Emergence and evolution of antimicrobial resistance genes and mutations inNeisseria gonorrhoeae
Authors: Yahara Koji , Ma Kevin C. , Mortimer Tatum D. , Shimuta Ken , Nakayama Shu-ichi , Hirabayashi Aki , Suzuki Masato , Jinnai Michio , Ohya Hitomi , Kuroki Toshiro , Watanabe Yuko , Yasuda Mitsuru , Deguchi Takashi , Eldholm Vegard , Harrison Odile B. , Maiden Martin C. J. , Grad Yonatan H. , Ohnishi Makoto 
Published: October 2020

Antimicrobial resistance inNeisseria gonorrhoeaeis a global health concern. Strains from two internationally circulating sequence types, ST-7363 and ST-1901, have acquired resistance to treatment with third-generation cephalosporins mainly due to the emergence of mosaicpenAalleles. These two STs were first detected in Japan; however, when and how the mosaicpenAalleles emerged and spread to other countries remains unknown. Here, we addressed the evolution ofpenAalleles by obtaining complete genomes from three Japanese ST-1901 clinical isolates harboring mosaicpenAallele 34 (penA-34) dating from 2005 and generating a phylogenetic representation of 1,075 strains sampled from 37 countries. We also sequenced the genomes of 103 Japanese ST-7363N. gonorrhoeaeisolates from 1996-2005 and reconstructed a phylogeny including 88 previously sequenced genomes. Based on an estimate of the time of emergence of ST-1901 harboring mosaicpenA-34and ST-7363 harboring mosaicpenA-10, and >300 additional genome sequences of Japanese strains representing multiple STs isolated in 1996-2015, we suggest thatpenA-34 in ST-1901 was generated frompenA-10 via recombination with anotherNeisseriaspecies, followed by a second recombination event with a gonococcal strain harboring wildtypepenA-1. Following the acquisition ofpenA-10 in ST-7363, a dominant sub-lineage rapidly acquired fluoroquinolone resistance mutations at GyrA 95 and ParC 87-88, possibly due to independent mutations rather than horizontal gene transfer. Literature data suggest the emergence of these resistance determinants may reflect selection from the standard treatment regimens in Japan at that time. Our findings highlight how recombination and antibiotic use across and withinNeisseriaspecies intersect in driving the emergence and spread of drug-resistant gonorrhea.

Author summary

Antimicrobial resistance is recognized as one of the greatest threats to human health, andNeisseria gonorrhoeaeresistance is classified as one of the most urgent. The two major internationally spreading lineages resistant. to first line drugs likely originated in Japan, but when and how their genetic resistance determinants emerged remain unknown. In this study, we conducted an evolutionary analysis using clinicalN. gonorrhoeaeisolates from 37 countries, including a historical collection of Japanese isolates, to investigate the emergence of resistance in each of the two major lineages. We showed that thepenAallele responsible for resistance to cephalosporins, the first-line treatment for gonorrhea, was possibly generated by two recombination events, one from anotherNeisseriaspecies and one from anotherN. gonorrhoeaelineage. We also showed that mutations responsible for resistance to a previously widely used antibiotic treatment occurred twice independently in one of the two major lineages. The emergence of the genetic resistance determinants potentially reflects selection from the standard treatment regimen at that time. Our findings highlight how recombination (horizontal gene transfer) and antibiotic use across and within a bacterial species intersect in driving the emergence and spread of antimicrobial resistance genes and mutations.