Emergence of a Neisseria gonorrhoeae clone with reduced cephalosporin susceptibility between 2014 and 2019 in Amsterdam, The Netherlands, revealed by genomic population analysis

Antimicrobial susceptibility profile of Neisseria gonorrhoeae from patients attending a medical laboratory, Institut Pasteur de Madagascar between 2014 and 2020: phenotypical and genomic characterisation in a subset of Neisseria gonorrhoeae isolates

OBJECTIVES

Antimicrobial-resistant Neisseria gonorrhoeae (NG) is a concern. Little is known about antimicrobial susceptibility profiles and associated genetic resistance mechanisms of NG in Madagascar. We report susceptibility data of NG isolates obtained by the medical laboratory (CBC) of the Institut Pasteur de Madagascar, Antananarivo, Madagascar, during 2014-2020. We present antimicrobial resistance mechanisms data and phenotype profiles of a subset of isolates.

METHODS

We retrieved retrospective data (N=395) from patients with NG isolated during 2014-2020 by the CBC. We retested 46 viable isolates including 6 found ceftriaxone and 2 azithromycin resistant, as well as 33 isolated from 2020. We determined minimal inhibitory concentrations for ceftriaxone, ciprofloxacin, azithromycin, penicillin, tetracycline and spectinomycin using Etest. We obtained whole-genome sequences and identified the gene determinants associated with antimicrobial resistance and the sequence types (STs).

RESULTS

Over the study period, ceftriaxone-resistant isolates exceeded the threshold of 5% in 2017 (7.4% (4 of 54)) and 2020 (7.1% (3 of 42)). All retested isolates were found susceptible to ceftriaxone, azithromycin and spectinomycin, and resistant to ciprofloxacin. The majority were resistant to penicillin (83% (38 of 46)) and tetracycline (87% (40 of 46)). We detected chromosomal mutations associated with antibiotic resistance in gyrA, parC, penA, ponA, porB and mtrR genes. None of the retested isolates carried the mosaic penA gene. The high rate of resistance to penicillin and tetracycline is explained by the presence of bla TEM (94.7% (36 of 38)) and tetM (97.5% (39 of 40)). We found a high number of circulating multilocus STs. Almost half of them were new types, and one new type was among the four most predominant.

CONCLUSIONS

Our report provides a detailed dataset obtained through phenotypical and genotypical methods which will serve as a baseline for future surveillance of NG. We could not confirm the occurrence of ceftriaxone-resistant isolates. Our results highlight the importance of implementing quality-assured gonococcal antimicrobial resistance surveillance in Madagascar.

Identification of high-level ceftriaxone-resistant Neisseria gonorrhoeae isolates with diverse penA alleles in Zhejiang, China

OBJECTIVES

The prevalence of ceftriaxone-resistant Neisseria gonorrhoeae poses a significant threat to the effectiveness of gonorrhoea treatment. The aim of the present study was to analyse the characteristics of ceftriaxone-resistant N. gonorrhoeae, with a specific focus on high-level ceftriaxone-resistant strains.

METHODS

A total of 207 strains of N. gonorrhoeae were collected from hospitals in Zhejiang, China, between 2019 and 2020. From this collection, we selected 8 strains of ceftriaxone-resistant N. gonorrhoeae for whole-genome sequencing, genotyping, and molecular profile analysis. For clonal strains (FC428-like), we conducted a phylogenetic analysis to understand their origin and evolutionary path.

RESULTS

Among the selected strains, 5 demonstrated high-level ceftriaxone resistance (MIC 1-2 mg/L). The genotyping results showed that these isolates had a higher diversity of penA alleles than expected. Four isolates had mosaic penA-60.001 allele and the remaining four had different non-mosaic penA alleles. Phylogenetic analysis suggested that the emergence of FC428-like clones containing penA-60.001 may result from further dissemination of different FC428 subclones from different regions of China. The identification of high-level ceftriaxone resistance in non-mosaic penA gonococci, specifically in the ZJ20-3 isolate (penA-21.001) with an MIC of 2 mg/L, is a groundbreaking discovery.

CONCLUSIONS

We present a comprehensive analysis of ceftriaxone-resistant N. gonorrhoeae isolates in Zhejiang, highlighting a significant diversity of penA alleles. The identification of strains exhibiting resistance to ceftriaxone at high levels in our study underscores the potential threat to existing protocols for gonorrhoea treatment. Consequently, we strongly emphasize the urgent need to enhance surveillance initiatives focused on ceftriaxone-resistant N. gonorrhoeae.

Genome-based epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in Spain: A prospective multicentre study

BACKGROUND

Whole-genome sequencing (WGS) of Neisseria gonorrhoeae isolates combined with epidemiological and phenotypic data provides better understanding of population dynamics.

AIM

The objective of this study was to investigate the molecular epidemiology of N. gonorrhoeae isolates from three centres in Spain and determine associations of antimicrobial resistance.

METHODS

Genetic characterization was performed in 170 N. gonorrhoeae isolates. WGS was carried out with the HiSeq platform (Illumina). Genome assemblies were submitted to the PubMLST Neisseria database website to determine NG-MAST, MLST and NG-STAR. Antimicrobial resistance genes and point mutations were identified with PubMLST. Phylogenomic comparison was based on whole-genome single nucleotide polymorphism analysis.

RESULTS

Twenty-six MLST, 49 NG-MAST and 41 NG-STAR sequence types were detected, the most prevalent being MLST-ST9363 (27.1%), NG-MAST ST569 (12.4%) and NG-STAR ST193 (14.7%). Phylogenetic analysis identified 13 clusters comprising 69% of the isolates, with two of note: one involved cefixime-resistant isolates from Barcelona presenting a mosaic penA X and belonging to MLST-ST7363 and the other involved azithromycin-resistant isolates from Mallorca that possessed the C2611T mutation in the four 23S rRNA alleles belonging to MLST-ST1901.

CONCLUSION

The population of N. gonorrhoeae is quite heterogeneous in Spain. Our results agree with previous data published in Europe, albeit with some differences in distribution between regions. This study describes the circulation of two gonococcal populations with a specific resistance profile and sequence type in a specific geographic area. WGS is an effective tool for epidemiological surveillance of gonococcal infection and detection of resistance genes.

Dissemination of Neisseria gonorrhoeae with decreased susceptibility to extended-spectrum cephalosporins in Southern China, 2021: a genome-wide surveillance from 20 cities

BACKGROUND

Antimicrobial resistance (AMR) of untreatable gonococcal infection is an emerging threat, especially in Guangdong, a prosperous province in Southern China.

METHODS

N.gonorrhoeae was isolated from 20 cities in Guangdong and determined antimicrobial susceptibility. Through whole-genome sequencing (WGS), multilocus sequence typing (MLST), N.gonorrhoeae multiantigen sequence typing (NG-MAST), and N.gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) were obtained based on the PubMLST database ( https://pubmlst.org/ ). Phylogenetic analysis was used for dissemination and tracking analysis.

RESULTS

Antimicrobial susceptibility was performed on 347 isolates, and 50 isolates were identified as decreased susceptibility (DS) to cephalosporins. Of which 16.0% (8/50) were ceftriaxone DS, 38.0% (19/50) were cefixime DS, and 46.0% (23/50) were both ceftriaxone and cefixime DS. In all, the dual-resistant rate of the cephalosporin-DS isolates was 96.0% for penicillin and 98.0% for tetracycline-resistant, and 10.0% (5/50) were resistant to azithromycin. All cephalosporin-DS isolates were resistant to ciprofloxacin but sensitive to spectinomycin. The predominant MLSTs were ST7363 (16%, 8/50), ST1903 (14%, 7/50), ST1901 (12%, 6/50), and ST7365 (10%, 5/50). Besides some isolates that failed genotyping (NA), NG-STAR ST1143 (n = 6) and NG-MAST ST17748 (n = 4) were the most prevalent. Twelve isolates with mosaic penA-60.001 allele retained the most elevated cephalosporin MIC (Minimum Inhibitory Concentration). Phylogenetic analysis revealed that epidemic penA-60.001 clones, either domestic or foreign, had spread to nine cities in Guangdong, and 9/12 clones were from the Pearl River Delta region.

CONCLUSIONS

N. gonorrhoeae with cephalosporins-DS was extensively disseminated in Guangdong, Southern China, requiring strict surveillance.

Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests

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.

Global status of Azithromycin and Erythromycin Resistance Rates in Neisseria gonorrhoeae: A Systematic Review and Meta-analysis

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).

Trends and regional variations of gonococcal antimicrobial resistance in the Netherlands, 2013 to 2019

Background

Gonococcal antimicrobial resistance is emerging worldwide and is monitored in the Netherlands in 18 of 24 Sexual Health Centres (SHC).

Aim

To report trends, predictors and regional variation of gonococcal azithromycin resistance (AZI-R, minimum inhibitory concentration (MIC) > 1 mg/L) and ceftriaxone decreased susceptibility (CEF-DS, MIC > 0.032 mg/L) in 2013–2019.

Methods

SHC reported data on individual characteristics, sexually transmitted infection diagnoses, and susceptibility testing (MIC, measured by Etest). We used multilevel logistic regression analysis to identify AZI-R/CEF-DS predictors, correcting for SHC region. Population differences’ effect on regional variance of AZI-R and CEF-DS was assessed with a separate multilevel model.

Results

The study included 13,172 isolates, predominantly (n = 9,751; 74%) from men who have sex with men (MSM). Between 2013 and 2019, annual proportions of AZI-R isolates appeared to increase from 2.8% (37/1,304) to 9.3% (210/2,264), while those of CEF-DS seemed to decrease from 7.0% (91/1,306) to 2.9% (65/2,276). Among SHC regions, 0.0‒16.9% isolates were AZI-R and 0.0−7.0% CEF-DS; population characteristics could not explain regional variance. Pharyngeal strain origin and consultation year were significantly associated with AZI-R and CEF-DS for MSM, women, and heterosexual men. Among women and heterosexual men ≥ 4 partners was associated with CEF-DS, and ≥ 10 with AZI-R.

Conclusions

No resistance or decreasing susceptibility was found for CEF, the first line gonorrhoea treatment in the Netherlands. Similar to trends worldwide, AZI-R appeared to increase. Regional differences between SHC support nationwide surveillance with regional-level reporting. The increased risk of resistance/decreased susceptibility in pharyngeal strains underlines the importance of including extragenital infections in gonococcal resistance surveillance.

Resistance-Guided Therapy for Neisseria gonorrhoeae

Antimicrobial-resistant Neisseria gonorrhoeae infections are a threat to public health. Novel strategies for combating such resistance include the development of molecular assays to facilitate real-time prediction of antimicrobial susceptibility. Resistance to ciprofloxacin is determined by the presence of a single mutation at codon 91 of the gyrase A gene; molecular assays to guide therapy are commercially available. Resistance to cefixime is conferred via 1 of 6 critical mutations in either the mosaic penA gene or specific loci in the nonmosaic region. Resistance to ceftriaxone is conferred through mutations in 1 of 4 genes: penA, ponA, penB, and mtr; however, the ability to predict reduced susceptibility based on those genes varies by geographic region. Here, we highlight the work done toward the development of 3 such assays for ciprofloxacin, cefixime, and ceftriaxone, discuss the status of our current understanding and ongoing challenges, and suggest future directions.

The Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance

The bacterial accessory genome provides the genetic flexibility needed to facilitate environment and host adaptation. In Neisseria gonorrhoeae, known accessory elements include plasmids which can transfer and mediate antimicrobial resistance (AMR); however, chromosomal accessory genes could also play a role in AMR. Here, the gonococcal accessory genome was characterized using gene-by-gene approaches and its association with the core genome and AMR were assessed. The gonococcal accessory gene pool consisted of 247 genes, which were mainly genes located on large mobile genetic elements, phage associated genes, or genes encoding putative secretion systems. Accessory elements showed similar synteny across genomes, indicating either a predisposition for particular genomic locations or ancestral inheritance that are conserved during strain expansion. Significant associations were found between the prevalence of accessory elements and core genome multi-locus sequence types (cgMLST), consistent with a structured gonococcal population despite frequent horizontal gene transfer (HGT). Increased prevalence of putative DNA exchange regulators was significantly associated with AMR, which included a putative secretion system, methyltransferases and a toxin-antitoxin system. Although frequent HGT results in high genetic diversity in the gonococcus, we found that this is mediated by a small gene pool. In fact, a highly organized genome composition was identified with a strong association between the accessory and core genome. Increased prevalence of DNA exchange regulators in antimicrobial resistant isolates suggests that genetic material exchange plays a role in the development or maintenance of AMR. These findings enhance our understanding of gonococcal genome architecture and have important implications for gonococcal population biology. IMPORTANCE The emergence of antimicrobial resistance (AMR) against third generation cephalosporins in Neisseria gonorrhoeae is a major public health concern, as these are antibiotics of last resort for the effective treatment of gonorrhea. Although the resistance mechanisms against this class of antibiotics have not been entirely resolved, resistance against other classes of antibiotics, such as tetracyclines, is known to be mediated through plasmids, which are known gonococcal extra-chromosomal accessory elements. A complete assessment of the chromosomal accessory genome content and its role in AMR has not yet been undertaken. Here, we comprehensively characterize the gonococcal accessory genome to better understand genome architecture as well as the evolution and mechanisms of AMR in this species.

Reliability of Genetic Alterations in Predicting Ceftriaxone Resistance in Neisseria gonorrhoeae Globally

Antimicrobial resistance in N. gonorrhoeae is increasing globally, and ceftriaxone is the recommended treatment for empirical therapy in most settings. Developing molecular assays to detect decreased ceftriaxone susceptibility is critical. Using PathogenWatch, a public database of N. gonorrhoeae genomes, antibiotic susceptibility data and DNA sequences of different genes associated with ceftriaxone resistance were extracted. That information was used to determine the sensitivity and specificity of different molecular markers and algorithms to predict decreased susceptibility to ceftriaxone. A total of 12,943 N. gonorrhoeae genomes were extracted from the PathogenWatch database, of which 9,540 genomes were used in the analysis. The sensitivity and specificity of specific molecular markers and algorithms were largely consistent with prior reports. Small variation (<10%) in either sensitivity or specificity occurred. Certain algorithms using different molecular markers at various prevalence of decreased ceftriaxone susceptibility identified a potentially clinically useful range of positive and negative predictive values. We validated previously described mutations and algorithms in a large public database containing a global collection of N. gonorrhoeae genomes. Certain mutations and algorithms resulted in sensitivity and specificity values consistent with those of prior studies. Further research is needed to integrate these markers and algorithms into the development of molecular assays to predict decreased ceftriaxone susceptibility. IMPORTANCE Antimicrobial resistance in Neisseria gonorrhoeae (N. gonorrhoeae), the causative agent of gonorrhea, is rising globally. Ceftriaxone is the last remaining antibiotic for empirical treatment of gonorrhea. Developing molecular tests to predict ceftriaxone resistance can help to improve detection and surveillance of ceftriaxone resistance. Here, we utilized PathogenWatch, a public global online database of N. gonorrhoeae genomes, to evaluate different genetic markers in predicting decreased susceptibility to ceftriaxone. We compiled MICs for ceftriaxone from the PathogenWatch database and used a computational approach to extract all the genetic markers from the genomic data. We determined the sensitivity and specificity for predicting decreased ceftriaxone susceptibility among several combinations of genetic markers. We identified several combinations of genetic markers with high predictive values for decreased susceptibility to ceftriaxone. These combinations of genetic markers might be promising candidates for future molecular tests to predict ceftriaxone resistance.

Horizontal Gene Transfer of Fluoroquinolone Resistance-Conferring Genes From Commensal Neisseria to Neisseria gonorrhoeae: A Global Phylogenetic Analysis of 20,047 Isolates

Antimicrobial resistance in Neisseria gonorrhoeae is an important global health concern. The genetically related commensal Neisseria act as a reservoir of resistance genes, and horizontal gene transfer (HGT) has been shown to play an important role in the genesis of resistance to cephalosporins and macrolides in N. gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes gyrA/gyrB and parC/parE responsible for fluoroquinolone resistance. Even though the role of gyrB and parE in quinolone resistance is unclear, the subunits gyrB and parE were included as zoliflodacin, a promising new drug to treat N. gonorrhoeae targets the gyrB subunit. We analyzed a collection of 20,047 isolates; 18,800 N. gonorrhoeae, 1,238 commensal Neisseria spp., and nine Neisseria meningitidis. Comparative genomic analyses identified HGT events in genes, gyrA, gyrB, parC, and parE. Recombination events were predicted in N. gonorrhoeae and Neisseria commensals. Neisseria lactamica, Neisseria macacae, and Neisseria mucosa were identified as likely progenitors of the HGT events in gyrA, gyrB, and parE, respectively.