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

Meng Zhang; Yanhua Yu; Qian Wang; Ran Chen; Yueling Wang; Yuanyuan Bai; Zhen Song; Xinglun Lu; Yingying Hao

doi:10.3389/fmicb.2022.1071385

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

Front Microbiol. 2023 Jan 4:13:1071385. doi: 10.3389/fmicb.2022.1071385. eCollection 2022.

Authors

Meng Zhang^{1

2}, Yanhua Yu³, Qian Wang⁴, Ran Chen¹, Yueling Wang⁴, Yuanyuan Bai⁴, Zhen Song⁴, Xinglun Lu⁴, Yingying Hao^{1

4}

Affiliations

¹ Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
² Department of Clinical Laboratory, Liaocheng Second People's Hospital, Liaocheng, Shandong, China.
³ Department of Clinical Laboratory, Beijing Youan Hospital, Capital Medical University, Beijing, China.
⁴ Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.

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 bla _NDM-1, bla _OXA-10, bla _PER-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 bla _NDM-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-bla _NDM-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]-bla _NDM-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.

Keywords: IS26; ISKox2; Providencia rettgeri; blaNDM-1; blaOXA-10; blaPER-4; class-1 integrons (IntI).