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Hooshiar MH, Sholeh M, Beig M, Azizian K, Kouhsari E. Global trends of antimicrobial resistance rates in Neisseria gonorrhoeae: a systematic review and meta-analysis. Front Pharmacol 2024; 15:1284665. [PMID: 39035993 PMCID: PMC11258497 DOI: 10.3389/fphar.2024.1284665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 06/05/2024] [Indexed: 07/23/2024] Open
Abstract
Background Antimicrobial resistance (AMR) of Neisseria gonorrhoeae (NG) is a significant public health concern. Objective The objective of our study was to assess global AMR rates and test them both temporally and geographically. Methods We conducted a systematic search of relevant reports from international databases up to 2021. The R statistical package was used for all statistical analyses. Results A total of 225 articles were analyzed, and 432,880 NG isolates were examined. The weighted pooled resistance (WPR) rate of different antibiotics was as follows: ciprofloxacin, 51.6%; tetracycline, 45.4%; trimethoprim/sulfamethoxazole, 42.4%; chloramphenicol, 4.1%; kanamycin, 2.1%; gentamicin, 0.6%; and spectinomycin, 0.3%. The resistance to spectinomycin, gentamicin, and kanamycin decreased over time. Significant differences in antibiotic resistance rates were found between the countries. Conclusion Our findings reveal a continuous increase in resistance to some antibiotics (tetracycline and ciprofloxacin) historically used for gonorrhea, even after discontinuation. However, encouraging trends of decreasing resistance to spectinomycin, gentamicin, and kanamycin were observed. Continued global monitoring of AMR profiles in NG isolates is essential for informing appropriate treatment strategies and mitigating the threat of untreatable gonorrhea.
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Affiliation(s)
| | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Beig
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Khalil Azizian
- Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Zoonoses Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
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Núñez-Samudio V, Herrera M, Herrera G, Pimentel-Peralta G, Landires I. The Molecular Genetic Epidemiology and Antimicrobial Resistance of Neisseria gonorrhoeae Strains Obtained from Clinical Isolates in Central Panama. Microorganisms 2023; 11:2572. [PMID: 37894230 PMCID: PMC10608929 DOI: 10.3390/microorganisms11102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
We aim to analyze Neisseria gonorrhoeae isolates in central Panama, characterize the associated gonococcal antimicrobial resistance (AMR) and conduct molecular epidemiology and genetic typing. We conducted a retrospective study based on N. gonorrhoeae hospital isolates collected between 2013 and 2018. AMR was determined using dilution agar and Etest®. Molecular typing was conducted using the Multilocus Sequence Typing (ST) scheme. The isolates analyzed (n = 30) showed resistance to penicillin (38%), tetracycline (40%), and ciprofloxacin (30%), and sensitivity to extended-spectrum cephalosporins and azithromycin. We identified 11 STs, the most frequent of which was ST1901 among the strains with decreased sensitivity and resistance to three types of antibiotics. We identified eight variations for the penA gene, all non-mosaic, with type II LVG as the most frequent (50%). To the best of our knowledge, we conducted the first Central American genomic study that analyzes a collection of gonococcal isolates, which represents a benchmark for future epidemiological and molecular genetic studies. The high prevalence of ciprofloxacin, tetracycline, and penicillin resistance, in addition to the identification of the worldwide spread of multidrug-resistant clone ST1901, should prompt the continuous and reinforced surveillance of AMR, including the molecular epidemiology of N. gonorrhoeae in Panama.
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Affiliation(s)
- Virginia Núñez-Samudio
- Instituto de Ciencias Médicas, Las Tablas 0710, Los Santos, Panama;
- Sección de Epidemiología, Departamento de Salud Pública, Región de Salud de Herrera, Ministry of Health, Chitré 0601, Herrera, Panama
| | - Mellissa Herrera
- Laboratorio Clínico, Hospital Luis “Chicho” Fábrega, Región de Salud Veraguas, Ministry of Health, Santiago 0923, Veraguas, Panama; (M.H.); (G.H.)
| | - Genarino Herrera
- Laboratorio Clínico, Hospital Luis “Chicho” Fábrega, Región de Salud Veraguas, Ministry of Health, Santiago 0923, Veraguas, Panama; (M.H.); (G.H.)
| | | | - Iván Landires
- Instituto de Ciencias Médicas, Las Tablas 0710, Los Santos, Panama;
- Hospital Regional Dr. Joaquín Pablo Franco Sayas, Región de Salud de Los Santos, Ministry of Health, Las Tablas 0710, Los Santos, Panama
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Sandoval MM, Bardach A, Rojas-Roque C, Alconada T, Gomez JA, Pinto T, Palermo C, Ciapponi A. Antimicrobial resistance of Neisseria gonorrhoeae in Latin American countries: a systematic review. J Antimicrob Chemother 2023; 78:1322-1336. [PMID: 37192385 PMCID: PMC10232280 DOI: 10.1093/jac/dkad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/23/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Detailed information is needed on the dynamic pattern of antimicrobial resistance (AMR) in Neisseria gonorrhoeae in Latin America and the Caribbean (LAC). OBJECTIVES To conduct a systematic review of AMR in N. gonorrhoeae in LAC. METHODS Electronic searches without language restrictions were conducted in PubMed, Embase, Cochrane Library, EconLIT, Cumulative Index of Nursing and Allied Health Literature, Centre for Reviews and Dissemination, and Latin American and Caribbean Literature in Health Sciences. Studies were eligible if published between 1 January 2011 and 13 February 2021, conducted in any LAC country (regardless of age, sex and population) and measured frequency and/or patterns of AMR to any antimicrobial in N. gonorrhoeae. The WHO Global Gonococcal Antimicrobial Surveillance Programme (WHO-GASP) for LAC countries and Latin American AMR SurveillanceNetwork databases were searched. AMR study quality was evaluated according to WHO recommendations. RESULTS AMR data for 38, 417 isolates collected in 1990-2018 were included from 31 publications, reporting data from Argentina, Brazil, Colombia, Peru, Uruguay, Venezuela and WHO-GASP. Resistance to extended-spectrum cephalosporins was infrequent (0.09%-8.5%). Resistance to azithromycin was up to 32% in the published studies and up to 61% in WHO-GASP. Resistance to penicillin, tetracycline and ciprofloxacin was high (17.6%-98%, 20.7%-90% and 5.9%-89%, respectively). Resistance to gentamicin was not reported, and resistance to spectinomycin was reported in one study. CONCLUSIONS This review provides data on resistance to azithromycin, potentially important given its use as first-line empirical treatment, and indicates the need for improved surveillance of gonococcal AMR in LAC. Trial registration: Registered in PROSPERO, CRD42021253342.
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Affiliation(s)
| | - Ariel Bardach
- Instituto de Efectividad Clínica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina
- Centro de Investigaciones Epidemiológicas y Salud Pública (CIESP-IECS), CONICET, Buenos Aires, Argentina
| | - Carlos Rojas-Roque
- Instituto de Efectividad Clínica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina
| | - Tomás Alconada
- Instituto de Efectividad Clínica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina
| | | | | | - Carolina Palermo
- Instituto de Efectividad Clínica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina
| | - Agustin Ciapponi
- Instituto de Efectividad Clínica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina
- Centro de Investigaciones Epidemiológicas y Salud Pública (CIESP-IECS), CONICET, Buenos Aires, Argentina
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de Oliveira VF, Coracini Tonacio A, Marchi AP, Farrel Côrtes M, Luiza Bazzo M, Takeshigue Lemos G, Bortolotto Bampi JV, Patricia Sanchez Espinoza E, Luiz Tarsia Duarte E, Cristina Ruedas Martins R, Alves Dos Santos S, Vieira Perdigão Neto L, Ramalho da Costa-Lourenço AP, Regina Bonelli R, Rita Elmore M, Rossi F, Hughes G, Figueiredo Costa S. Neisseria gonorrhoeae arthritis in a patient with systemic lupus: resistance and virulence profiles. Microbes Infect 2023; 25:105037. [PMID: 35940402 DOI: 10.1016/j.micinf.2022.105037] [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: 03/08/2022] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023]
Abstract
In this study, we describe a case report of gonococcal arthritis in a Systemic Lupus Erythematosus patient. Although several mechanisms favor disseminated gonococcal infection (DGI) in patients immunosuppressed by SLE, this association is rarely reported in literature. We performed whole genome sequencing (WGS) of the etiologic agent involved and molecular analysis using a global collection of Neisseria gonorrhoeae strains. Ours is the only sample derived from synovial fluid identified in this collection, the others being from the usual anatomical sites. Antimicrobial susceptibility was determined by disk diffusion and Etest, and WGS was conducted to determine multilocus sequence typing profiles, group isolates based on core genome single nucleotide polymorphisms (SNP), and identify virulence genes and antimicrobial resistance determinants. The N. gonorrhoeae samples in the global collection were highly heterogeneous. The SNP tree had a total 19,532 SNPs in 320 samples. Our sample displayed resistance to ciprofloxacin (MIC = 2 μg/mL) and tetracycline (zone diameter = 0 mm) belonged to ST 1588 and was not closely related to any isolate in the global collection of N. gonorrhoeae strains. The isolate had genetic features related to beta-lactam, tetracycline and quinolone resistance. Seventy-one virulence genes were identified in our sample, belonging to the following classes: adherence, efflux pump, immune modulator, invasion, iron uptake, protease and stress adaptation. Moreover, no virulence genes for immune evasion and toxin were identified.
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Affiliation(s)
- Vítor Falcão de Oliveira
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil.
| | - Adriana Coracini Tonacio
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil.
| | - Ana Paula Marchi
- Laboratório de Investigação Médica, Bacteriologia e Resistência Antimicrobiana, Instituto de Medicina Tropical da FMUSP (LIM 49), Av. Dr. Enéas Carvalho de Aguiar, 470, CEP: 05403-000, São Paulo, Brazil.
| | - Marina Farrel Côrtes
- Laboratório de Investigação Médica, Bacteriologia e Resistência Antimicrobiana, Instituto de Medicina Tropical da FMUSP (LIM 49), Av. Dr. Enéas Carvalho de Aguiar, 470, CEP: 05403-000, São Paulo, Brazil.
| | | | - Gabriela Takeshigue Lemos
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil.
| | - Jose Victor Bortolotto Bampi
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil.
| | - Evelyn Patricia Sanchez Espinoza
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil.
| | - Edson Luiz Tarsia Duarte
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil.
| | - Roberta Cristina Ruedas Martins
- Laboratório de Investigação Médica, Bacteriologia e Resistência Antimicrobiana, Instituto de Medicina Tropical da FMUSP (LIM 49), Av. Dr. Enéas Carvalho de Aguiar, 470, CEP: 05403-000, São Paulo, Brazil.
| | - Sânia Alves Dos Santos
- Laboratório de Investigação Médica, Bacteriologia e Resistência Antimicrobiana, Instituto de Medicina Tropical da FMUSP (LIM 49), Av. Dr. Enéas Carvalho de Aguiar, 470, CEP: 05403-000, São Paulo, Brazil.
| | - Lauro Vieira Perdigão Neto
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil.
| | - Ana Paula Ramalho da Costa-Lourenço
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bloco I, Laboratório I2-59, Cidade Universitária, CEP: 21941-902, Rio de Janeiro, Brazil.
| | - Raquel Regina Bonelli
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bloco I, Laboratório I2-59, Cidade Universitária, CEP: 21941-902, Rio de Janeiro, Brazil.
| | - Maria Rita Elmore
- Sessão de Microbiologia, Divisão de Laboratório de Laboratório Central, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. Av. Dr. Enéas de Carvalho Aguiar, 155, CEP: 05403-010, São Paulo, Brazil.
| | - Flavia Rossi
- Sessão de Microbiologia, Divisão de Laboratório de Laboratório Central, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. Av. Dr. Enéas de Carvalho Aguiar, 155, CEP: 05403-010, São Paulo, Brazil.
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, United Kingdom.
| | - Silvia Figueiredo Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 255, CEP: 01246-903, São Paulo, Brazil; Laboratório de Investigação Médica, Bacteriologia e Resistência Antimicrobiana, Instituto de Medicina Tropical da FMUSP (LIM 49), Av. Dr. Enéas Carvalho de Aguiar, 470, CEP: 05403-000, São Paulo, Brazil.
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Lu Z, Tadi DA, Fu J, Azizian K, Kouhsari E. Global status of Azithromycin and Erythromycin Resistance Rates in Neisseria gonorrhoeae: A Systematic Review and Meta-analysis. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:465-478. [PMID: 36568835 PMCID: PMC9765340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background: The widespread development of antibiotic resistance or decreased susceptibility in Neisseria gonorrhoeae (NG) infection is a global and significant human public health issue. Objectives: Therefore, this meta-analysis aimed to estimate worldwide resistance rates of NG to the azithromycin and erythromycin according to years, regions, and antimicrobial susceptibility testing (AST). Methods: We systematically searched the published studies in PubMed, Scopus, and Embase from 1988 to 2021. All analyses were conducted using Stata software. Results: The 134 reports included in the meta-analysis were performed in 51 countries and examined 165,172 NG isolates. Most of the included studies were from Asia (50 studies) and Europe (46 studies). In the metadata, the global prevalence over the past 30 years were 6% for azithromycin and 48% for erythromycin. There was substantial change in the prevalence of macrolides NG resistance over time (P <0.01). In this metadata, among 58 countries reporting resistance data for azithromycin, 17 (29.3%) countries reported that >5% of specimens had azithromycin resistance. Conclusions: The implications of this study emphasize the rigorous or improved antimicrobial stewardship, early diagnosis, contact tracing, and enhanced intensive global surveillance system are crucial for control of further spreading of gonococcal emergence of antimicrobial resistance (AMR).
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Affiliation(s)
- Zhiwei Lu
- Graduate School, Zhejiang Chinese Medical University,
Hangzhou, Zhejiang, China,Hangzhou Heyunjia Hospital, Hangzhou, Zhejiang,
China
| | - Danyal Abbasi Tadi
- Department of Veterinary, Azad University of Shahr-e
Kord, Shahr-e Kord, Iran
| | - Jinchao Fu
- Department of General Practice, Shulan (Hangzhou)
Hospital Affiliated to Zhejiang Shuren University Shulan International Medical
College, Hangzhou, Zhejiang, China,To whom all correspondence should be addressed:
Jinchao Fu, ; Ebrahim Kouhsari,
; ORCID:
https://www.orcid.org/0000-0001-5893-6483
| | - Khalil Azizian
- Department of Microbiology, Faculty of Medicine,
Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan
University of Medical Sciences, Gorgan, Iran,Department of Laboratory Sciences, Faculty of
Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran,To whom all correspondence should be addressed:
Jinchao Fu, ; Ebrahim Kouhsari,
; ORCID:
https://www.orcid.org/0000-0001-5893-6483
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Cassu-Corsi D, Santos FF, Cayô R, Martins WM, Nodari CS, Almeida LG, Martins RA, Carvalho da Silva RJ, Vasconcelos ATR, Pignatari AC, Gales AC. Genomic analyses of ciprofloxacin-resistant Neisseria gonorrhoeae isolates recovered from the largest South American metropolitan area. Genomics 2022; 114:110287. [DOI: 10.1016/j.ygeno.2022.110287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/11/2021] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
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High-Resolution Melting Analysis to Detect Antimicrobial Resistance Determinants in South African Neisseria gonorrhoeae Clinical Isolates and Specimens. Int J Microbiol 2022; 2022:9094328. [PMID: 35087590 PMCID: PMC8789472 DOI: 10.1155/2022/9094328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/06/2022] [Indexed: 12/02/2022] Open
Abstract
Background Antimicrobial resistance is limiting treatment options for Neisseria gonorrhoeae infections. To aid or replace culture and the syndromic management approach, molecular assays are required for antimicrobial susceptibility testing to guide appropriate and rapid treatment. Objective We aimed to detect single-nucleotide polymorphisms and plasmids associated with antimicrobial resistance from N. gonorrhoeae isolates from a clinic population in South Africa, using real-time PCR as a rapid test for AMR detection. Methods N. gonorrhoeae isolates, from female and male patients presenting for care at a sexually transmitted infections clinic in Durban, South Africa, were analysed using phenotypic and genotypic methods for identification and antibiotic susceptibility testing (AST). Real-time PCR and high-resolution melting analysis were used to detect porA pseudogene (species-specific marker) and resistance-associated targets. Whole-genome sequencing was used as the gold standard for the presence of point mutations. Results The real-time porA pseudogene assay identified all N. gonorrhoeae-positive isolates and specimens. Concordance between molecular detection (real-time PCR and HRM) and resistance phenotype was ≥92% for blaTEM (HLR penicillin), rpsJ_V57M (tetracycline), tetM (tetracycline), and gyrA_S91F (ciprofloxacin). Resistance determinants 16SrRNA_C1192U (spectinomycin), mtrR_G45D (azithromycin), and penA_D545S, penA_mosaic (cefixime/ceftriaxone) correlated with the WHO control isolates. Conclusions Eight resistance-associated targets correlated with phenotypic culture results. The porA pseudogene reliably detected N. gonorrhoeae. Larger cohorts are required to validate the utility of these targets as a convenient culture-free diagnostic tool, to guide STI management in a South African population.
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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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Golparian D, Bazzo ML, Golfetto L, Gaspar PC, Schörner MA, Schwartz Benzaken A, Ramos MC, Ferreira WA, Alonso Neto JB, Mendes Pereira GF, Unemo M. Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015-16. J Antimicrob Chemother 2021; 75:3163-3172. [PMID: 32785692 DOI: 10.1093/jac/dkaa318] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/22/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is imperative internationally, but only eight (22.9%) countries in the WHO Region of the Americas reported complete AMR data to the WHO Global Gonococcal Antimicrobial Surveillance Program (WHO GASP) in 2016. Genomic studies are ideal for enhanced understanding of gonococcal populations, including the spread of AMR strains. To elucidate the circulating gonococcal lineages/sublineages, including their AMR determinants, and the baseline genomic diversity among gonococcal strains in Brazil, we conducted WGS on 548 isolates obtained in 2015-16 across all five macroregions in Brazil. METHODS A total of 548 gonococcal isolates cultured across Brazil in 2015-16 were genome sequenced. AMR was determined using agar dilution and/or Etest. Genome sequences of isolates from Argentina (n = 158) and the 2016 WHO reference strains (n = 14) were included in the analysis. RESULTS We found 302, 68 and 214 different NG-MAST, MLST and NG-STAR STs, respectively. The phylogenomic analysis identified one main antimicrobial-susceptible lineage and one AMR lineage, which was divided into two sublineages with different AMR profiles. Determination of NG-STAR networks of clonal complexes was shown as a new and valuable molecular epidemiological analysis. Several novel mosaic mtrD (and mtrR and mtrE) variants associated with azithromycin resistance were identified. CONCLUSIONS We describe the first genomic baseline data to support the Brazilian GASP. The high prevalence of resistance to ciprofloxacin, tetracycline and benzylpenicillin, and the high number of isolates with mosaic penA and azithromycin resistance mutations, should prompt continued and strengthened AMR surveillance, including WGS, of N. gonorrhoeae in Brazil.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Maria Luiza Bazzo
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Lisléia Golfetto
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Pamela Cristina Gaspar
- Department of Diseases of Chronic Condition and Sexually Transmitted Infection, Secretariat of Health Surveillance, Ministry of Health of Brazil, Brasília, Brazil
| | - Marcos André Schörner
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | | | | | - José Boullosa Alonso Neto
- Department of Diseases of Chronic Condition and Sexually Transmitted Infection, Secretariat of Health Surveillance, Ministry of Health of Brazil, Brasília, Brazil
| | - Gerson Fernando Mendes Pereira
- Department of Diseases of Chronic Condition and Sexually Transmitted Infection, Secretariat of Health Surveillance, Ministry of Health of Brazil, Brasília, Brazil
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Yahara K, Ma KC, Mortimer TD, Shimuta K, Nakayama SI, Hirabayashi A, Suzuki M, Jinnai M, Ohya H, Kuroki T, Watanabe Y, Yasuda M, Deguchi T, Eldholm V, Harrison OB, Maiden MCJ, Grad YH, Ohnishi M. Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae. Genome Med 2021; 13:51. [PMID: 33785063 PMCID: PMC8008663 DOI: 10.1186/s13073-021-00860-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Antimicrobial resistance in Neisseria gonorrhoeae is a global health concern. Strains from two internationally circulating sequence types, ST-7363 and ST-1901, have acquired resistance to third-generation cephalosporins, mainly due to mosaic penA alleles. These two STs were first detected in Japan; however, the timeline, mechanism, and process of emergence and spread of these mosaic penA alleles to other countries remain unknown. METHODS We studied the evolution of penA alleles by obtaining the complete genomes from three Japanese ST-1901 clinical isolates harboring mosaic penA allele 34 (penA-34) dating from 2005 and generating a phylogenetic representation of 1075 strains sampled from 35 countries. We also sequenced the genomes of 103 Japanese ST-7363 N. gonorrhoeae isolates from 1996 to 2005 and reconstructed a phylogeny including 88 previously sequenced genomes. RESULTS Based on an estimate of the time-of-emergence of ST-1901 (harboring mosaic penA-34) and ST-7363 (harboring mosaic penA-10), and > 300 additional genome sequences of Japanese strains representing multiple STs isolated in 1996-2015, we suggest that penA-34 in ST-1901 was generated from penA-10 via recombination with another Neisseria species, followed by recombination with a gonococcal strain harboring wildtype penA-1. Following the acquisition of penA-10 in ST-7363, a dominant sub-lineage rapidly acquired fluoroquinolone resistance mutations at GyrA 95 and ParC 87-88, by independent mutations rather than horizontal gene transfer. Data in the literature suggest that the emergence of these resistance determinants may reflect selection from the standard treatment regimens in Japan at that time. CONCLUSIONS Our findings highlight how antibiotic use and recombination across and within Neisseria species intersect in driving the emergence and spread of drug-resistant gonorrhea.
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Affiliation(s)
- Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ken Shimuta
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Michio Jinnai
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Hitomi Ohya
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Toshiro Kuroki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
- Present address: Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari, Ehime, 794-8555, Japan
| | - Yuko Watanabe
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Mitsuru Yasuda
- Center for Nutrition Support and Infection Control, Gifu University Hospital, Gifu, Japan
| | - Takashi Deguchi
- Department of Urology, Kizawa Memorial Hospital, Gifu, Japan
| | - Vegard Eldholm
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
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11
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Tibayrenc M, Ayala FJ. Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria. ADVANCES IN PARASITOLOGY 2021; 111:75-117. [PMID: 33482977 DOI: 10.1016/bs.apar.2020.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Institut de recherche pour le développement, Montpellier Cedex 5, France.
| | - Francisco J Ayala
- Catedra Francisco Jose Ayala of Science, Technology, and Religion, University of Comillas, Madrid, Spain; 2 Locke Court, Irvine, CA, United States
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12
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Harrison OB, Cehovin A, Skett J, Jolley KA, Massari P, Genco CA, Tang CM, Maiden MCJ. Neisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance. J Infect Dis 2020; 222:1816-1825. [PMID: 32163580 PMCID: PMC7653085 DOI: 10.1093/infdis/jiaa002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods. METHODS In this study, we assess how the core genome can be used to improve our understanding of gonococcal population structure compared with current typing schemes. RESULTS A total of 1668 loci were identified as core to the gonococcal genome. These were organized into a core genome multilocus sequence typing scheme (N gonorrhoeae cgMLST v1.0). A clustering algorithm using a threshold of 400 allelic differences between isolates resolved gonococci into discrete and stable core genome groups, some of which persisted for multiple decades. These groups were associated with antimicrobial genotypes and non-overlapping NG-STAR and NG-MAST sequence types. The MLST-STs were more widely distributed among core genome groups. CONCLUSIONS Clustering with cgMLST identified globally distributed, persistent, gonococcal lineages improving understanding of the population biology of gonococci and revealing its population structure. These findings have implications for the emergence of antimicrobial resistance in gonococci and how this is associated with lineages, some of which are more predisposed to developing antimicrobial resistance than others.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Ana Cehovin
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jessica Skett
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Paola Massari
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Caroline Attardo Genco
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christoph M Tang
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
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13
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Evidence for Clonally Associated Increasing Rates of Azithromycin Resistant Neisseria gonorrhoeae in Rio de Janeiro, Brazil. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3180580. [PMID: 30800666 PMCID: PMC6360546 DOI: 10.1155/2019/3180580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/17/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022]
Abstract
Azithromycin is one of the drugs used in the combined therapy for syndromic treatment of gonorrhoea in many countries, including Brazil. Our research group, which receives isolates from clinical laboratories since 2006, has detected, after 2016, a tendency of rising rates of azithromycin resistance, with isolates showing higher minimal inhibitory concentrations (MICs) than those previously reported in this country. In this study, we report the susceptibility to azithromycin of 93 N. gonorrhoeae isolates obtained between 2014 and 2017. Strains with MIC ≥2 μg/mL were characterized according to azithromycin resistance mechanisms and strain typing. Results indicate that azithromycin resistance has emerged in all these years in unrelated MLST-STs, but after 2016 a clonal complex connected with ST1901 has been more frequently detected, grouping isolates with MIC varying from 2 to 64 μg/mL, with DelA mutations at the mtrR promoter region associated or not with mutations at rrl alleles. High rates of azithromycin resistance may compromise the use of this drug in the combined therapy with ceftriaxone. Inclusion of Rio de Janeiro in the Brazilian gonococcal surveillance program is important to evaluate if this data indicates an epidemiological phenomenon in the country.
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Abstract
Experimental infection of male volunteers with Neisseria gonorrhoeae is safe and reproduces the clinical features of naturally acquired gonococcal urethritis. The human model is useful for testing the importance of putative gonococcal virulence factors for urethral infection in men and the model presents opportunities to examine host immune responses that may be exploited or improved in development and testing of gonococcal vaccines. In this chapter, we describe methods for production, characterization, and storage of N. gonorrhoeae stocks for experimental human challenge, preparation and delivery of inoculum suspensions, monitoring experimental infection, and statistical considerations for data analysis.
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Affiliation(s)
- Marcia M Hobbs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Joseph A Duncan
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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15
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Mortimer TD, Grad YH. Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae. Ann N Y Acad Sci 2018; 1435:93-109. [PMID: 29876934 DOI: 10.1111/nyas.13871] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
Abstract
Infections with Neisseria gonorrhoeae, a sexually transmitted pathogen that causes urethritis, cervicitis, and more severe complications, are increasing. Gonorrhea is typically treated with antibiotics; however, N. gonorrhoeae has rapidly acquired resistance to many antibiotic classes, and lineages with reduced susceptibility to the currently recommended therapies are emerging worldwide. In this review, we discuss the contributions of whole genome sequencing (WGS) to our understanding of resistant N. gonorrhoeae. Genomics has illuminated the evolutionary origins and population structure of N. gonorrhoeae and the magnitude of horizontal gene transfer within and between Neisseria species. WGS can be used to predict the susceptibility of N. gonorrhoeae based on known resistance determinants, track the spread of these determinants throughout the N. gonorrhoeae population, and identify novel loci contributing to resistance. WGS has also allowed more detailed epidemiological analysis of transmission of N. gonorrhoeae between individuals and populations than previously used typing methods. Ongoing N. gonorrhoeae genomics will complement other laboratory techniques to understand the biology and evolution of the pathogen, improve diagnostics and treatment in the clinic, and inform public health policies to limit the impact of antibiotic resistance.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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