Department of Laboratory Medicine, National University Hospital, Singapore.
Environmental Health Institute, National Environment Agency, Singapore.
Microb Genom. 2021 Nov;7(11). doi: 10.1099/mgen.0.000708.
comprises three subspecies. These closely related strains are typically multi-drug-resistant and can cause difficult-to-treat infections. Dominant clusters of isolates with increased pathogenic potential have been demonstrated in pulmonary infections in the global cystic fibrosis (CF) population. An investigation was performed on isolates cultured from an Asian, predominantly non-CF population to explore the phylogenomic relationships within our population and compare it to global isolates. Whole-genome-sequencing was performed on isolates between 2017 and 2019. Bioinformatic analysis was performed to determine multi-locus-sequence-type, to establish the phylogenetic relationships between isolates, and to identify virulence and resistance determinants in these isolates. A total of 210 isolates were included, of which 68.5 % (144/210) were respiratory samples. These isolates consisted of 140 (66.6 %) . subsp. , 67 (31.9 %) . subsp. abscessus and three (1.4 %) . subsp. . Dominant sequence-types in our population were similar to those of global CF isolates, but SNP differences in our population were comparatively wider despite the isolates being from the same geographical region. ESX (ESAT-6 secretory) cluster three appeared to occur most commonly in ST4 and ST6 subsp. , but other virulence factors did not demonstrate an association with isolate subspecies or sample source. We demonstrate that although similar predominant sequence-types are seen in our patient population, cross-transmission is absent. The risk of patient-to-patient transmission appears to be largely limited to the vulnerable CF population, indicating infection from environmental sources remains more common than human-to-human transmission. Resistance and virulence factors are largely consistent across the subspecies with the exception of clarithromycin susceptibility and ESX-3.
该菌包含三个亚种。这些密切相关的菌株通常具有多重耐药性，并可能导致难以治疗的感染。在全球囊性纤维化 (CF) 人群的肺部感染中，已经证实了具有增加致病性潜力的分离株优势群。对来自亚洲、主要是非 CF 人群的分离株进行了一项调查，以探索我们人群中的系统发生关系，并将其与全球分离株进行比较。对 2017 年至 2019 年培养的 210 株分离株进行了全基因组测序。生物信息学分析用于确定多位点序列型，建立分离株之间的系统发育关系，并确定这些分离株中的毒力和耐药决定因素。共纳入 210 株分离株，其中 68.5%（144/210）为呼吸道样本。这些分离株包括 140 株（66.6%）. 亚种，67 株（31.9%）. 脓肿亚种和 3 株（1.4%）. 亚种。我们人群中的优势序列型与全球 CF 分离株相似，但尽管分离株来自同一地理区域，我们人群中的 SNP 差异却相对较宽。ESX（ESAT-6 分泌）簇 3 似乎在 ST4 和 ST6 亚种中最常见，但其他毒力因子与分离株亚种或样本来源没有关联。我们证明，尽管我们的患者人群中存在相似的主要序列型，但不存在交叉传播。患者之间传播的风险似乎主要局限于脆弱的 CF 人群，表明感染来自环境来源比人与人之间的传播更为常见。除克拉霉素敏感性和 ESX-3 外，耐药性和毒力因子在各亚种之间基本一致。
