Human gut microbiota – its diversity and impact on our health

The human digestive tract is the living environment for billions of cells of various microorganisms that are part of the human microflora. The use of modern molecular biology techniques, such as NGS (Next Generation Sequencing), made it possible to study the microorganisms inhabiting the intestines and to understand their impact on human health. The gut microbiota plays a significant role in the synthesis and metabolism of many nutrients and metabolites, including short-chain fatty acids (SCFA), amino acids, lipids, bile acids and vitamins. Many factors such as diet, age, climate, and socioeconomic conditions influence the diversity of the microbiota. Rapid changes in the composition of the microbiota (disturbance of homeostasis) can lead to dysbiosis - a condition associated not only with intestinal disorders, but also with numerous extraintestinal diseases. The present work is a review of current reports on: research techniques used to analyze microbiota, the impact of various factors on its diversity and the impact of microbiota on our health.

Staphylococcus prettenkoferi – biochemical properties, methods of species identification and clinical significance

Staphylococcus pettenkoferi was first isolated from blood culture a 25-years-old patient with fever of unknown etiology. Based on the literature analysis, it was found that it is an opportunistic microorganism. It causes blood stream infections and was an causative agent of osteomyelitis. Staphylococcus pettenkoferi is a component of the human microbiome, was found in a hospital environment and was also isolated from animals and their surroundings.

Evaluation of in-house ELISA and 11 commercial ELISA kits in the serological diagnosis of COVID-19

Introduction: ELISA-Immunoassays can complement the molecular diagnostic methods, and can be one of the important tools of sero-surveillance and vaccine evaluation. The aim of the presented study was to develop in-house ELISA and evaluate 11 commercial ELISA tests for detection of anti-SARS-CoV-2 antibodies in serum samples collected from COVID patients. Methods: In total, 237 serum samples obtained from 165 people with COVID-19 with RT-PCR confirmed SARS-CoV-2 virus infection were used for the study. The specificity of the developed in-house ELISA kit was tested using 170 serum samples obtained from patients with various bacterial and viral infections. The study used an in-house ELISA and 11 commercial ELISA kits developed by various manufacturers. Results: The presented study showed high sensitivity (81.0%) and specificity (97.2%) of the developed in-house kit in relation to the RT-PCR method. The sensitivity of the inhouse test significantly increased (98.1%) when only convalescents - persons at least 3 weeks after COVID-19 were examined. Commercial ELISA kits most frequently detected IgG antibodies (from 44.9% to 89.4%), especially in samples obtained later in the disease, and the least frequent detection of IgM antibodies (from 4.2% to 42.4%). Conclusions: All the presented ELISA kits may be used in serodiagnosis of COVID-19 however the detection of antibodies in individual tests differed quite significantly and was dependent on the period of the disease, on the class of immunoglobulins and the type of antigen used. The sensitivity of serological tests in the IgG class is clearly higher when examining samples obtained at least 2-3 weeks from the onset of clinical symptoms. Searching for IgA antibodies may be useful mainly in the early phase of the disease while IgM antibodies does not provide significant additional information. In the case of asymptomatic or mild infection, the level of antibodies is low which may be the cause problems with the correct interpretation of epidemiological surveys

Evaluation of the occurrence of genetic determinants of multi-drug resistance among Acinetobacter baumannii strains

Introduction: The aim of the study was the analysis of occurrence of genetic determinants of multi-drug resistance and the assessment of genetic relationship among Acinetobacter baumannii strains. Methods: Multiplex-PCR method was performed in order to: (1) confirm the phenotypic identification and (2) detect the presence of CHDL oxacillinases in the group of thirty A.baumannii strains. Further PCR studies included the analysis of the occurrence of genetic determinants associated with efflux pump, insertion sequence and biofilm formation. The relationship between bacterial strains was assayed using 6 primers in RAPD-PCR method. Results: Detection of the blaOXA-51-like gene confirmed that the strains belong to the A. baumannii species. In the multiplex-PCR, the presence of the blaOXA-23-like and blaOXA-40-like genes was detected in 3 (10%) and 27 (90%) isolates, respectively. Moreover, some strains showed the coexistence of the blaOXA-51-like and blaOXA-23-like genes (10%, n=3) or blaOXA-51-like and blaOXA-40-like (90%, n=27). In the group of analysed strains the presence of the efflux pump gene (adeA) and the insertion sequence ISAba1 were demonstrated in all tested isolates. Biofilm-related genes (abaI, csuE) were found in 100% and 97% (n=29) tested strains adequately. The RAPD-PCR studies revealed the presence of 10 unrelated genotypes. Conclusions: The obtained results suggest that the phenomenon of multi-drug resistance in the studied A. baumannii strains could be attributed to the occurrence of CHDL oxacillinases, AdeABC efflux pump, insertion sequence ISAba1 and the biofilm formation.

Evaluation of rapid, cassette immunochromatographic tests in the serological diagnosis of COVID-19

Introduction: Lateral flow assays (LFIA) are the technology behind low-cost, simple, rapid and portable detection devices popular in biomedicine. Lately, they are very common used in serodiagnosis of SARS-CoV-2 infections. The aim of the presented study was to assess the usefulness of selected LFIA in serological diagnosis of COVID-19. Methods: The usefulness of seven lateral flow assays in the serodiagnosis of COVID-19 was evaluated (VAZYME, DIAGNOSIS, PCL, INGEZIM, BIOSENSOR, ACCU-TELL, NOVAtest). The study used 107 serum samples obtained from 74 individuals with current SARS-CoV-2 infection confirmed by RT-PCR. The ELISA-IgG (Euroimmun) was used as the reference assay for sensitivity and specificity testing. Results: The highest percentage of positive results was obtained when searching for IgG antibodies with the NOVAtest (40.6%) and DIAGNOSIS (39.2%) sets and the lowest detection for the PCL set - 25.5%. In the case of searching for IgM antibodies in all sets, significantly lower percentages of positive results compared to the IgG class were recorded. In general, all lateral flow assays showed low sensitivity in relation to the Euroimmun ELISA-IgG. The DIAGNOSIS kit (64.5%) was characterized by the highest sensitivity, and the PCL kit was the lowest (38.7%). On the other hand, the specificity of all kits was very high, almost 100% in almost all cases. Conclusions: Lateral flow assays due to their low sensitivity are not suitable for quick diagnosis of the current SARS-CoV-2 infections and cannot be an alternative to genetic or even antigen tests. They may be used only to retrospectively test the presence of IgG antibodies. However, a negative results of LFIA in suspected disease or after vaccination should be confirmed by more sensitive serological tests.

AmpC cephalosporinases in Escherichia coli

Escherichia coli is an important pathogen causing nosocomial infections. A significant problem in the treatment of infections caused by these microorganisms is their increasing resistance to β-lactam antibiotics, including third and fourth generation cephalosporins. The production of β-lactamases enzymes such as extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases is among the main mechanisms for resistance to third generation cephalosporins. The genes encoding AmpC cephalosporinases are chromosomal (cAmpC) or plasmid-mediated (pAmpC). In E. coli, the expression of the ampC genes may be conditioned by the constitutive expression of low level ampC chromosomal genes. These strains remain susceptible to β-lactam antibiotics. However, mutations in the promoter region of the ampC may result in increased level of expression of chromosomal ampC genes. This can leads to resistance to cephalosporins. Resistance to cephalosporins in E. coli can be also associated with plasmid-mediated AmpC β−lactamases (pAmpC). In E. coli the presence of one or more plasmid-mediated AmpC β−lactamases along with the neglible expression of chromosomal encoded AmpC enzyme can leads to resistance to broad-spectrum cephalosporins. This review is focused on a resistance mechanisms associated with the production of AmpC cephalosporinases in clinical E. coli isolates.

Evaluation of survival of Candida albicans on PVC surfaces in the test of yeasticidal activity of disinfectant

Introduction: Candida albicans survival tests on PCV carriers are necessary for the proper determination of the effectiveness yeasticidal activity of disinfectants. C. albicans is a pathogenic microorganism that causes fungal diseases and therefore its spread in the medical and non-medical areas should be limited by disinfection. Methods: Survival of C. albicans was estimated with using principles of PN-EN 16615 standard. Suspension of C. albicans with interfering substances (0,3 g/l bovine albumin) was dry on PCV carriers under a laminar chamber without fan, at the ambient temperature for no longer than 60 minutes. C. albicans was recovered from the carriers immediately after drying and after contact time (1; 5, 10, 20, 40; 60 minutes). Results: The drying conditions applied reduced the recovery of C. albicans from 1.21 to 2.07 on a logarithmic decimal scale with respect to the test suspension with interfering substances. The difference between the recovery immediately after drying and the recovery after the tested contact times (up to 60 minutes) was insignificant. Conclusions: Achieving the number of C. albicans after the drying process, as provided for in PN-EN 16615, requires further improvement of the drying conditions or an increase of C. albicans suspension density before drying.

Fungal lesions of the nail plate in patients from the Warmian-Masurian Voivodeship - analysis and discussion of the results of studies carried out in 2014 - 2019

Introduction: The aim of the study was to analyze the results of mycological cultures obtained in the years 2014-2019. The study included an analysis of the incidence of mycosis with regard to their location, as well as the proportion of individual etiological factors in the infection. Methods: The study included materials from 999 patients who gave a total of 1103 cultures. The material was taken directly from the material and mycological cultures were established. Results: Positive results accounted for 35,8%. Trichophyton rubrum (44.2%) was the most common etiologic agent of dermatophytes. Among the yeast-like fungi, Candida albicans (8.8%) and Candida parapsilosis (7,6%) were the most common. Conclusions: Infectious lesions were mainly caused by dermatophytes, where Trichophyton rubrum and Trichophyton mentagrophytes dominated.

Reactive arthritis and erythema nodosum after gastrointestinal infections caused by Yersinia enterocolitica and Yersinia pseudotuberculossis

After gastrointestinal infection with Y. enterocolitica and Y. pseudotuberculosis, some patients may experience reactive arthritis and erythema nodosum. In the etiopathogenesis of these autoimmune complications, in addition to infectious agents, genetic factors, gender and age of the patients also play a role. In the study of the etiology of reactive arthritis and erythema nodosum after gastrointestinal infection, it is useful to investigate in the serum of patients specific antibodies for selected intestinal pathogens, including Yersinia antigens.

Oral carriage of methicillin-resistant Staphylococcus aureus strains among patients with diabetic foot ulcer

Introduction: Diabetic foot ulcer (DFU) caused by Staphylococcus aureus is one of the most feared complications of diabetes mellitus. The studies reporting the oral cavity as a potential reservoir of S. aureus in diabetic patients are sparse. The aim of the study was to compare the prevalence of methicillin-resistant Staphylococcus aureus strains in the oral and in the diabetic foot specimens from DFU patients. Materials and Methods: A total 80 specimens (40 oral swabs and 40 DFU swabs) were collected from diabetic patients with foot ulcer. The specimens were subcultured and the susceptibility of isolated S. aureus strains to antimicrobial agents was determined. Suspected methicillin-resistant S. aureus (MRSA) strains were further examined for the presence of modified PBP2a protein. Results: Less than one-fifth of patients with DFU had oral S. aureus carriage, however the colonization is significantly associated with S. aureus diabetic foot infection. S. aureus strains were isolated from 52.5% of DFU specimens, 17.5% were resistant to methicillin. S. aureus strains were isolated from 17.5% of oral specimens of diabetic patients; 2.5% were methicillin-resistant. The MRSA strains were isolated sevenfold more frequently from the diabetic foot than from the oral cavity. Conclusions: Although diabetic foot infections caused by an endogenous S. aureus strains colonizing the oral cavity of diabetic patients seems unlikely, it is evidently important to monitor the oral S. aureus carriage in diabetic patients and their resistance to antibiotics.