Genomic epidemiology of Neisseria gonorrhoeae in Shenzhen, China, during 2019-2020: increased spread of ceftriaxone-resistant isolates brings insights for strengthening public health responses

Abstract

The antimicrobial resistance (AMR) in gonorrhea poses global threat of increasing public health concern. In response to this concern, molecular surveillance has been widely utilized to detail the changes in the evolution and distribution of Neisseria gonorrhoeae during AMR transmission. In this study, we performed a comprehensive molecular surveillance of 664 N. gonorrhoeae isolates collected in Shenzhen, one of the cities with the largest mobile population in China, 2019-2020. In 2020, ceftriaxone showed an unprecedented high resistance rate of 24.87%, and 67.83% of the ceftriaxone-resistant (Cro-R) isolates harbored a nonmosaic penA allele. The Cro-R isolates with nonmosaic penA alleles showed a tremendous increasing trend from 0.00% in 2014 to 20.45% in 2020, which proves the need for monitoring nonmosaic penA-related resistance. Importantly, genotyping indicated that multilocus sequence typing ST11231 (35.71%) had a notable rate of ceftriaxone resistance, which might become the focus of future surveillance. Whole-genome sequencing analysis showed that the internationally spreading FC428 clones have circulated in Shenzhen region with typical ceftriaxone resistance (MIC ≥ 0.5 mg/L) maintained. Our surveillance combined with genomic analysis provides current information to update gonorrhea management guidelines and emphasizes that continuous AMR surveillance for N. gonorrhoeae is essential. IMPORTANCE We conducted a comprehensive molecular epidemiology analysis for antimicrobial-resistant Neisseria gonorrhoeae in Shenzhen during 2019-2020, which provided important data for personalized treatment and adjustment of monitoring strategy. Briefly, the proportion of ceftriaxone-resistant (Cro-R) isolates reached a stunning prevalence rate of 24.87% in 2020. A typical increment of Cro-R isolates with nonmosaic penA alleles proves the necessity of monitoring nonmosaic AMR mechanism and involving it into developing molecular detection methods. Whole-genome sequencing analysis showed that the international spreading FC428 clone has been circulating in Shenzhen with typical ceftriaxone resistance (MIC ≥ 0.5 mg/L) maintained. In summary, we conducted a comprehensive epidemiology study, providing significant data for therapy management. Our results not only improve the understanding of the distribution and transmission of AMR in N. gonorrhoeae but also provide effective AMR data for improving surveillance strategies in China.

Keywords: N. gonorrhoeae sequence typing for antimicrobial resistance; antimicrobial resistance; molecular surveillance; multilocus sequence typing; whole-genome sequencing.

Fig 1

Major antimicrobial susceptibility of N. gonorrhoeae in Shenzhen, China, 2014–2020. Percentages of gonococcal isolates resistant to (A) Cip, (B) Azi, (C) Pen, and (D) Cro. Bars in dashes boxes were data from our previous research in Shenzhen for 2014–2018. Cip-R, resistant to ciprofloxacin; Azi-R, resistant to azithromycin; Pen-R, resistant to penicillin; Cro-R, resistant to ceftriaxone.

Fig 2

Group 0 of goeBURST analysis. The frequency of occurrence is represented by the font size of MLST STs and the size of the nodes. Node color: purple, group founder; desaturated blue, subgroup founder; light gray, common node. Link color: black, link drawn without recourse to tiebreak rules; blue, link drawn using tiebreak rule 1 (number of SLVs); green, link drawn using tiebreak rule 2 (number of DLVs); red, link drawn using tiebreak rule 3 (number of TLVs).

Fig 3

Phylogenetic tree of 281 NG-STAR STs constructed using MEGA 11. The external color trips that range from inner to outer are as follows: trip 1, mosaic or nonmosaic penA allele, crimson, mosaic penA, cadet blue, nonmosaic penA; trip 2, bar chart showing number of isolates in each ST; trip 3, number of Cro-R isolates in each ST; trip 4, number of Azi-R isolates in each ST. STs indexed in the main text were indicated with arrows outside trips.

Fig 4

Maximum-likelihood phylogeny of 664 Shenzhen gonococcal isolates, 34 previously reported FC428 clones, and WHO-F. The maximum-likelihood phylogeny was constructed based on 46,305 SNP sites along the whole genome. The external color trips that range from inner to outer are as follows: trip 1, previously reported FC428 clones; trip 2, any mosaic penA alleles; trip 3, ceftriaxone MIC; trip 4, susceptibility categories of ceftriaxone (R, resistant; S, susceptible); trip 5, azithromycin MIC; trip 6, susceptibility categories of azithromycin (R, resistant; S, susceptible); trip 7, predominant NG-STAR STs; trip 8, predominant MLST STs. The percentages of Cro-R and Azi-R in FC428 subclade and A2543 subclade are represented by pie charts.