Resistome, Mobilome and Virulome Analysis of Shewanella algae and Vibrio spp. Strains Isolated in Italian Aquaculture Centers

Abstract

Antimicrobial resistance is a major public health concern restricted not only to healthcare settings but also to veterinary and environmental ones. In this study, we analyzed, by whole genome sequencing (WGS) the resistome, mobilome and virulome of 12 multidrug-resistant (MDR) marine strains belonging to Shewanellaceae and Vibrionaceae families collected at aquaculture centers in Italy. The results evidenced the presence of several resistance mechanisms including enzyme and efflux pump systems conferring resistance to beta-lactams, quinolones, tetracyclines, macrolides, polymyxins, chloramphenicol, fosfomycin, erythromycin, detergents and heavy metals. Mobilome analysis did not find circular elements but class I integrons, integrative and conjugative element (ICE) associated modules, prophages and different insertion sequence (IS) family transposases. These mobile genetic elements (MGEs) are usually present in other aquatic bacteria but also in Enterobacteriaceae suggesting their transferability among autochthonous and allochthonous bacteria of the resilient microbiota. Regarding the presence of virulence factors, hemolytic activity was detected both in the Shewanella algae and in Vibrio spp. strains. To conclude, these data indicate the role as a reservoir of resistance and virulence genes in the environment of the aquatic microbiota present in the examined Italian fish farms that potentially might be transferred to bacteria of medical interest.

Vibrio Species in an Urban Tropical Estuary: Antimicrobial Susceptibility, Interaction with Environmental Parameters, and Possible Public Health Outcomes

“…Tetracyclines, aminoglycosides, third-generation cephalosporins, and fluoroquinolones are usually employed for the treatment of Vibrio spp. infections [ 55 ]. In this study, resistance to all the aforementioned drugs was detected, being third-generation cephalosporins and aminoglycosides the classes with the highest resistance percentages.…”

Genetic Environment Surrounding bla OXA-55-like in Clinical Isolates of Shewanella algae Clade and Enhanced Expression of bla OXA-55-like in a Carbapenem-Resistant Isolate

“…This study confirmed the universal occurrence of bla OXA-55-like in the chromosomes of S. algae isolates, and the diversity of bla OXA-55-like nucleotide sequences among the isolates is suggestive of the stable long-term persistence of the gene. Although several carbapenem-resistant isolates of S. algae have been reported, the mechanisms and the extent of involvement of bla OXA-55-like in carbapenem resistance are unknown ( 4 , 14 ). In this study, we cloned bla OXA-55-like genes with slightly different nucleotide sequences from nine S. algae isolates and introduced them into E. coli DH5α, but no differences in the MICs of broad-spectrum cephalosporins or carbapenems were observed.…”

“…Shewanella spp. are susceptible to most antimicrobial agents, including β-lactams, but several clinical isolates resistant to carbapenems have been reported ( 3 , 4 ).…”

“…Although recent genetic analysis studies have confirmed the presence of bla OXA-55 in S. algae isolates, the extent of the involvement of bla OXA-55 in β-lactam resistance, especially carbapenem resistance, in this species is unknown ( 4 ). In addition, whether the genetic environment of bla OXA is common to the different strains of S. algae and to closely related species of the S. algae clade, such as Shewanella carassii , Shewanella chilikensis , and Shewanella indica , is unconfirmed.…”

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

“…A recent study has described the presence of β-lactams resistant clones of S. algae along the Italian Adriatic coast, containing AmpC and OXA-55-like β-lactamases [ 315 ]. Further, these authors have described the possible role of S. algae as a reservoir of ARGs, such as qnrA and β-lactamase genes (that confer resistance to quinolones and β-lactams, respectively), which could be transferred from the aquatic microbiota of Italian fish farms to bacteria of medical interest [ 316 ]. Actually, it has been proposed that S. algae are the origin of the quinolone resistance gene qnrA , widely distributed among plasmids present in several organisms [ 317 ], and different Shewanella species (as well as A. baumannii , see above) are considered as potential origins of some OXA-type β-lactamases [ 318 ].…”