Antimicrobial Resistance Mechanisms, Multilocus Sequence Typing, and NG-STAR Sequence Types of Diverse Neisseria gonorrhoeae Isolates in KwaZulu-Natal, South Africa

Abstract

Antimicrobial resistance (AMR) is a major challenge to managing infectious diseases. Africa has the highest incidence of gonorrhoea, but there is a lack of comprehensive data from sparse surveillance programs. This study investigated the molecular epidemiology and AMR profiles of Neisseria gonorrhoeae isolates in KwaZulu-Natal province (KZN), South Africa. Repository isolates from patients attending public health care clinics for sexually transmitted infection (STI) care were used for phenotypic and genotypic analysis. An Etest was performed to determine antimicrobial susceptibility. Whole-genome sequencing (WGS) was used to determine epidemiology and to predict susceptibility by detecting resistance-associated genes and mutations. Among the 61 isolates, multiple sequence types were identified. Six isolates were novel, as determined by multilocus sequence typing. N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) determined 48 sequence types, of which 35 isolates had novel antimicrobial profiles. Two novel penA alleles and eight novel mtrR alleles were identified. Point mutations were detected in gyrA, parC, mtrR, penA, ponA, and porB1. This study revealed a high prevalence of AMR (penicillin 67%, tetracycline 89%, and ciprofloxacin 52%). However, spectinomycin, cefixime, ceftriaxone, and azithromycin remained 100% effective. This study is one of the first to comprehensively describe the epidemiology and AMR of N. gonorrhoeae in KZN, South Africa and Africa, using WGS. KZN has a wide strain diversity and most of these sequence types have been detected in multiple countries; however, more than half of our isolates have novel antimicrobial profiles. Continued surveillance is crucial to monitor the emergence of resistance to cefixime, ceftriaxone, and azithromycin.

Keywords: AMR; gonorrhoea; sexually transmitted diseases.

FIG 1

(a) AMR profiles of N. gonorrhoeae isolates collected from KwaZulu-Natal, South Africa, between 2013 and 2016. (b) Predominant AMR determinants for penicillin, tetracycline, and ciprofloxacin present per year.

FIG 2

Maximum likelihood phylogenetic tree using core genome SNP analysis for 61 KZN, South Africa N. gonorrhoeae isolates between 2013 and 2016, 14 WHO strains, and the reference genome FA 1090. Phenotypic susceptible (green)/intermediate (yellow)/resistant (purple) data using the EUCAST breakpoints shown for penicillin (PEN), ciprofloxacin (CIP), tetracycline (TET), spectinomycin (SPT), cefixime (CFM), ceftriaxone (CRO), and azithromycin (AZM). All KZN isolates were susceptible to SPT, AZM, CFM, and CRO. Resistance-associated genes/mutations are included as present (blue) or absent (gray).