Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA.
Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Lancet Microbe. 2022 May;3(5):e376-e381. doi: 10.1016/S2666-5247(22)00034-9. Epub 2022 Mar 24.
Neisseria gonorrhoeae poses an urgent public health threat because of increasing antimicrobial resistance; however, much of the circulating population remains susceptible to historical treatment regimens. Point-of-care diagnostics that report susceptibility could allow for reintroduction of these regimens, but development of such diagnostics has been restricted to ciprofloxacin, for which susceptibility can be predicted from a single locus. We aimed to define genetic variants associated with susceptibility to penicillin and tetracycline.
We collected publicly available global whole-genome sequencing data (n=12 045) from clinical N gonorrhoeae isolates, with phenotypic resistance data for penicillin (n=6935), and tetracycline (n=5727). Using conditional genome-wide association studies, we defined genetic variants associated with susceptibility to penicillin and tetracycline. We excluded isolates that could not be classified as either susceptible or resistant. To validate our results, we assembled 1479 genomes from the US Centers for Disease Control and Prevention (CDC)'s Gonococcal Isolate Surveillance Project, for which urethral specimens are collected at sentinel surveillance sites across the USA. We evaluated the sensitivity and specificity of susceptibility-associated alleles using Clinical & Laboratory Standards Institute breakpoints for susceptibility and non-resistance in both the global and validation datasets.
In our conditional penicillin genome-wide association study, the presence of a genetic variant defined by a non-mosaic penA allele without an insertion at codon 345 was associated with penicillin susceptibility and had the highest negative effect size (β) of significant variants (p=5·0x10, β -2·5). In combination with the absence of bla, this variant predicted penicillin susceptibility with high specificity (99·8%) and modest sensitivity (36·7%). For tetracycline, the wildtype allele at rpsJ codon 57, encoding valine, was associated with tetracycline susceptibility (p=5·6x10, β -1·6) after conditioning on the presence of tetM. The combination of rpsJ codon 57 allele and tetM absence predicted tetracycline susceptibility with high specificity (97·2%) and sensitivity (88·7%).
As few as two genetic loci can predict susceptibility to penicillin and tetracycline in N gonorrhoeae with high specificity. Molecular point-of-care diagnostics targeting these loci have the potential to increase available treatments for gonorrhoea.
National Institute of Allergy and Infectious Diseases, the National Science Foundation, and the Smith Family Foundation.
淋病奈瑟菌由于抗药性不断增强，对公共卫生构成了紧迫威胁；然而，大部分流行菌株仍然对历史治疗方案敏感。能够报告药敏结果的即时检测诊断方法可以重新使用这些方案，但此类检测方法的开发仅限于环丙沙星，因为可以从单个基因座预测其敏感性。本研究旨在确定与青霉素和四环素敏感性相关的遗传变异。
我们收集了来自临床淋病奈瑟菌分离株的公开可用的全球全基因组测序数据（n=12045），并获得了青霉素（n=6935）和四环素（n=5727）的表型耐药数据。使用条件全基因组关联研究，我们确定了与青霉素和四环素敏感性相关的遗传变异。我们排除了不能归类为敏感或耐药的分离株。为了验证我们的结果，我们从美国疾病控制与预防中心（CDC）的淋病分离株监测项目中组装了 1479 个基因组，这些基因组是从美国各地的哨点监测站点采集尿道标本获得的。我们使用临床和实验室标准协会（CLSI）的药敏和非耐药折点，在全球和验证数据集评估了与药敏相关的等位基因的灵敏度和特异性。
在我们的条件青霉素全基因组关联研究中，具有非镶嵌 penA 等位基因且不存在 345 位密码子插入的遗传变异与青霉素敏感性相关，且具有最高的显著变异的负效应大小（β）（p=5.0x10，β-2.5）。与 bla 缺失结合，该变异可高度特异性（99.8%）和适度敏感性（36.7%）预测青霉素敏感性。对于四环素，编码缬氨酸的 rpsJ 密码子 57 上的野生型等位基因与 tetM 存在时的四环素敏感性相关（p=5.6x10，β-1.6）。rpsJ 密码子 57 等位基因和 tetM 缺失的组合以高特异性（97.2%）和敏感性（88.7%）预测四环素敏感性。
淋病奈瑟菌中，只要两个遗传位点就可以高度特异性地预测对青霉素和四环素的敏感性。针对这些位点的分子即时检测诊断方法有可能增加淋病的治疗选择。
美国国立过敏和传染病研究所、美国国家科学基金会和史密夫家族基金会。
