CTX-M-15-Producing Shewanella Species Clinical Isolate Expressing OXA-535, a Chromosome-Encoded OXA-48 Variant, Putative Progenitor of the Plasmid-Encoded OXA-436

Abstract

spp. constitute a reservoir of antibiotic resistance determinants. In a bile sample, we identified three extended-spectrum-β-lactamase (ESBL)-producing bacteria (, , and sp. strain JAB-1) isolated from a child suffering from cholangitis. Our objectives were to characterize the genome and the resistome of the first ESBL-producing isolate of the genus and determine whether plasmidic exchange occurred between the three bacterial species. Bacterial isolates were characterized using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), standard biochemical tools, and antimicrobial susceptibility testing. sp. JAB-1 and ESBL gene-encoding plasmids were characterized using PacBio and Illumina whole-genome sequencing, respectively. The sp. JAB-1 chromosome-encoded OXA-48 variant was cloned and functionally characterized. Whole-genome sequencing (WGS) of the sp. clinical isolate JAB-1 revealed the presence of a 193-kb plasmid belonging to the IncA/C incompatibility group and harboring two ESBL genes, and gene-carrying plasmids belonging to the IncY and IncR incompatibility groups were also found in the and isolates from the same patient, respectively. A comparison of the genetic environment indicated the independent origin of these plasmids and dismissed transfers. Furthermore, characterization of the resistome of sp. JAB-1 revealed the presence of a chromosome-carried gene, likely the progenitor of the plasmid-carried gene, a novel-like gene. The expression of in showed the carbapenem-hydrolyzing activity of OXA-535. The production of OXA-535 in sp. JAB-1 could be evidenced using molecular and immunoenzymatic tests, but not with biochemical tests that monitor carbapenem hydrolysis. In this study, we have identified a CTX-M-15-producing species that was responsible for a hepatobiliary infection and that is likely the progenitor of OXA-436, a novel plasmid-encoded OXA-48-like class D carbapenemase.

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

“…Cases of human infections involving Shewanella are rare but may include skin and soft tissue infections, septicemia, hepatobiliary disease, otitis media and pneumonia. These infections are described in immunocompromised patients with renal failure, neutropenia, hepatobiliary disease, diabetes or those involved in trauma accidents [1][2][3][4][5]. Usually, the antibiotic therapy adopted includes beta-lactams, aminoglycosides and quinolones.…”

“…These bacteria are generally susceptible to third and fourth generation cephalosporins, carbapenems, beta-lactamase inhibitor combinations, aminoglycosides, chloramphenicol, erythromycin, aztreonam and quinolones [2,5,6]. However, resistance to these drugs is increasing due to the presence in their chromosome of class D beta-lactamase encoding genes (bla OXA ) conferring resistance to carbapenems, class C beta-lactamases (bla AmpC ) which decrease the susceptibility to cephalosporins and qnr genes responsible for resistance to quinolones [4,[7][8][9][10][11][12][13][14]. Furthermore, resistance to colistin, currently a last-resort antibiotic in human medicine, has been reported as well, due to the presence of the chromosomal eptA gene encoding for phosphoethanolamine transferase [12,15,16].…”

Evaluation of the Revogene Carba C Assay for Detection and Differentiation of Carbapenemase-Producing Gram-Negative Bacteria

“…The chromosomally encoded OXA-535 identified in a Shewanella species (39), which has only 91.3% amino acid identity with OXA-48, has not been detected (data not shown). OXA-535, although not present in Enterobacterales, was used because it is the progenitor of OXA-436, a distantly related OXA-48 variant responsible for an outbreak associated with several enterobacterial species in Denmark (39,40). It is thus likely that OXA-436 would not be detected by the Revogene Carba C assay, and further studies on the Revogene Carba C assay should be carried out to test OXA-436 producers.…”

“…With Enterobacterales, the Revogene Carba C assay detected all KPC, NDM, VIM, IMP, and OXA-48 producers, including OXA-48 variants with carbapenemase activity (OXA-162, -181, -204, and -232), those difficult to detect by phenotypic means (such as OXA-244 and -519) (36,37), and very recently identified variants (OXA-484, -505, -517, and -793) ( Table 1) (38). The chromosomally encoded OXA-535 identified in a Shewanella species (39), which has only 91.3% amino acid identity with OXA-48, has not been detected (data not shown). OXA-535, although not present in Enterobacterales, was used because it is the progenitor of OXA-436, a distantly related OXA-48 variant responsible for an outbreak associated with several enterobacterial species in Denmark (39,40).…”

Evaluation of the BD MAX Check-Points CPO Assay for the Detection of Carbapenemase Producers Directly from Rectal Swabs

“…The b-lactamase content of these isolates had been characterized by end-point PCR, followed by Sanger sequencing 24 or by whole genome sequencing. 30,31 Fifty-two non-CP or nontargeted carbapenemase producers were also included as controls. Nontargeted carbapenemases are carbapenemases different from those detected by the BD MAX Check-Points CPO assay (eg, IMI, NMCA, Sme, GES, FRI, LMB, TMB, GIM, AIM, SPM, DIM, OXA-198, OXA-23, OXA-40, and OXA-58) ( Table 2).…”