Characterization of Escherichia coli strains isolated from geese by detection of integron-mediated antimicrobial resistance

Dairy farm waste: A potential reservoir of diverse antibiotic resistance and virulence genes in aminoglycoside- and beta-lactam-resistant Escherichia coli in Gansu Province, China

Aminoglycosides (AGs) and beta-lactams are the most commonly used antimicrobials in animal settings, particularly on dairy farms. Dairy farm waste is an important reservoir of antibiotic resistance genes (ARGs) and virulence genes (VGs) in environmental Escherichia coli, which is an important indicator of environmental contamination and foodborne pathogen that potentially threaten human and animal health. In the present study, we aimed to characterize the ARGs and VGs in AG- and beta-lactam-resistant E. coli from dairy farm waste in Gansu Province, China. The dairy farm waste consisted of fecal (n = 265) and sewage (n = 54) samples processed using standard microbiological techniques and the Clinical & Laboratory Standards Institute guidelines. The total DNA of AG- and beta-lactam-resistant E. coli was extracted, and whole-genome sequencing (WGS) was performed using the Illumina NovaSeq platform and analyzed using various bioinformatics tools. In this study, among 84.3% (269/319) of the E. coli strains, 23.8% (64/269) were identified as AG- and beta-lactam-resistant E. coli. WGS analysis revealed a large pool of ARGs belonging to multiple classes such as AGs, beta-lactams, aminocoumarins, fluoroquinolones, macrolides, phenicol, tetracyclines, phosphonic acid, disinfecting and antiseptic agents, elfamycin, rifamycin, and multidrug resistance genes. Furthermore, virulome analysis of 64 E. coli strains revealed clinically important virulence factors associated with adherence, biofilm, invasion, auto-transportation, siderophores, secretion systems, toxins, anti-phagocytosis, quorum sensing, regulation, metabolism, and motility. We identified dairy farm feces and sewage waste as important reservoirs of antimicrobial resistance and virulence determinants in E. coli in Gansu, China, which can threaten human and animal health through ecological exposure and contamination of food and water. We recommend continuous large-scale surveillance in dairy farm settings to formulate protective guidelines for public health safety.

Genomic Characterization of Extended-Spectrum β-Lactamase (ESBL) Producing E. coli Harboring bla OXA-1-catB3-arr-3 Genes Isolated From Dairy Farm Environment in China

Anthropogenic activities in the environment affect the ecosystem and can play an important role in selecting and spreading antibiotic-resistant bacteria (ARB) and genes (ARGs). The dairy farm environment may serve as a hotspot and reservoir for exchanging and spreading ARGs, but studies are scarce. Here, we investigated and characterized the extended-spectrum β-lactamase producing Escherichia coli strains recovered from the dairy farm environment co-harboring bla OXA-1, catB3, and arr-3 genes. The isolates were identified and characterized by PCR, antimicrobial susceptibility testing, conjugation assay, whole genome sequencing (WGS), and multiple bioinformatics tools. Seven E. coli strains co-harboring bla OXA-1, catB3, and arr-3 genes were identified which belonged to distinct sequence types (STs) and carried diverse plasmid replicon types. The conjugation assay revealed a successful transfer of bla OXA-1, catB3, and arr-3 genes into the recipient E. coli J53 with a co-conjugation frequency ranging from (2.25 ± 0.3) × 10-4 to (3.85 ± 0.3) × 10-3. Bioinformatics analysis of WGS revealed the diversity of acquired ARGs, conferring resistance to aminoglycosides, beta-lactams, quinolones, tetracyclines, macrolides, trimethoprim-sulfamethoxazole, phosphonic, phenicol, and rifamycin. The genetic environment analysis showed that aac(6')-Ib-cr-bla OXA-1-catB3-arr-3-qacE1-sul1 was the common genetic backbone among the seven E. coli strains. Among the mobile genetic elements, insertion sequences were the predominant elements as compared to transposons. The phylogenetic analysis demonstrated a close relationship between the E. coli of this study and other strains of human-animal-environment origin retrieved from the NCBI database. This study presented the whole genome-based characterization of E. coli strains carrying the bla OXA-1-catB3-arr-3 genes. It provided evidence that the dairy environment may harbor a variety of ARGs and act as a potential reservoir for their spread in the ecosystem. The results recommend the routine surveillance of ARGs carrying bacteria in dairy environments and the need for additional studies to understand the dissemination mechanism within One Health perspective to prevent their further spread.

Antibiotic Resistance Genes Carried by Commensal Escherichia coli from Shelter Cats in Italy

Antimicrobial resistance is a widespread global health problem. The presence of resistant bacteria and antibiotic resistance genes has been demonstrated not only in humans but also in animals, including pets. Stray cats share the urban environment with people and pets. This may facilitate transmission of resistant bacteria and resistance genes between stray animals, people and domestic animals. Several studies have investigated the role of stray cats as a fecal carrier of ESBL-producing bacteria. However, there are many genes and resistance mechanisms that can be detected in commensal E. coli, which, because of its genetic plasticity, is considered an indicator for monitoring antibiotic resistance. In this study, rectal swabs were collected from stray cats from colonies and shelters in the city of Monza (Monza Brianza, Italy) to isolate commensal E. coli. Phenotypic tests, such as the minimum inhibitory concentration (MIC) and the double disc test (DDST), and molecular analyses to detect antimicrobial resistance genes (ARGs) were used to study the resistance of these isolates. The results obtained confirm that stray cats can carry ESBL-producing E. coli (6.7%) and genes conferring resistance to other important antibiotic classes such as tetracyclines and sulfonamides.

High rate of multidrug resistance and integrons in Escherichia coli isolates from diseased ducks in select regions of China

With the increasing number of ducks being raised and consumed, it is crucial to monitor the presence of multidrug resistant (MDR) bacteria in duck farming. Waterfowl, such as ducks, can contribute to the rapid dissemination of antibiotic resistance genes (ARGs). The objective of this study was to investigate the antimicrobial resistance (AMR), ARGs, and mobile genetic elements (MGEs), such as IS26, tbrC, ISEcp1 in Escherichia coli(E. coli) isolated from the intestinal contents of diseased ducks between 2021 and 2022 in Sichuan, Chongqing and Anhui, China. The AMR phenotypes of 201 isolated E. coli strains were determined using the minimum inhibitory concentrations (MICs) method. Subsequently, polymerase chain reaction and sequencing techniques were employed to screen for integron-integrase genes (intI1, intI2, intI3 genes), gene cassettes (GCs), MGEs, and ARGs. The results demonstrated that 96.5% of the E. coli isolates were resistant to at least 1 antibiotic, with 88.1% of the strains displaying MDR phenotype. The highest AMR phenotype observed was for trimethoprim-sulfamethoxazole (88.1%). Furthermore, class 1 and class 2 integrons were detected in 68.2% and 3.0% of all the isolates, respectively, whereas no class 3 integrons were found. Ten types of GCs were identified in the variable regions of class 1 and class 2 integrons. Moreover, 10 MGEs were observed in 46 combinations, with IS26 exhibiting the highest detection rate (89.6%). Among the 22 types of ARGs, tetA (77.1%) was the most frequently detected. In the conjugational transfer experiment, transconjugants were found to carry specific ARGs and MGEs, with their MIC values were significantly higher than those of recipient E. coli J53, indicating their status as MDR bacteria. This study emphasizes the necessity of monitoring MGEs, ARGs, and integrons in duck farms. It provides valuable insights into the complex formation mechanisms of AMR and may aid in preventing and controlling the spread of MDR bacteria in waterfowl breeding farm.