WGS of Commensal Neisseria Reveals Acquisition of a New Ribosomal Protection Protein (MsrD) as a Possible Explanation for High Level Azithromycin Resistance in Belgium

Abstract

In this study, we characterized all oropharyngeal and anorectal isolates of <i>Neisseria</i> spp. in a cohort of men who have sex with men. This resulted in a panel of pathogenic <i>Neisseria</i> (<i>N. gonorrhoeae</i> [n = 5] and <i>N. meningitidis</i> [n = 5]) and nonpathogenic <i>Neisseria</i> (<i>N. subflava</i> [n = 11], <i>N. mucosa</i> [n = 3] and <i>N. oralis</i> [n = 2]). A high proportion of strains in this panel were resistant to azithromycin (18/26) and ceftriaxone (3/26). Whole genome sequencing (WGS) of these strains identified numerous mutations that are known to confer reduced susceptibility to azithromycin and ceftriaxone in <i>N. gonorrhoeae</i>. The presence or absence of these known mutations did not explain the high level resistance to azithromycin (>256 mg/L) in the nonpathogenic isolates (8/16). After screening for antimicrobial resistance (AMR) genes, we found a ribosomal protection protein, Msr(D), in these highly azithromycin resistant nonpathogenic strains. The complete integration site originated from <i>Streptococcus pneumoniae</i> and is associated with high level resistance to azithromycin in many other bacterial species. This novel AMR resistance mechanism to azithromycin in nonpathogenic <i>Neisseria</i> could be a public health concern if it were to be transmitted to pathogenic <i>Neisseria</i>. This study demonstrates the utility of WGS-based surveillance of nonpathogenic <i>Neisseria</i>.