Cultivable oral bacteriota dysbiosis in mechanically ventilated COVID-19 patients.

Potential interactions between the SARS-CoV-2 virus and the human oral microbiota are currently investigated widely. Patients with COVID-19 requiring mechanical ventilation in an intensive care unit (ICU) setting are at high risk of developing severe complications, including ventilator-associated pneumonia, thus making oral health management important. The aim of this study was to evaluate the oral health status and assess the dysbiosis of cultivable oral bacteriota in COVID-19 patients hospitalized in an ICU with acute respiratory distress within 36 h following intubation. In this prospective cohort study, we recruited 56 adult COVID-19 patients that qualified for mechanical ventilation in the Temporary ICU for COVID-19 Patients of the University Hospital in Krakow. On admission to the ICU, oral health of patients was assessed using the modified Beck Oral Assessment Score (BOAS). Four oral habitats were sampled, namely the buccal mucosa, tongue, buccal dental surface and gingival pocket. Microorganisms were identified by MALDI/TOF mass spectrometry. The mean age of the study population was 66.5 ± 12.7 years, there were 24 (42.9%) females. All patients included in this study were intubated and ventilated in the ICU, with a corresponding high mortality rate (76.8%). On admission to ICU, 76.8% subjects scored 11-20 on the BOAS scale (median 12 [IQR 10-14]), indicating moderate or severe dysfunction of oral health. Potentially pathogenic bacteria were identified in the oral microbiota samples, including Acinetobacter baumannii, Enterococcus faecalis, Escherichia coli and Klebsiella pneumoniae in 23.2%, 39.3%, 17.9%, and 19.6% of patients, respectively. Lactobacillus spp. were present in 57.1% subjects. The mean CFU counts of all bacteria strains in dental brushes were 9.3E+5 (1.4E+6) and in gingival pockets 7.6E+5 (1.4E+6). The highest CFU counts were observed for Enterococcus spp. and, Lactobacillus spp., although these did not differ significantly from CFU counts of Streptococcus spp. and Staphylococcus spp. In this report we comprehensively characterized the oral health condition and cultivable oral bacteriota in COVID-19 patients hospitalized in an ICU with acute respiratory distress within 36 h following intubation. The oral bacteriota showed significant qualitative and quantitative dysbiosis. Hospitalization in an ICU and mechanical ventilation are important factors leading to oral dysbiosis in SARS-CoV-2 patients.

Coagulase-Negative Staphylococci Contained in Gut Microbiota as a Primary Source of Sepsis in Low- and Very Low Birth Weight Neonates.

BACKGROUND: There are only a few reports in the literature about translocation of coagulase-negative staphylococci (CoNS) as a primary cause of sepsis in neonates, although CoNS are among a short list of "translocating" bacteria when present in abundance. METHODS: 468 blood samples, 119 stool samples, and 8 catheter tips, from 311 neonates, were tested for presence of microorganisms. CoNS strains isolated from the blood and stool or from blood and catheter tip of the same newborn at approximately the same time were paired and typed with PFGE (Pulse-Field Gel Electrophoresis) method. The strains were then tested for the presence of adherence genes and biofilm formation. RESULTS: The strains with identical PFGE profiles in comparison to those with non-identical profiles differed in terms of the pattern of the virulence genes and showed a lack of the genes related to adherence, but more often presence of IS256, which is related to virulence. They also were phenotypically unable to adhere to intestinal Caco2 cells. CONCLUSIONS: A considerable proportion of CoNS strains isolated from bloodstream of VLBW/LWB neonates was identical to the strains isolated from faeces of the same neonates at the same time. These observations may offer indirect evidence indicating that at least some CoNS can translocate from the gastrointestinal tract of the premature neonates into the bloodstream and thus cause generalized infection.

Meningoencephalitis caused by Lactobacillus plantarum - case report.

Specific strains of Lactobacillus spp. are widely used as probiotic agents but it has been repeatedly reported that may have a pathogenic potential. We present the report on a case of meningoencephalitis caused by Lactobacillus plantarum in a 63-year-old man with newly diagnosed metastatic planoepitheliale lung cancer. The patient was hospitalised due to newly diagnosed cancer and during the course of hospitalisation developed symptoms of neuroinfection. On the basis of the symptoms and results of the conducted tests the patient was diagnosed with bacterial meningoencephalitis. In microbiological tests of the blood and cerebrospinal fluid L. plantarum was cultured. During the course of antibiotic therapy the patient's condition improved. Lactobacilli are now recognised as a causative agent of infection, most notably bacteraemia. To our knowledge, this is the fourth documented case of Lactobacillus-associated neuroinfection, and only the second in an adult. Lactobacilli cause mostly opportunistic infections in immunocompromised individuals.

The level of fecal calprotectin significantly correlates with Clostridium difficile infection severity.

INTRODUCTION: Fecal calprotectin (FC) rises significantly in intestinal inflammation accompanied by neutrophil activation - such as Clostridium difficile infection (CDI). The aim of the study was to evaluate the benefit of FC testing in assessing the severity of CDI. MATERIALS AND METHODS: The study group included 76 patients with CDI hospitalized in the Jagiellonian University Hospital in Krakow from July 2017 till January 2018. FC levels were measured using an EIA (Enzyme Immunoassay). Demographic, clinical information and blood tests were recorded using standardized data collection forms. The selection of patients into non-severe and severe groups was carried out in accordance with the ESCMID criteria (European Society of Clinical Microbiology and Infectious Diseases) and some modi cations to those criteria were proposed. RESULTS: the studied population included 76 patients (39 men and 37 women) with CDI aged from 24 to 98 years (mean: 72). Median calprotectin level was 739 (Q25-Q75: 612-799 µg/g), characteristic of patients with colitis. A statistically significant difference in FC concentration in patients with severe vs non-severe CDI was observed (severe - 770 vs non-severe - 659 µg/g, p = 0.009). FC directly correlated with platelets level; however, no correlation between FC level and the blood parameters prognostic for CDI (leukocyte, neutrophil count, albumin, creatinine levels) was found. CONCLUSION: FC level is an indication of ongoing intestinal inflammation in CDI patients. FC level significantly correlated with CDI severity, which demonstrates that FC could serve as a predictive marker for assessing CDI severity.

Prevalence of human pathogens of the clade Nakaseomyces in a culture collection-the first report on Candida bracarensis in Poland.

Human pathogens belonging to the Nakaseomyces clade include Candida glabrata sensu stricto, Candida nivariensis and Candida bracarensis. Their highly similar phenotypic characteristics often lead to misidentification by conventional laboratory methods. Therefore, limited information on the true epidemiology of the Candida glabrata species complex is available. Due to life-threatening infections caused by these species, it is crucial to supplement this knowledge. The aim of the study was to estimate the prevalence of C. bracarensis and C. nivariensis in a culture collection of C. glabrata complex isolates. The study covered 353 isolates identified by biochemical methods as C. glabrata, collected from paediatric and adult patients hospitalised at four medical centres in Southern Poland. The multiplex PCR was used to identify the strains. Further species confirmation was performed via sequencing and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) analysis. One isolate was recognised as C. bracarensis (0.28%). To our knowledge, it is the first isolate in Poland. C. glabrata sensu stricto species has been confirmed for all the remaining isolates. No C. nivariensis was found. Our study has shown that the prevalence of C. nivariensis and C. bracarensis strains is infrequent. However, it should be emphasised that the incidence of these strains may differ locally and depend on environmental factors and the population.

Comparison of nested, multiplex, qPCR; FISH; SeptiFast and blood culture methods in detection and identification of bacteria and fungi in blood of patients with sepsis.

BACKGROUND: Microbiological diagnosis of sepsis relies primarily on blood culture data. This study compares four diagnostic methods, i.e. those developed by us: nested, multiplex, qPCR (qPCR) and FISH with commercial methods: SeptiFast (Roche) (SF) and BacT/ALERT® 3D blood culture system (bioMérieux). Blood samples were derived from adult patients with clinical symptoms of sepsis, according to SIRS criteria, hospitalized in the Intensive Care Unit. RESULTS: Using qPCR, FISH, SF, and culture, microbial presence was found in 71.8%, 29.6%, 25.3%, and 36.6% of samples, respectively. It was demonstrated that qPCR was significantly more likely to detect microorganisms than the remaining methods; qPCR confirmed the results obtained with the SF kit in all cases wherein bacteria were detected with simultaneous confirmation of Gram-typing. All data collected through the FISH method were corroborated by qPCR. CONCLUSIONS: The qPCR and FISH methods described in this study may constitute alternatives to blood culture and to the few existing commercial molecular assays since they enable the detection of the majority of microbial species, and the qPCR method allows their identification in a higher number of samples than the SF test. FISH made it possible to show the presence of microbes in a blood sample even before its culture.

[Use of the percutaneous drainage in the treatment of patients with hepatic abscesses]. / Zastosowanie drenazu przezskórnego w leczeniu chorych z ropniami watroby.

AIM OF THE STUDY: The aim of this study was to review our results in managing liver abscess with the use of sonographically-guided percutaneous drainage. MATERIAL AND METHODS: There were 24 patients (including 12 male and 12 female patients) with liver abscesses treated from 1993 to 2009 in our department. Mean age in the male group amounted to 52 (17-70), while in the female group - 60 (46-72). The group of 22 patients (91,6%) were treated with the use of percutaneously inserted "pigtail drain". RESULTS: The group of 22 patients (11 male and 11 female patients) was treated with the use of percutaneous sonographically-guided drainage. Eschericha coli constituted the most common etiological factor isolated from the purulent content. An average drainage time amounted to 9,5 days. Percutaneous drainage proved ineffective only in 4 patients (2 male and 2 female). In 2 of those cases failure was due to recurrent obstruction of the catheter and in remaining 2--due to migration of the drain outside the abscess. 2 of those patients were treated successfully with another sonographically-guided drainage, while 2 patients required open surgical operation. CONCLUSIONS: Percutaneous sonographically-guided drainage together with antimicrobial therapy constitutes valuable method of choice in the management of liver abscess. The technique has small morbidity and complication ratio allowing avoidance of more invasive surgical interventions.

[Microbiological report of examination of samples recovered during exhumation of general Wladyslaw Sikorski's remains]. / Raport z badania mikrobiologicznego próbek materialów pobranych podczas ekshumacji szczatków generala Wladyslawa Sikorskiego.

Specimens obtained during autopsy of exhumed remains of general Wladyslaw Sikorski were examined applying aerobic and anaerobic cultures. The results are presented in the table.

[Etiological bacterial factors of respiratory system infections in the Intensive Care Unit Surgery Clinic]. / Bakteryjne czynniki etiologiczne zakazen ukladu oddechowego w Oddziale Intensywnej Terapii Kliniki Chirurgicznej.

Pneumonia is the most frequently occurring hospital-acquired infection in Intensive Care Units (ICU). The frequency of bacteriological pathogenic factors in the surgical ICU and efficiency of empiric antibiotic therapy used in ICU was assessed. The study included 239 ICU patients in the I Department of General Surgery and Gastroenterological Surgery Clinics of Jagiellonian University Hospital in 2006 year. The bronchoscope materials were worked out with the application of qualitative and quantitative diagnostic methods. Identification of bacteria strains was based on the qualification of their biochemical characteristics based on commercially available tests (bio-Merieux): ID 32E and ID 32GN for rod-shaped (bacilli) bacteria and tests ID 32 STAPH and api 20 STREP that were applied to identify spherical (cocci) bacteria. Sensitivity to medicines was marked in the automatic system VITEK 2 (bio-Merieux). The ability to produce extended spectrum beta-lactamases (ESBL) was marked with double disc test (DDT). The immunity to meticiline was marked with diffusion-disc test and with E test method (AB BIODISK). The most frequently isolated gram-negative bacteria (92.3%). Klebsiella pneumoniae, Serratia marcescens constituted the largest percentage of bacteria strains resistant to many antibiotics. Change of antibiotic used was necessary in 24.3% of patients.

Clinical presentation of extraintestinal infections caused by non-typhoid Salmonella serotypes among patients at the University Hospital in Cracow during an 7-year period.

The most characteristic finding in non-typhoid salmonella (NTS) infection is acute food related outbreaks of gastroenteritis, which is usually benign and self-limiting. However, more serious extraintestinal findings, such as bacteraemia and focal infections localized to any organ may appear. The objective of this paper is to describe the most important characteristic of the extraintestinal infections due to NTS serotypes observed in University Hospital, in Cracow between January 2000 and December 2006. To do so, we reviewed the clinical presentations, risk groups, complications and outcomes of in-patients, in which extraintestinal non-typhoid Salmonella serotypes were isolated, applying a clinomicrobiological protocol. Out of 30 patients with either bacteraemias (n = 22) or focal salmonella infections (n = 8), 12 had malignancies, 17 had immune dysfunction state, 9 had gastrointestinal disorders and 8 had chronic heart, pulmonary or kidney disease. Four of these patients (13%) who had hematological malignancies (2), renal transplantation (1) and pulmonary disease (1) died. Regarding the clinical picture, primary bacteraemia and focal infections occurred with similar frequency (33.3% and 26.7%, respectively); the remaining were bacteraemias secondary to gastroenteritis. The incidence rate (mean 0.30/1000 hospital admission/year) increased steadily from 0.19/1000 to 0.32/1000 hospital admission during the study period. From 30 Salmonella isolates from extraintestinal samples collected, only four isolates were resistant to ampicillin, ciprofloxacin or trimethoprim-sulfamethoxazole. This finding indicate that multidrug resistance does not represent a serious problem among NTS serotypes collected from the our medical center as monitored over a period of 7 years. Given this presentation, clinicians need to have a high index of suspicion and to consider preemptive therapy, especially in elderly patients who are likely to develop severe immunosuppression following interventions.

[Correlation between computed tomography and microbiological results in chronic sinusitis]. / Korelacja obrazu tomografii komputerowej w przewleklym zapaleniu zatok przynosowych z wynikami badan mikrobiologicznych.

This article presents the observed correlation between the advancement of inflammatory lesions in paranasal sinuses found on computed tomography and microbiological specimen results in chronic sinusitis. The examined study group consisted of 28 patients, aged 19-59 years, in whom endoscopic sinus surgery was performed. In each patient prior to planned surgery a sinus CT scan was performed the result of which was scored using the Lund-Mackay scale, bacteriological and mycological examinations of nasal mucous secretion were also performed. In the study group a positive correlation between the CT score point sum and the number of pathogen species (regression test: r = 0.46; p = 0.0141) was found. With each additional pathogen species found the CT grading rose by 2.3 points. We also found that in patients with positive bacterial culture the average CT score rose by 4.4 (ANOVA: F(1,23)= 3.69; p = 0.0333). However no rise was found in the case of fungi and no interaction between bacteria and fungi was found. In cases of advanced sinusitis where a high CT lesion score of is found antimicrobial therapy based on exact microbiological diagnostics should be given in the perioperative period.

[Alcaligenes xylosoxidans--a pathogen of chronic ear infection]. / Alcaligenes xylosoxidans--patogen przewleklego zapalenia ucha.

INTRODUCTION: We discuss a case of a 48-year old man admitted to our Department with symptoms of chronic ear infection, that didn't answer to typical conservative treatment. The culture of the discharge was positive for Alcaligenes xylosoxidans. MATERIAL AND METHODS: We report characteristic features of that bacteria and we compare them with features of other pathogens typical for otitis media. We present performed treatment too. RESULTS: Alcaligenes xylosoxidans is a nonfermenting gram-negative rod. It can be confused with other nonfermentive, gram-negative rods, especially Pseudomonas species, in clinical specimens so that its role as a significant pathogen may be underestimated. Alcaligenes xylosoxidans is a part of normal human flora, especially skin and gastrointestinal tract, and can cause serious infections in human (especially in patients with immunodeficiency and premature children). CONCLUSIONS: Reports about Alcaligenes xylosoxidans as a cause of chronic otitis media are very rare and it can be supposed to stay a new kind of ear infection.

[Infections with Van B phenotype Enterococcus faecium and E. faecalis in patients with immune deficiency during the course of hematologic neoplasms]. / Zakazenia fenotypem Van B Enterococcus faecium i E. faecalis u chorych z niedoborem immunologicznym w przebiegu chorób nowotworowych ukladu krwiotwórczego.

In this work, we have analyzed the second outbreak of VRE with the VanB phenotype to be identified in the country. The aim of this study was to characteristics of the types of resistance to glycopeptide antibiotic and to check the resistance patterns of these pathogens. A trial of monitoring the risk factors for colonization or infection with VRE as well as epidemiological investigation were undertaken. Genus identification of the isolates was performed according to the method of Facklam and Collins, and species were identified using the API 20 Strep test. MICs of different antimicrobial agents were determined by the E-test method. The isolates collected during the investigation demonstrated resistance to multiple antimicrobials, which is a common characteristic of VRE. Isolates were found to be uniformly resistant to penicillin, fluoroquinolones, tetracycline and to high concentrations of aminoglycosides. The only drugs with in vitro activity against the isolates were ampicillin (VRES), linezolid (VRES, VREM) and quinupristin-dalfopristin (VREM). Except for a single VREM isolate, they all revealed the typical VanB phenotype with resistance to vancomycin and susceptibility to teicoplanin. One of the VREM isolates turned out to be resistant to teicoplanin, which coincided with the use of this antibiotic in the patient's therapy. Its vanB gene variant differed by a single mutation from that found in other isolates; however, it also lacked a large part of the vanB gene claster, including the regulatory genes vanRB and -SB, and the vancomycin--inducible promoter PYB. Our studies have found an association between colonization or infection with VRE and the mean duration of hospital stay, previously administration of glycopeptide, cephalosporins and imipenem. These organisms were a common cause of monoethiological bloodstream infections.

[Bacterial and fungal bloodstream infections in patients at the University Hospital of Cracow]. / Bakteryjne i grzybicze zakazenia krwi u chorych w Oddzialach Klinicznych Szpitala Uniwersyteckiego w Krakowie.

In presented material evaluation of changes in sepsis and types of bloodstream infections of hospitalized patients in Wards of the University Hospital in Cracow were examined. Results of 9,138 blood cultures studied in years 1989-1999 were analysed. All of the blood samples were recovered from 4,656 infected adults at Clinics of the University Hospital in Cracow. Microbiological blood examinations were held in system of constant monitoring of isolated cultures applying BacT/Alert--colorimetric system (Organon Teknika). Cultured micro--organisms were identified using commercial biochemical tests (bio-Merieux). During period of research changes of profile of isolated microorganisms was observed. Percentage of blood infections of Enterococcus spp. etiology increased from 2.2% in 1989 to 9.8% in 1997-98 (p = 0.014). Dynamic growth of non-fermentative S. maltophilia bacilli to 5.5% (p = 0.036) and Serratia marcescens to 13.8% (p = 0.042) in 1999 was revealed. Designed according to our research review of fungal flora in years 1989-1999 revealed tendency of systematic growth of invasive candidemia frequency, from 1.1% to 10.4%. Diagnostic and therapeutic profile of Departments was in a strict connection with increase of the number and meaning of the politiological bacteremias (p = 0.036) in total number of systemic infections cases.