1
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Padeniya TN, Hui BB, Wood JG, Regan DG, Seib KL. Review of mathematical models of Neisseria gonorrhoeae vaccine impact: Implications for vaccine development. Vaccine 2024:S0264-410X(24)00380-3. [PMID: 38556390 DOI: 10.1016/j.vaccine.2024.03.068] [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: 11/23/2023] [Revised: 03/04/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
An effective prophylactic vaccine for prevention of Neisseria gonorrhoeae infection would have a major impact on sexual and reproductive health worldwide. Interest in developing gonorrhoea vaccines is growing due to the reported high rates of N. gonorrhoeae infections globally, and the threat of antimicrobial resistance. Several gonorrhoea vaccine candidates are currently under evaluation and various mathematical models have been used to assess the potential population-level impact a gonorrhoea vaccine may have once available. Here we review key aspects of gonorrhoea vaccine mathematical modelling studies, including model structures, populations considered, and assumptions used as well as vaccine characteristics and implementation scenarios investigated. The predicted vaccine impact varied between studies, ranging from as little as ∼17 % reduction in N. gonorrhoeae prevalence after 30 years up to 100 % reduction after 5 years. However, all studies predicted that even a partially effective gonorrhoea vaccine could have a substantial impact in reducing N. gonorrhoeae prevalence or incidence, particularly when high coverage is achieved within either important risk groups or the overall sexually active population. As expected, higher vaccine efficacy against acquisition of N. gonorrhoeae and longer duration of protection were linked to greater reductions in infections. A vaccine that alters onward transmission could also substantially reduce infections. Several gaps and research needs have been identified by researchers in the field and via this narrative literature review. For example, future modelling to inform gonorrhoea vaccine development and implementation should consider additional populations that are at high risk of N. gonorrhoeae infection, especially in low- and middle-income settings, as well as the impact of vaccination on the potential adverse sexual and reproductive health outcomes of infection. In addition, more detailed and robust epidemiological, biological, and behavioural data is needed to enable more accurate and robust modelling of gonorrhoea vaccine impact to inform future scientific and public health decision-making.
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Affiliation(s)
- Thilini N Padeniya
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.
| | - Ben B Hui
- The Kirby Institute, UNSW Sydney, New South Wales, Australia
| | - James G Wood
- School of Population Health, UNSW Sydney, New South Wales, Australia
| | - David G Regan
- The Kirby Institute, UNSW Sydney, New South Wales, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
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2
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell 2024; 187:1374-1386.e13. [PMID: 38428425 PMCID: PMC10962340 DOI: 10.1016/j.cell.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I Paredes
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
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3
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Murayama H, Nishi A, Endo A. Different time scales used for sexual partner surveys pose a challenge in modelling dynamics of sexually transmitted infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.25.23300526. [PMID: 38234724 PMCID: PMC10793542 DOI: 10.1101/2023.12.25.23300526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Mathematical models for sexually transmitted infections (STIs) are parameterised by empirical data on sexual behaviour (e.g. the number of partners over a given period) obtained from surveys. However, the time window for reporting sexual partnerships may vary between surveys and how data for different windows can be translated from one to another remains an open question. To highlight this issue, we compared the distributions of the number of sexual partners over one year and four weeks from the British National Surveys of Sexual Attitudes and Lifestyles. The results show that simple linear rescaling did not render the one-year and four-week partner distributions aligned. Parameterising STI models using survey-based sexual encounter rates without considering the implication of the reporting window used can lead to misleading results.
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Affiliation(s)
- Hiroaki Murayama
- School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Akihiro Nishi
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, US
| | - Akira Endo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- The Centre of Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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4
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.27.23293266. [PMID: 37577709 PMCID: PMC10418578 DOI: 10.1101/2023.07.27.23293266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case-reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I. Paredes
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T. McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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5
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Brand SPC, Cavallaro M, Cumming F, Turner C, Florence I, Blomquist P, Hilton J, Guzman-Rincon LM, House T, Nokes DJ, Keeling MJ. The role of vaccination and public awareness in forecasts of Mpox incidence in the United Kingdom. Nat Commun 2023; 14:4100. [PMID: 37433797 PMCID: PMC10336136 DOI: 10.1038/s41467-023-38816-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/15/2023] [Indexed: 07/13/2023] Open
Abstract
Beginning in May 2022, Mpox virus spread rapidly in high-income countries through close human-to-human contact primarily amongst communities of gay, bisexual and men who have sex with men (GBMSM). Behavioural change arising from increased knowledge and health warnings may have reduced the rate of transmission and modified Vaccinia-based vaccination is likely to be an effective longer-term intervention. We investigate the UK epidemic presenting 26-week projections using a stochastic discrete-population transmission model which includes GBMSM status, rate of formation of new sexual partnerships, and clique partitioning of the population. The Mpox cases peaked in mid-July; our analysis is that the decline was due to decreased transmission rate per infected individual and infection-induced immunity among GBMSM, especially those with the highest rate of new partners. Vaccination did not cause Mpox incidence to turn over, however, we predict that a rebound in cases due to behaviour reversion was prevented by high-risk group-targeted vaccination.
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Affiliation(s)
- Samuel P C Brand
- The Zeeman Institute for Systems Biology Infectious Disease Epidemiology Research (SBIDER), Coventry, UK.
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Massimo Cavallaro
- The Zeeman Institute for Systems Biology Infectious Disease Epidemiology Research (SBIDER), Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
| | | | | | | | | | - Joe Hilton
- The Zeeman Institute for Systems Biology Infectious Disease Epidemiology Research (SBIDER), Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Laura M Guzman-Rincon
- The Zeeman Institute for Systems Biology Infectious Disease Epidemiology Research (SBIDER), Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
| | - D James Nokes
- The Zeeman Institute for Systems Biology Infectious Disease Epidemiology Research (SBIDER), Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Matt J Keeling
- The Zeeman Institute for Systems Biology Infectious Disease Epidemiology Research (SBIDER), Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
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6
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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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7
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Ford L, Self JL, Wong KK, Hoekstra RM, Tauxe RV, Rose EB, Bruce BB. Power Law for Estimating Underdetection of Foodborne Disease Outbreaks, United States. Emerg Infect Dis 2023; 30:337-340. [PMID: 38270126 PMCID: PMC10826756 DOI: 10.3201/eid3002.230342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
We fit a power law distribution to US foodborne disease outbreaks to assess underdetection and underreporting. We predicted that 788 fewer than expected small outbreaks were identified annually during 1998-2017 and 365 fewer during 2018-2019, after whole-genome sequencing was implemented. Power law can help assess effectiveness of public health interventions.
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Affiliation(s)
| | | | - Karen K. Wong
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Robert V. Tauxe
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Beau B. Bruce
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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8
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Endo A, Murayama H, Abbott S, Ratnayake R, Pearson CAB, Edmunds WJ, Fearon E, Funk S. Heavy-tailed sexual contact networks and monkeypox epidemiology in the global outbreak, 2022. Science 2022; 378:90-94. [PMID: 36137054 DOI: 10.1126/science.add4507] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The outbreak of monkeypox across non-endemic regions confirmed in May 2022 shows epidemiological features distinct from previously imported outbreaks, most notably its observed growth and predominance amongst men who have sex with men (MSM). We use a transmission model fitted to empirical sexual partnership data to show that the heavy-tailed sexual partnership distribution, in which a handful of individuals have disproportionately many partners, can explain the sustained growth of monkeypox among MSM despite the absence of such patterns previously. We suggest that the basic reproduction number (R0) for monkeypox over the MSM sexual network may be substantially above 1, which poses challenges to outbreak containment. Ensuring support and tailored messaging to facilitate prevention and early detection among MSM with high numbers of partners is warranted.
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Affiliation(s)
- Akira Endo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Hiroaki Murayama
- School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Sam Abbott
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ruwan Ratnayake
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Carl A B Pearson
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, Republic of South Africa
| | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Elizabeth Fearon
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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9
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Khalid MA. Accuracy of Gram-stained smears as screening tests for Neisseria gonorrhoeae: Brief communication. Indian J Sex Transm Dis AIDS 2022; 43:238-240. [PMID: 36743115 PMCID: PMC9890992 DOI: 10.4103/ijstd.ijstd_132_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
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10
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Steinegger B, Iacopini I, Teixeira AS, Bracci A, Casanova-Ferrer P, Antonioni A, Valdano E. Non-selective distribution of infectious disease prevention may outperform risk-based targeting. Nat Commun 2022; 13:3028. [PMID: 35641538 PMCID: PMC9156732 DOI: 10.1038/s41467-022-30639-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/06/2022] [Indexed: 12/22/2022] Open
Abstract
Epidemic control often requires optimal distribution of available vaccines and prophylactic tools, to protect from infection those susceptible. Well-established theory recommends prioritizing those at the highest risk of exposure. But the risk is hard to estimate, especially for diseases involving stigma and marginalization. We address this conundrum by proving that one should target those at high risk only if the infection-averting efficacy of prevention is above a critical value, which we derive analytically. We apply this to the distribution of pre-exposure prophylaxis (PrEP) of the Human Immunodeficiency Virus (HIV) among men-having-sex-with-men (MSM), a population particularly vulnerable to HIV. PrEP is effective in averting infections, but its global scale-up has been slow, showing the need to revisit distribution strategies, currently risk-based. Using data from MSM communities in 58 countries, we find that non-selective PrEP distribution often outperforms risk-based, showing that a logistically simpler strategy is also more effective. Our theory may help design more feasible and successful prevention. Pre-exposure prophylaxis (PrEP) is an effective HIV prevention measure but identifying those most at risk to target for treatment is challenging. Here, the authors demonstrate that non-selective PrEP distribution outperforms targeted strategies when use is not consistent, and/or prevalence of untreated HIV is high.
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Affiliation(s)
- Benjamin Steinegger
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, Tarragona, Spain
| | - Iacopo Iacopini
- Department of Network and Data Science, Central European University, Vienna, Austria.,Aix Marseille Univ, Université de Toulon, CNRS, CPT, Marseille, France
| | - Andreia Sofia Teixeira
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,INESC-ID, Lisboa, Portugal
| | - Alberto Bracci
- Department of Mathematics, City, University of London, London, UK
| | - Pau Casanova-Ferrer
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Department of Mathematics, Carlos III University of Madrid, Leganés, Spain.,Department of Systems Biology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Alberto Antonioni
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Department of Mathematics, Carlos III University of Madrid, Leganés, Spain
| | - Eugenio Valdano
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.
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11
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Joseph SJ, Thomas Iv JC, Schmerer MW, Cartee J, St Cyr S, Schlanger K, Kersh EN, Raphael BH, Gernert KM. Global emergence and dissemination of Neisseria gonorrhoeae ST-9363 isolates with reduced susceptibility to azithromycin. Genome Biol Evol 2021; 14:6486421. [PMID: 34962987 DOI: 10.1093/gbe/evab287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2021] [Indexed: 11/12/2022] Open
Abstract
Neisseria gonorrhoeae multi-locus sequence type (ST) 9363 core-genogroup isolates have been associated with reduced azithromycin susceptibility (AZMrs) and show evidence of clonal expansion in the U.S. Here we analyze a global collection of ST-9363 core-genogroup genomes to shed light on the emergence and dissemination of this strain. The global population structure of ST-9363 core-genogroup falls into three lineages: Basal, European, and North American; with 32 clades within all lineages. Although, ST-9363 core-genogroup is inferred to have originated from Asia in the mid-19th century; we estimate the three modern lineages emerged from Europe in the late 1970s to early 1980s. The European lineage appears to have emerged and expanded from around 1986 to 1998, spreading into North America and Oceania in the mid-2000s with multiple introductions, along with multiple secondary reintroductions into Europe. Our results suggest two separate acquisition events of mosaic mtrR and mtrR promoter alleles: first during 2009-2011 and again during the 2012-2013 time, facilitating the clonal expansion of this core-genogroup with AZMrs in the U.S. By tracking phylodynamic evolutionary trajectories of clades that share distinct demography as well as population-based genomic statistics, we demonstrate how recombination and selective pressures in the mtrCDE efflux operon granted a fitness advantage to establish ST-9363 as a successful gonococcal lineage in the U.S. and elsewhere. Although it is difficult to pinpoint the exact timing and emergence of this young core-genogroup, it remains critically important to continue monitoring it, as it could acquire additional resistance markers.
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Affiliation(s)
- Sandeep J Joseph
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Jesse C Thomas Iv
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Matthew W Schmerer
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Jack Cartee
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Sancta St Cyr
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Karen Schlanger
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Ellen N Kersh
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Brian H Raphael
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
| | - Kim M Gernert
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia-30329, USA
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12
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Didelot X, Kendall M, Xu Y, White PJ, McCarthy N. Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo. Curr Protoc 2021; 1:e60. [PMID: 33617114 PMCID: PMC7995038 DOI: 10.1002/cpz1.60] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo. © 2021 The Authors. Basic Protocol 1: First steps with TransPhylo Basic Protocol 2: Simulation of outbreak data Basic Protocol 3: Inference of transmission Basic Protocol 4: Exploring the results of inference.
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Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of StatisticsUniversity of WarwickUnited Kingdom
| | - Michelle Kendall
- School of Life Sciences and Department of StatisticsUniversity of WarwickUnited Kingdom
| | - Yuanwei Xu
- Center for Computational Biology, Institute of Cancer and Genomic SciencesUniversity of BirminghamUnited Kingdom
| | - Peter J. White
- Department of Infectious Disease Epidemiology, School of Public HealthImperial College LondonUnited Kingdom
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public HealthImperial College LondonUnited Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling and Health Economics, School of Public HealthImperial College LondonUnited Kingdom
- Modelling and Economics Unit, National Infection ServicePublic Health EnglandLondonUnited Kingdom
| | - Noel McCarthy
- Warwick Medical SchoolUniversity of WarwickUnited Kingdom
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13
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Osnes MN, Didelot X, de Korne-Elenbaas J, Alfsnes K, Brynildsrud OB, Syversen G, Nilsen ØJ, De Blasio BF, Caugant DA, Eldholm V. Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway. Microb Genom 2020; 6:mgen000480. [PMID: 33200978 PMCID: PMC8116678 DOI: 10.1099/mgen.0.000480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 11/02/2020] [Indexed: 01/01/2023] Open
Abstract
Neisseria gonorrhoeae multilocus sequence type (ST)-7827 emerged in a dramatic fashion in Norway in the period 2016-2018. Here, we aim to shed light on the provenance and expansion of this ST. ST-7827 was found to be polyphyletic, but the majority of members belonged to a monophyletic clade we termed PopPUNK cluster 7827 (PC-7827). In Norway, both PC-7827 and ST-7827 isolates were almost exclusively isolated from men. Phylogeographical analyses demonstrated an Asian origin of the genogroup, with multiple inferred exports to Europe and the USA. The genogroup was uniformly resistant to fluoroquinolones, and associated with reduced susceptibility to both azithromycin and the extended-spectrum cephalosporins (ESCs) cefixime and ceftriaxone. From a genetic background including the penA allele 13.001, associated with reduced ESC susceptibility, we identified repeated events of acquisition of porB alleles associated with further reduction in ceftriaxone susceptibility. Transmission of the strain was significantly reduced in Norway in 2019, but our results indicate the existence of a recently established global reservoir. The worrisome drug-resistance profile and rapid emergence of PC-7827 calls for close monitoring of the situation.
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Affiliation(s)
- Magnus N. Osnes
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | | | - Kristian Alfsnes
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ola B. Brynildsrud
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Gaute Syversen
- Department of Microbiology, Oslo University Hospital Ullevål, Oslo, Norway
| | - Øivind Jul Nilsen
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Birgitte Freiesleben De Blasio
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Dominique A. Caugant
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Community Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- AMR Centre, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- AMR Centre, Norwegian Institute of Public Health, Oslo, Norway
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14
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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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15
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Leng T, Keeling MJ. Improving pairwise approximations for network models with susceptible-infected-susceptible dynamics. J Theor Biol 2020; 500:110328. [PMID: 32454058 DOI: 10.1016/j.jtbi.2020.110328] [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: 10/07/2019] [Revised: 04/02/2020] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
Abstract
Network models of disease spread play an important role in elucidating the impact of long-lasting infectious contacts on the dynamics of epidemics. Moment-closure approximation is a common method of generating low-dimensional deterministic models of epidemics on networks, which has found particular success for diseases with susceptible-infected-recovered (SIR) dynamics. However, the effect of network structure is arguably more important for sexually transmitted infections, where epidemiologically relevant contacts are comparatively rare and longstanding, and which are in general modelled via the susceptible-infected-susceptible (SIS)-paradigm. In this paper, we introduce an improvement to the standard pairwise approximation for network models with SIS-dynamics for two different network structures: the isolated open triple (three connected individuals in a line) and the k-regular network. This improvement is achieved by tracking the rate of change of errors between triple values and their standard pairwise approximation. For the isolated open triple, this improved pairwise model is exact, while for k-regular networks a closure is made at the level of triples to obtain a closed set of equations. This improved pairwise approximation provides an insight into the errors introduced by the standard pairwise approximation, and more closely matches both higher-order moment-closure approximations and explicit stochastic simulations with only a modest increase in dimensionality to the standard pairwise approximation.
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Affiliation(s)
- Trystan Leng
- EPSRC & MRC Centre for Doctoral Training in Mathematics for Real-World Systems, University of Warwick, United Kingdom.
| | - Matt J Keeling
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, Mathematics Institute and School of Life Sciences, University of Warwick, United Kingdom
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16
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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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