Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology

An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past. To prospectively elucidate the unique characteristics of this strain in the early stages of this outbreak, we applied whole genome sequencing on the Life Technologies Ion Torrent PGM? sequencer and Optical Mapping to characterize one outbreak isolate (LB226692) and a historic O104:H4 HUS isolate from 2001 (01-09591). Reference guided draft assemblies of both strains were completed with the newly introduced PGM? within 62 hours. The HUS-associated strains both carried genes typically found in two types of pathogenic E. coli, enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC). Phylogenetic analyses of 1,144 core E. coli genes indicate that the HUS-causing O104:H4 strains and the previously published sequence of the EAEC strain 55989 show a close relationship but are only distantly related to common EHEC serotypes. Though closely related, the outbreak strain differs from the 2001 strain in plasmid content and fimbrial genes. We propose a model in which EAEC 55989 and EHEC O104:H4 strains evolved from a common EHEC O104:H4 progenitor, and suggest that by stepwise gain and loss of chromosomal and plasmid-encoded virulence factors, a highly pathogenic hybrid of EAEC and EHEC emerged as the current outbreak clone. In conclusion, rapid next-generation technologies facilitated prospective whole genome characterization in the early stages of an outbreak.     

Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: Weak differentiation yet distinct associations with water availability

Populations residing near species' low‐latitude range margins (LLMs) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographical range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at single nucleotide polymorphisms (SNPs) located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographical structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive F_ST‐outlier loci, and genotype–environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species’ resilience to climate change‐related pressures.     

Roles of the amyloid precursor protein family in the peripheral nervous system

Compelling evidence from in vivo model systems within the past decade shows that the APP family of proteins is important for synaptic development and function in the central and peripheral nervous systems. The synaptic role promises to be complex and multifaceted for several reasons. The three family members have overlapping and redundant functions in mammals. They have both adhesive and signaling properties and may, in principle, act as both ligands and receptors. Moreover, they bind a multitude of synapse-specific proteins, and we predict that additional interacting protein partners will be discovered. Transgenic mice with modified or abolished expression of APP and APLPs have synaptic defects that are readily apparent. Studies of the neuromuscular junction (NMJ) in these transgenic mice have revealed molecular and functional deficits in neurotransmitter release, in organization of the postsynaptic receptors, and in coordinated intercellular development. The results summarized here from invertebrate and vertebrate systems confirm that the NMJ with its accessibility, large size, and homogeneity provides a model synapse for identifying and analyzing molecular pathways of APP actions.     

Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel

Chemical proteomics aims to characterize all of the proteins in the proteome with respect to their function, which is associated with their interaction with other molecules. We propose the identification of a subproteomic library of expressed proteins whose native structures are typified by the presence of hydrophobic surface sites, which are often involved in interactions with small molecules, membrane lipids, and other proteins, pertaining to their functions. We demonstrate that soluble globular proteins with hydrophobic surface sites can be detected selectively by staining on an electrophoretic gel run under nondenaturing conditions. The application of these staining techniques may help elucidate new catalytic, transport, and regulatory functionalities in complex proteomic screenings.     

Biology of Polypedilum n. sp. (Diptera: Chironomidae), a promising candidate agent for the biological control of the aquatic weed Lagarosiphon major (Hydrocharitaceae) in Ireland

Lagarosiphon major (Ridl.) Moss ex Wager (Hydrocharitaceae), an aquatic macrophyte native to Southern Africa that has become invasive in several countries worldwide, is a potential target for biological control. Biology studies were conducted on Polypedilum (Pentapedilum) n. sp. near reei Oyewo & Sæther (Diptera: Chironomidae), a midge whose larvae were discovered mining the plant's shoot tips in its native range. Field surveys indicated that the midge occurred only at a small number of sites but attained high densities (up to 370 shoots damaged/m²) that prevented further growth from the shoot tips. A population of the midge was imported into quarantine in Ireland to evaluate its potential as a candidate biological control agent. The adult stage is terrestrial and short-lived (4–5 d), with females depositing one–two egg packets into the water bodies. First-instar larvae fed externally on the stems and leaflets. Later instars fed on the apical meristems and burrowed into the shoot tips, with resultant damage stunting the apical growth. Larvae moved readily between shoots to complete their development and pupated within the tunnels excavated by the late instar larvae. Developmental time to adulthood ranged from 31 to 49 days at 20.7°C and a 15 L:9-D cycle. This is the first time that a chironomid has been imported and successfully cultured for consideration as a classical biological control agent. Several aspects of the midge's biology suggest that host specificity testing is warranted to determine its potential as a biocontrol agent of L. major.     

Timing is everything: international variations in historical sexual partnership concurrency and HIV prevalence

Background

Higher prevalence of concurrent partnerships is one hypothesis for the severity of the HIV epidemic in the countries of Southern Africa. But measures of the prevalence of concurrency alone do not adequately capture the impact concurrency will have on transmission dynamics. The importance of overlap duration and coital exposure are examined here.

Methodology/Principal Findings

We conducted a comparison of data from three studies of sexual behavior carried out in the early 1990s in Uganda, Thailand and the US. Using cumulative concurrency measures, the three countries appeared somewhat similar. Over 50% of both Thai and Ugandan men reported a concurrency within the last three partnerships and over 20% reported a concurrency in the last year, the corresponding rates among US men were nearly 20% for Blacks and Hispanics, and about 10% for other racial/ethnic groups. Concurrency measures that were more sensitive to overlap duration, however, showed large differences. The point prevalence of concurrency on the day of interview was over 10% among Ugandan men compared to 1% for Thai men. Ugandan concurrencies were much longer duration – a median of about two years – than either the Thai (1 day) or US concurrencies (4–9 months across all groups), and involved 5–10 times more coital risk exposure with the less frequent partner. In the US, Blacks and Hispanics reported higher prevalence, longer duration and greater coital exposure than Whites, but were lower than Ugandans on nearly every measure. Together, the differences in the prevalence, duration and coital exposure of concurrent partnerships observed align with the HIV prevalence differentials seen in these populations at the time the data were collected.

Conclusions/Significance

There were substantial variations in the patterns of concurrent partnerships within and between populations. More long-term overlapping partnerships, with regular coital exposure, were found in populations with greater HIV epidemic severity.     

Chromosomal dynamism in progeny of outbreak-related sorbitol-fermenting enterohemorrhagic Escherichia coli O157:NM

Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:NM (nonmotile) is a unique clone that causes outbreaks of hemorrhagic colitis and hemolytic-uremic syndrome. In well-defined clusters of cases, we have observed significant variability in pulsed-field gel electrophoresis (PFGE) patterns which could indicate coinfection by different strains. An analysis of randomly selected progeny colonies of an outbreak strain after subcultivation demonstrated that they displayed either the cognate PFGE outbreak pattern or one of four additional patterns and were <89% similar. These profound alterations were associated with changes in the genomic position of one of two Shiga toxin 2-encoding genes (stx2) in the outbreak strain or with the loss of this gene. The two stx2 alleles in the outbreak strain were identical but were flanked with phage-related sequences with only 77% sequence identity. Neither of these phages produced plaques, but one lysogenized E. coli K-12 and integrated in yecE in the lysogens and the wild-type strain. The presence of two stx2 genes which correlated with increased production of Stx2 in vitro but not with the clinical outcome of infection was also found in 14 (21%) of 67 SF EHEC O157:NM isolates from sporadic cases of human disease. The variability of PFGE patterns for the progeny of a single colony must be considered when interpreting PFGE patterns in SF EHEC O157-associated outbreaks.