Detection of tetracycline resistance genes and their diversity in Escherichia coli isolated from pig farm waste in Banten province, Indonesia

Antimicrobial resistance, virulence gene profiles, and phylogenetic groups of Escherichia coli isolated from healthy broilers and broilers with colibacillosis in Thailand

BACKGROUND

Multidrug resistance in Escherichia coli has a significant global impact on poultry production. This study aimed to determine the phenotypic and genotypic backgrounds of antimicrobial resistance (AMR) and virulence gene profiles of E. coli strains isolated from diseased and healthy broilers. A total of 211 E. coli isolates were recovered from diseased (n = 110) and healthy broilers (n = 101). All the isolates were subjected to antimicrobial susceptibility testing. A PCR-based technique was applied to screen AMR genes, virulence genes and analyze phylogenetic groups.

RESULTS

Phylogenetic groups B1 and D were the most prevalent for E. coli isolated from diseased and healthy birds. Among virulence genes, the detection rates of cva/cvi, iutA, iucD, iroN, iss and ompT were considerably greater in E.coli strains from diseased birds than in healthy birds. The virulence gene pattern of hlyF-iutA-iucD-iroN-iss-ompT (16.4%) was frequently observed in E.coli isolated from diseased birds, whereas approximately 22.8% of E.coli from healthy birds did not carry any virulence genes. Analysis of AMR profiles revealed that 58.3% of E.coli were resistant to multiple classes of antibiotics, and 96.7% carried at least one antibiotic resistance gene AMR genes.

CONCLUSION

The findings of this study demonstrate the variable distribution of phylogenetic groups and virulence genes. E.coli strains isolated from broilers had multidrug resistance profiles. The study emphasizes the need for continuous monitoring of AMR emergence in E. coli from broilers. This monitoring allows for early detection and implementation of strategies to control the spread of resistant strains.

Occurrence and distribution of antibiotic resistance genes in Rivers entering the sea from the South bank of Laizhou Bay, China

The distribution of antibiotic resistance genes (ARGs) in Laizhou Bay affects the local socio-economic development. The study aimed to investigate the distribution of ARGs in the rivers that flow into the sea around Laizhou Bay's southern shore. Water and sediment samples were collected from different typical sites of rivers entering the sea in Weifang, including Mi River, Bai Lang River, Yu River, Wei River, Jiaolai River, Xiaoqing River and Di River. The species and abundance of ARGs in the sediments were characterized and quantified by macro-genome high-throughput sequencing technology. The species distribution of ARGs was compared. In two sediment samples and seven water samples, 24 ARGs types and 1244 subtypes of ARGs were detected, in which multidrug-resistant class was the main ARGs type and FBJ murine osteosarcoma viral oncogene homolog B (fosB) was the dominant ARGs. The types of ARG in the top ten of these samples were the same, although the proportion was different. Dominant ARG subtypes accounted for more than 50% of all the nine samples. This article provides basic data support for pollution status and environmental risk assessment as well as remediation of ARGs in rivers entering the sea along the south coast of Laizhou Bay.

Whole genome sequencing analysis on antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia

IMPORTANCE

The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics.

OBJECTIVE

This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.

METHODS

Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder.

RESULTS

Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%.

CONCLUSIONS AND RELEVANCE

The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.

Occurrence and dissemination of antibiotic resistance genes in the Yellow River basin: focused on family farms

As an emerging contaminant, antibiotic resistance genes (ARGs) have attracted growing attention, owing to their widespread dissemination and potential risk in the farming environment. However, ARG pollution from family livestock farms in the Yellow River basin, one of the main irrigation water sources in the North China Plain, remains unclear. Herein, we targeted 21 typical family farms to assess the occurrence patterns of ARGs in livestock waste and its influence on ARGs in receiving environment by real-time quantitative PCR (qPCR). Results showed that common ARGs were highly prevalent in family livestock waste, and tet-ARGs and sul-ARGs were the most abundant in these family farms. Most ARG levels in fresh feces of different animals varied, as the trend of chicken farms (broilers > laying hens) > swine farms (piglets > fattening pigs > boars and sows) > cattle farms (dairy cattle > beef cattle). The effect of natural composting on removing ARGs for chicken manure was better than that for cattle manure, while lagoon storage was not effective in removing ARGs from family livestock wastewater. More troublesomely, considerable amounts of ARGs were discharged with manure application, further leading to the ARG increase in farmland soil (up to 58-119 times), which would exert adverse impacts on human health and ecological safety.