STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA.
Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA.
J Clin Microbiol. 2024 Nov 13;62(11):e0070424. doi: 10.1128/jcm.00704-24. Epub 2024 Oct 3.
(Nm) and (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase () gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm gene replaced the Ng pseudogenes, and . Together, this study demonstrates that closely related species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests.
（Nm）和（Ng）是人病原体，有时占据相同的解剖位置。Ng 是淋病的病原体，每年在全球感染 8700 万人，由于耐药性不断增加，它是一个紧迫的威胁。Ng 是尿道生殖道的病原体，可能感染口咽或直肠部位，通常无症状。相反，Nm 是一种机会性病原体。虽然它通常是口咽道的共生菌，但它也是细菌性脑膜炎的主要原因，全球有 120 万病例，导致严重的发病率和死亡率。由于它们共享的解剖位置和遗传相似性，Ng 和 Nm 之间可能发生水平基因转移（HGT），这给准确检测和治疗带来了挑战。通过淋病分离株监测项目和加强美国对抗耐药淋病的反应进行常规监测，在密尔沃基（MIL）发现了六个令人关注的泌尿生殖道分离株，其物种鉴定相互矛盾。虽然所有六个分离株均通过核酸扩增检测（NAAT）呈 Ng 阳性，基质辅助激光解吸/电离飞行时间鉴定分离株为 Ng，但两种生化试验 Gonochek-II 和 API NH 将其分类为 Nm。为了解决这一差异，我们对所有分离株进行了 Illumina MiSeq 全基因组测序（WGS），并使用了各种生物信息学工具。使用 WGS 数据的 BMScan 进行的物种检测分析鉴定所有分离株均为 Ng。此外，Kraken 显示超过 98%的 WGS 读数映射到 Ng 基因组，<1%映射到 Nm。重组分析在所有 MIL 分离株中鉴定出 γ-谷氨酰转肽酶（）基因内的推定 HGT，该基因是用于区分 Nm 和 Ng 的生化试验中的关键组成部分。进一步分析确定 Nm 是 HGT 事件的来源。具体来说，活跃的 Nm 基因取代了 Ng 假基因和。总的来说，这项研究表明，共享生态位的密切相关的物种发生了 HGT，这导致了生化试验后物种的错误鉴定。重要的是，NAAT 准确地检测到 Ng。这种错误鉴定突出了使用 WGS 不断评估诊断或细菌鉴定试验的重要性。
