背景:淋病奈瑟菌的抗菌素耐药性(AMR)对公共健康构成威胁,因为菌株已对可用于治疗淋病的抗微生物剂产生耐药性。全基因组测序(WGS)可以检测和预测耐药性,以加强淋病的控制和预防。在赞比亚,淋病奈瑟菌的分子流行病学数据很少。这项研究旨在确定从卢萨卡性传播感染(STI)诊所就诊的患者中分离出的淋病奈瑟菌的遗传多样性。赞比亚。
方法:进行了一项横断面研究,对2019年至2020年从122例淋病患者中分离出的38例淋病奈瑟菌进行了测序。AMR曲线通过E检验确定,并使用NucliSenseasyMaG磁性装置提取DNA。在IlluminaNextSeq550平台上进行全基因组测序。细菌分析管道(BAP),可随时在以下网址获得:https://cge。cbs.dtu.dk/services/CGEPipeline-1.1用于物种的识别,组装基因组,多位点序列分型(MLST),质粒和AMR基因的检测。使用CCphylo数据集确定单核苷酸多态性(SNP)的系统发育。
结果:最常见的STs分别为ST7363,ST1921和ST1582,其次是ST1583(13%),新颖的ST17026(7.9%),ST1588(7.9%),ST1596(5.3%),ST11181(5.3%),ST11750(2.6/%)和ST11241(2.6%)在38个基因分型分离株中。blaTeM-1B和tetM(55%)是AMR基因最普遍的组合,其次是blaTeM-1B(18.4%),tetM(15.8%),和blaTeM-1B的组合,ermT,tetL为分离株的2.6%。环丙沙星中AMR表型的预测,青霉素,四环素,阿奇霉素,还有头孢克肟.23.7%的突变组合是GryA(S91F),parC(E91G),ponA(L421)和rpsJ(V57M),其次是gyrA(S91F)的18.4%,ponA(L421P),rpsJ(V57M),和18.4%的gyrA(D95G,S91F),ponA(L421P),和rpsJ(V57M)。gyrA中的组合(D95G,S91F)和rpsJ(V57M),和gyrA(D95G,S91F),parC(E91F),ponA(L421P)和rpsJ(V57M)各占13.2%。质粒TEM-1(84.2%),tetM(15.8%),所有分离株均检测到淋球菌遗传岛(GGI)。
结论:这项研究揭示了淋病奈瑟菌与blaTEM-1,tetM,pona,gyra,和与青霉素高抗性相关的parC基因,四环素,和环丙沙星要求修订赞比亚的标准治疗指南和改进抗菌药物管理。
BACKGROUND: Antimicrobial resistance (AMR) of Neisseria gonorrhoeae is a threat to public health as strains have developed resistance to antimicrobials available for the treatment of gonorrhea. Whole genome sequencing (WGS) can detect and predict antimicrobial resistance to enhance the control and prevention of gonorrhea. Data on the molecular epidemiology of N. gonorrhoeae is sparse in Zambia. This study aimed to determine the genetic diversity of N. gonorrhoeae isolated from patients attending sexually transmitted infection (STI) clinics in Lusaka, Zambia.
METHODS: A cross-sectional study that sequenced 38 N. gonorrhoeae isolated from 122 patients with gonorrhea from 2019 to 2020 was conducted. The AMR profiles were determined by the E-test, and the DNA was extracted using the NucliSens easyMaG magnetic device. Whole genome sequencing was performed on the Illumina NextSeq550 platform. The Bacterial analysis pipeline (BAP) that is readily available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 was used for the identification of the species, assembling the genome, multi-locus sequence
typing (MLST), detection of plasmids and AMR genes. Phylogeny by single nucleotide polymorphisms (SNPs) was determined with the CCphylo dataset.
RESULTS: The most frequent STs with 18.4% of isolates each were ST7363, ST1921 and ST1582, followed by ST1583 (13%), novel ST17026 (7.9%), ST1588 (7.9%), ST1596 (5.3%), ST11181 (5.3%), ST11750 (2.6/%) and ST11241 (2.6%) among the 38 genotyped isolates. The blaTeM-1B and tetM (55%) was the most prevalent combination of AMR genes, followed by blaTeM-1B (18.4%), tetM (15.8%), and the combination of blaTeM-1B, ermT, and tetL was 2.6% of the isolates. The AMR phenotypes were predicted in ciprofloxacin, penicillin, tetracycline, azithromycin, and cefixime. The combination of mutations 23.7% was gryA (S91F), parC (E91G), ponA (L421) and rpsJ (V57M), followed by 18.4% in gyrA (S91F), ponA (L421P), rpsJ (V57M), and 18.4% in gyrA (D95G, S91F), ponA (L421P), and rpsJ (V57M). The combinations in gyrA (D95G, S91F) and rpsJ (V57M), and gyrA (D95G, S91F), parC (E91F), ponA (L421P) and rpsJ (V57M) were 13.2% each of the isolates. Plasmid TEM-1 (84.2%), tetM (15.8%), and gonococcal genetic island (GGI) was detected in all isolates.
CONCLUSIONS: This study revealed remarkable heterogeneity of N. gonorrhoeae with blaTEM-1, tetM, ponA, gyrA, and parC genes associated with high resistance to penicillin, tetracycline, and ciprofloxacin demanding revision of the standard treatment guidelines and improved antimicrobial stewardship in Zambia.