Genome sequence of enterovirus D68 from St. Louis, Missouri, USA, 2016

Enterovirus D68 (EV-D68) was rarely observed prior to a widespread outbreak in 2014. We observed its reemergence in St. Louis in 2016 and sequenced the EV-D68 genomes from two patient samples. The 2016 viruses in St. Louis differed from those we had sequenced from the 2014 outbreak but were similar to other viruses circulating nationally in 2016

Whole-genome sequencing of Klebsiella pneumoniae isolates to track strain progression in a single patient with recurrent urinary tract infection

Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Evidence suggests that some same-strain recurrences in women with frequent urinary tract infections (UTIs) may emanate from a persistent intravesicular reservoir. Our objective was to analyze K. pneumoniae isolates collected over weeks from multiple body sites of a single patient with recurrent UTI in order to track ordered strain progression across body sites, as has been employed across patients in outbreak settings. Whole-genome sequencing of 26 K. pneumoniae isolates was performed utilizing the Illumina platform. PacBio sequencing was used to create a refined reference genome of the original urinary isolate (TOP52). Sequence variation was evaluated by comparing the 26 isolate sequences to the reference genome sequence. Whole-genome sequencing of the K. pneumoniae isolates from six different body sites of this patient with recurrent UTI demonstrated 100% chromosomal sequence identity of the isolates, with only a small P2 plasmid deletion in a minority of isolates. No single nucleotide variants were detected. The complete absence of single-nucleotide variants from 26 K. pneumoniae isolates from multiple body sites collected over weeks from a patient with recurrent UTI suggests that, unlike in an outbreak situation with strains collected from numerous patients, other methods are necessary to discern strain progression within a single host over a relatively short time frame.</p

The Cunning Folk

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Enhanced virome sequencing using targeted sequence capture

Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications

The Korean War and the Post-war Prisoner of War Regime, 1945–1956

This paper examines the framework for the treatment of prisoners of war that emerged after 1945. It focuses on one of the key elements of the post-war prisoner of war (POW) regime, the role of neutral bodies – state authorities acting as ‘protecting powers’ or humanitarian agencies such as the International Committee of the Red Cross – in supervising the implementation of the 1949 POW convention. It examines the importance of neutral supervision for the POW regime, and shows how the events of the Korean War affected the willingness of states to comply with their obligations under the new convention

Examining public service motivation in the voluntary sector: implications for public management

Building on research about the nature of Public Service Motivation (PSM) and its application outside the public sector, the authors provide a qualitative based examination of PSM's relevance to voluntary sector employees. In doing so, they explore how far their motivations extend beyond those encompassed within current conceptualisations of PSM and whether PSM research can be enriched through the adoption of qualitative methodologies. The findings suggest that PSM accounts for some, but not all, of the motives of voluntary sector employees and indicate that public sector managers involved in outsourcing public services need to be sensitive to their distinctive features

The “Majestic Equality” of the Law: Conservatism, Radicalism, and Reform of the Civil Courts in Upper Canada, 1841-1853

The mid-nineteenth century was an age of reform in the civil courts of the common-law world. Why, in spite of the clamour for change within Upper Canada and the introduction of reforms in adjacent common-law jurisdictions, were Upper Canada’s leading lawyers and politicians so reluctant to act? The answer is found in the conservatism of the province’s leaders, which stemmed not only from the legal training of the lawyers, but also from the moderate conservative ideology of the Upper Canadian leadership as a whole. At an almost unprecedented time of public debate, when resentment to lawyers and the courts was being expressed and a radical critique of the courts and the profession was emerging, Upper Canada’s most influential residents managed to maintain political control and steadfastly refused to act in advance of the mother country

Comparison of metagenomic sequencing and the NanoString nCounter analysis system for the characterization of bacterial and viral communities in vaginal samples

DNA sequencing assays have been used to characterize the vaginal microbiome and to identify associations with clinical outcomes. The purpose of this study was to evaluate the utility of the NanoString nCounter platform, a more efficient assay compared to sequencing, for the characterization of vaginal microbial communities. A panel of NanoString nCounter probes was designed to detect common vaginal bacteria and viruses with relevance to reproductive health. A defined synthetic community of microbes and 43 clinical samples were interrogated with NanoString nCounter assays and compared to known compositions or metagenomic shotgun sequencing (MSS) results. The NanoString nCounter platform and MSS were able to distinguish closely related microbes. In clinical samples, the relative abundance of bacterial species was similar between the two assays. The assays sometimes disagreed when targets were present at low abundance. More viruses were detected by MSS than by nCounter. However, the nCounter assays are able to provide results in about 30 h with minimal hands-on time, whereas MSS requires at least 138 to 178 h with extensive hands-on time. The reagent cost for the two assays was similar, but the overall cost of the nCounter was lower due to the minimal hands-on time. MSS can be used to inform the design of a targeted multiplex panel for the assessment of vaginal microbial communities, thereby allowing for more cost-effective and rapid screening of patient samples for research studies. The sensitivity for low abundance microbes could be improved, possibly by adding additional target amplification cycles before nCounter assessment. This approach has potential as an assay with both research and clinical applications