166 results on '"Cole, MJ"'
Search Results
2. Assessing coal mine closures and mining community profiles for the just transition' in South Africa
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Cole, MJ, primary, Mthenjane, M, additional, and van ZyP, AT, additional
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- 2023
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3. A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch
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Sánchez-Busó L, Yeats CA, Taylor B, Goater RJ, Underwood A, Abudahab K, Argimón S, Ma KC, Mortimer TD, Golparian D, Cole MJ, Grad YH, Martin I, Raphael BH, Shafer WM, Town K, Wi T, Harris SR, Unemo M, and Aanensen DM
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Pathogenwatch ,Public health ,Surveillance ,Epidemiology ,Genomics ,Antimicrobial resistance ,Neisseria gonorrhoeae - Abstract
Background Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones and transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community-driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance. Methods Here we present a public health-focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch (). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization. Results AMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin-resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasising the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern. Conclusions The N. gonorrhoeae scheme in Pathogenwatch provides customised bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower-resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.
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- 2021
4. High susceptibility to zoliflodacin and conserved target (GyrB) for zoliflodacin among 1209 consecutive clinical Neisseria gonorrhoeae isolates from 25 European countries, 2018
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Ahlstrand J, Sánchez-Busó L, Day M, Aanensen D, Golparian D, Jacobsson S, Cole MJ, Torreblanca RA, Ásmundsdóttir LR, Balla E, De Baetselier I, Bercot B, Carannante A, Caugant D, Borrego MJ, Buder S, Cassar R, Cole M, Dam A, Eder C, Hoffmann S, Hunjak B, Jeverica S, Kirjavainen V, Maikanti-Charalambous P, Miriagou V, Mlynarczyk-Bonikowska B, Pakarna G, Patterson L, Pavlik P, Perrin M, Shepherd J, Stefanelli P, Unemo M, Jelena V, and Zákoucká H
- Abstract
Objectives: Novel antimicrobials for treatment of gonorrhoea are imperative. The first-in-class spiropyrimidinetrione zoliflodacin is promising and currently in an international Phase 3 randomized controlled clinical trial (RCT) for treatment of uncomplicated gonorrhoea. We evaluated the in vitro activity of and the genetic conservation of the target (GyrB) and other potential zoliflodacin resistance determinants among 1209 consecutive clinical Neisseria gonorrhoeae isolates obtained from 25 EU/European Economic Area (EEA) countries in 2018 and compared the activity of zoliflodacin with that of therapeutic antimicrobials currently used. Methods: MICs of zoliflodacin, ceftriaxone, cefixime, azithromycin and ciprofloxacin were determined using an agar dilution technique for zoliflodacin or using MIC gradient strip tests or an agar dilution technique for the other antimicrobials. Genome sequences were available for 96.1% of isolates. Results: Zoliflodacin modal MIC, MIC50, MIC90 and MIC range were 0.125, 0.125, 0.125 and
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- 2021
5. Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis
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Beale, MA, Marks, M, Cole, MJ, Lee, M-K, Pitt, R, Ruis, C, Balla, E, Crucitti, T, Ewens, M, Fernandez-Naval, C, Grankvist, A, Guiver, M, Kenyon, CR, Khairullin, R, Kularatne, R, Arando, M, Molini, BJ, Obukhov, A, Page, EE, Petrovay, F, Rietmeijer, C, Rowley, D, Shokoples, S, Smit, E, Sweeney, EL, Taiaroa, G, Vera, JH, Wenneras, C, Whiley, DM, Williamson, DA, Hughes, G, Naidu, P, Unemo, M, Krajden, M, Lukehart, SA, Morshed, MG, Fifer, H, Thomson, NR, Beale, MA, Marks, M, Cole, MJ, Lee, M-K, Pitt, R, Ruis, C, Balla, E, Crucitti, T, Ewens, M, Fernandez-Naval, C, Grankvist, A, Guiver, M, Kenyon, CR, Khairullin, R, Kularatne, R, Arando, M, Molini, BJ, Obukhov, A, Page, EE, Petrovay, F, Rietmeijer, C, Rowley, D, Shokoples, S, Smit, E, Sweeney, EL, Taiaroa, G, Vera, JH, Wenneras, C, Whiley, DM, Williamson, DA, Hughes, G, Naidu, P, Unemo, M, Krajden, M, Lukehart, SA, Morshed, MG, Fifer, H, and Thomson, NR
- Abstract
Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.
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- 2021
6. HYPERVELOCITY IMPACT IN LOW EARTH ORBIT: FINDING SUBTLE IMPACTOR SIGNATURES ON THE HUBBLE SPACE TELESCOPE
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Kearsley, AT, Colaux, JL, Wozniakiewicz, PJ, Gerlach, L, Anz-Meador, P, Liou, JC, Griffin, T, Reed, B, Opiela, J, Palitsin, VV, Grime, GW, Webb, RP, Jeynes, C, Spratt, J, Cole, MJ, Price, MC, Burchell, MJ, Salge, T, Kearsley, AT, Colaux, JL, Wozniakiewicz, PJ, Gerlach, L, Anz-Meador, P, Liou, JC, Griffin, T, Reed, B, Opiela, J, Palitsin, VV, Grime, GW, Webb, RP, Jeynes, C, Spratt, J, Cole, MJ, Price, MC, Burchell, MJ, and Salge, T
- Abstract
HYPERVELOCITY IMPACT IN LOW EARTH ORBIT: FINDING SUBTLE IMPACTOR SIGNATURES ON THE HUBBLE SPACE TELESCOPE A T Kearsley 1,2,5, J L Colaux 3, D K Ross 4, P J Wozniakiewicz 2,5, L Gerlach 6, P Anz-Meador 4, J-C Liou 7, T Griffin 8, B Reed 8, J Opiela 4, V V Palitsin 3, G W Grime 3, R P Webb 3, C Jeynes 3, J Spratt 2, M J Cole 5, M C Price 5 and M J Burchell 5. 1 Dunholme, Raven Hall Road, Ravenscar, YO13 0NA, UK (kearsleys@runbox.com); 2 Natural History Museum (NHM), Cromwell Road, London, UK. 3 Ion Beam Centre, University of Surrey, Guildford, UK. 4 ESCG-Jacobs, NASA-JSC, Houston, TX, USA. 5 School of Physical Sciences, University of Kent, Canterbury, Kent, UK. 6 European Space Agency (ESA, retired), Noordwijk, The Netherlands. 7 NASA Johnson Space Center, Houston, TX, USA. 8 NASA Goddard Space Flight Center (GSFC), Greenbelt, Maryland, USA. ABSTRACT Introduction Return of large surface area components from the Hubble Space Telescope (HST) during shuttle orbiter service missions has allowed inspection of large numbers of hyper-velocity impact features from long exposure in low Earth orbit (LEO). Particular attention has been paid to the origin of the impacting particles, whether artificial Orbital Debris (OD) or natural Micrometeoroid (MM). Extensive studies have been made of solar cells (Graham et al., 2001; Kearsley et al 2005, Moussi et al., 2005) and recently, the painted metal surface of the Wide Field and Planetary Camera 2 WFPC2 radiator shield (Anz-Meador et al., 2013; Colaux et al., 2014; Kearsley et al., 2014a; Ross et al., 2014). Both of these materials from HST have layers of complex chemical composition, into which particle fragments and melt may infiltrate during impact. Experimental light gas gun (LGG) impacts (e.g. Price et al., 2014) have shown that impactor remains may be dispersed and dilute, often as a very thin and patchy coating within an irregular impact-generated pit. In previous studies, the low concentration of particle residue, the rugged to, © 2017 The Authors. Published by Elsevier Ltd. Peer-review under responsibility of the scientific committee of the 14th Hypervelocity Impact Symposium 2017. This Open Access article is distributed under the terms of the Creative Commons Attribution Noncommercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and the source are cited. The files attached consist of the Published/publisher’s pdf version of the article and the author's conference presentation., NHM Repository
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- 2018
7. WGS to predict antibiotic MICs for Neisseria gonorrhoeae
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Eyre, D, De Silva, D, Cole, K, Peters, J, Cole, MJ, Grad, YH, Demczuk, W, Martin, I, Mulvey, MR, Crook, DW, Walker, AS, Peto, T, and Paul, J
- Abstract
Background: Tracking the spread of antimicrobial resistant Neisseria gonorrhoeae is a major priority for national surveillance programmes. Objectives: We investigate whether whole-genome sequencing, WGS, and simultaneous analysis of multiple resistance determinants can be used to predict antimicrobial susceptibilities to the level of minimum inhibitory concentrations, 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 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 rate (VME, phenotypically resistant, WGS-prediction sensitive) was 21/1577(1.3%, 95%CI 0.8-2.0%), and the major error rate (ME, phenotypically sensitive, WGS-prediction resistant) 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 5 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.
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- 2017
8. Whole-genome sequencing to determine Neisseria gonorrhoeae transmission: an observational study
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De Silva, D, Wilson, DJ, Crook, DW, Peto, TEA, Waldram, A, Eyre, DW, Peters, J, Cole, K, Cole, MJ, Cresswell, F, Dean, G, Dave, J, Thomas, DR, Foster, K, Didelot, X, Grad, Y, Walker, AS, and Paul, J
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- 2016
9. Direction-Dependent Communication Mechanisms in Individual-Based Models of Collective Behaviour
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Zmurchok, Cole MJ
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- 2014
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10. Analysis of residues resulting from mafic silicate impacts into aluminium 1100
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Wozniakiewicz, PJ, Kearsley, A, Burchell, MJ, Cole, MJ, and Bland, PA
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Accepted version
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- 2006
11. Sedatives for opiate withdrawal in newborn infants
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Osborn, DA, primary, Jeffery, HE, additional, and Cole, MJ, additional
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- 2002
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12. Opiate treatment for opiate withdrawal in newborn infants
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Osborn, DA, primary, Cole, MJ, additional, and Jeffery, HE, additional
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- 2002
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13. Neonatal gastrointestinal mucormycosis mimicking necrotizing enterocolitis
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Nissen, MD, primary, Jana, AK, additional, Cole, MJ, additional, Grierson, JM, additional, and Gilbert, GL, additional
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- 1999
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14. Acquisition of hepatitis C virus in hemodialysis patients: A prospective study by branched DNA signal amplification assay
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Fabrizi, F, primary, Martin, P, additional, Dixit, V, additional, Brezina, M, additional, Cole, MJ, additional, Gerosa, S, additional, Mousa, M, additional, and Gitnick, G, additional
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- 1998
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15. An analysis of yield reduction caused by stripe rust in Rongotea wheat.
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Gaunt, RE, primary and Cole, MJ, additional
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- 1991
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16. Challenges of CPD for physiotherapists working as lone practitioners in amputee rehabilitation.
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Cole MJ, Morris J, Scammell A, Cole, Mary Jane, Morris, Jane, and Scammell, Amy
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Objectives: The aim of this study was to explore the issues around continuing professional development (CPD) for physiotherapists working as lone practitioners in amputee rehabilitation in the United Kingdom (UK).Design: Qualitative method using a phenomenological approach via one to one semi-structured interviews and thematic data analysis.Setting and Participants: Ten physiotherapists with responsibility for amputee rehabilitation working as lone practitioners in hospitals or specialist centres in the UK.Results: CPD is valued and there is commitment towards the process. Current solutions are identified but there are frustrations around more structured CPD and organizational issues. These include inadequate access to learning opportunities, lack of professional feedback, insufficient time and limited learning skills.Conclusion: There are opportunities for improving CPD through organizational structures but specialist input is recommended to support lone practitioners and managers with the process, e.g., consultant or peripatetic therapists. [ABSTRACT FROM AUTHOR]- Published
- 2008
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17. An evaluation of patient perceptions to the value of the gait laboratory as part of the rehabilitation of primary lower limb amputees.
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Cole MJ, Durham S, and Ewins D
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The value of gait analysis for research and product development/evaluation in prosthetics is well understood. However, in the rehabilitation of amputees, the application of gait analysis beyond observation in the clinical setting is not routinely practiced, largely due to the cost and time taken to complete a fully instrumented data collection and analysis. To address the time issue, a weekly clinical gait service for primary amputees, based around a reduced data set from video and video vector technology, has been developed. In this clinic primary amputees are seen twice in the Gait Laboratory during their rehabilitation period, with the clinic time for each patient being no more than 15 minutes, which covers both data collection and review. A questionnaire was developed to evaluate the patients' perceptions of the clinic. The questionnaire was completed anonymously by 48 primary amputees over a 6-month period. The results from the questionnaire demonstrate that the clinic was perceived positively by the patients, and suggested areas of future development, e.g. the education of junior staff, and the need to include the patient's physiotherapist in the data collection and review process. [ABSTRACT FROM AUTHOR]
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- 2008
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18. The Effect of Acid and Bethanechol Stimulation in Patients with Symptomatic Hypertensive Peristaltic (Nutcracker) Esophagus Evidence That This Disorder May Be a Precursor of Diffuse Esophageal Spasm
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Cole Mj, Beck It, DaCosta Lr, and Paterson Wg
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Adult ,Spasm ,medicine.medical_specialty ,Manometry ,Pain ,Achalasia ,Bethanechol ,Esophageal Diseases ,Chest pain ,Gastroenterology ,Bethanechol Compounds ,Internal medicine ,medicine ,Humans ,Esophagus ,Aged ,business.industry ,Esophageal disease ,Nutcracker esophagus ,Middle Aged ,medicine.disease ,medicine.anatomical_structure ,Esophageal motility disorder ,Esophageal spasm ,Hydrochloric Acid ,medicine.symptom ,business ,medicine.drug - Abstract
The hypertensive peristaltic (nutcracker) esophagus represents a motility disorder characterized clinically by squeezing retrosternal chest pain and manometrically by high amplitude esophageal peristaltic contractions. This study was designed to examine whether the nutcracker esophagus is: (a) a distinct entity, (b) a member of the spectrum of primary esophageal dysmotilities (e.g., diffuse esophageal spasm and achalasia), or (c) is secondary to reflux-induced acid sensitivity. Thirteen patients with a nutcracker esophagus by baseline manometry were subsequently studied after acid perfusion and bethanechol stimulation (0.08 mg/kg). Records were analyzed for symptomatic response and motility changes. Eight of 13 (62%) experienced chest pain during acid perfusion, but none had significant motility changes documented during this period. After bethanechol injection, chest pain occurred in six of 12 (50%) patients; two had burning pain and in the other four (33%) their squeezing chest pain was reproduced. Changes in the motility tracing with evidence of disordered motility suggestive of diffuse esophageal spasm were seen after bethanechol in seven of the 12 tracings analyzed (58%), including all six patients who developed chest pain. We conclude that patients with nutcracker esophagus on baseline manometry may develop motility patterns consistent with diffuse esophageal spasm after provocation with bethanechol. We take this to suggest that the nutcracker esophagus is part of the continuum of primary motility disorders and may actually be a precursor of diffuse esophageal spasm.
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- 1986
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19. Neonatal effects of long-term maternal phenoxybenzamine therapy.
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Aplin SC, Yee KF, Cole MJ, Aplin, Stephanie C, Yee, Kevin F, and Cole, Michael J
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- 2004
20. '5-D' fluorescence microscopy
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Webb, Sed, Elson, Ds, Siegel, J., Leveque-Fort, S., Gu, Y., Parsons-Karavassilis, D., Cole, Mj, French, Pmw, Lever, Mj, Sucharov, Lo, Mark Neil, Juskaitis, R., Wilson, T., Anderssonengels, S., and Kaschke, Mf
21. Molecular detection of ceftriaxone resistance in Neisseria gonorrhoeae clinical specimens: a tool for public health control.
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Day MJ, Boampong D, Pitt R, Bari A, Rebec M, Saunders J, Fifer H, Mbisa JL, and Cole MJ
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- Humans, Real-Time Polymerase Chain Reaction, Microbial Sensitivity Tests, Alleles, Drug Resistance, Bacterial genetics, Public Health, Sensitivity and Specificity, Male, Neisseria gonorrhoeae genetics, Neisseria gonorrhoeae drug effects, Neisseria gonorrhoeae isolation & purification, Ceftriaxone pharmacology, Gonorrhea microbiology, Gonorrhea diagnosis, Anti-Bacterial Agents pharmacology
- Abstract
Objectives: This study aimed to validate and implement a rapid screening assay for molecular detection of the penA -60 allele that is associated with ceftriaxone resistance in Neisseria gonorrhoeae for use on both isolate lysates and clinical specimen DNA extracts., Methods: A N. gonorrhoeae penA real-time (RT)-PCR was adapted to include a species-specific pap confirmation target and a commercially available internal control to monitor for PCR inhibition.The modified assay was validated using N. gonorrhoeae -positive (n=24) and N. gonorrhoeae -negative (n=42) clinical specimens and isolate lysates. The panel included seven samples with resistance conferred by penA alleles targeted by the assay and four samples with different penA alleles. The feasibility of using the penA RT-PCR for molecular surveillance was assessed using clinical specimens from 54 individuals attending a London sexual health clinic who also had a N. gonorrhoeae isolate included in the 2020 Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP)., Results: The assay correctly identified N. gonorrhoeae specimens (n=7) with penA -60/64 alleles targeted by the assay. No penA false negatives/positives were detected, giving the penA target of the assay a sensitivity, specificity, positive and negative predicted values (PPV, NPV) of 100% (95% CIs; sensitivity; 56.1-100%, specificity; 93.6-100%, PPV; 56.1-100%, NPV; 93.6-100%).No cross-reactivity with other Neisseria species or other urogenital pathogens was detected. The N. gonorrhoeae target ( pap ) was detected in 73 out of 78 of the N. gonorrhoeae -positive specimens, resulting in 92.6% sensitivity (95% CI 83.0% to 97.3%), 100% specificity (95% CI 75.9% to 100%) and PPV, and a NPV of 89.4% (95% CI 52.5% to 90.9%). No penA -59/60/64 alleles were detected within the clinical specimens from the GRASP 2020 feasibility molecular surveillance study (n=54 individuals)., Conclusion: The implementation of this PCR assay for patient management, public health and surveillance purposes enables the rapid detection of gonococcal ceftriaxone resistance conferred by the most widely circulating penA alleles., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2024
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22. Effects of telemetry collars on two free-roaming feral equid species.
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Schoenecker KA, King SRB, Hennig JD, Cole MJ, Scasta JD, and Beck JL
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- Animals, Horses, Female, Male, Telemetry, Equidae physiology, Geographic Information Systems
- Abstract
There are two species of free-roaming feral equids in North America: horses (Equus caballus) and donkeys or "burros" (E. asinus). Both species were introduced as domestic animals to North America in the early 1500s and currently inhabit rangelands across the western United States, Canada, and all continents except Antarctica. Despite their global distribution, little is known about their fine scale spatial ecology. Contemporary research tools to assess space use include global positioning system (GPS) tracking collars, but older models were problematic due to stiff collar belting causing poor fit. We tested modern designs of GPS collars on n = 105 horses and n = 60 burros for 4 years in five populations (3 horse, 2 burro) across the western United States, to assess whether collars posed welfare risks to horses or burros. We found no difference in survival of collared versus uncollared mares and jennies, and no difference in survival of their foals. In 4036 of 4307 observations for horses (93.7%) and 2115 of 2258 observations for burros (93.6%), collars were observed symmetrical, maintaining proper fit on the neck. Fur effects from collars (sweaty neck, indented fur, broken fur) were seen in 3% of horse observations and 25% of burro observations. Superficial effects (chafes and marks on skin surface) were seen in 2% of horse observations and 11% of burro observations; no severe effects from collars were seen. Body condition was not affected by collars; mean body condition of collared horses was 4.70 ± 0.54 (mean ± s.d) and 4.71 ± 0.65 for collared burros. Behavior results indicated minimal effects; collared horses stood slightly more than uncollared, and collared burros stood and foraged more in one population, but not in the other. For 6.3% of observations of horses and 6.4% of observations of burros, we found an effect of time wearing a collar on the cumulative sum of fur effects which increased over time (burros: rs = 0.87, P = <0.0001; horses: rs = 0.31, P = 0.002). Burros also showed an increase over time in the number of superficial effects, but horses did not. Collars occasionally moved into the wrong position, shifting forward over the ears; we observed this on 19 horses and 1 burro. Of those, most collars went over the ears in summer (n = 12). All collars were equipped with a remote release mechanism as well as a timed-release mechanism for redundancy, thus removed when observed in wrong position to avoid rubbing or discomfort. Our finding of no consequential physical effects in 98% of horse observations, and 89% of burro observations suggests the consequences of collars on free-roaming equid welfare and survival is biologically insignificant, although collars should be monitored regularly and continue to be equipped with a remote release mechanism to remove a collar if needed. With frequent welfare-driven, visual monitoring, collaring of free-roaming equids can be a safe and useful tool to increase our understanding of their spatial ecology, demography, habitat use, behavior, and interactions with other wildlife., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)
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- 2024
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23. Antimicrobial-resistant Neisseria gonorrhoeae in Europe in 2020 compared with in 2013 and 2018: a retrospective genomic surveillance study.
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Golparian D, Cole MJ, Sánchez-Busó L, Day M, Jacobsson S, Uthayakumaran T, Abad R, Bercot B, Caugant DA, Heuer D, Jansen K, Pleininger S, Stefanelli P, Aanensen DM, Bluemel B, and Unemo M
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- Humans, Retrospective Studies, Europe epidemiology, Male, Female, Adult, Genome, Bacterial genetics, Middle Aged, Young Adult, Genomics, Azithromycin pharmacology, Azithromycin therapeutic use, Adolescent, Neisseria gonorrhoeae drug effects, Neisseria gonorrhoeae genetics, Gonorrhea epidemiology, Gonorrhea drug therapy, Gonorrhea microbiology, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Microbial Sensitivity Tests, Drug Resistance, Bacterial genetics, Whole Genome Sequencing
- Abstract
Background: Regular quality-assured whole-genome sequencing linked to antimicrobial resistance (AMR) and patient metadata is imperative to elucidate the shifting gonorrhoea epidemiology, both nationally and internationally. We aimed to examine the gonococcal population in the European Economic Area (EEA) in 2020, elucidate emerging and disappearing gonococcal lineages associated with AMR and patient metadata, compare with 2013 and 2018 whole-genome sequencing data, and explain changes in gonococcal AMR and gonorrhoea epidemiology., Methods: In this retrospective genomic surveillance study, we analysed consecutive gonococcal isolates that were collected in EEA countries through the European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP) in 2020, and made comparisons with Euro-GASP data from 2013 and 2018. All isolates had linked AMR data (based on minimum inhibitory concentration determination) and patient metadata. We performed whole-genome sequencing and molecular typing and AMR determinants were derived from quality-checked whole-genome sequencing data. Links between genomic lineages, AMR, and patient metadata were examined., Findings: 1932 gonococcal isolates collected in 2020 in 21 EEA countries were included. The majority (81·2%, 147 of 181 isolates) of azithromycin resistance (present in 9·4%, 181 of 1932) was explained by the continued expansion of the Neisseria gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) clonal complexes (CCs) 63, 168, and 213 (with mtrD/mtrR promoter mosaic 2) and the novel NG-STAR CC1031 (semi-mosaic mtrD variant 13), associated with men who have sex with men and anorectal or oropharyngeal infections. The declining cefixime resistance (0·5%, nine of 1932) and negligible ceftriaxone resistance (0·1%, one of 1932) was largely because of the progressive disappearance of NG-STAR CC90 (with mosaic penA allele), which was predominant in 2013. No known resistance determinants for novel antimicrobials (zoliflodacin, gepotidacin, and lefamulin) were found., Interpretation: Azithromycin-resistant clones, mainly with mtrD mosaic or semi-mosaic variants, appear to be stabilising at a relatively high level in the EEA. This mostly low-level azithromycin resistance might threaten the recommended ceftriaxone-azithromycin therapy, but the negligible ceftriaxone resistance is encouraging. The decreased genomic population diversity and increased clonality could be explained in part by the COVID-19 pandemic resulting in lower importation of novel strains into Europe., Funding: European Centre for Disease Prevention and Control and Örebro University Hospital., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
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- 2024
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24. High tetracycline resistance percentages in Neisseria gonorrhoeae in Europe: is doxycycline post-exposure prophylaxis unlikely to reduce the incident gonorrhoea cases?
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Unemo M, Cole MJ, Kodmon C, Day M, and Jacobsson S
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Competing Interests: We declare no competing interest.
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- 2024
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25. Baseline Cannabinoid Use Is Associated with Increased Sedation Requirements for Outpatient Endoscopy.
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Nasser Y, Biala S, Chau M, Partridge ACR, Yang JY, Lethebe BC, Stinton LM, Cooray M, Cole MJ, Ma C, Chen YI, Andrews CN, and Forbes N
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- Adult, Humans, Prospective Studies, Outpatients, Endoscopy, Gastrointestinal adverse effects, Fentanyl adverse effects, Diphenhydramine adverse effects, Surveys and Questionnaires, Midazolam adverse effects, Cannabinoids
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Background and Aims: Given the underlying properties of cannabinoids, we aimed to assess associations between cannabinoid use and sedation requirements for esophagogastroduodenoscopy (EGD) and colonoscopy. Methods: A prospective cohort study was conducted at three endoscopy units. Adult outpatients undergoing EGD or colonoscopy with endoscopist-directed conscious sedation (EDCS) were given questionnaires on cannabinoid use and relevant parameters. Outcomes included intraprocedural midazolam, fentanyl, and diphenhydramine use, procedural tolerability, and adverse events. Multivariable logistic regression was performed to yield adjusted odds ratios (AORs) of outcomes. Results: A total of 419 patients were included. Baseline cannabinoid use was associated with high midazolam use, defined as ≥5 mg, during EGD (AOR 2.89, 95% confidence interval, CI: 1.19-7.50), but not during colonoscopy (AOR 0.89, 95% CI 0.41-1.91). Baseline cannabinoid use was associated with the administration of any diphenhydramine during EGD (AOR 3.04, 95% CI: 1.29-7.30) with a similar nonsignificant trend for colonoscopy (AOR 2.36, 95% CI: 0.81-7.04). Baseline cannabinoid use was associated with increased odds of requiring high total sedation, defined as any of midazolam ≥5 mg, fentanyl ≥100 mcg, or any diphenhydramine during EGD (AOR 3.72, 95% CI: 1.35-11.68). Cannabinoid use was not independently associated with fentanyl use, intraprocedural awareness, discomfort, or adverse events. Conclusions: Baseline cannabinoid use was associated with higher sedation use during endoscopy with EDCS, particularly with midazolam and diphenhydramine. Given increasingly widespread cannabinoid use, endoscopists should be equipped with optimal sedation strategies for this population. As part of the informed consent process, cannabis users should be counseled that they may require higher sedation doses to achieve the same effect.
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- 2024
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26. Antibody correlates of protection against Delta infection after vaccination: A nested case-control within the UK-based SIREN study.
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Atti A, Insalata F, Carr EJ, Otter AD, Foulkes S, Wu MY, Cole MJ, Linley E, Semper A, Brooks T, Hopkins S, Charlett A, Beale R, and Hall V
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- Humans, Case-Control Studies, Antibodies, Neutralizing, Vaccination, Antibodies, Viral, United Kingdom epidemiology, Vaccines, Hepatitis D
- Abstract
Objectives: To investigate serological correlates of protection against SARS-CoV-2 B.1.617.2 (Delta) infection after two vaccinations., Methods: We performed a case-control study, where cases were Delta infections after the second vaccine dose and controls were vaccinated, never infected participants, matched by age, gender and region. Sera were tested for anti-SARS-CoV-2 Spike antibody levels (anti-S) and neutralising antibody titres (nAbT), using live virus microneutralisation against Ancestral, Delta and Omicron (BA.1, B.1.1.529). We modelled the decay of anti-S and nAbT for both groups, inferring levels at matched calendar times since the second vaccination. We assessed differences in inferred antibody titres between groups and used conditional logistic regression to explore the relationship between titres and odds of infection., Results: In total, 130 sequence-confirmed Delta cases and 318 controls were included. Anti-S and Ancestral nAbT decayed similarly between groups, but faster in cases for Delta nAbT (p = 0.02) and Omicron nAbT (p = 0.002). At seven days before infection, controls had higher anti-S levels (p < 0.0001) and nAbT (p < 0.0001; all variants) at matched calendar time. A two-fold increase in anti-S levels was associated with a 29% ([95% CI 14-42%]; p = 0.001) reduction in odds of Delta infection. Delta nAbT>40 were associated with reduced odds of Delta infection (89%, [69-96%]; p < 0.0001), with additional benefits for titres >100 (p = 0.009) and >400 (p = 0.007)., Conclusions: We have identified correlates of protection against SARS-CoV-2 Delta, with potential implications for vaccine deployment, development, and public health response., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. All authors confirmed they have no completing interest to declare., (Crown Copyright © 2023. Published by Elsevier Ltd. All rights reserved.)
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- 2023
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27. Genomic epidemiology of syphilis in England: a population-based study.
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Beale MA, Thorn L, Cole MJ, Pitt R, Charles H, Ewens M, French P, Guiver M, Page EE, Smit E, Vera JH, Sinka K, Hughes G, Marks M, Fifer H, and Thomson NR
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- Humans, Male, Female, Homosexuality, Male, England epidemiology, Genomics, Syphilis epidemiology, Sexual and Gender Minorities
- Abstract
Background: Syphilis is a sexually transmitted bacterial infection caused by Treponema pallidum subspecies pallidum. Since 2012, syphilis rates have risen dramatically in many high-income countries, including England. Although this increase in syphilis prevalence is known to be associated with high-risk sexual activity in gay, bisexual, and other men who have sex with men (GBMSM), cases are rising in heterosexual men and women. The transmission dynamics within and between sexual networks of GBMSM and heterosexual people are not well understood. We aimed to investigate if whole genome sequencing could be used to supplement or enhance epidemiological insights around syphilis transmission., Methods: We linked national patient demographic, geospatial, and behavioural metadata to whole T pallidum genome sequences previously generated from patient samples collected from across England between Jan 1, 2012, and Oct 31, 2018, and performed detailed phylogenomic analyses., Findings: Of 497 English samples submitted for sequencing, we recovered 240 genomes (198 from the UK Health Security Agency reference laboratory and 42 from other laboratories). Three duplicate samples (same patient and collection date) were included in the main phylogenies, but removed from further analyses of English populations, leaving 237 genomes. 220 (92·8%) of 237 samples were from men, nine (3·8%) were from women, and eight (3·4%) were of unknown gender. Samples were mostly from London (n=118 [49·8%]), followed by southeast England (n=29 [12·2%]), northeast England (n=24 [10·1%]), and southwest England (n=15 [6·3%]). 180 (76·0%) of 237 genomes came from GBMSM, compared with 25 (10·5%) from those identifying as men who have sex with women, 15 (6·3%) from men with unrecorded sexual orientation, nine (3·8%) from those identifying as women who have sex with men, and eight (3·4%) from people of unknown gender and sexual orientation. Phylogenomic analysis and clustering revealed two dominant T pallidum sublineages in England. Sublineage 1 was found throughout England and across all patient groups, whereas sublineage 14 occurred predominantly in GBMSM older than 34 years and was absent from samples sequenced from the north of England. These different spatiotemporal trends, linked to demography or behaviour in the dominant sublineages, suggest they represent different sexual networks. By focusing on different regions of England we were able to distinguish a local heterosexual transmission cluster from a background of transmission in GBMSM., Interpretation: These findings show that, despite extremely close genetic relationships between T pallidum genomes globally, genomics can still be used to identify putative transmission clusters for epidemiological follow-up. This could be of value for deconvoluting putative outbreaks and for informing public health interventions., Funding: Wellcome funding to the Sanger Institute, UK Research and Innovation, National Institute for Health and Care Research, European and Developing Countries Clinical Trials Partnership, and UK Health Security Agency., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2023 Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
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- 2023
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28. Projecting the development of antimicrobial resistance in Neisseria gonorrhoeae from antimicrobial surveillance data: a mathematical modelling study.
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Riou J, Althaus CL, Allen H, Cole MJ, Grad YH, Heijne JCM, Unemo M, and Low N
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- Male, Humans, Female, Neisseria gonorrhoeae genetics, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Cefixime pharmacology, Cefixime therapeutic use, Ceftriaxone pharmacology, Ceftriaxone therapeutic use, Azithromycin pharmacology, Azithromycin therapeutic use, Homosexuality, Male, Drug Resistance, Bacterial, Ciprofloxacin pharmacology, Ciprofloxacin therapeutic use, Microbial Sensitivity Tests, Gonorrhea drug therapy, Gonorrhea epidemiology, Sexual and Gender Minorities
- Abstract
Background: The World Health Organization recommends changing the first-line antimicrobial treatment for gonorrhoea when ≥ 5% of Neisseria gonorrhoeae cases fail treatment or are resistant. Susceptibility to ceftriaxone, the last remaining treatment option has been decreasing in many countries. We used antimicrobial resistance surveillance data and developed mathematical models to project the time to reach the 5% threshold for resistance to first-line antimicrobials used for N. gonorrhoeae., Methods: We used data from the Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP) in England and Wales from 2000-2018 about minimum inhibitory concentrations (MIC) for ciprofloxacin, azithromycin, cefixime and ceftriaxone and antimicrobial treatment in two groups, heterosexual men and women (HMW) and men who have sex with men (MSM). We developed two susceptible-infected-susceptible models to fit these data and produce projections of the proportion of resistance until 2030. The single-step model represents the situation in which a single mutation results in antimicrobial resistance. In the multi-step model, the sequential accumulation of resistance mutations is reflected by changes in the MIC distribution., Results: The single-step model described resistance to ciprofloxacin well. Both single-step and multi-step models could describe azithromycin and cefixime resistance, with projected resistance levels higher with the multi-step than the single step model. For ceftriaxone, with very few observed cases of full resistance, the multi-step model was needed to describe long-term dynamics of resistance. Extrapolating from the observed upward drift in MIC values, the multi-step model projected ≥ 5% resistance to ceftriaxone could be reached by 2030, based on treatment pressure alone. Ceftriaxone resistance was projected to rise to 13.2% (95% credible interval [CrI]: 0.7-44.8%) among HMW and 19.6% (95%CrI: 2.6-54.4%) among MSM by 2030., Conclusions: New first-line antimicrobials for gonorrhoea treatment are needed. In the meantime, public health authorities should strengthen surveillance for AMR in N. gonorrhoeae and implement strategies for continued antimicrobial stewardship. Our models show the utility of long-term representative surveillance of gonococcal antimicrobial susceptibility data and can be adapted for use in, and for comparison with, other countries., (© 2023. The Author(s).)
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- 2023
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29. Incidence and Predictors of Incidental Biochemical and Radiologic Pancreatic Alterations Following Uncomplicated ERCP.
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Chau M, Samnani S, Bazerbachi F, Mirakhur A, Ruan Y, Howarth M, Bass S, Cole MJ, Lei Y, Li S, Turbide C, Mohamed R, Brenner DR, Heitman SJ, Elmunzer BJ, and Forbes N
- Abstract
Background: Despite post-ERCP pancreatitis (PEP) being a major focus of outcomes research in endoscopic retrograde cholangiopancreatography (ERCP), little is known regarding the frequency with which asymptomatic biochemical and/or radiologic pancreatic alterations occur in patients following ERCP., Methods: Adult inpatients undergoing ERCP were identified from a prospective ERCP registry. Patients with any abdominal pain, confirmed PEP, or pancreatitis or abnormal pancreatic enzymes preceding ERCP were excluded. Primary outcomes were asymptomatic lipase elevation on bloodwork within 24 h of ERCP or asymptomatic cross-sectional imaging findings consistent with acute pancreatitis in the absence of clinical PEP within 14 days. Multinomial logistic regression and multiple logistic regression were used to examine associations between exposures and lipase levels and between PEP or imaging findings, respectively., Results: In total, 646 and 187 patients were analyzed as part of the biochemical and radiologic cohorts, respectively. A total of 26.0% of patients had asymptomatic elevations in lipase above the upper limit of normal (ULN) within 24 h, and 9.4% had elevations >3× ULN. A total of 20.9% of patients had incidental findings of enlargement, inflammation/edema/fat stranding, peri-pancreatic fluid collections, and/or necrosis on cross-sectional imaging within 14 days. Pancreatic contrast injection was associated with higher odds of asymptomatic lipasemia (adjusted odds ratio, AOR, 7.22; 95% confidence intervals, CI, 1.13 to 46.02), as was the use of the double-wire technique (AOR 15.74; 95% 1.15 to 214.74) and placement of a common bile duct stent (AOR 4.19; 95% CI 1.37 to 12.77). Over 10 cannulation attempts were associated with the presence of one or more radiologic finding(s) (AOR 33.95; 95% CI 1.64, to 704.13)., Conclusions: Significant rates of incidental biochemical and/or radiologic pancreatic abnormalities are present following ERCP. Clinicians should be aware of our findings to minimize misclassification and better direct healthcare utilization.
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- 2023
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30. Effect of Disposable Elevator Cap Duodenoscopes on Persistent Microbial Contamination and Technical Performance of Endoscopic Retrograde Cholangiopancreatography: The ICECAP Randomized Clinical Trial.
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Forbes N, Elmunzer BJ, Allain T, Parkins MD, Sheth PM, Waddell BJ, Du K, Douchant K, Oladipo O, Saleem A, Cartwright S, Chau M, Howarth M, McKay J, Nashad T, Ruan Y, Bishay K, Gonzalez-Moreno E, Meng ZW, Bass S, Bechara R, Cole MJ, Jalink DW, Mohamed R, Turbide C, Belletrutti PJ, Kayal A, Kumar PR, Hilsden RJ, Buret AG, Hookey L, and Heitman SJ
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- Humans, Female, Middle Aged, Male, Elevators and Escalators, Disinfection, Data Collection, Duodenoscopes adverse effects, Duodenoscopes microbiology, Cholangiopancreatography, Endoscopic Retrograde instrumentation
- Abstract
Importance: Infection transmission following endoscopic retrograde cholangiopancreatography (ERCP) can occur due to persistent contamination of duodenoscopes despite high-level disinfection to completely eliminate microorganisms on the instrument., Objective: To determine (1) contamination rates after high-level disinfection and (2) technical performance of duodenoscopes with disposable elevator caps compared with those with standard designs., Design, Setting, and Participants: In this parallel-arm multicenter randomized clinical trial at 2 tertiary ERCP centers in Canada, all patients 18 years and older and undergoing ERCP for any indication were eligible., Intervention: The intervention was use of duodenoscopes with disposable elevator caps compared with duodenoscopes with a standard design., Main Outcomes and Measures: Coprimary outcomes were persistent microbial contamination of the duodenoscope elevator or channel, defined as growth of at least 10 colony-forming units of any organism or any growth of gram-negative bacteria following high-level disinfection (superiority outcome), and technical success of ERCP according to a priori criteria (noninferiority outcome with an a priori noninferiority margin of 7%), assessed by blinded reviewers., Results: From December 2019 to February 2022, 518 patients were enrolled (259 disposable elevator cap duodenoscopes, 259 standard duodenoscopes). Patients had a mean (SD) age of 60.7 (17.0) years and 258 (49.8%) were female. No significant differences were observed between study groups, including in ERCP difficulty. Persistent microbial contamination was detected in 11.2% (24 of 214) of standard duodenoscopes and 3.8% (8 of 208) of disposable elevator cap duodenoscopes (P = .004), corresponding to a relative risk of 0.34 (95% CI, 0.16-0.75) and number needed to treat of 13.6 (95% CI, 8.1-42.7) to avoid persistent contamination. Technical success using the disposable cap scope was noninferior to that of the standard scope (94.6% vs 90.7%, P = .13). There were no differences between study groups in adverse events and other secondary outcomes., Conclusions and Relevance: In this randomized clinical trial, disposable elevator cap duodenoscopes exhibited reduced contamination following high-level disinfection compared with standard scope designs, without affecting the technical performance and safety of ERCP., Trial Registration: ClinicalTrials.gov Identifier: NCT04040504.
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- 2023
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31. Is there an association between previous infection with Neisseria gonorrhoeae and gonococcal AMR? A cross-sectional analysis of national and sentinel surveillance data in England, 2015-2019.
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Allen H, Merrick R, Ivanov Z, Pitt R, Mohammed H, Sinka K, Hughes G, Fifer H, and Cole MJ
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- Male, Female, Humans, Neisseria gonorrhoeae, Ceftriaxone therapeutic use, Ceftriaxone pharmacology, Cefixime pharmacology, Cefixime therapeutic use, Homosexuality, Male, Cross-Sectional Studies, Sentinel Surveillance, Drug Resistance, Bacterial, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, England epidemiology, Microbial Sensitivity Tests, Gonorrhea drug therapy, Gonorrhea epidemiology, Gonorrhea diagnosis, Sexual and Gender Minorities
- Abstract
Objectives: Quarterly STI screening is recommended for high-risk gay, bisexual and other men who have sex with men (MSM) in the UK, but frequent antibiotic exposure could potentially increase the risk of antimicrobial resistance (AMR) developing in Neisseria gonorrhoeae . We investigated whether repeat diagnosis of gonorrhoea in those attending sexual health services (SHS) was associated with reduced antimicrobial susceptibility., Methods: Antimicrobial susceptibility data relating to the most recent gonorrhoea diagnosis for each individual included in the Gonococcal Resistance to Antimicrobials Surveillance Programme (2015-2019) were matched to their historical records in the national GUMCAD STI surveillance data set (2012-2019). The number of gonorrhoea diagnoses in the previous 3 years was calculated for each SHS attendee. Logistic regression was used to examine the associations between the number of diagnoses and reduced susceptibility to ceftriaxone (minimum inhibitory concentration (MIC) >0.03 mg/L), cefixime (MIC >0.06 mg/L) and azithromycin (MIC >0.25 mg/L) at the time of the latest diagnosis., Results: Of 6161 individuals included in the analysis, 3913 (63.5%) were MSM, 1220 (19.8%) were heterosexual men and 814 (13.2%) were women. Among MSM, 2476 (63.3%) had 1 past gonorrhoea diagnosis, 1295 (33.1%) had 2-4, 140 (3.6%) 5-9, and 2 (0.1%) ≥10. Most women and heterosexual men (91.7%) had one past gonorrhoea diagnosis; none had more than four. Reduced ceftriaxone and cefixime susceptibility was more common among MSM with two to four gonorrhoea diagnoses (3.8% and 5.8%, respectively) compared with those with one (2.2% and 3.9%, respectively). After adjusting for potential confounding, this association remained (adjusted OR: 1.59, 95% CI 1.07 to 2.37, p=0.02; adjusted OR: 1.54, 95% CI 1.11 to 2.14, p=0.01). No evidence was found for any other associations., Conclusions: Among MSM, repeat diagnosis of gonorrhoea may be associated with reduced ceftriaxone and cefixime susceptibility. As these are last-line therapies for gonorrhoea, further research is needed to assess the impact of intensive STI screening on AMR., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2023
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32. Early Warning Surveillance for SARS-CoV-2 Omicron Variants, United Kingdom, November 2021-September 2022.
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Foulkes S, Monk EJM, Sparkes D, Hettiarachchi N, Milligan ID, Munro K, Taylor-Kerr A, Platt N, Howells A, Kyaw JYA, Adaji E, Gallagher E, Khawam J, Wellington E, Price L, Crossman D, Norman C, de Lacy E, Cromey L, Corrigan D, Lackenby A, Barbero P, Elegunde B, Zambon M, Chand MA, Brown CS, Islam J, Atti A, Hopkins S, Hall VJ, and Cole MJ
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- Humans, Animals, SARS-CoV-2 genetics, United Kingdom epidemiology, Health Personnel, Reinfection, Urodela, COVID-19 diagnosis, COVID-19 epidemiology
- Abstract
Since June 2020, the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study has conducted routine PCR testing in UK healthcare workers and sequenced PCR-positive samples. SIREN detected increases in infections and reinfections and delected Omicron subvariant waves emergence contemporaneous with national surveillance. SIREN's sentinel surveillance methods can be used for variant surveillance.
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- 2023
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33. Antibody correlates of protection from SARS-CoV-2 reinfection prior to vaccination: A nested case-control within the SIREN study.
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Atti A, Insalata F, Carr EJ, Otter AD, Castillo-Olivares J, Wu M, Harvey R, Howell M, Chan A, Lyall J, Temperton N, Cantoni D, da Costa K, Nadesalingam A, Taylor-Kerr A, Hettiarachchi N, Tranquillini C, Hewson J, Cole MJ, Foulkes S, Munro K, Monk EJM, Milligan ID, Linley E, Chand MA, Brown CS, Islam J, Semper A, Charlett A, Heeney JL, Beale R, Zambon M, Hopkins S, Brooks T, and Hall V
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- Antibodies, Viral, Case-Control Studies, Humans, Reinfection prevention & control, Vaccination, COVID-19 prevention & control, SARS-CoV-2
- Abstract
Objectives: To investigate serological differences between SARS-CoV-2 reinfection cases and contemporary controls, to identify antibody correlates of protection against reinfection., Methods: We performed a case-control study, comparing reinfection cases with singly infected individuals pre-vaccination, matched by gender, age, region and timing of first infection. Serum samples were tested for anti-SARS-CoV-2 spike (anti-S), anti-SARS-CoV-2 nucleocapsid (anti-N), live virus microneutralisation (LV-N) and pseudovirus microneutralisation (PV-N). Results were analysed using fixed effect linear regression and fitted into conditional logistic regression models., Results: We identified 23 cases and 92 controls. First infections occurred before November 2020; reinfections occurred before February 2021, pre-vaccination. Anti-S levels, LV-N and PV-N titres were significantly lower among cases; no difference was found for anti-N levels. Increasing anti-S levels were associated with reduced risk of reinfection (OR 0·63, CI 0·47-0·85), but no association for anti-N levels (OR 0·88, CI 0·73-1·05). Titres >40 were correlated with protection against reinfection for LV-N Wuhan (OR 0·02, CI 0·001-0·31) and LV-N Alpha (OR 0·07, CI 0·009-0·62). For PV-N, titres >100 were associated with protection against Wuhan (OR 0·14, CI 0·03-0·64) and Alpha (0·06, CI 0·008-0·40)., Conclusions: Before vaccination, protection against SARS-CoV-2 reinfection was directly correlated with anti-S levels, PV-N and LV-N titres, but not with anti-N levels. Detectable LV-N titres were sufficient for protection, whilst PV-N titres >100 were required for a protective effect., Trial Registration Number: ISRCTN11041050., Competing Interests: Declaration of Competing Interest All authors declare no competing interests., (Copyright © 2022. Published by Elsevier Ltd.)
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- 2022
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34. Test Performance Characteristics of Dynamic Liver Enzyme Trends in the Prediction of Choledocholithiasis.
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Lei Y, Lethebe BC, Wishart E, Bazerbachi F, Elmunzer BJ, Thosani N, Buxbaum JL, Chen YI, Bass S, Cole MJ, Turbide C, Brenner DR, Heitman SJ, Mohamed R, and Forbes N
- Abstract
(1) Background: Various methods to predict the presence or absence of choledocholithiasis (CDL) have been proposed. We aimed to assess the performance characteristics of dynamic liver enzyme trends in the prediction of CDL. (2) Methods: This was a single-center retrospective cohort study. All adult in-patients undergoing endoscopy for suspected CDL between 1 January 2012 and 7 October 2018 were identified, with patients with prior cholecystectomy, prior sphincterotomy, or indwelling biliary prostheses were excluded. Available laboratory parameters within 72 h preceding the procedure were recorded, allowing for the assessment of trends. Dynamic enzyme trends were defined as any increase or decrease by 30% and 50% within 72 h of the index procedure. (3) Results: A total of 878 patients were included. Mean age was 61.8 years, with 58.6% female. Increases in alkaline phosphatase (ALP) of at least 30% or 50% were both specific for the presence of CDL, with specificities of 82.7% (95% CI 69.7-91.8%) and 88.5% (95% CI 76.6-95.6%), respectively. Decreases in bilirubin or ALP of at least 50% were highly specific for the absence of CDL, with specificities of 91.7% (95% CI 85.7-95.8%) and 100.0% (97.2-100.0%), respectively. (4) Conclusions: Several liver enzyme trends appear to be specific for the absence or presence of stones; in particular, significant decreases in total bilirubin or ALP of at least 30-50% over the prior 72 h appear to be especially predictive of an absence of intraductal findings during endoscopy.
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- 2022
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35. No widespread dissemination of Chlamydia trachomatis diagnostic-escape variants and the impact of Neisseria gonorrhoeae positivity on the Aptima Combo 2 assay.
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Cole MJ, Davis GS, Fifer H, Saunders JM, Unemo M, Hadad R, Roberts DJ, Fazal M, Day MJ, Minshull J, Muir P, Horner PJ, Gill NO, and Folkard K
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- Chlamydia trachomatis genetics, Humans, Neisseria gonorrhoeae genetics, Nucleic Acid Amplification Techniques methods, RNA, Ribosomal, 23S genetics, Sensitivity and Specificity, Chlamydia Infections diagnosis, Gonorrhea diagnosis
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Objectives: A Finnish Chlamydia trachomatis (CT) new variant was detected in 2019 that escaped detection in the Hologic Aptima Combo 2 (AC2) assay due to a C1515T mutation in the CT 23S rRNA target region. Reflex testing of CT-negative/CT-equivocal specimens as well as those positive for Neisseria gonorrhoeae (NG) with the Hologic Aptima CT (ACT) assay was recommended to identify any CT variants., Methods: From June to October 2019, specimens with discrepant AC2/ACT CT results were submitted to Public Health England and screened for detectable CT DNA using an inhouse real-time (RT)-PCR. When enough DNA was present, partial CT 23S rRNA gene sequencing was performed. Analysis of available relative light units and interpretative data was performed., Results: A total of 317 discordant AC2/ACT specimens were collected from 315 patients. Three hundred were tested on the RT-PCR; 53.3% (n=160) were negative and 46.7% (n=140) were positive. Due to low DNA load in most specimens, sequencing was successful for only 36 specimens. The CT 23S rRNA wild-type sequence was present in 32 specimens, and two variants with C1514T or G1523A mutation were detected in four specimens from three patients. Of the discordant specimens with NG interpretation, 36.6% of NG-negative/CT-negative AC2 specimens had detectable CT DNA on the inhouse RT-PCR vs 53.3% of NG-positive/CT-negative specimens., Conclusions: No widespread dissemination of AC2 diagnostic-escape CT variants has occurred in England. We however identified the impact of NG positivity on the discordant AC2/ACT specimens; a proportion appeared due to NG positivity and the associated NG signal, rather than any diagnostic-escape variants or low DNA load. Several patients with gonorrhoea may therefore receive false-negative AC2 CT results. Single diagnostic targets and multiplex diagnostic assays have their limitations such as providing selection pressure for escape mutants and potentially reduced sensitivity, respectively. These limitations must be considered when establishing diagnostic pathways., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2022
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36. Significant increase in azithromycin "resistance" and susceptibility to ceftriaxone and cefixime in Neisseria gonorrhoeae isolates in 26 European countries, 2019.
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Day MJ, Jacobsson S, Spiteri G, Kulishev C, Sajedi N, Woodford N, Blumel B, van der Werf MJ, Amato-Gauci AJ, Unemo M, and Cole MJ
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- Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Azithromycin pharmacology, Azithromycin therapeutic use, Cefixime pharmacology, Cefixime therapeutic use, Ceftriaxone pharmacology, Ceftriaxone therapeutic use, Ciprofloxacin pharmacology, Ciprofloxacin therapeutic use, Drug Resistance, Bacterial, Female, Homosexuality, Male, Humans, Male, Microbial Sensitivity Tests, Neisseria gonorrhoeae, Anti-Infective Agents therapeutic use, Gonorrhea drug therapy, Gonorrhea epidemiology, Pharyngitis drug therapy, Sexual and Gender Minorities
- Abstract
Background: The European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP) performs annual sentinel surveillance of Neisseria gonorrhoeae susceptibility to therapeutically relevant antimicrobials across the European Union/European Economic Area (EU/EEA). We present the Euro-GASP results from 2019 (26 countries), linked to patient epidemiological data, and compared with data from previous years., Methods: Agar dilution and minimum inhibitory concentration (MIC) gradient strip methodologies were used to determine the antimicrobial susceptibility (using EUCAST clinical breakpoints, where available) of 3239 N. gonorrhoeae isolates from 26 countries across the EU/EEA. Significance of differences compared with Euro-GASP results in previous years was analysed using Z-test and the Pearson's χ2 test was used to assess significance of odds ratios for associations between patient epidemiological data and antimicrobial resistance., Results: European N. gonorrhoeae isolates collected between 2016 and 2019 displayed shifting MIC distributions for; ceftriaxone, with highly susceptible isolates increasing over time and occasional resistant isolates each year; cefixime, with highly-susceptible isolates becoming increasingly common; azithromycin, with a shift away from lower MICs towards higher MICs above the EUCAST epidemiological cut-off (ECOFF); and ciprofloxacin which is displaying a similar shift in MICs as observed for azithromycin. In 2019, two isolates displayed ceftriaxone resistance, but both isolates had MICs below the azithromycin ECOFF. Cefixime resistance (0.8%) was associated with patient sex, with resistance higher in females compared with male heterosexuals and men-who-have-sex-with-men (MSM). The number of countries reporting isolates with azithromycin MICs above the ECOFF increased from 76.9% (20/26) in 2016 to 92.3% (24/26) in 2019. Isolates with azithromycin MICs above the ECOFF (9.0%) were associated with pharyngeal infection sites. Following multivariable analysis, ciprofloxacin resistance remained associated with isolates from MSM and heterosexual males compared with females, the absence of a concurrent chlamydial infection, pharyngeal infection sites and patients ≥ 25 years of age., Conclusions: Resistance to ceftriaxone and cefixime remained uncommon in EU/EEA countries in 2019 with a significant decrease in cefixime resistance observed between 2016 and 2019. The significant increase in azithromycin "resistance" (azithromycin MICs above the ECOFF) threatens the effectiveness of the dual therapy (ceftriaxone + azithromycin), i.e., for ceftriaxone-resistant cases, currently recommended in many countries internationally and requires close monitoring., (© 2022. The Author(s).)
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- 2022
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37. Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study.
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Sánchez-Busó L, Cole MJ, Spiteri G, Day M, Jacobsson S, Golparian D, Sajedi N, Yeats CA, Abudahab K, Underwood A, Bluemel B, Aanensen DM, and Unemo M
- Subjects
- Anti-Bacterial Agents pharmacology, Azithromycin pharmacology, Cefixime therapeutic use, Ceftriaxone pharmacology, Drug Resistance, Bacterial genetics, Europe epidemiology, Genomics, Homosexuality, Male, Humans, Male, Microbial Sensitivity Tests, Neisseria gonorrhoeae genetics, Gonorrhea drug therapy, Sexual and Gender Minorities
- Abstract
Background: Genomic surveillance using quality-assured whole-genome sequencing (WGS) together with epidemiological and antimicrobial resistance (AMR) data is essential to characterise the circulating Neisseria gonorrhoeae lineages and their association to patient groups (defined by demographic and epidemiological factors). In 2013, the European gonococcal population was characterised genomically for the first time. We describe the European gonococcal population in 2018 and identify emerging or vanishing lineages associated with AMR and epidemiological characteristics of patients, to elucidate recent changes in AMR and gonorrhoea epidemiology in Europe., Methods: We did WGS on 2375 gonococcal isolates from 2018 (mainly Sept 1-Nov 30) in 26 EU and EEA countries. Molecular typing and AMR determinants were extracted from quality-checked genomic data. Association analyses identified links between genomic lineages, AMR, and epidemiological data., Findings: Azithromycin-resistant N gonorrhoeae (8·0% [191/2375] in 2018) is rising in Europe due to the introduction or emergence and subsequent expansion of a novel N gonorrhoeae multi-antigen sequence typing (NG-MAST) genogroup, G12302 (132 [5·6%] of 2375; N gonorrhoeae sequence typing for antimicrobial resistance [NG-STAR] clonal complex [CC]168/63), carrying a mosaic mtrR promoter and mtrD sequence and found in 24 countries in 2018. CC63 was associated with pharyngeal infections in men who have sex with men. Susceptibility to ceftriaxone and cefixime is increasing, as the resistance-associated lineage, NG-MAST G1407 (51 [2·1%] of 2375), is progressively vanishing since 2009-10., Interpretation: Enhanced gonococcal AMR surveillance is imperative worldwide. WGS, linked to epidemiological and AMR data, is essential to elucidate the dynamics in gonorrhoea epidemiology and gonococcal populations as well as to predict AMR. When feasible, WGS should supplement the national and international AMR surveillance programmes to elucidate AMR changes over time. In the EU and EEA, increasing low-level azithromycin resistance could threaten the recommended ceftriaxone-azithromycin dual therapy, and an evidence-based clinical azithromycin resistance breakpoint is needed. Nevertheless, increasing ceftriaxone susceptibility, declining cefixime resistance, and absence of known resistance mutations for new treatments (zoliflodacin, gepotidacin) are promising., Funding: European Centre for Disease Prevention and Control, Centre for Genomic Pathogen Surveillance, Örebro University Hospital, Wellcome., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
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- 2022
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38. Capacity-Building in Community-Based Drug Treatment Services.
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Cole MJ
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- Capacity Building, Health Services Accessibility, Humans, Community Health Services, Human Rights
- Abstract
Globally, there are not enough services to meet the enormous demand for evidence-based community-based drug treatment. Further, the effectiveness of available services varies as much as the diversity of their treatment regimens. Capacity-building can help increase the scale and improve the quality of those interventions. Maximizing the impact of capacity-building requires a comprehensive and systematic approach considering three levels-the individual worker, organization, and service sector-and it starts with assessment and planning. This paper describes the areas to consider and steps to follow when planning and implementing a comprehensive capacity-building approach in community-based drug treatment services. Utilizing an empowerment model for capacity-building can increase the stakeholders and resources engaged in the process. Better engagement with community stakeholders increases the likelihood that capacity-building outcomes will be sustainable. Further, the institutionalization of capacity-building can establish and promote an organizational culture of continuous learning., Competing Interests: Competing interests: None declared., (Copyright © 2022 Cole.)
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- 2022
39. Detection of markers predictive of macrolide and fluoroquinolone resistance in Mycoplasma genitalium from patients attending sexual health services.
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Day MJ, Cole MJ, Fifer H, Woodford N, and Pitt R
- Subjects
- Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, DNA, Bacterial genetics, Drug Resistance, Bacterial genetics, Fluoroquinolones pharmacology, Fluoroquinolones therapeutic use, Health Services, Humans, Macrolides pharmacology, Macrolides therapeutic use, Mutation, Prevalence, RNA, Ribosomal, 23S genetics, Mycoplasma Infections drug therapy, Mycoplasma Infections epidemiology, Mycoplasma genitalium genetics
- Abstract
Objectives: This study sought to provide data on the prevalence of macrolide (23S rRNA) and fluoroquinolone ( parC ) resistance-associated mutations seen in Mycoplasma genitalium -positive specimens received in the UK national reference laboratory., Methods: In total, 2580 clinical specimens from patients with suspected or confirmed M. genitalium infection were received at the national reference laboratory between September 2017 and November 2018. M. genitalium -positive clinical specimens were identified using a reverse transcription-PCR targeting two M. genitalium genes: MgPa and gap . Resistance-associated single nucleotide poylmorphisms were sought in all positive specimens by sequence analysis of the 23S rRNA and parC genes., Results: Eighteen per cent (458 of 2580) of clinical specimens were positive for M. genitalium and 389 had sequence data for both macrolide and fluoroquinolone resistance markers. Of these, 71% (275 of 389) had macrolide resistance-associated mutations, 8% (31 of 389) had fluoroquinolone resistance-associated mutations (S83I/R and D87Y/N) and 7% (26 of 389) had mutations associated with resistance to both antimicrobials. Only 28% (108 of 389) had no mutations associated with resistance to either class of antibiotic. Five specimens had mutations of unknown clinical significance in the parC gene (eg, G81C and S83N)., Conclusions: Mutations associated with resistance to macrolides were very frequent. By contrast, susceptibility to the second-line treatment, moxifloxacin (a fluoroquinolone), was estimated at 92% based on the absence of resistance-associated mutations. The few specimens with mutations of unknown clinical significance in the parC gene were excluded from the analysis and so the actual level of fluoroquinolone susceptibility may be slightly lower than that reported here. Surveillance of antimicrobial resistance in M. genitalium is imperative for this to remain a treatable infection., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2022
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40. The European response to control and manage multi- and extensively drug-resistant Neisseria gonorrhoeae .
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Cole MJ, Day M, Jacobsson S, Amato-Gauci AJ, Spiteri G, and Unemo M
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- Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Ceftriaxone pharmacology, Ceftriaxone therapeutic use, Drug Resistance, Bacterial, Humans, Microbial Sensitivity Tests, Gonorrhea diagnosis, Gonorrhea drug therapy, Gonorrhea epidemiology, Neisseria gonorrhoeae
- Abstract
Because cefixime and ceftriaxone resistance in Neisseria gonorrhoeae and gonorrhoea treatment failures were increasing, a response plan to control and manage multidrug-resistant N. gonorrhoeae (MDR-NG) in Europe was published in 2012. The three main areas of the plan were to: (i) strengthen surveillance of antimicrobial resistance (AMR), (ii) implement monitoring of treatment failures and (iii) establish a communication strategy to increase awareness and disseminate AMR results. Since 2012, several additional extensively drug-resistant N. gonorrhoeae (XDR-NG) strains have emerged, and strains with high-level ceftriaxone resistance spread internationally. This prompted an evaluation and review of the 2012 European Centre for Disease Prevention and Control (ECDC) response plan, revealing an overall improvement in many aspects of monitoring AMR in N. gonorrhoeae ; however, treatment failure monitoring was a weakness. Accordingly, the plan was updated in 2019 to further support European Union/European Economic Area (EU/EEA) countries in controlling and managing the threat of MDR/XDR-NG in Europe through further strengthening of AMR surveillance and clinical management including treatment failure monitoring. The plan will be assessed biennially to ensure its effectiveness and its value. Along with prevention, diagnostic, treatment and epidemiological surveillance strategies, AMR surveillance is essential for effective control of gonorrhoea.
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- 2022
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41. Use of genomics to investigate Neisseria gonorrhoeae antimicrobial susceptibility testing discrepancies.
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Fifer H, Schaefer U, Pitt R, Allen H, Day M, Woodford N, and Cole MJ
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- Genomics, Humans, Microbial Sensitivity Tests, Neisseria gonorrhoeae genetics, Anti-Infective Agents, Gonorrhea diagnosis
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- 2022
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42. Serological profile of first SARS-CoV-2 reinfection cases detected within the SIREN study.
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Atti A, Ferrari M, Castillo-Olivares J, Monk EJM, Gopal R, Patel M, Hoschler K, Cole MJ, Semper A, Hewson J, Otter AD, Foulkes S, Islam J, Mirfenderesky M, Jain S, Murira J, Favager C, Nastouli E, Chand MA, Brown CS, Heeney JL, Brooks T, Hall VJ, Hopkins S, and Zambon M
- Subjects
- Antibodies, Viral immunology, Humans, Immunity, Humoral, Reinfection, COVID-19, SARS-CoV-2
- Abstract
Competing Interests: Declarations of Competing Interest None.
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- 2022
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43. Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.
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Beale MA, Marks M, Cole MJ, Lee MK, Pitt R, Ruis C, Balla E, Crucitti T, Ewens M, Fernández-Naval C, Grankvist A, Guiver M, Kenyon CR, Khairullin R, Kularatne R, Arando M, Molini BJ, Obukhov A, Page EE, Petrovay F, Rietmeijer C, Rowley D, Shokoples S, Smit E, Sweeney EL, Taiaroa G, Vera JH, Wennerås C, Whiley DM, Williamson DA, Hughes G, Naidu P, Unemo M, Krajden M, Lukehart SA, Morshed MG, Fifer H, and Thomson NR
- Subjects
- Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial, Genome, Bacterial, Humans, Macrolides pharmacology, Treponema pallidum classification, Treponema pallidum genetics, Treponema pallidum physiology, Phylogeny, Syphilis microbiology, Treponema pallidum isolation & purification
- Abstract
Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides., (© 2021. The Author(s).)
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- 2021
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44. WHO global antimicrobial resistance surveillance for Neisseria gonorrhoeae 2017-18: a retrospective observational study.
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Unemo M, Lahra MM, Escher M, Eremin S, Cole MJ, Galarza P, Ndowa F, Martin I, Dillon JR, Galas M, Ramon-Pardo P, Weinstock H, and Wi T
- Subjects
- Anti-Bacterial Agents pharmacology, Azithromycin pharmacology, Cefixime pharmacology, Ceftriaxone pharmacology, Ciprofloxacin pharmacology, Drug Resistance, Bacterial, Humans, World Health Organization, Gonorrhea diagnosis, Neisseria gonorrhoeae
- Abstract
Background: Gonorrhoea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are major health concerns globally. Increased global surveillance of gonococcal AMR is essential. We aimed to describe the 2017-18 data from WHO's global gonococcal AMR surveillance, and to discuss priorities essential for the effective management and control of gonorrhoea., Methods: We did a retrospective observational study of the AMR data of gonococcal isolates reported to WHO by 73 countries in 2017-18. WHO recommends that each country collects at least 100 gonococcal isolates per year, and that quantitative methods to determine the minimum inhibitory concentration of antimicrobials, interpreted by internationally standardised resistance breakpoints, are used., Findings: In 2017-18, 73 countries provided AMR data for one or more drug. Decreased susceptibility or resistance to ceftriaxone was reported by 21 (31%) of 68 reporting countries and to cefixime by 24 (47%) of 51 reporting countries. Resistance to azithromycin was reported by 51 (84%) of 61 reporting countries and to ciprofloxacin by all 70 (100%) reporting countries. The annual proportion of decreased susceptibility or resistance across countries was 0-21% to ceftriaxone and 0-22% to cefixime, and that of resistance was 0-60% to azithromycin and 0-100% to ciprofloxacin. The number of countries reporting gonococcal AMR and resistant isolates, and the number of examined isolates, have increased since 2015-16. Surveillance remains scarce in central America and the Caribbean and eastern Europe, and in the WHO African, Eastern Mediterranean, and South-East Asian regions., Interpretation: In many countries, ciprofloxacin resistance was exceedingly high, azithromycin resistance was increasing, and decreased susceptibility or resistance to ceftriaxone and cefixime continued to emerge. WHO's global surveillance of gonococcal AMR needs to expand internationally to provide imperative data for national and international management guidelines and public health policies. Improved prevention, early diagnosis, treatment of index patients and partners, enhanced surveillance (eg, infection, AMR, treatment failures, and antimicrobial use or misuse), and increased knowledge on antimicrobial selection, stewardship, and pharmacokinetics or pharmacodynamics are essential. The development of rapid, accurate, and affordable point-of-care gonococcal diagnostic tests, new antimicrobials, and gonococcal vaccines is imperative., Funding: None., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
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- 2021
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45. Prevalence of Chlamydia trachomatis and Mycoplasma genitalium coinfections and M. genitalium antimicrobial resistance in rectal specimens.
- Author
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Pitt R, Fifer H, Woodford N, Hopkins S, and Cole MJ
- Subjects
- Adult, Anti-Bacterial Agents therapeutic use, Chlamydia Infections drug therapy, Chlamydia trachomatis genetics, Coinfection drug therapy, Coinfection microbiology, Female, Genome, Bacterial, Humans, Male, Mycoplasma Infections drug therapy, Mycoplasma genitalium genetics, Prevalence, United Kingdom epidemiology, Anti-Bacterial Agents pharmacology, Chlamydia Infections epidemiology, Chlamydia trachomatis drug effects, Coinfection epidemiology, Drug Resistance, Multiple, Bacterial, Mycoplasma Infections epidemiology, Mycoplasma genitalium drug effects, Rectum microbiology
- Abstract
Competing Interests: Competing interests: None declared.
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- 2021
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46. Endosonography-guided transmural drainage of pancreatic fluid collections: comparative outcomes by stent type.
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Kayal A, Taghizadeh N, Ishikawa T, Gonzalez-Moreno E, Bass S, Cole MJ, Heitman SJ, Mohamed R, Turbide C, Chen YI, and Forbes N
- Subjects
- Humans, Retrospective Studies, Stents, Treatment Outcome, Drainage, Endosonography
- Abstract
Background: Pancreatic fluid collections (PFCs), including walled-off necrosis (WON), are commonly described sequelae of pancreatitis. Endosonography-guided PFC drainage can be performed using plastic stents (PS), fully covered self-expanding metal stents (FCSEMS), or lumen-apposing metal stents (LAMS). We performed a retrospective study comparing clinical outcomes and adverse events by stent type., Methods: In this historical cohort, patients undergoing endosonography-guided PFC drainage from 2010 to 2019 were divided into groups: those treated with (1) PS, (2) FCSEMS, and (3) LAMS. Clinical success, the primary outcome, was defined as complete resolution or size reduction of ≥ 50%, with resolution of symptoms and no reintervention required at 3 months following the index procedure. Adverse events (AEs) and procedure times were also evaluated., Results: Fifty-eight patients were included. Procedure times were significantly shorter with LAMS (21.4 ± 10.8 min versus 53.0 ± 24.4 min for FCSEMS and 65.9 ± 23.4 min for PS, p < 0.001). Clinical success rates for WON were higher with LAMS compared with FCSEMS (95.7% vs 66.7%, respectively; p = 0.04). For all PFCs, treatment with LAMS trended towards higher clinical success rates compared with PS and FCSEMS (96.3% vs 81.8% vs 77.8%, respectively; p = 0.14). Early AEs (within 1 week) occurred at significantly lower rates in the LAMS group compared to PS and FCSEMS (0% vs 33.3% vs 10.6%, respectively; p = 0.006), as did late AEs (7.4% vs 44.5% vs 40%, respectively; p = 0.01)., Conclusions: LAMS is superior in terms of WON clinical success, favorable in terms of lower adverse event profile, and shorter in terms of procedural time compared to FCSEMS and PS. LAMS can be considered as an initial approach for WON, given that clinical success in WON is lower when using PS or FCSEMS, though more high-quality data are needed.
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- 2021
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47. SARS-CoV-2 infection rates of antibody-positive compared with antibody-negative health-care workers in England: a large, multicentre, prospective cohort study (SIREN).
- Author
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Hall VJ, Foulkes S, Charlett A, Atti A, Monk EJM, Simmons R, Wellington E, Cole MJ, Saei A, Oguti B, Munro K, Wallace S, Kirwan PD, Shrotri M, Vusirikala A, Rokadiya S, Kall M, Zambon M, Ramsay M, Brooks T, Brown CS, Chand MA, and Hopkins S
- Subjects
- Adult, Asymptomatic Infections, COVID-19 diagnosis, COVID-19 Nucleic Acid Testing, England, Female, Follow-Up Studies, Humans, Male, Middle Aged, Pandemics, Prospective Studies, Reinfection, Risk Factors, SARS-CoV-2, Antibodies, Viral blood, COVID-19 epidemiology, COVID-19 immunology, Health Personnel
- Abstract
Background: Increased understanding of whether individuals who have recovered from COVID-19 are protected from future SARS-CoV-2 infection is an urgent requirement. We aimed to investigate whether antibodies against SARS-CoV-2 were associated with a decreased risk of symptomatic and asymptomatic reinfection., Methods: A large, multicentre, prospective cohort study was done, with participants recruited from publicly funded hospitals in all regions of England. All health-care workers, support staff, and administrative staff working at hospitals who could remain engaged in follow-up for 12 months were eligible to join The SARS-CoV-2 Immunity and Reinfection Evaluation study. Participants were excluded if they had no PCR tests after enrolment, enrolled after Dec 31, 2020, or had insufficient PCR and antibody data for cohort assignment. Participants attended regular SARS-CoV-2 PCR and antibody testing (every 2-4 weeks) and completed questionnaires every 2 weeks on symptoms and exposures. At enrolment, participants were assigned to either the positive cohort (antibody positive, or previous positive PCR or antibody test) or negative cohort (antibody negative, no previous positive PCR or antibody test). The primary outcome was a reinfection in the positive cohort or a primary infection in the negative cohort, determined by PCR tests. Potential reinfections were clinically reviewed and classified according to case definitions (confirmed, probable, or possible) and symptom-status, depending on the hierarchy of evidence. Primary infections in the negative cohort were defined as a first positive PCR test and seroconversions were excluded when not associated with a positive PCR test. A proportional hazards frailty model using a Poisson distribution was used to estimate incidence rate ratios (IRR) to compare infection rates in the two cohorts., Findings: From June 18, 2020, to Dec 31, 2020, 30 625 participants were enrolled into the study. 51 participants withdrew from the study, 4913 were excluded, and 25 661 participants (with linked data on antibody and PCR testing) were included in the analysis. Data were extracted from all sources on Feb 5, 2021, and include data up to and including Jan 11, 2021. 155 infections were detected in the baseline positive cohort of 8278 participants, collectively contributing 2 047 113 person-days of follow-up. This compares with 1704 new PCR positive infections in the negative cohort of 17 383 participants, contributing 2 971 436 person-days of follow-up. The incidence density was 7·6 reinfections per 100 000 person-days in the positive cohort, compared with 57·3 primary infections per 100 000 person-days in the negative cohort, between June, 2020, and January, 2021. The adjusted IRR was 0·159 for all reinfections (95% CI 0·13-0·19) compared with PCR-confirmed primary infections. The median interval between primary infection and reinfection was more than 200 days., Interpretation: A previous history of SARS-CoV-2 infection was associated with an 84% lower risk of infection, with median protective effect observed 7 months following primary infection. This time period is the minimum probable effect because seroconversions were not included. This study shows that previous infection with SARS-CoV-2 induces effective immunity to future infections in most individuals., Funding: Department of Health and Social Care of the UK Government, Public Health England, The National Institute for Health Research, with contributions from the Scottish, Welsh and Northern Irish governments., Competing Interests: Declaration of interests We declare no competing interests., (Crown copyright © 2021 Published by Elsevier Ltd. All rights reserved.)
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- 2021
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48. What's left in the cupboard? Older antimicrobials for treating gonorrhoea.
- Author
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Fifer H, Livermore DM, Uthayakumaran T, Woodford N, and Cole MJ
- Subjects
- Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Azithromycin pharmacology, Ceftriaxone pharmacology, Drug Resistance, Bacterial, Humans, Microbial Sensitivity Tests, Neisseria gonorrhoeae, Anti-Infective Agents pharmacology, Gonorrhea drug therapy
- Abstract
Background: Neisseria gonorrhoeae has developed resistance to all antimicrobials used to treat gonorrhoea, with even ceftriaxone being undermined. It is therefore important to examine any potential to redeploy older antimicrobials routinely used for other infections to treat ceftriaxone-resistant gonococcal infections., Objectives: We examined the susceptibility of N. gonorrhoeae to aztreonam, chloramphenicol, co-trimoxazole, fosfomycin, piperacillin/tazobactam and rifampicin., Methods: N. gonorrhoeae isolates (n = 94) were selected to include a range of antimicrobial susceptibilities: 58 were collected in the Gonococcal Resistance to Antimicrobials Surveillance Programme; 17 were clinical isolates referred to the PHE reference laboratory; and 19 were control strains. MICs were determined by agar dilution for the six study antimicrobials and for ceftriaxone and azithromycin as comparators., Results: There was correlation between piperacillin/tazobactam and ceftriaxone MICs, but all five isolates with high ceftriaxone MICs (>0.5 mg/L) were inhibited by piperacillin/tazobactam at 0.06-0.5 mg/L. Aztreonam MICs for ceftriaxone-resistant isolates exceeded those of ceftriaxone. Among non-β-lactams, fosfomycin and co-trimoxazole had low, tightly clustered MICs, suggesting widespread susceptibility, rifampicin split the collection into highly susceptible and highly resistant groups and chloramphenicol had a wide MIC distribution., Conclusions: Although unsuitable for empirical use, piperacillin/tazobactam, fosfomycin, co-trimoxazole, rifampicin and, possibly, chloramphenicol could be considered for individual patients with ceftriaxone-resistant gonococcal infection once MICs are known. Wider surveillance of the susceptibility of N. gonorrhoeae to these agents is needed, along with clinical trials and the establishment of clinical breakpoints for N gonorrhoeae., (© Crown copyright 2021.)
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- 2021
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49. High susceptibility to zoliflodacin and conserved target (GyrB) for zoliflodacin among 1209 consecutive clinical Neisseria gonorrhoeae isolates from 25 European countries, 2018.
- Author
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Unemo M, Ahlstrand J, Sánchez-Busó L, Day M, Aanensen D, Golparian D, Jacobsson S, and Cole MJ
- Subjects
- Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Azithromycin pharmacology, Barbiturates, Ceftriaxone pharmacology, Ciprofloxacin pharmacology, Drug Resistance, Bacterial, Europe, Humans, Isoxazoles, Microbial Sensitivity Tests, Morpholines, Oxazolidinones, Spiro Compounds, Gonorrhea drug therapy, Neisseria gonorrhoeae genetics
- Abstract
Objectives: Novel antimicrobials for treatment of gonorrhoea are imperative. The first-in-class spiropyrimidinetrione zoliflodacin is promising and currently in an international Phase 3 randomized controlled clinical trial (RCT) for treatment of uncomplicated gonorrhoea. We evaluated the in vitro activity of and the genetic conservation of the target (GyrB) and other potential zoliflodacin resistance determinants among 1209 consecutive clinical Neisseria gonorrhoeae isolates obtained from 25 EU/European Economic Area (EEA) countries in 2018 and compared the activity of zoliflodacin with that of therapeutic antimicrobials currently used., Methods: MICs of zoliflodacin, ceftriaxone, cefixime, azithromycin and ciprofloxacin were determined using an agar dilution technique for zoliflodacin or using MIC gradient strip tests or an agar dilution technique for the other antimicrobials. Genome sequences were available for 96.1% of isolates., Results: Zoliflodacin modal MIC, MIC50, MIC90 and MIC range were 0.125, 0.125, 0.125 and ≤0.004-0.5 mg/L, respectively. The resistance was 49.9%, 6.7%, 1.6% and 0.2% to ciprofloxacin, azithromycin, cefixime and ceftriaxone, respectively. Zoliflodacin did not show any cross-resistance to other tested antimicrobials. GyrB was highly conserved and no zoliflodacin gyrB resistance mutations were found. No fluoroquinolone target GyrA or ParC resistance mutations or mutations causing overexpression of the MtrCDE efflux pump substantially affected the MICs of zoliflodacin., Conclusions: The in vitro susceptibility to zoliflodacin was high and the zoliflodacin target GyrB was conserved among EU/EEA gonococcal isolates in 2018. This study supports further clinical development of zoliflodacin. However, additional zoliflodacin data regarding particularly the treatment of pharyngeal gonorrhoea, pharmacokinetics/pharmacodynamics and resistance selection, including suppression, would be valuable., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
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- 2021
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50. Associations between antimicrobial susceptibility/resistance of Neisseria gonorrhoeae isolates in European Union/European Economic Area and patients' gender, sexual orientation and anatomical site of infection, 2009-2016.
- Author
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Jacobsson S, Cole MJ, Spiteri G, Day M, and Unemo M
- Subjects
- Azithromycin therapeutic use, Cefixime therapeutic use, Ceftriaxone therapeutic use, Ciprofloxacin therapeutic use, European Union, Female, Gonorrhea drug therapy, Gonorrhea epidemiology, Heterosexuality, Homosexuality, Male, Humans, Male, Microbial Sensitivity Tests, Neisseria gonorrhoeae isolation & purification, Sexual Behavior, Anti-Bacterial Agents therapeutic use, Drug Resistance, Bacterial, Gonorrhea microbiology, Neisseria gonorrhoeae drug effects, Sex Factors, Sexual and Gender Minorities
- Abstract
Background: The emergence and spread of antimicrobial resistance (AMR) in Neisseria gonorrhoeae, nationally and internationally, is a serious threat to the management and control of gonorrhoea. Limited and conflicting data regarding the epidemiological drivers of gonococcal AMR internationally have been published. We examined the antimicrobial susceptibility/resistance of gonococcal isolates (n = 15,803) collected across 27 European Union/European Economic Area (EU/EEA) countries in 2009-2016, in conjunction to epidemiological and clinical data of the corresponding patients, to elucidate associations between antimicrobial susceptibility/resistance and patients' gender, sexual orientation and anatomical site of infection., Methods: In total, 15,803 N. gonorrhoeae isolates from the European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP), 2009-2016, were examined. Associations between gonococcal susceptibility/resistance and patients' gender, sexual orientation and anatomical site of infection were investigated using univariate and multivariate logistic regression analysis. Statistical significance was determined by Pearson χ
2 -test or Fisher's exact test with two-tailed p-values of < 0.05 indicating significance., Results: The overall gonococcal resistance from 2009 to 2016 was 51.7% (range during the years: 46.5-63.5%), 7.1% (4.5-13.2%), 4.3% (1.8-8.7%), and 0.2% (0.0-0.5%) to ciprofloxacin, azithromycin, cefixime, and ceftriaxone, respectively. The level of resistance combined with decreased susceptibility to ceftriaxone was 10.2% (5.7-15.5%). Resistance to cefixime and ciprofloxacin, and resistance combined with decreased susceptibility to ceftriaxone were positively associated with urogenital infections and heterosexual males, males with sexual orientation not reported and females (except for ciprofloxacin), i.e. when compared to men-who-have-sex-with-men (MSM). Azithromycin resistance was positively associated with heterosexual males, but no association was significant regarding anatomical site of infection., Conclusions: Overall, sexual orientation was the main variable associated with gonococcal AMR. Strongest positive associations were identified with heterosexual patients, particularly males, and not MSM. To provide evidence-based understanding and mitigate gonococcal AMR emergence and spread, associations between antimicrobial susceptibility/resistance and patients' gender, sexual orientation and anatomical site of infection need to be further investigated in different geographic settings. In general, these insights will support identification of groups at increased risk and targeted public health actions such as intensified screening, 3-site testing using molecular diagnostics, sexual contact tracing, and surveillance of treatment failures.- Published
- 2021
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