First Report of IMI-2-Producing Enterobacter bugandensis and CTX-M-55-Producing Escherichia coli isolated from Healthy Volunteers in Tunisia

Rym Ben Sallem; Ameni Arfaoui; Afef Najjari; Isabel Carvalho; Abdelmalek Lekired; Hadda-Imen Ouzari; Karim Ben Slama; Alex Wong; Carmen Torres; Naouel Klibi

doi:10.3390/antibiotics12010116

First Report of IMI-2-Producing Enterobacter bugandensis and CTX-M-55-Producing Escherichia coli isolated from Healthy Volunteers in Tunisia

Antibiotics (Basel). 2023 Jan 8;12(1):116. doi: 10.3390/antibiotics12010116.

Authors

Rym Ben Sallem^{1

2

3}, Ameni Arfaoui¹, Afef Najjari¹, Isabel Carvalho^{4

5}, Abdelmalek Lekired¹, Hadda-Imen Ouzari¹, Karim Ben Slama², Alex Wong⁶, Carmen Torres⁴, Naouel Klibi¹

Affiliations

¹ Laboratory of Microorganisms and Active Biomolecules (LR03ES03), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia.
² Bioresources, Environment and Biotechnology Laboratory (LR22ES04), Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia.
³ Department of Sciences, Sainte Anne University, 1695 Route 1, Clare, NS B0W 1M0, Canada.
⁴ Biochemistry and Molecular Biology, University of La Rioja, 26006 Logrono, Spain.
⁵ Department of Veterinary Sciences, University of Trás-os-Montes-and Alto Douro, 5000-801 Vila Real, Portugal.
⁶ Department of Biology, Carleton University, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada.

Abstract

The aim of this study was to characterize the prevalence of fecal carriage of extended-spectrum beta-lactamases and carbapenemase-producing Gram-negative bacteria among healthy humans in Tunisia. Fifty-one rectal swabs of healthy volunteers were plated on MacConkey agar plates supplemented with cefotaxime or imipenem. The occurrences of resistance genes, integrons, and phylogroup typing were investigated using PCR and sequencing. The genetic relatedness of isolates was determined by pulsed-field-gel-electrophoresis (PFGE) and multilocus-sequence-typing (MLST). Whole-genome-sequencing (WGS) was performed for the carbapenem-resistant isolate. Sixteen ESBL-producing Escherichia coli isolates and one carbapenem-resistant Enterobacter bugandensis were detected out of the fifty-one fecal samples. The ESBL-producing E. coli strains contained genes encoding CTX-M-15 (n = 9), CTX-M-1 (n = 3), CTX-M-27 (n = 3), and CTX-M-55 (n = 1). Three CTX-M-1-producers were of lineages ST131, ST7366, and ST1158; two CTX-M-15-producers belonged to lineage ST925 and ST5100; one CTX-M-27-producer belonged to ST2887, and one CTX-M-15-producer belonged to ST744. Six isolates contained class 1 integrons with the following four gene cassette arrangements: dfrA5 (two isolates), dfrA12-orf-aadA2 (two isolates), dfrA17-aadA5 (one isolate), and aadA1 (one isolate). E. bugandensis belonged to ST1095, produced IMI-2 carbapenemase, and contained qnrE1 and fosA genes. A genome-sequence analysis of the E. bugandensis strain revealed new mutations in the bla_ACT and qnr genes. Our results reveal an alarming rate of ESBL-E. coli in healthy humans in Tunisia and the first description of IMI-2 in E. bugandensis.

Keywords: E. bugandensis; ESBL; IMI-2; Tunisia; carbapenemases; healthy humans.

Grants and funding

R.B.S. received a post-doctoral fellowship from the Innovet-AMR project GA-092018F, IDRC Grant number 109048. A.A. received a grant from the Tunisian Ministry of Higher Education and Scientific Research. The work performed at the University of La Rioja was financed by MCIN/AEI/10.13039/501100011033 of Spain.