Project description:Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E. coli, 5 Shigella spp., 21 E. albertii, 12 E. fergusonii and 5 other species) and design primers for the following species-specific regions: a 212bp region of the cyclic di-GMP regulator gene (cdgR, AW869_22935 from genome K-12 MG1655, CP014225) for E. coli/Shigella; a 393bp region of the DNA-binding transcriptional activator of cysteine biosynthesis gene (EAKF1_ch4033 from genome KF1, CP007025) for E. albertii; and a 575bp region of the palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase (EFER_0790 from genome ATCC 35469, CU928158) for E. fergusonii. We incorporated the species-specific primers into a conventional multiplex PCR assay and assessed its performance with a collection of 97 Enterobacteriaceae strains. The assay was 100% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies.
Project description:Here, we report the complete genome sequence of colistin-resistant Escherichia fergusonii strain EFCF056, isolated from chicken feces. This genome contains six plasmids, including a 204,246-bp plasmid harboring the colistin resistance gene mcr-1 These results will increase our understanding of plasmid-mediated mcr-1 gene presence and transmission in E. fergusonii.
Project description:Although Escherichia fergusonii has been identified for decades, it has rarely been recovered from clinical specimens and its clinical significance remains unclear. We describe a case of E. fergusonii bacteremia in a diabetic patient with pancreatic cancer. The isolate was confirmed by three commercial identification systems and 16S rRNA gene sequence analysis. The patient's clinical condition gradually improved, and repeated blood cultures were negative after antibiotic treatment with an in vitro active agent (ceftriaxone).
Project description:We report here the genome sequences of 55 strains belonging to the genus Escherichia from multiple animal and environmental sources. These strains include representatives of Escherichia albertii, Escherichia fergusonii, and six additional genetically distinct lineages of Escherichia spp., one of which is newly discovered and is being reported for the first time here.
