Frequently asked questions

Yes, at the moment we have 26 primer sets available to target certain taxonomy group of bacteria and pathogens.

Yes, our cloud-based Resistomap Platform processes the quantitative AMR data and transforms it into clear, actionable insights, giving clients comprehensive information on AMR levels over time and across geographical locations.

Our analyses generate key metrics, such as Antibiotic Resistance Gene Index (ARGI), AMR Gene Removal, and AMR Comparative Risk Score

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Yes, you can still send us your DNA samples. However, there will be an extra dilution service fee.

Yes, we offer DNA extraction service for isolating environmental DNA from any sample type. We use commercial DNA isolation kits from QIAGEN and automate the process of DNA extraction using a QIACube machine. We store leftover samples for one month, after which the samples will be discarded.

We deliver analysis results within 10 working days. For three or more chips, the analysis process may take longer.

In Resistomap we provide antibiotic resistance monitoring services starting from sampling to the final analysis of the SmartChip qPCR results.

For optimal SmartChip qPCR analysis, samples should have a DNA concentration of 10 ng/µl and a 260/280 quality ratio between 1.8 and 2.0 ± 0.1, measured using NanoDrop One, and a volume of 100 µl. We recommend diluting samples in molecular grade qPCR water.

Please include an aliquot of your water if a no-template control (NTC) sample is included in the analysis. If sample concentrations or volumes are not optimal, we can accept a volume of 50 µl for the analysis of fewer than 100 genes and a minimum concentration of 3 ng/µl.

Optimal sample concentration and quality help us ensure the best possible results. A dilution service fee will be applied if samples exceed the suitable concentration range and require dilution before analysis. The fee for the dilution service starts at 100€/chip analysis and increases based on the number of samples.

For sample shipment instructions, please contact laboratory@resistomap.com

We recommend using safe-lock 1.5 mL microtubes to avoid evaporation or spilling during transportation. Please label the tubes individually in numerical order only, e.g., 1-25.

DO NOT USE PCR tubes for sending your samples.

Also, please avoid sending samples on 96-well plates. Based on our experience there is more cross contamination during transport compared to when sending samples on individual 1.5 ml microcentrifuge tubes. If using microcentrifuge tubes is not possible, please follow the pipetting order shown in this template.

Finally, please provide information about your samples in the Sample specification sheet, which we will send you before you send the samples.

When sending samples with dry ice the following things need to be considered: the local regulations, as there might be restrictions regarding shipments with dry ice; the samples need to be packed in a styrofoam box which will go inside a cardboard box. UN1845 label is needed on the side of the box with the weight of the shipped dry ice. Please be careful and wear protective gloves when handling the dry ice as careless handling might lead to frostbites.

Mondays, to avoid any unnecessary delays in the shipment.

No, usually there are only a few µL leftover from DNA samples after the SmartChip qPCR analysis. However, if you order the DNA extraction service at our facility, we can send back the leftover DNA extraction samples.

Yes, we can organise the sample pickup and transport for you using our courier partner DHL.

For solid samples, we recommend a dry/wet weight of 1 g. The solid samples should be stored in a zip lock plastic bag or a safe-lock 1.5 mL microtube and delivered on dry ice to our facility in Helsinki, Finland.

We require 1-10 L of water for river, lake, and seawater samples. For wastewater, we require 100 mL from influent and 250 mL from effluent. The sample should be filtered/concentrated using a hydrophilic membrane filter with a pore size of 0.2 µm. We recommend using PES membrane. Each concentrated water-filter should be stored in an individual 50 mL-falcon tube and delivered on dry ice to our facility in Helsinki, Finland.

We accept all types of samples, e.g., soil, sediment, sludge, manure, stool, meat, tissue, swabs, river, lake, wastewater, and seawater.

We have over 600 previously validated primer sets available in our database. A single SmartChip analysis can measure up to 384 genes. Our database includes assays targeting:

• Antibiotic resistance genes (ARGs), including:
  • aminoglycoside, amphenicol, beta-lactam, florfenicol, multidrug efflux pumps, macrolide–lincosamide–streptogramin B (MLSB), trimethoprim, tetracycline, and vancomycin
• Genes targeting other antibacterials, such as:
  • nisin, bacitracin, antiseptics, and mercury
• Genes associated with mobile genetic elements (MGEs) and integrons

Each SmartChip analysis also includes the 16S rRNA gene, which is required for our relative abundance calculations.

You can customise the target genes for your project. We will provide a list of available assays for selection during project planning. Please note that the 16S rRNA gene must be selected.

The customisation options for chip analysis are:

• 6 genes: 256 samples
• 12 genes: 128 samples
• 24 genes: 72 samples
• 36 genes: 48 samples
• 48 genes: 36 samples
• 54 genes: 32 samples
• 72 genes: 24 samples
• 80 genes: 21 samples
• 96 genes: 18 samples
• 120 genes: 14 samples
• 144 genes: 12 samples
• 216 genes: 8 samples
• 248 genes: 6 samples
• 296 genes: 5 samples
• 384 genes: 4 samples

Yes, all of our analyses include 3 technical replicates per sample and assay by default. The Resistomap Platform processes all replicates, applies Ct value and efficiency cutoff rules and excludes the least reliable one based on Ct value standard deviation and qPCR efficiency to ensure accurate results. The detailed analysis pipeline is described on the Resistomap Platform. Additionally, raw data for all replicates can be downloaded directly from Resistomap Platform and if you’re not using the Platform, the full replicate data is included in your result delivery.

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For sample with optimal 10ng/µL concentration a total of 2 ng/µL of DNA sample is measured in each 100 nL qPCR reaction

Yes, at the moment we have 26 primer sets available to target certain taxonomy group of bacteria and pathogens.

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Yes, you can measure the gene copy numbers by providing at least four to five serially diluted samples as the standard curve of the target gene. The standard curve samples will be measured with the other samples in the same chip analysis. You can calculate the target gene copy numbers based on the Ct values of the diluted samples used as the standard curve.

The ARG 1.0 and ARG 2.0 primer sets were developed to detect and quantify up to 384 genes in parallel and in one measurement using the SmartChip Real-Time PCR system. We updated the 384 gene ARG 2.0 primer sets to the ARG 2.1 primer sets according to the current antibiotic resistance gene database (CARD) to maintain the specificity of primer sets.

Yes, if the primer sets are already validated, have annealing temperatures of 60 °C in quantitative PCR, and a positive control of the gene is available.

It takes at least 1-3 months to optimise and validate new genes. Providing us the positive control of the new gene will make the validation process faster.

Each primer set was designed to target a specific region in an antibiotic resistance gene (ARG). For ARG variations, more primers have been designed to cover all known ARG variations.

Resistomap Platform is  our cloud-based Resistomap Platform processes the quantitative AMR data and transforms it into clear, actionable insights, giving clients comprehensive information on AMR levels over time and across geographical locations. With Resistomap Platform, you can share and present the results efficiently to your colleagues by giving them access to your project.

Our analyses also generate key metrics, such as Antibiotic Resistance Gene Index (ARGI), AMR Gene Removal, and AMR Comparative Risk Score.

The results are provided as a raw data in .xlsx format or available for exploration using our analysis service Resistomap Platform.

Yes, you can measure the gene copy numbers by providing at least four to five serially diluted samples as the standard curve of the target gene. The standard curve samples will be measured with the other samples in the same chip analysis. You can calculate the target gene copy numbers based on the Ct values of the diluted samples used as the standard curve.

We use the delta Ct calculation (https://doi.org/10.1021/acs.est.7b00551). Delta Ct = Ct of genes - Ct  of 16S rRNA gene. The relative quantification is calculated with formula: 2^-delta Ct.

The result can be used for both binary and quantitative studies. However, the quantification is based on the abundance of the genes or gene copy numbers relative to the amount of 16S rRNA gene in each sample.

We deliver analysis results within 10 working days. For three or more chips, the analysis process may take longer.

The results are quantitative.

SmartChip qPCR measures the relative abundance of each gene in comparison to 16S rRNA genes. In the Resistomap Platform, we estimate gene abundances by comparing gene copy numbers to the known copy numbers of 16S rRNA genes in each sample. To calculate the 16S rRNA gene copy numbers, we use a standard curve specifically measured for 16S rRNA genes within the SmartChip qPCR process.

The Resistomap Platform enables you to use, share, and present your analysis results efficiently. It offers an interactive way to display gene counts, abundances, and copy numbers relative to 16S rRNA genes, along with a heat map of gene profiles. You can filter results based on your interests—such as viewing gene abundances for specific antibiotic groups or sorting by sample type—and easily share results with colleagues by granting them access to your project. Paired with key metrics, such as Antibiotic Resistance Gene Index (ARGI), AMR Gene Removal, and AMR Comparative Risk Score, it is the most complete platform for antimicrobial resistance to date.

Yes, we can analyse raw data from the SmartChip qPCR measurement to provide meaningful gene abundances in each sample. We deliver the analysis results via Resistomap Platform, an interactive online dashboard, which displays the numbers, abundances, and copy numbers of detected genes relative to the 16S rRNA genes, as well as a heatmap of gene profiles.