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.

Escherichia coli is the leading cause of Gram-negative neonatal septicemia in the United States. Invasion and passage across the neonatal gut after ingestion of maternal E. coli strains produce bacteremia. In this study, we compared the virulence properties of the neonatal E. coli bacteremia clinical isolate SCB34 with the archetypal neonatal E. coli meningitis strain RS218. Whole-genome sequencing data was used to compare the protein coding sequences among these clinical isolates and 33 other representative E. coli strains. Oral inoculation of newborn animals with either strain produced septicemia, whereas intraperitoneal injection caused septicemia only in pups infected with RS218 but not in those injected with SCB34. In addition to being virulent only through the oral route, SCB34 demonstrated significantly greater invasion and transcytosis of polarized intestinal epithelial cells in vitro as compared to RS218. Protein coding sequences comparisons highlighted the presence of known virulence factors that are shared among several of these isolates, and revealed the existence of proteins exclusively encoded in SCB34, many of which remain uncharacterized. Our study demonstrates that oral acquisition is crucial for the virulence properties of the neonatal bacteremia clinical isolate SCB34. This characteristic, along with its enhanced ability to invade and transcytose intestinal epithelium are likely determined by the specific virulence factors that predominate in this strain.