Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates

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. Multilocus 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

Prevalenca in dejavniki, povezani z bolnišničnimi okužbami v slovenskih bolnišnicah za akutno oskrbo : rezultati tretje nacionalne presečne raziskave

Introduction. 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. Methods. 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. Results. 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] 4.195% confidence intervals [CI]: 3.1–5.4), peripheral vascular catheter (aOR 3.095% CI: 2.3–3.9), urinary catheter (aOR 1.895% CI: 1.4–2.3). Conclusions. 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.Izhodišča. Tretja slovenska nacionalna presečna raziskava bolnišničnih okužb (BO) je potekala v okviru evropske presečne raziskave okužb, povezanih z zdravstvom in uporabe protimikrobnih zdravil v bolnišnicah za akutno oskrbo. Naši cilji so bili oceniti prevalenco vseh vrst BO in opredeliti dejavnike, ki so povezani z BO. Metode. V enodnevno presečno raziskavo smo vključili vse bolnike, ki so bili na izbrani dan v novembru 2017 zdravljeni v slovenskih bolnišnicah za akutno oskrbo. Z deskriptivnimi analizami smo opisali značilnosti bolnikov, izpostavljenost invazivnim posegom in ocenili prevalenco različnih vrst BO. Z univariatnimi in multivariatnimi analizami povezanosti BO z možnimi dejavniki tveganja smo opredelili dejavnike tveganja. Rezultati. Na dan raziskave je imelo BO 4,4 % (95 % interval zaupanja (IZ): 3,9 %–4,9 %) bolnikov in dodatnih 2,2 % (95% IZ: 1,8 %–2,6 %) bolnikov je bilo še vedno zdravljenih zaradi BO, torej je imelo BO 6,6 % (95% IZ: 6,0 %–7,3 %) bolnikov oziroma je bila prevalenca BO 6,6 %. Na 100 bolnikov je bilo 7,1 epizod BO, ker so nekateri bolniki imeli več kot eno epizodo. Najvišja je bila prevalenca pljučnic (1,8 %), sledile so okužbe kirurške rane (1,5 %) in okužbe sečil (1,2 %). Prevalenca okužb krvi je bila 0,3 %. Delež bolnikov z vsaj eno BO je bil najvišji v enotah za intenzivno zdravljenje (30,6 %). Na 100 bolnikov v enotah za intenzivno zdravljenje je bilo 38,3 epizod BO. V primerjavi z bolniki brez različnih invazivnih posegov so imeli bolniki s centralnim žilnim katetrom 4,1-krat višji obet BO (prilagojeno razmerje obetov (pRO) 4,195 % interval zaupanja (IZ): 3,1–5,4), bolniki s perifernim žilnim katetrom 3,0-krat višji obet BO (pRO 3,095 % IZ: 2,3–3,9), bolniki z urinskim katetrom 1,8-krat višji obet BO (pRO 1,895 % IZ: 1,4–2,3) in bolniki z operacijo v času hospitalizacije 1,6-krat višji obet BO (pRO 1,695% IZ: 1,2–2,0). Zaključki. Prevalenca BO v slovenskih bolnišnicah za akutno oskrbo je bila v letu 2017 precejšnja. Predvsem je bila visoka v enotah za intenzivno zdravljenje. Preprečevanje in obvladovanje BO je pomembna javnozdravstvena prednostna naloga. Za preprečevanje in obvladovanje BO, ki temelji na dokazih, je treba vzpostaviti nacionalno epidemiološko spremljanje BO tudi v enotah za intenzivno zdravljenje

Sensitivity and specificity of the method used for ascertainment of healthcare-associated infections in the second Slovenian national prevalence survey

The second Slovenian national healthcare-associated infections (HAIs) prevalence survey (SNHPS) was conducted in acute-care hospitals in 2011. The objective was to assess the sensitivity and specificity of the method used for the ascertainment of six types of HAIs (bloodstream infections, catheter-associated infections, lower respiratory tract infections, pneumoniae, surgical site infections, and urinary tract infections) in the University Medical Centre Ljubljana (UMCL)

Prevalence of and factors associated with healthcare-associated infections in Slovenian acute care hospitals: Results of the third national survey

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

The prevalence of and risk factors for healthcare-associated infections in Slovenia: results of the second national survey

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

Impact of early valve surgery on outcome of staphylococcus aureus prosthetic valve infective endocarditis: Analysis in the international collaboration of endocarditis-prospective cohort study

© The Author 2014. Background. The impact of early valve surgery (EVS) on the outcome of Staphylococcus aureus (SA) prosthetic valve infective endocarditis (PVIE) is unresolved. The objective of this study was to evaluate the association between EVS, performed within the first 60 days of hospitalization, and outcome of SA PVIE within the International Collaboration on Endocarditis-Prospective Cohort Study. Methods. Participants were enrolled between June 2000 and December 2006. Cox proportional hazards modeling that included surgery as a time-dependent covariate and propensity adjustment for likelihood to receive cardiac surgery was used to evaluate the impact of EVS and 1-year all-cause mortality on patients with definite left-sided S. aureus PVIE and no history of injection drug use. Results. EVS was performed in 74 of the 168 (44.3%) patients. One-year mortality was significantly higher among patients with S. aureus PVIE than in patients with non-S. aureus PVIE (48.2% vs 32.9%; P

Robust saliva-based RNA extraction-free one-step nucleic acid amplification test for mass SARS-CoV-2 monitoring

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