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

Microorganisms

卷:9

Mariem Ben Khedher¹  Lalaoui Rym¹  David Lupande-Mwenebitu¹  Jean-Marc Rolain¹  Larbi Zakaria Nabti¹  Sami Khabthani¹  Seydina M. Diene¹  Octavie Lunguya-Metila²  Marie-France Phoba²  Alix Pantel³  Jean-Philippe Lavigne³ 

[1] Faculté de Pharmacie, Aix Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;

[2] Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa 127, Democratic Republic of the Congo;

[3] VBIC, INSERM U1047, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Université de Montpellier, 30000 Nîmes, France;

关键词: bla_NDM-1;    Providencia vermicola;    antibacterial resistance genes;    NRPS/PKS cluster;    comparative genomics;    MDR recombinant plasmid;   

DOI  :  10.3390/microorganisms9081751

来源: DOAJ

【 摘 要 】

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 bla_CMY-6 and bla_NDM-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 bla_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.

【 授权许可】

Unknown