An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

Abstract

The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species E. cloacae, K. pneumoniae and E. coli emerged from their common ancestry. A representative MGI from E. cloacae was named MIR17-GI, because it harbors the novel β-lactamase gene variant blaMIR17. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective E. cloacae isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst Enterobacteriaceae. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.

Exoproteomic profiling uncovers critical determinants for virulence of livestock-associated and human-originated Staphylococcus aureus ST398 strains

“…Relevant features of the 30 S. aureus strains with ST398 used in this study are presented in Table 1 . All strains were isolated, typed and whole-genome sequenced by Illumina sequencing as previously described [ 22 ], allowing their phylogenetic distinction as LA-ST398 or human-originated ST398 using RAxML v7.0.4.…”

Less Is More: Toward a Genome-Reduced Bacillus Cell Factory for “Difficult Proteins”

“…Next generation sequencing was used to determine the copy number of plasmid pRAG3:: isaA in B. subtilis 168 and PG10 as described previously. 31 Total DNA extraction for sequencing was performed from colonies using the Ultraclean Microbial DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, US) according to the manufacturer’s protocol. DNA concentrations were determined using a Qubit 2.0 fluorometer and the dsDNA HS and/or BR assay kit (Life technologies, Carlsbad, CA, US).…”

Development of a MALDI-TOF MS-based screening panel for accelerated differential detection of carbapenemases in Enterobacterales using the direct-on-target microdroplet growth assay

“…In addition to the identification of carbapenemases, the detection of AmpC production was included in the screening panel as a complementary feature, due to the decreased susceptibility to carbapenems that these enzymes may cause [32][33][34] . DOT-MGA coincided with the PCR in one AmpC-positive isolate.…”