Biodiverziteta patogenih flavobakterij pri šarenkah (Oncorhynchus mykiss) in dinamika okužb v nekaterih slovenskih ribogojnicah

Pavlin, Katarina (avtor), Švara, Tanja (mentor), Ocepek, Matjaž (komentor)

Namen raziskave je bil preučiti biodiverziteto bakterij iz rodu Flavobacterium in etiologijo flavobakterijskih bolezni pri gojeni šarenki (Oncorhynchus mykiss) v Sloveniji v vseh letnih časih, raziskati vpliv okužbe na zdravje rib s kvalitativno in semikvantitativno oceno patoanatomskih in histopatoloških sprememb, določiti občutljivost flavobakterij za protimikrobna zdravila z uporabo standardizirane mikrodilucijske metode ter analizirati korelacije med temperaturo vode, pH in vsebnostjo raztopljenega kisika ter flavobakterijskimi okužbami. Skupno smo vzorčili 540 šarenk, in sicer v dveh ribogojnicah v okviru longitudinalnega vzorčenja v vseh letnih časih ter v dveh drugih ribogojnicah po prijavi povišanega pogina. V raziskavi smo ugotovili prisotnost znanih patogenov Flavobacterium psychrophilum in Flavobacterium branchiophilum pri 23,7 % oziroma 2,04 % rib ter opisali z okužbo povezane patološke spremembe. Poleg tega rezultati nakazujejo, da lahko vrsti F. hercynium in F. hydatis povzročata patološke spremembe pri ribah. Ugotovili smo tudi številne druge manj znane flavobakterije in identificirali 41 potencialno novih vrst, vendar njihova patogenost še ni pojasnjena. Testiranje protimikrobne občutljivosti (AST) je pokazalo, da so bakterije rodu Flavobacterium večinoma multirezistentne. Visok delež izolatov F. psychrophilum je bil zunaj območja divjega tipa za oksitetraciklin in kinolone; poleg tega so izolati imeli visoke minimalne inhibitorne koncentracije (MIC) za ceftazidim in trimetoprim/sulfametoksazol. Vsi izolati so bili divjega tipa za florfenikol. Manj znane vrste flavobakterij so imele visoke MIC za vsaj tri skupine protimikrobnih zdravil, nekatere pa za vseh deset testiranih učinkovin. Prilagoditev standardizirane metode za F. psychrophilum je omogočila uspešno AST F. branchiophilum in drugih za gojenje zahtevnih flavobakterij. Okužbe s F. psychrophilum so bile statistično značilno povezane s povišanim pH vode na dotoku bazena ter zimskim obdobjem. Nasprotno pa so bile okužbe s F. branchiophilum povezane s povišanimi temperaturami vode, znižanjem raztopljenega kisika na iztoku bazena ter poletnim obdobjem. Raziskava prispeva k boljšemu razumevanju flavobakterijskih okužb v slovenskem ribogojstvu, omogoča oblikovanje premišljenih strategij za zdravljenje in obvladovanje bolezni ter predstavlja osnovo za nadaljnje raziskave biodiverzitete flavobakterij in njihovega vpliva na zdravje rib.

• Jezik: Angleški jezik
• Ključne besede: Flavobacterium, masna spektrometrija, ionizacija v matriksu z lasersko desorpcijo – čas preleta ionov (MALDI-TOF MS), sekvenciranje celotnega genoma (WGS), patologija, občutljivost za protimikrobna zdravila, kakovost vode
• Vrsta gradiva: Doktorsko delo/naloga
• Organizacija: VF - Veterinarska fakulteta
• Leto izida: 2025
• PID: 20.500.12556/RUL-174386
• Datum objave v RUL: 02.10.2025

Sekundarni jezik

• Jezik: Slovenski jezik
• Naslov: Biodiversity of pathogenic flavobacteria in rainbow trout (Oncorhynchus mykiss) and dynamics of infections in selected Slovene fish farms

Izvleček

This research aimed to investigate the biodiversity of Flavobacterium species and the aetiology of flavobacterial diseases in Slovene farmed rainbow trout (Oncorhynchus mykiss) throughout all seasons, assess the impact of infection on fish health by qualitative and semiquantitative evaluation of gross and histopathological lesions, determine antimicrobial susceptibility of flavobacteria using the standardised broth microdilution method and evaluate associations between water temperature, pH, dissolved oxygen, and flavobacterial infections. A total of 540 rainbow trout were sampled, namely longitudinally across all seasons in two farms and in two additional farms following mortality reports. We confirmed the presence of two known pathogens, Flavobacterium psychrophilum and Flavobacterium branchiophilum, in 23.7% and 2.04% of fish, respectively, and described associated pathological lesions. Our results also show that F. hercynium and F. hydatis can cause pathological lesions in fish. Numerous other lesser-known flavobacteria and 41 putative new species were identified, although their pathogenic potential remains to be clarified. Antimicrobial susceptibility testing revealed that Flavobacterium species were predominantly multidrug-resistant. F. psychrophilum showed high non-wild-type frequencies for oxytetracycline and quinolones and high minimum inhibitory concentrations (MICs) for ceftazidime and trimethoprim/sulfamethoxazole. However, all isolates were wild type for florfenicol. Lesser-known species exhibited high MICs across at least three antimicrobial classes, and some for all 10 antimicrobials tested. Adjustment of the standardised method for F. psychrophilum enabled successful testing of F. branchiophilum and other fastidious flavobacteria. F. psychrophilum infections were associated significantly with elevated water pH at the inlet and winter season. In contrast, F. branchiophilum infections correlated with increased water temperatures, decreased dissolved oxygen at the outlet, and the summer season. This research contributes to a better understanding of flavobacterial infections in Slovene aquaculture, enables informed strategies for disease treatment and control, and provides a foundation for future studies on flavobacterial biodiversity and their impact on fish health.

• Ključne besede: Flavobacterium, matrix-assisted laser-desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), pathology, antimicrobial susceptibility, water quality