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Shortly after the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cases of viral, bacterial, and fungal coinfections in hospitalized patients became evident. This retrospective study investigates the prevalence of multiple pathogen co-detections in 1472 lower respiratory tract (LRT) samples from 229 SARS-CoV-2-positive patients treated in the largest intensive care unit (ICU) in Slovenia. In addition to SARS-CoV-2, (rt)RT-PCR tests were used to detect cytomegalovirus (CMV), Epstein–Barr virus (EBV), herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), varicella zoster virus (VZV), and atypical bacteria: Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila/spp. At least one co-detection was observed in 89.1% of patients. EBV, HSV-1, and CMV were the most common, with 74.7%, 58.1%, and 38.0% of positive patients, respectively. The median detection time of EBV, HSV-1, and CMV after initial SARS-CoV-2 confirmation was 11 to 20 days. Bronchoalveolar lavage (BAL) and tracheal aspirate (TA) samples showed equivalent performance for the detection of EBV, CMV, and HSV-1 in patients with both available samples. Our results indicate that SARS-CoV-2 infection could be a risk factor for latent herpesvirus reactivation, especially HSV-1, EBV, and CMV. However, additional studies are needed to elucidate the clinical importance of these findings. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has strained healthcare systems globally. Shortages of hospital beds, reassignment of healthcare workers to COVID-19-dedicated wards, an increased workload, and evolving infection prevention and control measures have potentially contributed to the spread of multidrug-resistant bacteria (MDRB). To determine the impact of the COVID-19 pandemic at the University Medical Center Ljubljana, a tertiary teaching hospital, we analyzed the monthly incidence of select bacterial species per patient from 2018 to 2022. The analysis was performed for all isolates and for MDRB isolates. The data were analyzed separately for isolates from all clinical samples, from blood culture only, and from clinical and surveillance samples. Our findings revealed an increased incidence density of patients with Enterococcus faecium, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa isolates from clinical samples during the COVID-19 period in the studied hospital. Notably, the incidence density of MDRB isolates—vancomycin-resistant E. faecium, extended-spectrum betalactamase-producing K. pneumoniae, and betalactam-resistant P. aeruginosa—from clinical samples increased during the COVID-19 period. There were no statistically significant differences in the incidence density of patients with blood culture MDRB isolates. We observed an increase in the overall MDRB burden (patients with MDRB isolates from both clinical and surveillance samples per 1000 patient days) in the COVID-19 period in the studied hospital for vancomycin-resistant E. faecium, carbapenem-resistant K. pneumoniae, and betalactam-resistant P. aeruginosa and a decrease in the methicillin-resistant S. aureus burden. [ABSTRACT FROM AUTHOR]

To better understand the natural history of anogenital warts (AGWs) and the dynamics of HPV6/11 infection in regional hairs, 32 newly diagnosed male patients with AGWs and 32 age-matched healthy controls were closely followed. During enrollment and six follow-up visits (every 2.6 months), 43 AGW tissues and 1232 anogenital and eyebrow hair samples were collected. This is the closest longitudinal monitoring of AGW patients to date. Patients were treated according to standards of care. The HPV6/11 prevalence was 19.9% in the patients' hair samples (HPV6 B1 in 53.1%) and 0% in the controls. The highest HPV6/11 prevalence was found in pubic hairs (29.0%) and the lowest in eyebrows (7.1%). The odds of having HPV6/11-positive hairs increased with smoking, shaving the anogenital region, and age. A close association between HPV6/11 presence in hairs and clinically visible AGWs was observed. The proportion of patients with visible AGWs and HPV6/11-positive hairs declined during follow-up with similar trends. No particular HPV6/11 variant was linked with an increased AGW recurrence, but the sublineage HPV6 B1 showed significantly higher clearance from hairs. Despite treatment, 78.1% and 62.5% of the AGW patients experienced one and two or more post-initial AGW episodes, respectively. The patients with HPV6/11-positive hairs or visible AGWs at a preceding visit demonstrated substantially higher odds of presenting with visible AGWs at a subsequent visit. [ABSTRACT FROM AUTHOR]

Purpose: To evaluate the effect of a full-mouth disinfection protocol (FMD) on periodontal parameters, glycaemic control and subgingival microbiota of periodontal patients with type 1 and type 2 diabetes, as well as those without diabetes. Materials and Methods: This study included 33 patients with periodontitis. Eleven of them were type 1 diabetes patients, 11 were type 2 diabetes patients, and 11 were non-diabetics. At baseline and 3 months after the FMD, the periodontal parameters of each patient were recorded, samples of capillary blood for the chairside assessment of HbA1c were taken, and plaque samples from the two deepest periodontal pockets were collected to test for the presence of Aggregatibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythia (Tf) and Treponema denticola (Td). Results: Bleeding on probing (BOP), probing pocket depth (PPD), clinical attachment level (CAL) and glycated haemoglobin (HbA1c) decreased statistically significantly (p < 0.05) in all three groups 3 months after FMD. Only the proportion of Pg in the control group decreased statistically significantly (p < 0.05), while the proportion of other bacteria decreased or remained the same, whereby the differences were not statistically significant. Moreover, the proportion of Aa in type 1 diabetics increased statistically significantly (p < 0.05). Conclusion: The FMD protocol improves periodontal parameters and glycaemic control of type 1 and type 2 diabetes patients with periodontitis. [ABSTRACT FROM AUTHOR]

Purpose: To investigate the subgingival microbiological profiles of patients with periodontitis, to determine their stage and grade scores and to evaluate the differences in the microbiota among different stages and grades. Materials and Methods: Sixty-seven (n = 67) periodontitis patients were selected. Periodontitis staging and grading, following the 2018 classification system, were defined. Following a clinical examination, subgingival samples were taken from the deepest periodontal pocket of each quadrant for cultivation, identification and quantification. The prevalence, proportion and counts of nine selected periodontal pathogens were determined, and differences between periodontitis stages III and IV and grades B and C were assessed. Results: All nine cultivable periodontal bacteria were detected, of which the most prevalent was P. intermedia (91.0%) and the least prevalent were E. corrodens (9.0%) and C. ochracea (9.0%). The frequency of detection of the two main target pathogens, A. actinomycetemcomitans and P. gingivalis, was 41.8% and 76.1%, respectively. The prevalence (grade B: 80.6%, grade C: 55.6%, p = 0.035) and total counts (grade B: 19.8 colony forming units - CFU/ml-4 (1.9-52.8); grade C: 4.0 CFU/ml-4 (0.0-26.4); p = 0.022) of F. nucleatum were statistically significantly higher in grade B than in grade C periodontitis patients, whereas the counts of P. gingivalis and A. actinomycetemcomitans were similar between grades and stages. Conclusion: Our study suggests that relevant differences between the various grades of periodontitis exist only in the numbers of F. nucleatum. Prevalence and quantities of other cultivable species between different stages and grades of periodontitis seem to be similar. [ABSTRACT FROM AUTHOR]

Background: Repeated rotation of empiric antibiotic treatment strategies is hypothesized to reduce antibiotic resistance. Clinical rotation studies failed to change unit-wide prevalence of antibiotic resistant bacteria (ARB) carriage, including an international cluster-randomized crossover study. Unit-wide effects may differ from individual effects due to "ecological fallacy". This post-hoc analysis of a cluster-randomized crossover study assesses differences between cycling and mixing rotation strategies in acquisition of carriage with Gram-negative ARB in individual patients. Methods: This was a controlled cluster-randomized crossover study in 7 ICUs in 5 European countries. Clinical cultures taken as routine care were used for endpoint assessment. Patients with a first negative culture and at least one culture collected in total were included. Community acquisitions (2 days of admission or less) were excluded. Primary outcome was ICU-acquisition of Enterobacterales species with reduced susceptibility to: third- or fourth generation cephalosporins or piperacillin-tazobactam, and Acinetobacter species and Pseudomonas aeruginosa with reduced susceptibility for piperacillin-tazobactam or carbapenems. Cycling (altering first-line empiric therapy for Gram-negative bacteria, every other 6-weeks), to mixing (changing antibiotic type every empiric antibiotic course). Rotated antibiotics were third- or fourth generation cephalosporins, piperacillin-tazobactam and carbapenems. Results: For this analysis 1,613 admissions were eligible (855 and 758 during cycling and mixing, respectively), with 16,437 microbiological cultures obtained. Incidences of acquisition with ARB during ICU-stay were 7.3% (n = 62) and 5.1% (n = 39) during cycling and mixing, respectively (p-value 0.13), after a mean of 17.7 (median 15) and 20.8 (median 13) days. Adjusted odds ratio for acquisition of ARB carriage during mixing was 0.62 (95% CI 0.38 to 1.00). Acquired carriage with ARB were Enterobacterales species (n = 61), Pseudomonas aeruginosa (n = 38) and Acinetobacter species (n = 20), with no statistically significant differences between interventions. Conclusions: There was no statistically significant difference in individual patients' risk of acquiring carriage with Gram-negative ARB during cycling and mixing. These findings substantiate the absence of difference between cycling and mixing on the epidemiology of Gram-negative ARB in ICU. Trial registration: This trial is registered with ClinicalTrials.gov, registered 10 January 2011, NCT01293071. [ABSTRACT FROM AUTHOR]

This study focuses on the feasibility of collaborative robot implementation in a medical microbiology laboratory by demonstrating fine tasks using kinesthetic teaching. Fine tasks require sub-millimetre positioning accuracy. Bacterial colony picking and identification was used as a case study. Colonies were picked from Petri dishes and identified using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry. We picked and identified 56 colonies (36 colonies of Gram-negative Acinetobacter baumannii and 20 colonies of Gram-positive Staphylococcus epidermidis). The overall identification error rate was around 11%, although it was significantly lower for Gram-positive bacteria (5%) than Gram-negative bacteria (13.9%). Based on the identification scores, it was concluded that the system works similarly well as a manual operator. It was determined that tasks were successfully demonstrated using kinesthetic teaching and generalized using dynamic movement primitives (DMP). Further improvement of the identification error rate is possible by choosing a different deposited sample treatment method (e.g., semi-extraction, wet deposition). [ABSTRACT FROM AUTHOR]

Objectives: To determine the prevalence, viral load, tissue tropism, and genetic variability of novel human papillomavirus (HPV) type 179, which is etiologically associated with sporadic cases of common warts in immunocompromised patients, and phylogenetically related HPV types 135 and 146. Methods: The representative collection of 850 HPV-associated clinical samples (oral/nasopharyngeal/anal, archival specimens of oral/oropharyngeal/conjunctival/cervical/skin cancer, benign lesions of the larynx/conjunctiva/skin, and eyebrows), obtained from immunocompetent individuals, was tested for the presence of HPV179, HPV135, and HPV146 using type-specific real-time PCRs. To assess the genetic diversity of the HPVs investigated in the non-coding long control region (LCR), several highly sensitive nested PCR protocols were developed for each HPV type. The genetic diversity of HPV179 was additionally determined in 12 HPV179 isolates from different anatomical sites of an only immunocompromised patient included in the study. Results: HPV179, HPV135, and HPV146 were detected in 1.4, 2.0, and 1.5% of the samples tested, respectively, with no preference for cutaneous or mucosal epithelial cells. One (with five single nucleotide polymorphisms; SNPs), four (with one to six SNPs), and four (with one to eight SNPs) genetic variants of HPV179, HPV135, and HPV146, respectively, were identified among eligible samples. HPV179 isolates from the immunocompromised patient exhibited the identical LCR nucleotide sequence, suggesting that HPV179 can cause generalized HPV infections. Conclusions: HPV179, HPV135, and HPV146 have a mucocutaneous tissue tropism and are associated with sporadic infections in immunocompromised and immunocompetent individuals. Because the majority of mutations were found outside the major functional domains of the respective LCRs, we assume that HPV179, HPV135, and HPV146 genetic variants pathogenically do not differ from their prototypes. In addition, no association was found between specific HPV179, HPV135, and HPV146 genetic variants and anatomical sites of infection and/or specific neoplasms. [ABSTRACT FROM AUTHOR]

Objectives: The first hospital outbreak of carbapenemase-producing Enterobacteriaceae in Slovenia occurred in 2014–2016. Whole genome sequencing was used to analyse the population of carbapenem-resistant Klebsiella pneumoniae collected in Slovenia in 2014–2017, including OXA-48 and/or NDM-1 producing strains from the outbreak. Methods: A total of 32 K. pneumoniae isolates were analysed using short-read sequencing. Multi-locus sequence typing and core genome multi-locus sequence typing were used to infer genetic relatedness. Antimicrobial resistance markers, virulence factors, plasmid content and wzi types were determined. Long-read sequencing was used for six isolates for detailed analysis of plasmids and their possible transmission. Results: Overall, we detected 10 different sequence types (STs), the most common being ST437 (40.6%). Isolates from the initial outbreak belonged to ST437 (12/16) and ST147 (4/16). A second outbreak of four ST15 isolates was discovered. A new ST (ST3390) and two new wzi types (wzi-556, wzi-559) were identified. blaOXA-48 was found in 17 (53.1%) isolates, blaNDM-1 in five (15.6%), and a combination of blaOXA-48/NDM-1 in seven (21.9%) isolates. Identical plasmids carrying blaOXA-48 were found in outbreak isolates sequenced with long-read sequencing technology. Conclusions: Whole genome sequencing of Slovenian carbapenem-resistant K. pneumoniae isolates revealed multiple clusters of STs, two of which were involved in the first hospital outbreak of carbapenem producing K. pneumoniae in Slovenia. Transmission of the plasmid carrying blaOXA-48 between two STs was likely to have occurred. A previously unidentified second outbreak was also discovered, highlighting the importance of whole genome sequencing in detection and/or characterization of hospital outbreaks and surveillance of drug-resistant bacterial clones. [ABSTRACT FROM AUTHOR]

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Purpose: To characterize the normal bacterial flora and evaluate the presence of periodontopathogenic bacteria around dental implants and to correlate them with the periodontal flora or, in completely edentulous patients, the alveolar gingival flora. Materials and Methods: Clinical and radiographic parameters were recorded to exclude peri-implantitis in 34 partially edentulous and 19 completely edentulous patients. Partially edentulous patients were subdivided into two subgroups based on the depth of the periodontal pocket: ≤ 4 mm (n = 19) and > 4 mm (n = 15). Microbial samples were collected from periimplant sulci, the deepest periodontal sulci, and, for completely edentulous patients, from the alveolar gingiva. Predominant aerobic bacteria were determined by microbiologic culturing, and multiplex polymerase chain reaction was used to detect five periodontopathogenic bacteria: Porphyromonas gingivalis, Tannerella forsythensis, Treponema denticola, Prevotella intermedia, and Actinobacillus actinomycetemcomitans. Results: In all the examined patients, oral streptococci were the most frequent aerobic peri-implant bacteria. The frequency of four periodontopathogenic bacteria in tooth sulci (A actino - mycetemcomitans, P gingivalis, T forsythensis, T denticola) was significantly higher around natural teeth with deeper periodontal pockets, but there was no significant difference in the frequency of the same bacteria in peri-implant sulci in the two partially edentulous subgroups. In contrast, there were no such bacteria in the peri-implant sulci or the alveolar gingiva of completely edentulous patients. Conclusions: In healthy peri-implant sulci, oral streptococci constitute the predominant bacterial flora. In partially edentulous patients four periodontopathogenic bacteria were detected around implants, and none of these bacteria were found around implants in completely edentulous patients. [ABSTRACT FROM AUTHOR]