Emergence of multidrug-resistant Providencia rettgeri clone in food-producing animals: A public health threat

Abstract

The occurrence of carbapenemases encoding genes in Providencia rettgeri is a critical public health concern since this species has intrinsic resistance to several antimicrobials, including polymyxins. The identification of this multidrug-resistant (MDR) pathogen outside the hospital setting has become increasingly frequent, and raises an alert for the global health agencies, as they indicate a possible spread of such pathogens. Herein, we described three MDR P. rettgeri isolates carrying a diversity of antimicrobial resistance genes (ARGs) isolated from stool samples of swine and bovine in Brazil. Molecular analysis revealed that all isolates belonged to the same clone. The whole genome sequencing (WGS) of a representative isolate (PVR-188) was performed by MiSeq Illumina® platform, while the assembling and annotation was achieved using SPAdes and Prooka, respectively. The WGS analyses indicated the presence of ARGs that confer resistance to β-lactams (bla _NDM-1, bla _CTX-M-2), quinolones (qnrD1), aminoglycosides (aadA2, aadA1, aph(3')-Via), phenicol (catB2), sulfonamides (sul1, sul2), and trimethoprim (dfrA12, dfrA1). The presence of three plasmid replicons (Col3M, IncQ1, and IncT) was detected, but no phage sequences were found. The phylogenetic analyses confirmed the genomic relationship of the PVR-188 with P. rettgeri isolates recovered from animals and humans in the USA and Malaysia. In conclusion, we report the occurrence of MDR P. rettgeri clone colonizing the gut microbiota of food-producing animals in Brazil, revealing the spread of this pathogen beyond hospital boundaries.

Keywords: Carbapenemases; Enterobacterales; Genomic surveillance; Gram-negative bacilli; One Health; Resistome.

Fig. 1

SNP-based phylogenetic tree analysis of PVR-188 isolate and 28other P. rettgeri genomes recovered from distinct hosts worldwide and deposited in the GenBank®/NCBI database until December 2023.

Fig. 2

Heat map of the resistome of P. rettgeri isolates isolated from humans and animals from different geographic regions. NI: not informed.