Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

Gut Pathogens

Saisong Xiao¹  Yun Li²  Diangeng Li³  Xian Zhao³  Zhongyi Fan³  Xuege Jiang³  Yi Yu³  Changting Liu³  Peng Wang³  Xuelin Zhang⁴ 

[1] 0000 0001 1431 9176, grid.24695.3c, Department of Anesthesiology, Dongzhimen Hospital Beijing University of Chinese Medicine, 100700, Beijing, China;0000 0004 1761 8894, grid.414252.4, Respiratory Diseases Department, The Eighth Medical Center of PLA General Hospital, 100091, Beijing, China;0000 0004 1761 8894, grid.414252.4, Respiratory Diseases Department, The Second Medical Center of PLA General Hospital, 100853, Beijing, China;0000 0004 1761 8894, grid.414252.4, Respiratory Diseases Department, The Second Medical Center of PLA General Hospital, 100853, Beijing, China;0000 0004 1761 8894, grid.414252.4, Hyperbaric Oxygen Department, The First Medical Center of PLA General Hospital, 100853, Beijing, China;

关键词: Escherichia coli;    Antibiotic resistance;    High-throughput sequencing;    ESBL;    KPC;   

DOI  :  10.1186/s13099-019-0298-5

来源: publisher

【 摘 要 】

BackgroundMultidrug resistance is a growing global public health threat with far more serious consequences than generally anticipated. In this study, we investigated the antibiotic resistance and genomic traits of a clinical strain of Escherichia coli LCT-EC001.ResultsLCT-EC001 was resistant to 16 kinds of widely used antibiotics, including fourth-generation cephalosporins and carbapenems. In total, up to 68 determinants associated with antibiotic resistance were identified, including 8 beta-lactamase genes (notably producing ESBLs and KPCs), 31 multidrug efflux system genes, 6 outer membrane transport system genes, 4 aminoglycoside-modifying enzyme genes, 10 two-component regulatory system genes, and 9 other enzyme or transcriptional regulator genes, covering nearly all known drug-resistance mechanisms in E. coli. More than half of the resistance genes were located close to mobile genetic elements, such as plasmids, transposons, genomics islands, and insertion sequences. Phylogenetic analysis revealed that this strain may have evolved from E. coli K-12 but is a completely new MLST type.ConclusionsAntibiotic resistance was extremely severe in E. coli LCT-EC001, mainly due to mobile genetic elements that allowed the gain of a large quantity of resistance genes. The antibiotic resistance genes of E. coli LCT-EC001 can probably be transferred to other bacteria. To the best of our knowledge, this is the first report of a strain of E. coli which has such a large amount of antibiotic resistance genes. Apart from providing an E. coli reference genome with an extremely high multidrug-resistant background for future analyses, this work also offers a strategy for investigating the complement and characteristics of genes contributing to drug resistance at the whole-genome level.

【 授权许可】

CC BY