Bovine respiratory disease causes significant economic losses in cattle farming due to mortality, treatment costs, and reduced productivity. It involves viral and bacterial infections, with Pasteurella multocida and Mannheimia haemolytica key bacterial pathogens. These bacteria contribute to severe pneumonia and are often found together. Poland has one of the highest levels of antimicrobial use in food-producing animals among European Union countries. A total of 70 bacterial strains were analyzed, 48 P. multocida and 22 M. haemolytica, collected from affected calves’ respiratory tracts. The bacterial species were confirmed molecularly using PCR, which was also employed to detect antimicrobial resistance and virulence-associated genes. Antimicrobial susceptibility was determined using the broth microdilution method. Antimicrobial resistance varied between the two bacterial species studied. The highest resistance in P. multocida was to chlortetracycline 79.2% (38/48) and oxytetracycline 81.3% (39/48), while M. haemolytica showed 63.6% (14/22) resistance to penicillin and tilmicosin. The highest susceptibility was found for fluoroquinolones: P. multocida demonstrated 91.7% (44/48) susceptibility to enrofloxacin and 87.5% (42/48) to danofloxacin, while 77.3% (17/22) of M. haemolytica were susceptible to both tested fluoroquinolones. The tetH and tetR genes were observed only in P. multocida, at frequencies of 20.8% (10/48) and 16.7% (8/48), respectively. Both species carried the mphE and msrE genes, though at lower frequencies. All M. haemolytica contained the lkt, gs60, and gcp genes. All P. multocida carried the sodA gene, while the hgbB and ompH genes were present in 37.5% (18/48) and 20.8% (10/48) of strains, respectively. The highest resistance was observed against the most commonly used antibiotics in the European Union, although the resistance differed between the studied bacterial species and each strain exhibited the presence of at least one virulence gene.

Fungi are a typical part of the microbiome of poultry houses, but some of the genera can be pathogenic for poultry and humans. An investigation was conducted on 200 duck eggs from 10 flocks to determine total fungal contamination on the eggshells. The colony types were identified morphologically and microscopically, and a representative group was identified using PCR. The resistance profiles for all obtained Aspergillus isolates were conducted. The dominating genera on eggshells were Penicillium, Alternaria and Aspergillus and the number of fungal colonies ranged from 0 to 7100. Aspergillus fumigatus was cultured from 9.5% eggshells, and all isolates were obtained from three flocks. The minimum inhibitory concentration (MIC) values for A. fumigatus isolates ranged from 0.094–32 μg/mL for amphotericin B (MIC 50 1 mg/L and MIC 90 32 μg/mL), 0.125–32 μg/mL for caspofungin (MIC 50 0.38 μg/mL and MIC 90 32 μg/mL), 0.19–32 μg/mL for itraconazole (MIC 50 1.5 μg/mL and MIC 90 32 μg/mL), 0.047–12 μg/mL for posaconazole (MIC 50 0.5 μg/mL and MIC 90 8 μg/mL) and 0.023–32 μg/mL for voriconazole (MIC 50 0.19 μg/mL and MIC 90 32 μg/mL). A total of 73.7% of the isolates were resistant to posaconazole and 68.4% to itraconazole. Nearly half of the strains (47.4%) showed resistance to amphotericin B and 31.6% to voriconazole. Because of the lack of antifungals registered for poultry, hygiene and the regular disinfection of litter in particular are needed to prevent the contamination of the eggs by fungi for both animal and human health.