10.17037/DATA.00003087
Data extracted from published peer-reviewed and grey literature that summarise antimicrobial sensitivity testing data and sensitivity results.
| Variable name | Variable description | Answer code | Answer label | Variable type |
| Study ID no. | Study ID number | Numeric | ||
| Title | Study title | String | ||
| Authors | Study authors | String | ||
| Publication (FT) | the journal name | String | ||
| Publication Year | 5-year intervals for publication date | Numeric | ||
| Funding (FT) | The main funding body/bodies | String | ||
| Study Design | What types of studies are being conducted on this topic; also quality of evidence (randomized controlled trials provide best quality, descriptive studies are poor) | String | ||
| Prevalence/Cross-sectional | a study where both the exposure and outcome are known with the aim being to calculate prevalence in a group | |||
| Experimental Trial | a controlled trial where exposures are assigned by the investigator; can be random or not | |||
| Cohort | a study that follows a group of participants with a known exposure to determine their outcome; can be prospective or retrospective | |||
| Case Control | a study that investigates a group of participants with a known outcome to determine common exposures; prospective or retrospective, usually determines odds ratios | |||
| SR & MA | systematic review & meta-analysis | |||
| Descriptive | case studies or case series | |||
| Qualitative | studies where data is collected through interviews and questionnaires of participants, also includes mixed-methods studies | |||
| Longitudinal/Time Series | observational studies conducted over long periods of time (10-20 years) | |||
| Quantitative Assessment | risk analyses, economic studies | |||
| Grey | Conference proceedings, workshops etc | |||
| Country (FT) | Country name | String | ||
| LMIC | Low- or Middle-Income Country (LMIC) | String | ||
| Y | Yes | |||
| N | No | |||
| City/Area (FT) | Write the city or region if reported (less important than country) | String | ||
| Domestic vs Imported Foods | String | |||
| D | Domestic | |||
| I | Imported | |||
| Study Objective (FT) | The goals of the authors – what did they want to find out | String | ||
| Sample Information | ||||
| Sampling Method Used | Sampling method used | String | ||
| Non-probability | includes convenience (e.g. selected fruit samples sold near the lab or collected fruit samples until a contaminated sample was found), judgement (selected samples of the fruit most likely to be contaminated with AMR), purposive sampling (selected samples of the most popular fruit type) | |||
| Probability | any random selection of samples, should be stated explicitly; also includes cluster sampling | |||
| Not reported | if the type of sampling isn’t described, choose ‘not reported’ | |||
| NA | for grey literature, SR& MAs, Descriptive and Quantitative analyses | |||
| Sample Source | Sample source category | String | ||
| Farm Crop – Vegetable | ||||
| Farm Crop – Fruit | ||||
| Soil | ||||
| Manure | ||||
| Other Fertilizer (e.g. chemical, compost, biochar) | ||||
| Human Feces | ||||
| Irrigation Water | ||||
| Harvest/Processing (e.g. picking, washing, packaging) | ||||
| Retail – Vegetable | ||||
| Retail – Fruit | ||||
| RTE (ready-to-eat: foods eaten without further cooking or preparation required: e.g. bagged spinach or juice) | ||||
| Other (can use for genomic studies if it’s unclear where the DNA came from) | ||||
| Specific Sample Type (FT) | Write down the specific sample name (banana; poultry litter; compost etc). I think we will include RTE foods that do not contain non-food crop samples (e.g. fruit juice, salad can be included but not chicken salad etc). | String | ||
| Sample Group | Sample group | Sample group | String | |
| Culinary Herbs | ||||
| Fruit Crops | ||||
| Human Biosamples | ||||
| Irrigation water | ||||
| Lettuce | ||||
| Manure | ||||
| Pulses & Grain | ||||
| Pulses & Grains | ||||
| Root Crops | ||||
| RTE Produce | ||||
| Salad Crops | ||||
| Soil | ||||
| Vegetables | ||||
| Undefined | ||||
| Number of Samples (FT) | List out the number of samples taken of each sample type, if reported | Numeric | ||
| Number of Positive Samples (FT) | NA | Not applicable | ||
| Methods | Number of Positive Samples (FT) | Number of Positive Samples (FT) | Number of Positive Samples (FT) | Number of Positive Samples (FT) |
| Microbes Isolated | String | |||
| Acinetobacter baumanii | Acinetobacter baumanii | |||
| Aspergillus fumigatus | Aspergillus fumigatus (fungi) | |||
| Bacillus spp | Bacillus spp (any species but especially B. cereus) | |||
| E. coli and Salmonella | Enterococcus faecium/ E. faecalis | |||
| Enterococcus faecalis | Erwinia amylovora (bacterial cause of fire blight in apple and pear crops. Not a human pathogen but horizontal gene transfer to human pathogens of resistant genes reported) | |||
| Enterococcus faecium | Escherichia coli: all serotypes | |||
| Enterococcus faecium/faecalis | Klebsiella pneumoniae | |||
| Escherichia coli | Escherichia coli | |||
| Klebsiella pneumoniae | Klebsiella pneumoniae | |||
| Listeria monocytogenes | Listeria monocytogenes | |||
| Mixed | Mixed | |||
| NA | Not applicable | |||
| Salmonella enterica | Salmonella enterica: all serotypes | |||
| Shigella spp | Shigella spp | |||
| Staphylococcus aureus | Staphylococcus aureus | |||
| Xanthomonas spp | Xanthomonas spp (especially X. oryzae, which causes bacterial blight in rice) | |||
| Serovar/Serotype Reported (FT) | Mainly for E. coli and Salmonella: if serotypes are reported, list these | String | ||
| Number of Isolates (FT) | Number of microbial isolates detected on samples | Numeric | ||
| NA | Not applicable | |||
| AMR Detection Method | AMR detection method | String | ||
| Agar dilution | ||||
| Broth Microdilution | Broth Microdilution: microtiter plates are filled with broth and the bacteria as well as varying concentrations of the antimicrobial and then incubated. MIC is determined by the concentration that inhibited growth. | |||
| DDST | DDST: double disc synergy test | |||
| Disk Diffusion | Disk diffusion: antibiotic discs are placed on agar where bacteria have grown. The zone of inhibition is the area where the antibiotic stopped bacterial growth (also called Kirby-Bauer or agar-diffusion test). | |||
| E-test | E-test: a strip with a continuous gradient of antimicrobial on one side | |||
| FAME | FAME: Fatty acid methyl ester | |||
| Metagenomic | Metagenomics: study of genetic material derived from the environment. Also called community genomics or environmental genomics. | |||
| Modified plate-dilution technique | Modified plate-dilution technique | |||
| NA | Not applicable | |||
| NR | Not Relevant | |||
| PCR | PCR: polymerase chain reaction – a method to amplify DNA through thermal cycling | |||
| qPCR | qPCR: quantitative PCR, also called real-time or RTPCR. | |||
| Sequencing | Sequencing: the process of determining the nucleotide order of a DNA fragment; whole genome sequencing determines the complete structure of a genome. Also called third-generation sequencing, WGS, Next-generation or high-throughput sequencing. | |||
| WGS | WGS: whole genome sequencing | |||
| Interpretive Criteria | What are the most common tests used? Bar chart. | String | ||
| Antibiogram Committee of the French Society of Microbiology | ||||
| CLSI | CLSI: Clinical and Laboratory Standards Institute | |||
| DIN standards | DIN: drug identification number | |||
| EUCAST | EUCAST: European Committee on Antimicrobial Susceptibility Testing | |||
| NA | Not applicable | |||
| NCCLS | NCCLS: National Committee for Clinical Laboratory Standards | |||
| Breakpoint Criteria | String | |||
| Clinical | Clinical breakpoint values: the highest plasma drug concentration that can safely be achieved in the patient. Determined using several clinical criteria and updated annually. | |||
| Epidemiological | Epidemiological Cutoff Values: measures of a drug MIC distribution that separate bacterial populations into those representative of a wild-type population and those with acquired or mutational resistance to the drug. Usually abbreviated ECV (CLSI) or ECOFF (EUCAST). | |||
| NA | Not applicable | |||
| Not Specified | Not specified | |||
| Statistical Methods (FT) | List any statistical methods/tests used | String | ||
| AMP | AMP: ampicillin | String | ||
| % | String | |||
| AMX | AMX: amoxicillin | String | ||
| %2 | String | |||
| IPM | IPM: imipenem | String | ||
| %3 | String | |||
| STR | STR: streptomycin | String | ||
| %4 | String | |||
| GEN | GEN: gentamycin | String | ||
| %5 | String | |||
| TET | KAS: kasugomycin (only used on crops) | String | ||
| %6 | String | |||
| CAZ | CAZ: ceftazidime | String | ||
| %7 | String | |||
| CTX | CTX: cefotaxime | String | ||
| %8 | String | |||
| CST | CST: colistin | String | ||
| %9 | String | |||
| CIP | CIP: ciprofloxacin | String | ||
| %10 | String | |||
| VAN | VAN: vancomycin | String | ||
| %11 | String | |||
| CHL | CHL: chloramphenicol | String | ||
| %12 | String | |||
| MDR | MDR: multidrug resistance (resistance to more than 3 antibiotics) | String | ||
| %13 | String | |||
| DMI | DMI: demethylation inhibitor (fungicides, e.g. imidazole class) | String | ||
| ARG | ||||
| Reported Resistance Genes (FT) | List the reported resistance genes per sample (e.g. crop type) if possible. Ensure samples were not pooled together before testing for ARG, as otherwise may not be able to distinguish what origin was. If too many genes to write out (>100) you can include a reference to the table they are listed instead of typing them out. | String | ||
| Proportion of AMR-contaminated or ARG-positive samples (FT) | If the proportion of samples that are contaminated with resistant microbes has been calculated, list the absolute numbers and percentage here. If the proportion has not been calculated but the absolute values are listed somewhere, please still report them. | String |