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Analysis of 594 isolates of Escherichia coli sequence type (ST)131 and its single locus variants carrying carbapenemase genes from 17 European Union/European Economic Area countries revealed acquisition of 18 carbapenemase variants, mainly in ST131 clades A and C. Most frequent were bla OXA-244 (n = 230) and bla OXA-48 (n = 224), detected in 14 and 12 countries, respectively. Isolates carrying bla OXA-244 have increased rapidly since 2021. The increasing detection of carbapenemase genes in the E. coli high-risk lineage ST131 is a public health concern.

The diarrheagenic Escherichia coli (DEC) is the major cause of diarrheal diseases in Africa, including Ethiopia. However, the genetic diversity of E. coli pathotypes found in Ethiopia has not been studied well. This study aimed to characterize potential DEC belonging to enteropathogenic (EPEC), Shiga toxin-producing (STEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), and enteroinvasive (EIEC) E. coli pathotypes from stool specimens of patients attending primary healthcare units ( n = 260) in Addis Ababa and Hossana using whole-genome sequencing. Real-time PCR assays were used to identify DEC isolates belonging to EPEC, STEC, EAEC, ETEC, and EIEC pathotypes, which were then subjected to whole-genome sequencing on the Illumina platform. Twenty-four whole-genome nucleotide sequences of DEC strains with good enough quality were analyzed for virulence-associated genes (VAGs), antibiotic resistance genes (ARGs), phylogenetic groups, serogroups, and sequence types. The majority (62.5%) of DEC isolates belonged to the phylogenetic group B1. The identified DEC isolates belonged to 21 different serogroups and 17 different sequence types. All tested DEC isolates carried multiple VAGs and ARGs. The findings highlight the high diversity in the population structure of the studied DEC isolates, which is important for designing targeted interventions to reduce the diarrheal burden in Ethiopia.

The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of 260 E. coli isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 E. coli isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with IncF plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the E. coli isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs.

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., Competing Interests: The authors declare no conflicts of interest.

Antimicrobial resistance of Escherichia coli is a growing problem in both developed and developing countries. This study aimed to investigate the phenotypic antimicrobial resistance of E. coli isolates ( n = 260) isolated from the stool specimen of patients attending public health facilities in Addis Ababa and Hossana. This study also aimed to characterize phenotypically confirmed extended-spectrum beta-lactamase (ESBL)-producing E. coli isolates ( n = 22) using whole-genome sequencing. Resistance to 18 different antimicrobials was assessed using the disc diffusion method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The highest resistance rate among the E. coli isolates was found for ampicillin (52.7%), followed by trimethoprim-sulfamethoxazole (29.6%). Of all isolates, 50 (19.2%) were multidrug-resistant and 22 (8.5%) were ESBL producers. ESBL genes were detected in 94.7% of the sequenced E. coli isolates, and multiple β-lactamase genes were detected in 57.9% of the isolates. The predominant ESBL gene identified was bla CTX-M-15 (78.9%). The bla TEM-1B gene was detected in combination with other ESBL genes in 57.9% of the isolates, while only one of the sequenced isolates contained the bla TEM-1B gene alone. The bla CTX-M-3 gene was detected in three isolates. The genes bla CTX-M-15 and bla TEM-1B as well as bla CTX-M-15 and bla TEM-169 were confirmed to coexist in 52.6% and 10.5% of the sequenced E. coli isolates, respectively. In addition, bla OXA-1 was identified together with bla CTX-M-15 and bla TEM-1B in one isolate, and in one isolate, bla TEM-169 together with bla CTX-M-15 and bla TEM-1B was found. The results obtained show that measures need to be taken to reduce the spread of drug resistance and ensure the long-term use of available antimicrobials.

Introduction: Due to the paucity of recent literature on perianal streptococcal disease (PSD), we performed a comprehensive analysis of clinical characteristics of PSD and its management., Methods: We conducted a retrospective search in the laboratory information system of the Institute of Microbiology and Immunology, Ljubljana, Slovenia, between January 2006 and December 2016 and identified patients with suspected PSD. We reviewed patients' medical records and obtained data on patient age and sex, concomitant illnesses, duration of complaints, signs and symptoms of PSD, epidemiological history, date of diagnosis, microbiological characteristics of beta-hemolytic streptococcal isolates, additional laboratory findings, duration and type of systemic and/or topical therapy, and recurrence of PSD., Results: We identified 64 pediatric and eight adult PSD cases in total. The most common signs and symptoms were perianal erythema (67/72; 93.1%), anal fissures (28/72; 38.8%), itching (22/72; 30.6%), and blood-streaked stools (19/72; 26.4%). The duration of symptoms varied from < 1 week to > 1 year, with 58.3% of patients experiencing symptoms between 1 week and 6 months. The majority of patients received systemic (63/72; 87.5%) and topical (56/72; 77.8%) treatment., Conclusions: Although the signs and symptoms of PSD are non-specific, clinicians should be highly suspicious of the disease in adults and especially in preschool children with perianal complaints. Despite being a common disease, there is still considerable delay in correct diagnosis and treatment, prolonging the discomfort of PSD patients.

Our study evaluates the performance of two rapid phenotypical tests to detect colistin resistance in Enterobacterales: Alifax rapid AST colistin test using the HB&L system and Rapid Polymyxin NP test prepared in-house. A collection of well-characterized 53 colistin-susceptible and 66 colistin-resistantEnterobacterales isolates was used. The results obtained using both rapid tests were compared to the reference broth microdilution. Overall categorical agreement was 81.5% for Alifax test and 98.3% for Rapid Polymyxin NP test. Based on our results, the Rapid Polymyxin NP test is superior to the Alifax test that performed inadequate for Enterobacter spp., (© 2021. The Author(s).)

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%., (© 2021 Wiley-VCH GmbH.)

Acinetobacter baumannii primarily causes colonization, yet it can be an opportunistic pathogen associated with hospital-acquired infections. Many countries report rapid spread of carbapenem-resistant Acinetobacter baumannii (CRAb) which limits treatment options, with colistin frequently being the last line treatment option. The aim of our study was to evaluate a recently developed rapid method, namely the Rapid ResaPolymyxin test, for detection of colistin resistance (ColR) in Acinetobacter baumannii. This test was used for rapid screening of colistin resistance in a clinical setting where there is endemicity of CRAb isolates. A total of 82 A. baumannii clinical isolates were included in the evaluation. The majority of them were resistant to carbapenems (75/82, 91.5%). A total of 37 isolates (45.1%) were resistant to colistin, all being resistant to carbapenems. None of the ColR isolates carried the plasmid-mediated mcr-1 to -5 genes. The Rapid ResaPolymyxin NP test reached a 95.1% categorical agreement with results of reference broth microdilution method, with 93.3% sensitivity and specificity, and positive and negative predictive values being respectively at 92.3% and 97.7%. The Rapid ResaPolymyxin NP test performed well on our collection of clinical and surveillance CRAb isolates from the Central Slovenia region. The test is inexpensive and easy to integrate into laboratory workflow. The main value of the test is rapid categorization of susceptibility and resistance which has important implications with respect to the treatment strategy as well as the infection control measures.

Purpose. Increasing consumption of colistin as treatment for infections with multidrug-resistant (MDR) Gram-negative bacilli (GNB) has been accompanied by increasingly frequent reports of colistin-resistant (ColR) MDR GNB. Higher selective pressure creates a favourable environment that can facilitate the spread of ColR isolates. Monitoring of asymptomatic ColR GNB carriage can give us a better understanding of this emerging healthcare problem, particularly in wards with higher polymyxin selective pressure and prevalence of carbapenem-resistant GNB. Our aim was to assess the ColR GNB colonization rate in intensive care unit (ICU) patients and evaluate the performance of two surveillance protocols using a selective medium. Methodology. A prospective study included 739 surveillance samples (rectal swabs and tracheal aspirates) from 330 patients that were screened for ColR GNB carriage using SuperPolymyxin medium. Two approaches were used: direct sample plating and overnight pre-enrichment of samples followed by plating. Colistin resistance was confirmed with broth microdilution. ColR isolates were molecularly screened for plasmid-mediated mcr genes. Results. A total of 44/739 samples (45 ColR GNB isolates) were positive for ColR GNB, which included 31/330 (9.4 %) colonized patients; mcr genes were not detected. The direct plating method only identified 17/45 (37.8 %) isolates correctly, whereas the pre-enrichment protocol identified all 45 ColR GNB. Conclusion. The colonization rate among our ICU patients was 9.4  %. Based on our findings, the pre-enrichment step is necessary for the determination of ColR GNB carriage - even though the time to result takes an additional day, fewer than half of ColR GNB carriers were detected using the direct plating protocol.

Decreasing cephalosporin use was described as an effective intervention in decreasing the incidence of infections caused by Klebsiella pneumoniae harbouring extended-spectrum beta-lactamase (ESBLKP). Due to sustained increased levels of infections caused by ESBLKP, a multifaceted antibiotic stewardship intervention aimed to decrease cephalosporin use was carried out at a large medical unit of a teaching hospital. All cephalosporins except the first-generation were restricted and could only be prescribed after authorization by an infectious disease physician. The use of cephalosporins decreased significantly after intervention. The effect was most prominent for the third-generation cephalosporins (7.9-1.5 DDD/100 OBD). There was an increase in the consumption of piperacillin/tazobactam, carbapenems and fluoroquinolones. In contrast to our expectations the ESBLKP incidence increased, but the changes were not statistically significant. The intervention was successful in controlling the prescribing of cephalosporins, but had no impact on incidence of ESBLKP infections.

Staphylococcus aureus is among the most important human pathogens. It is associated with different infections and is a major cause of skin and soft tissue infections (SSTIs). The aim of our study was to compare S. aureus isolates associated with SSTIs with isolates obtained from healthy carriers in the Central Slovenia region in terms of antimicrobial susceptibility, genetic diversity by clonal complex (CC)/sequence type, spa type, and by toxin gene profiling. In total, 274 S. aureus isolates were collected prospectively by culturing wound samples from 461 SSTI patients and nasal samples from 451 healthy carriers. We have demonstrated high heterogeneity in terms of CCs and spa type in both groups of isolates. The main clone among SSTI strains was Panton-Valentine leukocidin gene (pvl) positive CC121, whereas the main clone among carrier strains was CC45 carrying a large range of toxin genes. The main spa type in both groups was t091. Pvl was more frequently present in SSTI strains (31.2% SSTI vs 3.6% carrier strains) and staphylococcal enterotoxin C was more frequently present in carrier strains (1.6% SSTI vs 17.0% carrier strains). We have also demonstrated that methicillin-resistant S. aureus was a rare cause (2.8%) of SSTIs in our region., (© 2016 APMIS. Published by John Wiley & Sons Ltd.)

Background: Increased life expectancy of human immunodeficiency virus (HIV)-infected patients appears to be coupled with increased incidence of cardiovascular disease (CVD)., Aim: The aim of our study was to determine the presence of early atherosclerosis among Slovenian HIV-infected patients below the age of 55 years., Methods: A total of 86 HIV-infected male patients below the age of 55 years participated in our study. Ankle-brachial index (ABI) was measured using a handheld Doppler ultrasonic probe and a blood pressure cuff. Carotid intima-media thickness (CIMT) was assessed by the B-mode high-resolution ultrasound technique. Low ABI, CIMT > 0.8 mm or presence of carotid plaques were considered markers of early atherosclerosis., Results: Average CIMT was lowest among treatment-naïve patients (0.65 mm); 10 (38.4 %) had CIMT > 0.8 mm, and carotid plaques were detected in 1 (3.8 %). Average CIMT among treated patients was 0.71 mm; 30 (50.0 %) had CIMT > 0.8 mm, and plaques were detected in 11 (18.3 %). Low ABI (≤ 0.90) was found in five patients (5.8 %) without symptoms of peripheral artery disease; two were treatment-naïve, and three received antiretroviral therapy. Early atherosclerosis was found in 43 (50.0 %) patients; 10 (38.4 %) were in treatment-naïve and 33 (55.0 %) in the treated group., Conclusions: Increased prevalence of early atherosclerosis among Slovenian HIV-infected patients below the age of 55 years has been demonstrated. Screening for early atherosclerosis should be implemented in the evaluation of young HIV-infected patients because a more aggressive treatment approach, aimed to delay the progression of atherosclerosis, may be warranted especially when carotid plaques are detected. We have shown that although ABI contributes to CVD risk assessment, CIMT assessment remains the more sensitive method.

We report our 1-year experience with modified GeneOhm MRSA assay (formerly IDI-MRSA) for pooled surveillance specimens in low methicillin-resistant Staphylococcus aureus (MRSA) prevalence clinical setting. We have successfully modified the GeneOhm MRSA assay protocol during the specimen preparation step by adding an extra washing step followed by pooling of up to 3 samples per patient (nose, skin, with or without throat) at the lysis step. The sensitivity of the modified assay compared with conventional cultivation was 94.3%, specificity 99.2%, negative predictive value 99.2%, and positive predictive value 94.3%. The modified test is reliable and performed well compared with conventional culture methods in our clinical setting with low-level prevalence of MRSA colonization. Our findings support the use of pooling of the patients samples as a cost-effective way of screening for MRSA colonization.

Analysis of time trends in newly diagnosed HIV-1 infected patients in Slovenia over a 10-year period (1996-2005) showed an increase in the number of newly diagnosed HIV-1 infected patients in 2004 and 2005 as well as increase in the number of newly diagnosed patients with primary/early HIV-1 infection. A retrospective analysis was performed in order to evaluate the clinical, epidemiological, laboratory and virological parameters of primary/early HIV-1 infection presenting with or without acute retroviral syndrome (ARS). Primary/early HIV-1 infection was diagnosed in 33 (19.5%) out of 169 newly diagnosed HIV-1 infected patients during the 10-year period. Most patients experienced ARS, the most commonly reported symptoms being fever, malaise and pharyngitis, followed by rash and lymphadenopathy. Median CD4 cell count was 415 cells/mm3, median CD8 cell count was 865 cells/mm3 and median HIV-1 viral load at the time of diagnosis was 5.1 loglo copies/mL. The increase in the number of newly diagnosed HIV-1 infected patients may be in part due to increased awareness among clinicians of the possibility of ARS, and the possibility of increased awareness of symptoms of ARS among persons at high risk of infection.

Background and Aim of the Study: Endocarditis due to Abiotrophia sp. is rare and often associated with negative blood cultures. The rates of treatment failure, infection relapse and mortality are higher than in endocarditis caused by other viridans streptococci., Methods: A retrospective review of A. defectiva endocarditis in a patient with prosthetic aortic valve and in a patient with Marfan syndrome was performed., Results: A. defectiva, susceptible to penicillin (MIC 0.064 mg/l and 0.016 mg/l, respectively) was isolated from blood cultures of both patients. Treatment with penicillin and gentamicin was started in both patients. Since the first patient developed a macular rash and leukopenia, penicillin was substituted with ceftriaxone. Both patients responded well to antibiotic treatment, did not need prosthetic valve insertion or reinsertion, and were without any sequelae at one year follow up., Conclusion: Standard treatment of bacterial endocarditis with penicillin and gentamicin was effective in both patients. In contrast to previous reports, the present patients had a favorable outcome on completion of treatment and at one-year follow up.