Background The morbidity and mortality associated with the multi drug resistant Gram negative bacterial infections pose a significant and growing challenge to clinical practitioners. Klebsiella pneumoniae, which is a substantial nosocomial pathogen and confer high levels of resistance to broad-spectrum antibiotics including carbapenems. The aim of this study is to determine the resistance profiles of Klebsiella pneumoniae strains isolated from various clinical specimens. Material and Method In this study, the antibiotic susceptibility profiles of 2452 Klebsiella pneumoniae strains isolated from various clinical specimens between July 2015 and November 2019 were considered retrospectively. Blood culture vials were incubated in Bac T / Alert 3D automated system, other samples were cultured on blood and Eosin Methylene-blue (EMB) medium. The identification and antibiotic susceptibility tests of the isolated bacteria were performed by VITEC 2 Compact ID-AST cards (BioMérieux, Marcy l’Etoile, Fransa) and the results were evaluated according to the standards of the Europian Committee on Antimicrobial Susceptibility testing (EUCAST). The first sample of each patient was included in the study. The strains with inappropriate results were re-studied with gradient agar diffusion test (BioMérieux, Marcy l’Etoile, Fransa). Results The study included a total of 2452 Klebsiella pneumoniae strains and the distribution of samples was as follows: 894 (36, 5 %) blood, 790 (32, 2%) bronchial lavage, 211 (8,6 %) wound, 148 (6 %) drainage, 148 (6 %) peritoneal fluid, 95 (3, 9 %) tracheal aspirates, 64 (2,6%) catheter, 62 (2,5 %) urine, 40 (1,6%) other samples (pleural fluid, cerebrospinal fluid, throat ). In this study, antibiotic susceptibility test results indicated that the resistance to tigecycline was lowest (0, 3%). High colistin resistance ratio (33, 5 %) in carbapenem-resistant Klebsiella pneumoniae was considered to be of concern. Conclusion In this study, high rates of resistance to carbapenems were noteworthy. Determination of hospital antimicrobial resistance rates will be useful in developing antibiotic use policies of each hospital, in the treatment of causative agents, in selecting antibiotics according to antimicrobial susceptibility. Show less

Objective Real-time surveillance of SARS-CoV-2 variants of concern (VOC) is of essential public health importance. Rapid Antigen Detection Tests (RAgDT) have become first-line COVID-19 diagnostic methods in many regions, but this strategy can hamper the surveillance of the virus variants due to their decentralized performance. The aim of this study was to assess the usefulness of the remaining sample of a widely used RAgDT (Panbio) for the surveillance of the B.1.1.7 VOC using molecular methods. Methods Symptomatic individuals and asymptomatic close contacts of confirmed cases were routinely screened for SARS-CoV-2 infection using the RAgDT in Primary Health Care Centers. After performing the test, the extraction tubes containing the remaining biological material of RAgDT-positive cases were sent to the clinical microbiology laboratory where RT-PCRs detecting key mutations of the VOC were conducted. Results A valid result was obtained in 1770/1812 (97.7%) RAgDT-positive cases. Variant B.1.1.7 was detected in 34.7% of the patients, increasing from 0% to 87.7% between the weeks beginning January 4 and March 15, 2021. Conclusion The sample remaining after performing the Panbio RAgDT allowed to monitor the emergence and circulation of the B.1.1.7, greatly improving the population screened for the molecular study of SARS-CoV-2 variants.   Show less

Bacteria of the genus Staphylococcus are pathogenic Gram-positive bacteria responsible for various infections, including skin suppuration, which can be severe or chronic. The objective of this study was to confirm Staphylococci strain’s identification isolated by bacteriological methods from biological products of CHU-B patients, by molecular methods based on the analysis of the gene coding for 16S rRNA. In total, 30 strains of Staphylococci were isolated including 8 (26.66%) community strains, 22 (73.33%) hospital strains. The products of the amplification of gene fragments encoding 16S rRNA from 10 strains of Staphylococci including 6 strains of Staphylococcus aureus (S. aureus) and 4 Coagulase Negative Staphylococci (CNS) were sequenced. The sequences obtained were subjected to bioinformatics analysis to confirm the results of conventional bacteriological methods. Six (6) S. aureus strains, 2 Staphylococcus haemolyticus strains, 1 uncultured bacterium clone nbw618g09c1, and one Staphylococcus sp. have been identified. These results made it possible to confirm the effectiveness of the molecular method and to show the limits of traditional bacteriological methods in the complete identification of bacteria. Show less

Typhoid fever, caused by the human restricted pathogen Salmonella Typhi, remains a major global public health concern. Even after successful treatment, approximately 3-5% of patients with typhoid fail to clear the bacteria within one year and become chronic carriers. Most typhoid carriers have gallstones in their gallbladder, and biofilm formation on gallstones is highly correlated with chronic carriage. This study’s goal was to identify asymptomatic typhoid carriers in an endemic setting in Kenya, and to compare acute versus chronic isolates. A cohort of typhoid fever patients identified through blood and/or stool culture, and their household contacts, were followed up after treatment to detect longitudinal S. Typhi stool shedding. An abdominal ultrasound scan was used to identify individuals with gallstones. A total of 32 index patients and 32 household contacts were successfully followed-up. Gallstones were detected in 4 cases and 1 household contact. The duration of S. Typhi shedding was significantly longer in individuals with gallstones compared to those without, P<0.001. Eighty-three (83) S. Typhi strains were tested for susceptibility to commonly used antimicrobials and examined by in vitro biofilm formation assays. Out of 37 infected individuals, 32.4% had infections caused by multidrug resistant (MDR) S. Typhi strains and only 18.9% were infected by susceptible strains. Non-MDR strains formed significantly better biofilms in vitro than the MDR strains (P<0.001). This study provides data on S. Typhi chronic carriage that will influence public health approaches aimed at reducing typhoid transmission and the burden of infection. Show less