scispace - formally typeset
Search or ask a question
Author

Michelle J Cole

Bio: Michelle J Cole is an academic researcher from Public Health England. The author has contributed to research in topics: Neisseria gonorrhoeae & Antibiotic resistance. The author has an hindex of 32, co-authored 100 publications receiving 2904 citations. Previous affiliations of Michelle J Cole include European Centre for Disease Prevention and Control & Health Protection Agency.


Papers
More filters
Journal ArticleDOI
V J Hall1, Sarah Foulkes2, Andre Charlett1, Ana Atti2  +302 moreInstitutions (3)
TL;DR: The SARS-CoV-2 Immunity and Reinfection Evaluation study as mentioned in this paper showed that a previous history of SARS infection was associated with an 84% lower risk of infection, with median protective effect observed 7 months following primary infection.

492 citations

Journal ArticleDOI
TL;DR: A heterosexual male was diagnosed with gonorrhoea in the United Kingdom following sexual intercourse with a locally resident female in Thailand and failed treatment with ceftriaxone plus doxycycline and subsequently spectinomycin, resulting in resistance arose from two mechanisms combining for the first time in a genetic background similar to a commonly circulating strain.
Abstract: We describe a gonorrhoea case with combined high-level azithromycin resistance and ceftriaxone resistance. In February 2018, a heterosexual male was diagnosed with gonorrhoea in the United Kingdom following sexual intercourse with a locally resident female in Thailand and failed treatment with ceftriaxone plus doxycycline and subsequently spectinomycin. Resistance arose from two mechanisms combining for the first time in a genetic background similar to a commonly circulating strain. Urgent action is essential to prevent further spread.

251 citations

Journal ArticleDOI
TL;DR: A WGS-based MIC prediction approach that allows reliable MIC prediction for five gonorrhoea antimicrobials is demonstrated and should allow reasonably precise prediction of MICs for a range of bacterial species.
Abstract: Background: Tracking the spread of antimicrobial-resistant Neisseria gonorrhoeae is a major priority for national surveillance programmes. / Objectives: We investigate whether WGS and simultaneous analysis of multiple resistance determinants can be used to predict antimicrobial susceptibilities to the level of MICs in N. gonorrhoeae. / Methods: WGS was used to identify previously reported potential resistance determinants in 681 N. gonorrhoeae isolates, from England, the USA and Canada, with phenotypes for cefixime, penicillin, azithromycin, ciprofloxacin and tetracycline determined as part of national surveillance programmes. Multivariate linear regression models were used to identify genetic predictors of MIC. Model performance was assessed using leave-one-out cross-validation. / Results: Overall 1785/3380 (53%) MIC values were predicted to the nearest doubling dilution and 3147 (93%) within ±1 doubling dilution and 3314 (98%) within ±2 doubling dilutions. MIC prediction performance was similar across the five antimicrobials tested. Prediction models included the majority of previously reported resistance determinants. Applying EUCAST breakpoints to MIC predictions, the overall very major error (VME; phenotypically resistant, WGS-prediction susceptible) rate was 21/1577 (1.3%, 95% CI 0.8%–2.0%) and the major error (ME; phenotypically susceptible, WGS-prediction resistant) rate was 20/1186 (1.7%, 1.0%–2.6%). VME rates met regulatory thresholds for all antimicrobials except cefixime and ME rates for all antimicrobials except tetracycline. Country of testing was a strongly significant predictor of MIC for all five antimicrobials. / Conclusions: We demonstrate a WGS-based MIC prediction approach that allows reliable MIC prediction for five gonorrhoea antimicrobials. Our approach should allow reasonably precise prediction of MICs for a range of bacterial species.

162 citations

Journal ArticleDOI
TL;DR: This work provides the first use of joint analysis of WGS and epidemiological data in an international programme for regional surveillance of sexually transmitted infections and provides a framework for genomic surveillance of gonococci through standardised sampling, use of W GS, and a shared information architecture for interpretation and dissemination.
Abstract: Summary Background Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction with linked epidemiological and phenotypic data, to describe the gonococcal population in 20 European countries. We aimed to detail changes in phenotypic antimicrobial resistance levels (and the reasons for these changes) and strain distribution (with a focus on antimicrobial resistance strains in risk groups), and to predict antimicrobial resistance from WGS data. Methods We carried out an observational study, in which we sequenced isolates taken from patients with gonorrhoea from the European Gonococcal Antimicrobial Surveillance Programme in 20 countries from September to November, 2013. We also developed a web platform that we used for automated antimicrobial resistance prediction, molecular typing ( N gonorrhoeae multi-antigen sequence typing [NG-MAST] and multilocus sequence typing), and phylogenetic clustering in conjunction with epidemiological and phenotypic data. Findings The multidrug-resistant NG-MAST genogroup G1407 was predominant and accounted for the most cephalosporin resistance, but the prevalence of this genogroup decreased from 248 (23%) of 1066 isolates in a previous study from 2009–10 to 174 (17%) of 1054 isolates in this survey in 2013. This genogroup previously showed an association with men who have sex with men, but changed to an association with heterosexual people (odds ratio=4·29). WGS provided substantially improved resolution and accuracy over NG-MAST and multilocus sequence typing, predicted antimicrobial resistance relatively well, and identified discrepant isolates, mixed infections or contaminants, and multidrug-resistant clades linked to risk groups. Interpretation To our knowledge, we provide the first use of joint analysis of WGS and epidemiological data in an international programme for regional surveillance of sexually transmitted infections. WGS provided enhanced understanding of the distribution of antimicrobial resistance clones, including replacement with clones that were more susceptible to antimicrobials, in several risk groups nationally and regionally. We provide a framework for genomic surveillance of gonococci through standardised sampling, use of WGS, and a shared information architecture for interpretation and dissemination by use of open access software. Funding The European Centre for Disease Prevention and Control, The Centre for Genomic Pathogen Surveillance, Orebro University Hospital, and Wellcome.

153 citations


Cited by
More filters
01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal Article
TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

2,436 citations

Journal ArticleDOI
Nuno R. Faria, Thomas A. Mellan1, Charles Whittaker1, Ingra Morales Claro2, Darlan da Silva Candido3, Darlan da Silva Candido2, Swapnil Mishra1, Myuki A E Crispim, Flavia C. S. Sales2, Iwona Hawryluk1, John T. McCrone4, Ruben J.G. Hulswit3, Lucas A M Franco2, Mariana S. Ramundo2, Jaqueline Goes de Jesus2, Pamela S Andrade2, Thais M. Coletti2, Giulia M. Ferreira5, Camila A. M. Silva2, Erika R. Manuli2, Rafael Henrique Moraes Pereira, Pedro S. Peixoto2, Moritz U. G. Kraemer3, Nelson Gaburo, Cecilia da C. Camilo, Henrique Hoeltgebaum1, William Marciel de Souza2, Esmenia C. Rocha2, Leandro Marques de Souza2, Mariana C. Pinho2, Leonardo José Tadeu de Araújo6, Frederico S V Malta, Aline B. de Lima, Joice do P. Silva, Danielle A G Zauli, Alessandro C. S. Ferreira, Ricardo P Schnekenberg3, Daniel J Laydon1, Patrick G T Walker1, Hannah M. Schlüter1, Ana L. P. dos Santos, Maria S. Vidal, Valentina S. Del Caro, Rosinaldo M. F. Filho, Helem M. dos Santos, Renato Santana Aguiar7, José Luiz Proença-Módena8, Bruce Walker Nelson9, James A. Hay10, Melodie Monod1, Xenia Miscouridou1, Helen Coupland1, Raphael Sonabend1, Michaela A. C. Vollmer1, Axel Gandy1, Carlos A. Prete2, Vitor H. Nascimento2, Marc A. Suchard11, Thomas A. Bowden3, Sergei L Kosakovsky Pond12, Chieh-Hsi Wu13, Oliver Ratmann1, Neil M. Ferguson1, Christopher Dye3, Nicholas J. Loman14, Philippe Lemey15, Andrew Rambaut4, Nelson Abrahim Fraiji, Maria Perpétuo Socorro Sampaio Carvalho, Oliver G. Pybus3, Oliver G. Pybus16, Seth Flaxman1, Samir Bhatt17, Samir Bhatt1, Ester Cerdeira Sabino2 
21 May 2021-Science
TL;DR: In this article, the authors used a two-category dynamical model that integrates genomic and mortality data to estimate that P.1 may be 1.7-to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.
Abstract: Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

985 citations

Journal ArticleDOI
TL;DR: Despite the high efficacy of the BNT162b2 messenger RNA vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rare breakthrough infections have been reported.
Abstract: Background Despite the high efficacy of the BNT162b2 messenger RNA vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rare breakthrough infections have been repo...

975 citations

Journal ArticleDOI
TL;DR: The study highlights the need to expand data collection efforts at country level and provides an initial baseline for monitoring progress of the World Health Organization global health sector strategy on sexually transmitted infections 2016–2021.
Abstract: Objective To generate estimates of the global prevalence and incidence of urogenital infection with chlamydia, gonorrhoea, trichomoniasis and syphilis in women and men, aged 15–49 years, in 2016.

860 citations