Extraintestinal pathogenic Escherichia coli (ExPEC) are a common cause of disease in both mammals and birds. A vaccine to prevent such infections would be desirable given the increasing antibiotic resistance of these bacteria. We have determined the genome sequence of ExPEC IHE3034 (ST95) isolated from a case of neonatal meningitis and compared this to available genome sequences of other ExPEC strains and a few nonpathogenic E. coli . We found 19 genomic islands present in the genome of IHE3034, which are absent in the nonpathogenic E. coli isolates. By using subtractive reverse vaccinology we identified 230 antigens present in ExPEC but absent (or present with low similarity) in nonpathogenic strains. Nine antigens were protective in a mouse challenge model. Some of them were also present in other pathogenic non-ExPEC strains, suggesting that a broadly protective E. coli vaccine may be possible. The gene encoding the most protective antigen was detected in most of the E. coli isolates, highly conserved in sequence and found to be exported by a type II secretion system which seems to be nonfunctional in nonpathogenic strains.

We examined the genetic structure among populations and regions for thespringtails Cryptopygus antarcticus antarcticus and Gomphiocephalus hodgsoni(Collembola) to identify potential historical refugia and subsequent colonizationroutes, and to examine population growth/expansion and relative ages ofpopulation divergence.Location Antarctic Peninsula for C. a. antarcticus; Antarctic continent (southernVictoria Land) for G. hodgsoni.Methods Samples were collected from 24 and 28 locations across the AntarcticPeninsula and southern Victoria Land regions for C. a. antarcticus andG. hodgsoni, respectively. We used population genetic, demographic and nestedclade analyses based on mitochondrial DNA (cytochrome c oxidase subunit I andsubunit II).Results Both species were found to have population structures compatiblewith the presence of historical glacial refugia on Pleistocene (2 Ma–present) timescales,followed by post-glacial expansion generating contemporary geographicallyisolated populations. However, G. hodgsoni populations were characterized by afragmented pattern with several ‘phylogroups’ (likely ancestral haplotypes presentin high frequency) retaining strong ancestral linkages among present-daypopulations. Conversely, C. a. antarcticus had an excess of rare haplotypes witha much reduced volume of ancestral lineages, possibly indicating historicalfounder/bottleneck events and widespread expansion.Main conclusions We infer that these differences reflect distinct evolutionaryhistories in each locality despite the resident species having similar life-historycharacteristics. We suggest that this has predominantly been influenced byvariation in the success of colonization events as a result of intrinsic historicalglaciological differences between the Antarctic Peninsula and continentalAntarctic environment

The ability to adhere and adapt to the human respiratory tract mucosa plays a pivotal role in the pathogenic lifestyle of nontypeable Haemophilus influenzae (NTHi). However, the temporal events associated with a successful colonization have not been fully characterized. In this study, by reconstituting the ciliated human bronchial epithelium in vitro, we monitored the global transcriptional changes in NTHi and infected mucosal epithelium simultaneously for up to 72 h by dual RNA sequencing. The initial stage of colonization was characterized by the binding of NTHi to ciliated cells. Temporal profiling of host mRNA signatures revealed significant dysregulation of the target cell cytoskeleton elicited by bacterial infection, with a profound effect on the intermediate filament network and junctional complexes. In response to environmental stimuli of the host epithelium, NTHi downregulated its central metabolism and increased the expression of transporters, indicating a change in the metabolic regime due to the availability of host substrates. Concurrently, the oxidative environment generated by infected cells instigated bacterial expression of stress-induced defense mechanisms, including the transport of exogenous glutathione and activation of the toxin-antitoxin system. The results of this analysis were validated by those of confocal microscopy, Western blotting, Bio-plex, and real-time quantitative reverse transcription-PCR (qRT-PCR). Notably, as part of our screening for novel signatures of infection, we identified a global profile of noncoding transcripts that are candidate small RNAs (sRNAs) regulated during human host infection in Haemophilus species. Our data, by providing a robust and comprehensive representation of the cross talk between the host and invading pathogen, provides important insights into NTHi pathogenesis and the development of efficacious preventive strategies.