Table 2.
Data extraction chart with description and example article.
| Data | Description | Example |
|---|---|---|
| Article characteristics | ||
| Citation | Article reference using APA 6th style | Leong, K. W., Cooley, L. A., Anderson, T. L., Gautam, S. S., McEwan, B., Wells, A., Wilson, F., Hughson, L., and O'Toole, R. F. (2018). Emergence of vancomycin-resistant Enterococcus faecium at an Australian Hospital: a whole genome sequencing analysis. Scientific Reports 8:6274. |
| Article type | List the study design or type | Cross-sectional |
| Research group country | Name the country from where the research group originates | Australia |
| Surveillance group | List the surveillance group(s) performing the study and/or with the isolate collection (if applicable) | Tasmania Infection Prevention and Control Healthcare Associated Infection Surveillance Program |
| Funders | List the funding groups for the study | - Royal Hobart Hospital Research Foundation grant - Tasmanian Infection Prevention and Control Unit |
| Introduction | ||
| Study objectives | Bullet point summary of stated objectives | - To better define hospital spread of VREfm at the RHH - Will correlate genomic information with epidemiologic data |
| Methods | ||
| Study location | List where the samples are from or where the study was performed | Royal Hobart Hospital (RHH) in Tasmania |
| Enterococcus spp. | List the enterococcal species isolated and studied | E. faecium |
| VREfm specific study (yes/no) | Yes: the study is specifically studying VREfm No: the study is not specifically looking for VREfm (although it may be included in the results) |
Yes |
| Sample sources | List the sources from where the isolates were obtained | - Human screening - Human clinical |
| AMS testing | List the methods used for antimicrobial susceptibility testing | Done in previous study—disc diffusion (EUCAST) |
| WGS Platform | List the WGS platform(s) used | Illumina MiSeq |
| Archive accession numbers provided (yes/no) | Yes: accession numbers provided No: accession numbers not provided |
Yes |
| Bioinformatic tools | List any bioinformatics tools used according to their purpose | Alignment: Snippy Phylogeny (SNPs): RaxML Assembly: Velvet AMR: Resfinder Typing: MLST Tool |
| Other genomics | List any other genomic analyses performed | None |
| Results | ||
| AMR phenotypes | List the antimicrobials to which resistance was found (percent or ratio of isolates in parentheses) Make note of any particular phenotypic patterns |
- Vancomycin (100%) |
| Sequence types and/or clonal complexes | List any sequence types and/or clonal complexes found | ST796 (47/80) ST80 (16/80) ST1421 (10/80) ST203 (4/80) ST78 (1/80) ST192 (1/80) ST555 (1/80) |
| AMR genes | List of AMR genes found through WGS, according to sample source If >10 AMR genes were found, reference where in the article they may be found, rather than providing an exhaustive list |
vanA vanB |
| Plasmids | List of any plasmids found | None described |
| Relatedness assessed | Brief description of the relatedness that was assessed | Study isolates to reference genome (SNPs) Comparison of genomic to epidemiologic data |
| Discussion | ||
| Addition to AMR knowledge | Summary of addition to knowledge about AMR in Enterococcus | - VREfm profile at RHH has shifted to ST796 and ST80 - Screening is important to detect isolates that may be involved in transmission - WGS is helpful for more accurate typing of E. faecium for better investigations |