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. 2022 Aug 3;10(8):1561.
doi: 10.3390/microorganisms10081561.

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

Maria Giufrè  1 , Giulia Errico  1 , Monica Monaco  1 , Maria Del Grosso  1 , Michela Sabbatucci  1   2 , Annalisa Pantosti  1 , Marina Cerquetti  1 , Michela Pagnotta  1 , Manuela Marra  3 , Maria Carollo  3 , Angelo Rossini  4 , Elena Fogato  5 , Elisabetta Cesana  6 , Flaminia Gentiloni Silverj  7 , Dorjan Zabzuni  6 , Marco Tinelli  6   8
Affiliations

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

Maria Giufrè et al. Microorganisms. .

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.

Keywords: MLST; carbapenemase; colonization; elderly; high-risk Escherichia coli clones; multidrug-resistance; whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Antimicrobial susceptibility profiles of 12 CP-E. coli isolates from intestinal carriage in elderly patients. Red/orange/grey color in each column indicates percentage of resistant/susceptible, increased exposure/susceptible isolates, respectively.
Figure 2
Figure 2
SNP-based phylogeny of CP-E. coli isolates from intestinal carriage in elderly patients. The maximum likelihood tree was rooted in a reference isolate E. coli strain K12 (accession no. NC_000913.2). Sequence type (ST) is shown for each isolate.
See this image and copyright information in PMC

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