目的:产碳青霉烯酶的肺炎克雷伯菌(KPC-Kp)的基因组监测对毒力至关重要,耐药性监测,和疫情遏制。
方法:通过全基因组测序(WGS)对2019-2021年从意大利北部3家医院分离的87株KPC-Kp菌株进行基因组分析,为了表征耐药性,病毒组,还有手机罩,并评估与表型抗性和临床表现的潜在关联。使用最大似然树和最小生成树来确定应变相关性并识别潜在的传播簇。
结果:总体而言,发现了15种不同的ST;主要的包括ST307(35,40.2%),ST512/1519(15,17.2%),ST20(12,13.8%),和ST101(7,8.1%)。发现33株(37.9%)KPC-Kp菌株在5个传播簇中(每个簇中的分离株数量中位数:5[3-10]),其中四个以医院内传播为特征。所有87株都带有Tn4401a转座子,携带blaKPC-3(48,55.2%),blaKPC-2(38,43.7%),在一例(1.2%)blaKPC-33中,后者基因赋予对头孢他啶/阿维巴坦(CZA)的抗性。30株(34.5%)存在孔蛋白突变;其中,7份(8.1%)携带多个Tn4401a拷贝。与没有孔蛋白突变或单个Tn4401a拷贝的菌株相比,这些菌株的特征在于CZA最低抑制浓度显着提高。分别,即使他们没有克服8ug/mL的阻力断点。每个菌株检测到中位数2个(IQR:1-2)毒力因子。与其他ST相比,在ST20中观察到最低数目(p<0.001)。虽然ST307与感染事件相关,对于ST20,可以观察到与定殖事件相关的趋势.
结论:基因组整合,阻力评分,和临床数据使我们能够定义2019年至2021年间意大利北部KPC-Kp的相对多样化,其特征是几乎没有大型传播链和罕见的医院间传播。我们的结果还提供了KPC-Kp基因组特征与某些抗菌药物或定植/感染状态的较高MIC水平之间相关性的初步证据。再次强调WGS在细菌监测中的重要性。
OBJECTIVE: Genomic surveillance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) is crucial for virulence, drug-resistance monitoring, and outbreak containment.
METHODS: Genomic analysis on 87 KPC-Kp strains isolated from 3 Northern Italy hospitals in 2019-2021 was performed by whole genome sequencing (WGS), to characterize resistome, virulome, and mobilome, and to assess potential associations with phenotype resistance and clinical presentation. Maximum Likelihood and Minimum Spanning Trees were used to determine strain correlations and identify potential transmission clusters.
RESULTS: Overall, 15 different STs were found; the predominant ones included ST307 (35, 40.2%), ST512/1519 (15, 17.2%), ST20 (12, 13.8%), and ST101 (7, 8.1%). 33 (37.9%) KPC-Kp strains were noticed to be in five transmission clusters (median number of isolates in each cluster: 5 [3-10]), four of them characterized by intra-hospital transmission. All 87 strains harbored Tn4401a transposon, carrying blaKPC-3 (48, 55.2%), blaKPC-2 (38, 43.7%), and in one case (1.2%) blaKPC-33, the latter gene conferred resistance to ceftazidime/avibactam (CZA). Thirty strains (34.5%) harbored porin mutations; of them, 7 (8.1%) carried multiple Tn4401a copies. These strains were characterized by significantly higher CZA minimum inhibitory concentration compared with strains with no porin mutations or single Tn4401a copy, respectively, even if they did not overcome the resistance breakpoint of 8 ug/mL. Median 2 (IQR:1-2) virulence factors per strain were detected. The lowest number was observed in ST20 compared to the other STs (p<0.001). While ST307 was associated with infection events, a trend associated with colonization events could be observed for ST20.
CONCLUSIONS: Integration of genomic, resistance score, and clinical data allowed us to define a relative diversification of KPC-Kp in Northern Italy between 2019 and 2021, characterized by few large transmission chains and rare inter-hospital transmission. Our results also provided initial evidence of correlation between KPC-Kp genomic signatures and higher MIC levels to some antimicrobial agents or colonization/infection status, once again underlining WGS\'s importance in bacterial surveillance.