Population genetic and evolution analysis of Vibrio isolated from Turkish fish farms

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 applicationsThis research was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) [No: 118O420]. This research was carried out in accordance with the ethical standards of the 2012-14/04 Local Ethics Commission report. We are pleased to Dollvet Veterinary Vaccine Pharmaceutical Biological Substance Production Industry and Trade Inc. for supporting us with strainsS

Epidemiology of pemphigus in Turkey: One-year prospective study of 220 cases

Pemphigus is a group of rare and life-threatening autoimmune blistering diseases of the skin and mucous membranes. Although they occur worldwide, their incidence shows wide geographical variation, and prospective data on the epidemiology of pemphigus are very limited. Objective of this work is to evaluate the incidence and epidemiological and clinical features of patients with pemphigus in Turkey. All patients newly diagnosed with pemphigus between June 2013 and June 2014 were prospectively enrolled in 33 dermatology departments in 20 different provinces from all seven regions of Turkey. Disease parameters including demography and clinical findings were recorded. A total of 220 patients were diagnosed with pemphigus during the 1-year period, with an annual incidence of 4.7 per million people in Turkey. Patients were predominantly women, with a male to female ratio of 1:1.41. The mean age at onset was 48.9 years. Pemphigus vulgaris (PV) was the commonest clinical subtype (n=192; 87.3%), followed by pemphigus foliaceus (n=21; 9.6%). The most common clinical subtype of PV was the mucocutaneous type (n=83; 43.2%). The mean Pemphigus Disease Area Index was 28.14±22.21 (mean ± Standard Deviation).  The incidence rate of pemphigus in Turkey is similar to the countries of South-East Europe, higher than those reported for the Central and Northern European countries and lower than the countries around the Mediterranean Sea and Iran. Pemphigus is more frequent in middle-aged people and is more common in women. The most frequent subtype was PV, with a 9-fold higher incidence than pemphigus foliaceus.   </p

Molecular characterization and antimicrobial resistance profile of fecal contaminants and spoilage bacteria that emerge in rainbow trout (Oncorhynchus mykiss) farms

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 gyrB housekeeping gene regions. The sequencing results obtained from the 16S rRNA and gyrB 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 gyrB 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 floR, tetC, tetD, and tetE. 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

Identification and Genotyping of Chryseobacterium aquaticum isolated from farmed salmonids showing clinical disease signs in Turkey

Flavobacterial diseases in fish are caused by multiple bacterialspecies within the family Flavobacteriaceaeand are responsible for devastating losses in wild and farmed fish stocks aroundthe world. With therecent advances in molecular biology, several novel genera within the family Flavobacteriaceae (e.g., Chryseobacterium, Elizabethkingia and Tenacibaculum) have emerged that encompass pathogens of fish, amphibians,reptiles, birds, and mammals, including humans1. Members of thegenus Chryseobacterium have emergedas serious fish pathogens on multiple continents. During the last ten yearsalone, numerous novel Chryseobacteriumspp., including C. piscicola2,C. chaponense3, C. viscerum4, and C. oncorhynchi5 were described and recovered from systemicallyinfected fishes exhibiting clinical disease signs worldwide1. Theobjective of this study was to identify and genotyping of C. aquaticum isolates in rainbow trout. Herein, twenty-seven, C. aquaticum isolates recovered fromfarmed rainbow trout exhibiting clinical signs such as darkening of skin color,exophthalmia, and caudal fin root. The identification of the isolates was performed through biochemical tests and 16SrRNA sequence analysis with using 27F and 1387R universal primers. The isolateswere compared through a phylogeneticanalysis with C. aquaticum sequences accessedin GenBank which were isolated from rainbow trout in Iran and water isolates inNew Zealand and South Korea6. We report that our C. aquaticum isolates were found to have close relationship betweeneach other. Also, the isolates of Iran and South Korea showed 99.5% similaritywith our isolates.&nbsp;In conclusion, this is the first report of C. aquaticum recovered from rainbowtrout in Turkey. Its pathogenicity wasnot assessed previously.1 Further research is needed to determiningthe virulence mechanisms and pathogenesis of C. aquaticum.&nbsp;</p

Genome analysis and antimicrobial resistance characteristics of Chryseobacterium aquaticum isolated from farmed salmonids

© 2021 Elsevier B.V.Fish diseases caused by bacterial genera belonging to the family Flavobacteriaceae, especially Tenacibaculum, Flavobacterium, and Chryseobacterium, are responsible for losses in wild and farmed fish around the world. In the last decade, the genus Chryseobacterium has rapidly grown in parallel with numerous novel Chryseobacterium species described from systemic infections of fish. Members of the family Flavobacteriaceae, isolated from fish, the environment, and clinical samples, have been reported to show low susceptibility to a broad range of antimicrobials. In this study, seventy C. aquaticum strains were isolated from diseased salmonids in Turkey. The phylogenetic analysis of all C. aquaticum strains, together with the reference strains in GenBank, which were obtained from different sources, including fish, plants, soil, water, and other animals, was performed by 16S rRNA gene sequence analysis. The antimicrobial susceptibility of each C. aquaticum strain was determined by a minimum inhibitory concentration (MIC) test. The isolate with the highest level of antimicrobial resistance, strain C-174, underwent a more detailed whole-genome sequence analysis for virulence and antimicrobial resistance genes (AMR) genes, genome size, and guanine-cytosine (GC) content. Phylogenetically, the 70 strains isolated from Turkey were assigned to three genogroups. Strains previously recovered from the rainbow trout, brown trout, and Siberian sturgeon were genetically very close to our strains. Most of the strains isolated in this study grew even in the presence of high concentrations of the tested antimicrobials, excluding enrofloxacin. Strain C-174 carried 74 putative functional genes encoding AMR and virulence. The number of putative AMR genes detected in the genome of strain C-174 was 46. The regulatory mechanisms of these genes involve antibiotic efflux (13), antibiotic target alteration (17), antibiotic inactivation (7), antibiotic target replacement (3), and antibiotic target protection (6). AMR genes confer resistance to multiple antibiotic groups, including among others, macrolides, fluoroquinolones, beta-lactams, tetracyclines, phenicols, sulphonamides, and diaminopyrimidines. We concluded that antimicrobial resistance could be of intrinsic nature. Furthermore, we detected three putative virulence genes in the genome of strain C-174 that have not been reported for C. aquaticum before. The results of this study demonstrated a strong correlation between these genes in the genome of C-174 and mortality in the rainbow trout

Identification of the new Pseudomonas species for aquaculture and important biochemical characteristics

Introduction: The genus Pseudomonas is one of the most complex Gram-negative bacterialgenera as it currently is the genus with the largest number of species. While Pseudomonas causesevere disease for humans, the incidence or transmission route not known very well from aquacultureto humans. Recently, there are many possible novel Pseudomonas species identified,but a few of them identified from fish. In the present study, the identification of Pseudomonasspecies recovered from farmed salmonid species and the determination of the most importantbiochemical characteristics were aimed.Methodology: Pseudomonas species were isolated from farmed salmonids in Turkey, 2013 -2018. The strains were identified by 16S rRNA gene sequence analysis with the similarity indexon NCBI database. Growth condition of Pseudomonas spp. on different salinity, incubationtemperature, distilled and tap water were showed by using Tryptic soy broth media. In addition,the fluorescent pigment and biofilm production were determined by using Pseudomonas selectiveagar and broth media.Results: The Pseudomonas species isolated from rainbow trout (Onchorhynchus mykiss), localtrout species (Salvelinus fontinalis, Salmo trutta magrostigma, Salmo trutta labrax), Carp(Cyrpinus carpio) and also farm water samples. More than ten different Pseudomonas specieswere identified with the similarity of NCBI database such as P. jessenii, P. madelii, P. gessardiiand a number of them are possible for novel species. The most of our isolates could growth on0 - 6% NaCl-TSB medium, distilled and tap water and also 4 - 37 °C incubation temperature.Conclusion: This is the first comprehensive research about Pseudomonas species determinationon aquaculture in Turkey. The identified species were determined in the first time in salmonidsand also some of them are possible novel Pseudomonas species isolated from aquaculture. Alsoour findings showed that the Pseudomonas can growth on distilled and tap water in additionbroad range of salinity and incubation temperature. Thus, the transmission of this agent fromaquaculture to human/animal/environment via water pose a big risk factor.Keywords: Pseudomonas, new species, biochemical characteristicsFunding: Scientific and Technological Research Council (TUBITAK) of Turkey, project number:118O420.</p

Phenotypic, Phylogenetic Characterization and Antimicrobial Susceptibility Determination of Chryseobacterium piscicola Isolates Recovered from Diseased Rainbow Trout

Twelve Chryseobacterium piscicola isolates recovered from rainbow trout weighing1-4 grams showing signs of anorexia, exophthalmos, darkening, and dorsal fin erosion were usedin our study. In addition to conventional microbiological tests, comprehensive phenotypiccharacterization has been performed using the Biolog GENIII microplate. Molecularidentification and characterization were performed using the 16S rRNA region. Antimicrobialsusceptibilities of the isolates were determined using the Kirby-Bauer disk diffusion method. Ourisolates were identified as C. piscicola in molecular identification performed by sequence analysisbased on the 16S rRNA region. In a phylogenetic analysis of our isolates, obtained from threedifferent hosts in America, Chile, and Finland, five genogroups were determined with highsimilarity rate. Isolates from Finland, Chile, the United States, and Turkey (only C-316) werefound in the same genogroup. It was determined that the phylogenetic analysis created with the16S rRNA region could not distinguish the host from which the bacteria was isolated. Thephenotypic characterization of six representative isolates selected according to phylogeneticanalysis was determined with the Biolog GENIII microplate. Based on the Biolog GENIII resultsof the representative isolates, the results of 40 out of 94 tests were found to be variable. With thisresult, it was found that C. piscicola isolates were not phenotypically homogeneous. Besides, itwas found that the zone diameters of our isolates against florfenicol, enrofloxacin, andsulfamethoxazole/trimethoprim</p