HIV-1 subtype diversity and phylogenetic insight into non-B subtype transmission in Slovenia, 1989-2013.

INTRODUCTION: Disease progression, drug resistance mutations, and treatment strategies may vary by HIV-1 subtype. This study determined HIV-1 subtypes circulating in Slovenia, a Central European country with an HIV-1 epidemic driven by men who have sex with men, focusing on molecular epidemiology of non-B subtypes. METHODS: A total of 367 HIV-1 sequences were included. Subtype was assigned by employing eight different HIV subtyping tools coupled with maximum likelihood phylogenetic analyses. RESULTS: The subtyping tools COMET, jpHMM, and REGA 3.0 exhibited the best performance on the dataset studied. Phylogenetic analyses showed a 14.7% prevalence of non-B subtypes, with subtype A detected most frequently (4.9%), followed by CRF02_AG (2.4%), subtype C (1.1%), subtypes D, G, and CRF01_AE (0.8% each), and subtypes F and CRF22_01A1 (0.3% each). A subtype could not be assigned to 12 sequences (3.3%), indicating potential unique recombinant forms. Non-B subtypes were significantly associated with a heterosexual route of transmission and infection acquired in Eastern Europe, Africa, or Asia. CONCLUSION: In a country where subtype B is predominant, non-B subtypes were observed in one out of seven patients, a non-negligible proportion, which underlines the importance of systematic surveillance of HIV subtype diversity and the corresponding molecular epidemiology.

Pre-exposure prophylaxis for HIV with oral tenofovir disoproxil fumarate/emtricitabine in men who have sex with men: Slovenian national demonstration project.

Prevalence of HIV in Slovenia is low, and men who have sex with men (MSM) have the highest risk for infection. Rates of enrolment into HIV care, initiation of antiretroviral therapy and reaching an undetectable viral load in HIV-infected patients are very high. Prevention of HIV infection for MSM with PrEP is not formally available in Slovenia. The aim of this study was to demonstrate possible implementation of PrEP in Slovenia. Sixty-nine (n = 69) MSM with increased risk for HIV received PrEP with oral tenofovir disproxil fumarate /emtricitabine and acquisition were followed for a mean of 566.6 days. They had 71 episodes of STIs (incidence 61.7 per 100 person-years). No one got acquired HIV infection. Estimated glomerular filtration rate (EGFR) was significantly lower 4 (p = 0.014) and 19 (p = 0.021) months after inclusion; however, there was no clinically significant renal failure (mean EGFR 110-115 mL/min). Self-reported body weight significantly increased after 7 months (p < 0.05). Overall EGFR and self-reported body weight did not change significantly. No significant change in adherence (overall mean 81.0%; 95% CI 77.5%-84.6%; p = 0.728), condom use (p = 0.077) and number of sexual partners (overall mean 2.36 per 30 days; 95% CI 2.06 to 2.65; p = 0.235) was found throughout the study. Participants reported 110 graded adverse effects (AE), 104 (94.5%) grade 1-2 and 6 (5.5%) grade 3-4. No participant discontinued PrEP due to AE. The study showed successful implementation of PrEP among MSM at high risk for HIV infection in Slovenia. Based on the results of our study, PrEP should be formally available in Slovenia.

Prevalence of And Factors Associated with Healthcare-associated Infections in Slovenian Acute Care Hospitals: Results of the Third National Survey.

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] 4.1; 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). 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.

HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011-2016 update.

HIV-positive individuals that have a detected transmitted drug resistance (TDR) at baseline have a higher risk of virological failure with antiretroviral therapy (ART). This study offers an update on the prevalence of TDR in Slovenia, looks for onward transmission of TDR, and reassesses the need for baseline drug resistance testing. Blinded questionnaires and partial pol sequences were obtained from 54.5% (168/308) of all of the patients diagnosed with HIV-1 from 2011 to 2016. Subtype B was detected in 82.7% (139/168) of patients, followed by subtype A (8.3%), subtype C (2.4%), and CRF01_AE (1.8%). Surveillance drug resistance mutations (SDRMs) were found in four individuals (2.4%), all of them men who have sex with men (MSM) and infected with subtype B. K103N was detected in two patients and T68D and T215D in one person each, corresponding to a prevalence of 0%, 1.2%, and 1.2% of TDR to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs), and non-NRTIs (NNRTIs), respectively. The impact of mutations on drug susceptibility was found to be most pronounced for NNRTIs. No forward spread of TDR within the country was observed; however, phylogenetic analysis revealed several new introductions of HIV into Slovenia in recent years, possibly due to increased risky behavior by MSM. This was indirectly confirmed by a substantial increase in syphilis cases and HIV-1 non-B subtypes during the study period. A drug-resistant HIV variant with good transmission fitness is thus more likely to be imported into Slovenia in the near future, and so TDR should be closely monitored.

Contribution of sonicate-fluid cultures and broad-range PCR to microbiological diagnosis in vascular graft infections.

BACKGROUND: Vascular graft infections (VGI) are associated with considerable morbidity and mortality, and antimicrobial treatment is an important adjunct to surgical treatment. While microbial aetiology of VGI is often difficult to determine, other techniques such as sonication of implanted material may be used to enhance the recovery of biofilm-associated organisms. METHODS: We performed a retrospective analysis of 22 consecutive patients treated for VGI at University Medical Centre Ljubljana from May 2011 through January 2015. Explanted vascular grafts were flooded with sterile Ringer solution, sonicated for 1 min at a frequency of 40 kHz and inoculated on solid and liquid culture media. Aerobic and anaerobic cultures were performed, incubated for 14 days and any significant bacterial growth was quantitatively evaluated. Additionally, broad-range PCR from sonicate fluid was performed. Microbiological results were compared with the results of preoperatively taken blood cultures and the results of intraoperative tissue cultures (material from peri-graft collection). RESULTS: Identification of the causative organism (irrespective of the method) was achieved in 95.8%. Preoperative blood cultures were positive in 35.3%, intraoperative tissue cultures in 31.8%, sonicate fluid culture in 79.2%, while broad-range PCR from sonicate fluid was positive in 66.7%. In 37.5% the pathogen detected in sonicate fluid culture or broad-range PCR was the only positive microbiological result. CONCLUSIONS: Sonicate fluid culture and broad-range PCR from explanted vascular grafts may contribute to optimization of antimicrobial treatment. Optimal timing of antibiotic therapy before explantation should be further assessed to improve diagnostic yield.

Antibiotic prescribing in long-term care facilities for the elderly: EVIPNet evidence brief for policy, number 3

The Ministry of Health of Slovenia commissioned this evidence brief for policy, to be published under the aegis of the WHO European Evidence-informed Policy Network, to develop evidence-informed options for the country to consider in tackling the problem of prescribing broad-spectrum antibiotics to elderly people in long-term care facilities. Such treatment is taking place without proper diagnosis of infection and microbiological testing, and without indication, choice, dose or duration of therapy, thus representing the key driving factor for antimicrobial resistance. The work was carried out within the framework of the Biennial Collaborative Agreement between the Ministry of Health and WHO, involving high-level national policy institutions and national experts, and supported by the technical experts of WHO Regional Office for Europe. The Slovene National Institute for Public Health convened a working group comprising representatives from the clinical field, pharmacology, public health and health care management. The group identified, selected, appraised and synthesized relevant research evidence on the problem, three options for tackling it and considerations in implementing them. The three options are: surveillance, monitoring and audit/feedback on antibiotic consumption and antimicrobial resistance in long-term care facilities; development and implementation of guidelines and clinical pathways for diagnosing and treating infections; and continuous medical education for health care professionals and provision of health information to residents of long-term care facilities and their relatives/visitors.

Acute kidney injury in critically-ill adult patients with seasonal influenza infection.

BACKGROUND: Acute kidney injury (AKI) occurs in 22.4 - 100% of critically-ill hospitalized patients with influenza infection. In up to 2/3, it is severe enough to necessitate renal replacement therapy. We aimed to document the incidence of AKI among patients with influenza-related critical illness and its relation to clinical outcomes. METHODS: We conducted a retrospective observational study of all adult patients with acute respiratory illness and laboratory-confirmed influenza infection admitted to non-surgical intensive care units at the University Medical Centre Ljubljana between January 1, 2016, and March 31, 2016. RESULT: Our sample consisted of 28 adult patients with mean age in years of 57.5 ± 20.2. Incidence of AKI was 71.4%. Mortality was 28.6% (35% in patients with AKI and 41.6% in patients who required renal replacement therapy). CONCLUSIONS: Influenza-related critical illness is rare but can cause AKI in a large proportion of affected patients. In this setting, requirement for renal replacement therapy could be associated with increased mortality risk.
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Longitudinal trends of recent HIV-1 infections in Slovenia (1986-2012) determined using an incidence algorithm.

Resolving dilemma whether the rise in the number of HIV diagnoses represents an actual increase in HIV transmissions or is a result of improved HIV surveillance is crucial before implementing national HIV prevention strategies. Annual proportions of recent infections (RI) among newly diagnosed persons infected with HIV-1 in Slovenia during 27 years (1986-2012) were determined using an algorithm consisting of routine baseline CD4 and HIV viral load measurements and the Aware BED EIA HIV-1 Incidence Test (BED test). The study included the highest coverage of persons diagnosed with HIV during the entire duration of an HIV epidemic in a given country/region (71%). Out of 416 patients, 170 (40.9%) had a baseline CD4 cell count less than 200 cells/mm(3) and/or HIV-1 viral load less than 400 copies/ml and were characterized as having a long-standing infection (LSI). The remaining 246 patients were additionally tested using the BED test. Overall, 23% (97/416) of the patients were labeled RI. The characteristics significantly associated with RI were as follows: younger age, acute retroviral syndrome, CDC class A and other than C, no AIDS defining illnesses, HIV test performed in the past, a higher viral load, and a higher CD4 cell count. An interesting trend in the proportion of RI was observed, with a peak in 2005 (47% of RI) and the lowest point in 2008 (12%) in parallel with a rise in the numbers of new HIV diagnoses. This study could help promote the idea of introducing periodic HIV incidence monitoring using a simple and affordable algorithm.

Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe.

BACKGROUND: The HIV-1 epidemic in Slovenia, a small Central European country, has some characteristics that make it an ideal model to study HIV-1 transmission. The epidemic is predominantly affecting men who have sex with men infected with subtype B (89% of all patients), has a low prevalence (less than 1/1000) and is growing slowly. The aim of the present study was to analyze in detail the evolutionary history and the determinants of transmission. METHODS: A total of 223 partial pol gene sequences from therapy naïve individuals were included, representing 52% of all patients newly diagnosed in 13 years (2000-2012) and analyzed together with genetically similar worldwide sequences, selected in a BLAST search. RESULTS: Combined analysis (maximum likelihood and Bayesian) of HIV-1 transmission chains revealed 8 major clusters (n ≥ 10 patients), 1 group of 4 patients, 2 trios and 12 transmission pairs, thus leaving only 43 (19.3%) Slovenian patients infected with subtype B without a local epidemiological link, indicating a predominance of local transmission of HIV-1 infection. Bayesian analysis performed on a full set of sequences estimated several introductions of HIV-1 into Slovenia, with the most recent common ancestor (tMRCA) of the earliest Slovenian cluster dated to the late 1980s, although tMRCAs obtained from separate independent analysis of each cluster showed considerably more recent estimates. These findings indicate inconsistencies in molecular clock estimation, which we further explored. We hypothesize that these inconsistent dating estimates across the tree could be caused by an evolutionary rate acceleration of HIV-1 after entering the Slovenia epidemic that is not taken into account by the molecular clock model. It could be caused by a lower transmission rate in this setting, as demonstrated by the low epidemic growth rate estimated by Bayesian skyline plot analysis. CONCLUSIONS: HIV-1 subtype B was introduced into Slovenia at several time points from the late 80s onward. The majority of patients had a local transmission link, indicating a closed HIV community. The observed slower epidemic rate suggests that individuals with a long-lasting infection are the driving force of the epidemic in this region.

Tick borne encephalitis without cerebrospinal fluid pleocytosis.

BACKGROUND: Tick borne encephalitis is the most frequent vector-transmitted infectious disease of the central nervous system in Europe and Asia. The disease caused by European subtype of tick borne encephalitis virus has typically a biphasic clinical course with the second phase presenting as meningitis, meningoencephalitis, or meningoencephalomyelitis. Cerebrospinal fluid pleocytosis is considered a condition sine qua non for the diagnosis of neurologic involvement in tick borne encephalitis, which in routine clinical practice is confirmed by demonstration of serum IgM and IgG antibodies to tick borne encephalitis virus. CASE PRESENTATION: Here we present a patient from Slovenia, an area highly endemic for tick borne encephalitis, with encephalitis but without cerebrospinal fluid pleocytosis in whom tick borne encephalitis virus infection of the central nervous system was demonstrated. CONCLUSION: Cerebrospinal fluid pleocytosis is not mandatory in encephalitis caused by tick borne encephalitis virus. In daily clinical practice, in patients with neurologic symptoms/signs compatible with tick borne encephalitis and the risk of exposure to ticks in a tick borne encephalitis endemic region, the search for central nervous system infection with tick borne encephalitis virus is warranted despite the lack of cerebrospinal fluid pleocytosis.

Prevalence, genotype distribution, and risk factors for hepatitis C infection among HIV-infected individuals in Slovenia: a 1986-2013 update.

INTRODUCTION: Since the introduction of highly active antiretroviral therapy, chronic hepatitis C has become one of the leading causes of non-AIDS-related morbidity and mortality in patients with HIV infection. Two previous Slovenian nationwide studies published in 2002 and 2009 showed a very low prevalence of hepatitis C virus (HCV) infection among Slovenian HIV-infected individuals (14.5% and 10.7%, respectively). METHODS AND RESULTS: The presence of HCV infection was tested in 579/639 (90.6%) patients that were confirmed as HIV-positive in Slovenia by the end of 2013. Among them, 7.6% (44/579) of HIV-infected individuals were anti-HCV-positive, and 33/44 (75%) anti-HCV-positive patients were also HCV RNA-positive. HCV genotype 1 was most prevalent among HIV-infected patients (68%), followed by genotype 3 (20%), genotype 4 (8%), and genotype 2 (4%). Anti-HCV positivity was significantly higher in those that acquired HIV by the parenteral route (91.8%) than in those that acquired HIV by the sexual route (2.8%). DISCUSSION: Slovenia remains among the countries with the lowest prevalence of HCV infection in HIV-infected individuals. Because the burden of HIV among men who have sex with men in Slovenia is disproportionately high and increasing rapidly, the current favorable situation could change quickly and should be therefore monitored regularly.

Short communication: prevalence of HIV type 1 transmitted drug resistance in Slovenia: 2005-2010.

Slovenia is a small European country with a total of 547 HIV-infected individuals cumulatively reported by the end of 2011. However, the estimated incidence rate of HIV infections increased from 7.0 per million in 2003 to 26.8 per million in 2011. In this study, we assessed the prevalence of transmitted drug resistance (TDR) in the past 6 years (2005-2010) and analyzed the time trend of the proportion of men having sex with men (MSM) and HIV-1 subtype B among newly diagnosed individuals in a 15-year period (1996-2010) in Slovenia. Among 150 patients included in the study, representing 63% of HIV-1 newly diagnosed patients in 2005-2010, TDR was found in seven patients (4.7%). The prevalence of TDR to nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and protease inhibitors was 2% (3/150), 2% (3/150), and 0.7% (1/150), respectively. The majority of patients were infected with subtype B (134/150, 89%), while subtype A was detected in 6.0% (9/150), subtype D in 1.3% (2/150), and subtype G and CRF02_AG in 0.7% (one patient each). Three of 150 sequences could not be typed. Infection with subtype B was found to be significantly associated with male gender, Slovenia being reported as the country of the patient's nationality and origin of the virus, CDC class A, mode of transmission with homosexual/bisexual contact, sex with an anonymous person, and a higher CD4(+) count. Among patients carrying the subtype B virus, an MSM transmission route was reported in 87% of patients. Although the prevalence of TDR in Slovenia is still below the European average, active surveillance should be continued, especially among MSM, the most vulnerable population for HIV-1 infection in this part of Europe.