Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones

• Published in: mSphere 2018-07, Vol.3 (4)
• Main Authors: Roer, Louise, Overballe-Petersen, Søren, Hansen, Frank, Schønning, Kristian, Wang, Mikala, Røder, Bent L, Hansen, Dennis S, Justesen, Ulrik S, Andersen, Leif P, Fulgsang-Damgaard, David, Hopkins, Katie L, Woodford, Neil, Falgenhauer, Linda, Chakraborty, Trinad, Samuelsen, Ørjan, Sjöström, Karin, Johannesen, Thor B, Ng, Kim, Nielsen, Jens, Ethelberg, Steen, Stegger, Marc, Hammerum, Anette M, Hasman, Henrik
• Format: Article
• Language: English
• Subjects: Antimicrobial agents; Antimicrobial resistance; Bacterial Proteins - genetics; Basale medisinske, odontologiske og veterinærmedisinske fag: 710; Basic medical, dental and veterinary science disciplines: 710; BEAST; beta-Lactamases - genetics; Carbapenemase; Carbapenems; Cephalosporins; Clinical Science and Epidemiology; Cloning; Denmark - epidemiology; Disease Outbreaks; Disease transmission; Drug resistance; E coli; Epidemics; Epidemiology; Escherichia coli; Escherichia coli Infections - epidemiology; Escherichia coli Infections - microbiology; evolution; Evolution, Molecular; Extraintestinal Pathogenic Escherichia coli - classification; Extraintestinal Pathogenic Escherichia coli - genetics; Extraintestinal Pathogenic Escherichia coli - isolation & purification; Farmakologi: 728; Fluoroquinolones; Genes; Genomes; Genotype; Health surveillance; high-risk clone; Hospitals; Humans; Infections; Medical disciplines: 700; Medical microbiology: 715; Medisinsk mikrobiologi: 715; Medisinske Fag: 700; Metadata; Multidrug resistance; Multilocus Sequence Typing; outbreak; Outbreaks; Pathogenicity; Patients; Pharmacology: 728; Phylogenetics; Plasmids; Prevalence; Prospective Studies; Public health; Septicemia; Urinary tract; VDP; Whole Genome Sequencing
• ISSN: 2379-5042; 2379-5042
• DOI: 10.1128/MSPHERE.00337-18

sequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410 isolates from Danish patients. Furthermore, ST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genes and of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework of ST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. The B2/H24R and B3/H24Rx clades emerged around 1987, concurrently with the C1/H30R and C2/H30Rx clades in ST131. B3/H24Rx appears to have evolved by the acquisition of the extended-spectrum β-lactamase (ESBL)-encoding gene and an IncFII plasmid, encoding IncFIA and IncFIB. Around 2003, the carbapenem-resistant clade B4/H24RxC emerged when ST410 acquired an IncX3 plasmid carrying a carbapenemase gene. Around 2014, the clade B4/H24RxC acquired a second carbapenemase gene, , on a conserved IncFII plasmid. From an epidemiological investigation of 49 ST410 isolates from Danish patients, we identified five possible regional outbreaks, of which one outbreak involved nine patients with - and -carrying B4/H24RxC isolates. The accumulated multidrug resistance in ST410 over the past two decades, together with its proven potential of transmission between patients, poses a high risk in clinical settings, and thus, ST410 should be considered a lineage with emerging "high-risk" clones, which should be monitored closely in the future. Extraintestinal pathogenic (ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a "high-risk" clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of the ST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage sho