Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis

Abstract

Background Escherichia coli (E. coli) is a common human pathogen, responsible for a broad spectrum of infections. Sites of infection can vary, but the hepato-biliary system is of particular concern due to the infection-associated formation of gallstones and the spread of pathogens from the bile ducts into the bloodstream. Case presentation The presented case is striking, as the detected isolate showed a positive string test. This hypermucoviscous phenotype is atypical for E. coli and a particular feature of hypervirulent Klebsiella pneumoniae (K. pneumoniae) variants. Objectives To provide new insights into the genomic background of an E. coli strain with an unusual hypermucoviscous phenotype using hybrid short- and long-read sequencing approaches. Results Complete hybrid assemblies of the E. coli genome and plasmids were done and used for genome based typing. Isolate 537–20 was assigned to the multilocus sequence type ST88 and serotype O8:H4. The strain showed a close relationship to avian pathogenic strains. Analysis of the chromosome and plasmids revealed the presence of several virulence factors, such as the Conserved Virulence Plasmidic (CVP) region on plasmid 537-20_1, including several iron acquisition genes (sitABCD, iroABCDEN, iucABCD, hbd) and the iutA gene encoding the receptor of the siderophore aerobactin. The hypermucoviscous phenotype could be caused by encapsulation of putative K. pneumoniae origin. Conclusions Hybrid sequencing enabled detailed genomic characterization of the hypermucoviscous E. coli strain, revealing virulence factors that have their putative origin in K. pneumoniae.

Genomic insights into ESBL-producing Escherichia coli isolated from non-human primates in the Peruvian Amazon

“…This characteristic resembles the HMV phenotype observed in certain virulent Klebsiella pneumoniae strains, providing an advantage for invasive infections ( 16 , 36 ). While the identification of HMV strains in E. coli is uncommon, it has been described in livestock and clinical strains ( 37 , 38 ). Analysis of the ECPI21 genome identified a highly conserved Klebsiella -capsule type K31 (98.86% identity; Figure 4C ).…”

“…Functional assays are necessary to confirm the association between K31 capsule type and the HMV phenotype observed in ECPI21. The coexistence of ESBL and HMV phenotypes should be a significant concern for public health due to their potentially enhanced virulence ( 16 , 36 – 38 ).…”

Molecular Markers and Antimicrobial Resistance Patterns of Extraintestinal Pathogenic Escherichia coli from Camel Calves Including Colistin-Resistant and Hypermucoviscuous Strains

“…While being a frequent trait of hypervirulent Klebsiella pneumoniae strains [ 26 ], it is rarely reported from E. coli. In all reported cases so far, the strains were ExPEC [ 16 , 27 , 28 , 29 ]. One study speculates that this trait could be a frequent, but overlooked, characteristic of UPEC strains [ 16 ].…”

Emergence of a NDM-1-producing ST25 Klebsiella pneumoniae strain causing neonatal sepsis in China

“…A string test was done using a standard inoculation loop to gently lift a colony of DY1928 grown on a blood agar plate to detect the hypermucoid phenotype, and the string test was rated as positive if a mucoid string of > 5 mm was observed ( Neumann et al, 2022 ). Biofilm formation assay was conducted according to the methods described in previous studies ( Heiden et al, 2020 ).…”