20.500.12556/DKUM-65278 Molecular identification of several clinically important bacteria including enterobacteria by partial 16S ribosomal RNA gene sequence comparison Molekularna identifikacija klinično pomembnih bakterij, vključno enterobakterij s primerjavo delnega nukleotidnega zaporedja gena za 16S ribosomsko RNK Background: The correct identification of bacterial isolates is paramount for the correct diagnosis and treatment of patients. The standard approach for bacterial identification relies on phenotypic tests, which are often time-consuming and unreliable when identifying atypical strains. We instead hypothesized a molecular approach; fast and reliable identification could be achieved by comparing a 16S ribosomal RNA gene sequence with publicly available sequences. Methods: In the present study, DNA from seventeen bacterial species was extracted and amplified by PCR, and then a partial 16S ribosomal RNA gene sequence was obtained and compared with sequences deposited in public DNA sequence databases; EMBL/GeneBank/DDBJ and RDP-II. Results: Bacterial species, belonging to several families; Coriobacteriaceae, Bacteroidaceae, Clostri- diaceae, Staphylococcaceae, as well as three out of nine Enterobacteriaceae were specifically identified by partial 16S ribosomal RNA gene sequence to the species level. For six other species of enteric bacteria specific identification of species failed, since the results of genotypic identification yielded several species. Conclusions: We conclude identification of bacteria with partial 16S ribosomal RNA gene sequence is an efficient complement to phenotypic identification, except for enteric bacteria. Za učinkovito diagnostiko bakterijskih okužb in zdravljenje je potrebna hitra in natančna identifikacija bakterije. Običajen postopek je fenotipska identifikacija, ki je pogosto zahtevna in nenatančna za atipične izolate. V naši študiji smo predpostavili, da je možno identificirati bakterije s primerjavo delnih nukleotidnih zaporedij genov, ki kodirajo 16S ribosomsko RNKs primerjavo z nukleotidnimi zaporedji v javno dostopnih podatkovnih bazah za zaporedja DNK: EMBL, GenBank, DDBJ in RDP-II. Še posebej nas je zanimala možnost identifikacije enterobakterij, saj mnogi avtorji navajajo, da te skupine bakterij ni moč ločiti na osnovi zaporedij genov 16S ribosomske RNK. Za izvedbo študije smo pridobili 15 tipskih sevov in dva klinična izolata iz zbirke Zavoda za zdravstveno varstvo Maribor, katerih rutinska fenotipska identifikacija je težavna. Iz bakterij smo izolirali DNK ter z verižno reakcijo s polimerazo (PCR) pomnožili variabilen odsek gena za 16S ribosomsko RNK. Pridelke PCR smo očistili in poslali na sekveniranje s prednjim začetnim oligonukleotidom v podjetje Macrogen, Koreja (www.macrogen.com). Pridobljena nukleotidna zaporedja DNK smo nato z dvema iskalnima algoritmoma; BLAST, v bazah GeneBank/EMBL/DDBJ, ter z algoritmom Sequence match v bazi RDP-II primerjali z vloženimi nukleotidnimi zaporedji, za morebitno identifikacijo vrste. Specifično smo uspeli identificirati vrste: Staphylococcus epidermidis,Bacteroides fragilis, Clostridium perfringens, Peptostreptococcus anaerobius, Eggerthella lenta, Enterobacter cloacae, Yersinia enterocolitica, Proteus mirabilis, Streptococcus pyogenes, Enterococcus faecalis. Medtem ko Escherichia coli, Serratia marcescens, Shigella flexneri, Klebsiella pneumoniae, Citrobacter freundii nismo uspeli nedvoumno identificirati, čeprav je klinično nujno. Vendar menimo, da je opisan genotipski pristop za identifikacijo vrste bakterije učinkovito dopolnilo fenotipski identifikaciji, še posebno pri identifikaciji atipičnih izolatov. molecular identification bacteria 16S rDNA sequences molekularna identifikacija nukleotidno zaporedje bakterije true false true Angleški jezik Slovenski jezik Znanstveno delo 2017-03-28 11:23:59 2017-03-28 11:25:10 2022-07-07 03:09:04 2019-07-11 15:13:15 2008 0 0 str. 547-552 št. 9 Letn. 77 2008 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 1318-0347 577 32893696 12712726 1318-0347 URN:SI:UM:DK:JKONMUN3 Zdravniski_vestnik_2008_Simenc,_Golle,_Potocnik_MOLECULAR_IDENTIFICATION_OF_SEVERAL_CLINICALLY_IMPORTANT_BACTERIA_INCLUDING_ENTEROBACTER.pdf Zdravniski_vestnik_2008_Simenc,_Golle,_Potocnik_MOLECULAR_IDENTIFICATION_OF_SEVERAL_CLINICALLY_IMPORTANT_BACTERIA_INCLUDING_ENTEROBACTER.pdf 1 A29CA1940D2A6B5BA585D46AE828B44D c45f6637b900b0453476ea4604d68388e2aaab02ba612dae491e4deec16d6bc9 06f936c8-7c0e-11eb-bb7a-00155d0001ca https://dk.um.si/Dokument.php?lang=slv&id=110242 http://vestnik.szd.si/index.php/ZdravVest/article/view/498 1 https://dk.um.si/Dokument.php?lang=slv&id=110241 Medicinska fakulteta 0 0 0