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Abstract: Mycobacterium abscessus complex (MABC) is a taxonomic group of rapidly growing, nontuberculous mycobacteria that are found as etiologic agents of various types of infections. They are considered as emerging human pathogens. MABC consists of 3 subspecies - M. abscessus subsp. bolletti, M. abscessus subsp. massiliense and M. abscessus subsp. abscessus. Here we present a novel method for subspecies differentiation of M. abscessus named Subspecies-Specific Sequence Detection (SSSD). This method is based on the presence of signature sequences present within the genomes of each subspecies of MABC. We tested this method against a virtual database of 1505 genome sequences of MABC. Further, we detected signature sequences of MABC in 45 microbiological samples through DNA hybridization. SSSD showed high levels of sensitivity and specificity for differentiation of subspecies of MABC, comparable to those obtained by rpoB sequence typing.
Keywords: Mycobacterium abscessus complex, nontuberculous mycobacteria, diagnosis
Published in DiRROS: 23.11.2020; Views: 12039; Downloads: 1007
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Keywords: Dezinsekcija, deratizacija
Published in DiRROS: 16.11.2020; Views: 1249; Downloads: 0

Abstract: Izhodišča. Medularni rak ščitnice (MRŠ) je redek endokrini tumor, ki se v približno 25 % primerov pojavlja v družinski obliki bolezni v sklopu multiple endokrine neoplazije tipa 2, v 75 % pa je bolezen sporadična. Namen dela je bil oceniti incidenco MRŠ ter pogostost in vrsto RET-mutacij v slovenski populaciji bolnikov med letoma 1995 in 2015.Metode. Retrospektivno smo analizirali podatke Registra raka Republike Slovenije in Registra bolnikov z MRŠ Onkološkega Inštituta v Ljubljani, zbrane med letoma 1995 in 2015. V ključili smo 143 bolnikov s potrjenim MRŠ in 43 njihovih zdravih sorodnikov, ki so bili napoteni na genetsko svetovanje in testira-nje. Genomsko DNK smo izolirali iz levkocitov periferne krvi. Eksone 10, 11, 13, 14, 15 in 16 RET protoonkogena smo pomnožili z verižno reakcijo s polimerazo. Točkovne mutacije RET proto-onkogena smo odkrili z metodo SSCA in DNA-sekvenciranjem. Zaznane mutacije so bile potrjene z restrikcijskimi encimi.Rezultati. Zarodno mutacijo RET protoonkogena smo odkrili pri 51 osebah; med njimi je bilo 37 bolnikov z MRŠ, kar predsta-vlja 25,9 % vseh bolnikov z MRŠ. Odkrili smo osem različnih mutacij RET protoonkogena. Najpogosteje smo potrdili mutacijo v kodonih 634 in 618, sledili so kodoni 790, 804 in 918. Povprečna groba letna incidenčna stopnja MRŠ v Sloveniji za opazovano obdobje znaša 0,34/100.000 prebivalcev.Zaključek. Ocenjena povprečna groba letna incidenčna stopnja MRŠ v Sloveniji je bila 0,34/100.000. Poleg tega smo ugotovili, da se RET-mutacija pojavlja v naši populaciji bolnikov v 25,9 % ter da najpogosteje prizadene kodona 634 in 618.
Keywords: medularni karcinom ščitnice, multipla endokrina neoplazija 2, genetsko svetovanje, incidenca
Published in DiRROS: 09.09.2020; Views: 2030; Downloads: 581
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Abstract: Drug resistant tuberculosis (TB), especially multidrug (MDR) and extensively drug-resistant (XDR) TB, is still a serious problem in global TB control. Slovenia and North Macedonia are low-incidence countries with TB incidence rates of 5.4 and 10.4 in 2017, respectively. In both countries, the percentage of drug resistant TB is very low with sporadic cases of MDR-TB. However, global burden of drug-resistant TB continues to increase imposing huge impact on public health systems and strongly stimulating the detection of gene variants related with drug resistance in TB. Next-generation sequencing (NGS) can provide comprehensive analysis of gene variants linked to drug resistance in Mycobacterium tuberculosis. Therefore, the aim of our study was to examine the feasibility of a full-length gene analysis for the drug resistance related genes (inhA, katG, rpoB, embB) using Ion Torrent technology and to compare the NGS results with those obtained from conventional phenotypic drug susceptibility testing (DST) in TB isolates. Between 1996 and 2017, we retrospectively selected 56 TB strains from our National mycobacterial culture collection. Of those, 33 TB isolates from Slovenian patients were isolated from various clinical samples and subjected to phenotypic DST testing in Laboratory for Mycobacteria (University Clinic Golnik, Slovenia). The remaining 23 TB isolates were isolated from Macedonian patients and sent to our laboratory for assistance in phenotypic DST testing. TB strains included were either mono-, poly- or multidrug resistant. For control purposes, we also randomly selected five TB strains susceptible to first-line anti-TB drugs. High concordance between genetic (Ion Torrent technology) and standard phenotypic DST testing for isoniazid, rifampicin and ethambutol was observed, with percent of agreement of 77%, 93.4% and 93.3%, sensitivities of 68.2%, 100% and 100%, and specificities of 100%, 80% and 88.2%, respectively. In conclusion, the genotypic DST using Ion Torrent semiconductor NGS successfully predicted drug resistance with significant shortening of time needed to obtain the resistance profiles from several weeks to just a few days.
Keywords: drug resistant tuberculosis, next-generation sequencing, low-incidence countries, phenotypic drug susceptibility testing
Published in DiRROS: 24.07.2020; Views: 1867; Downloads: 1051
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