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Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30  T and Flavobacterium bizetiae, 99.0 % for strain F-65  T and Flavobacterium branchiarum, 98.7 % for strain F-126  T and Flavobacterium tructae, 98.2 % for strain F-323  T and Flavobacterium cupreum while 99.7 % identity level was detected for strain F-70  T and Flavobacterium geliluteum. In addition, strains F-33, Fl-77, and F-70  T shared 100 % identical 16S rRNA genes, while strains F-323  T and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus Flavobacterium. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30  T , F-65  T , F-70  T , F126 T and F-323  T represent five novel species within the genus Flavobacterium for which Flavobacterium piscisymbiosum sp. nov. F-30  T (=JCM 34194  T  = KCTC 82254  T ), Flavobacterium pisciphilum sp. nov. F-65  T (=JCM 34197  T  = KCTC 82257  T ), Flavobacterium flavipigmentatum sp. nov. F-70  T (Fl-33 = Fl-77 = JCM 34198  T  = KCTC 82258  T ), Flavobacterium lipolyticum sp. nov. F-126  T (JCM 34199  T  = KCTC 82259  T ) and Flavobacterium cupriresistens sp. nov. F-323  T (Fl-318 = JCM 34200  T  = KCTC 82260  T ), are proposed., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Our study focused exclusively on analyzing Escherichia coli ( E. coli ) contamination in fresh raw mussels and ready-to-eat (RTE) stuffed mussels obtained from authorized and regulated facilities. However, it is critical to recognize that such contamination represents a significant public health threat in regions where unauthorized harvesting and sales practices are prevalent. This study aimed to comprehensively assess the prevalence, molecular characteristics, and antibacterial resistance profiles of E. coli in fresh raw mussels and RTE stuffed mussels. E. coli counts in fresh raw mussel samples ranged from 1 to 2.89 log CFU/g before cooking, with a significant reduction observed post-cooking. RTE stuffed mussel samples predominantly exhibited negligible E. coli presence (<1 log CFU/g). A phylogenetic analysis revealed a dominance of phylogroup A, with variations in the distribution observed across different sampling months. Antibacterial resistance was prevalent among the E. coli isolates, notably showing resistance to ampicillin, streptomycin, and cefotaxime. Extended-spectrum β-lactamase ( ESβL ) production was rare, with only one positive isolate detected. A variety of antibacterial resistance genes, including tetB and sul1 , were identified among the isolates. Notably, virulence factor genes associated with pathogenicity were absent. In light of these findings, it is imperative to maintain rigorous compliance with quality and safety standards at all stages of the mussel production process, encompassing harvesting, processing, cooking, and consumption. Continuous monitoring, implementation of rigorous hygiene protocols, and responsible antibacterial drug use are crucial measures in mitigating food safety risks and combating antibacterial resistance. Stakeholders, including seafood industry players, regulatory agencies, and healthcare professionals, are essential to ensure effective risk mitigation and safeguard public health in the context of seafood consumption.

Flavobacterium psychrophilum, a devastating fish pathogen, is responsible for bacterial cold-water disease (BCWD), also known as rainbow trout fry syndrome. F. psychrophilum is the main causative agent of outbreaks in rainbow trout farms, especially at early live stages. In the present study, we aimed to characterize F. psychrophilum Turkish isolates. Eighteen isolates were retrieved from BCWD outbreaks between 2014 and 2021. In vitro phenotypic characterization showed gelatin and casein hydrolysis capacities and in vitro adhesion for all isolates, whereas elastinolytic activity was present for 16 of 18 isolates. We used complete genome sequencing to infer MLST-type, serotype and phylogenetic reconstruction. Strikingly, one strain isolated from Coruh trout (FP-369) belongs to ST393, a previously undescribed ST, and is phylogenetically distant from the other isolates. However, all strains retrieved from rainbow trout belong to the well-characterized clonal complex CC-ST10, 12 of 17 were tightly connected in a single cluster. Several serotypes (Types -1, -2 and -3) were represented among isolates, but no correlation was observed with geographic origins. This analysis suggests a regional dissemination of an epidemic, disease-producing bacterial population. This study provides a basis for epidemiological surveillance of isolates circulating in Turkey and phenotypic data for future molecular studies of virulence traits of this important fish pathogen., (© 2024 The Authors. Journal of Fish Diseases published by John Wiley & Sons Ltd.)

Two yellow-coloured strains, F-29 T and F-340 T , were isolated from fish farms in Antalya and Mugla in 2015 and 2017 during surveillance studies. The 16S rRNA gene sequence analysis showed that both strains belong to the genus Flavobacterium . A polyphasic approach involving a comprehensive genome analysis was employed to ascertain the taxonomic provenance of the strains. The overall genome-relatedness indices of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genus Flavobacterium were found to be well below the established thresholds of 70 and 95 %, respectively. The whole-genome-based phylogenetic analysis revealed that strain F-29 T is closely related to Flavobacterium granuli (dDDH 39.3 % and ANI 89.4 %), while strain F-340 T has a close relationship with the type strain of Flavobacterium pygoscelis (dDDH 25.6 % and ANI 81.5 %). Both strains were psychrotolerant with an optimum growth temperature of 25 °C. The chemotaxonomic characteristics of the strains were typical of the genus Flavobacterium . Both strains had phosphatidylethanolamine, aminolipids and unidentified lipids in their polar lipid profile and MK-6 as the isoprenoid quinone. The major fatty acids were iso-C 15 : 0 and anteiso-C 15 : 0 . The genome size of the strains was 3.5 Mb, while G+C contents were 35.3 mol% for strain F-29 T and 33.4 mol% for strain F-340 T . Overall, the characterizations confirmed that both strains are representatives of two novel species within the genus Flavobacterium , for which the names Flavobacterium acetivorans sp. nov. and Flavobacterium galactosidilyticum sp. nov. are proposed, with F-29 T (JCM 34193 T =KCTC 82253 T ) and F-340 T (JCM 34203 T =KCTC 82263 T ) as the type strains, respectively.

Helicobacter pylori is a pathogen associated with gastroduodenal diseases. This study aimed; (i) to investigate H. pylori presence by invasive tests in adult dyspeptic patients, (ii) to determine antibiotic susceptibility and genotypic characteristics of the H. pylori isolates, and (iii) to investigate the relationship between the H. pylori genotypes and the histopathological findings. In this cross-sectional study, gastric biopsy samples from 208 adult dyspeptic patients were used for culture, tissue Polymerase Chain Reaction (PCR), and histopathological analysis. Antibiotic susceptibility of the H. pylori isolates was analyzed by gradient method. Analysis of the virulence genes was performed by monoplex PCR. Genetic profiles (from A to H) were created based on the virulence genes presence. Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) was used for the genotyping of the H. pylori isolates. The mean age of the patients was 46 (± 15) years and 128 (61.5%) of them were female. H. pylori positivity was detected by culture, tissue PCR and histopathological examination in 59 (28.4%), 114 (54.8%) and 81 (38.9%) patients, respectively. The overall prevalence of H. pylori was found to be 63% (131/208). All H. pylori isolates were susceptible to tetracycline and amoxicillin. The resistance rates for metronidazole, clarithromycin, levofloxacin, and rifampicin were 67.2%, 27.9%, 34.4% and 13.11%, respectively. Multi drug resistance (MDR) was detected at the rate of 45.9% (28/61). While the most common virulence gene was cagA (93.44%), the least common was vacAm1 (23%). The predominant genetic profile was profile A (47.5%). ERIC-PCR results revealed a total of 26 different patterns. A high prevalence of H. pylori was detected in adult dyspeptic patients as in developing countries. It was observed significant genotypic heterogeneity and virulence gene diversity within the isolates. A considerable resistance rate detected against antibiotics such as clarithromycin, metronidazole, and levofloxacin, which are frequently used in the eradication of H. pylori, should be taken into consideration when creating regional empirical treatment regimens., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

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., (© 2023 The Authors. Journal of Fish Diseases published by John Wiley & Sons Ltd.)

Brucellosis is a chronic disease caused by Brucella species with a wide range of hosts, from marine mammals to terrestrial species, but with strict host preferences. With the zoonotic character, the prevalence of human brucellosis cases is a reflection of animal infections. This study aimed to identify 192 Brucella isolates obtained from various sources by Bruce-ladder PCR and to determine their antibiotic susceptibilities by gradient diffusion method (E-test). As a result of the PCR, all human isolates (n = 57) were identified as B. melitensis. While 58 (82.9%) of the cattle isolates were identified as B. abortus, 59 (90.8%) of the sheep isolates were identified as B. melitensis. In addition, 12 (17.1%) of the cattle isolates and 6 (9.2%) of the sheep isolates were determined as B. melitensis and B. abortus, respectively. The primary host change behavior of B. melitensis was 1.9 times higher than that of B. abortus. While gentamicin and ciprofloxacin susceptibilities of Brucella isolates were 100%, tetracycline, doxycycline, streptomycin, trimethoprim/sulfamethoxazole and rifampicin susceptibilities were 99%, 99%, 97.4%, 91.7% and 83.9%, respectively. The lowest sensitivity of the isolates was determined against to cefoperazone as 26%. A triple-drug resistance was detected in 1 B. abortus isolate that included simultaneous resistance to cefoperazone, rifampicin, and trimethoprim/sulfamethoxazole. The high susceptibility profiles we found against to antibiotics such as tetracycline, doxycycline gentamicin and ciprofloxacin, used widely in treatment, are encouraging. However, the change in the canonical Brucella species-primary host preference suggests the need to reconsider eradication program, including updating vaccine formulations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

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.

The strain M-43 T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43 T . The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25 T , M. odoratimimus subsp. odoratimimus CCUG 39352 T and M. odoratimimus subsp. xuanwuensis DSM27251 T , respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43 T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43 T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251 T , M. profundi D25 T , and M. odoratimimus subsp. odoratimimus ATCC BAA-634 T , were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43 T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C 15:0 and summed feature 9 (iso-C 17:1 ω9c and/or 10-methyl C 16:0 ). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43 T as the type strain (JCM 34205 T  = KCTC 82265 T )., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Four strains, designated as C-2, C-17 T , C-39 T 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-17 T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089 T while strains C-2, C-39 T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775 T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17 T , C-39 T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17 T and C-39 T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C 15:0 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 secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17 T and C-39 T 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-17 T (=JCM 34190 T  = KCTC 82250 T ) and C-39 T (=JCM 34191 T  = KCTC 822251 T ), respectively, are proposed., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

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  = DSM 112312 T ) and faydin-H23 T (=LMG 32236 T  = CECT 30508 T ) as respective type strains., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

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 ω8 c , C 15 : 0 iso, and summed feature 3 (C 16 : 1 ω6 c and/or C 16 : 1 ω7 c ). 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 ).

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 gyr A and atp A 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-H70 T as the type strain (=DSM 112556 T =LMG 32335 T ).

Seventy-four Gram-negative, motile, slightly curved rod-shaped, microaerophilic, oxidase-positive and catalase-negative isolates, recovered from fecal samples of the Anatolian ground squirrel (Spermophilus xanthoprymnus) in Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that all isolates belonged to the genus Campylobacter. 16S rRNA gene sequence analyses revealed the closest match as Campylobacter curvus DSM 6644 T with identity levels of 96.41-96.70%. Based on the 16S rRNA gene phylogeny of the 74 isolates, six isolates (faydin-G24, faydin-G52, faydin-G105, faydin-G114, faydin-G129 and faydin-G140 T ) were chosen as representatives for further characterization. The overall genome relatedness indices for the strain faydin-G140 T , compared to the most closely related type strain C. curvus ATCC 35224 T , were calculated as 15.2%, 72.5%, and 83.7% for digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANIb and ANIm), respectively. The G+C content and genome size of the strains ranged between 35.2-35.4 mol% and 1.7-1.8 Mb, respectively. Based on data obtained from the polyphasic taxonomy approach, including phenotypic characterization as well as genomic and chemotaxonomic analyses, these strains are concluded to represent a novel species, for which the name Campylobacter anatolicus sp. nov. is proposed with faydin-G140 T as the type strain (=DSM 112311 T  = LMG 32238 T )., (Copyright © 2021 Elsevier GmbH. All rights reserved.)

During a study aiming at isolation and genomic characterization of non-pathogenic fish symbionts, strain F-328 T was isolated from skin mucus of healthy-seeming rainbow trout (Oncorhynchus mykiss) and subjected to polyphasic characterization, including a comprehensive genome analysis. Strain F-328 T was Gram stain negative, none-gliding, strictly aerobic, and rod shaped. The 16S rRNA gene sequence of strain F-328 T exhibited the highest level of identity (98.9%) with F. turcicum F-339 T . The major fatty acids were iso-C 15:0 , C 15:1 ω6c, and summed feature 3 (C 16:1 ω7c, C 16:1 ω6c). The polar lipid profile consisted mainly of phosphatidylethanolamine and aminolipids, while the predominant menaquinone was MK-6. The DNA G + C content and genome size of the strain were 35.3% and 3.4 Mb, respectively. Strain F-328 T shows 93.8% average nucleotide identity and 53% digital DNA-DNA hybridization identity with the closest type strain F. turcicum F-339 T . In addition, strain F-328 T was found to carry antimicrobial resistance genes, which confer resistance to several antimicrobials, including aminoglycoside, macrolides, and streptogramin. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain F-328 T should be classified as a novel species of the genus Flavobacterium for which the name Flavobacterium erciyesense sp. nov. is proposed, with F-328 T as the type strain (= JCM 34201 T  = KCTC 82261 T )., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Two yellow-pigmented isolates, F-60 T and F-392, were isolated from the internal organs of an apparently healthy rainbow trout ( Oncorhynchus mykiss ). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60 T and F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain of Flavobacterium crassostreae LPB0076 T . A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium . Digital DNA-DNA hybridization (dDDH) and average nucleotide identity based on blast (ANIb) values for strains F-60 T and F-392 were calculated as 100 %. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium . The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623 T while those values for F. crassostreae LPB0076 T were obtained as 21.4-21.5 % and 76.3 %. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60 T as the type strain (=JCM 34196 T =KCTC 82256 T ).

Cells of strains P66 T , V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66 T was isolated from rainbow trout ( Oncorhynchus mykiss ) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica . The major fatty acid components were C 16:0 (29.91-31.68 %) and summed feature 3 (36.44-37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P. putida group of species. Genome comparisons by the average nucleotide identity based on blast and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas . These data permitted us to conclude that strains P66 T , V1 and W15Feb18 belong to a novel species in the genus Pseudomonas , for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66 T (=CECT 30176 T =CCUG 74872 T ). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).

During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47 T , F-339 T , F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47 T and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719 T while strains F-339 T and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2 T . A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47 T , F-339 T and their close neighbours F. frigoris DSM 15719 T and F. caseinilyticum AT-3-2 T , respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47 T and F-339 T are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47 T and F-339 T represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47 T (=JCM 34195 T =KCTC 82255 T ) and Flavobacterium turcicum sp. nov. F-339 T (=JCM 34202 T =KCTC 82262 T ) are proposed, respectively., (Copyright © 2021 Elsevier GmbH. All rights reserved.)

The present study was aimed at determining antimicrobial susceptibility by a CLSI standard microdilution testing protocol and detecting the resistance genes of motile Aeromonas species isolated from cultured fish. The importance of the minimum inhibitory concentrations was assessed based on statistically determined epidemiological cut-off values calculated by normalized resistance analysis. Unfortunately, CLSI epidemiological cut-off values are available only for Aeromonas salmonicida, and there is no further detailed data on Aeromonas isolated from aquatic animals. The antimicrobial susceptibilities of pre-identified motile Aeromonas species to florfenicol, tetracycline and sulfamethoxazole were determined by calculating epidemiological cut-off values with fully automated and freely available Excel spreadsheets, applying the normalized resistance interpretation (NRI) method. Furthermore, the presence of the antimicrobial resistance genes floR, tetA, tetB, tetC, tetD, tetE, tetH, sulI, sulII and sulIII was detected by PCR analysis and confirmed by sequence analysis. The presence of up to six different genes (multiple antimicrobial resistance) was determined in the Aeromonas isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: Significance and Impact of the Study: In this study, we investigated phenotypic and genotypic antimicrobial resistance characteristics by a novel method based on epidemiological cut-off values. This is the second comprehensive study on the antimicrobial susceptibility characteristics of Aeromonas species using NRI and epidemiological cut-off values. The present research is related to our previous researches focussed on the identification of motile Aeromonads, their prevalence in relation to different fish lengths, seasons and regions, and covered the investigation of Lactococcus garvieae, Yersinia ruckeri, Flavobacterium spp., Enterobacter spp. and Citrobacter spp., (© 2020 The Society for Applied Microbiology.)

A study of 91 isolates from fish farms in Turkey showed that isolates P7 T , P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalis and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7 T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16-88.29% and 38.10-38.20%, respectively. These data confirm that isolates P7 T , P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7 T as a type strain (=CCUG 74260 T = and CECT30107 T )., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Six Gram negative, motile bacteria were isolated from rainbow trout ( Oncorhynchus mykiss ). The 16S rRNA sequence similarity values grouped them in the Pseudomonas mandelii (strains P49, P50 T , 154a T and P154b), Pseudomonas fluorescens (strain P115 T ) and Pseudomonas koreensis (strain P155 T ) phylogenetic subgroups in the genus Pseudomonas . The DNA G+C content ranged from 58.5 to 60 mol%. The strains were characterized phenotypically using API 20NE and Biolog GENIII tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. Multi-locus sequence analysis with four housekeeping gene sequences ( rpoD , rpoB , gyrB and 16S rRNA) together with genome comparisons by average nucleotide identity and genome-to-genome distance calculations were performed. Results showed that the similarity values of these strains to known species type strains were lower than the thresholds established for species in the genus Pseudomonas . Based on these data, we concluded that strains P49, P50 T , P115 T , P154a T , P154b and P155 T belonged to four novel species. The names proposed are: Pseudomonas piscium sp. nov. for strains P49 and P50 T with P50 T (=CECT 30175 T =CCUG 74871 T ) as the type strain; Pseudomonas pisciculturae sp. nov. for strain P115 T (CECT 30173 T =CCUG 74873 T ) ; Pseudomonas mucoides sp. nov. for strains P154a T and P154b with P154a T (=CECT 30177 T =CCUG 74874 T ) as the type strain; and Pseudomonas neuropathica sp. nov. for strain P155 T (=CECT 30178 T =CCUG 74875 T ).

Fecal contaminants are a major public concern that directly affect human health in the fish production industry. In this study, we aimed to determine the fecal coliform, spoilage bacteria, and antimicrobial-resistant bacterial contamination in rainbow trout ( Oncorhynchus mykiss) farms. Fish were sampled from rainbow trout farms that have a high production capacity and are established on spring water, stream water, and dammed lakes in six different regions of Turkey. A total of seven Enterobacter subspecies, two strains of Pseudomonas spp., and one isolate each of Morganella and Stenotrophomonas were characterized based on biochemical and molecular methods, including the 16S rRNA and gyr B housekeeping gene regions. The sequencing results obtained from the 16S rRNA and gyr B gene regions were deposited in the GenBank database and compared with isolates from different countries, which were registered in the database. Resistance to 10 different antimicrobial compounds was determined using the broth microdilution method, and molecular resistance genes against florfenicol, tetracycline, and sulfamethoxazole were identified by PCR. All detected resistance genes were confirmed by sequencing analyses. E. cloacae , E. asburiae , Pseudomonas spp., S. maltophilia, and M. psychrotolerans were identified using the gyr B housekeeping gene, while isolates showed different biochemical characteristics. All isolates were found to be phenotypically resistant to sulfamethoxazole, and some isolates were resistant to tetracycline, florfenicol, amoxicillin, and doxycycline; the resistance genes of these isolates included flo R, tet C, tet D, and tet E. We showed that fecal coliforms, spoilage bacteria, and antimicrobial resistant bacteria were present in farmed rainbow trout, and they pose a threat for human health and must be controlled in the farming stage of fish production., Competing Interests: We have no conflicts of interest to declare.

The aims of this study were to determine the prevalence and phylogenetic relationship of motile Aeromonas spp. that might be pathogenic species for rainbow trout in infected/mix infection cases (based upon different outbreaks on fish farms). A total of 99 motile Aeromonas isolates (and three reference strains) were analysed that were isolated from four different fish species in different sizes of fish (0.1-3,000 g), different months and water temperatures (6.1-21.2°C). The biochemical characteristics of the isolates were determined using conventional tests and a rapid test kit. Additionally, molecular identification was performed using the gyrB housekeeping gene region and with glycerophospholipid-cholesterol acyltransferase polymerase chain reaction (GCAT-PCR). The sequencing results obtained from the gyrB gene region were deposited in the GenBank database, and phylogenetic relationships were determined with the BioNumerics 7.6 database. Nearly half of the Aeromonas isolates that were isolated from rainbow trout showing signs of disease were determined to be possible infectious agents. Aeromonas species exhibit biochemical variability for many characters, so some Aeromonas species tested negative for GCAT-PCR despite that this test was created especially for Aeromonas identification. The phylogenetic tree based upon gyrB contained 10 different phylogroups that were based on 96% cut-off value in gyrB gene region., (© 2018 John Wiley & Sons Ltd.)

Turkey was the largest rainbow trout producer of the European countries in 2016, and the reason for this production is mainly attributed to its egg and fry production. Flavobacterium psychrophilum cause the highest rates of mortality in the starting to feeding stages of the fish. In the present study, twenty-five F. psychrophilum isolates recovered from rainbow trout, coruh trout and brook trout were analysed by RAPD-PCR, ERIC-PCR, REP-PCR and PCR-RFLP, including 16S rRNA, gyrA and gyrB gene regions and PCR-based serotyping method. The PCR-based molecular analysis showed that the isolates could not be differentiated exactly according to isolation source and geographical region. Most isolates were of type-1 and type-2, and some of them were of type-0 and type-3; in addition, one isolate showed a unique serotype. The combined analysis results showed that F. psychrophilum isolates discriminated as five different genotypes and all isolates were successfully discriminated based on host., (© 2018 John Wiley & Sons Ltd.)

Aquaculture has become an important candidate as an animal protein source through its growth over the last decade. Based upon a report from the Food and Agriculture Organization of the United Nations, it is the fastest growing sector of the food industry, yet the pathogenicity of many biological agents involved in aquaculture is still unknown. In this study, we isolated Pantoe agglomerans from diseased rainbow trout on several occasions and also attempted to determine their phenotypic and genotypic characteristics, including antimicrobial resistance, of four bacterial isolates. In the present study, P. agglomerans was isolated from diseased rainbow trout as a pathogenic agent. The identification of the P. agglomerans isolates from the rainbow trout was performed through biochemical tests and 16S rRNA sequence analysis. These isolates were predominately biochemically homogeneous, although some features were different, such as seen in methyl-red, mannose and lipase activity tests. All four studied isolates were identified as 99% identical to P. agglomerans based on sequence analysis. The isolates were compared through a phylogenetic analysis with P. agglomerans sequences recovered from 16 other countries and accessed from the GenBank database. All isolates in our study were at least 98.2% similar to sequences from GenBank. Furthermore, the phenotypic antimicrobial susceptibility of the isolates in this study was analyzed through both disc diffusion and broth micro dilution minimum inhibitory concentration (MIC) tests. Although there were some differences between two phenotypic antimicrobial tests, all studied isolates were found susceptible to different antimicrobials. In addition genotypic antimicrobial resistance characteristics were assessed by the presence of antimicrobial resistance genes (ARGs), in which qnrS and sul2 were detected for the first time in P. agglomerans., (Copyright © 2018. Published by Elsevier Ltd.)

Aim: Over the last decade, Citrobacter species have been responsible for infections in fish and many species and also new Citrobacter species have been identified. In this study, molecular identifications and the phenotypic and genotypic antimicrobial-resistance characteristics of atypical and typical Citrobacter species were determined., Materials and Methods: Seven Citrobacter isolates were investigated from rainbow trout of different lengths with signs of disease. Biochemical characteristics were determined using conventional tests and rapid test kits; moreover, molecular identifications were conducted with 16S rRNA and the gyrB housekeeping gene region. The sequencing results obtained from the gyrB gene region were deposited in the GenBank database and compared with isolates from different countries that were registered in the database. Resistances to florfenicol, sulfonamides, and tetracycline antimicrobials were determined using the broth micro dilution method, and molecular resistance genes against these antimicrobials were identified. All detected resistance genes were confirmed by sequence analyses., Results: It was determined that three of the Citrobacter species with biochemical characteristics were atypical and showed oxidase-positive reactions. All the Citrobacter species were identified as Citrobacter sp. using the 16S rRNA gene; three isolates were identified as Citrobacter gillenii and four as Citrobacter sp. based on gyrB gene sequence analysis. Some isolates were found in the same group as other countries' isolates in the GenBank database, while isolates with high identities were found in different genogroups. All isolates were found to be phenotypically resistant to sulfamethoxazole and susceptible to tetracycline; these isolates' resistance genes included sulI, tetA, tetB, and tetD., (Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)