Meningococcal quinolone resistance originated from several commensal Neisseria species

Quinolone resistance is increasing in Neisseria meningitidis, with high prevalence in China (>70%), but its origin is unknown. The aim of this study was to investigate donors of mutation-harboring gyrA alleles in N. meningitidis. A total of 198 N. meningitidis and 293 commensal Neisseria isolates were collected during 2005 and 2018 in Shanghai, China. Minimum inhibitory concentrations (MICs) of ciprofloxacin were determined by agar dilution method. Resistance-associated genes gyrA and parC were sequenced and analyzed. A few Neisseria isolates were performed Illumina sequencing. The prevalence of quinolone resistance in N. meningitidis and commensal Neisseria was 67.7% (134/198) and 99.3% (291/293), respectively. All the 134 quinolone-resistant N. meningitidis isolates possessed mutations in T91 (n=123) and/or D95 (n=12) of GyrA, with 7 isolates also harboring ParC mutations and showing higher MICs. Phylogenetic analysis of gyrA sequence identified six clusters. Among the 71 mutation-harboring gyrA alleles represented by 221 N. meningitidis isolates and genomes (n=221), 12 alleles (n=103, 46.6%) were included in N. meningitidis cluster, while 20 alleles (n=56) in N. lactamica cluster, 27 alleles (n=49) in N. cinerea cluster, and 9 alleles (n=10) in N. subflava cluster. Genomic analyses identified the exact N. lactimica donors of seven mutation-harboring gyrA alleles (gyrA92, gyrA97, gyrA98, gyrA114, gyrA116, gyrA151, and gyrA230) and the N. subflava donor isolate of gyrA171, with recombinant fragment ranging from 634bp to 7499bp. Over half of quinolone-resistant N. meningitidis isolates acquired resistance by horizontal gene transfer from three commensal Neisseria species. Quinolone resistance in N. meningitidis increases in a stepwise manner.