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Wang D, Li Y, Zhang C, Zeng Y, Peng J, Wang F. Genomic epidemiology of Neisseria gonorrhoeae in Shenzhen, China, during 2019-2020: increased spread of ceftriaxone-resistant isolates brings insights for strengthening public health responses. Microbiol Spectr 2023; 11:e0172823. [PMID: 37732794 PMCID: PMC10580820 DOI: 10.1128/spectrum.01728-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
The antimicrobial resistance (AMR) in gonorrhea poses global threat of increasing public health concern. In response to this concern, molecular surveillance has been widely utilized to detail the changes in the evolution and distribution of Neisseria gonorrhoeae during AMR transmission. In this study, we performed a comprehensive molecular surveillance of 664 N. gonorrhoeae isolates collected in Shenzhen, one of the cities with the largest mobile population in China, 2019-2020. In 2020, ceftriaxone showed an unprecedented high resistance rate of 24.87%, and 67.83% of the ceftriaxone-resistant (Cro-R) isolates harbored a nonmosaic penA allele. The Cro-R isolates with nonmosaic penA alleles showed a tremendous increasing trend from 0.00% in 2014 to 20.45% in 2020, which proves the need for monitoring nonmosaic penA-related resistance. Importantly, genotyping indicated that multilocus sequence typing ST11231 (35.71%) had a notable rate of ceftriaxone resistance, which might become the focus of future surveillance. Whole-genome sequencing analysis showed that the internationally spreading FC428 clones have circulated in Shenzhen region with typical ceftriaxone resistance (MIC ≥ 0.5 mg/L) maintained. Our surveillance combined with genomic analysis provides current information to update gonorrhea management guidelines and emphasizes that continuous AMR surveillance for N. gonorrhoeae is essential. IMPORTANCE We conducted a comprehensive molecular epidemiology analysis for antimicrobial-resistant Neisseria gonorrhoeae in Shenzhen during 2019-2020, which provided important data for personalized treatment and adjustment of monitoring strategy. Briefly, the proportion of ceftriaxone-resistant (Cro-R) isolates reached a stunning prevalence rate of 24.87% in 2020. A typical increment of Cro-R isolates with nonmosaic penA alleles proves the necessity of monitoring nonmosaic AMR mechanism and involving it into developing molecular detection methods. Whole-genome sequencing analysis showed that the international spreading FC428 clone has been circulating in Shenzhen with typical ceftriaxone resistance (MIC ≥ 0.5 mg/L) maintained. In summary, we conducted a comprehensive epidemiology study, providing significant data for therapy management. Our results not only improve the understanding of the distribution and transmission of AMR in N. gonorrhoeae but also provide effective AMR data for improving surveillance strategies in China.
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Affiliation(s)
- Di Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yamei Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chi Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yaling Zeng
- Shenzhen Center for Chronic Disease Control, Shenzhen Institute of Dermatology, Shenzhen, People’s Republic of China, China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Feng Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen Institute of Dermatology, Shenzhen, People’s Republic of China, China
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Helekal D, Keeling M, Grad YH, Didelot X. Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data. J R Soc Interface 2023; 20:20230074. [PMID: 37312496 PMCID: PMC10265023 DOI: 10.1098/rsif.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023] Open
Abstract
Increasing levels of antibiotic resistance in many bacterial pathogen populations are a major threat to public health. Resistance to an antibiotic provides a fitness benefit when the bacteria are exposed to this antibiotic, but resistance also often comes at a cost to the resistant pathogen relative to susceptible counterparts. We lack a good understanding of these benefits and costs of resistance for many bacterial pathogens and antibiotics, but estimating them could lead to better use of antibiotics in a way that reduces or prevents the spread of resistance. Here, we propose a new model for the joint epidemiology of susceptible and resistant variants, which includes explicit parameters for the cost and benefit of resistance. We show how Bayesian inference can be performed under this model using phylogenetic data from susceptible and resistant lineages and that by combining data from both we are able to disentangle and estimate the resistance cost and benefit parameters separately. We applied our inferential methodology to several simulated datasets to demonstrate good scalability and accuracy. We analysed a dataset of Neisseria gonorrhoeae genomes collected between 2000 and 2013 in the USA. We found that two unrelated lineages resistant to fluoroquinolones shared similar epidemic dynamics and resistance parameters. Fluoroquinolones were abandoned for the treatment of gonorrhoea due to increasing levels of resistance, but our results suggest that they could be used to treat a minority of around 10% of cases without causing resistance to grow again.
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Affiliation(s)
- David Helekal
- Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick, Coventry, UK
| | - Matt Keeling
- Mathematics Institute and School of Life Sciences, University of Warwick, Coventry, UK
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, TH Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
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Herrero M, Broner S, Cruells A, Esteve S, Ferré L, Mendioroz J, Jané M, Ciruela P. Epidemiology and antimicrobial resistance profile of Neisseria gonorrhoeae in Catalonia, Spain, 2016-2019. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04601-0. [PMID: 37162616 DOI: 10.1007/s10096-023-04601-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023]
Abstract
Antimicrobial resistance data for Neisseria gonorrhoeae is globally sparse and resistant strains are emerging in Catalonia. We aim to describe epidemiological and antimicrobial resistance in all patients infected with N. gonorrhoeae during the period from 2016 to 2019, using available antimicrobial susceptibility data. We retrospectively analysed confirmed N. gonorrhoeae cases notified to Catalonia's microbiological reporting system. Antibiotic susceptibility testing (azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, spectinomycin, and tetracycline) was assessed using clinical breakpoints published by the European Committee on Antimicrobial Susceptibility Testing. Incidence rates were calculated and proportions were compared using the χ2 test or Fisher's exact test, and analysed using the Statistical Package for Social Sciences (SPSS 18.0). A total of 14,251 confirmed cases of N. gonorrhoeae were notified. Incidence increased from 30.7 cases/100,000 person-years (p < 0.001) in 2016 to 64.7 in 2019. Culture was available in 6,292 isolates (44.2%), of which 5,377 (85.5%) were resistant to at least one of the antibiotics tested. Azithromycin resistance rose from 6.1% in 2016 to 16% in 2019 (p < 0.001). Only 1.0% (45 cases) were resistant to ceftriaxone. Multidrug-resistant N. gonorrhoeae increased from 0.25% in 2016 to 0.42% in 2019 (p = 0.521). One case presented extensively drug-resistant N. gonorrhoeae. In Catalonia, 10% of the N. gonorrhoeae isolates were resistant to azithromycin in the 2016-2019 period. According to World Health Organization guidelines, resistance above 5% indicates an alert to review treatment guidelines. Antimicrobial susceptibility testing in clinical practice followed by surveillance and interventions are essential to monitor trends and prevent the spread of antimicrobial resistance.
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Affiliation(s)
- Mercè Herrero
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain.
| | - Sonia Broner
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain
| | - Adrià Cruells
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain
| | - Silvia Esteve
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain
| | - Lourdes Ferré
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain
| | - Jacobo Mendioroz
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain
- Research Support Unit of Central Catalonia, Jordi Gol i Gurina University Research Institute for Primary Health Care, 08272, Sant Fruitós de Bages, Spain
| | - Mireia Jané
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP), Carlos III Health Institute, 28029, Madrid, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Pilar Ciruela
- Subdirectorate General for Public Health Surveillance and Emergency Response, Catalan Public Health Agency, Government of Catalonia, 08005, Barcelona, Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP), Carlos III Health Institute, 28029, Madrid, Spain
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Riou J, Althaus CL, Allen H, Cole MJ, Grad YH, Heijne JCM, Unemo M, Low N. Projecting the development of antimicrobial resistance in Neisseria gonorrhoeae from antimicrobial surveillance data: a mathematical modelling study. BMC Infect Dis 2023; 23:252. [PMID: 37081443 PMCID: PMC10116452 DOI: 10.1186/s12879-023-08200-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023] Open
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.
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Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | - Janneke C M Heijne
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands
| | | | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Zhao S, Hu I, Lou J, Chong MK, Cao L, He D, Zee BC, Wang MH. The mechanism shaping the logistic growth of mutation proportion in epidemics at population scale. Infect Dis Model 2022; 8:107-121. [PMID: 36632179 PMCID: PMC9811219 DOI: 10.1016/j.idm.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/19/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022] Open
Abstract
Virus evolution is a common process of pathogen adaption to host population and environment. Frequently, a small but important fraction of virus mutations are reported to contribute to higher risks of host infection, which is one of the major determinants of infectious diseases outbreaks at population scale. The key mutations contributing to transmission advantage of a genetic variant often grow and reach fixation rapidly. Based on classic epidemiology theories of disease transmission, we proposed a mechanistic explanation of the process that between-host transmission advantage may shape the observed logistic curve of the mutation proportion in population. The logistic growth of mutation is further generalized by incorporating time-varying selective pressure to account for impacts of external factors on pathogen adaptiveness. The proposed model is implemented in real-world data of COVID-19 to capture the emerging trends and changing dynamics of the B.1.1.7 strains of SARS-CoV-2 in England. The model characterizes and establishes the underlying theoretical mechanism that shapes the logistic growth of mutation in population.
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Affiliation(s)
- Shi Zhao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Inchi Hu
- Department of Information Systems, Business Statistics and Operations Management, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jingzhi Lou
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Marc K.C. Chong
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Lirong Cao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Benny C.Y. Zee
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Maggie H. Wang
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China,Corresponding author. JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China.
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Grunnill M, Hall I, Finnie T. Check your assumptions: Further scrutiny of basic model frameworks of antimicrobial resistance. J Theor Biol 2022; 554:111277. [PMID: 36150539 DOI: 10.1016/j.jtbi.2022.111277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/14/2023]
Abstract
Since the mid-1990s, growing concerns over antimicrobial resistant (AMR) organisms has led to an increase in the use of mathematical models to explore the inter-host transmission of such infections. Previous work reviewing such models categorised them into generic frameworks based on their underlying assumptions. These assumptions dictated the coexistence between AMR and antimicrobial sensitive strains. We add to this work performing stability analyses of the frameworks, along with simulating them deterministically and stochastically. Stability analyses found that many of these assumptions lead to models having the same equilibria, but showed differences in the equilibria's stability between models. Deterministic simulations reveal that assuming replacement of one infecting strain by another leads to an unusual antimicrobial treatment threshold. Increasing beyond this threshold causes a discontinuous increase in disease burden. The cost of AMR to pathogen fitness (lowered transmission) dictates both the threshold of treatment that causes the discontinuous increase in disease burden and the size of that increase. It was also shown that Superinfection states can be biased against resident strains and so favour coexistence of both strains. Stochastic simulations demonstrated that differing scenario starting conditions can guide models to converge upon equilibria that they may not have under deterministic simulation. These findings highlight the importance of checking assumptions when modelling AMR and strain competition more widely.
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Affiliation(s)
- Martin Grunnill
- Laboratory of Applied Mathematics (LIAM), York University, North York, M3J 3K1, Ontario, Canada.
| | - Ian Hall
- Department of Mathematics, University of Manchester, Manchester, M13 9PL, Greater Manchester, United Kingdom
| | - Thomas Finnie
- Directorate of Emergency Preparedness, Resilience and Response, UK Health Security Agency, Porton Down, Salisbury, SP4 0JG, Wiltshire, United Kingdom
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White PJ, Nikitin D, Whittles LK. We need estimates of gonorrhoea vaccine protection and symptomaticity by sex and anatomical site. THE LANCET. INFECTIOUS DISEASES 2022; 22:937. [PMID: 35752179 DOI: 10.1016/s1473-3099(22)00343-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/17/2022] [Indexed: 11/15/2022]
Affiliation(s)
- Peter J White
- Medical Research Council Centre for Global Infectious Disease Analysis and National Institute for Health and Care Research Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London W2 1PG, UK; Modelling and Economics Unit, UK Health Security Agency, London, UK.
| | - Dariya Nikitin
- Medical Research Council Centre for Global Infectious Disease Analysis and National Institute for Health and Care Research Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London W2 1PG, UK
| | - Lilith K Whittles
- Medical Research Council Centre for Global Infectious Disease Analysis and National Institute for Health and Care Research Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London W2 1PG, UK
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Barbee LA, St Cyr SB. Management of Neisseria gonorrhoeae in the United States: Summary of Evidence From the Development of the 2020 Gonorrhea Treatment Recommendations and the 2021 Centers for Disease Control and Prevention Sexually Transmitted Infection Treatment Guidelines. Clin Infect Dis 2022; 74:S95-S111. [PMID: 35416971 DOI: 10.1093/cid/ciac043] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Neisseria gonorrhoeae has developed resistance to all first-line recommended therapies, making gonococcal antimicrobial resistance a major public health concern given limited antibiotic options currently and an even smaller antimicrobial development pipeline. Since the release of the Centers for Disease Control and Prevention (CDC) 2015 STD Treatment Guidelines, azithromycin, part of the 2015 dual-drug treatment regimen, has had a rapid rise in resistance. The 2020 CDC Gonorrhea Treatment Recommendations and the 2021 Sexually Transmitted Infections (STI) Treatment Guidelines were developed weighing the priorities of treating the individual, protecting the population, and preventing antimicrobial resistance. METHODS Gonorrhea subject matter experts (SME) generated 8 key questions and conducted a literature review of updated data from 2013 to 2019 on gonorrhea antimicrobial resistance, treatment failures, clinical trials, and other key topics. More than 2200 abstracts were assessed, and 248 clinically relevant articles were thoroughly reviewed. SMEs also evaluated N gonorrhoeae antimicrobial resistance data from the Gonococcal Isolate Surveillance Project (GISP). EVIDENCE Although there have been reports of ceftriaxone treatment failures internationally, GISP data suggest that ceftriaxone minimal inhibitory concentrations (MICs) have remained stable in the United States, with < 0.1% exhibiting an "alert value" MIC (> 0.25 mcg/mL). However, GISP documented a rapid rise in the proportion of isolates with an elevated MIC (≥ 2.0 mcg/mL) to azithromycin-nearly 5% in 2018. At the same time, new pharmacokinetic/pharmacodynamic data are available, and there is greater recognition of the need for antimicrobial stewardship. SUMMARY The 2021 CDC STI Treatment Guidelines now recommend 500mg ceftriaxone intramuscularly once for the treatment of uncomplicated gonorrhea at all anatomic sites. If coinfection with chlamydia has not been excluded, cotreatment with doxycycline 100mg twice daily for 7 days should be added. Few alternative therapies exist for persons with cephalosporin allergies; there are no recommended alternative therapies for N gonorrhoeae infection of the throat.
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Affiliation(s)
- Lindley A Barbee
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,University of Washington, Seattle, Washington, USA.,Public Health - Seattle & King County HIV/STD Program, Seattle, Washington, USA
| | - Sancta B St Cyr
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Whittles LK, Didelot X, White PJ. Public health impact and cost-effectiveness of gonorrhoea vaccination: an integrated transmission-dynamic health-economic modelling analysis. THE LANCET INFECTIOUS DISEASES 2022; 22:1030-1041. [PMID: 35427491 PMCID: PMC9217755 DOI: 10.1016/s1473-3099(21)00744-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/14/2021] [Accepted: 11/11/2021] [Indexed: 12/19/2022]
Abstract
Background Gonorrhoea is a rapidly growing public health threat, with rising incidence and increasing drug resistance. Evidence that the MeNZB and four-component serogroup B meningococcal (4CMenB) vaccines, designed against Neisseria meningitidis, can also offer protection against gonorrhoea has created interest in using 4CMenB for this purpose and for developing gonorrhoea-specific vaccines. However, cost-effectiveness, and how the efficacy and duration of protection affect a gonorrhoea vaccine's value, have not been assessed. Methods We developed an integrated transmission-dynamic health-economic model, calibrated using Bayesian methods to surveillance data (from the Genitourinary Medicine Clinic Activity Dataset and the Gonococcal Resistance to Antimicrobials Surveillance Programme) on men who have sex with men (MSM) in England. We considered vaccination of MSM from the perspective of sexual health clinics, with and without vaccination offered to all adolescents in schools (vaccination before entry [VbE]), comparing three realistic approaches to targeting: vaccination on attendance (VoA) for testing; vaccination on diagnosis (VoD) with gonorrhoea; or vaccination according to risk (VaR), offered to patients diagnosed with gonorrhoea plus individuals who test negative but report having more than five sexual partners per year. For the primary analysis, vaccine impact was assessed relative to no vaccination in a conservative baseline scenario wherein time-varying behavioural parameters (sexual risk behaviour and screening rates) stabilise. To calculate the value of vaccination per dose administered, the value of vaccination was calculated by summing the averted costs of testing and treatment, and the monetary value of quality-adjusted life-year (QALY) gains with a QALY valued at £20 000. Costs were in 2018–19 GB£, and both costs and QALYs were discounted at 3·5% per year. We analysed the effects of varying vaccine uptake (0·5, 1, or 2 times HPV vaccine uptake by MSM in sexual health clinics in England), vaccine efficacy (1–100%) and duration of protection (1–20 years), and the time-horizon considered (10 years and 20 years). In addition, we calculated incremental cost-effectiveness ratios for the use of 4CMenB using assumed vaccine prices. Findings VbE has little impact on gonorrhoea diagnoses, with only 1·7% of MSM vaccinated per year. VoA has the largest impact but requires more vaccine doses than any other strategy, whereas VoD has a moderate impact but requires many fewer doses than VoA. VaR has almost the same impact as VoA but with fewer doses administered than VoA. VaR is the most cost-effective strategy for vaccines of moderate efficacy or duration of protection (or both), although VoD is more cost-effective for very protective and long-lasting vaccines. Even under conservative assumptions (efficacy equivalent to that of MeNZB and protection lasting for 18 months after two-dose primary vaccination and 36 months after single-dose booster vaccination), 4CMenB administered under VaR would likely be cost-saving at its current National Health Service price, averting an estimated mean 110 200 cases (95% credible interval 36 500–223 600), gaining a mean 100·3 QALYs (31·0–215·8), and saving a mean £7·9 million (0·0–20·5) over 10 years. A hypothetical gonorrhoea vaccine's value is increased more by improving its efficacy than its duration of protection—eg, 30% protection lasting 2 years has a median value of £48 (22–85) per dose over 10 years; doubling efficacy increases the value to £102 (53–144) whereas doubling the duration of protection increases it to £72 (34–120). Interpretation We recommend that vaccination of MSM against gonorrhoea according to risk in sexual health clinics in England with the 4CMenB vaccine be considered. Development of gonorrhoea-specific vaccines should prioritise maximising efficacy over duration of protection. Funding Medical Research Council (UK), National Institute for Health Research (UK).
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Affiliation(s)
- Lilith K Whittles
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, UK
| | - Xavier Didelot
- School of Life Sciences, University of Warwick, Coventry, UK; Department of Statistics, University of Warwick, Coventry, UK; NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Coventry, UK
| | - Peter J White
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, UK; Modelling and Economics Unit, National Infection Service, Public Health England, London, UK.
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The non-pharmaceutical interventions may affect the advantage in transmission of mutated variants during epidemics: A conceptual model for COVID-19. J Theor Biol 2022; 542:111105. [PMID: 35331730 PMCID: PMC8934756 DOI: 10.1016/j.jtbi.2022.111105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/25/2022]
Abstract
As the COVID-19 pandemic continues, genetic mutations in SARS-CoV-2 emerge, and some of them are found more contagious than the previously identified strains, acting as the major mechanism for many large-scale epidemics. The transmission advantage of mutated variants is widely believed as an innate biological feature that is difficult to be altered by artificial factors. In this study, we explore how non-pharmaceutical interventions (NPI) may affect transmission advantage. A two-strain compartmental epidemic model is proposed and simulated to investigate the biological mechanism of the relationships among different NPIs, the changes in transmissibility of each strain and transmission advantage. Although the NPIs are effective in flattening the epidemic curve, we demonstrate that NPIs probably lead to a decline in transmission advantage, which is likely to occur if the NPIs become intensive. Our findings uncover the mechanistic relationship between NPIs and transmission advantage dynamically, and highlight the important role of NPIs not only in controlling the intensity of epidemics but also in slowing or even containing the growth of the proportion of variants.
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11
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Barlow E, Morton A, Megiddo I, Colson A. Optimal subscription models to pay for antibiotics. Soc Sci Med 2022; 298:114818. [PMID: 35247782 PMCID: PMC9005781 DOI: 10.1016/j.socscimed.2022.114818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
Novel subscription payment schemes are one of the approaches being explored to tackle the threat of antimicrobial resistance. Under these schemes, some or all of the payment is made via a fixed “subscription” payment, which provides a funder unlimited access to the treatment for a specific duration, rather than relying purely on a price per pill. Subscription-based schemes guarantee pharmaceutical firms income that incentivises investment in developing new antibiotics, and can promote responsible stewardship. From the pharmaceutical perspective, revenue is disassociated from sales, removing benefits from push marketing strategies. We investigate this from the funder perspective, and consider that the funder plays a key role in promoting responsible antibiotic stewardship by choosing the price per pill for providers such that this encourages appropriate antibiotic use. This choice determines the payment structure, and we investigate the impact of this choice through the lens of social welfare. We present a mathematical model of subscription payment schemes, explicitly featuring fixed and volume-based payment components for a given treatment price. Total welfare returned at a societal level is then estimated (incorporating financial costs and monetised benefits). We consider a practical application of the model to development of novel antibiotic treatment for Gonorrhoea, and examine the optimal treatment price under different parameterisations. Specifically, we analyse two contrasting scenarios - one where a new antibiotic's prioritised role is reducing transmission, and one where a more pressing requirement is conserving the antibiotic as an effective last defence. Critically, this analysis demonstrates that effective roll-out of a subscription payment scheme for a new antibiotic requires a comprehensive assessment of the benefits gained from treatment. We discuss the insights this work presents on the nature of these payment schemes, and how these insights can enable decision-makers to take the first steps in determining effective structuring of subscription payment schemes. Policymakers and insurers are currently designing antibiotics subscription schemes. Social welfare returned from these payment schemes is modelled mathematically. Payment structures maximising social welfare are identified under different scenarios. If reduced transmission is a priority, subscription-only payments are near-optimal. If preserving an antibiotic is a priority, optimal structures include per-use payments.
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Affiliation(s)
- Euan Barlow
- Department of Management Science, Strathclyde Business School, University of Strathclyde, Glasgow, UK.
| | - Alec Morton
- Department of Management Science, Strathclyde Business School, University of Strathclyde, Glasgow, UK
| | - Itamar Megiddo
- Department of Management Science, Strathclyde Business School, University of Strathclyde, Glasgow, UK
| | - Abigail Colson
- Department of Management Science, Strathclyde Business School, University of Strathclyde, Glasgow, UK
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12
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A multiplex molecular assay for detection of six penA codons to predict decreased susceptibility to cephalosporins in
Neisseria gonorrhoeae. Antimicrob Agents Chemother 2022; 66:e0170921. [DOI: 10.1128/aac.01709-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emerging cephalosporin-resistant
Neisseria gonorrhoeae
poses an urgent threat to the continued efficacy of the last-line monotherapy for gonorrhea. Consequently, high-throughput, accurate, and reasonable molecular assays are urgently needed for strengthening antimicrobial-resistance surveillance in
N. gonorrhoeae
. In this study, we designed a high-throughput multiplex method that incorporates high-resolution melting technology and is based on a 6-codon assay (among the most parsimonious assays) developed following comprehensive and systematic reviews. The results showed that our method can precisely distinguish specific single-nucleotide polymorphisms in resistance-associated genes with a specificity and sensitivity of 100% and a detection limit as low as 10 copies per reaction. This method can be directly applied to clinical samples without cumbersome culture and successfully predicted all cephalosporin-resistant isolates (sensitivity: 100%). The method presented here represents a technique for rapid testing of antimicrobial resistance and will serve as a valuable tool for tailor-made antimicrobial therapy and for monitoring the transmission of cephalosporin-resistant strains.
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13
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Kanesaka I, Ohno A, Katsuse AK, Takahashi H, Kobayashi I. The emergence of the ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone by transfer of resistance from an oral Neisseria subflava reservoir of resistance. J Antimicrob Chemother 2021; 77:364-373. [PMID: 34747462 DOI: 10.1093/jac/dkab390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/05/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone was first discovered in Japan in 2015. OBJECTIVES We investigated the possibility of horizontal gene transfer from Neisseria subflava harbouring the mosaic-like PBP-2 in the emergence of the FC428 clone. We also analysed whether there were fitness costs associated with the sustained international dissemination of the clone. METHODS Sequencing of the penA gene in ceftriaxone-resistant N. subflava strains was performed. For transformation experiments between donor N. subflava and ciprofloxacin-resistant wild-type penA N. gonorrhoeae recipient, the full-length PCR amplification product of the penA gene, including DUS regions, was used as the donor DNA. Biological fitness of the transformants was measured by growth competition assays. The impact of QRDR and mtrR mutations, which have been reported as compensatory mutations, on fitness was also assessed. RESULTS The penA mosaic allele of the FC428 clone showed 100%, 91.8%, and 89.8% homology, respectively, with penA genes of three ceftriaxone-resistant N. subflava strains, No. 30, No. 9 and No. 14. Results were consistent with homologous recombination with the donated penA mosaic allele. In co-cultures with the parent strain, transformants showed comparable growth indicating that a gyrA mutation compensates for the fitness cost of mosaic penA alleles. CONCLUSIONS Our findings support the hypothesis that the FC428 clone was generated by transformation of the mosaic penA allele from oropharyngeal N. subflava to N. gonorrhoeae. Furthermore, it suggests that mutations in the gyrA QRDR region compensate for fitness costs and contribute to the continued transmission of the FC428 clone.
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Affiliation(s)
- Izumo Kanesaka
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, 4-16-20, Omori-nishi, Ota-ku, Tokyo 143-0015, Japan
| | - Akira Ohno
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, 4-16-20, Omori-nishi, Ota-ku, Tokyo 143-0015, Japan
| | - Akiko Kanayama Katsuse
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, 4-16-20, Omori-nishi, Ota-ku, Tokyo 143-0015, Japan
| | - Hiroshi Takahashi
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, 4-16-20, Omori-nishi, Ota-ku, Tokyo 143-0015, Japan
| | - Intetsu Kobayashi
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, 4-16-20, Omori-nishi, Ota-ku, Tokyo 143-0015, Japan
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14
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Ladhani SN, Borrow R, Ramsay ME. Killing 2 Cocci With 1 Vaccine: Unleashing the Full Potential of an Adolescent Meningococcal B Immunization Program. Clin Infect Dis 2021; 73:e238-e240. [PMID: 33340311 DOI: 10.1093/cid/ciaa1644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shamez N Ladhani
- Immunisation and Countermeasures Division, Public Health England, London, United Kingdom.,Paediatric Infectious Diseases Research Group, St. George's University of London, London, United Kingdom
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom
| | - Mary E Ramsay
- Immunisation and Countermeasures Division, Public Health England, London, United Kingdom.,London School of Hygiene and Tropical Medicine, London, United Kingdom
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15
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Yahara K, Ma KC, Mortimer TD, Shimuta K, Nakayama SI, Hirabayashi A, Suzuki M, Jinnai M, Ohya H, Kuroki T, Watanabe Y, Yasuda M, Deguchi T, Eldholm V, Harrison OB, Maiden MCJ, Grad YH, Ohnishi M. Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae. Genome Med 2021; 13:51. [PMID: 33785063 PMCID: PMC8008663 DOI: 10.1186/s13073-021-00860-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Antimicrobial resistance in Neisseria gonorrhoeae is a global health concern. Strains from two internationally circulating sequence types, ST-7363 and ST-1901, have acquired resistance to third-generation cephalosporins, mainly due to mosaic penA alleles. These two STs were first detected in Japan; however, the timeline, mechanism, and process of emergence and spread of these mosaic penA alleles to other countries remain unknown. METHODS We studied the evolution of penA alleles by obtaining the complete genomes from three Japanese ST-1901 clinical isolates harboring mosaic penA allele 34 (penA-34) dating from 2005 and generating a phylogenetic representation of 1075 strains sampled from 35 countries. We also sequenced the genomes of 103 Japanese ST-7363 N. gonorrhoeae isolates from 1996 to 2005 and reconstructed a phylogeny including 88 previously sequenced genomes. RESULTS Based on an estimate of the time-of-emergence of ST-1901 (harboring mosaic penA-34) and ST-7363 (harboring mosaic penA-10), and > 300 additional genome sequences of Japanese strains representing multiple STs isolated in 1996-2015, we suggest that penA-34 in ST-1901 was generated from penA-10 via recombination with another Neisseria species, followed by recombination with a gonococcal strain harboring wildtype penA-1. Following the acquisition of penA-10 in ST-7363, a dominant sub-lineage rapidly acquired fluoroquinolone resistance mutations at GyrA 95 and ParC 87-88, by independent mutations rather than horizontal gene transfer. Data in the literature suggest that the emergence of these resistance determinants may reflect selection from the standard treatment regimens in Japan at that time. CONCLUSIONS Our findings highlight how antibiotic use and recombination across and within Neisseria species intersect in driving the emergence and spread of drug-resistant gonorrhea.
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Affiliation(s)
- Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ken Shimuta
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Michio Jinnai
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Hitomi Ohya
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Toshiro Kuroki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
- Present address: Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari, Ehime, 794-8555, Japan
| | - Yuko Watanabe
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Mitsuru Yasuda
- Center for Nutrition Support and Infection Control, Gifu University Hospital, Gifu, Japan
| | - Takashi Deguchi
- Department of Urology, Kizawa Memorial Hospital, Gifu, Japan
| | - Vegard Eldholm
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
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16
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Vegvari C, Grad YH, White PJ, Didelot X, Whittles LK, Scangarella-Oman NE, Mitrani-Gold FS, Dumont E, Perry CR, Gilchrist K, Hossain M, Mortimer TD, Anderson RM, Gardiner D. Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea. ACTA ACUST UNITED AC 2021; 25. [PMID: 33124551 PMCID: PMC7596916 DOI: 10.2807/1560-7917.es.2020.25.43.1900210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background The first cases of extensively drug resistant gonorrhoea were recorded in the United Kingdom in 2018. There is a public health need for strategies on how to deploy existing and novel antibiotics to minimise the risk of resistance development. As rapid point-of-care tests (POCTs) to predict susceptibility are coming to clinical use, coupling the introduction of an antibiotic with diagnostics that can slow resistance emergence may offer a novel paradigm for maximising antibiotic benefits. Gepotidacin is a novel antibiotic with known resistance and resistance-predisposing mutations. In particular, a mutation that confers resistance to ciprofloxacin acts as the ‘stepping-stone’ mutation to gepotidacin resistance. Aim To investigate how POCTs detecting Neisseria gonorrhoeae resistance mutations for ciprofloxacin and gepotidacin can be used to minimise the risk of resistance development to gepotidacin. Methods We use individual-based stochastic simulations to formally investigate the aim. Results The level of testing needed to reduce the risk of resistance development depends on the mutation rate under treatment and the prevalence of stepping-stone mutations. A POCT is most effective if the mutation rate under antibiotic treatment is no more than two orders of magnitude above the mutation rate without treatment and the prevalence of stepping-stone mutations is 1–13%. Conclusion Mutation frequencies and rates should be considered when estimating the POCT usage required to reduce the risk of resistance development in a given population. Molecular POCTs for resistance mutations and stepping-stone mutations to resistance are likely to become important tools in antibiotic stewardship.
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Affiliation(s)
- Carolin Vegvari
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Yonatan H Grad
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Peter J White
- Modelling and Economics Unit, National Infection Service, Public Health England, London, United Kingdom.,MRC Centre for Global Infectious Disease Analysis and NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Xavier Didelot
- Current affiliation: School of Life Sciences and Department of Statistics, University of Warwick, United Kingdom.,MRC Centre for Global Infectious Disease Analysis and NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis and NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | | | | | - Etienne Dumont
- GlaxoSmithKline, Collegeville, Pennsylvania, United States
| | | | - Kim Gilchrist
- Current affiliation: Pfizer, Inc, Pennsylvania, United States.,GlaxoSmithKline, Collegeville, Pennsylvania, United States
| | | | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Roy M Anderson
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - David Gardiner
- GlaxoSmithKline, Collegeville, Pennsylvania, United States
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17
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Volz EM, Carsten W, Grad YH, Frost SDW, Dennis AM, Didelot X. Identification of Hidden Population Structure in Time-Scaled Phylogenies. Syst Biol 2021; 69:884-896. [PMID: 32049340 PMCID: PMC8559910 DOI: 10.1093/sysbio/syaa009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/09/2020] [Accepted: 01/23/2020] [Indexed: 11/13/2022] Open
Abstract
Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealized genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance. [Antimicrobial resistance; coalescent; HIV; population structure.].
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Affiliation(s)
- Erik M Volz
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, Imperial College London, Norfolk Place, W2 1PG London, UK
| | - Wiuf Carsten
- Department of Mathematical Sciences, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, TH Chan School of Public Health, Harvard University, 677 Huntington Ave, Boston, MA 02115, USA
| | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, UK.,The Alan Turing Institute, 96 Euston Rd, London NW1 2DB, London, UK
| | - Ann M Dennis
- Department of Medicine, University of North Carolina Chapel Hill, 321 S Columbia St, Chapel Hill, NC 27516, USA
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, CV4 7AL, UK
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18
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Whittles LK, White PJ, Didelot X. Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics. Clin Infect Dis 2020; 71:1912-1919. [PMID: 31905399 PMCID: PMC7643747 DOI: 10.1093/cid/ciz1241] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/02/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Gonorrhea incidence is increasing rapidly in many countries, while antibiotic resistance is making treatment more difficult. Combined with evidence that two meningococcal vaccines are likely partially protective against gonorrhea, this has renewed interest in a gonococcal vaccine, and several candidates are in development. Key questions are how protective and long-lasting a vaccine needs to be, and how to target it. We assessed vaccination's potential impact and the feasibility of achieving the World Health Organization's (WHO) target of reducing gonorrhea incidence by 90% during 2018-2030, by comparing realistic vaccination strategies under a range of scenarios of vaccine efficacy and duration of protection, and emergence of extensively-resistant gonorrhea. METHODS We developed a stochastic transmission-dynamic model, incorporating asymptomatic and symptomatic infection and heterogeneous sexual behavior in men who have sex with men (MSM). We used data from England, which has a comprehensive, consistent nationwide surveillance system. Using particle Markov chain Monte Carlo methods, we fitted to gonorrhea incidence in 2008-2017, then used Bayesian forecasting to examine an extensive range of scenarios. RESULTS Even in the worst-case scenario of untreatable infection emerging, the WHO target is achievable if all MSM attending sexual health clinics receive a vaccine offering ≥ 52% protection for ≥ 6 years. A vaccine conferring 31% protection (as estimated for MeNZB) for 2-4 years could reduce incidence in 2030 by 45% in the worst-case scenario, and by 75% if > 70% of resistant gonorrhea remains treatable. CONCLUSIONS Even a partially-protective vaccine, delivered through a realistic targeting strategy, could substantially reduce gonorrhea incidence, despite antibiotic resistance.
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Affiliation(s)
- Lilith K Whittles
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling Methodology, School of Public Health, Imperial College London, London, United Kingdom
| | - Peter J White
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling Methodology, School of Public Health, Imperial College London, London, United Kingdom
- Modelling and Economics Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Xavier Didelot
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
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19
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Men and Women Have Similar Neisseria gonorrhoeae Bacterial Loads: a Comparison of Three Anatomical Sites. J Clin Microbiol 2020; 58:JCM.01171-20. [PMID: 32817230 DOI: 10.1128/jcm.01171-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/08/2020] [Indexed: 02/07/2023] Open
Abstract
Neisseria gonorrhoeae is a common bacterial sexually transmitted infection (STI). Currently, there are limited data on the bacterial load in both men and women and on both genital and extragenital sites. Therefore, we quantified N. gonorrhoeae bacterial loads in a large population of women, heterosexual men, and men who have sex with men (MSM) at three different anatomical sites. N. gonorrhoeae-positive samples (n = 1265) of STI clinic consultations (n = 944) were tested for N. gonorrhoeae with the Roche Cobas 4800 system, and quantification cycle (Cq) values were used as an inversely proportional measure for N. gonorrhoeae bacterial load after interpolation from a standard curve. Bacterial loads were compared between sample materials and sexes using t tests. The following mean N. gonorrhoeae loads were observed: urine, 4.5 ± 1.0 log10 CFU/ml; vaginal swabs, 4.3 ± 1.1 log10 CFU/ml; anorectal swabs (women), 4.0 ± 1.2 log10 CFU/ml; anorectal swabs (men), 4.5 ± 1.3 log10 CFU/ml; oropharyngeal swabs (women), 2.8 ± 0.9 log10 CFU/ml; and oropharyngeal swabs (men), 3.2 ± 1.0 log10 CFU/ml. Oropharyngeal swabs had a significantly lower N. gonorrhoeae load (P < 0.001) than genital and anorectal samples. Loads did not differ between men and women. This is the first study that determined N. gonorrhoeae load in both women and men at three anatomical sites. The substantial N. gonorrhoeae load at all sample sites suggest that all sites may have transmission potential. However, the oropharyngeal site presents the lowest bacterial load. Men and women have a similar N. gonorrhoeae loads on separate anatomical sites, arguing for similar transmission potential and similar clinical relevance.
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20
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Strong Environment-Genotype Interactions Determine the Fitness Costs of Antibiotic Resistance In Vitro and in an Insect Model of Infection. Antimicrob Agents Chemother 2020; 64:AAC.01033-20. [PMID: 32661001 DOI: 10.1128/aac.01033-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/08/2020] [Indexed: 11/20/2022] Open
Abstract
The acquisition of antibiotic resistance commonly imposes fitness costs, a reduction in the fitness of bacteria in the absence of drugs. These costs have been quantified primarily using in vitro experiments and a small number of in vivo studies in mice, and it is commonly assumed that these diverse methods are consistent. Here, we used an insect model of infection to compare the fitness costs of antibiotic resistance in vivo to those in vitro Experiments explored diverse mechanisms of resistance in a Gram-positive pathogen, Bacillus thuringiensis, and a Gram-negative intestinal symbiont, Enterobacter cloacae Rifampin resistance in B. thuringiensis showed fitness costs that were typically elevated in vivo, although these were modulated by genotype-environment interactions. In contrast, resistance to cefotaxime via derepression of AmpC β-lactamase in E. cloacae resulted in no detectable costs in vivo or in vitro, while spontaneous resistance to nalidixic acid, and carriage of the IncP plasmid RP4, imposed costs that increased in vivo Overall, fitness costs in vitro were a poor predictor of fitness costs in vivo because of strong genotype-environment interactions throughout this study. Insect infections provide a cheap and accessible means of assessing the fitness consequences of resistance mutations, data that are important for understanding the evolution and spread of resistance. This study emphasizes that the fitness costs imposed by particular mutations or different modes of resistance are extremely variable and that only a subset of these mutations is likely to be prevalent outside the laboratory.
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21
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Zhang J, van der Veen S. Neisseria gonorrhoeae 23S rRNA A2059G mutation is the only determinant necessary for high-level azithromycin resistance and improves in vivo biological fitness. J Antimicrob Chemother 2020; 74:407-415. [PMID: 30376120 DOI: 10.1093/jac/dky438] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Objectives The global emergence of Neisseria gonorrhoeae isolates displaying high-level azithromycin resistance is a major concern for the currently recommended azithromycin/ceftriaxone dual therapy. N. gonorrhoeae high-level azithromycin resistance has been associated with an A2059G mutation in 23S rRNA. Here we investigated the specific contribution of this 23S rRNA A2059G mutation to high-level azithromycin resistance and its impact on biological fitness. Methods A2059G/G2059A alleles were specifically cloned into all four genomic copies of 23S rDNA of an azithromycin-susceptible isolate and a high-level azithromycin-resistant isolate. WT and mutant strains were subsequently investigated for azithromycin susceptibility using the agar dilution method. In addition, their biological fitness was studied by comparative liquid growth in the presence of hydrophobic and amphipathic compounds, by competition assays in a mouse vaginal tract infection model and by competition assays for invasion and intracellular survival. Results Azithromycin susceptibility analyses showed that the 23S rRNA A2059G mutation is the only genetic determinant required for N. gonorrhoeae to display the high-level azithromycin resistance phenotype. Further analysis of biological fitness showed that strains containing 2059G outcompeted isogenic strains containing 2059A for colonization in the mouse vaginal tract infection model and for invasion of HeLa cervical epithelial cells. Furthermore, the A2059G mutation enhanced growth in the presence of lithocholic acid or Triton X-100. Conclusions Our findings that the 23S rRNA A2059G mutation is sufficient for high-level azithromycin resistance and that this mutation generally enhanced the biological fitness of N. gonorrhoeae have important implications for the currently recommended treatment policies and antimicrobial stewardship programmes.
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Affiliation(s)
- Jianglin Zhang
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Stijn van der Veen
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Dermatology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Yaesoubi R, Cohen T, Hsu K, Gift TL, Chesson H, Salomon JA, Grad YH. Adaptive guidelines for the treatment of gonorrhea to increase the effective life span of antibiotics among men who have sex with men in the United States: A mathematical modeling study. PLoS Med 2020; 17:e1003077. [PMID: 32243443 PMCID: PMC7122693 DOI: 10.1371/journal.pmed.1003077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The rise of gonococcal antimicrobial resistance highlights the need for strategies that extend the clinically useful life span of antibiotics. Because there is limited evidence to support the current practice of switching empiric first-line antibiotic when resistance exceeds 5% in the population, our objective was to compare the impact of alternative strategies on the effective life spans of antibiotics and the overall burden of gonorrhea. METHODS AND FINDINGS We developed and calibrated a mathematical model of gonorrhea transmission among men who have sex with men (MSM) in the United States. We calibrated the model to the estimated prevalence of gonorrhea, the rate of gonorrhea cases, and the proportion of cases presenting symptoms among MSM in the US. We used this model to project the effective life span of antibiotics and the number of gonorrhea cases expected under current and alternative surveillance strategies over a 50-year simulation period. We demonstrate that compared to the current practice, a strategy that uses quarterly (as opposed to yearly) surveillance estimates and incorporates both the estimated prevalence of resistance and the trend in the prevalence of resistance to determine treatment guidelines could extend the effective life span of antibiotics by 0.83 years. This is equivalent to successfully treating an additional 80.1 (95% uncertainty interval: [47.7, 111.9]) gonorrhea cases per 100,000 MSM population each year with the first-line antibiotics without worsening the burden of gonorrhea. If the annual number of isolates tested for drug susceptibility is doubled, this strategy could increase the effective life span of antibiotics by 0.94 years, which is equivalent to successfully treating an additional 91.1 (54.3, 127.3) gonorrhea cases per 100,000 MSM population each year without increasing the incidence of gonorrhea. Study limitations include that our conclusions might not be generalizable to other settings because our model describes the transmission of gonorrhea among the US MSM population, and, to better capture uncertainty in the characteristics of current and future antibiotics, we chose to model hypothetical drugs with characteristics similar to the antibiotics commonly used in gonorrhea treatment. CONCLUSIONS Our results suggest that use of data from surveillance programs could be expanded to prolong the clinical effectiveness of antibiotics without increasing the burden of the disease. This highlights the importance of maintaining effective surveillance systems and the engagement of policy makers to turn surveillance findings into timely and effective decisions.
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Affiliation(s)
- Reza Yaesoubi
- Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, United States of America
- * E-mail:
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Katherine Hsu
- Massachusetts Department of Public Health, Boston, Massachusetts, United States of America
| | - Thomas L. Gift
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Harrell Chesson
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joshua A. Salomon
- Center for Primary Care & Outcomes Research, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
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Chen HH, Stringer A, Eguale T, Rao GG, Ozawa S. Impact of Antibiotic Resistance on Treatment of Pneumococcal Disease in Ethiopia: An Agent-Based Modeling Simulation. Am J Trop Med Hyg 2020; 101:1042-1053. [PMID: 31516111 DOI: 10.4269/ajtmh.18-0930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antimicrobial resistance (AMR) is a growing threat to global health. Although AMR endangers continued effectiveness of antibiotics, the impact of AMR has been poorly estimated in low-income countries. This study sought to quantify the effect of AMR on treatments for pediatric pneumococcal disease in Ethiopia. We developed the DREAMR (Dynamic Representation of the Economics of AMR) model that simulate children younger than 5 years who acquire pneumococcal disease (pneumonia, meningitis, and acute otitis media) and seek treatment from various health facilities in Ethiopia over a year. We examined the AMR levels of three antibiotics (penicillin, amoxicillin, and ceftriaxone), treatment failures, and attributable deaths. We used the cost-of-illness method to assess the resulting economic impact of AMR from a societal perspective by estimating the direct and indirect treatment costs and productivity losses. Findings showed that AMR against antibiotics that were used to treat pneumococcal disease led to 195,763 treatment failures per year, which contributed to 2,925 child deaths annually in Ethiopia. Antimicrobial resistance resulted in a first-line treatment failure rate of 29.4%. In 1 year, the proportion of nonsusceptible Streptococcus pneumoniae bacteria increased by 2.1% and 0.5% for amoxicillin and penicillin, and reduced by 0.3% for less commonly used ceftriaxone. Annual costs of AMR to treat pneumococcal disease were around US$15.8 million, including US$3.3 million for ineffective first-line treatments, US$3.7 million for second-line treatments, and US$8.9 million for long-term productivity losses. Antibiotic stewardship to reduce misuse and overuse of antibiotics is essential to maintain the effectiveness of antibiotics, and lessen the health and economic burden of AMR.
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Affiliation(s)
- Hui-Han Chen
- Division of Practice Advancement and Clinical Education, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrew Stringer
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gauri G Rao
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sachiko Ozawa
- Division of Practice Advancement and Clinical Education, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Maternal and Child Health, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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24
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Knight GM, Davies NG, Colijn C, Coll F, Donker T, Gifford DR, Glover RE, Jit M, Klemm E, Lehtinen S, Lindsay JA, Lipsitch M, Llewelyn MJ, Mateus ALP, Robotham JV, Sharland M, Stekel D, Yakob L, Atkins KE. Mathematical modelling for antibiotic resistance control policy: do we know enough? BMC Infect Dis 2019; 19:1011. [PMID: 31783803 PMCID: PMC6884858 DOI: 10.1186/s12879-019-4630-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Antibiotics remain the cornerstone of modern medicine. Yet there exists an inherent dilemma in their use: we are able to prevent harm by administering antibiotic treatment as necessary to both humans and animals, but we must be mindful of limiting the spread of resistance and safeguarding the efficacy of antibiotics for current and future generations. Policies that strike the right balance must be informed by a transparent rationale that relies on a robust evidence base. MAIN TEXT One way to generate the evidence base needed to inform policies for managing antibiotic resistance is by using mathematical models. These models can distil the key drivers of the dynamics of resistance transmission from complex infection and evolutionary processes, as well as predict likely responses to policy change in silico. Here, we ask whether we know enough about antibiotic resistance for mathematical modelling to robustly and effectively inform policy. We consider in turn the challenges associated with capturing antibiotic resistance evolution using mathematical models, and with translating mathematical modelling evidence into policy. CONCLUSIONS We suggest that in spite of promising advances, we lack a complete understanding of key principles. From this we advocate for priority areas of future empirical and theoretical research.
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Affiliation(s)
- Gwenan M Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
| | - Nicholas G Davies
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Francesc Coll
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, LSHTM, London, UK
| | - Tjibbe Donker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Danna R Gifford
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Rebecca E Glover
- Department of Health Services Research and Policy, Faculty of Public Health and Policy, LSHTM, London, UK
| | - Mark Jit
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | | | - Sonja Lehtinen
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jodi A Lindsay
- Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London, UK
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Martin J Llewelyn
- Department of Global Health and Infection, Brighton and Sussex Medical School, Brighton, UK
| | - Ana L P Mateus
- Population Sciences and Pathobiology Department, Royal Veterinary College, London, UK
| | - Julie V Robotham
- Modelling and Economics Unit, National Infection Service, Public Health England, London, UK
| | - Mike Sharland
- Paediatric Infectious Disease Research Group, St George's University of London, London, UK
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Loughborough, UK
| | - Laith Yakob
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, LSHTM, London, UK
| | - Katherine E Atkins
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
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Negative frequency dependent selection on plasmid carriage and low fitness costs maintain extended spectrum β-lactamases in Escherichia coli. Sci Rep 2019; 9:17211. [PMID: 31748602 PMCID: PMC6868128 DOI: 10.1038/s41598-019-53575-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/22/2019] [Indexed: 12/16/2022] Open
Abstract
Plasmids may maintain antibiotic resistance genes in bacterial populations through conjugation, in the absence of direct selection pressure. However, the costs and benefits of conjugation for plasmid and bacterial fitness are not well understood. Using invasion and competition experiments with plasmid mutants we explicitly tested how conjugation contributes to the maintenance of a plasmid bearing a single extended-spectrum ß-lactamase (ESBL) gene (blaCTX-M-14). Surprisingly, conjugation had little impact on overall frequencies, although it imposed a substantial fitness cost. Instead, stability resulted from the plasmid conferring fitness benefits when rare. Frequency dependent fitness did not require a functional blaCTX-M-14 gene, and was independent of culture media. Fitness benefits when rare are associated with the core plasmid backbone but are able to drive up frequencies of antibiotic resistance because fitness burden of the blaCTX-M-14 gene is very low. Negative frequency dependent fitness can contribute to maintaining a stable frequency of resistance genes in the absence of selection pressure from antimicrobials. In addition, persistent, low cost resistance has broad implications for antimicrobial stewardship.
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26
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Smid JH, Althaus CL, Low N, Unemo M, Herrmann B. Rise and fall of the new variant of Chlamydia trachomatis in Sweden: mathematical modelling study. Sex Transm Infect 2019; 96:375-379. [PMID: 31586947 PMCID: PMC7402554 DOI: 10.1136/sextrans-2019-054057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/13/2019] [Accepted: 09/23/2019] [Indexed: 02/04/2023] Open
Abstract
Objectives A new variant of Chlamydia trachomatis (nvCT) was discovered in Sweden in 2006. The nvCT has a plasmid deletion, which escaped detection by two nucleic acid amplification tests (Abbott-Roche, AR), which were used in 14 of 21 Swedish counties. The objectives of this study were to assess when and where nvCT emerged in Sweden, the proportion of nvCT in each county and the role of a potential fitness difference between nvCT and co-circulating wild-type strains (wtCT). Methods We used a compartmental mathematical model describing the spatial and temporal spread of nvCT and wtCT. We parameterised the model using sexual behaviour data and Swedish spatial and demographic data. We used Bayesian inference to fit the model to surveillance data about reported diagnoses of chlamydia infection in each county and data from four counties that assessed the proportion of nvCT in multiple years. Results Model results indicated that nvCT emerged in central Sweden (Dalarna, Gävleborg, Västernorrland), reaching a proportion of 1% of prevalent CT infections in late 2002 or early 2003. The diagnostic selective advantage enabled rapid spread of nvCT in the presence of high treatment rates. After detection, the proportion of nvCT decreased from 30%–70% in AR counties and 5%–20% in counties that Becton Dickinson tests, to around 5% in 2015 in all counties. The decrease in nvCT was consistent with an estimated fitness cost of around 5% in transmissibility or 17% reduction in infectious duration. Conclusions We reconstructed the course of a natural experiment in which a mutant strain of C. trachomatis spread across Sweden. Our modelling study provides support, for the first time, of a reduced transmissibility or infectious duration of nvCT. This mathematical model improved our understanding of the first nvCT epidemic in Sweden and can be adapted to investigate the impact of future diagnostic escape mutants.
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Affiliation(s)
- Joost H Smid
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bjőrn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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27
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Zienkiewicz AK, Verschueren van Rees N, Homer M, Ong JJ, Christensen H, Hill D, Looker KJ, Horner P, Hughes G, Turner KME. Agent-based modelling study of antimicrobial-resistant Neisseria gonorrhoeae transmission in men who have sex with men: towards individualised diagnosis and treatment. Sex Health 2019; 16:514-522. [PMID: 31476277 DOI: 10.1071/sh18235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 07/29/2019] [Indexed: 12/15/2022]
Abstract
Background Antimicrobial-resistant (AMR) gonorrhoea is a global public health threat. Discriminatory point-of-care tests (POCT) to detect drug sensitivity are under development, enabling individualised resistance-guided therapy. METHODS An individual-based dynamic transmission model of gonorrhoea infection in MSM living in London has been developed, incorporating ciprofloxacin-sensitive and resistant strains. The time-dependent sexual contact network is captured by periodically restructuring active connections to reflect the transience of contacts. Different strategies to improve treatment selection were explored, including discriminatory POCT and selecting partner treatment based on either the index case or partner susceptibility. Outcomes included population prevalence of gonorrhoea and drug dose counts. RESULTS It is shown that using POCT to detect ciprofloxacin-sensitive infections could result in a large decrease in ceftriaxone doses (by 70% compared with the reference case in the simulations of this study). It also suggests that ceftriaxone use can be reduced with existing technologies, albeit to a lesser degree; either using index case sensitivity profiles to direct treatment of partners, or testing notified partners with strain discriminatory laboratory tests before treatment, reduced ceftriaxone use in our model (by 27% and 47% respectively). CONCLUSIONS POCT to detect ciprofloxacin-sensitive gonorrhoea are likely to dramatically reduce reliance on ceftriaxone, but requires the implementation of new technology. In the meantime, the proportion of unnecessary ceftriaxone treatment by testing partners before treatment could be reduced significantly. Alternatively, index case sensitivity profiles could be used to select effective treatments for partners.
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Affiliation(s)
- Adam K Zienkiewicz
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, UK; and School of Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol BS40 5DU, UK
| | - Nicolás Verschueren van Rees
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, UK; and School of Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol BS40 5DU, UK
| | - Martin Homer
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, UK
| | - Jason J Ong
- Clinical Research and Development, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; and Central Clinical School, Monash University, Clayton, Vic. 3800, Australia; and Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Hannah Christensen
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Darryl Hill
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Katharine J Looker
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Paddy Horner
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Gwenda Hughes
- Instituto de Medicina Tropical, Universidade de São Paulo, Avenuenida Dr Enéas Carvalho de Aguiar, 470, CEP 05403-000, São Paulo, Brasil; and Blood Safety, Hepatitis, STI & HIV Division, National Infection Service, Public Health England, NW9 5EQ, UK
| | - Katy M E Turner
- School of Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol BS40 5DU, UK; and Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; and Corresponding author.
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29
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Raymond B. Five rules for resistance management in the antibiotic apocalypse, a road map for integrated microbial management. Evol Appl 2019; 12:1079-1091. [PMID: 31297143 PMCID: PMC6597870 DOI: 10.1111/eva.12808] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Resistance to new antimicrobials can become widespread within 2-3 years. Resistance problems are particularly acute for bacteria that can experience selection as both harmless commensals and pathogenic hospital-acquired infections. New drugs, although welcome, cannot tackle the antimicrobial resistance crisis alone: new drugs must be partnered with more sustainable patterns of use. However, the broader experience of resistance management in other disciplines, and the assumptions on which resistance rests, is not widely appreciated in clinical and microbiological disciplines. Improved awareness of the field of resistance management could improve clinical outcomes and help shape novel solutions. Here, the aim is to develop a pragmatic approach to developing a sustainable integrated means of using antimicrobials, based on an interdisciplinary synthesis of best practice, recent theory and recent clinical data. This synthesis emphasizes the importance of pre-emptive action and the value of reducing the supply of genetic novelty to bacteria under selection. The weight of resistance management experience also cautions against strategies that over-rely on the fitness costs of resistance or low doses. The potential (and pitfalls) of shorter courses, antibiotic combinations and antibiotic mixing or cycling are discussed in depth. Importantly, some of variability in the success of clinical trials of mixing approaches can be explained by the number and diversity of drugs in a trial, as well as whether trials encompass single wards or the wider transmission network that is a hospital. Consideration of the importance of data, and of the initially low frequency of resistance, leads to a number of additional recommendations. Overall, reduction in selection pressure, interference with the transmission of problematic genotypes and multidrug approaches (combinations, mixing or cycling) are all likely to be required for sustainability and the protection of forthcoming drugs.
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30
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Whittles LK, White PJ, Didelot X. A dynamic power-law sexual network model of gonorrhoea outbreaks. PLoS Comput Biol 2019; 15:e1006748. [PMID: 30849080 PMCID: PMC6426262 DOI: 10.1371/journal.pcbi.1006748] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 03/20/2019] [Accepted: 01/04/2019] [Indexed: 11/26/2022] Open
Abstract
Human networks of sexual contacts are dynamic by nature, with partnerships forming and breaking continuously over time. Sexual behaviours are also highly heterogeneous, so that the number of partners reported by individuals over a given period of time is typically distributed as a power-law. Both the dynamism and heterogeneity of sexual partnerships are likely to have an effect in the patterns of spread of sexually transmitted diseases. To represent these two fundamental properties of sexual networks, we developed a stochastic process of dynamic partnership formation and dissolution, which results in power-law numbers of partners over time. Model parameters can be set to produce realistic conditions in terms of the exponent of the power-law distribution, of the number of individuals without relationships and of the average duration of relationships. Using an outbreak of antibiotic resistant gonorrhoea amongst men have sex with men as a case study, we show that our realistic dynamic network exhibits different properties compared to the frequently used static networks or homogeneous mixing models. We also consider an approximation to our dynamic network model in terms of a much simpler branching process. We estimate the parameters of the generation time distribution and offspring distribution which can be used for example in the context of outbreak reconstruction based on genomic data. Finally, we investigate the impact of a range of interventions against gonorrhoea, including increased condom use, more frequent screening and immunisation, concluding that the latter shows great promise to reduce the burden of gonorrhoea, even if the vaccine was only partially effective or applied to only a random subset of the population.
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Affiliation(s)
- Lilith K. Whittles
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Peter J. White
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Modelling and Economics Unit, National Infection Service, Public Health England, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- NIHR Health Protection Research Unit in Modelling Methodology, School of Public Health, Imperial College London, London, United Kingdom
| | - Xavier Didelot
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
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31
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Blanquart F. Evolutionary epidemiology models to predict the dynamics of antibiotic resistance. Evol Appl 2019; 12:365-383. [PMID: 30828361 PMCID: PMC6383707 DOI: 10.1111/eva.12753] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
The evolution of resistance to antibiotics is a major public health problem and an example of rapid adaptation under natural selection by antibiotics. The dynamics of antibiotic resistance within and between hosts can be understood in the light of mathematical models that describe the epidemiology and evolution of the bacterial population. "Between-host" models describe the spread of resistance in the host community, and in more specific settings such as hospitalized hosts (treated by antibiotics at a high rate), or farm animals. These models make predictions on the best strategies to limit the spread of resistance, such as reducing transmission or adapting the prescription of several antibiotics. Models can be fitted to epidemiological data in the context of intensive care units or hospitals to predict the impact of interventions on resistance. It has proven harder to explain the dynamics of resistance in the community at large, in particular because models often do not reproduce the observed coexistence of drug-sensitive and drug-resistant strains. "Within-host" models describe the evolution of resistance within the treated host. They show that the risk of resistance emergence is maximal at an intermediate antibiotic dose, and some models successfully explain experimental data. New models that include the complex host population structure, the interaction between resistance-determining loci and other loci, or integrating the within- and between-host levels will allow better interpretation of epidemiological and genomic data from common pathogens and better prediction of the evolution of resistance.
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Affiliation(s)
- François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERMPSL Research UniversityParisFrance
- IAME, UMR 1137, INSERMUniversité Paris DiderotParisFrance
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32
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Volz EM, Didelot X. Modeling the Growth and Decline of Pathogen Effective Population Size Provides Insight into Epidemic Dynamics and Drivers of Antimicrobial Resistance. Syst Biol 2018; 67:719-728. [PMID: 29432602 PMCID: PMC6005154 DOI: 10.1093/sysbio/syy007] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/04/2018] [Indexed: 12/15/2022] Open
Abstract
Nonparametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stochastic processes with stationary increments which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that nonparametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a nonparametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data are sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of \documentclass[12pt]{minimal}
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}{}$\beta$\end{document}-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://github.com/mrc-ide/skygrowth.
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Affiliation(s)
- Erik M Volz
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, W2 1PG, UK
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, W2 1PG, UK
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33
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Yahara K, Nakayama SI, Shimuta K, Lee KI, Morita M, Kawahata T, Kuroki T, Watanabe Y, Ohya H, Yasuda M, Deguchi T, Didelot X, Ohnishi M. Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microb Genom 2018; 4:e000205. [PMID: 30063202 PMCID: PMC6159555 DOI: 10.1099/mgen.0.000205] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
The first extensively drug resistant (XDR) Neisseria gonorrhoeae strain with high resistance to the extended-spectrum cephalosporin ceftriaxone was identified in 2009 in Japan, but no other strain with this antimicrobial-resistance profile has been reported since. However, surveillance to date has been based on phenotypic methods and sequence typing, not genome sequencing. Therefore, little is known about the local population structure at the genomic level, and how resistance determinants and lineages are distributed and evolve. We analysed the whole-genome sequence data and the antimicrobial-susceptibility testing results of 204 strains sampled in a region where the first XDR ceftriaxone-resistant N. gonorrhoeae was isolated, complemented with 67 additional genomes from other time frames and locations within Japan. Strains resistant to ceftriaxone were not found, but we discovered a sequence type (ST)7363 sub-lineage susceptible to ceftriaxone and cefixime in which the mosaic penA allele responsible for reduced susceptibility had reverted to a susceptible allele by recombination. Approximately 85 % of isolates showed resistance to fluoroquinolones (ciprofloxacin) explained by linked amino acid substitutions at positions 91 and 95 of GyrA with 99 % sensitivity and 100 % specificity. Approximately 10 % showed resistance to macrolides (azithromycin), for which genetic determinants are less clear. Furthermore, we revealed different evolutionary paths of the two major lineages: single acquisition of penA X in the ST7363-associated lineage, followed by multiple independent acquisitions of the penA X and XXXIV in the ST1901-associated lineage. Our study provides a detailed picture of the distribution of resistance determinants and disentangles the evolution of the two major lineages spreading worldwide.
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Affiliation(s)
- Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken-ichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takuya Kawahata
- Virology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Toshiro Kuroki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan
- Present address: Faculty of Veterinary Medicine, Okayama University of Science, 1-3, Ikoinooka, Imabari, Ehime 794-8555, Japan
| | - Yuko Watanabe
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan
| | - Hitomi Ohya
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan
| | - Mitsuru Yasuda
- Department of Urology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Takashi Deguchi
- Department of Urology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Makoto Ohnishi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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Whittles LK, White PJ, Paul J, Didelot X. Epidemiological Trends of Antibiotic Resistant Gonorrhoea in the United Kingdom. Antibiotics (Basel) 2018; 7:antibiotics7030060. [PMID: 30011825 PMCID: PMC6165062 DOI: 10.3390/antibiotics7030060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 11/16/2022] Open
Abstract
Gonorrhoea is one of the most common sexually-transmitted bacterial infections, globally and in the United Kingdom. The levels of antibiotic resistance in gonorrhoea reported in recent years represent a critical public health issue. From penicillins to cefixime, the gonococcus has become resistant to all antibiotics that have been previously used against it, in each case only a matter of years after introduction as a first-line therapy. After each instance of resistance emergence, the treatment recommendations have required revision, to the point that only a few antibiotics can reliably be prescribed to treat infected individuals. Most countries, including the UK, now recommend that gonorrhoea be treated with a dual therapy combining ceftriaxone and azithromycin. While this treatment is still currently effective for the vast majority of cases, there are concerning signs that this will not always remain the case, and there is no readily apparent alternative. Here, we review the use of antibiotics and epidemiological trends of antibiotic resistance in gonorrhoea from surveillance data over the past 15 years in the UK and describe how surveillance could be improved.
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Affiliation(s)
- Lilith K Whittles
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
| | - Peter J White
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
- MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London W2 1PG, UK.
- NIHR Health Protection Research Unit in Modelling Methodology, School of Public Health, Imperial College London, London W2 1PG, UK.
- Modelling and Economics Unit, National Infection Service, Public Health England, London NW9 5EQ, UK.
| | - John Paul
- Department of Microbiology, Public Health England Collaborative Centre, Royal Sussex County Hospital, Brighton BN2 5BE, UK.
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer BN1 9PH, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
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Whittles LK, Didelot X, Grad YH, White PJ. Testing for gonorrhoea should routinely include the pharynx. THE LANCET. INFECTIOUS DISEASES 2018; 18:716-717. [PMID: 29976520 PMCID: PMC7349805 DOI: 10.1016/s1473-3099(18)30341-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/14/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Lilith K Whittles
- MRC Centre for Outbreak Analysis and Modelling and NIHR Health Protection Research Unit in Modelling Methodology, Imperial College London, London, W2 1PG, UK
| | - Xavier Didelot
- MRC Centre for Outbreak Analysis and Modelling and NIHR Health Protection Research Unit in Modelling Methodology, Imperial College London, London, W2 1PG, UK
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter J White
- MRC Centre for Outbreak Analysis and Modelling and NIHR Health Protection Research Unit in Modelling Methodology, Imperial College London, London, W2 1PG, UK; Modelling and Economics Unit, National Infection Service, Public Health England, London, UK.
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Mortimer TD, Grad YH. Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae. Ann N Y Acad Sci 2018; 1435:93-109. [PMID: 29876934 DOI: 10.1111/nyas.13871] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
Abstract
Infections with Neisseria gonorrhoeae, a sexually transmitted pathogen that causes urethritis, cervicitis, and more severe complications, are increasing. Gonorrhea is typically treated with antibiotics; however, N. gonorrhoeae has rapidly acquired resistance to many antibiotic classes, and lineages with reduced susceptibility to the currently recommended therapies are emerging worldwide. In this review, we discuss the contributions of whole genome sequencing (WGS) to our understanding of resistant N. gonorrhoeae. Genomics has illuminated the evolutionary origins and population structure of N. gonorrhoeae and the magnitude of horizontal gene transfer within and between Neisseria species. WGS can be used to predict the susceptibility of N. gonorrhoeae based on known resistance determinants, track the spread of these determinants throughout the N. gonorrhoeae population, and identify novel loci contributing to resistance. WGS has also allowed more detailed epidemiological analysis of transmission of N. gonorrhoeae between individuals and populations than previously used typing methods. Ongoing N. gonorrhoeae genomics will complement other laboratory techniques to understand the biology and evolution of the pathogen, improve diagnostics and treatment in the clinic, and inform public health policies to limit the impact of antibiotic resistance.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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Abstract
In an Editorial, Guest Editors Nicola Low and Nathalie Broutet discuss the Collection on sexually transmitted infections in the context of research priorities in the field.
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Affiliation(s)
- Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nathalie J. Broutet
- Department of Reproductive Health Research, World Health Organization, Geneva, Switzerland
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Unemo M, Althaus CL. Fitness cost and benefit of antimicrobial resistance in Neisseria gonorrhoeae: Multidisciplinary approaches are needed. PLoS Med 2017; 14:e1002423. [PMID: 29088232 PMCID: PMC5663331 DOI: 10.1371/journal.pmed.1002423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In a Perspective on the research article by Didelot and colleagues, Magnus Unemo and Christian Althaus discuss the value of modelling studies to inform antimicrobial resistance management and the limitations of the current evidence base informing such models.
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Affiliation(s)
- Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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