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Antibiotics have been widely used for improving human and animal health and well-being for many decades. However, the enormous antibiotic usage in agriculture especially for livestock leads to considerable quantities of antibiotic residues in associated food products and can reach potentially hazardous levels for consumers. Therefore, timely detection and systematical surveillance on residual antibiotics in food materials are of significance to minimize the negative impact caused by such unwanted antibiotic leftovers. To this end, we constructed a cloud-platform-based system (ARSCP) for comprehensive surveillance of antibiotic residues in food materials. With the system, we collected 126,560 samples from 68 chicken farms across China and detected the antibiotic residues using a rapid detection colorimetric commercial (Explorer 2.0) kit and UPLC-MS/MS. Only 108 (0.085 %) of the samples contained residual antibiotics exceeding the MRLs and all data were subjected to ARSCP system to provide a landscape of antibiotic residues in China. As a proof-of-concept, we provided an overview of residual antibiotics based on data from China, but the system is generally applicable to track and monitor the antibiotic residues globally when the data from other countries are incorporated. We used the combined Explorer 2.0 and MS data to construct ARSCP, an antimicrobial residue surveillance cloud platform for raw chicken samples. ARSCP can be used for rapid detection and real-time monitoring of antibiotic residues in animal food and provides both data management and risk warning functions. This system provides a solution to improve the management of facilities that must monitor antibiotic MRLs in food animal products that can reduce the pollution of antibiotics to the environment., Competing Interests: Declaration of competing interest None to declare., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The emergence of novel plasmid-mediated high-level tigecycline resistance genes tet(X) in the Enterobacteriaceae has increased public health risk for treating severe bacterial infections. Despite growing reports of tet(X)-positive isolates detected in animal sources, the epidemiological association of animal- and environment-derived isolates with human-derived isolates remains unclear. Here, we performed a comprehensive analysis of tet(X4)-positive Escherichia coli isolates collected in a hospital in Guangdong province, China. A total of 48 tet(X4)-positive E. coli isolates were obtained from 1001 fecal samples. The tet(X4)-positive E. coli isolates were genetically diverse but certain strains that belonged to ST48, ST10, and ST877 etc. also have clonally transmitted. Most of the tet(X4) genes from these patient isolates were located on conjugative plasmids that were successfully transferred (64.6%) and generally coexisted with other antibiotic resistance genes including aadA, floR, bla TEM and qnrS. More importantly, we found the IncX1 type plasmid was a common vector for tet(X4) and was prevalent in these patient-derived strains (31.3%). This plasmid type has been detected in animal-derived strains from different species in different regions demonstrating its strong transmission ability and wide host range. Furthermore, phylogenetic analysis revealed that certain strains of patient and animal origin were closely related indicating that the tet(X4)-positive E. coli isolates were likely to have cross-sectorial clonal transmission between humans, animals, and farm environments. Our research greatly expands the limited epidemiological knowledge of tet(X4)-positive strains in clinical settings and provides definitive evidence for the epidemiological link between human-derived tet(X4)-positive isolates and animal-derived isolates., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

Overuse of antibiotics in animal husbandry has led to an increase of antibiotic resistance microorganisms as well as antibiotic-resistance genes (ARGs). Duck farming in China is practiced on a large and diverse scale and the overuse of antibiotics in this field is gaining attention recently. We evaluated the diversity of ARGs from five duck farms using a functional metagenomic approach and constructed five libraries. A total of seventy-six resistant determinants were identified, of which sixty-one were gene variants or novel genes. The novel genes contained five β-lactamase-encoding genes designated as bla DWA1 , bla DWA2 , bla DWA3 , bla DWA4 and bla DWB1 , respectively, and two genes conferring resistance to fosfomycin designated as fosA-like1 and fosA-like2. Three of the five β-lactamase-encoding genes were further identified as extended-spectrum β-lactamases (ESBL) that can hydrolyze both penicillins and cephalosporins. Besides, two of the five β-lactamase-encoding genes were associated with mobile genetic elements, indicating a high potential for transfer of the genes to other bacterial hosts. The two novel fosA-like genes were able to increase the MICs of the test Escherichia coli strain from 2 μg/mL to as high as 256 μg/mL(up to 128-fold increase). Our study provides a reference for ARGs prevalence in duck farm wastes and implies that they are an important resistome reservoir, especially for novel ARGs with high spread potential., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Vast reservoirs of antibiotic resistance genes (ARG) are discharged into the environment via pig manure. We used metagenomic analysis to follow the distribution and shifts of ARGs and their bacterial hosts along wastewater treatment in three large pig farms. The predominating ARGs potentially encoded resistance to tetracycline (28.13%), aminoglycosides (23.64%), macrolide-lincosamide-streptogramin (MLS) (12.17%), sulfonamides (11.53%), multidrug (8.74%) and chloramphenicol (6.18%). The total relative ARG abundance increased along the treatment pathway prior to anaerobic digestion that had a similar degradative capacity for different ARGs and these ARGs were reduced by about 25% after digestion, but ARGs enriched erratically in manured soils. Distinctive ARG distribution patterns were found according to the three sample locations; feces, soil and wastewater and the differences were primarily due to the tetracycline ARGs (feces > wastewater > soil), sulfonamide ARGs (soil > wastewater > feces) and MLS ARGs (feces > wastewater > soil). Metagenomic assembly-based host analyses indicated the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were primary ARG carriers. The Streptococcaceae increased the abundance of multidrug, MLS and aminoglycoside ARGs in feces; Moraxellaceae were the primary contributors to the high abundance of multidrug ARGs in wastewater; the Comamonadaceae led to the higher abundance of bacA in wastewater and soil than feces. We found a high level of heterogeneity for both ARGs and ARG-hosts in the wastewater treatment system and in the agricultural soils for these pig farms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)