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Aranega-Bou P, Cornbill C, Rodger G, Bird M, Moore G, Roohi A, Hopkins KL, Hopkins S, Ribeca P, Stoesser N, Lipworth SI. WITHDRAWN: Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae , Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks. medRxiv 2024:2023.04.24.23289028. [PMID: 37214917 PMCID: PMC10193520 DOI: 10.1101/2023.04.24.23289028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The authors have withdrawn their manuscript due to becoming aware of methodology issues related to the curation of the training set used to determine cut-off values for Biotyper cluster assignation and lack of replicate measurements on different days for the isolates analysed. It is therefore unclear whether the conclusions of the manuscript are founded and no further work is possible to correct these issues as the instrument is no longer available to the authors. If you have any questions, please contact the corresponding author.
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Rodger G, Chau K, Aranega-Bou P, Roohi A, Moore G, Hopkins KL, Hopkins S, Walker AS, Stoesser N. A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing. J Hosp Infect 2024; 144:128-136. [PMID: 38145816 DOI: 10.1016/j.jhin.2023.11.021] [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] [Received: 09/27/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterize these factors are lacking. AIMS To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ('resistome') composition of sink trap samples for metagenomic sequencing. METHODS Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a 'real-world' pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22 °C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0). FINDINGS The limits of detection for each antibiotic were: 3 μg/L (ampicillin), 10 μg/L (doxycycline), 20 μg/L (sulfamethoxazole) and 8 μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterized 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulphonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22 °C for up to five days. CONCLUSIONS Dipsticks can be used to detect antibiotic residues and characterize water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.
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Affiliation(s)
- G Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - P Aranega-Bou
- Biosafety, Air and Water Microbiology Group, UK Health Security Agency, Porton Down, UK
| | - A Roohi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - G Moore
- Biosafety, Air and Water Microbiology Group, UK Health Security Agency, Porton Down, UK
| | | | - S Hopkins
- UK Health Security Agency, Colindale, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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Chau KK, Goodall T, Bowes M, Easterbrook K, Brett H, Hughes J, Crook DW, Read DS, Walker AS, Stoesser N. High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Microb Genom 2023; 9. [PMID: 37145848 DOI: 10.1099/mgen.0.000983] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.
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Affiliation(s)
- Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - M Bowes
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - K Easterbrook
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - H Brett
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - J Hughes
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - D W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - D S Read
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
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Chau KK, Barker L, Budgell EP, Vihta KD, Sims N, Kasprzyk-Hordern B, Harriss E, Crook DW, Read DS, Walker AS, Stoesser N. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. Environ Int 2022; 162:107171. [PMID: 35290866 PMCID: PMC8960996 DOI: 10.1016/j.envint.2022.107171] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/23/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
OBJECTIVES We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) evidence of concordance between wastewater-human AMR prevalence estimates, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin's concordance correlation coefficient (CCC) to quantify concordance between AMR prevalence estimates in wastewater and human compartments (where CCC = 1 reflects perfect concordance), and logistic regression to identify study features (e.g. sampling methods) associated with high agreement studies (defined as >70% of within-study wastewater-human AMR prevalence comparisons within ±10%). RESULTS Of 8,867 records and 441 full-text methods reviewed, 33 studies were included. AMR prevalence data was extractable from 24 studies conducting phenotypic-only (n = 7), genotypic-only (n = 1) or combined (n = 16) AMR detection. Overall concordance of wastewater-human AMR prevalence estimates was reasonably high for both phenotypic (CCC = 0.85 [95% CI 0.8-0.89]) and genotypic approaches (CCC = 0.88 (95% CI 0.84-0.9)) despite diverse study designs, bacterial species investigated and phenotypic/genotypic targets. No significant relationships between methodological approaches and high agreement studies were identified using logistic regression; however, this was limited by inconsistent reporting of study features, significant heterogeneity in approaches and limited sample size. Based on a secondary, descriptive synthesis, studies conducting composite sampling of wastewater influent, longitudinal sampling >12 months, and time-/location-matched sampling of wastewater and human compartments generally had higher agreement. CONCLUSION Wastewater-based surveillance of AMR appears promising, with high overall concordance between wastewater and human AMR prevalence estimates in studies irrespective of heterogenous approaches. However, our review suggests future work would benefit from: time-/location-matched sampling of wastewater and human populations, composite sampling of influent, and sampling >12 months for longitudinal studies. Further research and clear and consistent reporting of study methods is required to identify optimal practice.
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Affiliation(s)
- K K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - L Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - E P Budgell
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - K D Vihta
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - N Sims
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - B Kasprzyk-Hordern
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - E Harriss
- Bodleian Healthcare Libraries, University of Oxford, Oxford OX3 9DU, United Kingdom.
| | - D W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - D S Read
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, United Kingdom.
| | - A S Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, United Kingdom.
| | - N Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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McGlen SE, Stoesser N, Woodrow C, Dudley J, Newton D, Lasserson D. Tocilizumab for treatment of SARS-CoV-2 infection at home: A case report. Acute Med 2022; 21:53-55. [PMID: 35342912 DOI: 10.52964/amja.0894] [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: 11/13/2022]
Abstract
SARS-CoV-2 virtual wards have successfully developed to monitor and escalate patients to hospital throughout the pandemic. Here we describe the case of an 84 year old man who received his complete care for severe SARS-CoV-2 pneumonitis at home, including the administration of oxygen, dexamethasone and tocilizumab.
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Affiliation(s)
- S E McGlen
- MPharm, Oxford University Hospitals NHS Foundation Trust
| | - N Stoesser
- DPhil, Oxford University Hospitals NHS Foundation Trust and Nuffield Department of Medicine, University of Oxford
| | - C Woodrow
- MRCP, PhD, Oxford Univeristy Hospitals NHS Foundation Trust and Medical Sciences Division University of Oxford
| | - J Dudley
- RN, BSc, Oxford University Hospitals NHS Foundation Trust
| | | | - D Lasserson
- MD FRCPEdin, Oxford University Hospitals NHS Foundation Trust and Warwick Medical School, University of Warwick
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Reynolds ME, Phan HTT, George S, Hubbard ATM, Stoesser N, Maciuca IE, Crook DW, Timofte D. Occurrence and characterization of Escherichia coli ST410 co-harbouring blaNDM-5, blaCMY-42 and blaTEM-190 in a dog from the UK. J Antimicrob Chemother 2021; 74:1207-1211. [PMID: 30753576 DOI: 10.1093/jac/dkz017] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND/OBJECTIVES Carbapenemase-producing Enterobacteriaceae (CPE) are a public health threat, and have been found in humans, animals and the environment. Carbapenems are not authorized for use in EU or UK companion animals, and the prevalence of carbapenem-resistant Gram-negative bacilli (CRGNB) in this population is unknown. METHODS We investigated CRGNB isolated from animal specimens received by one diagnostic laboratory from 34 UK veterinary practices (September 2015-December 2016). Any Gram-negative isolates from clinical specimens showing reduced susceptibility to fluoroquinolones and/or aminoglycosides and/or cephalosporins were investigated phenotypically and genotypically for carbapenemases. A complete genome assembly (Illumina/Nanopore) was generated for the single isolate identified to investigate the genetic context for carbapenem resistance. RESULTS One ST410 Escherichia coli isolate [(CARB35); 1/191, 0.5%], cultured from a wound in a springer spaniel, harboured a known carbapenem resistance gene (blaNDM-5). The gene was located in the chromosome on an integrated 100 kb IncF plasmid, also harbouring other drug resistance genes (mrx, sul1, ant1 and dfrA). The isolate also contained blaCMY-42 and blaTEM-190 on two separate plasmids (IncI1 and IncFII, respectively) that showed homology with other publicly available plasmid sequences from Italy and Myanmar. CONCLUSIONS Even though the use of carbapenems in companion animals is restricted, the concurrent presence of blaCMY-42 and other antimicrobial resistance genes could lead to co-selection of carbapenemase genes in this population. Further studies investigating the selection and flow of plasmids carrying important resistance genes amongst humans and companion animals are needed.
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Affiliation(s)
- M E Reynolds
- Axiom Veterinary Laboratories Ltd, The Manor House, Brunel Road, Newton Abbot, UK
| | - H T T Phan
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - S George
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - A T M Hubbard
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - N Stoesser
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - I E Maciuca
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Cheshire, UK
| | - D W Crook
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - D Timofte
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Cheshire, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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Kizny Gordon A, Phan HTT, Lipworth SI, Cheong E, Gottlieb T, George S, Peto TEA, Mathers AJ, Walker AS, Crook DW, Stoesser N. Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital. J Antimicrob Chemother 2020; 75:873-882. [PMID: 31960024 PMCID: PMC7069471 DOI: 10.1093/jac/dkz526] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/20/2019] [Revised: 11/16/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety. OBJECTIVES To investigate the genomic dynamics of a 10 year (2006-15) outbreak of blaIMP-4-containing organisms in a burns unit in a hospital in Sydney, Australia. METHODS All carbapenem-non-susceptible or MDR clinical isolates (2006-15) and a random selection of equivalent or ESBL-producing environmental isolates (2012-15) were sequenced [short-read (Illumina), long-read (Oxford Nanopore Technology)]. Sequence data were used to assess genetic relatedness of isolates (Mash; mapping and recombination-adjusted phylogenies), perform in silico typing (MLST, resistance genes and plasmid replicons) and reconstruct a subset of blaIMP plasmids for comparative plasmid genomics. RESULTS A total of 46/58 clinical and 67/96 environmental isolates contained blaIMP-4. All blaIMP-4-positive organisms contained five or more other resistance genes. Enterobacter cloacae was the predominant organism, with 12 other species mainly found in either the environment or patients, some persisting despite several cleaning methods. On phylogenetic analysis there were three genetic clusters of E. cloacae containing both clinical and environmental isolates, and an additional four clusters restricted to either reservoir. blaIMP-4 was mostly found as part of a cassette array (blaIMP-4-qacG2-aacA4-catB3) in a class 1 integron within a previously described IncM2 plasmid (pEl1573), with almost complete conservation of this cassette across the species over the 10 years. Several other plasmids were also implicated, including an IncF plasmid backbone not previously widely described in association with blaIMP-4. CONCLUSIONS Genetic backgrounds disseminating blaIMP-4 can persist, diversify and evolve amongst both human and environmental reservoirs during a prolonged outbreak despite intensive prevention efforts.
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Affiliation(s)
- A Kizny Gordon
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H T T Phan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - S I Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - E Cheong
- Department of Microbiology & Infectious Diseases, Concord Repatriation General Hospital, Sydney, Australia
- University of Sydney, Sydney, Australia
| | - T Gottlieb
- Department of Microbiology & Infectious Diseases, Concord Repatriation General Hospital, Sydney, Australia
- University of Sydney, Sydney, Australia
| | - S George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - T E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - A J Mathers
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - D W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Phan HTT, Stoesser N, Maciuca IE, Toma F, Szekely E, Flonta M, Hubbard ATM, Pankhurst L, Do T, Peto TEA, Walker AS, Crook DW, Timofte D. Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania. J Antimicrob Chemother 2019; 73:672-679. [PMID: 29237003 PMCID: PMC5890751 DOI: 10.1093/jac/dkx456] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 08/21/2017] [Accepted: 11/06/2017] [Indexed: 11/30/2022] Open
Abstract
Background and Objectives Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase blaNDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010–15, including a neonatal NDM-1 S. marcescens outbreak. Methods Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference. Results 44/45 isolates were successfully sequenced (S. marcescens, n = 33; K. pneumoniae, n = 7; E. cloacae, n = 4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites. Conclusions The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.
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Affiliation(s)
- H T T Phan
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - N Stoesser
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - I E Maciuca
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, UK
| | - F Toma
- Microbiology Department, University of Medicine and Pharmacy, Targu Mures, Romania
| | - E Szekely
- Microbiology Department, University of Medicine and Pharmacy, Targu Mures, Romania
| | - M Flonta
- Clinical Hospital of Infectious Diseases, Cluj-Napoca, Romania
| | - A T M Hubbard
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - L Pankhurst
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - T Do
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - T E A Peto
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - A S Walker
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - D W Crook
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - D Timofte
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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van Aartsen JJ, Moore CE, Parry CM, Turner P, Phot N, Mao S, Suy K, Davies T, Giess A, Sheppard AE, Peto TEA, Day NPJ, Crook DW, Walker AS, Stoesser N. Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia. BMC Microbiol 2019; 19:59. [PMID: 30866820 PMCID: PMC6417137 DOI: 10.1186/s12866-019-1431-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/04/2019] [Indexed: 01/11/2023] Open
Abstract
Background Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. The aim of this study was to determine gastrointestinal colonisation prevalence of ESC-resistant E. coli (ESC-R-EC) and K. pneumoniae (ESC-R-KP) in Cambodian children/adolescents and associated socio-demographic risk factors; and to characterise relevant resistance genes, their genetic contexts, and the genetic relatedness of ESC-R strains using whole genome sequencing (WGS). Results Faeces and questionnaire data were obtained from individuals < 16 years in north-western Cambodia, 2012. WGS of cultured ESC-R-EC/KP was performed (Illumina). Maximum likelihood phylogenies were used to characterise relatedness of isolates; ESC-R-associated resistance genes and their genetic contexts were identified from de novo assemblies using BLASTn and automated/manual annotation. 82/148 (55%) of children/adolescents were ESC-R-EC/KP colonised; 12/148 (8%) were co-colonised with both species. Independent risk factors for colonisation were hospitalisation (OR: 3.12, 95% CI [1.52–6.38]) and intestinal parasites (OR: 3.11 [1.29–7.51]); school attendance conferred decreased risk (OR: 0.44 [0.21–0.92]. ESC-R strains were diverse; the commonest ESC-R mechanisms were blaCTX-M 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for blaCTX-M-15, − 55 and − 27 frequently involved IS26. Chromosomal blaCTX-M integration was common in E. coli. Conclusions Gastrointestinal ESC-R-EC/KP colonisation is widespread in Cambodian children/adolescents; hospital admission and intestinal parasites are independent risk factors. The genetic contexts of blaCTX-M are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of blaCTX-M may result in stable propagation in these community-associated pathogens. Electronic supplementary material The online version of this article (10.1186/s12866-019-1431-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J J van Aartsen
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK. .,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, The Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK.
| | - C E Moore
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
| | - C M Parry
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - P Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - N Phot
- Angkor Hospital for Children, Siem Reap, Cambodia
| | - S Mao
- Angkor Hospital for Children, Siem Reap, Cambodia
| | - K Suy
- Angkor Hospital for Children, Siem Reap, Cambodia
| | - T Davies
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
| | - A Giess
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
| | - A E Sheppard
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
| | - T E A Peto
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
| | - N P J Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - D W Crook
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
| | - A S Walker
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK
| | - N Stoesser
- Nuffield Department of Clinical Medicine and the National Institute for Health Research Oxford Biomedical Research Centre (NIHR-OxBRC), University of Oxford, Oxford, UK. .,Department of Microbiology/Infectious Diseases, John Radcliffe Hospital, Headley Way, Headington, OX3 9DU, UK.
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Stoesser N, Sheppard AE, Peirano G, Anson LW, Pankhurst L, Sebra R, Phan HTT, Kasarskis A, Mathers AJ, Peto TEA, Bradford P, Motyl MR, Walker AS, Crook DW, Pitout JD. Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Sci Rep 2017; 7:5917. [PMID: 28725045 PMCID: PMC5517641 DOI: 10.1038/s41598-017-06256-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [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: 01/19/2017] [Accepted: 06/12/2017] [Indexed: 12/24/2022] Open
Abstract
The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla KPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10 kb). Here we characterize the genetic features of bla KPC emergence in global E. coli, 2008-2013, using both long- and short-read whole-genome sequencing. Amongst 43/45 successfully sequenced bla KPC-E. coli strains, we identified substantial strain diversity (n = 21 sequence types, 18% of annotated genes in the core genome); substantial plasmid diversity (≥9 replicon types); and substantial bla KPC-associated, mobile genetic element (MGE) diversity (50% not within complete Tn4401 elements). We also found evidence of inter-species, regional and international plasmid spread. In several cases bla KPC was found on high copy number, small Col-like plasmids, previously associated with horizontal transmission of resistance genes in the absence of antimicrobial selection pressures. E. coli is a common human pathogen, but also a commensal in multiple environmental and animal reservoirs, and easily transmissible. The association of bla KPC with a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms (e.g. bla TEM, bla CTX-M) suggests that it may become similarly prevalent.
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Affiliation(s)
- N Stoesser
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.
| | - A E Sheppard
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - G Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Alberta, Canada
| | - L W Anson
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - L Pankhurst
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - R Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, USA
| | - H T T Phan
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, United Kingdom
| | - A Kasarskis
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, USA
| | - A J Mathers
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.,Office of Hospital Epidemiology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - T E A Peto
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - P Bradford
- AstraZeneca Pharmaceuticals LP, Waltham, Massachusetts, USA
| | - M R Motyl
- Clinical Microbiology, Merck and Co Inc., Rahway, New Jersey, USA
| | - A S Walker
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - D W Crook
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - J D Pitout
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious diseases, University of Calgary, Alberta, Canada.,Snyder Institute for Chronic diseases, University of Calgary, Alberta, Canada.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
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Stoesser N, Sheppard AE, Shakya M, Sthapit B, Thorson S, Giess A, Kelly D, Pollard AJ, Peto TEA, Walker AS, Crook DW. Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing. J Antimicrob Chemother 2015; 70:1008-15. [PMID: 25558071 PMCID: PMC4356206 DOI: 10.1093/jac/dku521] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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] [Indexed: 02/06/2023] Open
Abstract
Objectives There are limited data on Enterobacter cloacae outbreaks and fewer describing these in association with NDM-1. With whole-genome sequencing, we tested the hypothesis that a cluster of 16 E. cloacae bacteraemia cases in a Nepali neonatal unit represented a single clonal outbreak, using a wider set of epidemiologically unrelated clinical E. cloacae isolates for comparison. Methods Forty-three isolates were analysed, including 23 E. cloacae and 3 Citrobacter sp. isolates obtained from blood cultures from 16 neonates over a 3 month period. These were compared with two contemporaneous community-associated drug-resistant isolates from adults, a unit soap dispenser isolate and a set of historical invasive isolates (n = 14) from the same geographical locality. Results There were two clear neonatal outbreaks and one isolated case in the unit. One outbreak was associated with an NDM-1 plasmid also identified in a historical community-associated strain. The smaller, second outbreak was likely associated with a contaminated soap dispenser. The two community-acquired adult cases and three sets of historical hospital-associated neonatal isolates represented four additional genetic clusters. Conclusions E. cloacae infections in this context represent several different transmission networks, operating at the community/hospital and host strain/plasmid levels. Wide sampling frames and high-resolution typing methods are needed to describe the complex molecular epidemiology of E. cloacae outbreaks, which is not appropriately reflected by routine susceptibility phenotypes. Soap dispensers may represent a reservoir for E. cloacae and bacterial strains and plasmids may persist in hospitals and in the community for long periods, sporadically being involved in outbreaks of disease.
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Affiliation(s)
- N Stoesser
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - A E Sheppard
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - M Shakya
- Department of Paediatrics, Patan Hospital, Kathmandu, Nepal
| | - B Sthapit
- Department of Paediatrics, Patan Hospital, Kathmandu, Nepal
| | - S Thorson
- Department of Paediatrics, Patan Hospital, Kathmandu, Nepal
| | - A Giess
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - D Kelly
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - A J Pollard
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - T E A Peto
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - A S Walker
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - D W Crook
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
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Pocock JM, Khun PA, Moore CE, Vuthy S, Stoesser N, Parry CM. Septic arthritis of the hip in a Cambodian child caused by multidrug-resistant Salmonella enterica serovar Typhi with intermediate susceptibility to ciprofloxacin treated with ceftriaxone and azithromycin. Paediatr Int Child Health 2014; 34:227-9. [PMID: 24749773 DOI: 10.1179/2046905514y.0000000123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Septic arthritis is a rare complication of typhoid fever. A 12-year-old boy without pre-existing disease attended a paediatric hospital in Cambodia with fever and left hip pain. A hip synovial fluid aspirate grew multidrug-resistant Salmonella enterica ser. Typhi with intermediate susceptibility to ciprofloxacin. Arthrotomy, 2 weeks of intravenous ceftriaxone and 4 weeks of oral azithromycin led to resolution of symptoms. The optimum management of septic arthritis in drug-resistant typhoid is undefined.
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Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo Elias C, Johnson JR, Walker AS, Peto TEA, Crook DW. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 2013; 68:2234-44. [PMID: 23722448 PMCID: PMC3772739 DOI: 10.1093/jac/dkt180] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [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] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms and predicting phenotype, and strain type, for both clinical and epidemiological purposes. This retrospective study aimed to determine the efficacy of whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae. METHODS Seventy-four E. coli and 69 K. pneumoniae bacteraemia isolates from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes were predicted from genomic sequences using BLASTn-based comparisons of de novo-assembled contigs with a study database of >100 known resistance-associated loci, including plasmid-associated and chromosomal genes. Predictions were made for seven commonly used antimicrobials: amoxicillin, co-amoxiclav, ceftriaxone, ceftazidime, ciprofloxacin, gentamicin and meropenem. Comparisons were made with phenotypic results obtained in duplicate by broth dilution (BD Phoenix). Discrepancies, either between duplicate BD Phoenix results or between genotype and phenotype, were resolved with gradient diffusion analyses. RESULTS A wide variety of antimicrobial resistance genes were identified, including blaCTX-M, blaLEN, blaOKP, blaOXA, blaSHV, blaTEM, aac(3')-Ia, aac-(3')-IId, aac-(3')-IIe, aac(6')-Ib-cr, aadA1a, aadA4, aadA5, aadA16, aph(6')-Id, aph(3')-Ia, qnrB and qnrS, as well as resistance-associated mutations in chromosomal gyrA and parC genes. The sensitivity of genome-based resistance prediction across all antibiotics for both species was 0.96 (95% CI: 0.94-0.98) and the specificity was 0.97 (95% CI: 0.95-0.98). Very major and major error rates were 1.2% and 2.1%, respectively. CONCLUSIONS Our method was as sensitive and specific as routinely deployed phenotypic methods. Validation against larger datasets and formal assessments of cost and turnaround time in a routine laboratory setting are warranted.
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Affiliation(s)
- N Stoesser
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital (Level 5), Headley Way, Headington OX3 9DU, UK
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Stoesser N, Emary K, Soklin S, Peng An K, Sophal S, Chhomrath S, Day NPJ, Limmathurotsakul D, Nget P, Pangnarith Y, Sona S, Kumar V, Moore CE, Chanpheaktra N, Parry CM. The value of intermittent point-prevalence surveys of healthcare-associated infections for evaluating infection control interventions at Angkor Hospital for Children, Siem Reap, Cambodia. Trans R Soc Trop Med Hyg 2013; 107:248-53. [PMID: 23418156 PMCID: PMC4023319 DOI: 10.1093/trstmh/trt005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [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] [Indexed: 11/29/2022] Open
Abstract
Background There are limited data on the epidemiology of paediatric healthcare-associated infection (HCAI) and infection control in low-income countries. We describe the value of intermittent point-prevalence surveys for monitoring HCAI and evaluating infection control interventions in a Cambodian paediatric hospital. Methods Hospital-wide, point-prevalence surveys were performed monthly in 2011. Infection control interventions introduced during this period included a hand hygiene programme and a ventilator-associated pneumonia (VAP) care bundle. Results Overall HCAI prevalence was 13.8/100 patients at-risk, with a significant decline over time. The highest HCAI rates (50%) were observed in critical care; the majority of HCAIs were respiratory (61%). Klebsiella pneumoniae was most commonly isolated and antimicrobial resistance was widespread. Hand hygiene compliance doubled to 51.6%, and total VAP cases/1000 patient-ventilator days fell from 30 to 10. Conclusion Rates of HCAI were substantial in our institution, and antimicrobial resistance a major concern. Point-prevalence surveys are effective for HCAI surveillance, and in monitoring trends in response to infection control interventions.
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Affiliation(s)
- N Stoesser
- Angkor Hospital for Children, Vithey Preah Sangreach Tep Vong & Um Chhay St., Sangkat Svay Dangkum Commune, Siem Reap, Cambodia.
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Khun P, Seng S, Emary K, Moore C, Soeng S, Ngoun C, Kumar V, Day N, Parry C, Stoesser N. Surveillance of healthcare-associated infection at Angkor Hospital for Children, Siem Reap, Cambodia. Int J Infect Dis 2012. [DOI: 10.1016/j.ijid.2012.05.482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Gruber P, Kennedy P, Stoesser N, Wendon J, Auzinger G. Right ventricular dysfunction in liver failure: a hemodynamic study. Crit Care 2008. [PMCID: PMC4088453 DOI: 10.1186/cc6303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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