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Walker AS, Pritchard E, House T, Robotham JV, Birrell PJ, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Studley R, Hay J, Vihta KD, Peto TEA, Stoesser N, Matthews PC, Eyre DW, Pouwels KB. Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time. eLife 2021; 10:e64683. [PMID: 34250907 PMCID: PMC8282332 DOI: 10.7554/elife.64683] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load). Methods We included all positive nose and throat swabs 26 April 2020 to 13 March 2021 from the UK's national COVID-19 Infection Survey, tested by RT-PCR for the N, S, and ORF1ab genes. We investigated predictors of median Ct value using quantile regression. Results Of 3,312,159 nose and throat swabs, 27,902 (0.83%) were RT-PCR-positive, 10,317 (37%), 11,012 (40%), and 6550 (23%) for 3, 2, or 1 of the N, S, and ORF1ab genes, respectively, with median Ct = 29.2 (~215 copies/ml; IQR Ct = 21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity, and age. Single-gene positives almost invariably had Ct > 30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4808 (78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody negative. Conclusions Marked variation in community SARS-CoV-2 Ct values suggests that they could be a useful epidemiological early-warning indicator. Funding Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.
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Pritchard E, Matthews PC, Stoesser N, Eyre DW, Gethings O, Vihta KD, Jones J, House T, VanSteenHouse H, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Rourke E, Studley R, Crook D, Peto TEA, Walker AS, Pouwels KB. Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom. Nat Med 2021; 27:1370-1378. [PMID: 34108716 PMCID: PMC8363500 DOI: 10.1038/s41591-021-01410-w] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
The effectiveness of COVID-19 vaccination in preventing new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the general community is still unclear. Here, we used the Office for National Statistics COVID-19 Infection Survey—a large community-based survey of individuals living in randomly selected private households across the United Kingdom—to assess the effectiveness of the BNT162b2 (Pfizer–BioNTech) and ChAdOx1 nCoV-19 (Oxford–AstraZeneca; ChAdOx1) vaccines against any new SARS-CoV-2 PCR-positive tests, split according to self-reported symptoms, cycle threshold value (<30 versus ≥30; as a surrogate for viral load) and gene positivity pattern (compatible with B.1.1.7 or not). Using 1,945,071 real-time PCR results from nose and throat swabs taken from 383,812 participants between 1 December 2020 and 8 May 2021, we found that vaccination with the ChAdOx1 or BNT162b2 vaccines already reduced SARS-CoV-2 infections ≥21 d after the first dose (61% (95% confidence interval (CI) = 54–68%) versus 66% (95% CI = 60–71%), respectively), with greater reductions observed after a second dose (79% (95% CI = 65–88%) versus 80% (95% CI = 73–85%), respectively). The largest reductions were observed for symptomatic infections and/or infections with a higher viral burden. Overall, COVID-19 vaccination reduced the number of new SARS-CoV-2 infections, with the largest benefit received after two vaccinations and against symptomatic and high viral burden infections, and with no evidence of a difference between the BNT162b2 and ChAdOx1 vaccines. Results from the Office of National Statistics COVID-19 Infection Survey in the United Kingdom demonstrate that the ChAdOx1 nCoV-19 and BNT162b2 vaccines reduce the incidence of new SARS-CoV-2 infections by up to 65% with a single dose and up to 80% after two doses, with no significant differences in efficacy observed between the two vaccines.
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Auguet OT, Niehus R, Gweon HS, Berkley JA, Waichungo J, Njim T, Edgeworth JD, Batra R, Chau K, Swann J, Walker SA, Peto TE, Crook DW, Lamble S, Turner P, Cooper BS, Stoesser N. Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK. EClinicalMedicine 2021; 36:100910. [PMID: 34124634 PMCID: PMC8173267 DOI: 10.1016/j.eclinm.2021.100910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) in Enterobacterales is a global health threat. Capacity for individual-level surveillance remains limited in many countries, whilst population-level surveillance approaches could inform empiric antibiotic treatment guidelines. METHODS In this exploratory study, a novel approach to population-level prediction of AMR in Enterobacterales clinical isolates using metagenomic (Illumina) profiling of pooled DNA extracts from human faecal samples was developed and tested. Taxonomic and AMR gene profiles were used to derive taxonomy-adjusted population-level AMR metrics. Bayesian modelling, and model comparison based on cross-validation, were used to evaluate the capacity of each metric to predict the number of resistant Enterobacterales invasive infections at a population-level, using available bloodstream/cerebrospinal fluid infection data. FINDINGS Population metagenomes comprised samples from 177, 157, and 156 individuals in Kenya, the UK, and Cambodia, respectively, collected between September 2014 and April 2016. Clinical data from independent populations included 910, 3356 and 197 bacterial isolates from blood/cerebrospinal fluid infections in Kenya, the UK and Cambodia, respectively (samples collected between January 2010 and May 2017). Enterobacterales were common colonisers and pathogens, and faecal taxonomic/AMR gene distributions and proportions of antimicrobial-resistant Enterobacterales infections differed by setting. A model including terms reflecting the metagenomic abundance of the commonest clinical Enterobacterales species, and of AMR genes known to either increase the minimum inhibitory concentration (MIC) or confer clinically-relevant resistance, had a higher predictive performance in determining population-level resistance in clinical Enterobacterales isolates compared to models considering only AMR gene information, only taxonomic information, or an intercept-only baseline model (difference in expected log predictive density compared to best model, estimated using leave-one-out cross-validation: intercept-only model = -223 [95% credible interval (CI): -330,-116]; model considering only AMR gene information = -186 [95% CI: -281,-91]; model considering only taxonomic information = -151 [95% CI: -232,-69]). INTERPRETATION Whilst our findings are exploratory and require validation, intermittent metagenomics of pooled samples could represent an effective approach for AMR surveillance and to predict population-level AMR in clinical isolates, complementary to ongoing development of laboratory infrastructures processing individual samples.
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Shaw LP, Chau KK, Kavanagh J, AbuOun M, Stubberfield E, Gweon HS, Barker L, Rodger G, Bowes MJ, Hubbard ATM, Pickford H, Swann J, Gilson D, Smith RP, Hoosdally SJ, Sebra R, Brett H, Peto TEA, Bailey MJ, Crook DW, Read DS, Anjum MF, Walker AS, Stoesser N. Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. SCIENCE ADVANCES 2021; 7:eabe3868. [PMID: 33837077 PMCID: PMC8034854 DOI: 10.1126/sciadv.abe3868] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/22/2021] [Indexed: 05/07/2023]
Abstract
Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.
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Townsend A, Rijal P, Xiao J, Tan TK, Huang KYA, Schimanski L, Huo J, Gupta N, Rahikainen R, Matthews PC, Crook D, Hoosdally S, Dunachie S, Barnes E, Street T, Conlon CP, Frater J, Arancibia-Cárcamo CV, Rudkin J, Stoesser N, Karpe F, Neville M, Ploeg R, Oliveira M, Roberts DJ, Lamikanra AA, Tsang HP, Bown A, Vipond R, Mentzer AJ, Knight JC, Kwok AJ, Screaton GR, Mongkolsapaya J, Dejnirattisai W, Supasa P, Klenerman P, Dold C, Baillie JK, Moore SC, Openshaw PJM, Semple MG, Turtle LCW, Ainsworth M, Allcock A, Beer S, Bibi S, Skelly D, Stafford L, Jeffrey K, O'Donnell D, Clutterbuck E, Espinosa A, Mendoza M, Georgiou D, Lockett T, Martinez J, Perez E, Gallardo Sanchez V, Scozzafava G, Sobrinodiaz A, Thraves H, Joly E. A haemagglutination test for rapid detection of antibodies to SARS-CoV-2. Nat Commun 2021; 12:1951. [PMID: 33782398 PMCID: PMC8007702 DOI: 10.1038/s41467-021-22045-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/17/2021] [Indexed: 11/24/2022] Open
Abstract
Serological detection of antibodies to SARS-CoV-2 is essential for establishing rates of seroconversion in populations, and for seeking evidence for a level of antibody that may be protective against COVID-19 disease. Several high-performance commercial tests have been described, but these require centralised laboratory facilities that are comparatively expensive, and therefore not available universally. Red cell agglutination tests do not require special equipment, are read by eye, have short development times, low cost and can be applied at the Point of Care. Here we describe a quantitative Haemagglutination test (HAT) for the detection of antibodies to the receptor binding domain of the SARS-CoV-2 spike protein. The HAT has a sensitivity of 90% and specificity of 99% for detection of antibodies after a PCR diagnosed infection. We will supply aliquots of the test reagent sufficient for ten thousand test wells free of charge to qualified research groups anywhere in the world.
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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] [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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Lipworth S, Vihta KD, Chau KK, Kavanagh J, Davies T, George S, Barker L, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections. Clin Infect Dis 2021; 73:2276-2282. [PMID: 33411882 PMCID: PMC8677521 DOI: 10.1093/cid/ciab006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The incidence of bloodstream infections (BSIs) caused by Escherichia coli and Klebsiella pneumoniae is increasing, with substantial associated morbidity, mortality and antimicrobial resistance. Unbiased serotyping studies to guide vaccine target selection are limited. METHODS We conducted unselected, population-level genomic surveillance of bloodstream E. coli and Klebsiella pneumoniae isolates from 2008-2018 in Oxfordshire, UK. We supplemented this with an analysis of publicly available global sequencing data (n=3678). RESULTS We sequenced 3478 E. coli isolates (3278 passed quality control) and 556 K. pneumoniae isolates (535 (K-antigen) and 549 (O-antigen) passed quality control). The four most common E. coli O-antigens (O1/O2/O6/O25) were identified in 1499/3278 isolates; the incidence of these O-types increased over time (IRRy=1.14, 95% CI:1.11-1.16). These O-types accounted for 616/1434 multidrug resistant (MDR) and 173/256 extended-spectrum beta-lactamase(ESBL)-resistant isolates in Oxfordshire, but only 19/90 carbapenem-resistant isolates across all studies. For Klebsiella pneumoniae, the most common O-antigens (O2v2/O1v1/O3b/O1v2) accounted for 410/549 isolates; the incidence of BSIs caused by these also increased annually (IRRy=1.09; 95% CI:1.05-1.12). These O-types accounted for 122/148 MDR and 106/123 ESBL isolates in Oxfordshire and 557/734 carbapenem-resistant isolates across all studies. Conversely we observed substantial capsular antigen diversity. Analysis of 3678 isolates from global studies demonstrated the generalisability of these findings. For E. coli, based on serotyping, the ExPEC4V and ExPEC10V vaccines under investigation would cover 46% and 72% of Oxfordshire isolates respectively, and 47% and 71% of MDR isolates. CONCLUSIONS O-antigen targeted vaccines may be useful in reducing the morbidity, mortality and antimicrobial resistance associated with E. coli and K. pneumoniae BSIs.
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Ainsworth M, Andersson M, Auckland K, Baillie JK, Barnes E, Beer S, Beveridge A, Bibi S, Blackwell L, Borak M, Bown A, Brooks T, Burgess-Brown NA, Camara S, Catton M, Chau KK, Christott T, Clutterbuck E, Coker J, Cornall RJ, Cox S, Crawford-Jones D, Crook DW, D'Arcangelo S, Dejnirattsai W, Dequaire JMM, Dimitriadis S, Dingle KE, Doherty G, Dold C, Dong T, Dunachie SJ, Ebner D, Emmenegger M, Espinosa A, Eyre DW, Fairhead R, Fassih S, Feehily C, Felle S, Fernandez-Cid A, Fernandez Mendoza M, Foord TH, Fordwoh T, Fox McKee D, Frater J, Gallardo Sanchez V, Gent N, Georgiou D, Groves CJ, Hallis B, Hammond PM, Hatch SB, Harvala HJ, Hill J, Hoosdally SJ, Horsington B, Howarth A, James T, Jeffery K, Jones E, Justice A, Karpe F, Kavanagh J, Kim DS, Kirton R, Klenerman P, Knight JC, Koukouflis L, Kwok A, Leuschner U, Levin R, Linder A, Lockett T, Lumley SF, Marinou S, Marsden BD, Martinez J, Martins Ferreira L, Mason L, Matthews PC, Mentzer AJ, Mobbs A, Mongkolsapaya J, Morrow J, Mukhopadhyay SMM, Neville MJ, Oakley S, Oliveira M, Otter A, Paddon K, Pascoe J, Peng Y, Perez E, Perumal PK, Peto TEA, Pickford H, Ploeg RJ, Pollard AJ, Richardson A, Ritter TG, Roberts DJ, Rodger G, Rollier CS, Rowe C, Rudkin JK, Screaton G, Semple MG, Sienkiewicz A, Silva-Reyes L, Skelly DT, Sobrino Diaz A, Stafford L, Stockdale L, Stoesser N, Street T, Stuart DI, Sweed A, Taylor A, Thraves H, Tsang HP, Verheul MK, Vipond R, Walker TM, Wareing S, Warren Y, Wells C, Wilson C, Withycombe K, Young RK. Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison. THE LANCET. INFECTIOUS DISEASES 2020; 20:1390-1400. [PMID: 32979318 PMCID: PMC7511171 DOI: 10.1016/s1473-3099(20)30634-4] [Citation(s) in RCA: 260] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic in 2020. Testing is crucial for mitigating public health and economic effects. Serology is considered key to population-level surveillance and potentially individual-level risk assessment. However, immunoassay performance has not been compared on large, identical sample sets. We aimed to investigate the performance of four high-throughput commercial SARS-CoV-2 antibody immunoassays and a novel 384-well ELISA. METHODS We did a head-to-head assessment of SARS-CoV-2 IgG assay (Abbott, Chicago, IL, USA), LIAISON SARS-CoV-2 S1/S2 IgG assay (DiaSorin, Saluggia, Italy), Elecsys Anti-SARS-CoV-2 assay (Roche, Basel, Switzerland), SARS-CoV-2 Total assay (Siemens, Munich, Germany), and a novel 384-well ELISA (the Oxford immunoassay). We derived sensitivity and specificity from 976 pre-pandemic blood samples (collected between Sept 4, 2014, and Oct 4, 2016) and 536 blood samples from patients with laboratory-confirmed SARS-CoV-2 infection, collected at least 20 days post symptom onset (collected between Feb 1, 2020, and May 31, 2020). Receiver operating characteristic (ROC) curves were used to assess assay thresholds. FINDINGS At the manufacturers' thresholds, for the Abbott assay sensitivity was 92·7% (95% CI 90·2-94·8) and specificity was 99·9% (99·4-100%); for the DiaSorin assay sensitivity was 96·2% (94·2-97·7) and specificity was 98·9% (98·0-99·4); for the Oxford immunoassay sensitivity was 99·1% (97·8-99·7) and specificity was 99·0% (98·1-99·5); for the Roche assay sensitivity was 97·2% (95·4-98·4) and specificity was 99·8% (99·3-100); and for the Siemens assay sensitivity was 98·1% (96·6-99·1) and specificity was 99·9% (99·4-100%). All assays achieved a sensitivity of at least 98% with thresholds optimised to achieve a specificity of at least 98% on samples taken 30 days or more post symptom onset. INTERPRETATION Four commercial, widely available assays and a scalable 384-well ELISA can be used for SARS-CoV-2 serological testing to achieve sensitivity and specificity of at least 98%. The Siemens assay and Oxford immunoassay achieved these metrics without further optimisation. This benchmark study in immunoassay assessment should enable refinements of testing strategies and the best use of serological testing resource to benefit individuals and population health. FUNDING Public Health England and UK National Institute for Health Research.
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Lipworth S, Pickford H, Sanderson N, Chau KK, Kavanagh J, Barker L, Vaughan A, Swann J, Andersson M, Jeffery K, Morgan M, Peto TEA, Crook DW, Stoesser N, Walker AS. Optimized use of Oxford Nanopore flowcells for hybrid assemblies. Microb Genom 2020; 6:mgen000453. [PMID: 33174830 PMCID: PMC7725331 DOI: 10.1099/mgen.0.000453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/25/2020] [Indexed: 01/16/2023] Open
Abstract
Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the carriage of clinically important genes (e.g. those involved in antimicrobial resistance/virulence). The widespread application of this technique is currently primarily limited by cost. Recent data have suggested that non-inferior, and even superior, hybrid assemblies can be produced using a fraction of the total output from a multiplexed nanopore [Oxford Nanopore Technologies (ONT)] flowcell run. In this study we sought to determine the optimal minimal running time for flowcells when acquiring reads for hybrid assembly. We then evaluated whether the ONT wash kit might allow users to exploit shorter running times by sequencing multiple libraries per flowcell. After 24 h of sequencing, most chromosomes and plasmids had circularized and there was no benefit associated with longer running times. Quality was similar at 12 h, suggesting that shorter running times are likely to be acceptable for certain applications (e.g. plasmid genomics). The ONT wash kit was highly effective in removing DNA between libraries. Contamination between libraries did not appear to affect subsequent hybrid assemblies, even when the same barcodes were used successively on a single flowcell. Utilizing shorter run times in combination with between-library nuclease washes allows at least 36 Enterobacteriaceae isolates to be sequenced per flowcell, significantly reducing the per-isolate sequencing cost. Ultimately this will facilitate large-scale studies utilizing hybrid assembly, advancing our understanding of the genomics of key human pathogens.
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Andersson MI, Arancibia-Carcamo CV, Auckland K, Baillie JK, Barnes E, Beneke T, Bibi S, Brooks T, Carroll M, Crook D, Dingle K, Dold C, Downs LO, Dunn L, Eyre DW, Gilbert Jaramillo J, Harvala H, Hoosdally S, Ijaz S, James T, James W, Jeffery K, Justice A, Klenerman P, Knight JC, Knight M, Liu X, Lumley SF, Matthews PC, McNaughton AL, Mentzer AJ, Mongkolsapaya J, Oakley S, Oliveira MS, Peto T, Ploeg RJ, Ratcliff J, Robbins MJ, Roberts DJ, Rudkin J, Russell RA, Screaton G, Semple MG, Skelly D, Simmonds P, Stoesser N, Turtle L, Wareing S, Zambon M. SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus. Wellcome Open Res 2020; 5:181. [PMID: 33283055 PMCID: PMC7689603 DOI: 10.12688/wellcomeopenres.16002.2] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=462 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/494 (0%, 95%CI 0-0.7%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. There was a relationship between RT-PCR negativity and the presence of total SARS-CoV-2 antibody (p=0.02). Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.
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Lumley SF, Eyre DW, McNaughton AL, Howarth A, Hoosdally S, Hatch SB, Kavanagh J, Chau KK, Downs LO, Cox S, Dunn L, Justice A, Wareing S, Dingle K, Rudkin J, Auckland K, Fyfe A, Bolton J, Paton R, Mentzer AJ, Jeffery K, Andersson MI, James T, Peto TEA, Marsden BD, Screaton G, Cornall RJ, Klenerman P, Ebner D, Stuart DI, Crook DW, Stoesser N, Kennedy SH, Thompson C, Gupta S, Matthews PC. SARS-CoV-2 antibody prevalence, titres and neutralising activity in an antenatal cohort, United Kingdom, 14 April to 15 June 2020. Euro Surveill 2020; 25:2001721. [PMID: 33094717 PMCID: PMC7651878 DOI: 10.2807/1560-7917.es.2020.25.41.2001721] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/22/2020] [Indexed: 12/29/2022] Open
Abstract
SARS-CoV-2 IgG screening of 1,000 antenatal serum samples in the Oxford area, United Kingdom, between 14 April and 15 June 2020, yielded a 5.3% seroprevalence, mirroring contemporaneous regional data. Among the 53 positive samples, 39 showed in vitro neutralisation activity, correlating with IgG titre (Pearson's correlation p<0.0001). While SARS-CoV-2 seroprevalence in pregnancy cohorts could potentially inform population surveillance, clinical correlates of infection and immunity in pregnancy, and antenatal epidemiology evolution over time need further study.
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Eyre DW, Lumley SF, O'Donnell D, Campbell M, Sims E, Lawson E, Warren F, James T, Cox S, Howarth A, Doherty G, Hatch SB, Kavanagh J, Chau KK, Fowler PW, Swann J, Volk D, Yang-Turner F, Stoesser N, Matthews PC, Dudareva M, Davies T, Shaw RH, Peto L, Downs LO, Vogt A, Amini A, Young BC, Drennan PG, Mentzer AJ, Skelly DT, Karpe F, Neville MJ, Andersson M, Brent AJ, Jones N, Martins Ferreira L, Christott T, Marsden BD, Hoosdally S, Cornall R, Crook DW, Stuart DI, Screaton G, Peto TEA, Holthof B, O'Donnell AM, Ebner D, Conlon CP, Jeffery K, Walker TM. Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study. eLife 2020; 9:e60675. [PMID: 32820721 PMCID: PMC7486122 DOI: 10.7554/elife.60675] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022] Open
Abstract
We conducted voluntary Covid-19 testing programmes for symptomatic and asymptomatic staff at a UK teaching hospital using naso-/oro-pharyngeal PCR testing and immunoassays for IgG antibodies. 1128/10,034 (11.2%) staff had evidence of Covid-19 at some time. Using questionnaire data provided on potential risk-factors, staff with a confirmed household contact were at greatest risk (adjusted odds ratio [aOR] 4.82 [95%CI 3.45-6.72]). Higher rates of Covid-19 were seen in staff working in Covid-19-facing areas (22.6% vs. 8.6% elsewhere) (aOR 2.47 [1.99-3.08]). Controlling for Covid-19-facing status, risks were heterogenous across the hospital, with higher rates in acute medicine (1.52 [1.07-2.16]) and sporadic outbreaks in areas with few or no Covid-19 patients. Covid-19 intensive care unit staff were relatively protected (0.44 [0.28-0.69]), likely by a bundle of PPE-related measures. Positive results were more likely in Black (1.66 [1.25-2.21]) and Asian (1.51 [1.28-1.77]) staff, independent of role or working location, and in porters and cleaners (2.06 [1.34-3.15]).
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Cusack TP, Phimolsarnnousith V, Duangmala K, Phoumin P, Turton J, Hopkins KL, Woodford N, Shetty N, Stoesser N, Phan HTT, Dance DAB. Molecular characterization of carbapenem-resistant Escherichia coli and Acinetobacter baumannii in the Lao People's Democratic Republic. J Antimicrob Chemother 2020; 74:2810-2821. [PMID: 31167025 PMCID: PMC6736291 DOI: 10.1093/jac/dkz234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Andersson MI, Arancibia-Carcamo CV, Auckland K, Baillie JK, Barnes E, Beneke T, Bibi S, Brooks T, Carroll M, Crook D, Dingle K, Dold C, Downs LO, Dunn L, Eyre DW, Gilbert Jaramillo J, Harvala H, Hoosdally S, Ijaz S, James T, James W, Jeffery K, Justice A, Klenerman P, Knight JC, Knight M, Liu X, Lumley SF, Matthews PC, McNaughton AL, Mentzer AJ, Mongkolsapaya J, Oakley S, Oliveira MS, Peto T, Ploeg RJ, Ratcliff J, Robbins MJ, Roberts DJ, Rudkin J, Russell RA, Screaton G, Semple MG, Skelly D, Simmonds P, Stoesser N, Turtle L, Wareing S, Zambon M. SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus. Wellcome Open Res 2020; 5:181. [PMID: 33283055 PMCID: PMC7689603 DOI: 10.12688/wellcomeopenres.16002.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 11/13/2023] Open
Abstract
Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=462 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/494 (0%, 95%CI 0-0.7%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.
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Constantinides B, Chau KK, Quan TP, Rodger G, Andersson MI, Jeffery K, Lipworth S, Gweon HS, Peniket A, Pike G, Millo J, Byukusenge M, Holdaway M, Gibbons C, Mathers AJ, Crook DW, Peto TE, Walker AS, Stoesser N. Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Microb Genom 2020; 6:mgen000391. [PMID: 32553019 PMCID: PMC7478627 DOI: 10.1099/mgen.0.000391] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/24/2020] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of E. coli, Klebsiella pneumoniae and Klebsiella oxytoca, including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2 %; 95 % CI 0.05-11 %) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10 % of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including blaCTX-M, blaSHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.
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Shen C, Zhong LL, Yang Y, Doi Y, Paterson DL, Stoesser N, Ma F, El-Sayed Ahmed MAEG, Feng S, Huang S, Li HY, Huang X, Wen X, Zhao Z, Lin M, Chen G, Liang W, Liang Y, Xia Y, Dai M, Chen DQ, Zhang L, Liao K, Tian GB. Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing-based molecular epidemiological study. LANCET MICROBE 2020; 1:e34-e43. [DOI: 10.1016/s2666-5247(20)30005-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/10/2020] [Accepted: 03/27/2020] [Indexed: 11/29/2022]
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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] [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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Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N, Shaw LP, Stoesser N, Peto TEA, Crook DW, Walker AS. Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines. Gigascience 2020; 9:giaa007. [PMID: 32025702 PMCID: PMC7002876 DOI: 10.1093/gigascience/giaa007] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 12/02/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Accurately identifying single-nucleotide polymorphisms (SNPs) from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP-calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia, and Klebsiella. RESULTS We evaluated the performance of 209 SNP-calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic bacteria such as Escherichia coli but less dominant for clonal species such as Mycobacterium tuberculosis. CONCLUSIONS The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest-performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often used the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup, or Strelka.
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Crellen T, Turner P, Pol S, Baker S, Nguyen Thi Nguyen T, Stoesser N, Day NPJ, Turner C, Cooper BS. Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country. eLife 2019; 8:e50468. [PMID: 31793878 PMCID: PMC6977969 DOI: 10.7554/elife.50468] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Multidrug-resistant Klebsiella pneumoniae is an increasing cause of infant mortality in developing countries. We aimed to develop a quantitative understanding of the drivers of this epidemic by estimating the effects of antibiotics on nosocomial transmission risk, comparing competing hypotheses about mechanisms of spread, and quantifying the impact of potential interventions. Using a sequence of dynamic models, we analysed data from a one-year prospective carriage study in a Cambodian neonatal intensive care unit with hyperendemic third-generation cephalosporin-resistant K. pneumoniae. All widely-used antibiotics except imipenem were associated with an increased daily acquisition risk, with an odds ratio for the most common combination (ampicillin + gentamicin) of 1.96 (95% CrI 1.18, 3.36). Models incorporating genomic data found that colonisation pressure was associated with a higher transmission risk, indicated sequence type heterogeneity in transmissibility, and showed that within-ward transmission was insufficient to maintain endemicity. Simulations indicated that increasing the nurse-patient ratio could be an effective intervention.
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Gweon HS, Shaw LP, Swann J, De Maio N, AbuOun M, Niehus R, Hubbard ATM, Bowes MJ, Bailey MJ, Peto TEA, Hoosdally SJ, Walker AS, Sebra RP, Crook DW, Anjum MF, Read DS, Stoesser N. The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples. ENVIRONMENTAL MICROBIOME 2019; 14:7. [PMID: 33902704 PMCID: PMC8204541 DOI: 10.1186/s40793-019-0347-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/28/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, 'ResPipe'. RESULTS Taxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve < 1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment. CONCLUSIONS Sequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available ( https://gitlab.com/hsgweon/ResPipe ).
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Mathers AJ, Sheppard A, Stoesser N, Crook D, Barry KE, Eyre D, Vegesana KB, Parikh H. 505. Making of a “Super-Duper Bug”: Plasmid-Mediated Resistance Accumulation in a Carbapenemase-Producing Klebsiella quasipneumoniae from Patients and the Environment. Open Forum Infect Dis 2019. [PMCID: PMC6811105 DOI: 10.1093/ofid/ofz360.574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Carbapenemase-producing Enterobacteriaceae can form a reservoir in hospital wastewater biofilms. Klebsiella quasipneumoniae is increasingly recognized as an emerging nosocomial threat, frequently carrying antimicrobial resistance (AMR) genes on plasmids. The dynamics of AMR gene and plasmid gain/loss over time in this species remain unclear. Methods Klebsiella pneumoniae carbapenemase producing-K. quasipneumoniae (KPC-Kq) isolates from patients and wastewater sites from drains and toilets were sequenced (Illumina). Sequence assemblies (SPAdes) were probed in silico for AMR genes and plasmid Incompatibility types (using AMRFinder and PlasmidFinder databases, respectively). For related isolates (<100 SNV) cultured from the same sites longitudinally, we compared the accumulation of AMR genes in patients and environmental reservoirs over time. Results From 2009 to 2016 there were a total of 15 KPC-Kq isolates from 8 patients and 17 environmental isolates from 11 rooms. The mean number of resistance genes identified in patients and environmental isolates were 15 and 14, respectively (P = NS), with five resistance genes carried by all isolates including blaKPC. There was an average of 4.4 unique incompatibility types from patients and 4.0 from the environment (P = NS). For the longitudinal subset, there were 17 related isolates from two patients and two sink drains. One hospitalized patient with repeated antimicrobial exposure had a KPC-Kq initial isolate with 3 plasmid types and 13 AMR genes and died one year later with a KPC-Kq isolated from blood with 11 plasmid types and 25 AMR genes. The other patient was primarily an outpatient with little antimicrobial exposure. His KPC-Kq lost 1 plasmid and 3 AMR genes over 15 months. One KPC-Kq strain in the environment lost 3 plasmid types and 8 AMR genes over 4 months; the other was unchanged over 5 months. Conclusion KPC-Kq has been seen in both patients and the environment for several years at our institution. Sequencing of longitudinal isolates revealed that under antimicrobial pressure a patient KPC-Kq accumulated multiple plasmids and AMR genes. This same accumulation was not witnessed environmental sites over time although the numbers are small and will require confirmatory work. Disclosures All authors: No reported disclosures.
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Zhong LL, Phan HTT, Shen C, Vihta KD, Sheppard AE, Huang X, Zeng KJ, Li HY, Zhang XF, Patil S, Crook DW, Walker AS, Xing Y, Lin JL, Feng LQ, Doi Y, Xia Y, Stoesser N, Tian GB. High Rates of Human Fecal Carriage of mcr-1-Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families. Clin Infect Dis 2019; 66:676-685. [PMID: 29040419 DOI: 10.1093/cid/cix885] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/07/2017] [Indexed: 12/21/2022] Open
Abstract
Background mcr-1-mediated colistin resistance in Enterobacteriaceae is concerning, as colistin is used in treating multidrug-resistant Enterobacteriaceae infections. We identified trends in human fecal mcr-1-positivity rates and colonization with mcr-1-positive, third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae in Guangzhou, China, and investigated the genetic contexts of mcr-1 in mcr-1-positive 3GC-R strains. Methods Fecal samples were collected from in-/out-patients submitting specimens to 3 hospitals (2011-2016). mcr-1 carriage trends were assessed using iterative sequential regression. A subset of mcr-1-positive isolates was sequenced (whole-genome sequencing [WGS], Illumina), and genetic contexts (flanking regions, plasmids) of mcr-1 were characterized. Results Of 8022 fecal samples collected, 497 (6.2%) were mcr-1 positive, and 182 (2.3%) harbored mcr-1-positive 3GC-R Enterobacteriaceae. We observed marked increases in mcr-1 (0% [April 2011] to 31% [March 2016]) and more recent (since January 2014; 0% [April 2011] to 15% [March 2016]) increases in human colonization with mcr-1-positive 3GC-R Enterobacteriaceae (P < .001). mcr-1-positive 3GC-R isolates were commonly multidrug resistant. WGS of mcr-1-positive 3GC-R isolates (70 Escherichia coli, 3 Klebsiella pneumoniae) demonstrated bacterial strain diversity; mcr-1 in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequent mcr-1 chromosomal integration; and high mobility of the mcr-1-associated insertion sequence ISApl1. Sequence data were consistent with plasmid spread among animal/human reservoirs. Conclusions The high prevalence of mcr-1 in multidrug-resistant E. coli colonizing humans is a clinical threat; diverse genetic mechanisms (strains/plasmids/insertion sequences) have contributed to the dissemination of mcr-1, and will facilitate its persistence.
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De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N. Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. Microb Genom 2019; 5:e000294. [PMID: 31483244 PMCID: PMC6807382 DOI: 10.1099/mgen.0.000294] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/19/2019] [Indexed: 01/23/2023] Open
Abstract
Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the long-read assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.
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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] [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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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] [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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