Biotechnology

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Browsing Biotechnology by Author "Abera Admasie"

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    Isolation and Molecular Characterization of Campylobacter Jejuni and Campylobacter Coli Isolated from Ethiopian Dairy Supply Chain and Evaluation of their Associated Risk Factors and Antimicrobial Resistance
    (Addis Ababa University, 2024-03) Abera Admasie; Tesfaye Sisay
    Campylobacter is among the leading bacterial foodborne pathogens, causing a high foodborne disease burden worldwide. There is a limited information on the prevalence, risk factor, and whole genome sequencing of Campylobacter in Ethiopian milk and milk products in major milk sheds in Ethiopia. To this end, a cross-sectional study was carried out to isolate and characterize the genomic diversity,antimicrobial resistance patterns and associated risk factors of Campylobacter species from milk and dairy products collected from representative regional sites (Oromia, Amhara, and SNNP). in Ethiopia. A total of 1140 dairy food samples were collected in the dry and wet seasons of which 456 samples were used for seasonal comparison. Samples were tested for Campylobacter by following the ISO 10272-1:2017 standard and confirmed by PCR with Illumina MiSeq instrument (v3 600-cycle cartridge) for the paired-end sequencing run. Amrfinderplus_db NCBI was used to detect gyrA and 50S_L22_A103V gene mutations. NCBI Pathogen Detection database was used for the genomic similarity . A total of 141 Campylobacter isolates were tested for susceptibility to three antibiotics using a disk diffusion method.. The result indicated that Campylobacter was detected in 12% of tested food samples. The highest prevalence of Campylobacter jejuni and Campylobacter coli was found in raw milk (19%), followed by pasteurized milk (10 %) and cottage cheese (3%) (P<0.001). The prevalence did not differ significantly between the wet (20%) and dry (16%) seasons (P=0.27). However, there was a five times more chance of finding Campylobacter species in milk and milk products during the wet season than the dry season (COR = 4.5 (1.8-12), P = 0.002). in the Oromia region, Besides, 89% of the samples were contaminated with C. jejuni, and 11% with C. coli. Two different C. jejuni MLST sequence types, namely, ST 51 (clonal complex ST-443) and ST 2084 (clonal complex 353) were detected; they were clustered in different clades (B and C), respectively. Two ST 1628 and 2 ST 830 C. coli from clonal complex 828 were grouped into a single clade (C). Phenotypically, 89 %, 74%, and 57% of Campylobacter species were resistant to tetracycline, erythromycin, and ciprofloxacin respectively. Moreover, 43% of the tested isolates were resistant to more than two drugs. Genomically, ten isolates of 8 C. jejuni ST 2084 and 2 C. coli ST 1628 had a T86I mutation in the gryA gene, which is associated with resistance to Quinolone (ciprofloxacin), and all 14 C. jejuni carry 50S_L22_A103V gene, associated with resistance against Macrolide (erythromycin). Of these, all Campylobacter species carried CTD genes, chemotaxis-related genes (cheA, cheB, cheR, and cheY), and invasive genes (flaC, ciaB, and ciaC). We can conclude that 12% of Campylobacter species were present during the dry and wet seasons. The data also showed that , 43% of the isolates acquired more than two antibiotic resistance genes and a mutation was present in the 50S_L22_A103V and gryA genes in C. jejuni. The risk factor analysis showed that using warm water and soap for cleaning cow udders and teats on farms (AOR=0.3, P=0.023), filtering milk with a cloth, or plastic filter (AOR=0.065, P=0.005), and storing milk in an aluminum container (AOR=0.23, P=0.027) reduced the likelihood of detecting Campylobacter in raw milk. In contrast, Campylobacter detection was significantly higher in milk samples collected at collection centers with concrete floors (AOR=5.2, P=0.004). The odds of detecting Campylobacter in milk were 17 times greater (AOR=17, P=0.007) in milk processing facilities that did not calibrate a pasteurizer on an annual basis. Likewise,, having a separate refrigerator for milk storage reduced the occurrence of Campylobacter in retail (AOR=0.29, P=0.021). In conclusion, Compared to samples of pasteurized and cottage cheese, the raw milk was more contaminated. Additionally, a mutation was found in the 50S_L22_A103V and gryA genes of C. jejuni, and 43% of the isolates that were studied possessed more than two antibiotic resistance genes. Thus, understanding the genetic composition and prevalence of Campylobacter in the dairy supply chain may help identify potential contamination sources and create effective management plans that ensure the safety and caliber of dairy products.