The identification of patients infected and/or colonised by methicillin resistant
(MRSA) is necessary for the timely introduction of measures for infection control. We compared the diagnostic ...efficacy of combinations of MRSA surveillance swabs routinely taken by health institutions in the country.
All surveillance samples, which were sent for a microbiological analysis to detect MRSA with the culture method in 2014, in the three departments for medical microbiology of the National Laboratory for Health, Environment and Food, were included in this study.
Among 65,251 surveillance cultures from 13,274 persons, 1,233 (2.1%) were positive (490 positive persons). Prevailing positive surveillance cultures were throat swabs (31.3%), followed by nose swab (31.2%), skin swab (18.9%), perineum (16.4%) and wound swabs (1.4%). The contribution of other samples, such as aspirate, urine and excreta, was under 1%. We found no statistically significant differences in the frequency of detection of a positive patient, if the combination of samples NTS (nose, throat, skin) or NTP (nose, throat, perineum) was analysed. However, statistically significant differences were confirmed when any of the anatomic sites would be omitted from the sets of NTP and NTS (chi square; p<0.01). Adding additional samples resulted in only 24 additional positive patients (4.9%).
The results indicate that increasing the number of surveillance cultures above three does not add much to the sensitivity of MRSA surveillance, the exception could be wound. The swabs from the perineum and from the skin are exchangeable.
Background
SARS-CoV-2 infection does not confer long immunity. However, studies suggest that prior infection is associated with lower risk of reinfection and milder outcomes of recurrent infections. ...The aims of this retrospective observational case-control study were to describe the clinical and molecular characteristics of genetically confirmed Delta reinfection cases and to assess the potential protective role of preceding infection on the severity of reinfection.
Methods
We used next generation sequencing (NGS) to explore if cases with two positive real time RT-PCR tests > 90 days apart were infected with a different SARS-CoV-2 variant. Cases with confirmed reinfection between August 1st and October 31st, 2021 (the Delta wave) in Slovenia were matched 1:4 by age, sex and timeframe (week of positive test) with individuals with primary infection. Sociodemographic and epidemiologic data, vaccination status, and data on hospitalization and outcome of infection were retrieved from several centralized and standardized national databases. Additional epidemiologic surveys were performed on a limited number of cases and controls.
Results
We identified 628 cases of genetically confirmed reinfection during the study period and matched them with 2,512 control subjects with Delta primary infection. Primary infections in individuals with reinfection were mainly caused by B.1.258.17 (51.1%), followed by B.1.1.7 (15.1%) and reinfection was detected on average 271 days after primary infection (range 101–477 days). Our results show a substantially lower probability of hospitalization in cases with reinfection compared with controls (OR: 0.21,
p
= 0.017), but no significant difference was observed in intensive care unit admission and deaths. We observed a significantly lower proportion of vaccinated individuals among cases compared to controls (4.5% vs. 28.2%), suggesting that hybrid immunity leads to lower probability of reinfection. Detailed analysis of the temporal distribution of variants, responsible for reinfections, showed no significant differences in reinfection potential.
Conclusion
Reinfection with the SARS-CoV-2 Delta variant resulted in fewer hospitalizations compared to the primary Delta infection, suggesting that primary infection may, to some extent, produce at least short lasting protective immunity. This study provides additional insight into the reinfection dynamics that may allow appropriate public health measures to be taken in subsequent waves of the COVID-19 pandemic.
BACKGROUND Shiga toxin-producing E. coli or Vero cytotoxin-producing E. coli (VTEC) are characterised by the ability to produce either one or both cytotoxins referred to as Shiga toxin 1 (Stx1) and ...Shiga toxin 2 (Stx2). VTEC infection may result in life-threatening conditions such as haemolytic uremic syndrome (HUS) and thrombotic thrombocytopenic purpura (TTP). Due to different methods of monitoring and identification of these bacteria in recent years, the existing data on reported cases of VTEC infections probably do not reflect reality. Our study of VTEC strains isolated in different regions of Slovenia, showed serogroups, major virulence factors and specific epidemiological data that can serve as a basis for further laboratory and epidemiological surveillance of VTEC infections. METHODS A total of 66 VTEC strains, isolated from stool samples of patients with diarrhoea from the year 1993 to 2009, were collected at NIPH (National Institute of Public Health). The data of patient's age and gender, onset of illness and clinical manifestation of disease were gathered. The serogroups of isolated strains were determined with antisera following manufacturer's instructions. The ability to produce verocytotoxins was tested using the reversed passive latex agglutination method. The presence of genes for intimin (eae), enterohaemolysin (ehxA) and verotoxins (vtx1 and vtx2) were determined by polymerase chain reaction (PCR). RESULTS Infection with VTEC was encountered throughout the year, but most people were ill in the summer and autumn months. More than half of patients (57.6 %) were younger than five years. Collected VTEC strains belonged to serogroups O17, O26, O91, O103, O111, O113, O126, O128, O145, O148 and O157 (the most frequent were O157 and O26). A high percentage of VTEC strains showed the presence of intimin (86.4 %) and enterohaemolysin (86.4 %) genes. The gene for vtx1 was found in 22.7 % of strains, the vtx2 in 57.6 % of strains, while the presence of both genes was determined in 19.7 % of strains. The presence of the vtx2 gene was determined in all strains associated with HUS and TTP, most of them possessed the eae and ehxA genes too. These patients were mostly older people and young children. CONCLUSIONS Most infections with VTEC occurred in the warmer months of the year, most patient were small children. The severity of VTEC infection is determined by several factors such as the E. coli serogroup, the type of Shiga toxin produced and presence of other virulence genes. The most common serogroups among the study strains were O157 and O26. VTEC O26 has been the most commonly isolated serogroup in recent years, nevertheless more and more different serological groups began to emerge. In all strains associated with HUS and TTP, the vtx2 gene was determined. Further typing of verocytotoxin encoding genes will contribute to assess the risk for complications with VTEC infection. The study provides insights about the age of the patients, seasonal distribution of disease, serogroups and genotypes of the agent.
background Rotaviruses are the major cause of acute watery diarrhea in children up to 5 years of age. In 2007 and 2008 an extensive rotavirus molecular epidemiology study was conducted in Slovenia in ...order to provide information on rotavirus molecular epidemiology in our country. This study is part of the EuroRotaNet, European rotavirus surveillance study. Methods A total of 823 stool samples were collected from children with acute gastroenteritis in seven out of nine healthcare regions in Slovenia. The total RNA was extracted and first amplification of VP7 and VP4 genes was performed in RT-PCR. The RT-PCR product was used for genotyping in multiplex-nested PCR. Untypable strains were included in sequence analysis of VP7 and VP4 genes. Results Genotype distribution similar to that in other European countries was observed. G1P8, G2P4, G3P8, G4P8 and G9P8 were the most prevalent genotypes in 2007 and 2008, except of G3P8, not detected in 2008. Relatively high rate of possible zoonotic strains was detected in 2007 (2.5%). The emerging unusual strain G10P14 was the only potential zoonotic strain detected in 2007 and 2008. conclusions After the vaccine introduction in Slovenia in 2007, no specific changes in molecular epidemiology of rotaviruses was observed. This finding was expected since rotavirus vaccine coverage in 2007 in Slovenia was very low. Genotype G1P8 remains the most prevalent genotype. The rotavirus strain surveillance in Slovenia should be carried on to allow monitoring the spread of some unusual rotavirus genotypes, like G10. The G10 strains should be tracked especially in vaccinated children as no data on vaccine efficiency against infection with G10 strains was presented till now.
BackgroundSequencing of SARS-CoV-2 PCR-positive samples was introduced in Slovenia in January 2021. Our surveillance programme comprised three complementary schemes: (A) non-targeted sequencing of at ...least 10% of samples, (B) sequencing of samples positive after PCR screening for variants of concern (VOC) and (C) sequencing as per epidemiological indication.AimWe present the analysis of cumulative data of the non-targeted surveillance of SARS-CoV-2 and variant-dependent growth kinetics for the five most common variants in Slovenia for the first 9 months of 2021.MethodsSARS-CoV-2 PCR-positive samples, from January to September 2021, were selected for sequencing according to the national surveillance plan. Growth kinetics studies were done on Vero E6 cells.ResultsAltogether 15,175 genomes were sequenced and 64 variants were detected, of which three successively prevailed. Variant B.1.258.17 was detected in ca 80% of samples in January and was replaced, within 9 weeks, by the Alpha variant. The number of cases decreased substantially during the summer of 2021. However, the introduction of the Delta variant caused a fourth wave and completely outcompeted other variants. Other VOC were only detected in small numbers. Infection of Vero E6 cells showed higher replication rates for the variants Alpha and Delta, compared with B.1.258.17, B.1.258, and B.1.1.70, which dominated in Slovenia before the introduction of the Alpha and Delta variants.ConclusionInformation on SARS-CoV-2 variant diversity provided context to the epidemiological data of PCR-positive cases, contributed to control of the initial spread of known VOC and influenced epidemiological measures.
The first detailed epidemiological study of extended-spectrum beta-lactamase (ESBL)-producing organisms identified in Slovenia was carried out. It was performed on a group of 40 Klebsiella pneumoniae ...isolates that were randomly selected from all putative ESBL producers of this species recovered in a large hospital in Celje in 1997-2001. At least three different ESBLs, SHV-2, -5, and -12, were produced by the isolates and these enzymes seem to be common in nosocomial Enterobacteriaceae populations in countries of the region (e.g., Italy, Hungary, Croatia). The analysis revealed a complex epidemiology of the organisms, illustrated mostly by their high clonal variety but also by the diversity of their beta-lactamase and plasmid content, mating capability, and antimicrobial susceptibility. Although some cases of a 'fresh' dissemination of strains or plasmids could be identified, the overall situation should be described rather as endemic, and its complexity may be in part attributed to the late introduction of the ESBL detection procedure to the hospital.
Abstract
Background: August 2010 marked the beginning of the largest outbreak of legionellosis in a Slovenian nursing home. This article presents our experiences with the outbreak investigation. ...Methods: In order to collect the necessary patient epidemiological data, we used individual epidemiological questionnaires. Samples were available from 15 patients and were subject to laboratory investigation. Urine and sputum samples were difficult to obtain due to the underlying diseases of the patients. Serological diagnostics constituted an important part of the epidemiological investigation. Sixty-four environmental samples were taken to identify the sources of infection. By genotyping, we assessed the affinity of the allelic profile of Legionella pneumophila serogroup 1 in environmental samples and in patient samples. Results: Legionnaires' disease was diagnosed in 10 patients based on a combination of various tests. Legionella pneumophila serogroup 1, Legionella pneumophila serogroups 2-14, and Legionella sp., in concentrations of < 10 to 61,000 CFU/l, were isolated from 51 out of 64 environmental samples. The source of the outbreak was confirmed by genotyping the isolates from patients and the isolates from the water supply system. The 2 isolates had identical allelic profiles corresponding to that of L. pneumophila serogroup 1 allelic profile 2,3,9,10,2,1,6, designated sequence type 23 (according to the European Working Group for Legionella Infections). Conclusion: We describe a Legionella pneumophila serogroup 1 outbreak in a Slovenian nursing home. The source of infection was demonstrated using sequence-based typing. Water flow disturbances were determined as the most probable cause of Legionella growth. Overall, the risk of a Legionella outbreak is underestimated in Slovenia.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background: Antimicrobials are among the most commonly prescribed drugs in hospitals, received by 49 % to 61 % of General’s Hospital Celje inpatients, depending on time of observation.Methods: The ...World Health Organization recommends that the consumption of antimicrobial agents in hospitals should be presented as the Defined Daily Dose per 100 bed days. The project presents the available data on the consumption of antibacterial drugs at the level of general hospital. The data provide a basis for the study of ecological impact of antibiotic consumption, evaluation of the association between antibiotic consumption and resistance, assessment of quality indicators for antibiotic consumption and improvement in the prescribing of antibiotics.Results: Trends of antimicrobial resistance were followed by comparing the rates of resistance of the five frequent bacteria isolated in General Hospital Celje between years 2000 and 2005. The usage of fluoroquinolones and macrolides increased gradually throughout the study period, while usage of aminoglycosides decreased. The relationships between antibacterial drug use and bacterial susceptibility showed different patterns. The investigation showed a decrease in amoxicyllin/clavulanic acid resistance of Escherichia coli and Klebsiella pneumoniae despite increasing its use. The increased ciprofloxacin resistance of Pseudomonas aeruginosa and Acinetobacter spp. was followed by increased consumption of quinolones.Conclusions: The analysis of resistance levels and antibacterial consumption in the present study suggest different mechanisms for increased resistance. The significant trend of increased resistance to antibacterials over time constitutes an important warning system.
The emergence of pneumococcal strains resistant to penicillin caused a lot of problems in the therapy of invasive diseases, and added new dimensions to the role of immunisation. In addition to the ...currently available 23-valent pneumococcal polysaccharide vaccine (PPV) and a new 7-valent conjugate vaccine (PCV) (Prevnar, Wyeth Lederle), two new conjugate vaccines—a 9- and a 11-valent—are being developed. So far, the choice of most appropriate vaccines has depended on the established prevalence of serotypes causing invasive diseases and their antibiotic resistance in the Slovene children population. Between 1993 and 2001, 263 invasive pneumococcal strains isolated from children with invasive diseases were typed. During the period 1998–2001, the same 161 invasive strains were tested for their antibiotic sensitivity.
Streptococcus pneumoniae was identified as the major cause of invasive bacterial diseases in the Slovene children population, especially in children under 4 years of age. Distribution by age groups showed the highest incidence in children aged 0–1 years. The predominant serotypes in all age groups were serotypes 14, 1, 19F, 23F, 6B, 18C and 6A. The distribution of penicillin-intermediate and penicillin-resistant strains showed the predominance of serotypes 23F, 14 and 19F. As concerns infection with
S. pneumoniae serotypes, we have proved that children aged less than 5 years are more likely to be infected with penicillin-nonsusceptible or intermediate susceptible strains than older children. The 7-valent conjugate vaccine covers 74% of invasive strains in toddlers, but is less effective in older children.
We can conclude that the 9-valent vaccine formulation is optimal for our country, but further cost-effectiveness analysis must be done for recommendation of wide use.
At that moment it is reasonable to use the 7-valent conjugate vaccine for children with chronic cardiovascular, pulmonary, urinary and liver diseases, with asplenia, neoplasmia, diabetes, meningomyelocoele, before or after bone marrow transplantation and in cases of immunodeficiency.
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