A Whole-genome Sequencing Analysis of Neisseria gonorrhoeae Isolates in China: An Observational Study

Abstract

Background Tracking the spread of the Neisseria gonorrhoeae strains with decreased susceptibility or resistance to cephalosporins is a major priority for global surveillance programmes. Whole-genome sequencing (WGS) has been widely used by increasing countries in North America, Europe, and Pacific to determine the decreased susceptible or resistance determinants of Neisseria gonorrhoeae , track the spread of these determinants throughout the gonococcal population at national or regional level. However, no studies to date have examined the genomic epidemiology of gonorrhea in Asia where the antimicrobial resistant strains of Neisseria gonorrhoeae appears to have emerged before disseminating the strains globally. Methods We obtained clinical isolates and data from the China Gonococcal Resistance Surveillance Programme (China-GRSP) from 2012 to 2013. We sequenced the genomes of 435 clinical isolates of Neisseria gonorrhoeae , including 112 (25.6%) isolates with decreased susceptibility to ceftriaxone (Cfx-DS). We assessed the association between antimicrobial resistance genotype and phenotype. We also compared our data with the whole genome data of the isolates from the USA and the UK in the GenBank. Findings The most prevalent MLST STs in our gonococcal population were MLST ST7827 (n = 74), followed by ST7365 (n = 58), ST1600 (n = 38), ST7367 (n = 35), and ST7363 (n = 29). MLST ST1901 which was reported as the predominant ST in the US was not found in our population. A total of 2512 strains, including additional 2077 published NG strains, were further included for phylogenetic analysis. It generated two distinct lineages - lineage 1 and lineage 2. Analysis of MLST ST1901 in the database indicate that most of MLST ST1901 isolates in the lineage2.6 were Cfx-DS isolates while all isolates in the lineage 2.1 were sensitive to ceftriaxone (77/110 vs. 0/13; p < 0.001). ST1901/lineage 2.6 is a ceftriaxone resistant clone which cannot distinguished by MLST genotyping. In the isolates from our study, the MICs of ceftriaxone for ST7363/lineage 2.6 isolates ranged from 0.008–0.125 mg/L (mean ± SD; 0.054 ± 0.043 mg/L) while those for ST7363/lineage 2.8 isolates ranged from 0.032–0.250 mg/L (0.134 ± 0.085 mg/L). All ST7363/lineage 2.8 isolates contained penA mosaic alleles. Interpretation To our knowledge, current study is the first WGS-based analysis of gonococcal population at national level in Asia. China harbors the different predominant clones associated with decreased susceptibility to ceftriaxone from those clones circulated in other regions. The findings from the study can be not only used as baseline data for future studies in China but also contributable to our understanding on spread of N . gonorrhoeae and its resistant strains ...

Molecular epidemiological typing of Neisseria gonorrhoeae isolates identifies a novel association between genogroup G10557 (G7072) and decreased susceptibility to cefixime, Germany, 2014 to 2017

“…High proportions of these genogroups have also been detected in many other EU/EEA countries including Belgium, Hungary, Norway, Portugal, Slovenia, Spain and Switzerland, which might indicate putative transmissions [15,16,30]. Moreover, our study describes the gonococcal population in Germany as genetically diverse, which is in line with observations made worldwide [15,16,31,32].…”

The sudden emergence of aNeisseria gonorrhoeaestrain with reduced susceptibility to extended-spectrum cephalosporins, Norway

“…For datasets where this information was lacking, we downloaded and screened the sequence data in silico against the pubMLST database to determine the ST. We did not identify any ST-7827 members among recently published sequences from Japan (13) , the USA (14) or a global gonorrhea genomic study (8) . However, in a recent study from China, 74 out of 435 isolates belonged to ST-7827 (15) , and these were included in the current study. Information on all isolates is available in a supplementary excel file (Appendix 2: supplementary_ isolate_data ).…”

Multiplex High-Resolution Melting Assay for Simultaneous Identification of Molecular Markers Associated with Extended-Spectrum Cephalosporins and Azithromycin Resistance in Neisseria gonorrhoeae

“…The assay was validated on archived bacterial samples from the China Gonococcal Resistance Surveillance Program, which consisted of DNA from 218 gonococcal isolates. 24 The genome sequencing of all archived DNA specimens was performed during a previously described study. 24 In addition, 156 clinical isolates and 182 directly extracted clinical specimens (urethral/genital swabs and first void urine samples) were also used in the evaluation stage and were collected from Shenzhen Center for Chronic Disease Control in 2017 and 2018, respectively.…”

“…24 The genome sequencing of all archived DNA specimens was performed during a previously described study. 24 In addition, 156 clinical isolates and 182 directly extracted clinical specimens (urethral/genital swabs and first void urine samples) were also used in the evaluation stage and were collected from Shenzhen Center for Chronic Disease Control in 2017 and 2018, respectively. For the clinical isolates, 25 genomic DNA was extracted by using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany), according to the user's guide.…”

“…Analytical Performance of the Multiplex HRM Assays Using Archived DNA Samples Two-hundred and eighteen archived DNA specimens with genome sequencing were analyzed using WGS technology. 24 Each target produced melting peaks that corresponded to their respective control (mutant or wild type) melting ranges. The PPV, NPV, specificity, and sensitivity of each target using WGS as a gold standard are presented in Table 4.…”