scholarly journals Genomic epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates from Ukraine, 2013–2018

Apmis ◽  
2020 ◽  
Vol 128 (7) ◽  
pp. 465-475
Author(s):  
Iryna Boiko ◽  
Daniel Golparian ◽  
Susanne Jacobsson ◽  
Inna Krynytska ◽  
Arkadii Frankenberg ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Genomic Epidemiology ◽  
Resistance Determinants

scholarly journals Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

2017 ◽  
Vol 55 (5) ◽  
pp. 1454-1468 ◽  
Author(s):  
W. Demczuk ◽  
S. Sidhu ◽  
M. Unemo ◽  
D. M. Whiley ◽  
V. G. Allen ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Dna Sequences ◽  
Diversity Index ◽  
23S Rrna ◽  
Content Type ◽  
Typing Scheme ◽  
Resistance Determinants ◽  
Index Value ◽  
User Friendly

ABSTRACTA curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants inNeisseria gonorrhoeaewas developed and is publicly accessible (https://ngstar.canada.ca). TheN. gonorrhoeaeSequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA,mtrR,porB,ponA,gyrA,parC, and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entirepenAsequence, combining the historical nomenclature forpenAtypes I to XXXVIII with novel nucleotide sequence designations; the fullmtrRsequence and a portion of its promoter region; portions ofponA,porB,gyrA, andparC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n= 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n= 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n= 100; 13.0%), ST-42 and ST-91 (n= 45; 5.9%), ST-64 (n= 44; 5.72%), and ST-139 (n= 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n= 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n= 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 (n= 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 (n= 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistantN. gonorrhoeaestrains.

scholarly journals Equations To Predict Antimicrobial MICs in Neisseria gonorrhoeae Using Molecular Antimicrobial Resistance Determinants

2019 ◽  
Vol 64 (3) ◽  
Author(s):  
Walter Demczuk ◽  
Irene Martin ◽  
Pam Sawatzky ◽  
Vanessa Allen ◽  
Brigitte Lefebvre ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Training Data ◽  
Sequencing Analysis ◽  
Regression Equations ◽  
Validation Data ◽  
Data Set ◽  
Content Type ◽  
Resistance Determinants ◽  
Extended Spectrum

ABSTRACT The emergence of Neisseria gonorrhoeae strains that are resistant to azithromycin and extended-spectrum cephalosporins represents a public health threat, that of untreatable gonorrhea infections. Multivariate regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to the overall antimicrobial MICs for ceftriaxone, cefixime, azithromycin, tetracycline, ciprofloxacin, and penicillin. A training data set consisting of 1,280 N. gonorrhoeae strains was used to generate regression equations which were then applied to validation data sets of Canadian (n = 1,095) and international (n = 431) strains. The predicted MICs for extended-spectrum cephalosporins (ceftriaxone and cefixime) were fully explained by 5 amino acid substitutions in PenA, A311V, A501P/T/V, N513Y, A517G, and G543S; the presence of a disrupted mtrR promoter; and the PorB G120 and PonA L421P mutations. The correlation of predicted MICs within one doubling dilution to phenotypically determined MICs of the Canadian validation data set was 95.0% for ceftriaxone, 95.6% for cefixime, 91.4% for azithromycin, 98.2% for tetracycline, 90.4% for ciprofloxacin, and 92.3% for penicillin, with an overall sensitivity of 99.9% and specificity of 97.1%. The correlations of predicted MIC values to the phenotypically determined MICs were similar to those from phenotype MIC-only comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular data will facilitate the transition to whole-genome sequencing analysis from phenotypic testing and can fill the surveillance gap in an era of increased reliance on nucleic acid assay testing (NAAT) diagnostics to better monitor the dynamics of N. gonorrhoeae.

scholarly journals Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013–2014

2021 ◽  
Vol 12 (1) ◽  
pp. 17-25
Author(s):  
Alfred Villamin ◽  
Silvia Argimon ◽  
Karis Bohme ◽  
Melissa Masim ◽  
June Gayeta ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Sequence Data ◽  
The Philippines ◽  
Sequence Type ◽  
Surveillance Program ◽  
Gyra Gene ◽  
Genotypic Resistance ◽  
Genomic Epidemiology ◽  
Epidemiology Studies

Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health and is of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but genomic epidemiology studies on this pathogen are lacking in the Philippines. We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013–2014 by ARSP. The multilocus sequence type, multiantigen sequence type, presence of determinants of antimicrobial resistance and relatedness among the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. Ten of 21 isolates were resistant to penicillin, ciprofloxacin and tetracycline, due mainly to the presence of the blaTEM gene, the S91F mutation in the gyrA gene and the tetM gene, respectively. None of the isolates was resistant to ceftriaxone or cefixime. The concordance between phenotypic and genotypic resistance was 92.38% overall for five antibiotics in four classes. Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the N. gonorrhoeae multiantigen sequence typing types and the tree. Comparison with global genomes placed the Philippine genomes within global lineage A and led to the identification of an international transmission route.

scholarly journals Genomic Surveillance of Neisseria gonorrhoeae in the Philippines from 2013-2014

2020 ◽  
Author(s):  
Alfred S. Villamin ◽  
Silvia Argimón ◽  
Manuel C. Jamoralin ◽  
Karis D. Boehme ◽  
Melissa L. Masim ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Sequence Data ◽  
The Philippines ◽  
Sequence Type ◽  
Western Pacific ◽  
Surveillance Program ◽  
Genotypic Resistance ◽  
Genomic Epidemiology ◽  
The Western Pacific

AbstractAntimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health, and of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but studies of the genomic epidemiology of gonorrhoea in the Philippines are lacking.We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013-2014 by the ARSP. The multi-locus sequence type, multi-antigen sequence type, presence of antimicrobial resistance (AMR) determinants, and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined.Ten out of 21 isolates were resistant to penicillin, ciprofloxacin and tetracycline, mostly linked to the presence of blaTEM gene, the S91F mutation in the gyrA gene, and the tetM gene, respectively. None of the isolates were resistant to azithromycin, ceftriaxone or cefixime, although we identified the A24-deletion in the mtrR promoter in one isolate. The concordance between phenotypic and genotypic resistance was 92.38% overall for 5 antibiotics in 4 classes. Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the NG-MAST types and the tree. Comparison with global genomes placed the Philippine genomes within global Lineage A and led to the identification of an international transmission route.This first genomic survey of N. gonorrhoeae isolates collected by ARSP will be used to contextualize ongoing prospective surveillance, and it highlights the importance of genomic surveillance in the Western Pacific and other endemic regions to understand the spread of drug-resistant gonorrhoea worldwide.

scholarly journals Antimicrobial susceptibility of commensal Neisseria in a general population and men who have sex with men in Belgium

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Jolein Gyonne Elise Laumen ◽  
Christophe Van Dijck ◽  
Saïd Abdellati ◽  
Irith De Baetselier ◽  
Gabriela Serrano ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
General Population ◽  
Neisseria Gonorrhoeae ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Resistance Determinants ◽  
Antimicrobial Resistance Genes ◽  
Sex With Men ◽  
Commensal Neisseria ◽  
Tof Ms

AbstractNon-pathogenic Neisseria are a reservoir of antimicrobial resistance genes for pathogenic Neisseria meningitidis and Neisseria gonorrhoeae. Men who have sex with men (MSM) are at risk of co-colonization with resistant non-pathogenic and pathogenic Neisseria. We assessed if the antimicrobial susceptibility of non-pathogenic Neisseria among MSM differs from a general population and if antimicrobial exposure impacts susceptibility. We recruited 96 participants at our center in Belgium: 32 employees, 32 MSM who did not use antibiotics in the previous 6 months, and 32 MSM who did. Oropharyngeal Neisseria were cultured and identified with MALDI-TOF–MS. Minimum inhibitory concentrations for azithromycin, ceftriaxone and ciprofloxacin were determined using E-tests® and compared between groups with non-parametric tests. Non-pathogenic Neisseria from employees as well as MSM were remarkably resistant. Those from MSM were significantly less susceptible than employees to azithromycin and ciprofloxacin (p < 0.0001, p < 0.001), but not ceftriaxone (p = 0.3). Susceptibility did not differ significantly according to recent antimicrobial exposure in MSM. Surveilling antimicrobial susceptibility of non-pathogenic Neisseria may be a sensitive way to assess impact of antimicrobial exposure in a population. The high levels of antimicrobial resistance in this survey indicate that novel resistance determinants may be readily available for future transfer from non-pathogenic to pathogenic Neisseria.

scholarly journals Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae

2020 ◽  
Author(s):  
Koji Yahara ◽  
Kevin C. Ma ◽  
Tatum D. Mortimer ◽  
Ken Shimuta ◽  
Shu-ichi Nakayama ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Neisseria Gonorrhoeae ◽  
Standard Treatment ◽  
Genetic Resistance ◽  
Antibiotic Use ◽  
First Line ◽  
Resistance Determinants ◽  
Antimicrobial Resistance Genes

AbstractAntimicrobial 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 treatment with third-generation cephalosporins mainly due to the emergence of mosaic penA alleles. These two STs were first detected in Japan; however, when and how the mosaic penA alleles emerged and spread to other countries remains unknown. Here, we addressed the evolution of penA alleles by obtaining 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 1,075 strains sampled from 37 countries. We also sequenced the genomes of 103 Japanese ST-7363 N. gonorrhoeae isolates from 1996-2005 and reconstructed a phylogeny including 88 previously sequenced genomes. 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 a second recombination event 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, possibly due to independent mutations rather than horizontal gene transfer. Literature data suggest the emergence of these resistance determinants may reflect selection from the standard treatment regimens in Japan at that time. Our findings highlight how recombination and antibiotic use across and within Neisseria species intersect in driving the emergence and spread of drug-resistant gonorrhea.Author summaryAntimicrobial resistance is recognized as one of the greatest threats to human health, and Neisseria gonorrhoeae resistance is classified as one of the most urgent. The two major internationally spreading lineages resistant. to first line drugs likely originated in Japan, but when and how their genetic resistance determinants emerged remain unknown. In this study, we conducted an evolutionary analysis using clinical N. gonorrhoeae isolates from 37 countries, including a historical collection of Japanese isolates, to investigate the emergence of resistance in each of the two major lineages. We showed that the penA allele responsible for resistance to cephalosporins, the first-line treatment for gonorrhea, was possibly generated by two recombination events, one from another Neisseria species and one from another N. gonorrhoeae lineage. We also showed that mutations responsible for resistance to a previously widely used antibiotic treatment occurred twice independently in one of the two major lineages. The emergence of the genetic resistance determinants potentially reflects selection from the standard treatment regimen at that time. Our findings highlight how recombination (horizontal gene transfer) and antibiotic use across and within a bacterial species intersect in driving the emergence and spread of antimicrobial resistance genes and mutations.

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