Aleksander Deptuła’s research while affiliated with Nicolaus Copernicus University and other places

The gut microbiota serves a crucial role in the development of host immunity. Immunocompromised patients are particularly vulnerable to dysbiosis not only by virtue of a defect in the immune system but also due to increased susceptibility to infection and multiple courses of antibiotic therapy. Fecal microbiota transplantation is by far the most effective option for restoring gastrointestinal homeostasis. However, it is contraindicated in patients with significant primary and secondary immunodeficiencies. This article presents the case of a 59-year-old patient with common variable immunodeficiency, after splenectomy at age 39 for primary immune thrombocytopenia, who manifested diarrhea of up to 10 stools per day accompanied by secondary malnutrition and cachexia. The patient was admitted to the hospital on multiple occasions due to this condition, with stool PCR tests confirming a HHV-5 (Cytomegalovirus, CMV) infection. Following the administration of valganciclovir, the patient’s complaints diminished, although, upon cessation of the drug, the symptoms recurred. In addition, the patient had an intestinal infection with C. difficile etiology. Given that the patient’s therapeutic options had been exhausted, after obtaining informed consent from the patient and approval from the bioethics committee to conduct a medical experiment, treatment of diarrhea was undertaken by fecal microbiota transplantation with the certified preparation Mbiotix HBI from the Human Biome Institute. The patient underwent two transplants, with a one-week interval between them. The initial procedure was performed using the endoscopic method, while the subsequent was conducted using the capsule method. Following the administration of the applied treatment, the patient’s symptoms were successfully alleviated, and no adverse effects were observed. A microbiological analysis of the intestinal microbiota was conducted prior to and following transplantation via next-generation sequencing (NGS). No recurrence of symptoms was observed during the two-year follow-up period. To the best of our knowledge, this is the first fecal microbiota transplantation in an adult patient with primary and secondary immunodeficiency.

Pseudomonas aeruginosa is an opportunistic pathogen encoding several virulence factors in its genome, which is well-known for its ability to cause severe and life-threatening infections, particularly among cystic fibrosis patients. The organism is also a major cause of nosocomial infections, mainly affecting patients with immune deficiencies and burn wounds, ventilator-assisted patients, and patients affected by other malignancies. The extensively reported emergence of multidrug-resistant (MDR) P. aeruginosa strains poses additional challenges to the management of infections. The aim of this study was to compare the incidence rates of selected virulence-factor-encoding genes and the genotype distribution amongst clinical multidrug-sensitive (MDS) and MDR P. aeruginosa strains. The study involved 74 MDS and 57 MDR P. aeruginosa strains and the following virulence-factor-encoding genes: lasB, plC H, plC N, exoU, nan1, pilA, and pilB. The genotype distribution, with respect to the antimicrobial susceptibility profiles of the strains, was also analyzed. The lasB and plC N genes were present amongst several P. aeruginosa strains, including all the MDR P. aeruginosa, suggesting that their presence might be used as a marker for diagnostic purposes. A wide variety of genotype distributions were observed among the investigated isolates, with the MDS and MDR strains exhibiting, respectively, 18 and 9 distinct profiles. A higher prevalence of genes determining the virulence factors in the MDR strains was observed in this study, but more research is needed on the prevalence and expression levels of these genes in additional MDR strains.

Background Candida auris is an emerging pathogen that constitutes a serious global health threat. It is difficult to identify without specific approaches, and it can be misidentified with standard laboratory methods, what may lead to inappropriate management. Case Presentation We report, probably the first in Poland, C. auris isolation from blood cultures and wound swabs of a young male following meningococcal septicaemia, in February 2019. The patient had been previously hospitalized in the United Arab Emirates. The isolate was rapidly identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry and therefore clinicians were promptly informed on the alert pathogen isolation. The targeted antifungal treatment was successful and infection control measures seemed effective. ITS-based identification and subsequent whole genome sequencing showed that the C. auris isolate belongs to South Asian lineage (clade I). Conclusions C. auris is able to cause outbreaks in healthcare settings. Therefore, it is important to quickly identify C. auris isolates in hospital settings so that healthcare facilities can take proper precautions to limit its spread.

Objective: The aim of this retrospective study was to estimate the prevalence of healthcare-associated infections (HAI), microbiological data including resistance patterns and impact of HAI on patients' survival. Methods: Two-centre study on 172 patients was performed. Medical records of patients hospitalized in the two COVID-19 intensive care units (ICU) localized in Bydgoszcz between 1 October 2020 and 30 March 2021 were analysed retrospectively. Data collection included demographics, microbiological, clinical variables, and patient outcome. All infections were defined according to the HAI-Net ICU protocol of the European Centre for Disease Prevention and Control (ECDC). Detailed data concerning bloodstream infection (BSI), pneumonia (PN) and urinary tract infection (UTI) were collected. Results: In 97 patients (56.4%), 138 HAI cases were identified. Patients with HAI statistically more often had been administered antimicrobial therapy prior to the admission to ICU (59.8% vs. 34.7%, p < 0.05), and needed catecholamines during hospitalization (93.8% vs. 70.7%, p < 0.001). The risk of HAI increased by 50% if antimicrobial therapy had been applied before the admission to ICU, and was three times higher if during the hospitalization in ICU catecholamines infusion was needed. Mortality was higher in patients diagnosed with HAI (72.2% vs. 65.3%) but the difference was not statistically significant (p = 0.34). Conclusions: Further investigation of co-infections in critically ill patients with COVID-19 is required in order to identify HAI risk factors, define the role of empiric antimicrobial therapy and proper prevention strategies.

Lactic acid bacteria belonging to Lactobacillus spp. and Lacticaseibacillus spp. are a natural part of fermented milk and other food products, probiotic supplements and human microbiota. They mainly belong to mucosal microflora, especially oral, vaginal and intestinal. Lacticaseibacillus spp. strains included in probiotics are generally characterised as safe microorganisms, and the species are concerned bacteria with very low pathogenic potential. However, infections caused by Lactobacillus spp. and Lacticaseibacillus spp., including bacteraemia and endocarditis, occur occasionally. The aim of the study was to present two cases of bacteraemia due to Lacticaseibacillus rhamnosus associated with the use of a probiotic product. It afflicted patients in intensive care units. The investigation was preliminarily based on clinical and microbiological recognition of the cases. The initial observation was laboratory confirmed with the application of pulsed-field gel electrophoresis (PFGE) results. Identical PFGE patterns were obtained for the evaluated strains and the strains derived from a commercially available probiotic that was administered to those patients. The increasing number of studies describing opportunistic infections due to probiotic strains of Lacticaseibacillus spp. should result in verifying the safety of probiotic formulations used in immunocompromised patients and forming detailed guidelines for the use of probiotics among patients from several risk groups.

We aimed to describe the clinical presentation, treatment, outcome and report on factors associated with mortality over a 90-day period in Clostridioides difficile infection (CDI). Descriptive, univariate, and multivariate regression analyses were performed on data collected in a retrospective case-control study conducted in nine hospitals from seven European countries. A total of 624 patients were included, of which 415 were deceased (cases) and 209 were still alive 90 days after a CDI diagnosis (controls). The most common antibiotics used previously in both groups were β-lactams; previous exposure to fluoroquinolones was significantly (p = 0.0004) greater in deceased patients. Multivariate logistic regression showed that the factors independently related with death during CDI were older age, inadequate CDI therapy, cachexia, malignancy, Charlson Index, long-term care, elevated white blood cell count (WBC), C-reactive protein (CRP), bacteraemia, complications, and cognitive impairment. In addition, older age, higher levels of WBC, neutrophil, CRP or creatinine, the presence of malignancy, cognitive impairment, and complications were strongly correlated with shortening the time from CDI diagnosis to death. CDI prevention should be primarily focused on hospitalised elderly people receiving antibiotics. WBC, neutrophil count, CRP, creatinine, albumin and lactate levels should be tested in every hospitalised patient treated for CDI to assess the risk of a fatal outcome.

Background Studies have repeatedly highlighted the need for homogenisation of training content and opportunities in infection prevention and control (IPC) across European countries. Objectives To map current training opportunities for IPC professionals, define local needs and highlight differences, across 11 European countries (Cyprus, France, England, Germany, Greece, Italy, Netherlands, Poland, Romania, Spain, Switzerland). Sources From July 2018 to February 2019, IPC experts directly involved in IPC training and education in their countries and/or internationally were invited to complete a prespecified set of questions in order to provide a detailed description of IPC training opportunities and needs in their country. Conclusions IPC training among nurses and doctors varies greatly across countries, with differences in content and type of training (e.g., standardised curriculum, educational programme, clinical experience) duration, as well as in assessment and recognition/accreditation. The observed heterogeneity in IPC training between European countries can be eliminated through establishment of interdisciplinary region-wide training programmes, with common learning objectives, shared know-how and supported by national and international professional bodies.

Antimicrobial stewardship (AMS) and Infection prevention and control (IPC) are two key complementary strategies that combat development and spread of antimicrobial resistance. The ESGAP (ESCMID Study Group for AMS), EUCIC (European Committee on Infection Control) and TAE (Trainee Association of ESCMID) investigated how AMS and IPC activities and training are organized, if present, at national level in Europe. From February 2018 to May 2018, an internet-based cross-sectional survey was conducted through a 36-item questionnaire, involving up to three selected respondents per country, from 38 European countries in total (including Israel), belonging to the ESGAP/EUCIC/TAE networks. All 38 countries participated with at least one respondent, and a total of 81 respondents. Education and involvement in AMS programmes were mandatory during the postgraduate training of clinical microbiology and infectious diseases specialists in up to one-third of countries. IPC was acknowledged as a specialty in 32% of countries. Only 32% of countries had both guidance and national requirements regarding AMS programmes, in contrast to 61% for IPC. Formal national staffing standards for AMS and IPC hospital-based activities were present in 24% and 63% of countries, respectively. The backgrounds of professionals responsible for AMS and IPC programmes varied tremendously between countries. The organization and training of AMS and IPC in Europe are heterogeneous and national requirements for activities are frequently lacking.

Mucormycosis is a rare fungal infection in immunocompetent patients, whereas in immunocompromised, it may be systemic and disseminated infection associated with high mortality. Mucormycosis is one of the most rapidly progressing and fulminant forms of fungal infections; Mucor circinelloides is rarely isolated species, also from immunocompromised patients. The reported case of mucormycosis after a traffic accident indicates that it may be the result of a contamination of wound by M. circinelloides coming from the environment. The fungal strain was identified by phenotypic methods and confirmed by molecular methods. Etest method was used for susceptibility testing of the fungal strain. No mycotoxins were detected in the analyzed sample. The infection was successfully treated with amphotericin B, but amputation of the lower limb was necessary.