Whole Genome Sequencing and Molecular Analysis of Carbapenemase-Producing Escherichia coli from Intestinal Carriage in Elderly Inpatients

Abstract

The spread of carbapenemase-producing (CP) Enterobacterales is currently a worldwide concern, especially in the elderly. Twelve CP-E. coli isolated from rectal swabs of colonized inpatients aged ≥65 years from four hospitals in two Italian cities (Milan and Rome) were analyzed by whole genome sequencing (WGS) to obtain multi-locus sequence typing (MLST), identification of carbapenemase-encoding genes, resistome, plasmid content, and virulence genes. MLST analysis showed the presence of 10 unrelated lineages: ST410 (three isolates from three different hospitals in two cities) and ST12, ST38, ST69, ST95, ST131, ST189, ST648, ST1288, and ST1598 (one isolate each). Most isolates (9/12, 75%) contained a serine-β-lactamase gene (5 blaKPC-3, 2 blaKPC-2, and 2 blaOXA-181), while three isolates harbored a metallo-β-lactamase gene (two blaNDM-5 and one blaVIM-1). In most CP-E. coli, the presence of more than one plasmid was observed, with the predominance of IncF. Several virulence genes were detected. All isolates contained genes enhancing the bacterial fitness, such as gad and terC, and all isolates but one, fimH, encoding type 1 fimbriae. In conclusion, CP-E. coli clones colonizing elderly patients showed heterogeneous genetic backgrounds. We recommend strict surveillance to monitor and prevent the spread of successful, high-risk clones in healthcare settings.

Comparison of Lateral Flow Immunochromatography and Phenotypic Assays to PCR for the Detection of Carbapenemase-Producing Gram-Negative Bacteria, a Multicenter Experience in Mexico

“…Although it is a weakness that we found few Enterobacterales VIM-producers and few P. aeruginosa NDM-producers, and no Enterobacterales IMP-producers, it is worth mentioning that sensitivity and specificity of phenotypic methods, especially of Carba NP-EDTA and eCIM, exhibited a worse performance in comparison to other publications. An opportunity of study is the sequencing of the carbapenemase encoding-genes, which might elucidate possible new enzymes not reported by this assay or characterize the carbapenemases that were falsely negative by the NG-Test CARBA-5 ® [38,39].…”

Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece

“…A literature search at the NCBI database (last consulted on 28 December 2022) revealed that over 750 different plasmids might carry the bla NDM-1 encoding gene in E. coli [ 21 , 22 , 23 ]. Recently, a genomic epidemiological study of global carbapenemase-producing E. coli conducted between 2015–2017 in 62 countries showed that NDM-1 was the most frequent NDM-enzyme and was associated with various STs within diverse plasmids [ 24 ]; 13 different STs were identified obtained from Egypt, Morocco, Serbia, Romania, Guatemala, Kuwait, Philippines, Russia, Thailand and Vietnam [ 25 ].…”