First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture

Abstract

In this paper, we describe the first complete genome sequence of <i>Providencia vermicola</i> species, a clinical multidrug-resistant strain harboring the New Delhi Metallo-β-lactamase-1 (NDM-1) gene, isolated at the Kinshasa University Teaching Hospital, in Democratic Republic of the Congo. Whole genome sequencing of an imipenem-resistant clinical Gram-negative <i>P. vermicola</i> P8538 isolate was performed using MiSeq and Gridion, and then complete genome analysis, plasmid search, resistome analysis, and comparative genomics were performed. Genome assembly resulted in a circular chromosome sequence of 4,280,811-bp and 40.80% GC and a circular plasmid (pPV8538_NDM-1) of 151,684-bp and 51.93%GC, which was identified in an <i>Escherichia coli</i> P8540 strain isolated in the same hospital. Interestingly, comparative genomic analysis revealed multiple sequences acquisition within the <i>P. vermicola</i> P8538 chromosome, including three complete prophages, a siderophore biosynthesis NRPS cluster, a Type VI secretion system (T6SS), a urease gene cluster, and a complete Type-I-F CRISPR-Cas3 system. Β-lactamase genes, including <i>bla</i>_CMY-6 and <i>bla</i>_NDM-1, were found on the recombinant plasmid pPV8538_NDM-1, in addition to other antibiotic resistance genes such as <i>rmtC</i>, <i>aac6'</i>-<i>Ib3</i>, <i>aacA4</i>, <i>catA1</i>, <i>sul1</i>, <i>aac6'</i>-<i>Ib</i>-<i>cr</i>, <i>tetA</i>, and <i>tetB</i>. Genome comparison with <i>Providencia</i> species revealed 82.95% of average nucleotide identity (ANI), with <i>P. stuartii</i> species exhibiting 90.79% of proteome similarity. We report the first complete genome of <i>P. vermicola</i> species and for the first time the presence of the <i>bla</i>_NDM-1 gene in this species. This work highlights the need to improve surveillance and clinical practices in DR Congo in order to reduce or prevent the spread of such resistance.