Fifteen years of a nationwide culture collection of Neisseria gonorrhoeae antimicrobial resistance in Portugal

Pinto, Miguel; Rodrigues, João; Matias, Rui; Água-Doce, Ivone; Cordeiro, Dora; Correia, Cristina Belo; Gomes, João Paulo; Borrego, Maria José; PTGonoNet,

doi:10.1007/s10096-020-03907-7

Cited by 5 publications

(7 citation statements)

References 24 publications

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“…gonorrhoeae surveillance in the NRL. The laboratory surveillance and isolates collection built up on behalf of PTGonoNet, hosted at the NRL [31], has already strengthened our contribution to the EURO-GASP [6]. This has been achieved through the enrichment of the current geo-temporal and genomic diversity of N.…”

Section: Discussionmentioning

confidence: 99%

“…Ultimately, in the frame of the demanding short-term transition from traditional genotyping methods, the current comparative study is an important step towards the implementation of a WGS-based laboratory workflow for N. gonorrhoeae surveillance in the NRL. The laboratory surveillance and isolates collection built up on behalf of PTGonoNet, hosted at the NRL [ 31 ], has already strengthened our contribution to the EURO-GASP [ 6 ]. This has been achieved through the enrichment of the current geo-temporal and genomic diversity of N. gonorrhoeae , by adding WGS data of isolates spanning 15 years of N. gonorrhoeae surveillance in Portugal.…”

Section: Discussionmentioning

confidence: 99%

“… N. gonorrhoeae isolates analysed in the present study are part of the ongoing activity of the Portuguese National Laboratory Network for Neisseria gonorrhoeae Collection (PTGonoNet) hosted at the National Reference Laboratory for Sexually Transmitted Infections of the Portuguese National Institute of Health (NRL) [ 31 ]. Six hundred Portuguese isolates (herein designated as ‘PT isolates’) collected from 2003 up to 2017 from distinct specimens, spread across the country, and presenting different antimicrobial-susceptibility profiles were selected for analysis.…”

Section: Methodsmentioning

confidence: 99%

“…Six hundred Portuguese isolates (herein designated as ‘PT isolates’) collected from 2003 up to 2017 from distinct specimens, spread across the country, and presenting different antimicrobial-susceptibility profiles were selected for analysis. Regarding antimicrobial-susceptibility testing, MICs for azithromycin, benzylpenicillin, cefixime, ceftriaxone, ciprofloxacin, gentamicin, spectinomycin and tetracycline were determined by Etest (bioMérieux), as previously described [ 31 ]. For 117 isolates from 2006 up to 2010, no MIC values were available for some antibiotics, as antibiotic susceptibility was determined by agar dilution breakpoint technique at the time by Public Health England, which provided solely qualitative results [ 32 ] (Table S1).…”

Section: Methodsmentioning

confidence: 99%

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Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance

et al. 2021

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Neisseria gonorrhoeae , the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST ( N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance

et al. 2021

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“…Much work has been done to determine the genetic modulators of AMR in N. gonorrhoeae , 34–48 with a focus on the antibiotics for which antimicrobial susceptibility test (AST) phenotypes are available—thus, most data are for antibiotics in recent use (ceftriaxone, cefixime, azithromycin, and ciprofloxacin) as well as others for which surveillance programs often collect data (penicillin and tetracycline) 16,17,23,25,49–72 . Most of the loci that account for a large extent of resistance in circulating populations in areas of high surveillance have been well characterized, 66,73 with several recent additions to the list of genetic modulators being described, 18,74–77 including some of increasing prevalence, such as the mosaic mtr 78,79 (where mosaicism refers to interspecies recombination between N. gonorrhoeae and another Neisseria species).…”

Section: Introductionmentioning

confidence: 99%

Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests

Martin

Mortimer

Grad

2022

Annals of the New York Academy of Sciences

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Neisseria gonorrhoeae is an urgent public health threat due to the emergence of antibiotic resistance. As most isolates in the United States are susceptible to at least one antibiotic, rapid molecular antimicrobial susceptibility tests (ASTs) would offer the opportunity to tailor antibiotic therapy, thereby expanding treatment options. With genome sequence and antibiotic resistance phenotype data for nearly 20,000 clinical N. gonorrhoeae isolates now available, there is an opportunity to use statistical methods to develop sequence-based diagnostics that predict antibiotic susceptibility from genotype. N. gonorrhoeae, therefore, provides a useful example illustrating how to apply machine learning models to aid in the design of sequence-based ASTs. We present an overview of this framework, which begins with establishing the assay technology, the performance criteria, the population in which the diagnostic will be used, and the clinical goals, and extends to the choices that must be made to arrive at a set of features with the desired properties for predicting susceptibility phenotype from genotype. While we focus on the example of N. gonorrhoeae, the framework generalizes to other organisms for which large-scale genotype and antibiotic resistance data can be combined to aid in diagnostics development.

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Preclinical assessment of an antibiotic-free cationic surfactant-based cellulose hydrogel for sexually and perinatally transmitted infections

Calado,

Mendes,

Conniot

et al. 2024

Matter

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Fifteen years of a nationwide culture collection of Neisseria gonorrhoeae antimicrobial resistance in Portugal

Cited by 5 publications

References 24 publications

Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance

Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance

Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests

Preclinical assessment of an antibiotic-free cationic surfactant-based cellulose hydrogel for sexually and perinatally transmitted infections

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