Asymptomatic carriage isolates: multilocus sequence types, clades and toxin status.

<p>Participant id follows that used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078445#pone-0078445-g002" target="_blank">Figure 2</a>.</p

Asymptomatic study participants and samples.

<p>Asymptomatic study participants and samples.</p

Relationship between overnight hospital stays and antibiotic exposure in the last six months amongst <i>C. difficile</i> carriers and non-carriers.

<p>111 of the 112 participants with questionnaire data completed both questions on hospital exposure and antibiotic use.</p

Univariate risk factors for asymptomatic carriage of <i>C. difficile</i>.

<p>There were no <i>C. difficile</i> carriers with the following risk factors: inflammatory bowel disease (present in 1/112 (1%) participants), haematological malignancy (5/112 (4%)), gastrointestinal surgery (5/112 (4%) with surgery in current admission, 12/112 (11%) with past surgery), current nasogastric tube placement (3/112 (3%)), previous CDI (5/112 (4%)), contact with a CDI case (2/112 (2%)), vegetarian diet (7/112 (6%)), and overseas travel (4/112 (4%)). *Given the study design, most participants spent relatively short amounts of time in hospital prior to enrolment, median (IQR) 2 (1–6) days.</p

Temporal pattern of samples in participants with ≥1 positive sample.

<p>Asymptomatic positive and negative relate to samples obtained during the carriage study. Matching of study participants with the hospital admission and microbiology data allowed 4 participants with a subsequent symptomatic CDI positive samples to be identified, denoted symptomatic positive. 118 participants had consistently negative samples and are not plotted.</p

Multivariate risk factors for asymptomatic carriage of <i>C. difficile.</i>

<p>The left hand side of the table includes all participants with questionnaire data, the right hand side excludes 22 patients with loose or more frequent stool, but not meeting CDI diagnosis criteria (5 carriers and 17 non-carriers). No significant pairwise interactions were identified, but given the relatively small sample size the power to detect these is low. Excluding one participant with missing hospital exposure data.</p

Single nucleotide variants, SNVs, between 18 asymptomatic carriage samples and most closely genetically related prior and subsequent symptomatic/asymptomatic sample.

<p>Participants are ordered by the number of SNVs to the most closely related sample. The participant numbering follows the same scheme used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078445#pone-0078445-g002" target="_blank">Figure 2</a>.</p>*<p>indicates acquisition following an initially negative sample.</p>§<p>indicates subsequently developed disease with the same strain,</p>†<p>indicates subsequently developed disease with a different strain.</p

Epidemiological relationships between 4 asymptomatic study participants and genetically related cases.

<p>Study participants are shown in blue, with the exception of participant 3, shown in red in the first panel. Symptomatic cases are shown as different colours, and are distinct across different panels. Positive asymptomatic samples from study participants are shown as filled circles. Positive symptomatic samples are shown as crosses. EIA-negative culture-positive samples are shown as diamonds. Ward stays are shown as horizontal lines with capped ends. Wards sharing the same specialty and hospital share the same initial letter; adjacent wards forming a single unit have the same letter and number and are followed by a lower case letter.</p

Type and duration of antibiotic exposure at study enrolment in <i>C. difficile</i> carriers and non-carriers.

*<p>Of those taking multiple agents, 15 participants’ regimes included co-amoxiclav, 7 participants a macrolide, and 3 a cephalosporin.</p

Oxford Screening of CSF and Respiratory Samples ('OSCAR'): Supplementary resources for a project using Next Generation Sequencing (NGS) for identification of viruses from clinical laboratory samples

<p>This is a file set that describes the methods used in a small pilot study to investigate 'next generation sequencing' (NGS) derived from an Illumina platform, applied to clinical diagnostic samples following routine testing in a UK microbiology laboratory.</p><p>We briefly summarise the benefits and challenges of an NGS approach to diagnostics, and conclude with some potential methodological improvements.</p><p>The file set includes anonymised metadata for the samples tested (10 respiratory and 10 CSF).</p><p>Results have been made available through a separate DOI: 10.6084/m9.figshare.5712091 and the entire genomic metadata have been submitted to European Nucleotide Archive (ENA); (primary accession PRJEB22949). </p><p>This study was approved through the UK integrated research application system (REC reference 14/LO/1077).</p