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.
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.
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.
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.
Background
Candida bloodstream infections (BSI) became an important invasive disease in the late 20th century, in particular among immunocompromised patients. Although considerable progress has been ...made in the management of patients with invasive mycoses, Candida BSI are still widespread among hospitalised patients and are associated with relatively high mortality.
Objectives
We conducted a retrospective study to evaluate patient characteristics, incidence, species distribution and antifungal susceptibility of BSI isolates of Candida spp. as well as outcomes of Candida BSI from 2001 to 2012, before the widespread use of echinocandins. This is the first epidemiological study of Candida BSI in Slovenia so far.
Methods
All documented candidaemia cases from 2001 to 2012 in two major hospitals—University Medical Centre and Institute of Oncology in Ljubljana, Slovenia—were taken into consideration. Candida BSI were identified in 422 patients (250 male, 172 female). Laboratory and clinical data of these patients were retrospectively analysed. Mann‐Whitney U test was used to compare continuous variables and Fisher's exact test or chi‐squared test for categorical variables.
Results and conclusions
The average incidence of Candida BSI was 0.524/10.000 patient‐days (0,317/1000 admissions); 16/422 were younger than 1 year and 251/422 patients were over 60 years old. The most commonly isolated species were Candida albicans and Candida glabrata, followed by Candida parapsilosis. Majority of the patients had a single episode of Candida BSI, multiple episodes of Candida BSI occurred in 18/434 patients (4.1%); in 25/434 patients (5.8%) mixed Candida BSI were observed. Crude 30‐day case‐fatality rate was 55.4%.
We monitored trends of severe COVID-19 morbidity in Slovenia during weeks 13 to 37 2021. National weekly rates of severe acute respiratory infections (SARI) cases testing positive for SARS-CoV-2 at ...admission in all hospitals varied between 0.2 and 16.3 cases per 100,000 population. Of those without previous COVID-19 diagnosis, SARI COVID-19 admission rates ranged between 0.3 and 17.5 per 100,000 unvaccinated, and 0.0 and 7.3 per 100,000 fully vaccinated individuals. National SARI COVID-19 surveillance is essential in informing COVID-19 response.
Infective endocarditis is a growing problem with many shifts due to ever-increasing comorbid illnesses, invasive procedures, and increase in the elderly. We performed this multinational study to ...depict definite infective endocarditis. Adult patients with definite endocarditis hospitalized between January 1, 2015, and October 1, 2018, were included from 41 hospitals in 13 countries. We included microbiological features, types and severity of the disease, complications, but excluded therapeutic parameters. A total of 867 patients were included. A total of 631 (72.8%) patients had native valve endocarditis (NVE), 214 (24.7%) patients had prosthetic valve endocarditis (PVE), 21 (2.4%) patients had pacemaker lead endocarditis, and 1 patient had catheter port endocarditis. Eighteen percent of NVE patients were hospital-acquired. PVE patients were classified as early-onset in 24.9%. A total of 385 (44.4%) patients had major embolic events, most frequently to the brain (
n
= 227, 26.3%). Blood cultures yielded pathogens in 766 (88.4%). In 101 (11.6%) patients, blood cultures were negative. Molecular testing of vegetations disclosed pathogens in 65 cases. Overall, 795 (91.7%) endocarditis patients had any identified pathogen. Leading pathogens (
Staphylococcus aureus
(
n
= 267, 33.6%),
Streptococcus viridans
(
n
= 149, 18.7%), enterococci (
n
= 128, 16.1%), coagulase-negative staphylococci (
n
= 92, 11.6%)) displayed substantial resistance profiles. A total of 132 (15.2%) patients had cardiac abscesses; 693 (79.9%) patients had left-sided endocarditis. Aortic (
n
= 394, 45.4%) and mitral valves (
n
= 369, 42.5%) were most frequently involved. Mortality was more common in PVE than NVE (NVE (
n
= 101, 16%), PVE (
n
= 49, 22.9%),
p
= 0.042).
A total of 188 human (n = 92) and animal (n = 96) isolates of Clostridium difficile of different PCR ribotypes were screened for susceptibility to 30 antimicrobials using broth microdilution. When ...comparing the prevalence of antimicrobial resistance, the isolates of animal origin were significantly more often resistant to oxacillin, gentamicin and trimethoprim/sulfamethoxazole (P<0.01). The most significant difference between the animal and human populations (P = 0.0006) was found in the level of imipenem resistance, with a prevalence of 53.3 % in isolates of human origin and 28.1 % in isolates of animal origin. Overall, the results show similar MICs for the majority of tested antimicrobials for isolates from human and animal sources, which were collected from the same geographical region and in the same time interval. This supports the hypothesis that C. difficile could be transmissible between human and animal hosts. Resistant isolates have been found in all animal species tested, including food and companion animals, and also among non-toxigenic isolates. The isolates of the most prevalent PCR ribotype 014/020 had low resistance rates for moxifloxacin, erythromycin, rifampicin and daptomycin, but a high resistance rate for imipenem. Multiresistant strains were found in animals and humans, belonging to PCR ribotypes 012, 017, 027, 045, 046, 078 and 150, and also to non-toxigenic strains of PCR ribotypes 010 and SLO 080.
Early diagnosis with rapid detection of the virus plays a key role in preventing the spread of infection and in treating patients effectively. In order to address the need for a straightforward ...detection of SARS-CoV-2 infection and assessment of viral spread, we developed rapid, sensitive, extraction-free one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) tests for detecting SARS-CoV-2 in saliva. We analyzed over 700 matched pairs of saliva and nasopharyngeal swab (NSB) specimens from asymptomatic and symptomatic individuals. Saliva, as either an oral cavity swab or passive drool, was collected in an RNA stabilization buffer. The stabilized saliva specimens were heat-treated and directly analyzed without RNA extraction. The diagnostic sensitivity of saliva-based RT-qPCR was at least 95% in individuals with subclinical infection and outperformed RT-LAMP, which had at least 70% sensitivity when compared to NSBs analyzed with a clinical RT-qPCR test. The diagnostic sensitivity for passive drool saliva was higher than that of oral cavity swab specimens (95% and 87%, respectively). A rapid, sensitive one-step extraction-free RT-qPCR test for detecting SARS-CoV-2 in passive drool saliva is operationally simple and can be easily implemented using existing testing sites, thus allowing high-throughput, rapid, and repeated testing of large populations. Furthermore, saliva testing is adequate to detect individuals in an asymptomatic screening program and can help improve voluntary screening compliance for those individuals averse to various forms of nasal collections.
In the third Slovenian national healthcare-associated infections (HAIs) prevalence survey, conducted within the European point prevalence survey of HAIs and antimicrobial use in acute care hospitals, ...we estimated the prevalence of all types of HAIs and identified factors associated with them.
Patients were enrolled into a one-day cross-sectional study in November 2017. Descriptive analyses were performed to describe the characteristics of patients, their exposure to invasive procedures and the prevalence of different types of HAIs. Univariate and multivariate analyses of association of having at least one HAI with possible risk factors were performed to identify risk factors.
Among 5,743 patients, 4.4% had at least one HAI and an additional 2.2% were still treated for HAIs on the day of the survey, with a prevalence of HAIs of 6.6%. The prevalence of pneumoniae was the highest (1.8%), followed by surgical site infections (1.5%) and urinary tract infections (1.2%). Prevalence of blood stream infections was 0.3%. In intensive care units (ICUs), the prevalence of patients with at least one HAI was 30.6%. Factors associated with HAIs included central vascular catheter (adjusted odds ratio aOR 4.1; 95% confidence intervals CI: 3.1-5.4), peripheral vascular catheter (aOR 3.0; 95% CI: 2.3-3.9), urinary catheter (aOR 1.8; 95% CI: 1.4-2.3).
The prevalence of HAIs in Slovenian acute care hospitals in 2017 was substantial, especially in ICUs. HAIs prevention and control is an important public health priority. National surveillance of HAIs in ICUs should be developed to support evidence-based prevention and control.
In the second Slovenian national healthcare-associated infections (HAIs) prevalence survey, conducted within the European point prevalence survey of HAIs and antimicrobial use in acute-care ...hospitals, we estimated the prevalence of all types of HAIs and identified risk factors.
Patients from acute-care hospitals were enrolled into a one-day cross-sectional study in October 2011. Descriptive analyses were performed to describe the characteristics of patients, their exposure to invasive procedures and the prevalence of different types of HAIs. Univariate and multivariate analyses of association of having at least one HAI with possible risk factors were performed to identify risk factors.
Among 5628 patients, 3.8% had at least one HAI and additional 2.6% were still being treated for HAIs on the day of the survey; the prevalence of HAIs was 6.4%. The prevalence of urinary tract infections was the highest (1.4%), followed by pneumoniae (1.3%) and surgical site infections (1.2%). In intensive care units (ICUs), the prevalence of patients with at least one HAI was 35.7%. Risk factors for HAIs included central vascular catheter (adjusted odds ratio (aOR) 4.0; 95% confidence intervals (CI): 2.9-5.7), peripheral vascular catheter (aOR 2.0; 95% CI: 1.5-2.6), intubation (aOR 2.3; 95% CI: 1.4-3.5) and rapidly fatal underlying condition (aOR 2.1; 95% CI: 1.4-3.3).
The prevalence of HAIs in Slovenian acute-care hospitals in 2011 was substantial, especially in ICUs. HAIs prevention and control is an important public health priority. National surveillance of HAIs in ICUs should be developed to support evidence-based prevention and control.
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