Browsing by Author "Bicer, Yusuf"

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Citation - WoS: 1
Citation - Scopus: 1
Bacterial Microbiome Diversity Along Poultry Slaughtering Lines: Insights From Chicken Carcasses and Environmental Sources
(Sciendo, 2024) Telli, Arife Ezgi; Bicer, Yusuf; Telli, Nihat; Sönmez, Gonca; Turkal, Gamze; Güzel, İsmail
Introduction This study aimed to determine the bacterial diversity of chicken carcasses and their surrounding environment at various stages along a poultry slaughter line.Material and Methods Amplicon sequencing of the 16S rRNA gene was employed to assess the shifts in bacterial community diversity at both phylum and genus levels. Samples were collected from September to November 2021, targeting carcass surfaces at various operational stages (post-defeathering, post-evisceration, post-water chilling, and post-cooling), as well as from the internal environments and air of these units. The study took place in a vertically integrated poultry slaughterhouse in Konya, Turkey.Results Microbial diversity increased after the chilling and storage stages as a result of redistribution of the microorganisms after the physical effect of the slaughtering stages. The final product sample taken after storage had the highest bacterial abundance. The abundance at this stage was found to be strongly correlated with that at other slaughtering stages, as well as with the abundance in chilling water and on the personnel's hands. The common genera in chicken carcasses during slaughter stages were Macrococcus, Acinetobacter, Enterococcus, Escherichia-Shigella, Psychrobacter, Streptococcus, Lactococcus and Ligilactobacillus. Microbiome data in environmental samples indicated that the genera in highest relative abundance were Bacillus, Anoxybacillus, Acinetobacter and Psychrobacter. In air samples, the storage room had the highest diversity and in this place Bacillus spp. and Staphylococcus spp. were in the majority.Conclusion This study may provide some useful information to pinpoint the critical contamination sources in the poultry slaughtering process.
Co-Occurrence and Molecular Characterization of ESBL-Producing and Colistin-Resistant Escherichia Coli Isolates From Retail Raw Meat
(MDPI, 2025) Telli, Arife Ezgi; Telli, Nihat; Bicer, Yusuf; Turkal, Gamze; Yilmaz, Tahir; Ucar, Gurkan
Background: The emergence of extended-spectrum beta-lactamase (ESBL) producing and colistin-resistant Escherichia coli in retail meat poses a significant public health risk. Method: A total of 180 retail meat samples (chicken parts, internals, processed products; lamb; beef; fish) were purchased from markets and butcher shops across Turkiye. Presumptive ESBL-producing isolates were screened on chromogenic agar and phenotypically confirmed. Species identity was verified by uspA PCR, and resistance genes (blaCTX-M, blaTEM, blaOXA, blaSHV, mcr-1, mcr-2, mcr-3) were analyzed. Colistin MICs were determined by broth microdilution, while antimicrobial susceptibility of ESBL-positive isolates was assessed by disk diffusion. Results: Overall, ESBL-producing E. coli were detected in 21.7% (n = 39) of the 180 meat samples analyzed, with the highest prevalence observed in chicken parts (26/40, 65.0%) and giblets (6/10, 60%). All ESBL-E. coli isolates harbored blaCTX-M, with blaCTX-M-1 identified as the sole variant. The blaTEM gene was detected in 61.5% (24/39) of ESBL-positive E. coli isolates. Colistin resistance was identified in six isolates (15.4%), all of which carried the mcr-1 gene. Additionally, one lamb minced meat isolate harbored the mcr-2 gene. Co-occurrence analysis revealed that the most frequent resistance gene combination among ESBL-producing isolates was blaCTX-M1 + blaTEM, detected predominantly in chicken meat samples, while mcr-1 was observed only in isolates harboring single or limited resistance genes, suggesting a distinct acquisition pattern. Conclusions: A high prevalence of blaCTX-M-1 and the co-occurrence of mcr genes were detected in E. coli isolates from retail meat, particularly poultry. The detection of mcr-1/mcr-2 co-carriage in lamb meat, though rare, highlights the need for broader surveillance. These findings underscore the need for integrated monitoring and prudent antimicrobial use in food animals. The use of antibiotics as growth promoters is prohibited in T & uuml;rkiye, and therapeutic applications require a veterinary prescription; however, stronger enforcement remains essential to limit the dissemination of multidrug-resistant bacteria in the food chain.
Citation - WoS: 1
Citation - Scopus: 1
Extended-Spectrum (Esbl)-Producing Escherichia Coli in Laying Hens: Slaughterhouse Prevalence and Antibiotic Resistance Patterns
(Mdpi, 2025) Telli, Nihat; Telli, Arife Ezgi; Bicer, Yusuf; Turkal, Gamze
Background: Laying hens, which are widely utilized for consumption and export in various regions, experience prolonged antibiotic exposure due to their longer lifespan, increasing the risk of antibiotic resistance and impacting the microbial environment of poultry slaughterhouses. Given the significance of extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli in food safety, this study aimed to investigate the prevalence of ESBL genes in E. coli isolated from a laying hen slaughterhouse in Konya, Turkey. Methods: Sampling was conducted using a convenient sampling approach, and a total of 150 samples were collected from a single slaughterhouse over six visits during both warm (June-August) and cold (January-March) seasons to evaluate seasonal variations. Samples were categorized into environmental sources (personnel, air, wastewater, eggs) and carcass-related sources (cloaca, carcasses at critical control points, final product). Classical cultural and molecular techniques and antimicrobial susceptibility tests were used for ESBL presence and gene characterization. For sequence analysis, the bidirectional Sanger Gene sequence analysis method was applied. Results: PCR-based detection identified 10 of the 17 isolates as E. coli by amplifying the uspA gene, and bidirectional Sanger sequencing further confirmed these isolates at the species level. The E. coli isolates were detected at various sampling areas, including personnel, carcasses after evisceration, and raw wastewater samples collected at different time points. In the multiplex PCR analysis, most ESBL isolates were positive for the blaCTX-M gene. The co-existence of blaTEM and blaCTX-M genes was detected in five samples. Additionally, three genes (blaSHV, blaCTX-M, and blaOXA) were identified in a carcass sample after evisceration. All ESBL-producing isolates harbored the blaCTX-M1 gene, and multiple antibiotic resistance was observed across all isolates. The presence of these genes was strongly associated with resistance to ampicillin, amoxicillin-clavulanic acid, aztreonam, cefepime, cefpodoxime, cefuroxime, and cephalothin, highlighting the critical role of blaCTX-M in driving the multidrug resistance patterns observed in this study. The highest resistance rate (80%) was observed in "personnel" and "carcass samples after evisceration", while all isolates remained sensitive to carbapenems (imipenem and meropenem). Conclusions: Our findings highlight the importance of the laying hen slaughter line as a potential source of contamination with ESBL-producing E. coli, which poses significant implications for food safety and public health. These findings underscore the need for improved control measures to mitigate ESBL E. coli transmission in poultry processing and highlight the importance of optimizing antibiotic use strategies in laying hen farming.
From Raw to Fermented: Uncovering the Microbial Wealth of Dairy
(MDPI, 2025) Bicer, Yusuf; Telli, Arife Ezgi; Turkal, Gamze; Telli, Nihat; Ucar, Gurkan
Dairy products harbor complex and dynamic microbial communities that contribute to their sensory properties, safety, and cultural distinctiveness. Raw milk contains a diverse microbiota shaped by seasonality, storage conditions, lactation stage, animal health, farm management, and genetics, serving as a variable starting point for further processing. Fermentation, whether spontaneous or starter driven, selects for subsets of lactic acid bacteria (LAB), yeasts, and molds, resulting in microbial succession that underpins both artisanal and industrial products such as kefir and cheese. Kefir represents a balanced LAB-yeast symbiosis, with species composition influenced by grain origin, milk type, and processing parameters, whereas the cheese microbiota reflects the interplay of starter and non-starter LAB, coagulants, ripening conditions, and "house microbiota". Methodological factors-including DNA extraction, sequencing platform, and bioinformatic pipelines-further impact the reported microbial profiles, highlighting the need for standardization across studies. This review synthesizes current knowledge on raw milk, kefir, and cheese microbiomes, emphasizing the biological, technological, environmental, and methodological factors shaping microbial diversity. A holistic understanding of these drivers is essential to preserve product authenticity, ensure safety, and harness microbial resources for innovation in dairy biotechnology.