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    Antibiotic, heavy metal, and disinfectant resistance in chicken, cattle, and sheep origin E. coli and whole-genome sequencing analysis of a multidrug-resistant E. coli O100:H25 strain
    (Wiley, 2022) Çufaoğlu, Gizem; Cengiz, Görkem; Acar, Bahar Onaran; Yesilkaya, Busra; Ayaz, Naim Deniz; Levent, Gizem; Goncuoğlu, Muammer
    In this study, antibiotic, heavy metal, and disinfectant resistance profiles of E. coli and E. coli O157 isolates were determined, and whole-genome sequencing of a multidrug-resistant E. coli O100:H25 strain was reported. A total of 70 E. coli isolated from chicken neck skin and sheep cecum samples, and 32 E. coli O157 strains isolated from cattle carcass, sheep carcass, and slaughterhouse wastewater samples were explored. Minimum inhibitory concentrations (MICs) of one antibiotics, eight heavy metals, and three disinfectants were determined by the broth microdilution method. Twenty of those isolates exhibiting high MIC values against compounds tested were further analyzed by PCR for the presence of relevant resistance genes (n = 42). The majority of the isolates tested were resistant to erythromycin and/or fosfomycin (99% and 78%, respectively) and 89% of the isolates were multidrug-resistant. Among the heavy metals, and disinfectants that were quaternary ammonium compounds (QAC) tested, the highest prevalence of resistance was observed against nickel (71%) and followed by zinc (62%), and N-alkyl-dimethyl-benzyl-ammonium chloride (26%). While bla(AmpC), ermC, murA, and aadA were the most abundant antibiotic resistance genes, rcnA and zntA, and mdfA, sugE (c), and ydg(F) were also commonly observed as heavy metal and disinfectant genes, respectively. Additionally, whole-genome sequencing was performed for a single multidrug-resistant strain (E. coli P91). This strain was identified as serotype O100:H25, and harbored three Inc class plasmids and ant(2 '')-Ia, aph(3 ')-Ia, aph(3 '')-Ib, aph(6)-Id, bla(TEM-1A), dfrA5, mdf(A), sul1, sul2, and tet(A) genes along with the various heavy metal and disinfectant related genes. The findings of the study show that both phenotypic and genotypic antibiotic, heavy metal, and disinfectant resistance are highly prevalent in E. coli isolates that originated from food-producing animals. The use of antimicrobials in food-producing animals needs to be carefully evaluated since the coexistence of antibiotic, heavy metal, and disinfectant resistance genes may result in a coselection that yields the emergence and spread of highly persistent and resistant strains in agricultural settings.
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    Emerging details about COVID-19 and chronology of the pandemic in Turkey
    (2020) Göncüoğlu, Muammer; Cengiz, Görkem; Onaran, Bahar; Ayaz, Naim Deniz; Çufaoğlu, Gizem
    Coronaviruses are found in all mammalian and avian species. Due to its mild infection on upper respiratory tract, this virus was not considered as a serious human pathogen until the outbreaks of SARS-CoV and MERS-CoV in 2002 and 2012, respectively. Recently the third and the biggest outbreak of coronavirus “COVID-19” or “SARS-CoV-2” has erupted and the world is now in a struggle to combat this disease. Although everything has not yet been fully clarified about this new type of virus, the data obtained from the studies conducted so far provides guidance on how to deal with SARS-CoV-2. In this context, this review provides information about pathogenesis, clinical symptoms, presence in animals, potential transmission routes of SARS-CoV-2 as well as the detection methods used in the world and Turkey.
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    Mono- and Mixed-Species Biofilm Formation by Salmonella Infantis, Salmonella Kentucky, Enterococcus faecium, and Enterococcus faecalis
    (Istanbul Univ-Cerrahpasa, 2021) Çufaoğlu, Gizem; Onaran Acar, Bahar; Cengiz, Görkem; Ayaz, Naim Deniz; Göncüoğlu, Muammer
    It is crucial to understand the interactions between food-borne pathogens, as they are commonly encountered as multi-species biofilms in the food industry. Since Salmonella and Enterococcus are both found in poultry intestinal micro-biota, the multi-species biofilms of these strains gain more significance. This study aimed to reveal the synergistic and antagonistic effects of mono- and mixed-species biofilms of Salmonella Infantis, Salmonella Kentucky, Enterococcus faecium, and Enterococcus faecalis on each other. Biofilm formation of mono- and mixed-species at different concentrations (10(9), 10(7), 10(5), and 10(3) cfu/mL) were determined in Tryptic Soy Broth using polystyrene microplates at room temperature (21 +/- 1 degrees C) for 48 hours. According to the optical density measured at 590 nm, S. Infantis was determined as a strong biofilm producer, and S. Kentucky and E. faecium were defined as weak biofilm producers under the conditions applied in the study. No biofilm formation was observed in E. faecalis. In addition, while S. Infantis and S. Kentucky exhibited an antagonistic effect on each other when co-incubated, a synergistic effect was seen between the S. Infantis and Enterococcus spp. This study highlights the impact of microbial interactions in mixed-species biofilm formed by foodborne pathogens, and could help in future studies on combating biofilms, especially in poultry-based food processing environments.