Inhibitor-Resistant TEM- and OXA-1-Producing Escherichia coli Isolates Resistant to Amoxicillin-Clavulanate Are More Clonal and Possess Lower Virulence Gene Content than Susceptible Clinical Isolates

Abstract

In a previous prospective multicenter study in Spain, we found that OXA-1 and inhibitor-resistant TEM (IRT) ␤-lactamases constitute the most common plasmid-borne mechanisms of genuine amoxicillin-clavulanate (AMC) resistance in Escherichia coli. In the present study, we investigated the population structure and virulence traits of clinical AMC-resistant E. coli strains expressing OXA-1 or IRT and compared these traits to those in a control group of clinical AMC-susceptible E. coli isolates. All OXA-1-producing (n ‫؍‬ 67) and IRT-producing (n ‫؍‬ 45) isolates were matched by geographical and temporal origin to the AMCsusceptible control set (n ‫؍‬ 56). We performed multilocus sequence typing and phylogenetic group characterization for each isolate and then studied the isolates for the presence of 49 virulence factors (VFs) by PCR and sequencing. The most prevalent clone detected was distinct for each group: group C isolates of sequence type (ST) 88 (C/ST88) were the most common in OXA-1 producers, B2/ST131 isolates were the most common in IRT producers, and B2/ST73 isolates were the most common in AMCsusceptible isolates. The median numbers of isolates per ST were 3.72 in OXA-1 producers, 2.04 in IRT producers, and 1.69 in AMC-susceptible isolates; the proportions of STs represented by one unique isolate in each group were 19.4%, 31.1%, and 48.2%, respectively. The sum of all VFs detected, calculated as a virulence score, was significantly higher in AMC-susceptible isolates than OXA-1 and IRT producers (means, 12.5 versus 8.3 and 8.2, respectively). Our findings suggest that IRT-and OXA-1-producing E. coli isolates resistant to AMC have a different and less diverse population structure than AMC-susceptible clinical E. coli isolates. The AMC-susceptible population also contains more VFs than AMC-resistant isolates.

Molecular identification of aminoglycoside-modifying enzymes in clinical isolates of Escherichia coli resistant to amoxicillin/clavulanic acid isolated in Spain

“…Among the 257 AMC-resistant E. coli, all 5 isolates (1.9%) resistant to amikacin contained the aac(6 )-Ib gene. Although it has been described that the aac(6 )-Ib gene confers resistance to amikacin, kanamycin, tobramycin and netilmicin [7], when applying EUCAST (2) To (2) K, To (2) Gm (1) To (1) K (1) Susceptible (1) aph (3 )-Ia 21 (20.0) K, Nm As expected (20) As expected (20) Gm, K, Nm (1) Gm, K (1) aac(3)-IIa 9 (8.6) Gm, Nt, To As expected (8) As expected (2) Gm, K, Nt, To (1) Gm, To (2) Gm (5) aac (6 )-Ib, aac(3)-IIa 8 (7.6) Ak, Gm, K, Nt, To As expected (1) As expected (1) Gm, K, Nt, To (7) Gm, K, Nt, To (2) Gm, K, To (4) Gm, To (1) aac (3) breakpoints only 4 of the 25 isolates (16%) containing only the aac(6 )-Ib gene presented this specific pattern, whilst the remaining 21 isolates were resistant to one or more of gentamicin, tobramycin, netilmicin or kanamycin, but not to amikacin. Using breakpoints established by the CLSI, none of isolates carrying the aac(6 )-Ib gene had the expected resistance phenotype to aminoglycosides; in fact, this gene was detected in one strain susceptible to all tested aminoglycosides ( Table 2).…”

“…We also found that 23 of 25 strains producing CTX-M-15 had the aac(6 )-Ib-cr gene, of which 69.5% belonged to clonal complex ST131 and 30.5% were ST23 or ST10 [20]. On the other hand, it is also remarkable that 5 of 11 isolates hyperproducing chromosomal AmpC harboured the aac(6 )-Ib gene, in contrast with the results of Lindemann et al [12] who did not find aac(6 )-Ib in any of isolates with AmpC hyperproduction.…”

“…As shown in Table 4, the OXA-1 gene alone (the most prevalent mechanism of resistance to AMC [4]) was usually associated with ant(2 )-Ia (21/30 isolates; 70%); all isolates with ant(2 )-Ia belong to the clone ST88 phylogroup A (P < 0.0001) [20]. On the other hand, 18 strains (17.1%) producing both OXA-1 and ESBL (CTX-M-15) contained aac(6 )-Ib-cr alone or in combination with another AME gene.…”

Plasmid‐mediated resistance to cephalosporins and quinolones in Escherichia coli from American crows in the USA

“…The bla CMY-2 isolates from two sampling sites showed ESBL, AmpC and PMQR E. coli from American crows 2031 significant clonal similarity with dominance of ST88 and ST336 in California and ST48 and ST345 in New York, indicating their common source. ST88 has been described as both extraintestinal pathogenic E. coli (ExPEC) and avian pathogenic E. coli (APEC) (Maluta et al, 2014) and betalactamase-producing isolates of this clonal group have been reported in hospitals in France (Cremet et al, 2010) and Spain (Oteo et al, 2014) as well as from cases of bovine mastitis in the UK (Timofte et al, 2014). ST345 has been reported as APEC (Maluta et al, 2014) and the isolates of this ST have been found in wild birds in Europe (Jamborova et al, 2015), companion animals (Poirel et al, 2013) and human clinical samples in Asia (Yuan et al, 2012).…”

Carbapenemase-producing enterobacteriaceae recovered from a Spanish river ecosystem

“…coli strains were screened for the presence of 49 virulence factors (including 19 adhesins, 4 siderophores, 11 toxins, 6 capsule synthesis-associated genes, and 9 miscellaneous genes). Screening was performed by multiplex PCRs according to previously reported methodology [23]. In the case of K .…”