Whole genome sequence of EC16, a blaNDM-5-, blaCTX-M-55-, and fosA3-coproducing Escherichia coli ST167 clinical isolate from China

Huang, Junwei; Zhu, Jin; Gong, Daojun; Wu, Lin; Zhu, Yongze; Hu, Liqing

doi:10.1016/j.jgar.2022.04.001

Cited by 8 publications

(6 citation statements)

References 5 publications

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“…The prediction of tRNA coding regions was performed by the tRNAScan-SE server v.1.21 [12] program. Genomic comparisons were performed with the software Easy g2.2.3 [7].…”

Section: Introduction and Resultsmentioning

confidence: 99%

Characterization of a novel Pseudomonas aeruginosa phage species PaYy-2

Fang,

Ning

2024

Preprint

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A novel Pseudomonas aeruginosa phage, PaYy-2 was isolated from a lake in China and its genome has been sequenced and characterized. Payy-2 has a 92,348 bp double-stranded DNA genome encoding 168 proteins, which has 68% similarity with the genome of the known Pseudomonasphage YS35. According to the phylogenetic analysis, the putative RNA polymerase was similar to that of Pseudomonasphage SRT6（similar index 94%）and the putative terminase_large_subnit was similar to that of the phages YS35（similar index 96%）which belongs to the Pakpunavirus genus. We also observed the morphology of the new phage by TEM whcih demonstrated the phage tails and particles morphology. All these findings indicate that the PaYy-2 phage can be classified as a new species of the Pakpunavirus genus of the family Myoviridae for the first time.

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“…The prediction of tRNA coding regions was performed by the tRNAScan-SE server v.1.21 [12] program. Genomic comparisons were performed with the software Easy g2.2.3 [7].…”

Section: Introduction and Resultsmentioning

confidence: 99%

Characterization of a novel Pseudomonas aeruginosa phage species PaYy-2

Fang,

Ning

2024

Preprint

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“…This is an important issue, since polymyxins are considered to be the last resort of antibacterial agents against MDR E. coli [146]. Several clones harbour chromosomal pmrA and pmrB mutations and plasmid-mediated colistin resistance determinants (mcr-1,-3,-5,-9) [7,[18][19][20]38,56,57,60,102,105,106,111,130,141,142]. In addition, apart from the most frequently detailed ExPEC clones (ST131, ST69, CC10, ST405, ST38, ST457, ST410, ST48, ST58, ST88), a huge number of currently less widely known strains carry mcr-genes, such as ST57, ST156, ST224, ST345, ST393, ST850, ST3024, ST8900, ST12657 (Tables 3 and 4, Figure 2).…”

Section: Discussionmentioning

confidence: 99%

“…The nucleotide sequence information was submitted in GenBank under the BioProject accession number PRJNA784589 [20] (Table 1). In addition to β-lactam resistance, CC10 has also been marked by fluoroquinolone-resistance determinants (e.g., qnrS1, aac(6 )-Ib-cr) and the mcr-1 colistin-resistance gene [7,60,111,112]. In addition, bla OXA-48 associated with ST10; bla NDM-1 related to ST44, ST48, ST167, ST617; bla CTX-M-14,15,55 , fosA3, bla OXA-1 , bla NDM-1,9 , bla NDM-5 together with bla OXA-181 and co-carriage of bla OXA-48 in ST167; as well as bla KPC-2,3 with bla NDM-1 in ST617 have also been reported.…”

Section: St69 and Cc10 The Second And Third Most Common High-risk Clonesmentioning

confidence: 99%

“…Of these high-risk CC10 lineages, in the last few years, ST167 was clustered into subclades, and it was reported to be a predominant clone in China. This clone was also identified from a urine clinical sample as a qepA4 carrier [7,40,61,62,112,113].…”

Section: St69 and Cc10 The Second And Third Most Common High-risk Clonesmentioning

confidence: 99%

“…E. coli has a remarkable capacity to take up and to accumulate various genetic materials, including plasmids, integrons, and transposons through horizontal gene transfer; thus, E. coli can acquire different antibiotic resistance genes, enabling it to develop multiresistance [6,7]. Currently, extended-spectrum beta-lactamase (ESBL)-and carbapenemaseproducing E. coli are of great concern worldwide [8,9].…”

Section: Introductionmentioning

confidence: 99%

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Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli

Kocsis

Gulyás

Szabó

2022

Life

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Multiresistant Escherichia coli has been disseminated worldwide, and it is one of the major causative agents of nosocomial infections. E. coli has a remarkable and complex genomic plasticity for taking up and accumulating genetic elements; thus, multiresistant high-risk clones can evolve. In this review, we summarise all available data about internationally disseminated extraintestinal pathogenic high-risk E. coli clones based on whole-genome sequence (WGS) data and confirmed outbreaks. Based on genetic markers, E. coli is clustered into eight phylogenetic groups. Nowadays, the E. coli ST131 clone from phylogenetic group B2 is the predominant high-risk clone worldwide. Currently, strains of the C1-M27 subclade within clade C of ST131 are circulating and becoming prominent in Canada, China, Germany, Hungary and Japan. The C1-M27 subclade is characterised by blaCTX-M-27. Recently, the ST1193 clone has been reported as an emerging high-risk clone from phylogenetic group B2. ST38 clone carrying blaOXA-244 (a blaOXA-48-like carbapenemase gene) caused several outbreaks in Germany and Switzerland. Further high-risk international E. coli clones include ST10, ST69, ST73, ST405, ST410, ST457. High-risk E. coli strains are present in different niches, in the human intestinal tract and in animals, and persist in environment. These strains can be transmitted easily within the community as well as in hospital settings. WGS analysis is a useful tool for tracking the dissemination of resistance determinants, the emergence of high-risk mulitresistant E. coli clones and to analyse changes in the E. coli population on a genomic level.

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