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

Whole Genome Sequencing: Applications in Clinical Bacteriology

The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective for whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology. WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the applications of WGS in clinical bacteriology.

Gonorrhoea on the rise in Denmark since 2022: distinct clones drive increase in heterosexual individuals

A surge in gonorrhoea in Denmark has occurred since 2022, a 46% increase from 2021. National surveillance, leveraging mandatory reporting and epidemiological data, highlights three distinct clades linked to heterosexual transmission. Despite the rise, these exhibit high susceptibility, contrasting MSM-associated strains. Geographical hotspots and age-specific patterns further illuminate transmission dynamics. The combination of genomic and epidemiological data provides novel insights into the evolving landscape of gonorrhoea, indicating potential shifts in infection dynamics and transmissibility.

Systems Biology: New Insight into Antibiotic Resistance

Over the past few decades, antimicrobial resistance (AMR) has emerged as an important threat to public health, resulting from the global propagation of multidrug-resistant strains of various bacterial species. Knowledge of the intrinsic factors leading to this resistance is necessary to overcome these new strains. This has contributed to the increased use of omics technologies and their extrapolation to the system level. Understanding the mechanisms involved in antimicrobial resistance acquired by microorganisms at the system level is essential to obtain answers and explore options to combat this resistance. Therefore, the use of robust whole-genome sequencing approaches and other omics techniques such as transcriptomics, proteomics, and metabolomics provide fundamental insights into the physiology of antimicrobial resistance. To improve the efficiency of data obtained through omics approaches, and thus gain a predictive understanding of bacterial responses to antibiotics, the integration of mathematical models with genome-scale metabolic models (GEMs) is essential. In this context, here we outline recent efforts that have demonstrated that the use of omics technology and systems biology, as quantitative and robust hypothesis-generating frameworks, can improve the understanding of antibiotic resistance, and it is hoped that this emerging field can provide support for these new efforts.

Resistance profiles of Neisseria gonorrhoeae isolates in Vienna, Austria: a phenotypic and genetic characterization from 2013 to 2020

OBJECTIVES

International surveillance data show a constant rise in the number of Neisseria gonorrhoeae infections and an increase in drug resistance of N. gonorrhoeae. As recent N. gonorrhoeae surveillance data in Austria are scarce, this study investigated phenotypic and genotypic antimicrobial resistance in N. gonorrhoeae isolates.

METHODS

In total, 440 N. gonorrhoeae samples were collected at the Medical University of Vienna, and the minimal inhibitory concentrations (MICs) for a range of different antibiotics were determined. Sampling sites and treatments were recorded, and whole-genome sequencing of N. gonorrhoeae isolates was performed using allele libraries to determine genotypic resistance.

RESULTS

The median MICs for ceftriaxone, cefixime, azithromycin, ciprofloxacin, tetracycline and penicillin were <0.002 µg/mL, <0.016 µg/mL, 0.25 µg/mL, 2.0 µg/mL, 1.5 µg/mL and 0.25 µg/mL, respectively. Annual comparison showed that MICs were generally stable for all antimicrobial agents except azithromycin, for which an increase in median MIC was observed from 2017 (0.25 µg/mL). There was no genetic resistance to ceftriaxone; 8% of samples displayed resistance mutations against cefixime, primarily located in the penA gene. Resistance to azithromycin increased from 2% in 2013 to 12% in 2020. MtrD mosaic had the highest impact on azithromycin susceptibility; 47% of the resistant isolates showed this mutation. The majority of cases of gonorrhoea were treated successfully with either ceftriaxone or a ceftriaxone/azithromycin regime. Two treatment failures occurred under monotherapy with doxycycline. Overall, genotypic resistance corresponded significantly to all respective MICs.

CONCLUSIONS

The resistance rate of N. gonorrhoeae to antibiotics has remained stable in Vienna over the last decade, except for azithromycin. The strong correlation found between genetic and phenotypic patterns in this study holds promise for future diagnostics of N. gonorrhoeae resistance based on genotypes.

Surveillance and epidemiology of syphilis, gonorrhoea and chlamydia in the non-European Union countries of the World Health Organization European Region, 2015 to 2020

Background

Epidemics of sexually transmitted infections (STI) are a major public health challenge in the World Health Organization (WHO) European Region.

Aim

We aimed to provide an overview of case reporting and other surveillance data for syphilis, gonorrhoea and chlamydia for the non-European Union (EU)/European Economic Area (EEA) countries of the Centre and East part of the WHO European Region as per classification used by the WHO Regional Office for Europe (WHO/Europe) and the European Centre for Disease Prevention and Control.

Methods

Data were provided by the surveillance agencies of the Member States for the period 2015 to 2019 through the WHO/Europe Communicable Diseases Annual Reporting Form. We analysed reported cases, explored data reported to the WHO Gonococcal Antimicrobial Surveillance Programme (GASP) and performed a review of publications on antimicrobial resistance (AMR) in gonorrhoea in the period 2015 to 2020 using systematic methodology.

Results

From 2015 to 2019, in most of the countries with three or more data points, there was a pattern of decrease in reported syphilis, gonorrhoea and chlamydia cases, which is in contrast to the EU/EEA. The number of reported cases per 100,000 population was 0.4–26.5 for syphilis, 0–18.5 for gonorrhoea and 0–43.3 for chlamydia. Four countries reported recent data on AMR in gonorrhoea to GASP, and we identified further publications from Georgia, Russia and Ukraine.

Conclusion

We found wide heterogeneity in reported rates of STI. There is a strong need to improve availability and quality of STI surveillance data in the non-EU/EEA countries.

High-Resolution Melting Analysis to Detect Antimicrobial Resistance Determinants in South African Neisseria gonorrhoeae Clinical Isolates and Specimens

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 bla_TEM (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.

Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review

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.

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

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.

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

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.

Comparative performance of commercial Amies transport media with and without charcoal for Neisseria gonorrhoeae culture for gonococcal isolation and antimicrobial resistance monitoring in Ukraine

INTRODUCTION

Culture is the only laboratory method that provides live gonococcal isolates for monitoring antimicrobial resistance. Many clinical settings do not have direct access to laboratories for the immediate processing of biological samples. Validated and quality-assured transport media are recommended to maintain the viability of Neisseria gonorrhoeae.

METHODS

In total, 103 clinical samples were divided into two groups: 51 samples were stored in Amies agar gel medium containing charcoal and 52 samples were stored in agar gel medium without charcoal. All samples were stored at 4°C for 0.5-6 h and then transported in a thermo-protected box within 0.17-0.25 h to the laboratory of Ternopil Regional STI Clinic (Ukraine).

RESULTS

The recovery rate was significantly higher for charcoal-containing Amies medium than for charcoal-free Amies medium (86.27%, 44/51 vs. 59.62%, 31/52). A higher rate of specimens transported in charcoal-containing Amies medium was isolated within 24 h (84.31%, 43/51), whereas most isolates from charcoal-free Amies medium grew within 24 h (42.31%, 22/52) or 48 h (17.31%, 9/52). Growth beyond the first quadrant of the agar plate was registered for 59.09% (26/44) of charcoal-containing Amies samples, compared with only 19.35% (6/31) of charcoal-free Amies samples.

CONCLUSIONS

A high rate of N. gonorrhoeae recovery after transport has considerable public health implications for establishing national antimicrobial susceptibility programs. Charcoal-containing Amies medium had higher viability rate, and it could be used for diagnostic and isolation purposes in future antimicrobial susceptibility studies. Continuous validation studies of transport medium for N. gonorrhoeae culture are needed.

Typing of Neisseria Gonorrhoeae isolates in Shenzhen, China from 2014-2018 reveals the shift of genotypes associated with antimicrobial resistance

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 genotype and resistance phenotype that provides 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 during 2014-2018. In total, 909 isolates were collected from Shenzhen from 2014-2018. 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 data of logistic regression. Among 909 isolates, ST₈₁₂₃, ST₇₃₆₃, ST₁₉₀₁, ST₇₃₆₅, and ST₇₃₆₀ were most the common MLST sequence types (STs), and ST₃₄₈, ST₂₄₇₃, ST₄₉₇, and ST₁₉₉ were the most prevalent NG-STAR STs. The logistic regression analysis showed that NG-STAR_ST497, MLST_ST7365, and MLST_ST7360 were typically associated with decreased susceptibility to ceftriaxone. Furthermore, the internationally spreading ESC-resistant clone MLST_ST1901 has been prevalent at least in 2014 in Shenzhen and showed a significant increase during 2014-2018. Additionally, MLST_ST7363 owns the potential to become the next internationally spreading ceftriaxone-resistant ST. In conclusions, 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.