Non-pathogenic Neisseria species of the oropharynx as a reservoir of antimicrobial resistance: a cross-sectional study

Comprehensive analysis of the type VI secretion system in Neisseria: identification, distribution, and evolutionary insights

The genus Neisseria, a gram-negative diplococcus, includes commensal and pathogenic species that infect mucosal tissues, causing diseases such as gonorrhea and meningitis. The type VI secretion system (T6SS), a multifunctional molecular machine that facilitates the ability of gram-negative bacteria to deliver effectors for bacterial competition, virulence, and interaction with host cells, has been widely studied across various bacterial taxa. However, research on the T6SS in the genus Neisseria remains limited. In this study, we employed comparative genomics and pangenomics, among other bioinformatics approaches, to characterize the distribution of the T6SS and its related proteins, including effectors, immunity proteins and regulators, across different species within the genus. Through an analysis of 5,067 Neisseria genomes, we identified two complete T6SS loci. We found that more than half of the Neisseria species possess at least one complete T6SS locus. Further investigation revealed multiple T6SS-related loci. We also applied a statistics-based method for identifying T6SS-associated orthologous groups and revealed 64 new T6SS-associated proteins within the genus. Our research provides a comprehensive analysis of the T6SS in Neisseria, advancing the understanding of T6SS-related mechanisms.

Variability of antimicrobial susceptibility of commensal Neisseria species supports its use as a marker of excessive antimicrobial consumption - reflections from the results of a four-country study

This perspective explores the utility of commensal Neisseria species as an early warning sign of excessive antimicrobial consumption. Little is known as to how the prevalence and antimicrobial susceptibility of various commensal Neisseria species varies between populations around the world. We compared the prevalence and antimicrobial susceptibilities of oral commensal Neisseria species in the general population and cohorts of men who have sex with men (MSM) in four countries with available data - Belgium, Italy, Japan and Vietnam. In individuals where Neisseria spp. were detected, N. subflava was present in 70-100% of individuals in the different studies. The N. subflava azithromycin and ciprofloxacin minimum inhibitory concentrations (MICs) were higher in the MSM than in the general population. The MICs of all Neisseria spp. were very similar in the general populations of Belgium and Italy. For all Neisseria spp., azithromycin and ceftriaxone MICs were higher, whereas ciprofloxacin MICs were lower in Belgium and Italy than in Japan. The higher azithromycin and ciprofloxacin MICs observed in the cohorts of MSM compared to the general population and the higher ciprofloxacin MICs in Japan compared to Belgium and Italy are commensurate with the most commonly antimicrobial prescribed in these populations. Our results support using commensal Neisseria species as an early warning system of excessive antimicrobial consumption.

Dynamic pharyngeal carriage of Neisseria species in healthy population

Considering the significant role of commensal Neisseria carried in the pharynx on the variation of N.meningitidis and the acquisition of its resistance genes, understanding the true Neisseria population colonizing the human pharynx is of great significance. In this study, we carried out a five-month continuous survey of oropharyngeal carriage in a certain healthy population to reveal the long-term carriage status of different Neisseria species. Totally, 419 Neisseria strains were isolated from 203 out of 205 pharyngeal swabs of 49 participants. Using combined methods (MALDI-TOF-MS, rplF sequencing and genome sequencing), the isolates were identified as N.subflava (n = 290), N.mucosa (n = 52), N.oralis (n = 8), N.elongata group (n = 6) and non-species-confirmed (n = 63). N.subflava was isolated from all individuals and 168 swabs (81.95 %). N.mucosa, N.oralis, N.elongata and non-species-confirmed were isolated from 25 (45), 6 (7), 4 (5) and 20 (53) individuals (swabs) respectively. It was common that multiple Neisseria spp. or multiple clones of one species were isolated from a single sample. An identical strain could be isolated frequently from a single person within five months. These results indicate that Neisseria spp. and N.subflava are ubiquitous in human pharynx and both have diverse population; we should pay more attention to them when studying N.meningitidis or other respiratory pathogens; robust and handy method for identifying Neisseria species remains to be developed.

Antimicrobial Resistance of Neisseria gonorrhoeae Isolates among Men Who Have Sex with Men in Lower Silesia, Poland

Neisseria gonorrhoeae (NG) has developed resistance to nearly all antibiotics used for its treatment. However, very limited data are available regarding the antimicrobial resistance of NG isolates among MSM in Poland. The aim of this study was to evaluate the susceptibility of Neisseria gonorrhoeae isolates in this key population. We investigated the antimicrobial susceptibility of NG isolates to six antimicrobials (ceftriaxone, cefixime, azithromycin, ciprofloxacin, tetracycline, and benzylpenicillin). Minimum inhibitory concentrations (MICs; mg/L) were determined using Etests on gonococcal isolates. One hundred high-risk MSM were included in the study (25 HIV-positive and 75 HIV-negative using pre-exposure prophylaxis for HIV). The rate of NG infection was 28%. All NG isolates were susceptible to cefixime and ceftriaxone. Susceptibility to azithromycin was found in 69.2% (18/26) of the NG isolates and resistance in 30.8% (8/26) of NG isolates. Susceptibility to tetracycline was found in 50% (13/26) of the isolates and resistance in 50% (13/26) of the isolates. We observed gonorrhea to be more prevalent in patients with a higher number of oral sexual contacts. Increasing azithromycin resistance is especially concerning for future treatment options, especially if ceftriaxone/cefixime resistance starts to develop and for people with beta-lactam antibiotics allergies. Doxy-PEP might lose its partial efficacy for NG soon.

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.

Antimicrobial resistance determinants in the oropharyngeal microbiome of 'men having sex with men' attending an sexually transmitted infection clinic

BACKGROUND

'Men having sex with men' (MSM) represent a key population with a significant prevalence of pharyngeal Neisseria gonorrhoeae (NG) infections and a high rate of antimicrobial resistance genes in the pharyngeal microbiome. As NG can acquire antibiotic resistance genes from other commensal oropharyngeal bacteria, monitoring the prevalence of these resistance determinants is critical to curtail the spread of NG-resistant strains.

PURPOSE AND RESEARCH DESIGN

Here, we assessed the distribution of five resistance genes (pen (A), mtr (R), gyr (A), par (C), msr (D)) in the oropharynx of 164 MSM, attending an Outpatient clinic for STI screening.

RESULTS

The most frequently detected resistance gene was msr (D) (88.4%), followed by gyr (A) (67.1%). The distribution of resistance genes was not influenced by pharyngeal gonorrhea nor by the HIV status, whereas a younger age was associated with mtr (R) presence (p = .008). Subjects using mouthwash exhibited significantly lower levels of mtr (R) (p = .0005). Smoking habit was associated with a higher prevalence of par (C) (p = .02). A noteworthy association was observed between the presence of msr (D) gene and the use of antibiotics (p = .014).

CONCLUSIONS

Our findings reveal an enrichment of antimicrobial resistance genes in the oropharynx of MSM. These insights could aid in the development of screening programs and antimicrobial stewardship initiatives targeting populations at heightened risk of pharyngeal gonorrhea.

Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade

Introduction. Commensal Neisseria spp. are highly prevalent in the oropharynx as part of the healthy microbiome. N. meningitidis can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify N. meningitidis, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).Hypothesis/Gap statement. N. meningitidis may be misidentified by MALDI-TOF MS.Aim. To conduct genomic surveillance of oropharyngeal Neisseria spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal Neisseria spp. genomes.Methodology. We analysed whole genome sequence (WGS) data from 119 Neisseria spp. isolates from a surveillance programme for oropharyngeal Neisseria spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) rplF gene species identification. WGS data were used to further characterize Neisseria species found with supplementary analyses of Neisseria cinerea genomes.Results. Based on genomic species identification, isolates from the oropharyngeal Neisseria surveilence study were composed of the following species: N. meningitidis (n=23), N. subflava (n=61), N. mucosa (n=15), N. oralis (n=8), N. cinerea (n=5), N. elongata (n=3), N. lactamica (n=2), N. bacilliformis (n=1) and N. polysaccharea (n=1). Of these 119 isolates, four isolates identified as N. meningitidis (n=3) and N. subflava (n=1) by MALDI-TOF MS, were determined to be N. polysaccharea (n=1), N. cinerea (n=2) and N. mucosa (n=1) by rMLST. Phylogenetic analyses revealed that N. cinerea isolates from the general population (n=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, n=2, cluster two). The latter contained genomes misidentified as N. meningitidis using MALDI-TOF MS. These two N. cinerea clusters persisted after the inclusion of published N. cinerea WGS (n=42). Both N. cinerea clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.Conclusion. This study provides insights into the importance of genomic genus-wide Neisseria surveillance studies to improve the characterization and identification of the Neisseria genus.

Antimicrobial susceptibility of commensal Neisseria spp. in parents and their children in Belgium: a cross-sectional survey

BACKGROUND

commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species.

METHODS

we assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n = 38) and children (n = 50) of 35 families in Belgium.

RESULTS

various commensal Neisseria (n = 5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. Neisseria subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). Neisseria mucosa was more prevalent in children [41/50 (82%)] than parents [23/38 (60.5%); P < .05], while N. bacilliformis was more prevalent in parents [7/36 (19.4%)] than children [2/50 (4%); P < .05]. Neisseria bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5 mg/l; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents.

INTERPRETATION

the N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.

Measuring individual colony MICs is a more sensitive method to detect the effect of antimicrobials on antimicrobial susceptibility than the proportion of colonies resistant

The ResistAZM randomized controlled trial found that the receipt of ceftriaxone/azithromycin, compared to ceftriaxone was not associated with an increase in the proportion of oral commensal Neisseria spp. and streptococci with azithromycin resistance 14 days after treatment. We repeated the analyses by measuring the minimum inhibitory concentrations (MICs) of azithromycin and ceftriaxone for individual colonies of commensal Neisseria spp. and streptococci at day 0 and day 14 in both arms. The receipt of ceftriaxone/azithromycin but not ceftriaxone was associated with an increase in azithromycin MIC for both Neisseria spp. (P < 0.0001) and streptococci (P = 0.0076). Likewise, ceftriaxone/azithromycin but not ceftriaxone monotherapy was associated with an increase in ceftriaxone MICs in Neisseria spp. (P = 0.0035). Whereas the proportion method failed to detect an association between the receipt of azithromycin and increased macrolide resistance, the MIC distribution method detected this effect. The MIC distribution method is thus a more sensitive method to assess the effect of antimicrobials on antimicrobial susceptibility.

BACKGROUND

The ResistAZM randomized controlled trial found that the receipt of ceftriaxone/azithromycin, compared to ceftriaxone was not associated with an increase in the proportion of oral commensal Neisseria spp. and streptococci with azithromycin resistance 14 days after treatment.

METHODS

We repeated the analyses by measuring the minimum inhibitory concentrations (MICs) of azithromycin and ceftriaxone for individual colonies of commensal Neisseria spp. and streptococci at day 0 and day 14 in both arms.

RESULTS

The receipt of ceftriaxone/azithromycin but not ceftriaxone was associated with an increase in azithromycin MIC for both Neisseria spp. (P < 0.0001) and streptococci (P = 0.0076). Likewise, ceftriaxone/azithromycin but not ceftriaxone monotherapy was associated with an increase in ceftriaxone MICs in Neisseria spp. (P = 0.0035).

CONCLUSIONS

Whereas the proportion method failed to detect an association between the receipt of azithromycin and increased macrolide resistance, the MIC distribution method detected this effect. The MIC distribution method is thus a more sensitive method to assess the effect of antimicrobials on antimicrobial susceptibility.