A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms

Abstract

The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.

Machine learning and metagenomics enhance surveillance of antimicrobial resistance in chicken production in China

“…In our study 68 clinically relevant ARGs correlated with resistance to multiple antibiotics, and some of these antibiotics had no previously known association with these ARGs. In particular, the six ARGs (aadA16, aadA22, PER-1, AAC(6')-Ia, tet (39) and SHV-110) that we found associated to resistance to the highest number of antibiotics, had been previously found in earlier studies on poultry in China [34][35][36] , con rming our method. However, we found a cluster of further gut bacteria that correlated well with E. coli resistance to ve different antibiotics.…”

“…However, we found a cluster of further gut bacteria that correlated well with E. coli resistance to ve different antibiotics. These included Arcobacter (an emerging waterborne and foodborne zoonotic pathogen, responsible for gastroenteritis in humans 37 ), Acinetobacter (commensal in the poultry gut, but capable of causing extraintestinal diseases in both humans and poultry 38 ) and Sphingobacterium (clinically relevant in humans and animals 39 ). This result suggests that, in agreement with previous studies 11,14,40−44 , focusing exclusively on E. coli within the farm for surveillance purposes may not be as effective as monitoring a larger number of pathogens.…”

“…This analysis highlighted a core of 117 ARGs (68 clinically relevant, including bla CTX−M−64 , bla CTX−M−123 , fosB3 and dfra5) acting as predictors of more than three antibiotic resistances. Six ARGs (aadA16, aadA22, PER-1, AAC(6')-Ia, tet (39) and SHV-110) were found to be predictors of eight antibiotic resistances. The same analysis revealed 29 microbial species in the gut, acting as predictors of ve antibiotic resistances (aztreonam, chloramphenicol, cefotaxime, kanamycin and nalidixic acid).…”

“…11), between farms using and not using antibiotics (Supplementary Table 12). On the farms that received tetracycline antibiotics, the tetracycline class and tetracycline ARGs (tet (39), tet(B), tet(G), tet(Y), tetS and tetX) were found be signi cantly increased (adjusted p values < 0.05). In addition, in these farms there was also a signi cantly increased presence of genes from the classes: aminoglycoside, beta lactam, MLSB, MDR, phenicol, sulfonamide, trimethoprim, fosfomycin, glycopeptide and nucleoside (adjusted p values < 0.05).…”

Comparison of antibiotic resistance genes in swine manure storage pits of Iowa, USA

“…The tet36 gene was first discovered in swine manure pits, and is yet unclear whether it is enriched or persists in the environment upon manure application (Whittle et al, 2003;Kang et al, 2018;He et al, 2019). Less is known about the erm35 gene, except that it was detected in poultry manure with metagenomics (Błazėjewska et al, 2022;Wang and Chai, 2022). The erm35 gene may have potential as a swine indicator since it was detected so frequently with HT-qPCR in the current study.…”