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

David Lupande-Mwenebitu (1, 2) , Mariem Ben Khedher (1) , Sami Khabthani (1) , Lalaoui Rym (1, 3) , Marie-France Phoba (4) , Larbi Zakaria Nabti (5) , Octavie Lunguya-Metila (4) , Alix Pantel (6, 7) , Jean-Philippe Lavigne (7, 6) , Jean-Marc Rolain (1) , Seydina Diene (1)

1 MEPHI - Microbes évolution phylogénie et infections
2 Université catholique de Bukavu
3 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection
4 INRB - Institut National de Recherche Biomédicale [Kinshasa]
5 UFAS1 - Université Ferhat-Abbas Sétif 1 [Sétif]
6 CHU Nîmes - Centre Hospitalier Universitaire de Nîmes
7 VBMI - Virulence bactérienne et maladies infectieuses

In this paper, we describe the first complete genome sequence of Providencia vermicola 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 P. vermicola 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 Escherichia coli P8540 strain isolated in the same hospital. Interestingly, comparative genomic analysis revealed multiple sequences acquisition within the P. vermicola 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 blaCMY-6 and blaNDM-1, were found on the recombinant plasmid pPV8538_NDM-1, in addition to other antibiotic resistance genes such as rmtC, aac6’-Ib3, aacA4, catA1, sul1, aac6’-Ib-cr, tetA, and tetB. Genome comparison with Providencia species revealed 82.95% of average nucleotide identity (ANI), with P. stuartii species exhibiting 90.79% of proteome similarity. We report the first complete genome of P. vermicola species and for the first time the presence of the blaNDM-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.

Keywords: Antibacterial resistance genes; Providencia vermicola; NRPS/PKS cluster; MDR recombinant plasmid; BlaNDM-1; Comparative genomics

Domains: Life Sciences [q-bio]; Microbiology and Parasitology; Bacteriology; Life Sciences [q-bio]; Microbiology and Parasitology; Virology; Life Sciences [q-bio]; Microbiology and Parasitology; Parasitology; Life Sciences [q-bio]; Human health and pathology; Cardiology and cardiovascular system; Life Sciences [q-bio]; Human health and pathology; Emerging diseases; Life Sciences [q-bio]; Human health and pathology; Infectious diseases

David Lupande-Mwenebitu, Mariem Ben Khedher, Sami Khabthani, Lalaoui Rym, Marie-France Phoba, et al.. First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture. Microorganisms, 2021, 9 (8), pp.1751. ⟨10.3390/microorganisms9081751⟩. ⟨hal-03429615⟩