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 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.

An Integrative Approach to Study the Inhibition of Providencia vermicola FabD Using C2-Quaternary Indolinones

“…Our results are further supported by the fact that genome comparison of both P. vermicola and P. stuartii revealed a proteome similarity of 90.79%. 53 Similar evidence was also observed in another work where P. vermicola type strain in a clade showed 100 bootstrap support in the strains of both the species P. stuartii and P. thailandensis. 28…”

“…In a more recent study, it was found that P. vermicola also exhibits multi-drug resistance, which is a cause of major concern in terms of clinical significance. 53 The lowest concentration or the MIC for moL12 is 10 mg/mL (as shown in Figure 2).…”

Antibiotic Profiles and Draft Genome Sequences of Kerstersia gyiorum, Providencia stuartii, Providencia vermicola, and Alcaligenes faecalis Strains Recovered from Soft Tissue Biopsy Samples in Ghana

“… Providencia stuartii infections are difficult to manage ( 3 ) and are often resistant to multiple antibiotics ( 7 – 9 ). The NDM-1 carbapenemase gene has been detected in Providencia vermicola isolates ( 10 , 11 ).…”

Isolation and selection of siderophore-producing bacteria from roots of Simadu pineapple (Ananas comosus) in Subang District, West Java

“…The species Providencia vermicola P8438 was found to be the closest relative to isolate M7 and has multiple Mobile Genetic Elements (MGEs) genes, DNA segments that encode enzymes, and other proteins that facilitate the movement of genetic material between bacterial chromosomes. On the P. vermicola chromosome P8438, a Nonribosomal Peptide Synthase (NRPS) cluster was also found which functions for siderophore biosynthesis (Lupande-Mwenebitu et al, 2021). The genus Providencia spp.…”