Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
Sci Total Environ. 2024 Dec 1;954:176486. doi: 10.1016/j.scitotenv.2024.176486. Epub 2024 Sep 23.
To improve the understanding of antimicrobial resistance (AMR) in migratory birds derived-Enterobacter cloacae (E. cloacae) complex and its spread at the human-bird-environment interface, we isolated 11 strains of third-generation cephalosporin-resistant E. cloacae from 1003 specimens from 29 migratory bird species over two years in Chongming, Shanghai, China. The comprehensive analysis incorporated second- and third-generation sequencing techniques and extensive bioinformatic analysis. Four human-associated E. cloacae sequence types (STs), including ST432, ST412, ST1, and ST639, were found in migratory birds. We confirmed that the bla and bla genes were the major genotypes of the β-lactamase resistance genes in E. cloacae found in migratory birds. In addition, a thorough genomic analysis was performed on a global collection of 398 E. cloacae isolates carrying the bla gene from 46 different countries. China had the highest proportion with 19.10 % (76/398), followed by Singapore with 18.34 % (73/398), Nigeria with 15.83 % (63/398), and the USA with 14.07 % (56/398). The first transmission of E. cloacae carrying bla and bla was defined around 1894 and 1549, respectively. Time-based phylogenetic analysis revealed that host jumps among humans, birds, and the environment led to the emergence of modern strains with ESBL- and carbapenem-resistant genes from about 2004 to 2016. The detection rate of insertion sequences (IS) of E. cloacae carrying bla from human sources is higher than that from migratory bird sources, which is related to the different genetic environments caused by antibiotic selective pressure. It is crucial to have a comprehensive understanding of the characteristics exhibited by bla producing E. cloacae in different ecological environments. Our results contribute to the effective monitoring and implementation of proactive strategies to reduce the spread of multidrug-resistant E. cloacae.
为了提高对迁徙鸟类源阴沟肠杆菌（E. cloacae）复合耐药（AMR）的理解及其在人-鸟-环境界面传播的认识，我们从中国上海崇明岛 29 种迁徙鸟类的 1003 个样本中分离出了 11 株第三代头孢菌素耐药的阴沟肠杆菌。综合分析采用了二代和三代测序技术以及广泛的生物信息学分析。在迁徙鸟类中发现了 4 种与人类相关的阴沟肠杆菌序列型（ST），包括 ST432、ST412、ST1 和 ST639。我们证实，bla 和 bla 基因是迁徙鸟类源阴沟肠杆菌β-内酰胺酶耐药基因的主要基因型。此外，对来自 46 个不同国家的携带 bla 基因的 398 株阴沟肠杆菌全球分离株进行了全面的基因组分析。中国的比例最高，为 19.10%（76/398），其次是新加坡，为 18.34%（73/398），尼日利亚为 15.83%（63/398），美国为 14.07%（56/398）。首次定义了bla 和 bla 携带的 E. cloacae 的传播发生在 1894 年和 1549 年左右。基于时间的系统发育分析表明，人类、鸟类和环境之间的宿主跳跃导致了具有 ESBL 和碳青霉烯耐药基因的现代菌株的出现，这发生在 2004 年至 2016 年期间。从人类来源的bla 携带 E. cloacae 中检测到的插入序列（IS）的检出率高于从迁徙鸟类来源的检出率，这与抗生素选择压力引起的不同遗传环境有关。全面了解不同生态环境中bla 产生的 E. cloacae 的特征至关重要。我们的研究结果有助于对多药耐药性 E. cloacae 的传播进行有效监测和实施积极的防控策略。
