Pilot istraživanje Clostridium difficile infekcija u bolesnika s proljevom u zdravstvenim ustanovama u Tbilisiju, Gruzija

Background: Clostridium difficile infection (CDI) is the most frequent cause of healthcare-associated diarrhoea and is increasingly recognized in the community. The epidemiology of CDI in Georgia is unknown. Methods: Pilot surveillance for CDI among patients with diarrhoea was conducted in four hospital ICUs, and three outpatient clinics in Tbilisi, Georgia. Demographic, clinical and treatment data of patients with CDI were collected from medical records. A CDI diagnosis was made if the stool sample was positive for C. difficile toxin A and/or B by nucleic acid amplification test or enzyme immunoassay, or by culture of a toxin-producing C. difficile. Results: A total of 131 patients with new onset diarrhoeal illness were recruited. Of these, laboratory confirmed CDI was found in 24% (31/131): 32% (17/53) of adult and 20% (11/55) of paediatric ICU patients, 22% (2/9) adult and 7% (1/14) of paediatric outpatients. Presenting symptoms were fever (>380C) and diarrhoea with a median duration 7 days. Most CDI cases received antibiotics before diagnosis; 94% of adults and 91% of children diagnosed in the ICU (median: 12 days); the majority receiving simultaneously two or more antibiotics. In the outpatient settings, 100% of CDI case-patients received an antibiotic for a median duration of 7 days. Conclusions: This pilot surveillance demonstrated that C. difficile is a common cause of diarrhoea in hospitalized and community patients in Georgia. It highlights the need to improve the knowledge of medical providers regarding the burden of CDI and to establish diagnostic testing at hospital laboratories.Uvod: Infekcije uzrokovane Clostridium difficile (CDI) najčešći su uzrok proljeva povezanog sa zdravstvenom skrbi i sve se više prepoznaju u zajednici. Epidemiologija C.difficile infekcija u Gruziji nije poznata. Metode: Pilot istraživanje C.difficile infekcija kod bolesnika s proljevom provedeno je u četiri bolničke jedinice za intenzivno liječenje (JIL) i tri ambulantne klinike u Tbilisiju u Gruziji. Podaci o demografskim i kliničkim karakteristikama te liječenju bolesnika s CDI prikupljeni su iz povijesti bolesti. Dijagnoza C.difficile infekcije postavljena je ukoliko je uzorak stolice bio pozitivan na C. difficile toksin A i/ili B testom amplifikacije nukleinskih kiselina ili metodom enzimskog imunoeseja ili nalazom C. difficile koji proizvode toksine u kulturi. Rezultati: U istraživanje je bio uključen 131 bolesnik s novonastalom dijarealnom bolesti. Od toga je laboratorijski dokazana CDI utvrđena kod 24% (31/131) bolesnika: u 32% (17/53) odraslih i 20% (11/55) djece liječene u JIL-u, 22% (2/9) odraslih i 7% (1/14) pedijatrijskih ambulantnih bolesnika. Simptomi su bili povišena tjelesna temperatura (> 38 ° C) i proljev s prosječnim trajanjem od 7 dana. Većina bolesnika s CDI primila je antibiotik prije postavljanja dijagnoze; 94% odraslih i 91% djece liječene u JIL-u (medijan: 12 dana); većina je istodobno primala dva ili više antibiotika. U ambulantnom okruženju, 100% bolesnika s CDI primilo je antibiotik u prosječnom trajanju od 7 dana. Zaključak: Ovo pilot istraživanje pokazalo je da je C. difficile čest uzrok proljeva u hospitaliziranih i izvanbolničkih pacijenata u Gruziji. Ono naglašava potrebu za poboljšanjem znanja pružatelja zdravstvenih usluga vezano uz probleme koje nose infekcije uzrokovane C. difficile te uspostavom dijagnostičkih testova u bolničkim laboratorijima

Analysis of Three CRISPR Loci Among Yersinia pestis Stains from Georgia and Neighboring Countries

ObjectiveThe purpose of our study was CRISPR-based analysis of Y. pestis isolates from Georgia and neighboring countries.IntroductionParticular family of tandem repeats, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) found in a wide range of prokaryotic genomes. CRISPRs consist of highly conserved repeats interspaced with non-repetitive elements or "spacers" usually of viral origin. In the Yersinia pestis genome, three CRISPR elements YPa, YPb and YPc are found. The distribution of spacers and their arrays in Y. pestis strains is region and focus specific and can provide important information for genotyping and evolutionary research of bacteria.MethodsWhole-genome sequencing (WGS) of 14 Y. pestis strains from Georgia, Armenia, Azerbaijan, Russian Federation (RF) and Kirgizstan were performed using a combination of different next generation sequencing (NGS) platforms: Illumina, PacBio and 454 technologies. Identification of spacer sequences from CRISPR loci was conducted to evaluate the genetic diversity among the isolates. The spacers arrays were acquired and analyzed. DRs and spacers were identified and extracted. The selected spacer sequences were compared against the microbial genome database in GenBank. Leader sequences were obtained for each CRISPR locus and aligned using MAFFT software.ResultsIn all 14 sequenced genomes, three CRISPR elements were found. All alleles show the same organization, conserved 28 bp repeated sequence is interspaced with spacers, 31 or 34bp in length. A total of 18 spacers were found: seven for the YP1, six for the YP2 and five forYP3. According to the spacer arrays sequence, Biovar Microtus strains from Georgia and Armenia had the same allele sizes with the presence of seven motifs, for YP1 (a1b1c1d1e1m1n1), six motifs for YP2 (a2j2b2k2l2m2) and five for YP3 loci (a3b3c3d3e3) identical to PestoidesG (genotype 1). Spacers/spacer arrays of Biovar Medievalis strains from Georgia, Azerbaijen and Kabardino Balkaria (RF) were the same as KIM (genotype - 59).ConclusionsCRISPR analysis of Georgian strains identified two independent phylogenetic groups that is in agreement with previous study data (SNP typing, IS100 fingerprinting). Biovar Microrus strains from Transcaucasian highland placed within one of the most ancient branches of the evolutionary model of Y. pestis. This study enhances our understanding and fulfills the existing data of genetic characteristics of Y. pestis strains circulating in the region