The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence

Circulation of the Omicron variant with the reemergence of the N501Y mutation along with many others in the spike protein has once again stirred the academic community. Interestingly, tracing the genetic diversity of SARSCoV- 2 shed light on a less frequent N501Y þ Delta variant which has been in the global circulation for some time before the Omicron appearance. This paper aims to present the molecular characteristics of the SARS-CoV-2 Spike_N501Y þ Delta variant detected in Bosnia and Herzegovina. The study was conducted during November and December 2021. All patients were tested using real-time RT-PCR for detection of SARS-CoV-2. A representative number of SARS-CoV-2 positive samples was pre-screened using VirSNiP SARS-CoV-2 Spike N501Y kit. The characterization of the viruses was carried out with Illumina RNA Prep with enrichment and the Respiratory Virus Oligo Panel kit. Among the analyzed sequences, we found two isolates of the Delta variant that differ from their most related clade- GK AY.4.3 in additional mutations N501Y and L54F. In this study, we described the presence of a rare form of Delta variant with Spike_N501Y mutation in the shadow of the Omicron emergence. Despite the set of mutations in the Spike protein, this form of Delta variant does not indicate the large-scale consequences for the general population. Further functional studies of this form could provide more information about its antigenicity and infectivity

Seasonal and inter-seasonal RSV activity in the European Region during the COVID-19 pandemic from autumn 2020 to summer 2022

© 2023 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.Background: The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in early 2020 and subsequent implementation of public health and social measures (PHSM) disrupted the epidemiology of respiratory viruses. This work describes the epidemiology of respiratory syncytial virus (RSV) observed during two winter seasons (weeks 40–20) and inter-seasonal periods (weeks 21–39) during the pandemic between October 2020 and September 2022. Methods: Using data submitted to The European Surveillance System (TESSy) by countries or territories in the World Health Organization (WHO) European Region between weeks 40/2020 and 39/2022, we aggregated country-specific weekly RSV counts of sentinel, non-sentinel and Severe Acute Respiratory Infection (SARI) surveillance specimens and calculated percentage positivity. Results for both 2020/21 and 2021/22 seasons and inter-seasons were compared with pre-pandemic 2016/17 to 2019/20 seasons and inter-seasons. Results: Although more specimens were tested than in pre-COVID-19 pandemic seasons, very few RSV detections were reported during the 2020/21 season in all surveillance systems. During the 2021 inter-season, a gradual increase in detections was observed in all systems. In 2021/22, all systems saw early peaks of RSV infection, and during the 2022 inter-seasonal period, patterns of detections were closer to those seen before the COVID-19 pandemic. Conclusion: RSV surveillance continued throughout the COVID-19 pandemic, with an initial reduction in transmission, followed by very high and out-of-season RSV circulation (summer 2021) and then an early start of the 2021/22 season. As of the 2022/23 season, RSV circulation had not yet normalised.Peer reviewe

Catheter-Related Urinary Tract Infection in Patients Suffering from Spinal Cord Injuries

Urinary tract infection is commoner in patients with spinal cord injuries because of incomplete bladder emptying and the use of catheters that can result in the introduction of bacteria into the bladder. 145 patients suffering from spinal cord injuries, admitted to the Institute for physical medicine and rehabilitation, Centre for paraplegia of the Clinical Centre of the University of Sarajevo, were included. The patients were divided in three groups according to the method of bladder drainage: Group A (n=61) consisted of patients on clean intermittent catheterization; Group B (n=54) consisted of patients with indwelling catheters; Group C (n=30) consisted of patients who had performed self-catheterization. From a total of 4539 urine samples, 3963 (87,3%) were positive and 576 (12,7%) were sterile. More than 90% of the infected patients were asymptomatic. The overall rate of urinary infection amounted to about 2,1 episodes, and bacteriuria to 8,1 episodes per patient. 77% of infections (113/145) were acquired within seven days from catheterization. Infection was usually polymicrobial; the greatest number of urine samples 1770/3943 (44,9%) included more than one bacterium. The vast majority of cases of urinary tract infection and bacteriuria are caused by Gram-negative bacilli and enterococci, commensal organisms of the bowel and perineum, representative of those from the hospital environment. Providencia stuarti (18,9%) being the most common, followed by Proteus mirabilis (16,3%), Escherichia coli (11,8%), Pseudomonas aeruginosa (10,2%), Klebsiella pneumoniae (8,1%), Morganella morgani (5,4%), Acinetobacter baumannii (4,6%), Providencia rettgeri (3,5%). 15,7% of isolates were Gram-positive with Enterococcus faecalis (8,6%) as the most common. 55,3% of isolates were multidrug-resistant, and the highest rates of resistance were found among Acinetobacter baumannii (87,8%), Providencia rettgeri (86,7%), Pseudomonas aeruginosa (85,4%), Providencia stuarti (84,3%) and Morganella morgani (81,0%). Lower rates of resistance were found in Group C, i.e. patients on intermittent self- catheterisation. Eradication of organisms was achieved in only 53 (10,05%) of patients; hence, antibiotic therapy had no or very low effect. Significant correlations were found between the method of catheterization and the frequency of bacteriuria and urinary tract infections. The analysis of Group C showed a rate of lower urinary tract infection and bacteriuria than the other two Groups of patients. The objective of this study is the update of etiology and antimicrobial susceptibility in urinary tract infections in this group of patients. In addition, possible correlations between UTI and the type of bladder management were examined

Emergence of extensive drug-resistant (XDR) Acinetobacter baumanniiin the Clinical Center University of Sarajevo, Bosnia and Herzegovina

Aim Recently increased attention and interest for Acinetobacterbaumannii are the result of the occurrence of multidrug resistant (MDR), extensive drug resistant (XDR) and pandrug resistant (PDR) isolates around the world. The aim of this study was to examine the resistance of A. baumannii isolates to antimicrobials in Clinical Centre University of Sarajevo, Bosnia and Herzegovina. Methods Two hundred and fifty-seven A.baumannii isolates were collected between July 2011 and June 2012 in different wards and from different clinical samples. Multidrug resistant, XDR and PDR were defined according to international expert proposal for interim standard definitions for acquired resistance. Results A total of 257 A. baumannii isolates showed eleven different patterns of resistance, of which ten patterns corresponded to MDR and one corresponded to XDR (sensitive only to colistin). Multidrug resistant and XDR strains were the most common at Intensive Care Units and surgical departments. The largest numbers of isolates were found in wound swabs, blood and bronchial aspirate. Conclusion This is the first report of XDR A. baumannii in the 2000-bed Clinical Centre University of Sarajevo, Bosnia-Herzegovina. Although XDR strains have been detected, the resistance to colistin has not. The elevated prevalence of these strains indicates that local antibiotic prescription policies should be revised and infection prevention and control should be improved

Frequency and Distribution of Diarrhoeagenic Escherichia Coli Strains Isolated from Pediatric Patients with Diarrhoea in Bosnia and Herzegovina

Diarrhoeal disease is a major cause of illness and death among infants and young children worldwide. Among the Escherichia coli (E. coli) causing intestinal diseases, there are six well-described categories: enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), enteroinvasive E. coli (EIEC), entero-pathogenic E. coli (EPEC), enterohaemorrhagic E. coli (EHEC) and enterotoxigenic E. coli (ETEC). The aim of the present study was to investigate the relative contribution of different groups of diarrhoe-agenic E. coli (DEC) in paediatric patients with diarrhoea. Clinical stool specimens from 380 children with diarrhoea, with ages ranging from birth to < 12 years, were selected for the study over a period of 17 months (August 2007 to December 2008). The study showed that 85/380 children (22%) had diarrhoea due to diarrhoeagenic E. coli. The most prevalent was enteropathogenic E. coli (EPEC) isolated from 46/85 paediatric patients (54%), followed by enterotoxigenic (ETEC) isolated from 19/85 (22.3%), en-terohaemorrhagic (EHEC) from 18/85 (21.1%) and enteroinvasive (EIEC) from 2/85 patients (2.3%). The most prevalent serotypes of EPEC were O86:K61 and O44:K74 isolated from 10/46 (21.7%), O128:K67 from 6/46 patients (13%), followed by O158:K- and O126:K71 isolated from 4/46 patients (8.6%). Among the ETEC the most prevalent serotypes were O78:K80 isolated from 10/19 (56.7%) and O25:K11 from 9/19 patients (47.3%), especially during the first twelve months: 9/19 patients (47.3%). The most prevalent EHEC strain found in this study was O145:K- and O103:K-: 5/18 patients (27.8%). Two isolated strains of EIEC belong to serotype O164:K-. The average age of the patients was 2 years. Two patients with bloody diarrhoea had EHEC serotype O157:H7 which progressed to haemolytic-uremic syndrome (HUS). Our study shows that diarrhoeagenic E. coli is a significant causal agent of diarrhoeal diseases in paediatric patients in Bosnia and Herzegovina. This study is the first report about the frequency and most common serotypes of DEC in Bosnia and Herzegovina. Additionally, it is the first report of cases with an O157:K- infection which progressed to HUS, a serious and potentially fatal illness

Performance Characteristics and Utility of the Standard Q COVID-19 Antigen Test for Emergency Admissions to Healthcare Facilities

This study evaluated the performance of the COVID-19 Ag-RDT compared to the real-time reverse transcription-polymerase chain reaction (rtRT-PCR) for SARS-CoV-2 detection and its use among patients referred for emergency admission. A total of 120 nasopharyngeal swabs were collected from patients referred for emergency admission and immediately preceded for testing to the Unit of Clinical Microbiology. Out of 60 Ag positive tests, 53 (88.3%) were confirmed by rtRT-PCR, while 7 (11.7%) tested negative (false positives). Out of 60 Ag negative tests, 56 (93.3%) were confirmed negative by rtRT-PCR, and 4 (6.7%) were positive (false negatives). Ct value comparison was performed for 53 samples that were positive by both methods: 8 (15.1%) isolates had Ct value up to 20; 37 (69.8%) 21 to 30 and 8 (15.1%) 31 to 40, respectively. The sensitivity of the analyzed rapid Ag test was 92.9%, and specificity 88.9%. The accuracy of the Ag test was 90.8%. This study has shown that rapid Ag tests can be used in emergency admissions to healthcare facilities. However, rtRT-PCR should be considered after negative antigen test results in symptomatic patients, and after positive antigen test results in asymptomatic persons

Predominance of influenza virus A(H3N2) 3C.2a1b and A(H1N1)pdm09 6B.1A5A genetic subclades in the WHO European Region, 2018–2019

Network authors: Portugal - Raquel Guiomar, Pedro Pechirra, National Influenza Reference Laboratory, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, PortugalBackground: The 2018/2019 influenza season in the WHO European Region was dominated by influenza A (H1N1)pdm09 and (H3N2) viruses, with very few influenza B viruses detected. Methods: Countries in the European Region reported virus characterization data to The European Surveillance System for weeks 40/2018 to 20/2019. These virus antigenic and genetic characterization and haemagglutinin (HA) sequence data were analysed to describe and assess circulating viruses relative to the 2018/2019 vaccine virus components for the northern hemisphere. Results: Thirty countries reported 4776 viruses characterized genetically and 3311 viruses antigenically. All genetically characterized A(H1N1)pdm09 viruses fell in subclade 6B.1A, of which 90% carried the amino acid substitution S183P in the HA gene. Antigenic data indicated that circulating A(H1N1)pdm09 viruses were similar to the 2018/2019 vaccine virus. Genetic data showed that A(H3N2) viruses mostly fell in clade 3C.2a (75%) and 90% of which were subclade 3C.2a1b. A lower proportion fell in clade 3C.3a (23%) and were antigenically distinct from the vaccine virus. All B/Victoria viruses belonged to clade 1A; 30% carried a double amino acid deletion in HA and were genetically and antigenically similar to the vaccine virus component, while 55% carried a triple amino acid deletion or no deletion in HA; these were antigenically distinct from each other and from the vaccine component. All B/Yamagata viruses belonged to clade 3 and were antigenically similar to the virus component in the quadrivalent vaccine for 2018/2019. Conclusions: A simultaneous circulation of genetically and antigenically diverse A(H3N2) and B/Victoria viruses was observed and represented a challenge to vaccine strain selection.Highlights: Co-circulation of different clades/subclades of influenza A viruses in 2018/2019 in the Region; Most circulating A(H1N1)pdm09 viruses (6B.1A) carried S183P in hemagglutinin; Genetically heterogeneous A(H3N2) viruses, with co-circulation of clades 3C.2a and 3C.3a; Antigenically distinct A(H3N2) clade 3C.3a viruses were increasingly detected until 02/2019 and then decreased; Co-circulation of genetically and antigenically diverse A(H3N2) strains challenges vaccine strain selection.info:eu-repo/semantics/publishedVersio