdson Scott and  Andrew Conway Morris

11 January 2021


Summary:
A DNA test to identify secondary pneumonia in patients with severe COVID-19 has been created by Cambridge researchers. Bacteria samples need to be collected from patients and grown in a lab to identify them – this could take days. Now researchers have created a test which will detect the DNA of the bacteria within hours. Clinicians will then be able to start the right course of treatment a lot sooner. This new test is being rolled out at Cambridge University Hospitals.
Read the full news story.

Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS.

Publication: Journal of Antimicrobial Chemotherapy

Pérez-Vázquez M, Sola Campoy PJ, Ortega A, Bautista V, Monzón S, Ruiz-Carrascoso G, Mingorance J, González-Barberá EM, Gimeno C, Aracil B, Sáez D, Lara N, Fernández S, González-López JJ, Campos J, Kingsley RA, Dougan G, Oteo-Iglesias J; Spanish NDM Study Group .  J Antimicrob Chemother.

3 September 2019

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Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center.

Publication: Genome Biology

Ellington MJ, Heinz E, Wailan AM, Dorman MJ, de Goffau M, Cain AK, Henson SP, Gleadall N, Boinett CJ, Dougan G, Brown NM, Woodford N, Parkhill J, Török ME, Peacock SJ, Thomson NR.

2 September 2019

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Diagnostic host gene signature for distinguishing enteric fever from other febrile diseases.

Publication: EMBO Molecular Medicine

Blohmke CJ, Muller J, Gibani MM, Dobinson H, Shrestha S, Perinparajah S, Jin C, Hughes H, Blackwell L, Dongol S, Karkey A, Schreiber F, Pickard D, Basnyat B, Dougan G, Baker S, Pollard AJ, Darton TC.

30 August 2019

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Adaptation of host transmission cycle during Clostridium difficile speciation

Publication: Nature Genetics

Kumar N, Browne HP, Viciani E, Forster SC, Clare S, Harcourt K, Stares MD, Dougan G, Fairley DJ, Roberts P, Pirmohamed M, Clokie MRJ, Jensen MBF, Hargreaves KR, Ip M, Wieler LH, Seyboldt C, Norén T, Riley TV, Kuijper EJ, Wren BW, Lawley TD.

12 August 2019

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Antibiotic Resistance and Typhoid

Publication: Clinical Infectious Diseases

Dyson ZA, Klemm EJ, Palmer S, Dougan G.

7 March 2019

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