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

Abstract

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.

Providencia manganoxydans sp. nov., a Mn(II)-oxidizing bacterium isolated from heavy metal contaminated soils in Hunan Province, China

“…Even though the phylogenetic position at the 16S rRNA sequence level suggests a separate branch for LLDRA6 T within Providencia (Fig. 1), bootstrap values on branches ranging from 50-80 %, indicate that the clade topology around LLDRA6 T is insufficiently supported, probably because of the high similarity in 16S rRNA sequences, which is in agreement with the previous statement of insufficient resolution of 16S rRNA phylogenies for species delineation in Providencia [2,10,13]. Hence, in the present case, more evidences are needed to support the hypothetical theory that strain LLDRA6 T is the representative of a novel species in Providencia.…”

“…The species members of Providencia are mostly distributed in insects, invertebrates, vertebrates and humans [1][2][3][4][5][6]. Particularly, the majority of them are believed to be potentially pathogenic and can be frequently detected in human specimens of diarrhoea, urinary tract infections, wounds, burns and bacteraemia [13]. Recent studies have shown that bacterial strains within Providencia also inhabit heavy metal contaminated soils [14,15].…”

Occurrence of blaNDM-1-Positive Providencia spp. in a Pig Farm of China

“…Moreover, Providencia spp. have been found in a variety of organisms, including birds, fish, and fruit flies, and can be isolated directly from water [ 13 , 14 , 15 , 16 , 17 ]. The discovery of bla NDM-1 in Providencia is concerning because these bacteria are naturally resistant to tetracycline and colistin, making the clinical treatment of these infections extremely difficult [ 18 ].…”

Identification and comparison of somatic antigen composition for bacteria from Providencia genus

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Providencia is a genus of Gram-negative bacteria belonging to the Morganellaceae family. This genus includes nine species (P. stuartii, P. sneebia, P. rettgeri, P. rustigianii, P. heimbachae, P. burhodogranariea, P. alcalifaciens, P. huaxiensis, and P. vermicola) with varying degrees of virulence, capable of infecting humans and insects [1,2].For Gram-negative bacteria, the somatic antigen (O-antigen) has become one of the key virulence factors. It is the highly immunogenic part of lipopolysaccharides due to the distal location.

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“…Providencia is a genus of Gram-negative bacteria belonging to the Morganellaceae family. This genus includes nine species (P. stuartii, P. sneebia, P. rettgeri, P. rustigianii, P. heimbachae, P. burhodogranariea, P. alcalifaciens, P. huaxiensis , and P. vermicola ) with varying degrees of virulence, capable of infecting humans and insects [1, 2].…”