Azithromycin susceptibility of Neisseria gonorrhoeae in the USA in 2017: a genomic analysis of surveillance data

Abstract

BackgroundThe number of cases of gonorrhoea in the USA and worldwide caused by Neisseria gonorrhoeae is increasing (555 608 reported US cases in 2017, and 87 million cases worldwide in 2016). Many countries report declining in vitro susceptibility of azithromycin, which is a concern because azithromycin and ceftriaxone are the recommended dual treatment in many countries. We aimed to identify strain types associated with decreased susceptibility to azithromycin. MethodsWe did a genomic analysis of N gonorrhoeae isolates obtained by the US Gonococcal Isolate Surveillance Project. Isolates were whole-genome sequenced based on decreased susceptibility to azithromycin (minimal inhibitory concentration [MIC] ≥2 µg/mL, using agar dilution antibiotic susceptibility testing) and geographical representation. Bioinformatic analyses established genomic diversity, strain population dynamics, and antimicrobial resistance profiles. Findings 410 isolates were sorted into more than 20 unique phylogenetic clades. One predominant persistent clade (consisting of 97 isolates) included the most isolates with azithromycin MICs of 2 µg/mL or higher (61 of 97 [63%] vs 59 of 311 [19%]; p<0•0001) and carried a mosaic mtr (multiple transferable resistance) locus (68 of 97 [70%] vs two of 313 [1%]; p<0•0001). Of the remaining 313 isolates, 57 (18%) had decreased susceptibility to azithromycin (MIC ≥4 µg/mL), which was attributed to 23S rRNA variants (56 of 57 [98%]) and formed phylogenetically diverse clades, showing various levels of clonal expansion. Interpretation Reduced azithromycin susceptibility was associated with expanding and persistent clades harbouring two well described resistance mechanisms, mosaic mtr locus and 23S rRNA variants. Understanding the role of recombination, particularly within the mtr locus, on the fitness and expansion of strains with decreased susceptibility has important implications for the public health response to minimise gonorrhoea transmission. Funding US Centers for Disease Control and Prevention (CDC), CDC Combating Antibiotic Resistant Bacteria initiative,

Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations

“…Accordingly, we hypothesize that any influence A39T might have on mtrCDE depression requires the presence of other MtrR amino acid changes common in clinical strains such as R44Q or Y48D substitution ( 4 ); as shown in our fluorescence polarization-based DNA binding studies, R44 and Y48 are critical for high affinity DNA binding (Table 3 and Supplementary Figure S5 ). This hypothesis is further supported by the high frequency of accompanying mutations in clinical isolates of N. gonorrhoeae containing the A39T mutation ( 57 ) ( Supplementary Table S6 ).…”

“…Further, both mutations similarly elevated expression of mtrC and rpoH (Figure 4 ). These mutations could contribute to resistance in gonococcal isolates in tandem with other mtrR point mutations as suggested by the occurrence of accompanying mutations in the HTH motif or mtrCDE operator in a recent survey of clinical isolates in the USA ( 57 ) ( Supplementary Table S6 ).…”

A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

“…As described above, other mechanisms have also been recently discovered that increase the MIC of azithromycin (Table 2 ), such as mosaicism affecting the efflux pump-encoding mtrCDE genes and its repressor mtrR , mainly when the mosaic spans the mtrR promoter region and mtrD gene [ 23 , 24 ]. Some studies have recently reported the local expansion of azithromycin-resistant N. gonorrhoeae lineages carrying an mtr mosaic in the USA [ 122 , 123 , 134 ] and Australia [ 118 ]. However, the extent of the dispersion of this mechanism to other parts of the world has not been studied yet.…”

Update to CDC's Treatment Guidelines for Gonococcal Infection, 2020

“…During 2018, among men who have sex with men, the proportion of GISP isolates with an azithromycin alert value was 8.6%, compared with 2.9% among men who have sex with women only ( 1 ). Studies have associated development of reduced azithromycin susceptibility with azithromycin exposure among patients with N. gonorrhoeae infection ( 24 , 25 ).…”