Browsing by Author "SATICIOĞLU, İZZET BURÇİN"

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A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022
(Wiley, 2023-10-30) Duman, Muhammed; Altun, Soner; Satıcıoğlu, İzzet Burçin; Romalde, Jesus L.; DUMAN, MUHAMMED; ALTUN, SONER; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0002-2721-3204; AAD-4156-2019; AAG-8518-2021; T-1697-2019
Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram-negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram-positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.
Description of a novel fish pathogen, plesiomonas shigelloides subsp. oncorhynchi , isolated from rainbow trout ( oncorhynchus mykiss ): First genome analysis and comparative genomics
(Mdpi, 2023-04-01) Valdes, Elena Garcia; Ay, Hilal; Altun, Soner; SATICIOĞLU, İZZET BURÇİN; DUMAN, MUHAMMED; Duman, Muhammed; Altun, Soner; ALTUN, SONER; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; 0000-0001-7707-2705; 0000-0002-2721-3204; AAD-4156-2019
Plesiomonas shigelloides is the only species in its genus, and has zoonotic importance due to the serious implications resulting from the consumption of contaminated seafood. This is the first report on the genomic features of the whole-genome sequence (WGS) of P. shigelloides strain V-78, recovered from diseased rainbow trout, Oncorhynchus mykiss. The genome of P. shigelloides V-78 consists of 4,478,098 base pairs (bp), which encode 3730 proteins, and has a G + C content of 51.1%. The bioinformatics analysis of WGS of V-78 confirmed the presence of 121 tRNA genes and 42 rRNA genes (15 genes for 5S rRNA, 13 genes for 16S rRNA, and 14 genes for 23S rRNA). Comprehensive genome analyses revealed that the strain encodes for secondary metabolites, antimicrobial resistance, and virulence genes. The strain V-78 has 31 known antibiotic resistance models, which encode many antimicrobial resistances. In addition, strain V-78 has 42 different virulence genes, such as adhesion, secretion system, and motility. The digital DNA-DNA hybridization value against P. shigelloides NCTC 10360 was 74.2%, while the average nucleotide identity value was 97.1%. Based on the scrutinized analysis of genomic data, strain V-78 should be considered a novel subspecies of P. shigelloides, for which Plesiomonas shigelloides subsp. oncorhynchi is proposed.
Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds
(Elsevier Gmbh, 2022-05-13) Aydın, Fuat; Ay, Hilal; Kayman, Tuba; Karakaya, Emre; Abay, Seçil; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu; AAD-4156-2019
A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5-98.6% to H. mustelae ATCC 43772(T), while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478(T). Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8(T), faydin-H23(T) and their close neighbors H. anseris MIT 04-9362(T) and H. pametensis ATCC 51478(T), respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8(T) and faydin-H23(T) are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8(T)(=LMG 32237(T) = DSMZ 112312(T)) and faydin-H23(T)(=LMG 32236(T) = CECT 30508(T)) as respective type strains.
Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds (vol 45, 126326, 2022)
(Elsevier Gmbh, 2022-11-12) Aydın, Fuat; Ay, Hilal; Kayman, Tuba; Karakaya, Emre; Abay, Seçil; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; AAD-4156-2019
A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5-98.6% to H. mustelae ATCC 43772(T), while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478(T). Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8T, faydin-H23(T) and their close neighbors H. anseris MIT 04-9362T and H. pametensis ATCC 51478(T), respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G + C contents of the strains faydin-H8(T) and faydin-H23T are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8T (=LMG 32237(T) = DSM 112312(T)) and faydin-H23(T) (=LMG 32236(T) = CECT 30508(T)) as respective type strains.
General assessment of approaches to the identification of aquatic bacterial pathogens: A methodological review
(Wiley, 2022-08-08) Duman, Muhammed; DUMAN, MUHAMMED; Altun, Soner; ALTUN, SONER; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; 0000-0001-7707-2705; 0000-0002-2721-3204; T-1697-2019; AAD-4156-2019
In the evolving biosphere, pathogenic microorganisms that cause disease may undergo phenotypic changes. While some of these changes result in new variants or mutants, others lead to the emergence of novel pathogens. Such phenotypic changes as well as advances in technology and analytical methods and the identification of genomic sequences of microbial DNA have brought about new methodological approaches in the diagnosis of bacterial diseases. Although bacterial identification was originally based on phenotypic characteristics, later researchers claimed that bacteria could be accurately identified by only gene sequencing and generally by the sequencing of the 16S ribosomal RNA gene region. Currently, there is still disagreement between classical microbiologists and those using new genomic sequence technology over the best method for identification. Fish are cold-blooded animals, and fish pathogens generally exhibit psychrophilic characteristics. Many bacterial identification systems that are used to identify mesophilic bacteria remain useless for identifying fish pathogens because the optimum incubation temperatures for mesophilic bacteria are 35-37 degrees C. Bacteria that are pathogenic to piscine species require specific media for their cultivation at lower incubation temperatures (15-28 degrees C), and this limits both their growth in culture and subsequent identification by phenotype-based methods. This review presents a comprehensive overview of the isolation and identification of bacterial fish pathogens by optimal culture conditions, biochemical tests, colorimetric methods for rapid identification systems, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and immunological and molecular methods, as well as an overview of the detection of uncultivable bacteria and the use of anamnesis. We conclude that the accurate identification of fish pathogens requires the use of different methods, including phenotype- and genotype-based tests, and the evaluation of anamnesis.
Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey
(Elsevier Gmbh, 2022-11-18) Satıcıoğlu, İzzet Burçin; Ay, Hilal; Altun, Soner; Duman, Muhammed; SATICIOĞLU, İZZET BURÇİN; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; AAD-4156-2019; AAG-8518-2021; DYJ-5986-2022
Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic prove-nance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid qui -none and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 - 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to sec-ondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.
Helicobacter turcicus sp. nov., a catalase- negative new member of the helicobacter genus, isolated from anatolian ground squirrel (spermophilus xanthoprymnus) in Turkey
(Microbiology Soc, 2022-01-01) Aydın, Fuat; Karakaya, Emre; Kayman, Tuba; Abay, Seçil; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; 0000-0002-2721-3204; AAD-4156-2019
Eleven Gram-negative, curved and S-shaped, oxidase activity positive, catalase activity negative bacterial isolates recovered from faeces of Anatolian ground squirrel (Spermophilus xanthoprymnus) in the city of Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR revealed that these isolates belonged to the genus Helicobacter. The 16S rRNA gene sequence analysis revealed that the 11 isolates had over 99 % sequence identity with each other and were most closely related to Helicobacter ganmani CMRI H02(T) with 97.0-97.1 % identity levels and they formed a novel phylogenetic line within the genus Helicobacter. Faydin-H64 and Faydin-H70(T) strains were subjected to gyrA and atpA gene and whole genome sequence analyses. These two Helicobacter strains formed separate phylogenetic clades, divergent from other known Helicobacter species. The DNA G+C content and genome size of the strain Faydin-H70(T) were 35.3 mol% and 1.7 Mb, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain Faydin-H70(T) and its close phylogenetic neighbour H. winghamensis ATCC BAA-430(T) were determined as 81.7 and 34.9%, respectively. Pairwise sequence comparison showed that it was closely related to H. ganmani CMRI H02(T) however it shared the highest ANI and dDDH values with H. winghamensis ATCC BAA-430(T). The data obtained from the polyphasic taxonomy approach, including phenotypic characterization and whole-genome sequences, revealed that these strains represent a novel species within the genus Helicobacter, for which the name Helicobacter turcicus sp. nov., is proposed with Faydin-H70T as the type strain (=DSM 112556(T)=LMG 32335(T)).
Investigation of the genus flavobacterium as a reservoir for fish-pathogenic bacterial species: The case of flavobacterium collinsii
(Amer Soc Microbiology, 2023-03-28) Lee, Bo-Hyung; Nicolas, Pierre; Fradet, Benjamin; Bernardet, Jean-Francois; Rigaudeau, Dimitri; Rochat, Tatiana; Duchaud, Eric; Satıcıoğlu, Izzet Burcin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; AAD-4156-2019
Aquaculture has expanded significantly worldwide in the last decades and accounts for half of human fish consumption. However, infectious fish diseases are a major bottleneck for its sustainable development, and an increasing number of bacterial species from diseased fish raise a great concern.Bacteria of the genus Flavobacterium are recovered from a large variety of environments. Among the described species, Flavobacterium psychrophilum and Flavobacterium columnare cause considerable losses in fish farms. Alongside these well-known fish-pathogenic species, isolates belonging to the same genus recovered from diseased or apparently healthy wild, feral, and farmed fish have been suspected to be pathogenic. Here, we report the identification and genomic characterization of a Flavobacterium collinsii isolate (TRV642) retrieved from rainbow trout spleen. A phylogenetic tree of the genus built by aligning the core genome of 195 Flavobacterium species revealed that F. collinsii stands within a cluster of species associated with diseased fish, the closest one being F. tructae, which was recently confirmed as pathogenic. We evaluated the pathogenicity of F. collinsii TRV642 as well as of Flavobacterium bernardetii F-372(T), another recently described species reported as a possible emerging pathogen. Following intramuscular injection challenges in rainbow trout, no clinical signs or mortalities were observed with F. bernardetii. F. collinsii showed very low virulence but was isolated from the internal organs of survivors, indicating that the bacterium is able to survive inside the host and may provoke disease in fish under compromised conditions such as stress and/or wounds. Our results suggest that members of a phylogenetic cluster of fish-associated Flavobacterium species may be opportunistic fish pathogens causing disease under specific circumstances.IMPORTANCE Aquaculture has expanded significantly worldwide in the last decades and accounts for half of human fish consumption. However, infectious fish diseases are a major bottleneck for its sustainable development, and an increasing number of bacterial species from diseased fish raise a great concern. The current study revealed phylogenetic associations with ecological niches among the Flavobacterium species. We also focused on Flavobacterium collinsii, which belongs to a group of putative pathogenic species. The genome contents revealed a versatile metabolic repertoire suggesting the use of diverse nutrient sources, a characteristic of saprophytic or commensal bacteria. In a rainbow trout experimental challenge, the bacterium survived inside the host, likely escaping clearance by the immune system but without provoking massive mortality, suggesting opportunistic pathogenic behavior. This study highlights the importance of experimentally evaluating the pathogenicity of the numerous bacterial species retrieved from diseased fish.
Population genetic and evolution analysis of vibrio isolated from Turkish fish farms
(Elsevier, 2022-08-27) Bujan, Noemi; Romalde, Jesus L.; DUMAN, MUHAMMED; Altun, Soner; ALTUN, SONER; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; 0000-0001-7707-2705; 0000-0003-4786-4773; 0000-0002-2721-3204; T-1697-2019; AAD-4156-2019
The genus Vibrio includes important pathogenic species for human and aquatic organisms such as Vibrio cholera, V. parahaemolyticus, V. vulnificus, V. anguillarum or V. harveyi. At present, Vibrionaceae family consists of > 190 described species, classified into nine genera. Vibrio are widespread in shellfish, finfish and marine ecosystems and show resourceful ecologies, which recognized as one of the most diverse bacterial groups for illuminating the genome evolution. In the present study, to clarify the relationship among aquatic species in the genus, a multilocus sequence analysis (MLSA) and typing (MLST) approach was applied to characterize 51 Vibrio isolates from Turkish fish farms, 146 strains deposited in the PubMLST database and 59 type strains from GenBank. For all studied isolates (n = 256), diversity analysis, population structure, determination of recombination, demographic history and gene flow were performed based on the MLST scheme. Vibrio isolates, subjected to the study, showed a high diversity within the Vibrio population and also genetic interactions into the genus. We found 17 new described sequence types by MLST analysis that were isolated from rainbow trout, sea bream and sea bass in Turkish fish farms, which clearly indicate that the genes underwent recombination frequently. While predominant sequence types were found in the presented study, differences of genotypes need to be evaluated in a disease situation or preventing measurements. The findings about genetic recombination possibly helps to understand differences of Vibrio infections in fish. Furthermore, elucidating of genetic variability within species shed light on providing effective measurements in aquaculture by vaccine production and drug applications.
Shewanella oncorhynchi sp. nov., a novel member of the genus shewanella, isolated from rainbow trout (oncorhynchus mykiss)
(Microbiology Soc, 2022-01-01) Ay, Hilal; ALTUN, SONER; Duman, Muhammed; DUMAN, MUHAMMED; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; 0000-0001-7707-2705; 0000-0002-2721-3204; T-1697-2019; AAG-8518-2021 ; AAD-4156-2019
A strain, S-1(T) was isolated from rainbow trout (Oncorhynchus mykiss) exhibiting clinical symptoms of lens atrophy, inappetence, visual impairment and growth retardation. The strain was identified as representing a member of the genus Shewanella on the basis of the results of 16S rRNA gene sequence analysis. The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences indicated that S-1(T) clustered with Shewanella putrefaciens JCM 20190(T), Shewanella profunda DSM 15900(T), and Shewanella hafniensis P010(T), sharing 99.3, 98.8 and 87.7% 16S rRNA gene similarities, respectively. A polyphasic taxonomic approach including phenotypic, chemotaxonomic, and genomic characterization was employed to ascertain the taxonomic position of S-1(T) within the genus Shewanella. The overall genome relatedness indices (OGRI) for S-1(T) compared with the most closely related type strains S. hafniensis ATCC BAA-1207(T), Shewanella baltica NCTC 10735(T), S. putrefaciens ATCC 8071(T) and S. profunda DSM 15900(T) were calculated as 40.8, 40.1, 28.5 and 27.3% for digital DNA-DNA hybridization (dDDH), and 91.6, 91.0, 86.3 and 85.1% for average nucleotide identity (ANI), respectively. OGRI values between S-1(T) and its close neighbours confirmed that the strain represents a novel species in the genus Shewanella. The DNA G+C content of the strain is 45.2%. Major fatty acids were C-17:1.8 omega 8c, C(15:0)iso, and summed feature 3 (C-16:1 omega 6c and/or C-16:1 omega 7c). The predominant polar lipids were phosphatidylethanolamine, phospholipid, amino-phospholipid and unidentified lipids. The major respiratory quinones were ubiquinone-8, ubiquinone-7 and menaquinone-7. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Shewanella oncorhynchi sp. nov. is proposed, with S-1(T) as the type strain (JCM 34183(T)= KCTC 82249(T)).
Tentative epidemiological Cut-Off values and distribution of resistance genes in aquatic pseudomonas species isolated from rainbow trout
(Springer, 2023-05-01) Duman, Muhammed; Woo, Soo-Ji; Altun, Soner; Satıcıoğlu, İzzet Burçin; DUMAN, MUHAMMED; ALTUN, SONER; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0002-2721-3204; AAD-4156-2019; T-1697-2019; AAG-8518-2021
Epidemiological cut-off value (ECV) analysis for commonly used antimicrobials in aquaculture have not been established for many aquatic pathogens, including Pseudomonas. This study was the first to examine the categorization of 92 aquatic Pseudomonas isolates by calculating seven antimicrobials ECVs using two analytical methods: normalized resistance interpretation and ECOFFinder. Pseudomonas spp. isolates had decreased sensitivity to all antimicrobials examined except for doxycycline and ciprofloxacin. The PCR analysis of the 91 isolates of Pseudomonas spp. detected the tetracycline genes are predominant with the count of 41 genes, including tetA, tetC, tetD, tetM, tetS and tetH, following sulfonamide genes are in 21 isolates including sul1 and sul2, floR gene in 15 isolates and ermA gene in three isolates. Our findings provide an understanding of the antimicrobial categorization of Pseudomonas species, which are significant groups, subgroups, and species for aquaculture due to insufficiently defined breakpoints or cut-off values reported in CLSI and/or EUCAST.