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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.

This study determines and compares the frequency of human mastadenovirus (HAdV) presence in children with acute bronchiolitis (AB), acute gastroenteritis (AGE), and febrile seizures (FS), ascertains types of HAdVs associated with each individual syndrome and contrasts the findings with a control group of children. The presence of HAdVs was ascertained in simultaneously collected nasopharyngeal (NP) swabs and stool samples amplifying the hexon gene by RT-PCR; these were sequenced to determine the types of HAdVs. HAdVs were grouped into eight different genotypes. Of these, three (F40, F41, and A31) were found solely in stool samples, whereas the others (B3, C1, C2, C5, and C6) were found in both stool samples and NP swabs. The most common genotypes in NP swabs were C2 (found in children with AGE and FS) and C1 (only in children with FS), whereas in stool samples genotypes F41 (in children with AGE) and C2 (in children with AGE and FS) prevailed, and C2 was simultaneously present in both samples. HAdVs were more often detected in stool samples than in NP swabs in patients (with the highest estimated viral load in stool samples in children with AB and AGE) and healthy controls and were more common in NP swabs in children with AGE than in children with AB. In most patients, the characterized genotypes in NP swabs and stool samples were in concordance.

Mycoplasma pneumoniae ( Mp ) can cause several extrapulmonary manifestations, most frequently dermatological ones. It is largely unknown whether Mp genotype determines Mp -induced cutaneous disease. The aim of our study was to assess the association between Mp genotype and this clinical outcome. We performed a retrospective study of children referred with signs of acute Mp infection from 1 January 2014 to 31 December 2014. We compared the characteristics of children presenting as cutaneous disease, upper (URTI) and lower respiratory tract infection (LRTI). In addition, we separately analyzed the data of patients presenting with Mp -induced cutaneous disease. We evaluated data from 435 patients (mean age 7.3 years, SD 3.4 years; 52.0% boys) who had Mp PCR-positive pharyngeal swab, P1 genotype and/or multilocus variable-number tandem-repeat analysis (MLVA) genotype defined and no viral co-detection, presenting as cutaneous disease (38/435), URTI (46/435) or LRTI (351/435). The majority of patients had urticarial (55%, 21/38) or maculopapular eruptions (37%, 14/38). We found no association between Mp genotype and clinical outcome of cutaneous disease, nor any specific dermatological presentation. In the group with cutaneous disease, 18% (7/38) required hospital admission because of rash. We found that infection with MLVA-3,6,6,2 strains was more common in admitted patients than in outpatients (40% vs. 4%, p = 0.017) and significantly affected the likelihood of hospital admission in a logistic regression model. The results of our cohort study suggest that Mp genotype does not determine Mp -induced cutaneous disease or a specific dermatological presentation. Nevertheless, infections with certain MLVA strains could induce more severe cutaneous disease requiring hospitalization.

The multilocus variable-number tandem-repeat analysis (MLVA) typing method is commonly used in Mycoplasma pneumoniae (M. pneumoniae) epidemiology. It remains unknown if clinical manifestations of lower respiratory tract infections (LRTI) in children differ between different MLVA genotypes. We aimed to determine if specific M. pneumoniae MLVA genotypes indicate the severity of LRTI in children. We performed a retrospective study of children younger than 18 years with signs of acute M. pneumoniae LRTI from January 1, 2009, to December 31, 2014. All patients who were PCR-positive for M. pneumoniae from pharyngeal swabs and had MLVA genotype successfully defined were included in the study. We compared the epidemiological and clinical data of children infected with different MLVA genotypes. In total, 429 patients (mean age 7.4 years, SD 3.4 years; 54% boys) met the study inclusion criteria. We compared the data of patients infected with the three most common MLVA types: MLVA-3,5,6,2 (86/429), MLVA-3,6,6,2 (71/429) and MLVA-4,5,7,2 (256/429). MLVA-3,5,6,2-infected patients over 5 years of age presented with a significantly higher median C-reactive protein level (34 vs 23 vs 19 mg/L, p = .008) and a higher median white blood cell count (9.4 vs 7.9 vs 8.5 × 10 9 /L, p = .040) compared to MLVA-3,6,6,2- and MLVA-4,5,7,2-infected patients. No such difference was observed in the group of younger than 5 years. The results from our large cohort indicate that different MLVA genotypes may have different pathogenic potential and that children with MLVA-3,5,6,2 LRTI may present with higher inflammatory marker levels in comparison with other MLVA types., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Mycoplasma pneumoniae strains can be classified into two major genetic groups, P1 type 1 (P1-1) and P1 type 2 (P1-2). It remains unknown if clinical manifestations of lower respiratory tract infections (LRTI) in children differ between the two genotypes. We aimed to determine if the M. pneumoniae P1 genotype is associated with severity of LRTI in children. Medical charts of 420 children (≤15 years old) with signs of acute LRTI who were PCR positive for M. pneumoniae from pharyngeal swabs in a recent M. pneumoniae epidemic were analyzed. We used a culture and pyrosequencing approach for genotyping PCR-positive samples. We compared epidemiological and clinical data of children with either P1-1 or P1-2 LRTI. P1-2-infected children presented with a significantly higher median baseline C-reactive protein level and were admitted to the hospital more often. The P1 genotype had a significant predictive value in a multiple linear regression model predicting C-reactive protein levels in our study sample. Moreover, the P1 genotype significantly affected the likelihood of hospital admission in a logistic regression model. Our modeling results were also confirmed on an additional independent sample of children with M. pneumoniae LRTI. Results from our large patient group indicate that the two M. pneumoniae P1 genotypes may have different pathogenic potential and that LRTI with P1-2 strains may have a more severe disease course than those with P1-1 strains in children. P1 genotyping is not routinely performed but could be used as a predictor of M. pneumoniae LRTI severity, enabling patient-tailored treatments.

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.

Background: Carbapenemase-producing Enterobacteriaceae (CPE) occur only sporadically in Slovenia., Aim: To describe the first Slovenian carbapenemase-producing (CP) Klebsiella pneumoniae and Escherichia coli outbreak which occurred at the tertiary teaching hospital University Medical Centre Ljubljana from October 2014 to April 2015., Methods: A CPE-positive case was defined as any patient infected or colonized with CPE. A strict definition of a contact patient was adopted. Measures to prevent cross-transmission included cohorting of all CPE carriers with strict contact precautions and assignment of dedicated healthcare workers, cohorting of all contact patients until obtaining the result of screening cultures, systematic rectal screening of contact patients, and tagging of all CPE-positive cases and their contacts. Educational campaigns on CPEs were implemented. Clinical specimens were processed using standard procedures. Pulsed-field gel electrophoresis (PFGE) was used to determine relatedness. Multi-locus sequence typing was performed on CP K. pneumoniae isolates that belonged to different pulsotypes., Findings: Before the outbreak was brought under control, 40 patients were colonized or infected with OXA-48 and/or New Delhi metallo-β-lactamase (NDM)-producing CPE; in 38 patients OXA-48 and/or NDM-producing K. pneumoniae was detected, in seven OXA-48 and/or NDM-producing E. coli was found together with K. pneumoniae, and in two patients only CP E. coli was isolated. The outbreak was oligoclonal with two major CP K. pneumoniae clusters belonging to ST437 and ST147 in epidemiologically linked patients., Conclusion: Initial standard control measures failed to prevent the outbreak. Once the problem had been recognized, strict infection control measures and the education of healthcare workers contributed to the successful control of the outbreak., (Copyright © 2018 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Acrodermatitis chronica atrophicans is a late manifestation of European Lyme borreliosis and is characterized by high levels of borrelial IgG antibodies, slowly expanding skin redness usually beginning on distal parts of extremities, and corresponding histologic findings. It very rarely develops in children. The main prerequisite for the diagnosis is clinical suspicion. In the present article we report on two children with acrodermatitis chronica atrophicans and on the findings of a PubMed literature search on acrodermatitis chronica atrophicans in childhood, published in the past three decades., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Aim: Study's objective was to identify risk factors associated with bronchiolitis severity., Methods: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). Detection of respiratory viruses in nasopharyngeal swab was accomplished by RT-PCR. Severity was assessed by Wang Respiratory Score and hospitalization longer than 24 hours., Results: The study included 761 children. The three most frequently detected viruses were respiratory syncytial virus (RSV), human rhinovirus (hRV) and human bocavirus (hBoV) (57.5%, 272/473; 25.6%, 121/473; 18.4%, 87/473). Patient groups differed in Wang Respiratory Score for the severity of bronchiolitis (P < 0.001). No differences regarding the causative viruses were found. There was a lower proportion of children with the presence of more than one virus in PICU group compared to other two groups (P = 0.017). The three groups significantly differed in age, birthweight, comorbidities, bronchodilator treatment and antibiotic usage. However, multiple regression analysis revealed that younger age and the use of antibiotics were associated with bronchiolitis severity defined as hospitalization for >24 hours., Conclusions: Respiratory syncytial virus, hRV and hBoV were the most frequently detected viruses. The majority of patients admitted to the PICU had only one virus detected. Younger age and the use of antibiotics were associated with bronchiolitis severity., (© 2018 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.)

Mycoplasma pneumoniae (M. pneumoniae) isolates can be classified into two major genetic groups, P1 type 1 (MP1) and P1 type 2 (MP2), based on the DNA sequence of the P1 adhesion protein gene. The aim of our study was to determine if M. pneumoniae P1 genotype is associated with disease manifestation and severity of acute M. pneumoniae infection. We compared epidemiological and clinical data of children infected with either MP1 or MP2. In addition, we separately analysed data of patients presenting with individual manifestations of M. pneumoniae infection. Data of 356 patients infected with MP1 were compared with those of 126 patients infected with MP2. MP2-infected children presented with higher median baseline C-reactive protein levels and were admitted to the hospital more often. The distribution of P1 genotype varied among groups of patients with different manifestations of M. pneumoniae infection. MP2 was more common than MP1 among patients with neurological and cardiovascular manifestations, whereas MP1 was more prevalent in other manifestations. The results from our large cohort indicate that the two P1 subtypes may have different pathogenic potential and that infections with MP2 strains could be more virulent than those with MP1 strains.

Two nationwide Mycoplasma pneumoniae epidemics occurred in Slovenia between 2006 and 2016. The aim of this study was to assess which M. pneumoniae genotypes were present in our area during the selected timeframe, whether the origin of the epidemics was monoclonal or polyclonal and whether the proportion between detected genotypes changed over time. We were also interested in the presence of macrolide resistance (MR) and whether it could be linked to specific genotypes. We performed pyrosequencing of the P1 gene and multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) typing from 872 M. pneumoniae isolates obtained from respiratory tract infections (RTI)-suffering patients. Additionally, isolates were tested for the presence of MR implicated mutations in the 23S rRNA gene. The MLVA typing results revealed that three main genotypes, MLVA-3,5,6,2, MLVA-3,6,6,2 and MLVA-4,5,7,2, were constantly present and occasionally joined by less abundant, short-lived genotypes, which were detected mostly, but not exclusively, during epidemics. We also noticed a switch in abundance from MLVA-3,5,6,2 and MLVA-3,6,6,2, which dominated in the first epidemic (77.0%; 97/126), to MLVA-4,5,7,2 (71.6%; 428/598), which dominated in the second. Similar to this finding, the dominant P1 type also shifted from type 2 to type 1, although a complete P1 type shift was not observed, since both types remained in circulation. MR was detected in 0.8% (7/872) of M. pneumoniae isolates. Our results seem to suggest that MR remains sporadic in Slovenia at this point in time and that both recent epidemics were polyclonal in nature and, possibly, to some extent, fuelled by the P1 type dominance change.

The majority of children with febrile seizures have viral infections and viruses were detected in 22% to 63% of children in published studies. Using molecular methods, viruses were also detected in asymptomatic persons. A prospective study was conducted to detect respiratory and enteric viruses in 192 children with febrile seizures and compare the detection rates to those found in 156 healthy age-matched controls. A respiratory or enteric virus was detected in 72.9% of children with febrile seizures and in 51.4% of healthy controls. The viruses most strongly associated with febrile seizures were influenza, respiratory syncytial virus, parainfluenza, human coronavirus, and rotavirus. Compared to healthy controls, the age-adjusted odds ratios for nasopharynx virus positivity in febrile seizure patients were 79.4, 2.8, 7.2, and 4.9 for influenza virus, parainfluenza virus, respiratory syncytial virus, and human coronavirus, respectively, and 22.0 for rotavirus in stool. The detected virus did not influence clinical features of febrile seizure.

Background: Twenty-five percent to 50% of acute gastroenteritis (AGE) cases remain etiologically undiagnosed. Our main aim was to determine the most appropriate list of enteric pathogens to be included in the daily diagnostics scheme of AGE, ensuring the lowest possible diagnostic gap., Methods: Two hundred ninety seven children ≤6 years of age, admitted to hospital in Slovenia, October 2011 to October 2012, with AGE, and 88 ≤6 years old healthy children were included in the study. A broad spectrum of enteric pathogens was targeted with molecular methods, including 8 viruses, 6 bacteria and 2 parasites., Results: At least one enteric pathogen was detected in 91.2% of cases with AGE and 27.3% of controls. Viruses were the most prevalent (82.5% and 15.9%), followed by bacteria (27.3% and 10.2%) and parasites (3.0% and 1.1%) in cases and controls, respectively. A high proportion (41.8%) of mixed infections was observed in the cases. For cases with undetermined etiology (8.8%), stool samples were analyzed with next generation sequencing, and a potential viral pathogen was detected in 17 additional samples (5.8%)., Conclusions: Our study suggests that tests for rotaviruses, noroviruses genogroup II, adenoviruses 40/41, astroviruses, Campylobacter spp. and Salmonella sp. should be included in the initial diagnostic algorithm, which revealed the etiology in 83.5% of children tested. The use of molecular methods in diagnostics of gastroenteritis is preferable because of their high sensitivity, specificity, fast performance and the possibility of establishing the concentration of the target. The latter may be valuable for assessing the clinical significance of the detected enteric, particularly viral pathogens.

Unlabelled: Human coronaviruses (HCoVs) are associated with a variety of clinical presentations in children, but their role in disease remains uncertain. The objective of our prospective study was to investigate HCoVs associations with various clinical presentations in hospitalized children up to 6 years of age. Children hospitalized with acute bronchiolitis (AB), acute gastroenteritis (AGE), or febrile seizures (FS), and children admitted for elective surgical procedures (healthy controls) were included in the study. In patients with AB, AGE, and FS, a nasopharyngeal (NP) swab and blood sample were obtained upon admission and the follow-up visit 14 days later, whereas in children with AGE a stool sample was also acquired upon admission; in healthy controls a NP swab and stool sample were taken upon admission. Amplification of polymerase 1b gene was used to detect HCoVs in the specimens. HCoVs-positive specimens were also examined for the presence of several other viruses. HCoVs were most often detected in children with FS (19/192, 9.9%, 95% CI: 6-15%), followed by children with AGE (19/218, 8.7%, 95% CI: 5.3-13.3%) and AB (20/308, 6.5%, 95% CI: 4.0-9.8%). The presence of other viruses was a common finding, most frequent in the group of children with AB (19/20, 95%, 95% CI: 75.1-99.8%), followed by FS (10/19, 52.6%, 95% CI: 28.9-75.6%) and AGE (7/19, 36.8%, 95% CI: 16.3-61.6%). In healthy control children HCoVs were detected in 3/156 (1.9%, 95% CI: 0.4-5.5%) NP swabs and 1/150 (0.7%, 95% CI: 0.02-3.3%) stool samples. It seems that an etiological role of HCoVs is most likely in children with FS, considering that they had a higher proportion of positive HCoVs results than patients with AB and those with AGE, and had the highest viral load; however, the co-detection of other viruses was 52.6%., Trial Registration: ClinicalTrials.gov NCT00987519.

Background: Human coronaviruses (HCoVs) are a well-known cause of respiratory infections but their role in gastrointestinal infections is unclear. The objective of our study was to assess the significance of HCoVs in the etiology of acute gastroenteritis (AGE) in children <6  years of age., Methods: Stool samples and nasopharyngeal (NP) swabs collected from 260 children hospitalized for AGE (160 also had respiratory symptoms) and 157 otherwise healthy control children admitted for elective surgery were tested for the presence of four HCoVs using real time RT-PCR. Registered at ClinicalTrials.gov (reg. NCT00987519)., Results: HCoVs were more frequent in patients with AGE than in controls (23/260, 8.8% versus 4/151, 2.6%; odds ratio, OR 3.3; 95% confidence interval, CI 1.3-10.0; P = 0.01). Three of four HCoV-positive members in the control group, asymptomatic when sampled, recalled gastrointestinal or respiratory symptoms within the previous 14  days. In patients with AGE, HCoVs were present in NP samples more often than in stools (22/256, 8.6%, versus 6/260, 2.3%; P = 0.0004). In 5/6 children with HCoVs detected in stools, the viruses were also detected in NP swabs. Patients had a significantly higher probability of HCoV detection in stool (OR 4; 95% CI 1.4-15.3; P = 0.006) and also in stool and/or NP (OR 3.3, 95% CI 1.3-10.0; P = 0.01) than healthy controls. All four HCoVs species were detected in stool and NP samples., Conclusions: Although HCoVs were more frequently detected in patients with AGE than in the control group, high prevalence of HCoVs in NP swabs compounded by their low occurrence in stool samples and detection of other viruses in stool samples, indicate that HCoVs probably play only a minor role in causing gastrointestinal illness in children <6 years old.