P-1269. Genetic markers of antimicrobial resistance in oropharyngeal commensal Neisseria

TL;DR

This study identifies genetic markers of antibiotic resistance in non-harmful Neisseria bacteria in the throat, highlighting their potential to transfer resistance to harmful species like N. gonorrhoeae.

Contribution

The study reveals the role of commensal Neisseria as a reservoir for antimicrobial resistance genes and identifies specific markers like msr(D) and blaTEM-1B.

Findings

The msr(D) gene showed high predictive value for azithromycin resistance in Neisseria isolates.

The blaTEM-1B gene was highly specific for cefixime and ceftriaxone resistance.

Commensal Neisseria species may contribute to the spread of antimicrobial resistance through horizontal gene transfer.

Abstract

Non-pathogenic Neisseria species are of increasing significance given their potential of harboring antimicrobial resistant (AMR) genes and studies have shown horizontal gene transmission (HGT) can be responsible for antimicrobial resistance in pathogens such as Neisseria gonorrhoeae.

From 5/2022 – 12/2023, oral rinse specimen from men in a HIV pre-exposure prophylaxis (PrEP) program were plated on LBVT-SNR media for culture. Minimum inhibitory concentrations (MIC) to antibitoics were determined using E-tests. Isolates were sequenced using Illumina and analyzed using Geneious Prime software. Species identification resulted from NCBI blasts of 16s and rpoB gene-aligned sequences. AMR genes were identified using Resfinder (4.5.0) from the Center for Genomic Epidemiology.

In total, 48 Neisseria isolates were grown from 42 different individuals, with N. subflava being the most prevalent species (n=23). Of the 48 isolates, 41 (85%) were resistant to Azithromycin, 3 (6%) to Cefixime, 3 (6%) to Ceftriaxone, and 26 (54%) to doxycycline. The msr(D) gene was found to have sensitivity of 31.5%, specificity 85.7%, positive predictive value (PPV) 92.9%, and negative predictive value (NPV) 17.7% for overall Azithromycin resistance, yet sensitivity 83.3%, specificity 88.9%, PPV 71.4%, NPV 94.1% for high-level Azithromycin resistance (MIC ≥ 256 μg/mL). The blaTEM-1B gene had sensitivity of 100%, specificity 91.1%, PPV 41.8%, and NPV 100 % for both cefixime and ceftriaxone resistance. Detection of any tet gene (B/G/M) had a sensitivity 46.2%, specificity 81.8%, PPN 74.9%, and NPV 56.4% for doxycycline resistance.

Prevalence of AMR genes detected in multiple commensal Neisseria species showed the potential of HGT to pathogenic Neisseria species. Strikingly, 83% of isolates with high-level azithromycin resistance had the msr(D) gene. In this study, detection of msr(D) had high NPV for high-level resistance and high PPV for overall resistance to Azithromycin. Our study sheds light on the previously underappreciated dynamic of AMR gene reservoir and inter-species transfers in the oropharyngeal microbiome that may play an important role in the rapid increase of multi-drug-resistant N. gonorrhoeae.

Shangxin Yang, PhD, D(ABMM), Eurofins | Viracor Clinical Diagnostics: Advisor/Consultant