scholarly journals Antimicrobial resistance and molecular epidemiological typing of Neisseria gonorrhoeae isolates from Kyrgyzstan in Central Asia, 2012 and 2017

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Saliya Karymbaeva ◽  
Iryna Boiko ◽  
Susanne Jacobsson ◽  
Galina Mamaeva ◽  
Ainagul Ibraeva ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Central Asia ◽  
Treatment Guidelines ◽  
High Genetic Diversity ◽  
Significant Public Health ◽  
Clinical Breakpoints ◽  
Overall Resistance ◽  
First Time ◽  
Sequence Types

Abstract Background Gonorrhoea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are significant public health concerns globally. Nearly no gonococcal AMR data are available from Central Asia, and no data from Kyrgyzstan has been published. We examined, for the first time, AMR and molecular epidemiology of N. gonorrhoeae isolates cultured in Kyrgyzstan in 2012 and 2017, in order to inform refinements of the Kyrgyz national gonorrhoea management guidelines. Methods N. gonorrhoeae isolates cultured in 2012 (n = 84) and 2017 (n = 72) in Kyrgyzstan were examined. MICs of nine antimicrobials were determined using Etest and, where available, clinical breakpoints from the EUCAST were applied. N. gonorrhoeae multiantigen sequence typing (NG-MAST) was also performed. Results The overall resistance levels were high to ciprofloxacin (88.5%), tetracycline (56.9%), benzylpenicillin (39.1%), and kanamycin (4.7%). Resistance to cefixime (0.6%, n = 1 isolate), azithromycin (0.6%, n = 1), and gentamicin (0.6%, n = 1) was rare. No resistance to ceftriaxone or spectinomycin was found. However, the proportion of isolates with decreased susceptibility (MIC = 0.125 mg/L) to ceftriaxone and cefixime was 12.8 and 11.5%, respectively. Gonococcal isolates were assigned 69 sequence types, of which 52 (75.4%) were new. Conclusions The gonococcal population in Kyrgyzstan in 2012 and 2017 showed a high genetic diversity. Ceftriaxone, 500–1000 mg, in combination with azithromycin 2 g or doxycycline, particularly when chlamydial infection has not been excluded, should be recommended as empiric first-line treatment. Spectinomycin 2 g could be an alternative treatment, and given with azithromycin 2 g if pharyngeal gonorrhoea has not been excluded. Fluoroquinolones, aminoglycosides, benzylpenicillin, or tetracyclines should not be used for empiric treatment of gonorrhoea in Kyrgyzstan. Timely updating and high compliance to national gonorrhoea treatment guidelines based on quality-assured AMR data is imperative. Expanded and improved gonococcal AMR surveillance in Kyrgyzstan is crucial.

scholarly journals Antimicrobial resistance in Neisseria gonorrhoeae isolates and gonorrhoea treatment in the Republic of Belarus, Eastern Europe, 2009–2019

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Aliaksandra Aniskevich ◽  
Iryna Shimanskaya ◽  
Iryna Boiko ◽  
Tatyana Golubovskaya ◽  
Daniel Golparian ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Eastern Europe ◽  
Treatment Guidelines ◽  
Statistical Significance ◽  
Antimicrobial Treatment ◽  
National Guidelines ◽  
First Line ◽  
Exact Test ◽  
The Republic

Abstract Background Limited antimicrobial resistance (AMR) data for Neisseria gonorrhoeae are available in Eastern Europe. We investigated AMR in N. gonorrhoeae isolates in the Republic of Belarus from 2009 to 2019, antimicrobial treatment recommended nationally, and treatment given to patients with gonorrhoea. Methods N. gonorrhoeae isolates (n = 522) cultured in three regions of Belarus in 2009–2019 were examined. Determination of minimum inhibitory concentrations (MICs) of eight antimicrobials was performed using Etest. Resistance breakpoints from the European Committee on Antimicrobial Susceptibility Testing were applied where available. A Nitrocefin test identified β-lactamase production. Gonorrhoea treatment for 1652 patients was also analysed. Statistical significance was determined by the Z-test, Fisher’s exact test, or Mann-Whitney U test with p-values of < 0.05 indicating significance. Results In total, 27.8% of the N. gonorrhoeae isolates were resistant to tetracycline, 24.7% to ciprofloxacin, 7.0% to benzylpenicillin, 2.7% to cefixime, and 0.8% to azithromycin. No isolates were resistant to ceftriaxone, spectinomycin, or gentamicin. However, 14 (2.7%) isolates had a ceftriaxone MIC of 0.125 mg/L, exactly at the resistance breakpoint (MIC > 0.125 mg/L). Only one (0.2%) isolate, from 2013, produced β-lactamase. From 2009 to 2019, the levels of resistance to ciprofloxacin and tetracycline were relatively high and stable. Resistance to cefixime was not identified before 2013 but peaked at 22.2% in 2017. Only sporadic isolates with resistance to azithromycin were found in 2009 (n = 1), 2012 (n = 1), and 2018–2019 (n = 2). Overall, 862 (52.2%) patients received first-line treatment according to national guidelines (ceftriaxone 1 g). However, 154 (9.3%) patients received a nationally recommended alternative treatment (cefixime 400 mg or ofloxacin 400 mg), and 636 (38.5%) were given non-recommended treatment. Conclusions The gonococcal resistance to ciprofloxacin and tetracycline was high, however, the resistance to azithromycin was low and no resistance to ceftriaxone was identified. Ceftriaxone 1 g can continuously be recommended as empiric first-line gonorrhoea therapy in Belarus. Fluoroquinolones should not be prescribed for treatment if susceptibility has not been confirmed by testing. Timely updating and high compliance with national evidence-based gonorrhoea treatment guidelines based on quality-assured AMR data are imperative. The need for continued, improved and enhanced surveillance of gonococcal AMR in Belarus is evident.

Antimicrobial resistance mechanisms, MLST and NG-STAR sequence types of diverse Neisseria gonorrhoeae isolates in KwaZulu-Natal, South Africa

2021 ◽  
Author(s):  
Nireshni Mitchev ◽  
Ravesh Singh ◽  
Mushal Allam ◽  
Stanford Kwenda ◽  
Arshad Ismail ◽  
...  
Keyword(s):  
South Africa ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Point Mutations ◽  
Resistance Mechanisms ◽  
Public Healthcare ◽  
Multiple Sequence ◽  
Genotypic Analysis ◽  
Kwazulu Natal ◽  
Sequence Types

Objective: Antimicrobial resistance (AMR) is a major challenge to managing infectious diseases. Africa has the highest incidence of gonorrhoea but there is a lack of comprehensive data from sparse surveillance programs. This study investigated the molecular epidemiology and AMR profiles of Neisseria gonorrhoeae isolates in KwaZulu-Natal province (KZN), South Africa. Methods: Repository isolates, from patients attending public healthcare clinics for STI care, were used for phenotypic and genotypic analysis. Etest® was performed to determine antimicrobial susceptibility. Whole-genome sequencing (WGS) was used to determine epidemiology and to predict susceptibility by detecting resistance-associated genes and mutations. Results: Among the 61 isolates, multiple sequence types were identified. Six isolates were novel as determined by multilocus sequence typing. N.gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) determined 48 sequence types, of which 35 isolates had novel antimicrobial profiles. Two novel penA alleles and eight novel mtrR alleles were identified. Point mutations were detected in gyrA , parC , mtrR , penA , ponA and porB1 . This study revealed a high prevalence of AMR (penicillin 67%, tetracycline 89% and ciprofloxacin 52%). However, spectinomycin, cefixime, ceftriaxone and azithromycin remained 100% effective. Conclusion: This study is one of the first to comprehensively describe the epidemiology and AMR of N. gonorrhoeae in KZN, South Africa and Africa, using WGS. KZN has a wide strain diversity and most of these sequence types have been detected in multiple countries, however more than half of our isolates have novel antimicrobial profiles. Continued surveillance is crucial to monitor the emergence of resistance to cefixime, ceftriaxone and azithromycin.

scholarly journals Differences in Neisseria gonorrhoeae population structure and antimicrobial resistance pattern between men who have sex with men and heterosexuals

2016 ◽  
Vol 145 (2) ◽  
pp. 379-385 ◽  
Author(s):  
J. SERRA-PLADEVALL ◽  
M. J. BARBERÁ ◽  
A. E. CALLARISA ◽  
R. BARTOLOMÉ-COMAS ◽  
A. ANDREU
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Antimicrobial Susceptibility ◽  
Sexual Practices ◽  
Resistance Pattern ◽  
High Prevalence ◽  
Sex With Men ◽  
Resistance Rates ◽  
Sequence Types

SUMMARYThis study compared the antimicrobial susceptibility and genotypes of strains of Neisseria gonorrhoeae isolated from men who have sex with men (MSM) and from heterosexuals. One hundred and eleven strains were characterized from 107 patients, comprising 57 strains from 54 heterosexuals and 54 strains from 53 MSM. Antimicrobial resistance rates were higher in strains from heterosexual patients, with resistance to cefixime (P = 0·0159) and ciprofloxacin (P = 0·002) being significantly higher. Typing by N. gonorrhoeae multi-antigen sequence typing (NG-MAST) showed that the most prevalent sequence types (ST) and genogroups (G) respectively were ST2400, ST2992, and ST5793, and G1407, G2992, and G2400. A statistically significant association was observed for MSM and genogroups G2400 (P = 0·0005) and G2992 (P = 0·0488), and G1407 with heterosexuals (P = 0·0002). We conclude that in our region distinct populations of gonococci are circulating among subjects with different sexual practices, with their corresponding transmission patterns. Furthermore, the high prevalence of genotype G2400 in MSM, has not to our knowledge been previously described.

scholarly journals NG-MAST GENOTYPING OF NEISSERIA GONORRHOEAE STRAINS ISOLATED IN RUSSIAN FEDERATION IN 2012 - 2015

2016 ◽  
pp. 42-51 ◽  
Author(s):  
D. V. Vorobiev ◽  
V. S. Solomka ◽  
K. I. Plakhova ◽  
D. G. Deryabin ◽  
A. A. Kubanov
Keyword(s):  
Genetic Diversity ◽  
Neisseria Gonorrhoeae ◽  
Russian Federation ◽  
Variable Regions ◽  
The Russian Federation ◽  
First Time ◽  
Sequence Types

Aim. Characteristics of contemporary strains of N. gonorrhoeae using NG-MAST genotyping (.Neisseria gonorrhoeae multi-antigen sequence typing), isolation of dominating variants and analysis of their territorial distribution. Materials and methods. 440 strains of N. gonorrhoeae isolated in 2012 - 2015 in 19 subjects of the Russian Federation were used in the study. Genotyping was carried out based on sequencing of variable regions of porB and tbpB genes. Identification of alleles and sequence-types was carried out according to http://www.ng-mast.net. Results. 172 NG-MAST genotypes were identified, 100 of which -were described for the first time. 807,1152, 1544,5714 and 5941 were predominating sequence-types, typical for several subjects of the Russian Federation and some neighboring countries, as well as sequence-types 8583 and 9476 described for the first time, that were exclusively distributed in the regions of their emergence. Sequence-types 225, 1407 and 2992, that are epidemically significant in distant countries, were represented by single isolates in this study. Conclusion. A peculiar and significant genetic diversity of N. gonorrhoeae strains, circulating in the Russian Federation, with characteristic bond of several NG-MAST genotypes to one or several regions, was shown.

scholarly journals Typing of Neisseria gonorrhoeae Isolates in Shenzhen, China, from 2014 to 2018 Reveals the Shift of Genotypes Significantly Associated with Antimicrobial Resistance

2021 ◽  
Vol 65 (5) ◽  
Author(s):  
Yizhun Li ◽  
Yamei Li ◽  
Leshan Xiu ◽  
Yaling Zeng ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Molecular Epidemiology ◽  
Important Data ◽  
Content Type ◽  
Future Studies ◽  
Ideal Tool ◽  
Global Threat ◽  
Sequence Types

ABSTRACT The growing antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a serious global threat to gonococcal therapy. Molecular typing is an ideal tool to reveal the association between specific genotypes and resistance phenotypes that provide effective data for tracking the transmission of resistant clones of N. gonorrhoeae. In our study, we aimed to describe the molecular epidemiology of AMR and the distribution of resistance-associated genotypes in Shenzhen, China, during 2014 to 2018. In total, 909 isolates were collected from Shenzhen from 2014 to 2018. Two typing schemes, multilocus sequence typing (MLST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), were performed for all isolates. The distribution of resistance-associated genotypes was described using goeBURST analysis combined with logistic regression data. Among 909 isolates, sequence type 8123 (ST8123), ST7363, ST1901, ST7365, and ST7360 were the most common MLST sequence types, and ST348, ST2473, ST497, and ST199 were the most prevalent NG-STAR STs. Logistic regression analysis showed that NG-STARST497, MLSTST7365, and MLSTST7360 were typically associated with decreased susceptibility to ceftriaxone. Furthermore, the internationally spreading extended-spectrum cephalosporin (ESC)-resistant clone MLSTST1901 has been prevalent since at least 2014 in Shenzhen and showed a significant increase during 2014 to 2018. Additionally, MLSTST7363 owns the potential to become the next internationally spreading ceftriaxone-resistant ST. In conclusion, we performed a comprehensive epidemiological study to explore the correlation between AMR and specific STs, which provided important data for future studies of the molecular epidemiology of AMR in N. gonorrhoeae. Besides, these findings provide insight for adjusting surveillance strategies and therapy management in Shenzhen.

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

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Koji Yahara ◽  
Kevin C. Ma ◽  
Tatum D. Mortimer ◽  
Ken Shimuta ◽  
Shu-ichi Nakayama ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Acquired Resistance ◽  
Antibiotic Use ◽  
Health Concern ◽  
Fluoroquinolone Resistance ◽  
Resistance Mutations ◽  
Treatment Regimens ◽  
Antimicrobial Resistance Genes ◽  
Sequence Types

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.

scholarly journals High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

2020 ◽  
Author(s):  
Nicholas D Sanderson ◽  
Jeremy Swann ◽  
Leanne Barker ◽  
James Kavanagh ◽  
Sarah Hoosdally ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Health Concern ◽  
Clinical Samples ◽  
Metagenomic Sequencing ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Entire Genome ◽  
Culture Independent ◽  
Significant Public Health

AbstractThe rise of antimicrobial resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhoea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N. gonorrhoeae genome from metagenomic samples and robustly identifying antimicrobial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics challenge.Here we demonstrate an N. gonorrhoeae diagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20x reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information in N. gonorrhoeae infection.

scholarly journals Prevalence, Population Diversity and Antimicrobial Resistance of Campylobacter coli Isolated in Italian Swine at Slaughterhouse

2020 ◽  
Vol 8 (2) ◽  
pp. 222 ◽  
Author(s):  
Guido Di Donato ◽  
Francesca Marotta ◽  
Roberta Nuvoloni ◽  
Katiuscia Zilli ◽  
Diana Neri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Population Diversity ◽  
Campylobacter Coli ◽  
Gyra Gene ◽  
Genotypic Resistance ◽  
High Genetic Diversity ◽  
Genetic Profiles ◽  
Carcass Contamination ◽  
Sequence Types

Campylobacter spp. are among the microorganisms most commonly associated with foodborne disease. Swine are known to be the main reservoir of Campylobacter coli and a possible source infection of humans as a result of carcass contamination at slaughter. The aim of this study was to evaluate the prevalence of C. coli contamination in swine carcasses, the antimicrobial resistance (AMR) patterns of isolates and the genetic diversity between strains obtained from swine and those isolated from humans. The prevalence of contamination was higher on carcasses (50.4%) than in faeces (32.9%). The 162 C. coli isolated from swine were examined by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The results of PFGE indicated a high genetic diversity among the isolates, with 25 different PFGE types. MLST assigned 51 sequence types (STs) to isolates. The most common genotype was ST-854 (16.04%), ST-9264 (10.49 %) and ST-1016 (6.08 %). Results of AMR showed a high resistance to quinolones and fluoroquinolones together with aminoglycosides and tetracycline. Many strains were multi-resistant with predominant R-type TeSCipNa (57%). Five resistance genes were detected along with mutation in the gyrA gene. A strong correlation between phenotypic and genotypic resistance was found for fluoroquinolone and tetracycline. Genetic profiles obtained in swine isolates were compared to those of 11 human strains. All human strains and 64.19% of animal strains (104/162) were assigned to the ST-828 clonal complex.

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