Person: CARLI, KAMİL TAYFUN
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CARLI
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KAMİL TAYFUN
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Publication Comparison of mycoplasma gallisepticum infection in different samples and ages of chicken breeder flocks(Facta-fundacio Arnco Ciencia Tecnologia Avicolas, 2020-01-01) Demirbilek, Serpil Kahya; KAHYA DEMİRBİLEK, SERPİL; Ardıçlı, Özge; ARDIÇLI, ÖZGE; Çarlı, Kamil Tayfun; CARLI, KAMİL TAYFUN; Veteriner Fakültesi; Mikrobiyoloji Ana Bilim Dalı; 0000-0001-6077-0478; 0000-0001-6045-8644; AAG-7421-2021; AAH-2842-2021This study aimed to compare method-based and newly developed sample-based methods for Mycoplasma gallisepticum (MG) detection in different samples of breeder flocks suffering from respiratory disease problems by using culture, real-time PCR (rPCR) and ELISA from chicks and embryonated eggs. Overall, 450 samples of 19-day-old chicken embryo's trachea, 450 samples of 8-day-old chicken tracheal swabs and 900 blood samples of 20-, 27-, 34-, 40- and 46-week-old breeder chickens from 5 flocks were sampled for 26 weeks, and were all tested for MG by culture, MG-rPCR and MG-ELISA. Culturing assays and rPCR were applied to 450 mixture samples from 19-day-old chicken embryo's trachea and 450 tracheal swab samples (each pooled into groups of 3) from 8-day-old chicks from the same flocks. Also, 900 blood samples from the same 5 breeder flocks suffering from respiratory disease problems were tested by MG-ELISA.In individual sample-based analyses, 55 (18.3%) of the 300 pooled swab samples were positive for MG using culture methods, and 106 (35.3%) of the same samples were found positive by rPCR (sensitivity, specificity). The ELISAs indicated that 252 (28%) of the 900 breeding blood samples were MG seropositive. Using age-based analyses, the most positive period was 46 weeks, followed by 40 weeks, 34 weeks, 27 weeks and at least 20 weeks, in order of decreasing seropositivity. When comparing the culture and rPCR results of the two different sampling methods, chicken embryo's trachea yielded more positive results than did tracheal swabs from the same flocks. In conclusion, rPCR is a highly specific, sensitive and reliable method for MG identification.Publication Effect of Mentofin application on the clearance of Mycoplasma gallisepticum (MG) from naturally infected layer chickens' trachea(Ankara Üniversitesi, 2015-01-01) Kahya, Serpil; Onat, Kaan; Erköse, Evren; Temelli, Seran; Eyigör, Ayşegül; Çarlı, Kamil Tayfun; KAHYA DEMİRBİLEK, SERPİL; Erköse, Evren; TEMELLİ, SERAN; Eyigör, Ayşegül; CARLI, KAMİL TAYFUN; Veteriner Fakültesi; Gıda Hijyeni ve Teknolojisi Ana Bilim Dalı; AAI-1092-2021; AAH-2842-2021; AAI-1101-2021; JPM-2439-2023; E-3867-2010Aim of this study was to determine if Mentofin would have any effect on Mycoplasma gallisepticum (MG) clearance from the tracheal epithelium of chickens in commercial layer flocks, which were naturally infected with MG. Results indicated that, compared to the control group, there was a significant and continuous decline in MG infection in chickens of Mentofin group determined by culture and Real-Time Polymerase Chain Reaction (MGrPCR) (P<0,05). Serology results in the control group indicated an increase in MG positivity from 25% to 40% (P>0,05), while there was no change in the Mentofin group (P>0,05). Culture results for MG positivity decreased from 85% to 5% in the Mentofin group, while this decrease was from 80% to 35% in the control group (P<0,05). There was a prominent decrease from 100% to 20% in MGrPCR positives in the Mentofin group (P<0,05) compared to a non-significant change observed from 95% to 80% in the control group (P>0,05). Results of this study indicate that Mentofin clearly had an effect on MG clearance from the tracheal epithelium, supported by detection of decline in MG infection in layers.Publication Detection of mycoplasma gallisepticum and mycoplasma synoviae by real-time pcrs and mycoplasma gallisepticum-antibody detection by an elisa in chicken breeder flocks(Kafkas Univ, Veteriner Fakultesi Dergisi, 2015-05-01) Kahya, Serpil; Yılmaz, Özge; Eyigör, Ayşegül; Temelli, Seran; Çarlı, K. Tayfun; KAHYA DEMİRBİLEK, SERPİL; Yılmaz, Özge; Eyigör, Ayşegül; TEMELLİ, SERAN; CARLI, KAMİL TAYFUN; Veteriner Fakültesi; Mikrobiyoloji Ana Bilim Dalı; 0000-0002-9415-2106; AAI-1092-2021; AAI-1101-2021; AAG-7421-2021; AAH-2842-2021; HHL-6717-2022; E-3867-2010This study aimed to determine the prevalence of Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) in breeder flocks showing respiratory symptoms. A total of 77 flocks (2153 tracheal swabs and blood samples) were sampled and all were tested by MG real time PCR (MG-rPCR) and MG-ELISA, and 32 flocks were tested by MS real time PCR (MS-rPCR). In the first part of this study covering 28 flocks, all samples from chickens with marked clinical symptoms and high MG-antibody levels gave negative results with MG-rPCR(1). Therefore, the MG-lipoprotein gene-specific primers (MG-rPCR(1)) of this PCR were replaced with MG-16S rRNA primers (MG-rPCR(2)), as were the MS-16S rRNA primers (MS-rPCR), thus the study was pursued accordingly. All of the first 28 flocks, which were 100% positive by MG-ELISA, were MG-rPCR(1) negative, whereas in the second part of the study, other 49 flocks, which were 87.8% MG seropositive, were found 42.9% positive by MG-rPCR(2). In addition, 5 selected flocks from the first 28 were negative, whereas 7.4% of the 27 selected flocks from the second 49 were positive by MS-rPCR. Overall, 81 out of 432 MG-rPCR(1-2) (18.7%) performed from 77 flocks, and 13 out of 187 MS-rPCRs (6.9%) in 32 flocks were determined as positive. ELISA results indicated that there could be significantly high false-positives in serological tests, thus results should not be relied upon one test system. Also, this study revealed that, for the confirmation of Mycoplasma-infected flocks in laboratories, rPCR is a reliable method as long as suitable primers are selected, and that MG and MS prevalence is considerably high in winter season.Publication Detection of israel variant 2 (is/1494/06) genotype of infectious bronchitis virus in a layer chicken flock(Ankara Universitesi, 2021-01-01) Ongor, Hasan; Timurkaan, Necati; Coven, Fethiye; Karabulut, Burak; Eroksuz, Hatice; Cetinkaya, Burhan; Çarlı, Kamil Tayfun; CARLI, KAMİL TAYFUN; Veteriner Fakültesi; Mikrobiyoloji Ana Bilim Dalı; 0000-0001-6045-8644The aim of this study was to determine an infectious bronchitis (IB) infection, caused by an Israel variant 2 (IS/1494/06)-like IBV, in a layer chicken flock regularly vaccinated with vaccines containing IBV H120 and 4/91 strains. Mild respiratory symptoms, drop in egg production and soft-shelled eggs and eventually death were observed in a layer chicken flock. Clinical samples from four diseased chickens were examined for the detection and genotyping of IBV by virus isolation, a commercial real time reverse transcription polymerase chain reaction (rRT-PCR) and nucleotide sequencing. Both Israel variant 2 (IS-Var2) and 793/B serotypes were detected from samples by rRT-PCR, but sequencing results of a 345 bp part of S1 gene revealed that our IBV isolate, HFT-IBV, was IS/1494/06 (IS-Var2)-like with the 97.7% genetic similarity. These results suggested that immunity against vaccination with a combination of different genotypes (H120 and 4/91) could not be protective for IS-Var2 IBV field infection. In addition, identification of genotypes from the clinical samples, such as swabs and organ samples by commercial rRT-PCR assays failed to find correct IBV genotype responsible for the IB infection, whereas analysis of nucleotide sequencing of S1 gene of IBV as a gold standard test undoubtedly detected causative genotype of the infection. Also, the findings indicated that there is an urgent need for consider genotype- or protectotype-match vaccination strategies in the field to prevent vaccine- and IB-dependent economic losses of the poultry sector and logically protect chickens from IBV infection.Publication Exposure to avian coronavirus vaccines is associated with increased levels of SARS-CoV-2-cross-reactive antibodies(Wiley, 2022-07-23) Ardıçlı, Özge; Çarlı, Kamil Tayfun; Satitsuksanoa, Pattraporn; Dreher, Anita; Cusini, Alexia; Hutter, Sandra; Mirer, David; Rueckert, Beate; Jonsdottir, Hulda R.; Weber, Benjamin; Cervia, Carlo; Akdis, Mubeccel; Boyman, Onur; Eggel, Alexander; Brueggen, Marie-Charlotte; Akdis, Cezmi A.; van de Veen, Willem; ARDIÇLI, ÖZGE; CARLI, KAMİL TAYFUN; Veteriner Fakültesi; Mikrobiyoloji Ana Bilim Dalı; 0000-0001-6077-0478; AAG-7421-2021; CIN-4902-2022Background Although avian coronavirus infectious bronchitis virus (IBV) and SARS-CoV-2 belong to different genera of the Coronaviridae family, exposure to IBV may result in the development of cross-reactive antibodies to SARS-CoV-2 due to homologous epitopes. We aimed to investigate whether antibody responses to IBV cross-react with SARS-CoV-2 in poultry farm personnel who are occupationally exposed to aerosolized IBV vaccines. Methods We analyzed sera from poultry farm personnel, COVID-19 patients, and pre-pandemic controls. IgG levels against the SARS-CoV-2 antigens S1, RBD, S2, and N and peptides corresponding to the SARS-CoV-2 ORF3a, N, and S proteins as well as whole virus antigens of the four major S1-genotypes 4/91, IS/1494/06, M41, and D274 of IBV were investigated by in-house ELISAs. Moreover, live-virus neutralization test (VNT) was performed. Results A subgroup of poultry farm personnel showed elevated levels of specific IgG for all tested SARS-CoV-2 antigens compared with pre-pandemic controls. Moreover, poultry farm personnel, COVID-19 patients, and pre-pandemic controls showed specific IgG antibodies against IBV strains. These antibody titers were higher in long-term vaccine implementers. We observed a strong correlation between IBV-specific IgG and SARS-CoV-2 S1-, RBD-, S2-, and N-specific IgG in poultry farm personnel compared with pre-pandemic controls and COVID-19 patients. However, no neutralization was observed for these cross-reactive antibodies from poultry farm personnel using the VNT. Conclusion We report here for the first time the detection of cross-reactive IgG antibodies against SARS-CoV-2 antigens in humans exposed to IBV vaccines. These findings may be useful for further studies on the adaptive immunity against COVID-19.Publication Investigation of contagious agalactia by bacteriological and PCR methods in sheep and goats(Kafkas Üniversitesi, 2015-01-01) Göçmen, Hüban; Ülgen, Mihriban; Çarlı, K. Tayfun; Onat, Kaan; Kahya, Serpil; Özdemir, Ümit; Mat, Burak; Göçmen, Hüban; ÜLGEN, MİHRİBAN; CARLI, KAMİL TAYFUN; KAHYA DEMİRBİLEK, SERPİL; Veteriner Fakultesi; Veteriner Mikrobiyoloji Ana Bilim Dalı; 0000-0002-2245-5781; 0000-0002-6307-5179; AAG-8117-2021; B-9095-2018; AAH-2842-2021; E-3867-2010The aim of this study was diagnosis that occurrence of Contagious Agalactia by bacteriological and molecular methods in sheep and goats. A total of 339 samples from sheep and goats in Bursa, Balikesir, Canakkale and Edirne provinces were examined by bacteriological and molecular methods. The samples were 162 milk samples, 147 eye swabs, 15 joint fluids, 11 nasal swabs and 4 lung tissue. In bacteriological examination, 29 isolates were evaluated as Mycoplasma sp.. As a result of biochemical tests and growth inhibition tests, 29 (8.55%) Mycoplasma sp. were identified as 25 (7.37%) Mycoplasma agalactiae, 2 (0.58%) Mycoplasma ovipneumoniae and 2 (0.58%) Mycoplasma arginini. In molecular diagnosis, polC gene-PCR results could be detected M. agalactiae positive with 9.14% rate. As a result of this, 5 milk samples and 1 lung tissue sample were detected positive by polC-PCR while negative by bacteriological examination. The results of polC-PCR detected M. agalactiae positive with 14.19% rate of milk samples, 13.33% rate of joint fluids, 2.72% rate of eye swabs and 50% rate of lung tissue samples but nasal swabs were detected as negative. In this study, presence of Contagious Agalactia were investigated by bacteriological and molecular methods and M. agalactiae was detected as a main agent which cause disease however other Mycoplasma species which cause disease were not observed.Publication Presence of Salmonella in retail grade a eggs determined by the International Organization for Standardization 6579 method and a LightCycler polymerase chain reaction system(Ankara Üniversitesi, 2015-01-01) Temelli, Seran; Kahya, Serpil; Ata, Zafer; Çarlı, Kamil Tayfun; Eyigör, Ayşegül; TEMELLİ, SERAN; KAHYA DEMİRBİLEK, SERPİL; Ata, Zafer; CARLI, KAMİL TAYFUN; Eyigör, Ayşegül; Veteriner Fakültesi; Mikrobiyoloji Ana Bilim Dalı; AAI-1092-2021; W-7994-2019; AAH-2842-2021; AAI-1101-2021; AAH-2842-2021This study aims to determine the presence of Salmonella in naturally contaminated grade A eggs by the standard culture method International Organization for Standardization Method 6579 (ISO) and a specific real-time PCR system (LightCycler PCR-LCPCR) to complement ISO. A total of 1635 eggs pooled into 101 samples were randomly collected within one year period from 20 different retail markets in Bursa, Turkey, carrying eggs of 16 large egg producers/suppliers of 5 cities with intensive layer production. Preparation of the egg and shell for analyses, Salmonella isolations and identifications, and detections were performed according to ISO 6887-4:2003, ISO 6579 and LCPCR, respectively. Overall Salmonella detection rate by ISO and LCPCR were 15.8 % (16/101) and 46.5 % (47/101), respectively. Out of 101 inner parts, Salmonella was detected in 11 (10.9 %) samples by ISO, and in 31 (30.7 %) samples by LCPCR. Six of 101 shell samples (5.9 %) were found to harbor Salmonella by ISO, while 18 (17.8 %) shells were positive by LCPCR. All isolates were determined as Salmonella enterica subsp. enterica serovar Enteritidis. These findings indicate considerably high Salmonella contamination in retail grade A eggs. This should be under routine monitoring by rapid methods such as PCR, complemented by standard culture to evaluate and assess the significance of risk for public health.Publication First isolation of salmonella duisburg from quail flock(Sivar-soc Italiana Veterinari Animali Reddito, 2021-06-01) ARDIÇLI, ÖZGE; ARDIÇLI, ÖZGE; KAHYA DEMİRBİLEK, SERPİL; KAHYA DEMİRBİLEK, SERPİL; Kurnaz, Havva; Carli, Kamil Tayfun; CARLI, KAMİL TAYFUN; ÇARLI, KAMİL TAYFUN; Veteriner Fakültesi; 0000-0001-6077-0478; HOC-6049-2023; AAG-7421-2021The first isolation of Salmonella enterica subsp. enterica serovar Duisburg (S. Duisburg) (4,12,[27]:d:e,n,z(15)) from quails was presented in this case report. Internal organs and ileocecal parts of intestines were collected from quails at 20-day old age in the flock (total of 150 quails) located in South Marmara region of Turkey. Isolation was performed according to International Organization for Standardization Method 6579. Regarding the identification of Salmonella-suspected colonies, API 20E test strips and Phoenix 100 ID/AST system were used. Serotyping of the isolate was undertaken using the slide serum agglutination test. Minimum inhibitory concentration results showed that Salmonella isolate was susceptible to all the tested antimicrobials. Although the prominent species is chicken in poultry, quail breeding increases its importance and extensiveness. Therefore this study may be useful not only for current antibiotic practices in quail breeding but also for further studies on avian microbiology.Publication How do we use molecular knowledge in diagnosis and control of pandemic avian viruses?(Aves, 2022-01-01) Ardıçlı, Özge; Demirbilek, Serpil Kahya; Coven, Fethiye; Çarlı, Kamil Tayfun; ARDIÇLI, ÖZGE; KAHYA DEMİRBİLEK, SERPİL; CARLI, KAMİL TAYFUN; Veteriner Fakültesi; Mikrobiyoloji Ana Bilim Dalı; 0000-0001-6077-0478; 0000-0003-1928-7630; AAG-7421-2021; E-3867-2010; CNE-1191-2022Pandemic respiratory viruses of poultry have caused significant economic losses in the poultry industry since the 1930s, and molecular and genetic techniques are widely used for diagnosis and control of the infections. Knowledge of changes in the genetic and antigenic characteristics of the pandemic viruses during the time can be really important for human pandemic viruses such as severe acute respiratory syndrome virus-coronavirus-2 and human influenza virus. The use of these techniques plays a vital role in preventing the faulty results and the possible financial losses that may occur due to the limited findings obtained from conventional laboratory tests. In the light of this information, the purpose of this review is to provide an up-to-date assessment of the diagnosis and prevention of major respiratory viruses in poultry and a general and field-oriented scientific perspective that may be useful in the industry. In this context, current approaches for diagnosis and vaccination applications developed using molecular methods based on avian coronavirus infectious bronchitis virus, avian paramyxovirus-1 virus, and avian influenza virus, which are pandemic, are discussed, and solution suggestions for an effective fight are presented.Publication Pathogens isolated from bovine clinical mastitis and their antimicrobial resistance(Polish Soc Veterinary Sciences Editorial Office, 2022-01-01) Ardıçlı, Özge; Demirbilek, Serpil Kahya; Carlı, Kamil Tayfun; ARDIÇLI, ÖZGE; KAHYA DEMİRBİLEK, SERPİL; CARLI, KAMİL TAYFUN; Veteriner Fakültesi; Mikrobiyoloji Ana Bilim Dalı; 0000-0001-6077-0478; AAG-7421-2021; E-3867-2010; CNE-1191-2022This study aimed to isolate aerobic and microaerophilic bacteria from mastitis milk samples, as well as to determine their antibiotic resistance. A total of 196 bovine mastitis milk samples were tested by standard bacteriological methods and with API identification test kits. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disk diffusion method. The results revealed that the predominant isolate was S. aureus, with an isolation rate of 28%, followed by Streptococcus spp. (27%) and E. coli (19%). Isolation rates for Corynebacterium spp., Mycoplasma spp., and Pseudomonas aeruginosa were 11%, 6%, and 4%, respectively. Compared to the bacteria mentioned above, lower percentages were observed for Trueperella pyogenes (2%), Pasteurella multocida (2%), and Klebsiella pneumoniae (1%). A broad evaluation of antimicrobial resistance showed that the pathogens were resistant to tetracycline (68.63%), oxytetracycline (41.57%), ampicillin (39.08%), ceftiofur (38.1%), cephalexin (32.26%), penicillin (31.25%), amoxicillin/clavulanic acid (24.53%), enrofloxacin (24.44%), gentamycin (23.68%), and trimethoprim/sulfamethoxazole (22.09%). This study demonstrated that the sources of bacteria isolated from mastitis bovine milk samples were both contagious and environmental. More importantly, the present results demonstrate a critically high antimicrobial resistance in dairy cattle. For instance, E. coli isolates showed a crucial resistance to commonly used and recommended antimicrobials, including ceftiofur (100%), cephalexin (83.33%), and tetracycline (94.44%). The results of this study may provide valuable information about clinical aspects of bovine mastitis infections and current antimicrobial resistance levels in dairy cattle.