Phylogenomic analysis reveals persistence of gonococcal strains with reduced-susceptibility to extended-spectrum cephalosporins and mosaic penA-34

Intraspecies associations from strain-rich metagenome samples

Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference-based approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based, framework to accurately quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we uncover previously undetected clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will propel new mechanistic insights from accumulating metagenomic data.

Cyr SB, Schlanger K, Raphael BH, Kersh EN, Joseph SJ. Emergence and evolution of mosaic penA-60 and penA-237 alleles in a Neisseria gonorrhoeae core genogroup that was historically susceptible to extended spectrum cephalosporins

Introduction

Neisseria gonorrhoeae (Ng) has successively developed resistance to all previously recommended antimicrobial therapies, with ceftriaxone being the last option for monotherapy of gonorrhea. Global emergence and international spread of the FC428 clone derived mosaic penA-60 allele, associated with highlevel ceftriaxone minimum inhibitory concentrations (MICs) in non FC428 clone Ng lineages, has become an increasing concern. The penA-60 allele carrying Ng was first identified in the U.S. in Las Vegas, Nevada (2019; GCWGS-102723), with a multi-locus sequence type (MLST)-1901 strain, in a non FC428 clone Ng lineage, which is associated with a historically ceftriaxone susceptible core genogroup. Later in 2022, an allele genetically similar to penA-60, mosaic penA-237, was identified in the UK (H22-722) and France (F92) with high-level ceftriaxone MICs and both belonged to MLST-1901.

Methods

In this study, we assessed phylogenomic relatedness and antimicrobial resistance (AMR) determinant profiles of these three isolates with high-level ceftriaxone MICs among a global collection of 2,104 genomes belonging to the MLST-1901 core genome cluster group 31, which includes strains separated by a locus threshold of 200 or fewer differences (Ng_cgc_200). Recombination events in and around the penA coding region were catalogued and potential sources of inter species recombinant DNA were also inferred.

Results

The global population structure of MLST-1901 core genogroup falls into 4 major lineages. Isolates GCWGS-10723, F92, and H22-722 clustered within Lineage 1, which was dominated by non-mosaic penA-5 alleles. These three isolates formed a clade within Lineage 1 that consisted of isolates from North America and southeast Asia. Neisseria subflava and Neisseria sicca were identified as likely progenitors of two independent recombination events that may have led to the generation of mosaic penA-60 and penA-237, within a possible non-mosaic penA-5 background.

Discussions

Our study suggests that there are multiple evolutionary pathways that could generate concerning mosaic penA alleles via homologous recombination of historically susceptible Ng lineages with Neisseria commensals. Enhanced surveillance of gonococcal strains and Neisseria commensals is crucial for understanding of the evolution of AMR, particularly in less-studied regions (e.g., Asia), where high-level ceftriaxone MICs and multi-drug resistance are more prevalent.

Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care

OBJECTIVES

The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea.

METHODS

We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis.

RESULTS

We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n = 7) and gonorrhoea (n = 1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n = 2), inform antimicrobial therapy (n = 5) and identify cross-contamination (n = 1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management.

CONCLUSIONS

While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.

Mini-Multilocus Sequence Typing Scheme for the Global Population of Neisseria gonorrhoeae

The increasing problem of antimicrobial resistance in N. gonorrhoeae necessitates the development of molecular typing schemes that are suitable for rapid and mass screening. The objective of this study was to design and validate a mini-MLST scheme for N. gonorrhoeae based on global pathogen population data. Using sequences of seven housekeeping genes of 21,402 isolates with known MLSTs from the PubMLST database, we identified eighteen informative polymorphisms and obtained mini-MLST nucleotide profiles to predict MLSTs of isolates. We proposed a new MLST grouping system for N. gonorrhoeae based on mini-MLST profiles. Phylogenetic analysis revealed that MLST genogroups are a stable characteristic of the N. gonorrhoeae global population. The proposed grouping system has been shown to bring together isolates with similar antimicrobial susceptibility, as demonstrated by the characteristics of major genogroups. Established MLST prediction algorithms based on nucleotide profiles are now publicly available. The mini-MLST scheme was evaluated using a MLST detection/prediction method based on the original hydrogel DNA microarray. The results confirmed a high predictive ability up to the MLST genogroup. The proposed holistic approach to gonococcal population analysis can be used for the continuous surveillance of known and emerging resistant N. gonorrhoeae isolates.

penA profile of Neisseria gonorrhoeae in Guangdong, China: Novel penA alleles are related to decreased susceptibility to ceftriaxone or cefixime

BACKGROUND

Resistance to extended-spectrum cephalosporins (ESCs) has become a public health concern with the spread of Neisseria gonorrhoeae and increasing antimicrobial resistance. Mutation of penA, encoding penicillin-binding protein 2, represents a mechanism of ESC resistance. This study sought to assess penA alleles and mutations associated with decreased susceptibility (DS) to ESCs in N. gonorrhoeae.

MATERIALS AND METHODS

In 2021, 347 gonococci were collected in Guangdong, China. Minimum inhibitory concentations (MICs) of ceftriaxone and cefixime were determined, and whole-genome sequencing and phylogenetic analysis were performed. Multi-locus sequence typing (MLST) and conventional resistance determinants such as penA, mtrR, PonA and PorB were analysed. penA was genotyped and sequence-aligned using PubMLST.

RESULTS

Genome-wide phylogenetic analysis revealed that the prevalence of DS to ESCs was highest in Clade 11.1 (100.0%), Clade 2 (66.7%) and Clade 0 (55.7%), and the leading cause was strains with penA-60.001 or new penA alleles in clades. The penA phylogenetic tree is divided into two branches: non-mosaic penA and mosaic penA. The latter contained penA-60.001, penA-10 and penA-34. penA profile analysis indicated that A311V and T483S are closely related to DS to ESCs in mosaic penA. The new alleles NEIS1753_2840 and NEIS1753_2837 are closely related to penA-60.001, with DS to ceftriaxone and cefixime of 100%. NEIS1753_2660, a derivative of penA-10 (A486V), has increased DS to ceftriaxone. NEIS1753_2846, a derivative of penA-34.007 (G546S), has increased DS to cefixime.

CONCLUSION

This study identified critical penA alleles related to elevated MICs, and trends of gonococcus-evolved mutated penA associated with DS to ESCs in Guangdong.

Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century

Core genome multilocus sequence typing (cgMLST) is commonly used to classify bacterial strains into different types, for taxonomical and epidemiological applications. However, cgMLST schemes require central databases for the nomenclature of new alleles and sequence types, which must be synchronized worldwide and involve increasingly intensive calculation and storage demands. Here, we describe a distributed cgMLST (dcgMLST) scheme that does not require a central database of allelic sequences and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria. We classify 69,994 worldwide Neisseria strains into multi-level clusters that assign species, lineages, and local disease outbreaks. We divide Neisseria meningitidis into 168 endemic lineages and three epidemic lineages responsible for at least 9 epidemics in the past century. According to our analyses, the epidemic and endemic lineages experienced very different population dynamics in the past 100 years. Epidemic lineages repetitively emerged from endemic lineages, disseminated worldwide, and apparently disappeared rapidly afterward. We propose a stepwise model for the evolutionary trajectory of epidemic lineages in Neisseria, and expect that the development of similar dcgMLST schemes will facilitate epidemiological studies of other bacterial pathogens.

Antimicrobial Resistance Profiling and Genome Analysis of the penA-60.001 Neisseria gonorrhoeae Clinical Isolates in China in 2021

BACKGROUND

Neisseria gonorrhoeae antimicrobial resistance (AMR) is an urgent public health threat. With dissemination of FC428-related clones, the efficacy of ceftriaxone has become controversial.

METHODS

Agar dilution and whole genome sequencing were used to analyze AMR.

RESULTS

High resistance to penicillin (75.2%), tetracycline (87.9%), ciprofloxacin (98.3%), ceftriaxone (8.9%), cefixime (14.3%), and azithromycin (8.6%) was observed among 463 isolates first collected in China in 2021. All penA-60.001 clones exhibited resistance to ceftriaxone or cefixime, and 1 of the 12 cases was resistant to azithromycin. ngMAST and ngSTAR of penA-60.001 isolates showed that single-nucleotide polymorphisms in the porB, tbpB, ponA, gyrA, and parC genes were the major causes of different sequence types. MLST-7365 (n = 5) and MLST-1903 (n = 3) were main genotypes, and the other 4 strains featured MLST-10314, MLST-13871, MLST-7827 and MLST-1600. Furthermore, resistance markers (eg, penA, blaTEM-1, blaTEM-135) and virus factors were detected. Most penA-60.001 strains were fully mixed with global FC428-related clones; 2021-A2 and F89 had the same origin; and 2021-A1 exhibited a unique evolutionary trajectory.

CONCLUSIONS

Results provide the first demonstration of extremely severe AMR rates of N gonorrhoeae in China in 2021, particularly strains with ceftriaxone decreased susceptibility. The sustained transmission of penA-60.001 subclones might further threaten treatment effectiveness.

Emergence of a predominant sequence type ST7363 and the increasing trend of resistance to cefixime and ceftriaxone in Neisseria gonorrhoeae in Southern Taiwan, 2019-2021

BACKGROUND/PURPOSE

Multi-drug resistance and the presence of epidemic lineages of Neisseria gonorrhoeae locally and globally were important clinical and public health issues. We aimed to investigate the molecular epidemiology and the antimicrobial susceptibility profiles of N. gonorrhoeae in Southern Taiwan.

METHODS

Between 2019 and 2021, adult patients who had suspected gonorrhea and attended a urology clinic in southern Taiwan were recruited to participate in this study. Clinical data from medical records and a questionnaire, antimicrobial susceptibility testing using a disk diffusion test in accordance with the guidelines by the Clinical and Laboratory Standards Institute, and Multi-locus sequence typing (MLST) were analyzed.

RESULTS

A total of 500 patients participated in the surveillance study. Among them, 232 N. gonorrhoeae isolates were identified, but only 164 isolates were recovered for further research. ST7363 (n = 83, 50.61%) was found to be the predominant sequence type, followed by ST1583 (n = 24, 14.63%), ST1588 (n = 13, 7.93%), and ST7827 (n = 12, 7.32%). 100% resistance to penicillin and 99.4% non-susceptible rate of ciprofloxacin were observed. The azithromycin resistant rate being 15.24% and the cefixime non-susceptible rate being 17.07% were alarming, both with decreasing trends in susceptibilities during 2019-2021. The 25 azithromycin resistant isolates were mainly belonged to ST7363 (n = 12) and ST7827 (n = 3). Seven (4.2%) isolates were ceftriaxone non-susceptible. Among them, four were assigned to be ST 7827 and three belonged to ST7363.

CONCLUSION

We observed the emergence of a predominant sequence type ST7363 in southern Taiwan. Compared with previous Taiwan studies, the increasing trend of resistance to cefixime and ceftriaxone necessitates clinicians' alertness for clinical treatment response of the extended spectrum cephalosporins and the further surveillance monitor.

Genomic analysis of 1710 surveillance-based Neisseria gonorrhoeae isolates from the USA in 2019 identifies predominant strain types and chromosomal antimicrobial-resistance determinants

This study characterized high-quality whole-genome sequences of a sentinel, surveillance-based collection of 1710 Neisseria gonorrhoeae (GC) isolates from 2019 collected in the USA as part of the Gonococcal Isolate Surveillance Project (GISP). It aims to provide a detailed report of strain diversity, phylogenetic relationships and resistance determinant profiles associated with reduced susceptibilities to antibiotics of concern. The 1710 isolates represented 164 multilocus sequence types and 21 predominant phylogenetic clades. Common genomic determinants defined most strains' phenotypic, reduced susceptibility to current and historic antibiotics (e.g. bla _TEM plasmid for penicillin, tetM plasmid for tetracycline, gyrA for ciprofloxacin, 23S rRNA and/or mosaic mtr operon for azithromycin, and mosaic penA for cefixime and ceftriaxone). The most predominant phylogenetic clade accounted for 21 % of the isolates, included a majority of the isolates with low-level elevated MICs to azithromycin (2.0 µg ml^-1), carried a mosaic mtr operon and variants in PorB, and showed expansion with respect to data previously reported from 2018. The second largest clade predominantly carried the GyrA S91F variant, was largely ciprofloxacin resistant (MIC ≥1.0 µg ml^-1), and showed significant expansion with respect to 2018. Overall, a low proportion of isolates had medium- to high-level elevated MIC to azithromycin ((≥4.0 µg ml^-1), based on C2611T or A2059G 23S rRNA variants). One isolate carried the penA 60.001 allele resulting in elevated MICs to cefixime and ceftriaxone of 1.0 µg ml^-1. This high-resolution snapshot of genetic profiles of 1710 GC sequences, through a comparison with 2018 data (1479 GC sequences) within the sentinel system, highlights change in proportions and expansion of select GC strains and the associated genetic mechanisms of resistance. The knowledge gained through molecular surveillance may support rapid identification of outbreaks of concern. Continued monitoring may inform public health responses to limit the development and spread of antibiotic-resistant gonorrhoea.

Graphene in nanomedicine: A review on nano-bio factors and antibacterial activity

Graphene-based nanomaterials possess potent antibacterial activity and have engrossed immense interest among researchers as an active armour against pathogenic microbes. A comprehensive perception of the antibacterial activity of these nanomaterials is critical to the fabrication of highly effective antimicrobial nanomaterials, which results in highly efficient and enhanced activity. These materials owing to their antimicrobial activity are utilized as nanomedicine against various pathogenic microbes. The present article reviews the antimicrobial activity of graphene and its analogs such as graphene oxide, reduced graphene oxide as well as metal, metal oxide and polymeric composites. The review draws emphasis on the effect of various nano-bio factors on the antibacterial capability. It also provides an insight into the antibacterial properties of these materials along with a brief discussion on the discrepancies in their activities as evidenced by the scientific communities. In this way, the review is expected to shed light on future research and development in graphene-based nanomedicine.

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.

Systematic Review and Meta-Analysis to Estimate the Treatment Effect and Inform a Noninferiority Margin for a Phase 3 Noninferiority Trial in Uncomplicated Urogenital Gonorrhea

BACKGROUND

Active-controlled noninferiority studies are used to investigate novel agents for uncomplicated urogenital gonorrhea (uUGC) as placebo-controlled trials are unethical. A systematic literature review and meta-analysis were conducted to estimate the ceftriaxone and proxy-for-placebo microbiological treatment effect and determine an appropriate noninferiority margin for phase 3 trials.

METHODS

Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed. To account for interstudy variability, a weighted, noniterative random-effects model was fitted using "R" software to estimate the microbiological response rate and 95% confidence intervals (CIs) for ceftriaxone and proxy-for-placebo (treatment with an antibiotic the isolate was subsequently confirmed resistant to, or spontaneous resolution without treatment). I2 , τ2 , and P values were computed and included in the meta-analysis forest plot.

RESULTS

Seventeen studies were included in the meta-analysis; 14 reported ceftriaxone response in micro-intent-to-treat and microbiologically evaluable populations, and 3 reported proxy-for-placebo treatment response in uUGC (microbiologically evaluable population only). Microbiological treatment effect was estimated by subtracting the upper end of the CI for placebo from the lower end of the CI for ceftriaxone. Overall microbiological response was 98% (95% CI, 97-99) for ceftriaxone and 44% (95% CI, 34-54) for proxy-for-placebo, resulting in a microbiological treatment effect of 43%. A noninferiority margin of 15% preserved 65% of the ceftriaxone treatment effect, exceeding the 50% recommended per US Food and Drug Administration guidance for noninferiority studies.

CONCLUSIONS

Results of this systematic literature review and meta-analysis could help inform the design, conduct, and analysis of future clinical studies in uUGC.

Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections

The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.

First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016

The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.

Dissemination and genome analysis of high-level ceftriaxone-resistant penA 60.001 Neisseria gonorrhoeae strains from the Guangdong Gonococcal Antibiotics Susceptibility Programme (GD-GASP), 2016-2019

Background: After Neisseria gonorrhoeae FC428 was first found in Japan, ceftriaxone-resistant strains disseminated globally, and the gonococcal resistance rate increased remarkably. Epidemiological investigations are greatly significant for the analysis of antimicrobial resistance (AMR) trends, molecular features and evolution. Objectives: To clarify the AMR trend from 2016–2019 and reveal the molecular characteristics and evolution of ceftriaxone-resistant penA 60.001 isolates. Methods: The minimum inhibitory concentrations (MICs) of antibiotics against 4113 isolates were detected by the agar dilution method. N. gonorrhoeae multiantigen sequence typing (NG-MAST), multilocus sequence typing (MLST) and N.gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) were used to identify the sequence types. Genome analysis was conducted to analyze resistance genes, virulence factors, and evolutionary sources. Results: Isolates with decreased ceftriaxone susceptibility have increased from 2.05% (2016) to 16.18% (2019). Six ceftriaxone-resistant isolates possessing penA 60.001 appeared in Guangdong Province, and were resistant to ceftriaxone, penicillin, tetracycline, ciprofloxacin and cefixime, but susceptible to azithromycin and spectinomycin. Single-nucleotide polymorphisms (SNPs) in the porB gene were the major cause of different NG-MAST types. ST1903 was the main NG-STAR genotype and only strain-ZH545 was ST7365, with molecular features consistent with the MICs. Furthermore, different MLSTs suggested diverse evolutionary sources. Genome analysis revealed a set of virulence factors along with the resistance genes “penA” and “blaTEM-1B”. Half of penA 60.001 strains were fully mixed with global FC428-related strains. Conclusions: Global FC428-related clones have disseminated across Guangdong, possibly causing decreased ceftriaxone susceptibility. Enhanced gonococcal surveillance will help elucidate the trajectory of transmission and curb further dissemination.