Complete Genome Sequence of an Extensively Drug-Resistant Shewanella xiamenensis Strain Isolated from Algerian Hospital Effluents

Abstract

In this study, we present the first complete genome of an extensively drug-resistant strain of Shewanella xiamenensis, collected from hospital effluents in Algeria. This genome includes the chromosome and a large new plasmid harboring several drug-resistance genes.

GENOME ANNOUNCEMENT

Shewanella xiamenensis is a recently validated species (1) that has been reported in different parts of the world (2–6). Bacteria of the genus Shewanella are motile Gram-negative bacilli belonging to the Shewanellaceae family. They have been proposed to be a reservoir and vehicle of different antibiotic-resistance determinants (2, 3, 6–8). In S. xiamenensis, the bla_OXA-48-like genes encoding carbapenem-hydrolyzing enzymes have been reported and the bacterium is recognized as the progenitor of these genes (2–5). Recently, different resistance genes and mobile genetic elements have been identified in S. xiamenensis (6, 8).

Here, we present the first complete genome of S. xiamenensis T17, including the chromosome and a multidrug-resistance plasmid (pSx1). This extensively drug-resistant (XDR) isolate produces extended-spectrum β-lactamase and is resistant to penicillin, ampicillin, piperacillin, ticarcillin, cefotaxime, ceftazidime, cefepime, ertapenem, aztreonam, gentamicin, streptomycin, ciprofloxacin, trimethoprim-sulfamethoxazole, tetracycline, azithromycin, and chloramphenicol.

This XDR strain of S. xiamenensis was isolated from hospital effluents in 2012 in Tizi Ouzou, Algeria. The whole-genome sequencing was performed using the PacBio SMRTbell template prep kit version 1.0 (Pacific Biosciences, Menlo Park, CA, USA). The assembly of the long reads was done using the Hierarchical Genome Assembly Process (HGAP) version 3, and the high-quality unitigs were generated with the Quiver algorithm. The sequence annotation was performed by Prokka version 1.11. To our knowledge, only one draft genome of S. xiamenensis (strain BC01) is deposited in GenBank (accession number JGVI00000000) (9).

The chromosome size of S. xiamenensis T17 was 5,084,350 bp, and the plasmid size was 268,412 bp. A total of 4,587 open reading frames were detected on the chromosome and 297 on the plasmid. The bla_OXA-416 gene—a variant of the recently described bla_OXA-48 gene, which confers resistance to carbapenem—was detected in the chromosome of T17 (5). To date, plasmids identified in the genus Shewanella do not carry any drug-resistance genes. Analysis of this new plasmid showed the presence of bla_VEB-16 and bla_PSE-1 conferring resistance to β-lactams, qnrVC6 to quinolones, dfrA12 and dfrA23 to trimethoprim; aacC1, aac(6)-II, aadA1, and aadA2 to aminoglycosides; tetR, tetA(C), and tetA(G) to tetracyclines; sul1 and sul1Δ to sulfonamides; catA2 and cmlA9 to chloramphenicol; msr(E) and mph(E) to macrolides; and qacG to quaternary ammonium compounds. The acrA, acrB, and oep multidrug efflux pumps were also detected. These genes are carried by a new Tn1696 transposon derivative associated with several mobiles genetic elements. The mercury-resistance system, including merE, merD, merB, merA, merP, merT, and merR, was also identified (6). This high-quality genome sequence could be used as a reference for assembly genomes and could be investigated in different studies on Shewanella spp. and the evolution and transfer of resistance genes.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LDOA00000000. The version described in this paper is the first version, LDOA01000000.