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

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

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1071385

DOI=10.3389/fmicb.2022.1071385

ISSN=1664-302X

ABSTRACT=<p><italic>Providencia rettgeri</italic> 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 <italic>P</italic>. <italic>rettgeri</italic> 18004577 clinical strain recovered from the urine of a hospitalized patient in Shandong, China, in 2018. <italic>Providencia rettgeri</italic> 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 <italic>bla</italic><sub>NDM-1</sub>, <italic>bla</italic><sub>OXA-10</sub>, <italic>bla</italic><sub>PER-4</sub>, <italic>aph</italic>(<italic>3′</italic>)<italic>-VI</italic>, <italic>ant</italic>(<italic>2′′</italic>)<italic>-Ia</italic>, <italic>ant</italic>(<italic>3′</italic>)<italic>-Ia</italic>, <italic>sul1</italic>, <italic>catB8</italic>, <italic>catA1</italic>, <italic>mph</italic>(<italic>E</italic>), and <italic>tet</italic>. Conjugation experiments and whole-genome sequencing revealed that the <italic>bla</italic><sub>NDM-1</sub> gene could be transferred to the transconjugant <italic>via</italic> the formation of pJ18004577_NDM, a novel hybrid plasmid. Based on the genetic comparison, the main possible formation process for pJ18004577_<italic>NDM</italic> was the insertion of the [<italic>ΔISKox2-IS26-ΔISKox2</italic>]<italic>-aph</italic>(<italic>3′</italic>)<italic>-VI-bla</italic><sub>NDM-1</sub> translocatable unit module from p18004577_<italic>NDM</italic> into plasmid p18004577_Rts in the Russian doll insertion structure (<italic>ΔISKox2-IS26-ΔISKox2</italic>), which played a role similar to that of <italic>IS26</italic> using the “copy-in” route in the mobilization of [<italic>aph</italic>(<italic>3′</italic>)<italic>-VI</italic>]<italic>-bla</italic><sub>NDM-1</sub>. 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 <italic>P</italic>. <italic>rettgeri strains</italic> pan genome identified 415 core, 756 soft core, 5,744 shell, and 12,967 cloud genes, highlighting the “close” nature of <italic>P</italic>. <italic>rettgeri</italic> pan-genome. After a comprehensive pan-genome analysis, representative biological information was revealed that included phylogenetic distances, presence or absence of genes across the <italic>P</italic>. <italic>rettgeri</italic> bacteria clade, and functional distribution of proteins. Moreover, pan-genome analysis has been shown to be an effective approach to better understand <italic>P</italic>. <italic>rettgeri</italic> bacteria because it helps develop various tailored therapeutic strategies based on their biological similarities and differences.</p>