Comparative Genomic Analysis Reveals Genetic Mechanisms of the Variety of Pathogenicity, Antibiotic Resistance, and Environmental Adaptation of Providencia Genus

Yuan, Chao; Yi, Wei; Zhang, Si; Cheng, Juan; Cheng, Xiaolei; Qian, Chengqian; Wang, Yuhui; Zhang, Yang; Yin, Zhiqiu; Chen, Hong

doi:10.3389/fmicb.2020.572642

Cited by 33 publications

(47 citation statements)

References 77 publications

(91 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…assemblies GCA_014396895.1, GCA_010748935.1 and GCA_016618195.1) of three Providencia strains assigned to the species P. vermicola, namely strain G1 isolated from fish in Algeria, strain P8538 obtained from a clinical sample in Congo and strain LLDRA6 isolated from contaminated soil in China [ 43 ]. Comparative approaches have been used to explore the genomes of both clinical [ 44 ] and insect derived [ 45 ] Providencia bacteria. However, the species P. vermicola has not been covered by these studies, mainly due to the lack of a reliable reference genome.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

et al. 2021

View full text Add to dashboard Cite

Background Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

show abstract

Section: Introductionmentioning

confidence: 99%

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The genome analysis and comparative genomics of this clinical MDR P. vermicola P8538 isolate revealed significant genomic variations compared to other Providencia species. This may indicate the ability of this bacterium to colonize several hostile environments, given the presence of several MGEs in the genome, which is well documented in the literature [ 3 , 20 , 21 ]. We identified a conjugative and recombinant plasmid harboring antimicrobial resistance genes which was identified in two different pathogenic Enterobacterial species ( E. coli and P. vermicola ) from the same hospital, suggestive of a spread of the MDR plasmid within this healthcare setting.…”

Section: Discussionmentioning

confidence: 77%

“…Their specific power to deaminate specific amino acids by oxidation into their corresponding keto and ammonia acids is a particularity that differentiates them from other members of the Enterobacteriaceae family [ 1 , 2 ]. Unlike other bacteria in this family, Providencia species are rarely involved in nosocomial infections [ 3 ]. Two species of Providencia , including P. stuartii and P .…”

Section: Introductionmentioning

confidence: 99%

“…n. vermicola inhabitant of worms) [ 7 ] and is very rarely found as an etiological agent in humans, with only one described case of diarrhea in a 37-year-old patient in India [ 8 ]. Providencia species are reported to be found mainly in environments such as water and are mostly involved in infections of birds, fish, and certain insects such as fruit flies [ 3 , 9 ]. Prior to this study, there was no available genome of P. vermicola in the NCBI database.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2021

View full text Add to dashboard Cite

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.

show abstract

“…The main Providencia species involved in human pathology are P. stuartii and P. rettgeri which can produce urinary tract infections, pneumonia, meningitis, wound infections, endocarditis, osteomyelitis, intraabdominal and bloodstream infections in hospitalized patients [1], [2], [9], [10], [11], [12].…”

Section: Introductionmentioning

confidence: 99%

Providencia Species – Involvement in Pathology and Multidrug Resistance in a Romanian County Hospital

Idomir

2021

View full text Add to dashboard Cite

The aim of the study was to evaluate the distribution on hospital wards, the spectrum of infections and the pattern of antimicrobial resistance of Providencia strains identified between 01.01.2018-31.12.2020 in the samples of the patients hospitalized in the Clinical County Emergency Hospital of Brasov. 380 strains of Providencia species were identified in the medical and surgical wards, especially in ICU (76.84%), Internal medicine ward (5.79%) and General surgery (3.95%). More frequently, Providencia spp. were isolated from tracheobronchial secretions (35.79%), pus (22.89%) and urine (19.74%). The levels of antimicrobial resistance of Providencia strains were very high for all the tested antimicrobials.

show abstract

Comparative Genomic Analysis Reveals Genetic Mechanisms of the Variety of Pathogenicity, Antibiotic Resistance, and Environmental Adaptation of Providencia Genus

Cited by 33 publications

References 77 publications

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

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

Providencia Species – Involvement in Pathology and Multidrug Resistance in a Romanian County Hospital

Contact Info

Product

Resources

About