Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-Lactams

Abstract

The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.

Plasmid-Mediated Ampicillin, Quinolone, and Heavy Metal Co-Resistance among ESBL-Producing Isolates from the Yamuna River, New Delhi, India

“…A similar resistance pattern for β-lactam antibiotics was recorded by Lu et al from an urban river habitat in China [ 45 ]. Moreover, our results are also in line with other studies reporting a high level of resistance against β-lactam and non-β-lactam antibiotics [ 46 , 47 , 48 , 49 , 50 , 51 , 52 ]. This study found 34.2% and 20.5% resistance toward piperacillin + tazobactam and ampicillin + sulbactam combinations, respectively.…”

“…Plasmid-mediated CIT type AmpC β-lactamase was successfully amplified among 20.5% of bacterial strains. Bajaj et al, Martinez-Medina et al, and Loncaric et al also reported the similar occurrence of AmpC -type β-lactamase among bacterial isolates from river water and patient samples, respectively [ 9 , 52 , 55 ]. Furthermore, sequence analysis revealed the occurrence of bla CMY-2 and bla CMY-42 among 8 and 7 strains, respectively.…”

Phylogrouping and characterization of Escherichia coli isolated from colonic biopsies and fecal samples of patients with flare of inflammatory bowel disease in Iran

“…To our knowledge, only a very small fraction of studies have reported the antimicrobial resistance patterns of Enterobacteriaceae strains among IBD patients. In a study conducted by Martinez-Medina et al, it was reported that mucosa-associated E. coli isolates from CD patients were more frequently resistant to β-lactams than those isolated from the intestine of control subjects ( 67 ). Dogan et al reported that CD-associated E. coli frequently manifests resistance to commonly used antimicrobials, particularly, resistance to ciprofloxacin, rifaximin/rifampin, and trimethoprim/sulfamethoxazole ( 68 ).…”

TheE. colipathobiont LF82 encodes a unique variant of σ70that results in specific gene expression changes and altered phenotypes

“…The effects of changing amino acid 445 has not been previously reported. Inspection of genomes from other AIEC 31,32,34,51,62,[70][71][72]85,86 reveals the rpoD D445V allele is unique to LF82.…”