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Chromy D, Heissenberger D, Lippert K, Heger F, Indra A, Hyden P, Bauer WM, Grabmeier-Pfistershammer K, Willinger B, Weninger W, Pleininger S, Geusau A. Genotypic cluster analysis of Neisseria gonorrhoeae reveals a spectrum of sexual mixing including among HIV-serodiscordant men who have sex with men. Infect Dis (Lond) 2024:1-10. [PMID: 38907951 DOI: 10.1080/23744235.2024.2339864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 04/01/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Men who have sex with men (MSM) are more vulnerable to acquiring sexually transmitted infections (STIs). In 2019, for instance, 74% of European Neisseria gonorrhoeae (Ng) cases among males affected MSM. A recent report by the World Health Organization showed that most of the 2020' interim targets to end STIs by 2030 had not been met. A broadened understanding of STI transmission networks could guide future elimination strategies and reduce the STI burden. Therefore, we used whole-genome sequencing (WGS) to determine Ng-clusters and assess sexual mixing. METHODS WGS was performed on Ng-isolates collected at the Medical University of Vienna, Austria and was used for core genome multi-locus sequencing typing cluster analysis. Epidemiologic and infection-specific details were extracted from medical records. RESULTS Genomic analysis and demographic data were available for 415 isolates, and 43.9% (182/415) were allocated to 31 Ng-clusters. Nine clusters comprised samples from heterosexual individuals only (women N = 4, human immunodeficiency virus (HIV)-negative men N = 49, HIV-positive man N = 1), nine clusters included MSM only (HIV-negative N = 22, HIV-positive N = 13) and 13 clusters included both heterosexuals and MSM (HIV-negative N = 75, HIV-positive N = 18). Current use of HIV pre-exposure prophylaxis (PrEP) was reported by 22.8% of MSM. In multivariate analysis, only 'MSM' predicted clustering with isolates from HIV-positive individuals (adjusted odds ratio 10.24 (95% CI 5.02-20.90)). CONCLUSIONS Sexual mixing of HIV-positive, HIV-negative MSM and non-MSM was frequently observed. Furthermore, HIV-serodiscordant clustering highlights the importance of PrEP rollout to avert HIV transmission. Our findings can inform future STI prevention strategies and continuous surveillance efforts are required to keep up with transmission dynamics.
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Affiliation(s)
- David Chromy
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Department of Dermatology and Venereology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Kathrin Lippert
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Florian Heger
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Alexander Indra
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Paracelsus Medical University of Salzburg, Salzburg, Austria
| | - Patrick Hyden
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | | | - Birgit Willinger
- Department of Hygiene and Medical Microbiology, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Sonja Pleininger
- Department of Dermatology and Venereology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Alexandra Geusau
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
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Osman R, Dema E, David A, Hughes G, Field N, Cole M, Didelot X, Saunders J. Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care. J Infect 2024; 88:106168. [PMID: 38670270 DOI: 10.1016/j.jinf.2024.106168] [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] [Received: 01/10/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVES The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea. METHODS We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis. RESULTS We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n = 7) and gonorrhoea (n = 1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n = 2), inform antimicrobial therapy (n = 5) and identify cross-contamination (n = 1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management. CONCLUSIONS While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.
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Affiliation(s)
- Roeann Osman
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom.
| | - Emily Dema
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Alexandra David
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology and Dynamics, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Nigel Field
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Michelle Cole
- UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Genomics and Enabling Data at Warwick University, United Kingdom
| | - John Saunders
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom; UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
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Lyu H, Tang H, Feng Y, Hu S, Wang Y, Zhou L, Huang S, Li J, Zhu H, He X, Tang W, Zhou Y, Zhang L. Incidence and spontaneous clearance of gonorrhea and chlamydia infections among men who have sex with men: a prospective cohort study in Zhuhai, China. Front Public Health 2024; 12:1348686. [PMID: 38770362 PMCID: PMC11102956 DOI: 10.3389/fpubh.2024.1348686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Background Men who have sex with men (MSM) face significant risks of Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (NG) infection. Nevertheless, only limited studies have looked into the site-specific infection and clearance of CT/NG. In order to prevent transmission, it is essential to understand the underlying factors that drive infection and spontaneous clearance. Methods A 12-week cohort study examined the association between CT/NG infection, self-clearance, and sexual behaviors among MSM. The Willingness Service recruited participants who completed weekly questionnaires and provided urine, throat, and rectal swab samples. Results The study involved 151 men, in which 51 (33.8%) were diagnosed with CT/NG infection during the study period. HIV (OR = 11.31), kissing (OR = 1.59), receptive oral sex (OR = 36.64), and insertive anal sex (OR = 19.73) constituted significant risk factors. 100% condom use (OR = 5.78) and antibiotic (OR = 7.53) were more likely to cause spontaneous clearance. Discussion MSM may engage in riskier sexual behaviors due to insufficient knowledge and awareness of STI prevention, leading to increased susceptibility to NG/CT. It is crucial to concentrate on enhancing health education for MSM. Conclusion This study found that the rectum was the most prevalent site of CT/NG and sexual behavior can influence the infection. Additionally, the appropriate use of antibiotics and consistent condom use may contribute to clear spontaneously.
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Affiliation(s)
- Hang Lyu
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Haotong Tang
- Jieyang Center for Disease Control and Prevention, Jieyang, China
| | - Yunlong Feng
- Longhua District Center for Disease Control and Prevention, Shenzhen, China
| | - Shuyan Hu
- Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Yuyu Wang
- Longhua District Center for Disease Control and Prevention, Shenzhen, China
| | - Lanlan Zhou
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Shanzi Huang
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Jiarun Li
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Huamei Zhu
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Xi He
- Zhuhai Xutong Voluntary Services Center, Zhuhai, China
| | - Weiming Tang
- University of North Carolina Project-China, Guangzhou, China
- Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Yi Zhou
- Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Lei Zhang
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Artificial Intelligence and Modelling in Epidemiology Program, Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
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Mitjà O, Padovese V, Folch C, Rossoni I, Marks M, Rodríguez i Arias MA, Telenti A, Ciuffi A, Blondeel K, Mårdh O, Casabona J. Epidemiology and determinants of reemerging bacterial sexually transmitted infections (STIs) and emerging STIs in Europe. THE LANCET REGIONAL HEALTH. EUROPE 2023; 34:100742. [PMID: 37927427 PMCID: PMC10625005 DOI: 10.1016/j.lanepe.2023.100742] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
In this scoping review, we offer a comprehensive understanding of the current and recent epidemiology, challenges, and emerging issues related to bacterial sexually transmitted infections (STIs) in the WHO European Region. We endeavour in collating data from both EU/EEA and non- EU/EEA countries, thereby giving a complete picture of the region which highlights the higher notification rates in Northern and Western countries than other regions, likely due to differences in testing, access to testing, and surveillance capacity. We provide an up-to-date review on the current knowledge of determinants and persistent inequities in key populations as well as the use of molecular epidemiology for identifying transmission networks in gonorrhoea and syphilis, and detecting chlamydia mutations that evade molecular diagnosis. Finally, we explore the emerging STIs in the region and the evolving transmission routes of food and waterborne diseases into sexual transmission. Our findings call for harmonized STI surveillance systems, proactive strategies, and policies to address social factors, and staying vigilant for emerging STIs.
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Affiliation(s)
- Oriol Mitjà
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trías i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
- School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Valeska Padovese
- Genitourinary Clinic, Department of Dermatology and Venereology, Mater Dei Hospital, Msida, Malta
| | - Cinta Folch
- Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Health Department, Generalitat de Catalunya, Badalona, Spain
- Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
| | - Isotta Rossoni
- Van Vollenhoven Institute for Law, Governance and Society, Leiden University, Netherland
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, United Kingdom
- Division of Infection and Immunology, University College London, London, UK
- Hospital for Tropical Diseases, University College London Hospital, London, UK
| | - Miquel Angel Rodríguez i Arias
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trías i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
| | | | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Karel Blondeel
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Otilia Mårdh
- STI, Blood Borne Viruses and TB Section, Disease Programmes Unit, European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Jordi Casabona
- Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Health Department, Generalitat de Catalunya, Badalona, Spain
- Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
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Beale MA, Thorn L, Cole MJ, Pitt R, Charles H, Ewens M, French P, Guiver M, Page EE, Smit E, Vera JH, Sinka K, Hughes G, Marks M, Fifer H, Thomson NR. Genomic epidemiology of syphilis in England: a population-based study. THE LANCET. MICROBE 2023; 4:e770-e780. [PMID: 37722404 PMCID: PMC10547597 DOI: 10.1016/s2666-5247(23)00154-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Syphilis is a sexually transmitted bacterial infection caused by Treponema pallidum subspecies pallidum. Since 2012, syphilis rates have risen dramatically in many high-income countries, including England. Although this increase in syphilis prevalence is known to be associated with high-risk sexual activity in gay, bisexual, and other men who have sex with men (GBMSM), cases are rising in heterosexual men and women. The transmission dynamics within and between sexual networks of GBMSM and heterosexual people are not well understood. We aimed to investigate if whole genome sequencing could be used to supplement or enhance epidemiological insights around syphilis transmission. METHODS We linked national patient demographic, geospatial, and behavioural metadata to whole T pallidum genome sequences previously generated from patient samples collected from across England between Jan 1, 2012, and Oct 31, 2018, and performed detailed phylogenomic analyses. FINDINGS Of 497 English samples submitted for sequencing, we recovered 240 genomes (198 from the UK Health Security Agency reference laboratory and 42 from other laboratories). Three duplicate samples (same patient and collection date) were included in the main phylogenies, but removed from further analyses of English populations, leaving 237 genomes. 220 (92·8%) of 237 samples were from men, nine (3·8%) were from women, and eight (3·4%) were of unknown gender. Samples were mostly from London (n=118 [49·8%]), followed by southeast England (n=29 [12·2%]), northeast England (n=24 [10·1%]), and southwest England (n=15 [6·3%]). 180 (76·0%) of 237 genomes came from GBMSM, compared with 25 (10·5%) from those identifying as men who have sex with women, 15 (6·3%) from men with unrecorded sexual orientation, nine (3·8%) from those identifying as women who have sex with men, and eight (3·4%) from people of unknown gender and sexual orientation. Phylogenomic analysis and clustering revealed two dominant T pallidum sublineages in England. Sublineage 1 was found throughout England and across all patient groups, whereas sublineage 14 occurred predominantly in GBMSM older than 34 years and was absent from samples sequenced from the north of England. These different spatiotemporal trends, linked to demography or behaviour in the dominant sublineages, suggest they represent different sexual networks. By focusing on different regions of England we were able to distinguish a local heterosexual transmission cluster from a background of transmission in GBMSM. INTERPRETATION These findings show that, despite extremely close genetic relationships between T pallidum genomes globally, genomics can still be used to identify putative transmission clusters for epidemiological follow-up. This could be of value for deconvoluting putative outbreaks and for informing public health interventions. FUNDING Wellcome funding to the Sanger Institute, UK Research and Innovation, National Institute for Health and Care Research, European and Developing Countries Clinical Trials Partnership, and UK Health Security Agency.
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Affiliation(s)
- Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | - Louise Thorn
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK
| | - Michelle J Cole
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Rachel Pitt
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Hannah Charles
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK
| | - Michael Ewens
- Brotherton Wing Clinic, Brotherton Wing, Leeds General Infirmary, Leeds, UK
| | - Patrick French
- The Mortimer Market Centre, Central and North West London NHS Trust, London, UK
| | - Malcolm Guiver
- Laboratory Network, Manchester, UK Health Security Agency, Manchester Royal Infirmary, Manchester, UK
| | - Emma E Page
- Virology Department, Old Medical School, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Erasmus Smit
- Clinical Microbiology Department, Queen Elizabeth Hospital, Birmingham, UK; Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jaime H Vera
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Katy Sinka
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Marks
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, UK; Division of Infection and Immunity, University College London, London, UK
| | - Helen Fifer
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK.
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Learner ER, Grey JA, Bernstein K, Kirkcaldy RD, Torrone EA. Primary and Secondary Syphilis Among Men Who Have Sex With Men and Women, 2010 to 2019. Sex Transm Dis 2022; 49:794-796. [PMID: 35312656 PMCID: PMC9463392 DOI: 10.1097/olq.0000000000001623] [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] [Indexed: 11/26/2022]
Abstract
ABSTRACT The relative proportion of cases of primary and secondary syphilis among men who have sex with men and women reported through national case report data from 2010 to 2019 seemed stable overall and were stratified by race/ethnicity, region, and age group, but case counts increased.
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Affiliation(s)
- Emily R Learner
- From the Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
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Cartee JC, Joseph SJ, Weston E, Pham CD, Thomas JC, Schlanger K, St Cyr SB, Farley MM, Moore AE, Tunali AK, Cloud C, Raphael BH. Phylogenomic comparison of Neisseria gonorrhoeae causing disseminated gonococcal infections and uncomplicated gonorrhea in Georgia, United States. Open Forum Infect Dis 2022; 9:ofac247. [DOI: 10.1093/ofid/ofac247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Disseminated gonococcal infection (DGI) is a rare complication caused by the systemic dissemination of Neisseria gonorrhoeae (Ng) to normally sterile anatomical sites. Little is known about the genetic diversity of DGI gonococcal strains and how they relate to other gonococcal strains causing uncomplicated mucosal infections. We used whole genome sequencing to characterize DGI isolates (n = 30) collected from a surveillance system in Georgia (GA), USA during 2017-2020 to understand phylogenetic clustering among DGI as well as uncomplicated uro-and-extragenital gonococcal (UGI) isolates (n = 110) collected in Fulton County, GA during 2017-2019. We also investigated the presence or absence of genetic markers related to antimicrobial resistance (AMR) as well as surveyed the genomes for putative virulence genetic factors associated with normal human-serum (NHS) resistance that might facilitate DGI. We found that DGI strains demonstrated significant genetic variability similar to the population structure of isolates causing UGI, with sporadic incidences of geographically clustered DGI strains. DGI isolates contained various AMR markers and genetic mechanisms associated with NHS resistance. DGI isolates had a higher frequency of the porB1A allele compared with UGI (67% vs. 9%, p < 0.0001); however, no single NHS resistance marker was found in all DGI isolates. Continued DGI surveillance with genome-based characterization of DGI isolates is necessary to better understand specific factors that promote systemic dissemination.
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Affiliation(s)
- John C. Cartee
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Sandeep J. Joseph
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Emily Weston
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
- Current affiliation: Division of Global Health and Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Cau D. Pham
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Jesse C. Thomas
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Karen Schlanger
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Sancta B. St Cyr
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Monica M. Farley
- Emory University School of Medicine, Department of Medicine, Atlanta, GA, 30322, United States
- Atlanta VA Medical Center, Atlanta, GA, 30033, United States
| | - Ashley E. Moore
- Georgia Department of Public Health, Atlanta, GA, 30303, United States
| | - Amy K. Tunali
- Emory University School of Medicine, Department of Medicine, Atlanta, GA, 30322, United States
- Atlanta VA Medical Center, Atlanta, GA, 30033, United States
| | - Charletta Cloud
- Georgia Department of Public Health, Atlanta, GA, 30303, United States
| | - Brian H. Raphael
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
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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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9
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Donnell D, Zewdie K, Ratna N, Miller V, Saunders JM, Gill ON, Delpech V, Mohammed H. Association between rectal gonorrhoea and HIV incidence in men who have sex with men: a meta-analysis. Sex Transm Infect 2021; 98:492-496. [PMID: 34911750 DOI: 10.1136/sextrans-2021-055254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/26/2021] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Incidence of rectal gonorrhoea (GC) has been hypothesised as a correlate of HIV exposure in prevention trials of men who have sex with men (MSM). High rectal GC incidence in MSM trials of new biomedical prevention drugs may provide supportive evidence for ongoing HIV risk. Empirical evidence of correlation between rectal GC and HIV incidence is needed to assess whether high rectal GC rates reliably correlate with high risk of HIV. METHODS Rectal GC and HIV are routinely tested in sexual health clinics (SHCs) throughout England. Through routine surveillance data collected at visits to SHCs, we assessed HIV incidence and new rectal GC diagnoses in repeat visits by HIV-negative MSM between 2011 and 2018, predating widespread roll-out of pre-exposure prophylaxis. Meta-analysis regression assessed population-level association between HIV and rectal GC incidence over time. FINDINGS Between 2011 and 2018, HIV and rectal GC incidence was assessed in 541 056 HIV-negative MSM attending SHCs in England. HIV incidence among MSM attending SHCs fell from 1.26/100 person-years (PYs) in 2011 to 0.28/100 PYs in 2018. Rectal GC rates increased from 3.5/100 PYs to 11.1/100 PYs over the same period. The rate of HIV incidence decreased by 22.3% for each percent increase in rectal GC (95% CI -30.8 to -14.7, p<0.001). INTERPRETATION Among the population of MSM attending SHCs in England, rectal GC rates increased substantially while HIV incidence rates decreased between 2011 and 2018. HIV incidence likely decreased through expanded HIV testing, prompt antiretroviral treatment (ART) initiation and increased viral suppression in persons living with HIV, interventions that did not decrease rectal GC. Rectal GC may not be an ideal proxy for HIV incidence in trials, as HIV exposure risk is complex and context dependent, given effective HIV prevention interventions in MSM. INTRODUCTION
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Affiliation(s)
- Deborah Donnell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kidist Zewdie
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Natasha Ratna
- Blood Safety, Hepatitis, Sexually Transmitted Infections (STI) and HIV Division-National Infection Service, Public Health England, London, UK
| | - Veronica Miller
- School of Public Health, University of California System, Oakland, California, USA.,Forum for Collaborative Research, Washington, District of Columbia, USA
| | - John Michael Saunders
- HIV & STI Department, Public Health England, London, UK.,Research Department of Infection and Population Health, University College London, London, UK
| | - O Noel Gill
- HIV & STI Department, Public Health England, London, UK
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10
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Bai Y, Shao C, Hao Y, Wang Y, Jin Y. Using Whole Genome Sequencing to Trace, Control and Characterize a Hospital Infection of IMP-4-Producing Klebsiella pneumoniae ST2253 in a Neonatal Unit in a Tertiary Hospital, China. Front Public Health 2021; 9:755252. [PMID: 34976919 PMCID: PMC8715938 DOI: 10.3389/fpubh.2021.755252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/15/2021] [Indexed: 12/31/2022] Open
Abstract
Background: The purpose of this study is to use whole genome sequencing (WGS) combined with epidemiological data to track a hospital infection of the carbapenem-resistant Klebsiella pneumoniae (CRKP), which affected 3 neonatal patients in the neonatal intensive care unit (NICU). Methods: The minimum inhibitory concentrations for the antimicrobial agents were determined according to the guidelines of the Clinical and Laboratory Standards Institute. Beta-lactamases were investigated using the polymerase chain reaction and DNA sequencing. The transferability of the plasmid was investigated by a conjugation experiment. The clonal relationships were evaluated using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). WGS and single nucleotide polymorphisms (SNPs) analysis were performed on the CRKP isolates to investigate how the infection might progress. Results: Nine CRKP isolates were obtained from the NICU, seven from three patients, one from a duster cloth and one from the hand of a nurse, they all harbored blaIMP-4. Other resistance genes including blaKPC-2, blaIMP-4, blaSHV-1, blaTEM-1, blaCTX-M-15, and blaDHA-1 were also detected. PFGE analysis showed that IMP-4-producing K. pneumoniae were clonally related, and MLST assigned them to a new sequence type 2253. The SNP variations throughout the genome divided the 9 strains into three clades. Clade 1 comprised 7 strains (K1- K2 and K4-K8), whereas clade 2 and 3 consisted of only one strain each: K3 and K9, respectively.The sputum isolate K3 from patient 3 was the most distinct one differing from the other eight isolates by 239-275 SNPs. Conclusions: This is a report of using WGS to track a hospital infecion of IMP-4-producing K. pneumoniae ST2253 among neonates. Nosocomial surveillance systems are needed to limit the spread of the infection caused by these pathogens resulting from the environmental exposure in NICUs.
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11
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Town K, Learner ER, Chivukula VL, Mauk K, Reimche JL, Schmerer MW, Black J, Pathela P, Bhattacharyya S, Kerani RP, Gieseker KE, Fukuda A, Sankaran M, McNeil CJ, Spicknall IH, Raphael BH, St Cyr SB, Bernstein K, Kersh EN, Kirkcaldy RD, Schlanger K, Gernert KM. Exploring and Comparing the Structure of Sexual Networks Affected by Neisseria gonorrhoeae Using Sexual Partner Services Investigation and Genomic Data. Sex Transm Dis 2021; 48:S131-S136. [PMID: 34310528 DOI: 10.1097/olq.0000000000001520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Sexual networks are difficult to construct because of incomplete sexual partner data. The proximity of people within a network may be inferred from genetically similar infections. We explored genomic data combined with partner services investigation (PSI) data to extend our understanding of sexual networks affected by Neisseria gonorrhoeae (NG). METHODS We used 2017-2019 PSI and whole-genome sequencing (WGS) data from 8 jurisdictions participating in Centers for Disease Control and Prevention's Strengthening the US Response to Resistant Gonorrhea (SURRG) project. Clusters were identified from sexual contacts and through genetically similar NG isolates. Sexual mixing patterns were characterized by describing the clusters by the individual's gender and gender of their sex partners. RESULTS Our study included 4627 diagnoses of NG infection (81% sequenced), 2455 people received a PSI, 393 people were negative contacts of cases, and 495 were contacts with an unknown NG status. We identified 823 distinct clusters using PSI data combined with WGS data. Of cases that were not linked to any other case using PSI data, 37% were linked when using WGS data. Overall, 40% of PSI cases were allocated to a larger cluster when PSI and WGS data were combined compared with PSI data alone. Mixed clusters containing women, men who report sex with women, and men who report sex with men were common when using the WGS data either alone or in combination with the PSI data. CONCLUSIONS Combining PSI and WGS data improves our understanding of sexual network connectivity.
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Affiliation(s)
- Katy Town
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Emily R Learner
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Kerry Mauk
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Matthew W Schmerer
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Jamie Black
- Division of HIV/STD/Viral Hepatitis, Indiana Department of Health, Indianapolis, IN
| | - Preeti Pathela
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, Queens, NY
| | | | | | - Karen E Gieseker
- Colorado Department of Public Health and Environment, Denver, CO
| | | | | | - Candice J McNeil
- Department of Health, Wake Forest University School of Medicine/Guilford County, NC
| | - Ian H Spicknall
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Brian H Raphael
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Sancta B St Cyr
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Kyle Bernstein
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Ellen N Kersh
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Robert D Kirkcaldy
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Karen Schlanger
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Kim M Gernert
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
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12
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Kong LY, Wilson JD, Moura IB, Fawley W, Kelly L, Walker AS, Eyre DW, Wilcox MH. Utility of Whole Genome Sequencing in Assessing and Enhancing Partner Notification of Neisseria gonorrhoeae Infection. Sex Transm Dis 2021; 48:773-780. [PMID: 34110743 DOI: 10.1097/olq.0000000000001419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Gonorrhea is a sexually transmitted infection of global concern. We investigated whole-genome sequencing (WGS) as a tool to measure and enhance partner notification (PN) in gonorrhea management. METHODS Between May and November 2018, all N. gonorrhoeae isolated from patients attending Leeds Sexual Health, United Kingdom, underwent WGS. Reports listing sequences within 20 single-nucleotide polymorphisms (SNPs) of study isolates within a database containing select isolates from April 1, 2016, to November 15, 2018, were issued to clinicians. The proportion of cases with a potential transmission partner identified by PN was determined from patient and PN data. The WGS reports were reviewed to identify additional cases within 6 SNPs or less and verified for PN concordance. RESULTS Three hundred eighty isolates from 377 cases were successfully sequenced; 292 had traceable/contactable partners and 69 (18%) had a potential transmission partner identified by PN. Concordant PN and WGS links were identified in 47 partner pairs. Of 308 cases with no transmission partner by PN, 185 (60%) had a case within 6 SNPs or less; examination of these cases' PN data identified 7 partner pairs with previously unrecognized PN link, giving a total of 54 pairs; all had 4 or less SNP differences. The WGS clusters confirmed gaps in partner finding, at individual and group levels. Despite the clinic providing sexual health services to the whole city, 35 cases with multiple partners had no genetically related case, suggesting multiple undiagnosed infections. CONCLUSIONS Whole-genome sequencing could improve gonorrhea PN and control by identifying new links and clusters with significant gaps in partner finding.
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Affiliation(s)
| | | | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds
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13
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Campbell EM, Boyles A, Shankar A, Kim J, Knyazev S, Cintron R, Switzer WM. MicrobeTrace: Retooling molecular epidemiology for rapid public health response. PLoS Comput Biol 2021; 17:e1009300. [PMID: 34492010 PMCID: PMC8491948 DOI: 10.1371/journal.pcbi.1009300] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 10/05/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022] Open
Abstract
Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. MicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully operational without an internet connection. Using publicly available data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. Users can email microbetrace@cdc.gov for support. The source code is available at https://github.com/cdcgov/microbetrace. Rapid advances in the fields of data science and bioinformatics have significantly improved molecular epidemiology tools used in public health and have led to major changes in the way outbreak investigation and pathogen transmission studies are conducted. However, the need for specialized computer skills often impedes the use of many of these tools in the public heath domain. We bridge this knowledge gap by development of an intuitive, standalone tool called MicrobeTrace to securely integrate, visualize and explore pathogen epidemiologic data. MicrobeTrace is an easy to use browser-based tool which can effectively merge contact tracing and/or microbial genomic data with demographic or behavioral information, resulting in elegant and informative networks as well as multiple customizable visualizations. MicrobeTrace can be used offline, with analyses being performed locally in the field, ensuring secure and confidential use of personally identifiable information (PII). We provide real world examples of how MicrobeTrace has been used in public health, including COVID outbreak investigations.
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Affiliation(s)
- Ellsworth M Campbell
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Anthony Boyles
- Northrup Grumman, Atlanta, Georgia, United States of America
| | - Anupama Shankar
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jay Kim
- Northrup Grumman, Atlanta, Georgia, United States of America
| | - Sergey Knyazev
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America.,Department of Computer Science, Georgia State University, Atlanta, Georgia, United States of America
| | - Roxana Cintron
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - William M Switzer
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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14
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Shaskolskiy B, Kandinov I, Kravtsov D, Filippova M, Chestkov A, Solomka V, Kubanov A, Deryabin D, Dementieva E, Gryadunov D. Prediction of ceftriaxone MIC in Neisseria gonorrhoeae using DNA microarray technology and regression analysis. J Antimicrob Chemother 2021; 76:3151-3158. [PMID: 34458918 DOI: 10.1093/jac/dkab308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/26/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Decreased susceptibility of Neisseria gonorrhoeae to extended-spectrum cephalosporins is a major concern. Elucidation of the phenotypic and genetic characteristics of such isolates is a priority task. METHODS We developed a method for predicting the N. gonorrhoeae ceftriaxone susceptibility level (MICcro) by identifying genetic determinants of resistance using low-density hydrogel microarrays and a regression equation. A training dataset, containing 5631 isolates from the Pathogenwatch database and 181 isolates obtained in the Russian Federation during 2018-19, was used to build a regression model. The regression equation was tested on 14 WHO reference strains. Ceftriaxone resistance determinants for the 448 evaluated clinical isolates collected in Russia were identified using microarray analysis, and MICcro values were calculated using the regression equation and compared with those measured by the serial dilution method. RESULTS The regression equation for calculating MICcro values included 20 chromosomal resistance determinants. The greatest contributions to the increase in MICcro were shown to be PBP2: Ala-501→Pro, Ala-311→Val, Gly-545→Ser substitutions, Asp(345-346) insertion; and PorB: Gly-120→Arg substitution. The substitutions PBP2: Ala-501→Thr/Val, PorB: Gly-120→Asn/Asp/Lys and PBP1: Leu-421→Pro had weaker effects. For 94.4% of the isolates in the evaluation set, the predicted MICcro was within one doubling dilution of the experimentally determined MICcro. No ceftriaxone-resistant isolates were identified in the analysed samples from Russia, and no interpretative errors were detected in the MICcro calculations. CONCLUSIONS The developed strategy for predicting ceftriaxone MIC can be used for the continuous surveillance of known and emerging resistant N. gonorrhoeae isolates.
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Affiliation(s)
- Boris Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Ilya Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Dmitry Kravtsov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Marina Filippova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Alexander Chestkov
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Victoria Solomka
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Alexey Kubanov
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Dmitry Deryabin
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Ekaterina Dementieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Dmitry Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
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15
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Singh R, Kusalik A, Dillon JAR. Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. Brief Funct Genomics 2021; 21:78-89. [PMID: 34170311 DOI: 10.1093/bfgp/elab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/02/2023] Open
Abstract
Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.
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Affiliation(s)
- Reema Singh
- Department of Biochemistry, Microbiology and Immunology
| | - Anthony Kusalik
- Department of Computer Science at the University of Saskatchewan
| | - Jo-Anne R Dillon
- Department of Biochemistry Microbiology and Immunology, College of Medicine, c/o Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan S7N5E3, Canada
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16
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Manoharan-Basil SS, Laumen JGE, Van Dijck C, De Block T, De Baetselier I, Kenyon C. Evidence of Horizontal Gene Transfer of 50S Ribosomal Genes rplB, rplD, and rplY in Neisseria gonorrhoeae. Front Microbiol 2021; 12:683901. [PMID: 34177869 PMCID: PMC8222677 DOI: 10.3389/fmicb.2021.683901] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022] Open
Abstract
Horizontal gene transfer (HGT) in the penA and multidrug efflux pump genes has been shown to play a key role in the genesis of antimicrobial resistance in Neisseria gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes coding for the ribosomal proteins in the Neisseria genus. We did this in a collection of 11,659 isolates of Neisseria, including N. gonorrhoeae and commensal Neisseria species (N. cinerea, N. elongata, N. flavescens, N. mucosa, N. polysaccharea, and N. subflava). Comparative genomic analyses identified HGT events in three genes: rplB, rplD, and rplY coding for ribosomal proteins L2, L4 and L25, respectively. Recombination events were predicted in N. gonorrhoeae and N. cinerea, N. subflava, and N. lactamica were identified as likely progenitors. In total, 2,337, 2,355, and 1,127 isolates possessed L2, L4, and L25 HGT events. Strong associations were found between HGT in L2/L4 and the C2597T 23S rRNA mutation that confers reduced susceptibility to macrolides. Whilst previous studies have found evidence of HGT of entire genes coding for ribosomal proteins in other bacterial species, this is the first study to find evidence of HGT-mediated chimerization of ribosomal proteins.
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Affiliation(s)
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Tessa De Block
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Medicine, University of Cape Town, Cape Town, South Africa
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17
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Sánchez-Busó L, Yeats CA, Taylor B, Goater RJ, Underwood A, Abudahab K, Argimón S, Ma KC, Mortimer TD, Golparian D, Cole MJ, Grad YH, Martin I, Raphael BH, Shafer WM, Town K, Wi T, Harris SR, Unemo M, Aanensen DM. A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch. Genome Med 2021; 13:61. [PMID: 33875000 PMCID: PMC8054416 DOI: 10.1186/s13073-021-00858-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones and transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community-driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance. METHODS Here we present a public health-focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch ( https://pathogen.watch/ngonorrhoeae ). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization. RESULTS AMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin-resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasising the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern. CONCLUSIONS The N. gonorrhoeae scheme in Pathogenwatch provides customised bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower-resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.
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Affiliation(s)
- Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain.
| | - Corin A Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Benjamin Taylor
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - Richard J Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
- European Molecular Biology Lab, Heidelberg, Baden-Wuerttemberg, Germany
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - 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
| | - Daniel Golparian
- World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Michelle J Cole
- National Infection Service, Public Health England, London, UK
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. 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
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Brian H Raphael
- Division of STD prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - William M Shafer
- Department of Microbiology and Immunology and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
- Laboratories of Bacterial Pathogenesis, Veterans Affairs Medical Center, Decatur, GA, USA
| | - Katy Town
- Division of STD prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI Programmes, World Health Organization, Geneva, Switzerland
| | - Simon R Harris
- Microbiotica, Biodata Innovation Centre, Cambridge, Cambridgeshire, UK
| | - Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK.
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Phylogenomic analysis of Neisseria gonorrhoeae: a promising tool for tracking putative gonococcal sexual networks. THE LANCET. INFECTIOUS DISEASES 2020; 20:391-392. [PMID: 31978352 DOI: 10.1016/s1473-3099(19)30751-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/18/2019] [Indexed: 11/21/2022]
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