WGS-based surveillance of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark

Roer, Louise; Hansen, Frank; Thomsen, Martin Christen Frølund; Knudsen, Jenny Dahl; Hansen, Dennis Schrøder; Wang, Mikala; Samulioniené, Jurgita; Justesen, Ulrik Stenz; Røder, Bent; Schumacher, Helga; Østergaard, Claus; Andersen, Leif Percival; Dzajic, Esad; Søndergaard, Turid Snekloth; Stegger, Marc; Hammerum, Anette M.; Hasman, Henrik

doi:10.1093/jac/dkx092

Cited by 65 publications

(67 citation statements)

References 27 publications

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“…The EAEC pathotype did not occur in conjunction with any other ESBL-encoding gene; hence, the association between bla CTX-M-101 and the EAEC pathotype was highly significant (χ 2 , p<0.0001), suggesting that the resistance gene may be co-localized with EAEC-specific virulence genes on the pAA plasmid. As shown by Roer et al , the 27 ST131 strains with bla CTX-M-101 formed a distinct cluster with nine or fewer SNP differences, supporting a recent emergence ( 22 ).…”

Section: Resultsmentioning

confidence: 78%

“…To determine whether EAEC ST131 strains were present among contemporary Danish patients, we searched for EAEC-specific virulence genes within a recently published collection of 552 whole-genome sequenced ESBL-producing E. coli (ESBL- Ec ) isolates obtained from patients with BSIs in Denmark between 2014 and 2015 ( 22 ). ST131 accounted for 50% (n = 258) of the isolates ( 22 ). Among these, 25 isolates harbored the genes encoding AAF/V, AggR, Aar, Aap, AatPABCD, and ORF3/4 ( Suppl.…”

Section: Resultsmentioning

confidence: 99%

“…To determine whether the 12 EAEC ST131 isolates from the WHO collection were clonally related to other available EAEC ST131 isolates, a SNP-based phylogeny was constructed using 1) all 121 ST131 isolates from the WHO collection ( 10 ); 2) 93 German/US ST131 isolates from 2010-2012 ( 6 ); 3) the 27 Danish bla CTX-M-101 -containing ST131 isolates from 2014-2015 ( 22 ); and 4) 46 international fimH 27-carrying ST131 isolates from Enterobase. Focusing first on isolates within the H 22 clade ( Fig 2A ), WHO collection EAEC isolate C180-00, carrying fimH298 , clustered together with two fimH 298 EAEC EnteroBase isolates (SRA IDs SRR2970775 and SRR2970774) from Cambodia (2009-2010).…”

Section: Resultsmentioning

confidence: 99%

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Emergence of enteroaggregativeEscherichia coliwithin the ST131 lineage as a cause of extraintestinal infections

Boll

Stegger

Hasman

et al. 2018

Preprint

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26Escherichia coli sequence type 131 (ST131) is a major cause of urinary and bloodstream infections 27 and its association with extended-spectrum β-lactamases (ESBL) significantly complicates treatment. 28 Most notorious is its rapidly expanding H30-Rx clade (named for containing allele 30 of the type-1 29 fimbrial adhesin gene fimH and extensive antimicrobial resistance), which appears to have emerged 30 55 Escherichia coli sequence type 131 (ST131) is the dominant multidrug-resistant (MDR) 56 extraintestinal pathogenic E. coli (ExPEC) lineage worldwide, causing a wide range of infections 57 including bloodstream and urinary tract infections (BSIs/UTIs) (1-3). Its rise to global dominance 58 and pathogenicity is thought to have been primed by sequential acquisition of virulence-associated 59 genes followed by development of antibiotic resistance (4, 5). ST131 predominantly exhibits 60 serotype O25:H4 and is closely associated with fluoroquinolone resistance and the production of the 61 CTX-M-15 extended-spectrum β-lactamase (ESBL) (2, 6). The expansion of E. coli ST131 in the 62 United States has been driven mainly by a single clade, designated H30 because of its tight 63 association with allele 30 of the type-1 fimbrial adhesin gene, fimH. H30 has a prominent MDR-64 associated clade, H30R, which accounts for most fluoroquinolone resistance within ST131. H30R in 65 turn has two main sub-clades: H30R, which accounts for almost all ST131-associated CTX-M-14 66 and CTX-M-27 production (although most members are ESBL-negative), and H30Rx, which 67 accounts for almost all ST131-associated CTX-M-15 production (6). In addition to H30, other 68 distinct clades of ST131 are also circulating worldwide, most commonly associated to the 22 and 41 69 fimH alleles. While these non-H30 allelic variants are normally not associated with carriage of CTX-70 M-genes, cases of bla CTX-M-14 , bla CTX-M-15 and bla CTX-M-27 acquisition by ST131 lineages carrying 71 fimH22 or -H41 have been reported (4, 7). 72 ST131 isolates typically carry multiple ExPEC-associated virulence genes encoding 73 adhesins, toxins, and siderophores, whereas virulence genes typical of diarrheagenic E. coli (DEC) 74rarely have been reported (8, 9). However, we recently surveyed an international World Health 75 Organization (WHO) collection of historic E. coli for ST131 O25 isolates, assessing them for 76 temporal trends of antibiotic resistance and virulence traits. Among a total of 128 ST131 isolates we 77 found 12 (9%) that fulfilled molecular criteria for the enteroaggregative E. coli (EAEC) pathotype 78 (10). Pulsed-field gel electrophoresis (PFGE) analysis revealed a cluster comprising seven of these 79 6 EAEC isolates. Of these, sixincluding two urine isolates from patients with UTI, three fecal 80 isolates from patients with diarrhea, and one lower respiratory tract isolate (associated symptoms 81 unknown)were from Danish patients (1998)(1999)(2000), supporting the occurrence of an unrecognized 82 EAEC ST131-associated outbreak of UTI and po...

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Section: Resultsmentioning

confidence: 78%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Emergence of enteroaggregativeEscherichia coliwithin the ST131 lineage as a cause of extraintestinal infections

Boll

Stegger

Hasman

et al. 2018

Preprint

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“…Subtyping of fimH is especially relevant for the major E. coli clonal group ST131. Therefore, the 122 E. coli isolates from data set 2 previously predicted by Roer et al (6) to belong to ST131 by the Achtman MLST scheme (7) were further analyzed in relation to their fimH subtype. All 122 ST131 E. coli isolates harbored an fimH allele, with fimH30 being the most frequent (n ϭ 95, 78%) and representing the pandemic multidrug-resistant clonal group ST131-H30, followed by fimH27 (n ϭ 14, 11%), fimH41 (n ϭ 11, 9%), fimH22 (n ϭ 1, Ͻ1%), and fimH35 (n ϭ 1, Ͻ1%).…”

Section: Resultsmentioning

confidence: 99%

“…The data set covered 13 different fimH subtypes. Data set 2 comprised draft genomes obtained from whole-genome sequencing using a 250-bp paired-end Illumina data set of 243 third-generation-cephalosporin-resistant E. coli isolates originating from blood infections and submitted to Statens Serum Institut in 2014 as part of the surveillance of third-generation-cephalosporin-resistant E. coli (6). These 243 E. coli isolates covered 49 different STs, of which 122 isolates belonged to ST131 (11).…”

Section: Methodsmentioning

confidence: 99%

Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles

et al. 2017

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The aim of this study was to construct a valid publicly available method for in silico fimH subtyping of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multilocus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available at https://bitbucket.org/genomicepidemiology/fimtyper, the database is freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db, and a service implementing the software is available at https://cge.cbs.dtu.dk/services/FimTyper. FimTyper was validated on three data sets: one containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study (data set 1), one containing whole-genome sequence (WGS) data of 243 third-generation-cephalosporin-resistant E. coli isolates (data set 2), and one containing a randomly chosen subset of 40 E. coli isolates from data set 2 that were subjected to conventional fimH subtyping (data set 3). The combination of the three data sets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 42 fimH subtypes from the Sanger sequences from data set 1 and successfully analyzed all 243 draft genomes from data set 2. FimTyper subtyping of the Sanger sequences and WGS data from data set 3 were in complete agreement. Additionally, fimH subtyping was evaluated on a phylogenetic network of 122 sequence type 131 (ST131) E. coli isolates. There was perfect concordance between the typology and fimH-based subclones within ST131, with accurate identification of the pandemic multidrug-resistant clonal subgroup ST131-H30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH subtyping, highly suitable for surveillance and outbreak detection. KEYWORDS fimH, Escherichia coli, typing, whole-genome sequencing analysisT he fimH gene is part of the fim operon, which encodes a surface organelle named type 1 fimbriae found in most Escherichia coli strains (1). The FimH protein is located at the tip of the fimbrial structure and serves as a D-mannose-specific adhesin, which aids in immobilizing the bacterium on both biotic and abiotic surfaces (2, 3). Studies have shown only minor sequence variation within the fimH genes, which renders the fimH alleles feasible for use in high-resolution subtyping of multilocus sequence typing (MLST)-based E. coli clonal groups. The applicability of fimH subtyping has been shown to be particularly relevant within the highly virulent sequence type 131 (ST131) clonal group, where the resistant and multiresistant H30 subgroups carrying the fimH30 allele have been identified (4, 5). As ST131 E. coli is the most dominant human-pathogenic clonal group being reported in relation to bloodstream infections, the need to perform fimH subtyping is undisputed. Traditionally, typing of fimH alleles has been obtained

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OXA-48-like carbapenemases producing Enterobacteriaceae in different niches

Mairi

Pantel

Sotto

et al. 2017

Eur J Clin Microbiol Infect Dis

144

115

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The emergence of carbapenem-resistant enterobacterial species poses a serious threat to public health worldwide. OXA-48-type carbapenem-hydrolyzing class D β-lactamases are widely distributed among Enterobacteriaceae, with significant geographical differences. To date, 11 OXA-48-like variants have been identified, with classical OXA-48 being the most widespread. These enzymes show high-level hydrolytic activity against penicillins and low-level hydrolysis towards carbapenems. Since the first description of the OXA-48 carbapenemase in Turkey, bacterial strains producing the enzyme have been extensively reported in nosocomial and community outbreaks in many parts of the word, particularly in the Mediterranean area and European countries. The rapid spread of Enterobacteriaceae producing OXA-48-like enzymes in different ecosystems has become a serious issue recently. The number of reservoirs for such organisms is increasing, not only in hospitals, but also in the community, among animals (e.g., livestock, companion animals, and wildlife) and in the environment. This review aims to summarize the main characteristics of the OXA-48-type carbapenemases, covering genetic and enzymatic traits, their epidemiology, clonality and associated genes, correlation with extended-spectrum β-lactamases (ESBLs) or plasmidic AmpC (pAmpC) in different bacterial species worldwide.

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WGS-based surveillance of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark

Cited by 65 publications

References 27 publications

Emergence of enteroaggregativeEscherichia coliwithin the ST131 lineage as a cause of extraintestinal infections

Emergence of enteroaggregativeEscherichia coliwithin the ST131 lineage as a cause of extraintestinal infections

Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles

OXA-48-like carbapenemases producing Enterobacteriaceae in different niches

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