Epidemiology of potential source, risk attribution of Clostridium perfringens from Egyptian broiler farms and genetic diversity of multidrug resistance strains.

Clostridium perfringens induced necrotic enteritis (NE) became a persistent problem that had a major financial impact on the poultry business worldwide. Nevertheless, no prior research has assessed the related risk factors in Egyptian broiler farms. Thus, the purpose of this study is to perform an epidemiological analysis of C. perfringens occurrence, toxinotyping, and risk factors in El-Dakhlia and Damietta provinces, Egypt as well as their characteristics of antimicrobial resistance and molecular typing. From 25 broiler farms, 1100 samples were gathered. Antimicrobial resistance profiles and molecular typing were used to characterize the isolates. The findings revealed an overall prevalence of 26.3% (289/1100) from chickens' clinical samples (30.3%; 273/900) and farm environmental samples (8%; 16/200). Toxinotyping of 289 isolates showed that 165 (57.1%) isolates were C. perfringens type A, harboring only alpha toxin gene (cpa) while 124 (42.9%) isolates were C. perfringens type G, containing netB gene. The cpb2 genes were found in 66 (22.8%) isolates with the highest positive rate from dead birds. Additionally, the study found a number of possible risk variables that were substantially linked to the prevalence of C. perfringens, including location in Damietta, winter season, history of coccidia infection, use of antimicrobial growth promoters, birds older than 22 days, wet litter type, and biosecurity strategy. Univariate and multivariate analyses showed a significant association between C. perfringens infection and grower chickens (OR 2.09, 95% CI 1.05-4.21, p = 0.037) compared to starter chickens. The isolates displayed their highest resistance rate to sulfamethoxazole-trimethoprim (94.5%), erythromycin, imipenem (94.1% each), penicillin, ampicillin, streptomycin, gentamycin (90.7% each), ampicillin/sulbactam (89.9%), cefuroxime and cefepime (85.8%), nalidixic acid (85.1%), and tetracycline (78.9%). Remarkably, none of the strains were resistant to meropenem. Multidrug-resistant was observed in 94.5% strains with MAR index of 0.32-0.79. The resistance genes carried by different strains were obviously different, among which the detection rate of aminoglycoside resistance gene aphA1, was the highest (100%), followed by bla (85.8%), ermB, qnrS (85.1%), sul1 (80.6%), tetA(78.9%), drfA-1 (75.1%), qnrD, sul2 (60.2%), catA (57.4%), aadA (57.4%), ampC, mefA, qnrA (50.2%), bla (46%), and tetM (42.2%). Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) was used to classify these isolates into eight different genotypes according to sampling place and sample type. The epidemiological information from this study was helpful in determining the danger of clostridial infection linked to Egyptian broiler farms. Our results also show that in order to combat multidrug resistance, new medications and antibiotic substitutes are required. The importance of conducting more surveys to better understand the prevalence of C. perfringens infection under strict management circumstances for various flock purposes cannot be overstated.