Antibiotic resistance and molecular characterization of bacteremia Escherichia coli isolates from newborns in the United States

Abstract

Background Escherichia coli is a major cause of neonatal sepsis. Contemporary antibiotic resistance data and molecular characterization of neonatal E . coli bacteremia isolates in the US are limited. Methods E . coli blood isolates, antibiotic susceptibility data, and clinical characteristics were obtained from prospectively identified newborns from 2006 to 2016. The E . coli isolates were classified using an updated phylogrouping method and multi-locus sequence typing. The presence of several virulence traits was also determined. Results Forty-three newborns with E . coli bacteremia were identified. Mean gestational age was 32.3 (SD±5.4) weeks. Median age was 7 days (interquartile range 0–10). Mortality (28%) occurred exclusively in preterm newborns. Resistance to ampicillin was 67%, to gentamicin was 14%, and to ceftriaxone was 2%; one isolate produced extended-spectrum beta lactamases. Phylogroup B2 predominated. Sequence type (ST) 95 and ST131 prevailed; ST1193 emerged recently. All isolates carried fimH , nlpI , and ompA , and 46% carried the K1 capsule. E . coli from newborns with bacteremia diagnosed at <72 hours old had more virulence genes compared to E . coli from newborns ≥ 72 hours old. The hek/hra gene was more frequent in isolates from newborns who died than in isolates from survivors. Conclusion Antibiotic resistance in E . coli was prevalent in this large collection of bacteremia isolates from US newborns. Most strains belonged to distinctive extra-intestinal pathogenic E . coil phylogroups and STs. Further characterization of virulence genes in neonatal E . coli bacteremia strains is needed in larger numbers and in more geographically diverse areas.

Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016

“…On their side, Cole et al [28], studying 43 bacteremia E. coli isolates from newborns obtained between 2006 and 2016 in Oklahoma, found that ST95 was the most prevalent ST (11.3%) followed by ST131 (9.2%) and ST1193 (3.7%). Cole et al [28] noted that ST95 and ST131 isolates were present throughout the studied years, while ST1193 was only seen in the recent years. Overall, neither ST88 nor ST141 belong to the most prevalent clones in North America.…”

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects

“…The absence of the AR phenotype does not exclude the presence of AR genes, which may be expressed in vivo or can be involved in the diffusion and spread of AR genes [25]. However, the rapid emergence of resistant bacteria occurring worldwide attributed to the overuse and misuse of antibiotics, healthy subjects harbor an endogenous E. coli population still sensitive to a wide range of antibiotics, contrary to the pathogenic strains isolated from different clinical specimens [26,27,28]. The scarce relevance of commensal E. coli as an AR carrier disagrees with other studies [29,30,31,32] but is consistent with a recent analysis of metagenomes that investigated AR genes in the gut microbiota of healthy people.…”

Oligosaccharides increase the genotoxic effect of colibactin produced by pks+ Escherichia coli strains

“…Since complete eradication of pks+ E. coli from the gut microbiome is not feasible to reduce CRC risk [ 11 – 13 ], we aimed at regulating the genotoxin by using prebiotics, a major regulator of the gut microbiota metabolism [ 14 ]. Prebiotics are fermentable fibers, which include oligosaccharides, that have beneficial effects on intestinal health through the maintenance of mucosal integrity, and most importantly, through the promotion of beneficial bacteria feeding on prebiotics to generate short chain fatty acids [ 15 , 16 ].…”