Respiratory Samples Research Articles

Epidemiological, clinical and biological profile of COVID-19 in patients hospitalized at the Avicenne Military Hospital in Marrakech

In late December 2019, a series of cases of viral pneumonia caused by a novel coronavirus emerged in Wuhan, China, and quickly spread to all continents. This coronavirus, identified in respiratory tract samples, was named SARS-CoV-2 for Severe Acute Respiratory Syndrome Coronavirus-2 by the ICTV (International Committee on Taxonomy of Viruses). The disease it causes was designated COVID-19 for Coronavirus Disease 2019 by the Word Health Organization. Most often, SARS-CoV-2 infection is responsible for a mild or moderate form, with the most typical clinical presentation being that of a febrile respiratory infection with dry cough, dyspnea, fatigue, and myalgia. Approximately 10-15% of cases are severe, and 5% are critical. Cases of reinfection have been described. Treatment for COVID-19 is currently symptomatic, relying on supportive care. The present study aims to investigate the demographic, clinical, and diagnostic aspects, as well as the study of risk factors associated with SARS-CoV-2 infection among 318 patients admitted to the Avicenne Military Hospital in Marrakech during the first wave of the pandemic. This is a retrospective descriptive and analytical study involving 318 cases of SARS-CoV-2 infection, diagnosed at the microbiology-virology department, and followed up in various non-intensive care units of the Avicenna Military Hospital in Marrakech, during the period of the first wave of the epidemic in Morocco, schematically between March 22, 2020, and July 19, 2020. For patients who developed pneumonia, 20% were diabetic and 13.3% were hypertensive. A quarter of patients with pneumonia experienced desaturation upon admission. In the multivariate logistic regression model, risk factors associated with the development of pneumonia and the various disease outcomes included advanced age and absence of a history of contact with a confirmed case. In the univariate analysis, hyperleukocytosis, neutrophilia, lymphopenia, eosinopenia, anaemia, hyperferritinaemia with elevated aspartate aminotransferase, hyponatraemia and fasting hyperglycaemia were significantly associated with a higher risk of an unfavourable outcome. Patients who presented with pneumonia on admission had an unfavourable outcome during their hospitalisation compared with patients who did not develop pneumonia. The statistically significant risk factors associated with an unfavourable outcome were advanced age (>60 years) with p <0. 001: OR=1.194; 95%IC= [1.114-1.278], absence of contact with a confirmed case (p <0.001 : OR= 43.138; 95%IC= [8.893-209.263]), presence of comorbidity (P<0.001 : OR=11. 503; 95%CI= [3,306-40,028]), mainly diabetes (P<0.001: OR=16,971; 95%CI= [4,267-67,504]) and arterial hypertension (P<0.001: OR=18,812; 95%CI= [3,977-88,954]). The study of the epidemiological, clinical and biological characteristics of COVID 19 at the Avicenne military hospital in Marrakech has enabled us to gain a better understanding of the profile of our patients with SARS-CoV-2 infection, and then to detect shortcomings in terms of prophylaxis, diagnosis and management, in order to be able to provide the necessary solutions aimed at further improving the quality of care for this population.

Genomic characterization of circulating human respiratory syncytial viruses A and B in Kuwait using whole-genome sequencing.

The human respiratory syncytial virus (RSV) is considered one of the most common viruses that infect children globally. The virus is known to have extensive gene sequence variability within and between RSV groups A and B globally; however, there is no information on the whole-genome characterization and diversity of RSV in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with acute respiratory tract infection (ARTI) in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with ARTI in Kuwait. Between January 2020 and September 2022, 7,093 respiratory samples were collected from hospitalized infants, children, and adults and were analyzed for respiratory viruses by multiplex real-time PCR. Whole-genome sequencing using the Oxford Nanopore sequencing technology was performed on 84 RSV-positive samples. The results revealed a higher prevalence of group A (76%) than group B (24%) RSV isolates. Phylogenetic analysis showed that RSV-A strains clustered with the GA2.3.5 sub-genotype and RSV-B strains clustered with the GB5.0.5a sub-genotype; however, forming new lineages of RSV-A and RSV-B circulated in Kuwait during this period. Genetic variability was higher among the group A viruses than group B viruses, and the rate of synonymous and missense mutations was high in genes other than the G protein-coding gene. We also detected several known and unique molecular markers in different protein-coding genes. This is the first study in Kuwait to characterize the whole genomes of RSV A and B to identify the circulating genotypes, comprehend the genetic diversity and the evolution of the virus, and identify important genetic markers associated with specific genotypes.IMPORTANCEWhole-genome sequencing of respiratory syncytial virus (RSV) strains in Kuwait using MinION Nanopore technology was used to characterize and analyze the genotypes and sub-genotypes of the RSV circulating among patients with acute respiratory tract infections in Kuwait. This study also identified known and unknown gene mutations and imported genetic markers associated with specific genotypes. These results will assist in establishing a framework for RSV classification and allow for a better consideration of the mechanisms leading to the generation of diversity of RSV. In addition, these data will allow a comparison of vaccine viruses with those in Kuwait, providing useful insights into future vaccine and therapy strategies for RSV in Kuwait.

Neurological involvement related to the influenza virus in children: A 5-year single-centre retrospective study

IntroductionInflammation related to influenza virus infection can lead to multiple neurological presentations. Encephalitis is one of them, mostly accompanied by seizures, with different profiles depending on the epidemics and previous medical conditions. Materials and methodsAll children presenting neurological symptoms and positive for influenza virus RNA detection in a respiratory sample between November 2018 and April 2023, hospitalized in the Department of Paediatric Neurology of Toulouse Children's Hospital, were retrospectively analysed. ResultsAmong the 1,277 children diagnosed with influenza in our centre, 131 (10.3 %) were hospitalized for neurological features. The year 2020–2021 was marked by zero incidence of positive influenza tests, associated with the COVID-19 pandemic. Among the 131 patients included, 71.6 % were under 5 years old. Most of them (80.9 %) were infected by influenza A virus. The first neurological symptoms were mainly seizures in 73.3 % of patients. Possible or confirmed encephalitis was observed in 29 % of cases, including one acute necrotizing encephalopathy. Few children (6.1 %) presented with acute myositis. Twenty-seven patients (20.6 %) had a personal history of significant previous neurological disorders. Most patients (88.5 %) displayed a rapid favourable outcome, marked by the disappearance of their neurological symptoms within the first 2 days. Anti-epileptic drugs were introduced in 1.5 % of cases, and adapted in 16.8 %, mainly in patients with febrile status epilepticus and an abnormal EEG. ConclusionNeurological features were frequently associated with influenza infection in children; most were transient. Effects on long-term neurodevelopmental outcomes need to be clarified as our follow-up was limited, especially in children with pre-existing neurological conditions.

#1569 Cytomegalovirus (CMV) infection in renal transplant patients managed with early pre-emptive treatment

Abstract Background and Aims Human Cytomegalovirus (CMV) can cause significant morbidity in transplant recipients. Primary CMV infection in CMV seronegative recipients (R−) and reactivation of CMV in seropositive recipients (R+) post-transplant can lead to CMV end organ disease (EOD). At Royal Free Hospital (RFH), London, United Kingdom, CMV EOD is prevented through pre-emptive therapy (PET), which utilises quantitative real-time PCR (qPCR) in whole blood to monitor all transplant patients and guide therapeutic interventions (1). PET is started in D+R− transplant patients following the first detectable CMV DNA (≥200 copies/ml) in blood (2). For CMV seropositive patients, PET is started when CMV DNA is ≥3000 copies/ml. This differs from many transplant centres which provide CMV anti-viral prophylaxis for the first 3-6 months post-transplant to patients at high risk of developing CMV EOD. In this observational study, the effectiveness of our PET approach and differences in CMV viral replication kinetics was retrospectively analysed in renal transplant recipients of differing CMV serostatus. Method A retrospective review of results from electronic patient records and laboratory information management system for patients who underwent renal transplantation from April 2021 to January 2023 was conducted. Patients were divided into four groups based on organ donor and recipient CMV IgG serostatus (D+R−, D+R+, D−R+, D−R−). Those who were followed up for less than 90 days or had unknown donor serostatuses were excluded. Results A total of 227 patients who received renal transplantation between April 2021 to January 2023 were identified. Of which, 11% (25/227) were D+R−, 42.3% (96/227) were D+R+, 33% (75/227) were D−R+ and 13.7% (31/227) were D−R−. Within each group, 60% (15/25) of D+R−, 61.5% (59/96) of D+R+ and 48% (36/75) of D−R+ patients developed CMV viraemia during the monitoring period. Of CMV viraemic patients, all D+R− (15/15), 54.2% (32/59) of D+R+ and 27.8% (10/36) of D−R+ patients were treated with valganciclovir as per our PET protocol. None of the D−R− patients developed any CMV viraemia. The mean peak viral load for patients with viraemia requiring treatment with valganciclovir was 4772 copies/ml (range 210-30000 copies/ml) in D+R−, 5050 copies/ml (range 3000-30000 copies/ml) and 5050 copies/ml (range 3300-18000 copies/ml) in D+R+ and D−R+ groups respectively. The mean time to first viraemia was 59 days (range 15-332) for the D+R−, 40 days (range 7-177) for D+R+ and 43 days (range 15-91) for D−R+ patients. Furthermore, the mean duration of viraemia was 34 days for D+R−, 37.5 days for D+R+ and 30.5 days for D−R+ groups. 19 patients had CMV viraemia recurrence requiring re-treatment, 63%were D+R− (12/19), 32% were D+R+ (6/19) and 5% (1/19) were D−R+. Across all four groups, two patients developed CMV EOD. One D+R+ patient was found to have CMV in respiratory sample and one D−R+ patient had CMV on colon biopsy. One D+R− patient developed UL97 mutations (M460I and A594V) conferring ganciclovir resistance due to poor compliance and was treated with maribavir. Conclusion PET is a safe and effective approach which reduces the risk of CMV EOD and antiviral medication resistance in SOT patients. Our PET approach provides monitoring of all patients regardless of CMV serostatus thereby reducing the risk of CMV EOD in all patients by ensuring early treatment of viraemia.

Examination of upper respiratory tracts of Siirt-coloured mohair goats by scanning electron microscopy before and after plastination.

Present study was conducted to determine the changes in the surface structure of the upper respiratory tract of Siirt-coloured mohair goats by the silicone plastination method. Accordingly, the heads of 10 Siirt-coloured mohair goats procured from slaughterhouses were divided into two halves. Half of each head was plastinated. After macro-comparisons were made, the deformations of silicone plastination on the surface were examined by comparing the scanning electron microscope (SEM) findings of both upper respiratory tract tissue samples collected from plastinates and fresh material. When the data from scanning electron microscopy were analysed, cilia, cobblestone patterns, goblet cells and gland ducts on the epithelial surface were identified in areas on the upper respiratory tract. The SEM images of the plastinated tissues showed that the surface structures were degenerated due to the deformation of the surface epithelium. The plastination technique damaged the structures on the surface epithelium. Since the plastination technique and scanning electron microscopy have been studied together for the first time, we believe this would contribute to the scientific literature.

Routes of SARS-Cov2 transmission in the intensive care unit: A multicentric prospective study

BackgroundThe risk of SARS-CoV-2 transmission to health care workers in intensive care units (ICU) and the contribution of airborne and fomites to SARS-CoV-2 transmission remain unclear. To assess the rate of air and surface contamination and identify risk factors associated with this contamination in patients admitted to the ICU for acute respiratory failure due to SARS-CoV-2 pneumonia. MethodsProspective multicentric non-interventional study conducted from June 2020 to November 2020 in 3 French ICUs. For each enrolled patient, 3 predefined surfaces were swabbed, 2 air samples at 1 m and 3 m from the patient’s mouth and face masks of 3 health care workers (HCW) were collected within the first 48 h of SARS-CoV-2 positive PCR in a respiratory sample. Droplet digital PCR and quantitative PCR were performed on different samples, respectively. ResultsAmong 150 included patients, 5 (3.6%, 95%CI: 1.2% to 8.2%) had positive ddPCR on air samples at 1 m or 3 m. Seventy-one patients (53.3%, CI95%: 44.5% to 62.0%) had at least one surface positive. Face masks worn by HCW were positive in 6 patients (4.4%, CI: 1.6% to 9.4%). The threshold of RT-qPCR of the respiratory sample performed at inclusion (odds ratio, OR= 0.88, 95%CI: 0.83 to 0.93, p < 0.0001) and the presence of diarrhea (OR= 3.28, 95%CI: 1.09 to 9.88, p = 0.037) were significantly associated with the number of contaminated surfaces. ConclusionIn this study, including patients admitted to the ICU for acute respiratory failure " contact route " of transmission, i.e. through fomites, seems dominant. While presence of SARS-CoV-2 in the air is rare in this specific population, the presence of diarrhea is associated to surface contamination around Covid patients.

The effect of the COVID-19 pandemic on the incidence and resistance of Gram-negative bacilli and antimicrobial consumption in the intensive care units of a referral hospital in Buenos Aires

There was a reported increase in the antimicrobial consumption in hospitals during the COVID-19 pandemic, accompanied by an increase in infections due to multidrug-resistant (MDR) bacteria. This retrospective time series study from intensive care units in Buenos Aires examined changes in antibiotic consumption (defined daily doses/1000 patients/day), the incidence of Gram-negative bacilli (GNB) and the mechanism of resistance. Antibiotics were categorised into group 1 (agents against MDR GNB) and group 2 (agents against non-MDR infections). Bacteriological samples included respiratory samples and blood cultures. Periods were divided into pre-pandemic (July 2019 to March 2020) and pandemic (April 2020 to March 2022). Correlation coefficients (r) were analysed and the Mann-Whitney test was performed to compare both periods. During the study period, GNB incidence, group 1 antibiotic consumption and resistance mechanisms increased, whereas antibiotics decreased in group 2. A significant positive correlation was seen between the consumption of antibiotics in group 1 and the incidence of GNB (r = 0.63; P < 0.001) and resistance (r = 0.52; P = 0.002). Significant differences were found between pre-pandemic and pandemic periods regarding the medians of group 1 consumption (520 [408-570] vs. 753 [495-851] DDD/1000 patients/day; P = 0.029), incidence of GNB (12 [10-13] vs. 43 [25-52.5] cases/month; P < 0.001) and resistance mechanisms (5 [4-8] vs. 17 [10-25] cases/month; P < 0.001), extended-spectrum beta lactamases (2 [1-2] vs. 6 [3-8] cases/month; P < 0.001) and metallo-beta-lactamases (0 [0-0] vs. 6 [1.75-8.5] cases/month; P < 0.001). During the COVID-19 pandemic, the rise in GNB incidence and the amount of resistance mechanisms significantly correlated with the increase in consumption of agents against MDR strains.

The “COVID effect” in culture-based clinical microbiology: Changes induced by COVID-19 pandemic in a Hungarian tertiary care center

BackgroundThe presence of bacterial and fungal coinfections plays an important role in the mortality of patients with coronavirus 2019 (COVID-19). We compared data from the 3 years before and 3 years after the COVID-19 pandemic outbreak to evaluate its effect on the traits of bacterial and fungal diseases. MethodsWe retrospectively collected and analyzed data on positive respiratory tract samples (n = 13,133 samples from 7717 patients) and blood cultures (n = 23,652 from 9653 patients) between 2017 and 2022 from the Clinical Center of the University of Szeged, Hungary. We also evaluated antimicrobial susceptibility test results derived from 169,020 respiratory samples and 549,729 blood cultures to gain insight into changes in antimicrobial resistance. ResultsThe most common respiratory pathogen in the pre-COVID era was Pseudomonas aeruginosa, whereas Candida albicans was the most frequent during the pandemic. The number of respiratory isolates of Acinetobacter baumannii was also markedly increased. In blood cultures, Staphylococcus epidermidis, Escherichia coli, and S. aureus were dominant during the study period, and A. baumannii was widespread in blood cultures during the pandemic years. Resistance to ofloxacin, penicillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, ceftolozane-tazobactam, and itraconazole increased significantly in the COVID era. ConclusionsDuring the COVID-19 pandemic, there were changes in the prevalence of respiratory and blood culture pathogens at the Clinical Center of the University of Szeged. C. albicans became the predominant respiratory pathogen, and the number of A. baumannii isolates increased dramatically. Additionally, antimicrobial resistance notably increased during this period.

Evaluation of Gram Stain-Guided Antibiotic Therapy for Methicillin-Resistant Staphylococcus aureus Pneumonia in Intensive Care Unit Patients.

Background: Despite high negative predictive values (NPVs) seen with methicillin-resistant Staphylococcus aureus (MRSA) nares polymerase chain reaction (PCR) assays, utilization of both respiratory sample Gram stain and MRSA nares PCR in patients with pneumonia may contribute to overuse of laboratory resources. The purpose of this study was to evaluate if a Gram stain demonstrating no Gram-positive organisms from a respiratory sample is sufficient to allow for de-escalation of vancomycin therapy. Methods: This single center study retrospectively identified intensive care unit (ICU) patients started on vancomycin for presumed pneumonia at University of Wisconsin (UW) Health in Madison, WI between August 2022 and March 2023. Patients with respiratory sample demonstrating no Gram-positives on Gram stain met inclusion criteria if the sample was ordered within 24 h of vancomycin initiation. The primary outcome was NPV of respiratory sample Gram stain demonstrating no Gram-positive organisms with respect to MRSA detection of the respiratory culture. Secondary outcomes included the NPV of combined MRSA nares PCR plus respiratory sample Gram stain, and difference in time to event in patients that had both a respiratory sample and MRSA nares PCR ordered. Results: A total of 370 patients were screened for study eligibility; of which 99 patients met inclusion criteria. NPV of respiratory sample Gram stain was 99% for MRSA culture. The combined NPV of respiratory sample Gram stain plus MRSA nares PCR was 98.9% for MRSA culture (n = 88). Respiratory sample was ordered 2.3 h faster compared to MRSA nares PCR (4.3 vs 6.6 h, P = .036). Respiratory sample Gram stain resulted 4.5 h faster compared to MRSA nares PCR (10.7 vs 15.2 h, P = .002). Conclusion: Respiratory sample Gram stains demonstrating no Gram-positive organisms may be used to de-escalate vancomycin and deprioritize the use of MRSA nares PCR.

Impact and Occurrence of Herpesvirus and Aspergillosis Superinfection in Patients with Severe COVID-19 Pneumonia

Background: Pulmonary superinfections with Herpesviridae and Aspergillus spp. are common in severe coronavirus disease 2019 (COVID-19) pneumonia but their epidemiology and impact remain poorly understood. Methods: We conducted a retrospective observational study of 61 mechanically ventilated COVID-19 patients at Deventer Hospital’s ICU (2020–2021) who underwent bronchoalveolar lavage (BL) due to clinical deterioration. We analyzed blood and respiratory samples, treatment, and clinical outcomes. Results: Among 61 mechanically ventilated COVID-19 patients who underwent BL, 34 (55.7%) had superinfections, with 18 having COVID-19-associated pulmonary aspergillosis (CAPA), 7 having herpes simplex virus (HSV) infection, and 9 having both. Patients with HSV had later diagnoses (median 14 vs. 8 days, p = 0.014), longer mechanical ventilation (median 47 vs. 18.5 days, p = 0.015), and longer ICU stays (median 74 vs. 24 days, p = 0.021) compared to CAPA patients. At baseline, laboratory parameters and treatment (dexamethasone or tocilizumab) showed no significant association with superinfections. Mortality did not differ significantly among groups. Conclusion: In mechanically ventilated COVID-19 patients undergoing bronchoalveolar lavage, HSV reactivation occurred later in the course of illness and was associated with longer mechanical ventilation and ICU stays compared to CAPA. Baseline parameters did not predict superinfections.

Parallel use of low-complexity automated nucleic acid amplification tests on respiratory samples and stool with or without lateral flow lipoarabinomannan assays to detect pulmonary tuberculosis disease in children

Parallel use of low-complexity automated nucleic acid amplification tests on respiratory samples and stool with or without lateral flow lipoarabinomannan assays to detect pulmonary tuberculosis disease in children

Unravelling the acute respiratory infection landscape: virus type, viral load, health status and coinfection do matter.

Acute respiratory infections (ARI) are the most common infections in the general population and are mainly caused by respiratory viruses. Detecting several viruses in a respiratory sample is common. To better understand these viral codetections and potential interferences, we tested for the presence of viruses and developed quantitative PCR (Polymerase Chain Reaction) for the viruses most prevalent in coinfections: human rhinovirus (HRV) and respiratory syncytial virus (RSV), and quantified their viral loads according to coinfections and health status, age, cellular abundance and other variables. Samples from two different cohorts were analyzed: one included hospitalized infants under 12 months of age with acute bronchiolitis (n=719) and the other primary care patients of all ages with symptoms of ARI (n=685). We performed Multiplex PCR on nasopharyngeal swabs, and quantitative PCR on samples positive for HRV or/and RSV to determine viral loads (VL). Cellular abundance (CA) was also estimated by qPCR targeting the GAPDH gene. Genotyping was performed either directly from first-line molecular panel or by PCR and sequencing for HRV. The risks of viral codetection were 4.1 (IC95[1.8; 10.0]) and 93.9 1 (IC95[48.7; 190.7]) higher in infants hospitalized for bronchiolitis than in infants in primary care for RSV and HRV respectively (p<0.001). CA was higher in samples positive for multiple viruses than in mono-infected or negative samples (p<0.001), and higher in samples positive for RSV (p<0.001) and HRV (p<0.001) than in negative samples. We found a positive correlation between CA and VL for both RSV and HRV. HRV VL was higher in children than in the elderly (p<0.05), but not RSV VL. HRV VL was higher when detected alone than in samples coinfected with RSV-A and with RSV-B. There was a significant increase of RSV-A VL when codetecting with HRV (p=0.001) and when co-detecting with RSV-B+HRV versus RSV-A+ RSV-B (p=0.02). Many parameters influence the natural history of respiratory viral infections, and quantifying respiratory viral loads can help disentangle their contributions to viral outcome.

Metagenomics to Identify Viral Communities Associated with Porcine Respiratory Disease Complex in Tibetan Pigs in the Tibetan Plateau, China.

Tibetan pig is a unique pig breed native to the Qinghai-Tibet Plateau. To investigate viral communities associated with porcine respiratory disease complex (PRDC), 167 respiratory samples were collected from Tibetan pigs in the Ganzi Tibetan autonomous prefecture of Sichuan province. Following library construction and Illunima Novaseq sequencing, 18 distinct viruses belonging to 15 viral taxonomic families were identified in Tibetan pigs with PRDC. Among the 18 detected viruses, 3 viruses were associated with PRDC, including porcine circovirus type 2 (PCV-2), Torque teno sus virus (TTSuV), and porcine cytomegalovirus (PCMV). The genomic sequences of two PCV-2 strains, three TTSuV strains, and one novel Porprismacovirus strain were assembled by SOAPdenovo software (v2). Sequence alignment and phylogenetic analysis showed that both PCV-2 strains belonged to PCV-2d, three TTSuVs were classified to TTSuV2a and TTSuV2b genotypes, and the Porprismacovirus strain PPMV-SCgz-2022 showed a close genetic relationship with a virus of human origin. Recombination analysis indicated that PPMV-SCgz-2022 may have originated from recombination events between Human 16,806 × 66-213 strain and Porcine 17,668 × 82-593 strain. Furthermore, the high proportion of single infection or co-infection of PCV2/TTSuV2 provides insight into PRDC infection in Tibetan pigs. This is the first report of the viral communities in PRDC-affected Tibetan pigs in this region, and the results provides reference for the prevention and control of respiratory diseases in these animals.

Monitoring of antimicrobial resistance in respiratory tract pathogens during the COVID-19 pandemic: A retrospective study.

To understand the distribution and antimicrobial resistance (AMR) of pathogens in respiratory samples in Changle District People's Hospital in Fujian Province in recent years, and provide empirical guidance for infection control and clinical treatment in the region. A retrospective analysis was conducted on 5137 isolates of pathogens from respiratory samples collected from 2019 to 2022. The AMR patterns were systematically analyzed. For research purposes, the data was accessed on October 12, 2023. A total of 3517 isolates were included in the study, including 811 (23.06%) gram-positive bacteria and 2706 (76.94%) gram-negative bacteria. The top 3 gram-positive bacteria were Staphylococcus aureus with 455 isolates (12.94%), Streptococcus pneumoniae with 99 isolates (2.81%), and Staphylococcus hemolytic with 99 isolates (2.81%). The top 3 gram-negative bacteria were Klebsiella pneumoniae with 815 isolates (23.17%), Pseudomonas aeruginosa with 589 isolates (16.75%), and Acinetobacter baumannii with 328 isolates (9.33%). The proportion of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and K pneumoniae fluctuated between 41.9% and 70.5%, and 18.6% and 20.9%, respectively. The resistance rates of E coli, K pneumoniae, P aeruginosa, and A baumannii to carbapenems were 2.36%, 8.9%, 18.5%, and 19.6%, respectively. The prevalence of methicillin-resistant S aureus (MRSA) was 48.55%, but it decreased to 38.4% by 2022. The resistance rate of Staphylococcus haemolyticus to methicillin was 100%, and 1 case of vancomycin-resistant strain was detected. K pneumoniae, P aeruginosa, A baumannii, and S aureus are the main pathogens in respiratory samples. Although the resistance rates of some multidrug-resistant strains have decreased, ESBL-producing Enterobacteriaceae, carbapenem-resistant bacteria have still increased. Therefore, it is necessary to strengthen the monitoring of pathogen resistance, promote rational use of antibiotics, and promptly report findings.

Faecal shedding of SARS-CoV-2 from patients with asymptomatic and mild COVID-19 without gastrointestinal symptoms in Ghana

ObjectiveIn this study, we sought to determine whether faecal shedding occurs among SARS-COV-2 positive Ghanaians, as reported elsewhere. Hence we assayed for SARS-COV-2 in the stools of 48 SARS-COV-2 confirmed patients at the Ho Municipal Hospital in Ghana.ResultsOf the 48 COVID-19 patients, 45 (93.8%) had positive tests for SARS-CoV-2 faecal shedding. About 60% reported no respiratory symptoms, while only 2% (1 patient) reported gastrointestinal (GI) symptoms in the form of nausea. Other symptoms reported included headache (57.9%), weakness (57.9%), cough (52.6%), blocked/runny nose (47.4%), fever (31.6%), sore throat (31.6%), and shortness of breath (21.1%). One person complained of nausea (5.3%) Semi-quantitative comparison of the SARS COV-2 viral loads in matched respiratory and faecal samples using the cycle threshold (CT) values revealed no statistical differences. Furthermore, the duration between collection of respiratory and faecal samples did not have any direct influence on the differences in the CT values. This suggests that treatment and use of sewage for environmental surveillance of SARS COV-2 could be a potential public health countermeasure.

Serum procalcitonin as a diagnostic biomarker in dogs with bacterial respiratory diseases.

Procalcitonin (PCT) is a useful biomarker in humans in the identification of bacterial respiratory infections. The aim of this study was to investigate the utility of serum PCT measurements as a diagnostic biomarker in canine bacterial lower respiratory tract diseases. PCT concentrations were measured in serum samples with an ELISA method previously validated for dogs. All dogs underwent thorough clinical examinations, and the diagnosis of respiratory disease was based on clinical and laboratory findings, diagnostic imaging, as well as cytology and bacterial culture of respiratory samples. PCT concentrations between different cohorts of dogs were compared with an ANOVA-model. Sixty-two privately owned dogs with respiratory diseases, 25 with bacterial pneumonia (BP), 17 with bacterial bronchitis caused by Bordetella bronchiseptica (BB), and 20 with chronic bronchitis (CB) as well as 44 healthy controls were included in the study. Serum PCT concentrations in dogs with bacterial respiratory diseases (BP mean 51.8 ng/L ± standard deviation [SD] 40.6 ng/L and BB mean 61.4 ng/L ± SD 35.3 ng/L) were not significantly different when compared with dogs with a non-bacterial respiratory disease (CB mean 89.7 ± SD 73.5 ng/L) or healthy dogs (mean 51.0 ng/L ± SD 37.5 ng/L, p > .05 in all comparisons). These results indicate that despite being a valuable diagnostic, prognostic, and follow-up marker in humans with pneumonia, serum PCT concentrations are not elevated in dogs with bacterial respiratory diseases and, therefore, cannot be used as a diagnostic biomarker in dogs.

Proteome analysis, genetic characterization, and antibiotic resistance patterns of Klebsiella pneumoniae clinical isolates

Klebsiella pneumoniae (K. pneumoniae) is a member of the ESKAPE group and is responsible for severe community and healthcare-associated infections. Certain Klebsiella species have very similar phenotypes, which presents a challenge in identifying K. pneumoniae. Multidrug-resistant K. pneumoniae is also a serious global problem that needs to be addressed. A total of 190 isolates were isolated from urine (n = 69), respiratory (n = 52), wound (n = 48) and blood (n = 21) samples collected from various hospitals in the Al-Qassim, Saudi Arabia, between March 2021 and October 2022. Our study aimed to rapidly and accurately detect K. pneumoniae using the Peptide Mass Fingerprinting (PMF) technique, confirmed by real-time PCR. Additionally, screening for antibiotic susceptibility and resistance was conducted. The primary methods for identifying K. pneumoniae isolates were culture, Gram staining, and the Vitek® 2 ID Compact system. An automated MALDI Biotyper (MBT) instrument was used for proteome identification, which was subsequently confirmed using SYBR green real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Vitek® 2 AST-GN66 cards were utilized to evaluate the antimicrobial sensitivity of K. pneumoniae isolates. According to our results, Vitek® 2 Compact accurately identified 178 out of 190 (93.68%) K. pneumoniae isolates, while the PMF technique correctly detected 188 out of 190 (98.95%) isolates with a score value of 2.00 or higher. Principal component analysis was conducted using MBT Compass software to classify K. pneumoniae isolates based on their structure. Based on the analysis of the single peak intensities generated by MBT, the highest peak values were found at 3444, 5022, 5525, 6847, and 7537 m/z. K. pneumoniae gene testing confirmed the PMF results, with 90.53% detecting entrobactin, 70% detecting 16 S rRNA, and 32.63% detecting ferric iron uptake. The resistance of the K. pneumoniae isolates to antibiotics was as follows: 64.75% for cefazolin, 62.63% for trimethoprim/sulfamethoxazole, 59.45% for ampicillin, 58.42% for cefoxitin, 57.37% for ceftriaxone, 53.68% for cefepime, 52.11% for ampicillin-sulbactam, 50.53% for ceftazidime, 52.11% for ertapenem, and 49.47% for imipenem. Based on the results of the double-disk synergy test, 93 out of 190 (48.95%) K. pneumoniae isolates were extended-spectrum beta-lactamase. In conclusion, PMF is a powerful analytical technique used to identify K. pneumoniae isolates from clinical samples based on their proteomic characteristics. K. pneumoniae isolates have shown increasing resistance to antibiotics from different classes, including carbapenem, which poses a significant threat to human health as these infections may become difficult to treat.

Presence and Significance of Multiple Respiratory Viral Infections in Children Admitted to a Tertiary Pediatric Hospital in Italy

Viral co-infections are frequently observed among children, but whether specific viral interactions enhance or diminish the severity of respiratory disease is still controversial. This study aimed to investigate the type of viral mono- and co-infections by also evaluating viral correlations in 3525 respiratory samples from 3525 pediatric in/outpatients screened by the Allplex Respiratory Panel Assays and with a Severe Acute Respiratory Syndrome-COronaVirus 2 (SARS-CoV-2) test available. Overall, viral co-infections were detected in 37.8% of patients and were more frequently observed in specimens from children with lower respiratory tract infections compared to those with upper respiratory tract infections (47.1% vs. 36.0%, p = 0.003). SARS-CoV-2 and influenza A were more commonly detected in mono-infections, whereas human bocavirus showed the highest co-infection rate (87.8% in co-infection). After analyzing viral pairings using Spearman’s correlation test, it was noted that SARS-CoV-2 was negatively associated with all other respiratory viruses, whereas a markedly significant positive correlation (p &lt; 0.001) was observed for five viral pairings (involving adenovirus/human bocavirus/human enterovirus/metapneumoviruses/rhinovirus). The correlation between co-infection and clinical outcome may be linked to the type of virus(es) involved in the co-infection rather than simple co-presence. Further studies dedicated to this important point are needed, since it has obvious implications from a diagnostic and clinical point of view.

Retrospective Genotyping of Enteroviruses Using a Diagnostic Nanopore Sequencing Workflow.

Enteroviruses are among the most common viruses pathogenic to humans. They are associated with various forms of disease, ranging from mild respiratory illness to severe neurological diseases. In recent years, an increasing number of isolated cases of children developing meningitis or encephalitis as a result of enterovirus infection have been reported, as well as discrete enterovirus D68 outbreaks in North America in 2014 and 2016. We developed an assay to rapidly genotype enteroviruses by sequencing a region within the VP1 gene using nanopore Flongles. We retrospectively analyzed enterovirus-/rhinovirus-positive clinical samples from the Zurich, Switzerland area mainly collected during two seasons in 2019/2020 and 2021/2022. Respiratory, cerebrospinal fluid, and stool samples were analyzed. Whole-genome sequencing was performed on samples with ambiguous genotyping results and enterovirus D68-positive samples. Out of 255 isolates, a total of 95 different genotypes were found. A difference in the prevalence of enterovirus and rhinovirus infections was observed for both sample type and age group. In particular, children aged 0-4 years showed a higher frequency of enterovirus infections. Comparing the respiratory seasons, a higher prevalence was found, especially for enterovirus A and rhinovirus A after the SARS-CoV-2 pandemic. The enterovirus genotyping workflow provides a rapid diagnostic tool for individual analysis and continuous enterovirus surveillance.

Utility of a multiplex pathogen detection system directly from respiratory specimens for treatment and diagnostic stewardship.

The availability of syndrome-based panels for various ailments has widened the scope of diagnostics in many clinical settings. These panels can detect a multitude of pathogens responsible for a particular condition, which can lead to a timely diagnosis and better treatment outcomes. In contrast to traditional identification methods based on pathogen growth on culture, syndrome-based panels offer a quicker diagnosis, which can be especially beneficial in situations requiring urgent care, such as intensive care units. One such panel is the Biofire Filmarray Pneumonia plus Panel (BFP), which we have compared against microbiological culture and identification. The lower respiratory samples from patients were tested with BFP, culture, and identification with culture considered the gold standard. The phenotypic antibiotic susceptibility results (Vitek 2) were compared with the antimicrobial resistance (AMR) genes detected in BFP. Statistical analysis was carried out using GraphPad 7.0 and MS Excel (Microsoft Inc.). The results showed a positive percent agreement of 100% and a negative percent agreement of 47.8% with an overall agreement of 76.72% compared to culture. BFP was better at identifying fastidious bacteria, and the agreement with culture was higher for high bacterial identification numbers (107 and 106). There was also a correlation between the number of pathogens detected and growth in culture. Carbapenemase genes were detected in around 80% of phenotypically resistant samples and correlated with in-house PCR 60% of the time. Hence, BFP results need to be interpreted with caution especially when multiple pathogens are detected. Similarly, the presence or absence of AMR genes should be used to guide the therapy while being watchful of unusual resistance or susceptibility. The cost constraints and low throughput call for patient selection criteria and prioritization in emergency or resource-limited conditions.IMPORTANCEApplication of syndrome-based panels in clinical microbiology is of huge support in infectious conditions requiring urgent interventions, such as pneumonia. Interpreting the results requires caution; hence, we have compared the results obtained from Biofire Filmarray Pneumonia plus Panel with standard microbiological methods.