Genomic analysis of a multidrug‐resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln1483 and an A/C plasmid replicon. Issue 1 (23rd September 2019)

• Record Type: Journal Article
• Authors: Mbelle, Nontombi Marylucy; Osei Sekyere, John; Amoako, Daniel Gyamfi; Maningi, Nontuthuko Excellent; Modipane, Lesedi; Essack, Sabiha Yusuf; Feldman, Charles
• Is Part Of: Annals of the New York Academy of Sciences. Volume 1462:Issue 1(2020)
• Page Start: 92
• Page End: 103
• Publication Date: 2019-09-23
• Subjects: Providencia rettgeri -- IncA/C2 plasmid -- resistome -- mobilome -- virulence -- South Africa; Medical sciences -- Periodicals; Medicine -- Periodicals; Science -- Periodicals; 610
• DOI: 10.1111/nyas.14237
• Languages: English
• ISSNs: 0077-8923

Abstract

Abstract: Whole‐genome sequence analysis was performed on a multidrug‐resistant Providencia rettgeri PR002 clinical strain isolated from the urine of a hospitalized patient in Pretoria, South Africa, in 2013. The resistome, mobilome, pathogenicity island(s), as well as virulence and heavy‐metal resistance genes of the isolate, were characterized using whole‐genome sequencing and bioinformatic analysis. PR002 had a genome assembly size of 4, 832, 624 bp with a GC content of 40.7%, an A/C2 plasmid replicase gene, four integrons/gene cassettes, 17 resistance genes, and several virulence and heavy metal resistance genes, confirming PR002 as a human pathogen. A novel integron, In 1483, harboring the gene bla OXA‐2, was identified, with other uncharacterized class 1 integrons harboring aacA4cr and dfrA1 . Aac(3′)‐IIa and bla SCO‐1, as well as bla PER‐7, sul2, and tet (B), were found bracketed by composite Tn 3 transposons, and IS 91, IS 91, and IS 4 family insertion sequences, respectively. PR002 was resistant to all antibiotics tested except amikacin, carbapenems, cefotaxime‐clavulanate, ceftazidime‐clavulanate, cefoxitin, and fosfomycin. PR002 was closely related to PR1 (USA), PRET_2032 (SPAIN), DSM_1131, and NCTC7477 clinical P. rettgeri strains, but not close enough to suggest it was imported into South Africa from other countries. Multidrug resistance in P. rettgeri is rare, particularly in clinical settings, making this case an important incident requiring urgent attention. This is also the first report of an A/C plasmid in P. rettgeri . The array, multiplicity, and diversity of resistance and virulence genes in this strain are concerning, necessitating stringent infection control, antibiotic stewardship, and periodic resistance surveillance/monitoring policies to preempt further horizontal and vertical spread of these resistance genes. Abstract : Whole‐genome sequence analysis was performed on a multidrug‐resistant Providencia rettgeri PR002 clinical strain isolated from the urine of a hospitalized patient in Pretoria, South Africa, in 2013. The array, multiplicity, and diversity of resistance and virulence genes in this strain are concerning, necessitating stringent infection control, antibiotic stewardship and periodic resistance surveillance/monitoring policies to preempt further horizontal and vertical spread of these resistance genes.