Phage typing, antibiotic resistance and genomic rep-PCR fingerprinting of clinical Salmonella isolates from the Caucasus region

Abstract

Background: In reaction to the use of antibiotics in farming and veterinary practices, MDR phenotypes have emerged. As Salmonella enterica serovars are widely diverse and spread through the food chain, rapid increase in antibiotic resistance is also observed in clinical strains. Therefore, rapid identification and treatment solutions are direly needed to treat MDR infections. The use of lytic phage-based systems offers a triple benefit: rapid and cost effective typing using therapeutic agents, which can potentially lyse the examined MDR strains. Methods & Materials: In this study we have focused on isolates from patients with Salmonellosis, who have not yet received any antibiotic therapy. In total, 71 non-typhoid Salmonella enterica clinical isolates from the “Nork” Clinical Hospital of Infectious Diseases (Yerevan, Armenia) and 22 strains from the Referral Laboratory at the Republican Clinical Hospital of Infectious Diseases (RCHID, Tbilisi, Georgia) were selected. Serotyping by polyvalent antisera for flagellar (H) and lipopolysaccharide (O) antigens, and by biochemical analysis, were performed in the respective clinical settings. MALDI-TOF analysis was performed to confirm the identification at the genus level. Semi-automated rep-PCR fingerprinting profiles were determined using the DiversiLab® system and analyzed using Pearson's correlation analysis. The obtained clusters were compared with Salmonella group B, C, D, E, F, G, K, L, O, R reference libraries for serotype identification. Antibiotic resistance profiles were determined in accordance with the CLSI guidelines for standard disk diffusion assays. Phage typing was performed using the line spot-test method. Results: Species identification by phage typing confirmed the MALDI-TOF identifications. Forty-one percent of the tested clinical isolates were shown to be MDR, while none of the strains showed complete resistance to the tested phages. According to rep-PCR fingerprinting, 93 examined isolates clustered into 24 different cluster-serotypes. One isolate from RCHID showed 97.3% similarity with a Salmonella Dublin reference strain, one cluster harbored 14 strains with >95% similarity to a Salmonella typhimurium reference strain and another cluster consisted of 21 strains identified as Salmonella enteritidis. As expected, no correlation was observed between strain genotypes and phage types. Conclusion: A lytic phage-based characterization system can be relevant for epidemiological studies and rapid screening for therapeutic phage applications.