Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant

• Published in: Environmental pollution (1987) 2023-06, Vol.327, p.121517-121517, Article 121517
• Main Authors: Tripathi, Animesh, Kumar, Dinesh, Chavda, Priyank, Rathore, Dalip Singh, Pandit, Ramesh, Blake, Damer, Tomley, Fiona, Joshi, Madhvi, Joshi, Chaitanya G., Dubey, Suresh Kumar
• Format: Article
• Language: English
• Subjects: Animals; Anti-Bacterial Agents - analysis; Anti-Bacterial Agents - pharmacology; Anti-Infective Agents; Antibiotic resistance gene; Chickens; Drug Resistance, Bacterial - genetics; Genes, Bacterial; Humans; Manure - analysis; Plant microbiome; Poultry; Poultry litter; Resistome; Soil
• ISSN: 0269-7491; 1873-6424
• DOI: 10.1016/j.envpol.2023.121517

Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health. [Display omitted] •Prevalence of AMR genes in poultry litter, soil and plant were reported.•Copy number of relevant AMR genes were validated using droplet digital PCR.•Campylobacter jejuni was found in samples sequenced from broiler and layer litters.•Dominant pathogens of origin were represented by Staphylococcus, Enterococcus etc.•Transmission of AMR genes to plants via soil have been demonstrated.