Browsing by Author "Kiliç, A.O."

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Investigation of Antimicrobial Activities and 16S rRNA Sequences of Actinomycetes Isolated from Karst Caves in the Eastern Black Sea Region of Türkiye
(2023.01.01) Tüfekci, E.F.; Uzun, U.; Ertunga, N.S.; Biber, A.; Hidiroglu, I.A.; Tekkiliç, I.; Altay, B.; Kiliç, A.O.
Considering that most antibiotics originate from actinomycete group bacteria, especially the Streptomyces genus, it is predicted that novel actinomycetes isolated from extreme environments such as caves may bring novel antibiotics to the medical world. The study aimed to screen the antimicrobial activity of actinomycetes isolated from the three karst caves in Turkiye and to identify selected isolates with antimicrobial activity by molecular methods. One hundred seventy-nine actinomycetes isolated from Akcakale, Kirklar (Altintas), and Koprubasi Caves in Gumushane province in the Eastern Black Sea Region of Turkiye were included in the study. The antimicrobial activity of isolates was investigated using the modified cross-streak agar method against seven Gram-negative bacteria, three Gram -positive bacteria, and one yeast strain. Fifty-three isolates (29.6%) had antimicrobial activity against at least one of the tested microorganisms. The rate of isolates exhibiting antimicrobial activity against Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Chromobacterium violaceum, Klebsiella pneumoniae, Salmonella Typhimurium, Escherichia coli, Acinetobacter haemolyticus, Pseudomonas aeruginosa, Enterobacter aerogenes, and Candida albicans was 21.2%, 20.0%, 16.8%, 12.8%, 3.4%, 2.8%, 2.2%, 1.1%, 0.6%, 0.6%, and 0.6%, respectively. An actinomycete isolate, TRMS 124, showed antimicrobial activity against ten test microorganisms. The 16S ribosomal RNA (16S rRNA) sequencing was performed for the identification and phylogenetic analysis of 26 isolates randomly selected among actinomycetes that exhibited antimicrobial activity against at least three test microorganisms. As a result, it was determined that 24 isolates showed homology with various Streptomyces species and two isolates with Embleya scabrispora and Couchioplanes caeruleus, respectively. These results showed that karst caves could be good sources for isolating actinomycetes with the potential to produce antimicrobial compounds.
Prevalence and Molecular Characterization of ESBL/pAmpC Producing Faecal Escherichia coli Strains with Widespread Detection of CTX-M-15 Isolated from Healthy Poultry Flocks in Eastern Algeria
(2024) Akkari, H.; Heleili, N.; Ozgumus, O.B.; Merradi, M.; Reis, A.; Ayachi, A.; Akarsu, N.; Tufekci, E.F.; Kiliç, A.O.
The intensification of livestock farming has led to the widespread use of massive amounts of antibiotics worldwide. Poultry production, including white meat, eggs and the use of their excreta as fertiliser, has been identified as one of the most crucial reservoirs for the emergence and spread of resistant bacteria, including E. coli in poultry as an important opportunistic pathogen representing the greatest biological hazard to human and wildlife health. Thus, this study aimed to analyse E. coli in the faecal carriage of healthy poultry flocks and to investigate the phenotypic and genotypic characteristics of antimicrobial resistance, including integrons genes and phylogenetic groups. A total of 431 cloacal swabs from apparently healthy poultry from four regions in Eastern Algeria from December 2021 to October 2022. 360 E. coli were isolated; from broilers (n=151), broiler breeders (n=91), laying hens (n=72), and breeding hens (n=46). Among this, 281 isolates exhibited multidrug resistance (MDR) phenotype, 17 of the 360 E. coli isolates exhibited ESBL, and one isolate exhibited both ESBL/pAmpC. A representative collection of 183 among 281 MDR E. coli was selected for further analysis by PCR to detect genes encoding resistance to different antibiotics, and sequencing was performed on all positive PCR products of bla and bla genes. Phylogenetic groups were determined in 80 E. coli isolates (20 from each of the four kinds of poultry). The bla gene was found in 16 (94.11 %) ESBL-producing E. coli isolates within 11 strains co-expressing the bla gene and 8 strains co-expressing the bla gene. Sequence analysis showed frequent diversity in CTX-M-group-1, with bla being the most predominant (n=11), followed by bla (n=5). The bla gene was detected only in one ESBL/pAmpC isolate. Among the 183 tested isolates, various antimicrobial resistance genes were found (number of strains) bla (n=121), bla (n=12), tetA (n=100), tetB (n=29), sul1(n=67), sul2 (n=32), qnrS (n=45), qnrB (n=10), qnrA (n=1), catA1(n=13), aac-(6')-Ib (n=3). Furthermore, class 1 and class 2 integrons were found in 113 and 2 E. coli, respectively. The isolates were classified into multiple phylogroups, including A (35%), B1 (27.5%), B2 and D each (18.75%). The detection of integrons and different classes of resistance genes in the faecal carriage of healthy poultry production indicates that commensal E. coli could potentially act as a reservoir for antimicrobial resistance, posing a significant One Health challenge encompassing the interconnected domains of human, animal health and the environment. Here, we present the first investigation to describe the diversity of bla producing E. coli isolates with widespread detection of CTX-M-15 and CTX-M-1 in healthy breeders (Broiler and breeding hens) in Eastern Algeria.
Prevalence and molecular characterization of ESBL/pAmpC producing faecal Escherichia coli strains with widespread detection of CTX-M-15 isolated from healthy poultry flocks in Eastern Algeria
(Academic Press, 2024) Akkari, H.; Heleili, N.; Ozgumus, O.B.; Merradi, M.; Reis, A.; Ayachi, A.; Akarsu, N.; Tufekci, E.F.; Kiliç, A.O.
The intensification of livestock farming has led to the widespread use of massive amounts of antibiotics worldwide. Poultry production, including white meat, eggs and the use of their manure as fertiliser, has been identified as one of the most crucial reservoirs for the emergence and spread of resistant bacteria, including E. coli in poultry as an important opportunistic pathogen representing the greatest biological hazard to human and wildlife health. Thus, this study aimed to analyse E. coli in the faecal carriage of healthy poultry flocks and to investigate the phenotypic and genotypic characteristics of antimicrobial resistance, including integrons genes and phylogenetic groups. A total of 431 cloacal swabs from apparently healthy poultry from four regions in Eastern Algeria from December 2021 to October 2022. 360 E. coli were isolated; from broilers (n = 151), broiler breeders (n = 91), laying hens (n = 72), and breeding hens (n = 46). Among this, 281 isolates exhibited multidrug resistance (MDR) phenotype, 17 of the 360 E. coli isolates exhibited ESBL, and one isolate exhibited both ESBL/pAmpC. A representative collection of 183 among 281 MDR E. coli was selected for further analysis by PCR to detect genes encoding resistance to different antibiotics, and sequencing was performed on all positive PCR products of blaCTX-M and blaCMY-2 genes. Phylogenetic groups were determined in 80 E. coli isolates (20 from each of the four kinds of poultry). The blaCTX-M gene was found in 16 (94.11 %) ESBL-producing E. coli isolates within 11 strains co-expressing the blaSHV gene and 8 strains co-expressing the blaTEM gene. Sequence analysis showed frequent diversity in CTX-M-group-1, with blaCTX-M-15 being the most predominant (n = 11), followed by blaCTX-M-1 (n = 5). The blaCMY-2 gene was detected only in one ESBL/pAmpC isolate. Among the 183 tested isolates, various antimicrobial resistance genes were found (number of strains) blaTEM (n = 121), blaSHV (n = 12), tetA (n = 100), tetB (n = 29), sul1(n = 67), sul2 (n = 32), qnrS (n = 45), qnrB (n = 10), qnrA (n = 1), catA1(n = 13), aac-(6′)-Ib (n = 3). Furthermore, class 1 and class 2 integrons were found in 113 and 2 E. coli, respectively. The isolates were classified into multiple phylogroups, including A (35 %), B1 (27.5 %), B2 and D each (18.75 %). The detection of integrons and different classes of resistance genes in the faecal carriage of healthy poultry production indicates that commensal E. coli could potentially act as a reservoir for antimicrobial resistance, posing a significant One Health challenge encompassing the interconnected domains of human, animal health and the environment. Here, we present the first investigation to describe the diversity of blaCTX-M producing E. coli isolates with widespread detection of CTX-M-15 and CTX-M-1 in healthy breeders (Broiler and breeding hens) in Eastern Algeria