Conjugation of plasmid harboring blaNDM-1 in a clinical Providencia rettgeri strain through the formation of a fusion plasmid

Abstract

Providencia rettgeri has recently gained increased importance owing to the New Delhi metallo-β-lactamase (NDM) and other β-lactamases produced by its clinical isolates. These enzymes reduce the efficiency of antimicrobial therapy. Herein, we reported the findings of whole-genome sequence analysis and a comprehensive pan-genome analysis performed on a multidrug-resistant P. rettgeri 18004577 clinical strain recovered from the urine of a hospitalized patient in Shandong, China, in 2018. Providencia rettgeri 18004577 was found to have a genome assembly size of 4.6 Mb with a G + C content of 41%; a circular plasmid p18004577_NDM of 273.3 Kb, harboring an accessory multidrug-resistant region; and a circular, stable IncT plasmid p18004577_Rts of 146.2 Kb. Additionally, various resistance genes were identified in its genome, including blaNDM-1, blaOXA-10, blaPER-4, aph(3′)-VI, ant(2′′)-Ia, ant(3′)-Ia, sul1, catB8, catA1, mph(E), and tet. Conjugation experiments and whole-genome sequencing revealed that the blaNDM-1 gene could be transferred to the transconjugant via the formation of pJ18004577_NDM, a novel hybrid plasmid. Based on the genetic comparison, the main possible formation process for pJ18004577_NDM was the insertion of the [ΔISKox2-IS26-ΔISKox2]-aph(3′)-VI-blaNDM-1 translocatable unit module from p18004577_NDM into plasmid p18004577_Rts in the Russian doll insertion structure (ΔISKox2-IS26-ΔISKox2), which played a role similar to that of IS26 using the “copy-in” route in the mobilization of [aph(3′)-VI]-blaNDM-1. The array, multiplicity, and diversity of the resistance and virulence genes in this strain necessitate stringent infection control, antibiotic stewardship, and periodic resistance surveillance/monitoring policies to preempt further horizontal and vertical spread of the resistance genes. Roary analysis based on 30 P. rettgeri strains pan genome identified 415 core, 756 soft core, 5,744 shell, and 12,967 cloud genes, highlighting the “close” nature of P. rettgeri pan-genome. After a comprehensive pan-genome analysis, representative biological information was revealed that included phylogenetic distances, presence or absence of genes across the P. rettgeri bacteria clade, and functional distribution of proteins. Moreover, pan-genome analysis has been shown to be an effective approach to better understand P. rettgeri bacteria because it helps develop various tailored therapeutic strategies based on their biological similarities and differences.

Detection of NDM-1 and OXA-10 Co-Producing Providencia rettgeri Clinical Isolate

“…While Shen et al 15 and Piza-Buitrago et al 6 reported the co-existence of bla NDM-1 and bla OXA-10 in P. rettgeri , their study only clarified the transmission of bla NDM-1 through plasmids, but did not explain whether bla OXA-10 co-existed with bla NDM-1 on the same plasmid. Zhang et al 35 provided a comprehensive analysis of the genetic context of a circular plasmid measuring 273.2 Kb, which harbored bla NDM-1 , bla OXA-10 , and bla PER-4 genes in P. rettgeri . Horizontal transmission of interbacterial resistance can occur by conjugating plasmids and integrating conjugative elements.…”

Genomic epidemiology and heterogeneity of Providencia and their bla NDM-1 -carrying plasmids

“…Moreover, extensive use and frequent misuse of antibiotics have led to the emergence of extended-spectrum β-lactamase- or even carbapenemase-producing Providencia strains, exacerbating the MDR problem in Providencia [ 18 , 19 ]. It has been revealed that the frequent emergence of carbapenemase-producing Providencia strains is mainly due to the spread of bla NDM-1 gene [ 2 , 20 ]. IncC plasmids that carry bla NDM-1 have been widely detected in P. stuartii from distrust Romanian [ 21 ] and Italy hospitals [ 22 ], and several additional Inc (incompatible) groups of bla NDM-1 -harbouring plasmids have been identified in Providencia [ 18 , 23–26 ], indicating diverse types of plasmids contribute to the spread of bla NDM-1 in Providencia .…”