Detecting antibiotic and/or chemical use in aquatic animals using epigenetic means

A method of determining if a test animal and/or a test animal from which a product is derived has been treated and/or is currently undergoing treatment with at least one antibiotic and/or veterinary chemical, the method comprising:

• (a) determining the methylation status of at least one CpG site in genomic material contained in a biological sample obtained from the test animal,
• (b) comparing the methylation status of the CpG site from (a) with that of a control animal of the same biological taxon as the test animal, which was not treated and/or is not currently undergoing treatment with at least one antibiotic and/or veterinary chemical,
• wherein a difference in the test methylation status of (a) in the test animal compared to the CpG site in the control animal is indicative of the test animal having been treated and/or is currently undergoing treatment with at least one antibiotic and/or veterinary chemical;
• and
• wherein the test animal is an aquatic animal;
• and
• the veterinary chemical is an anti-parasitic, an anti-viral, a feed additive, a water additive, a disinfectant, glutaraldehyde, and/or formalin used in aquaculture.

A method of determining if a test animal and/or a test animal from which a product is derived has been treated and/or is currently undergoing treatment with at least one antibiotic, and if so, determining the distinct class of antibiotics with which the test animal is being treated and/or is currently undergoing treatment, the method comprising:

• (a) determining a test methylation profile from the genomic material contained in a biological sample obtained from the test animal and/or the animal-derived product sample;
• and
• (b) comparing the test methylation profile obtained from (a) with one or more predetermined reference methylation profiles, wherein each of the predetermined reference methylation profiles is from a different animal of the same biological taxon as the test animal, and each of the different animals was treated with a different class of antibiotics,
• wherein if the test methylation profile of (a) is significantly similar to one of the predetermined reference methylation profiles, the test animal is confirmed for being treated with the same class of antibiotics with which the animal with the predetermined reference profile is treated with and the test animal has been confirmed for having been treated and/or is currently undergoing treatment with the distinct class of antibiotics;
• and
• wherein the test animal is an aquatic animal.

A method of determining if a test animal and/or a test animal from which a product is derived has been treated and/or is currently undergoing treatment with at least one antibiotic, and if so, determining if the antibiotic is used as a growth promotant or as a therapeutant, the method comprising:

• (a) determining a test methylation profile from the genomic material contained in a biological sample obtained from the test animal and/or the animal-derived product;
• and
• (b) comparing the test methylation profile obtained from (a) with one or more predetermined reference methylation profiles, wherein each of the predetermined reference methylation profiles is from a different control animal of the same biological taxon as the test animal, and each of the different control animals was treated with the antibiotic as a growth promotant or therapeutant,
• wherein if the test methylation profile of (a) is significantly similar to one of the predetermined reference methylation profiles, the test animal is confirmed for being treated with the antibiotic in the same way that the control animal with the similar predetermined reference profile is treated and the test animal has been confirmed for having been treated and/or is currently undergoing treatment with the antibiotic as a growth promotant or therapeutant;
• and
• wherein the test animal is an aquatic animal.

A method of determining if a test animal from which a product is derived underwent a withdrawal period of no treatment with at least one antibiotic and/or veterinary chemical prior to the product being obtained, the method comprising:

• (a) determining a test methylation profile from the genomic material contained in a biological sample obtained from the animal-derived product;
• and
• (b) comparing the test methylation profile obtained from (a) with at least two predetermined reference methylation profiles, wherein at least one of the predetermined reference methylation profiles is from a control animal that underwent a withdrawal period and at the other one of the predetermined reference methylation profiles is from a control animal of the same biological taxon as the test animal, that did not undergo a withdrawal period before the product was obtained,
• wherein if the test methylation profile of (a) is significantly similar to the predetermined reference methylation profile, the test animal is confirmed for having undergone a withdrawal period or not;
• and
• wherein the test animal is an aquatic animal;
• and
• the veterinary chemical is an anti-parasitic, an anti-viral, a feed additive, a water additive, a disinfectant, glutaraldehyde, and/or formalin used in aquaculture.