Neonatal meningitis Eschericha coli (NMEC), a sub-pathotype of extra intestinal E. coli (ExPEC), is one of the most common causative agents of neonatal bacterial meningitis (NBM). NBM is a devastating disease affecting neonates less than four weeks old, causing acute onset of sepsis and invasion of the central nervous system. Without treatment, NBM is almost certainly fatal, but early intervention and empiric treatment, as well as new broad spectrum antibiotics, have reduced the mortality rates from 32% in 1975 to as low as 8.5% in the United States.

Recent studies have greatly improved knowledge of NMEC pathogenetic mechanisms by characterizing multiple NMEC virulence factors; however, nearly all experiments were performed using a single NMEC strain RS218 and its derivative mutants. Broader studies examining larger populations of NMEC have begun to show that some of the virulence factors critical for NMEC RS218 pathogenesis occur uncommonly in other NMEC, while other virulence factors identified using NMEC RS218 are present in multiple E. coli sub-pathotypes and even non-pathogenic E. coli. Such findings beg the questions, what genes define the NMEC sub-pathotype? How diverse are members of the NMEC sub-pathotype? And can another NMEC strain, other than NMEC RS218, serve as a more representative prototype of the NMEC group?

Additionally, other studies have found that some Avian Pathogenic E. coli (APEC) strains can cause NBM in the rat model of human disease, while some NMEC are able to cause disease in the day-old chick model of avian colibacillosis. Such findings suggest that NBM and avian colibacillosis, caused by ExPEC, could be zoonotic diseases, a contention that requires further study for both the benefit of human and animal health.

works of this dissertation seek to generate high quality genomic and plasmid sequences for a random population of NMEC and analyze these data in silico to better define the NMEC sub-pathotype.

Initial characterization began by sequence and assembly of a population of 48 NMEC strains from the United States and Europe, searching for novel virulence and resistance factors. As part of this comparative study of NMEC strains, a polymorphic analysis of ubiquitous E. coli genes, thought to contribute to the pathogenesis of ExPEC diseases but also occurring widely among non-pathogenic E. coli was undertaken. Analysis of the results showed that genes that are strongly linked to NMEC virulence in the literature, such as cnf1, sfaS, sfaC, and traJ, were found in less than 50% of the NMEC surveyed, while the K1 capsule, aslA, chuA, and papX were found in more than 75% of the strains. Analysis of the sequences of the ubiquitously occurring and well-known genes, fimH and ompA, demonstrated that both harbored polymorphisms in sites important to protein activity and substrate binding. When these NMEC polymorphisms were compared to those in other ExPEC sub-pathotypes (namely, uropathogenic E. coli and APEC), distinct polymorphic patterns were discerned that differentiated members of the three ExPEC sub-pathotypes. This finding is quite intriguing, as these genes encode a number of key processes in ExPEC pathogenesis, suggesting that they could explain tissue tropism, host specificity and/or capability of a strain to cause a specific syndrome. Future study will need to be done to explore these issues.

In addition to comparative analysis of NMEC chromosomes, the large putative virulence plasmids of several NMEC isolates were sequenced and compared to define the core and pan-plasmidome of NMEC. These sequences were also scanned for novel virulence and resistance genes, and the sequences compared to one another and to plasmids sequences of other ExPEC sub-pathotypes. Results show NMEC plasmids sequenced in this dissertation were genetically similar to plasmids of APEC strains. Neither core plasmid polymorphism phylogenies nor differences in plasmid-borne genes could distinguish APEC plasmids from NMEC plasmids.

Finally, high quality complete genomic sequences for NMEC O18 and APEC O18 strains with zoonotic potential were generated. NMEC O18 is a highly virulent NMEC strain able to cause similar disease in the rat model of human neonatal meningitis. Interestingly, it lacks cnf1 and traJ, both thought to be crucial for NMEC pathogenesis. APEC O18 is highly virulent in chick embryos and day old chicks but is also highly virulent in the rat model of human meningitis. This paper reports the first sequence of an APEC O18 strain causing neonatal meningitis at the same level as NMEC O18 and RS218.