Supplemental Material - Possibilities and Pitfalls for Dealing with Large Longitudinal Qualitative Datasets

Supplemental Material for Possibilities and Pitfalls for Dealing with Large Longitudinal Qualitative Datasets by Megan Devonald and Nicola Jones in International Journal of Qualitative Methods</p

Additional file 1: of Oral fosfomycin for treatment of urinary tract infection: a retrospective cohort study

Spreadsheet reporting 75 unique patients treated with fosfomycin for urinary tract infections. This excel file contains anonymised details of 75 unique adult patients treated with fosfomycin for urinary tract infections at Oxford University Hospitals NHS Foundation Trust from March 2013 through June 2015. Our original analysis also included patient sex, but this has been removed from the suppl. data file in order to protect anonymity. (XLSX 24 kb

Additional file 2: of Oral fosfomycin for treatment of urinary tract infection: a retrospective cohort study

Tabulated summary of studies that have informed current NICE guidelines for fosfomycin use in UTI. This table contains a brief summary of four studies from Europe/North America that are referenced by current NICE guidelines regarding the use of oral fosfomycin for treatment of UTI, including date of study, cohort location, study design and cure data. (DOCX 88 kb

Microbial diversity and antimicrobial resistance in faecalsamples from acute medical patients assessed through metagenomic sequencing

Antimicrobial resistance (AMR) is a threat to global public health. However, unsatisfactory approaches to directly measuring the AMR burden carried by individuals has hampered efforts to assess interventions aimed at reducing selection for AMR. Metagenomics can provide accurate detection and quantification of AMR genes within an individual person’s faecal flora (their gut “resistome”). Using this approach, we aimed to test the hypothesis that differences in antimicrobial use across different hospitals in the United Kingdom will result in observable differences in the resistome of individual patients. Three National Health Service acute Hospital Trusts with markedly different antibiotic use and Clostridioides difficile infection rates collected faecal samples from anonymous patients which were discarded after C. difficile testing over a period of 9 to 15 months. Metagenomic DNA was extracted from these samples and sequenced using an Illumina NovaSeq 6000 platform. The resulting sequencing reads were analysed for taxonomic composition and for the presence of AMR genes. Among 683 faecal metagenomes we found huge variation between individuals in terms of taxonomic diversity (Shannon Index range 0.10–3.99) and carriage of AMR genes (Median 1.50 genes/cell/sample overall). We found no statistically significant differences in diversity (median Shannon index 2.16 (IQR 1.71–2.56), 2.15 (IQR 1.62–2.50) and 2.26 (IQR 1.55–2.51)) or carriage of AMR genes (median 1.37 genes/cell/sample (IQR 0.70–3.24), 1.70 (IQR 0.70–4.52) and 1.43 (IQR 0.55–3.71)) at the three trusts respectively. This was also the case across the sample collection period within the trusts. While we have not demonstrated differences over place or time using metagenomic sequencing of faecal discards, other sampling frameworks may be more suitable to determine whether organisational level differences in antibiotic use are associated with individual-level differences in burden of AMR carriage