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Superinfection and recombination of infectious laryngotracheitis virus vaccines in the natural host.Vaccine Nov 2020Infectious laryngotracheitis virus (ILTV, Gallid alphaherpesvirus 1) causes severe respiratory disease in chickens and has a major impact on the poultry industry...
Infectious laryngotracheitis virus (ILTV, Gallid alphaherpesvirus 1) causes severe respiratory disease in chickens and has a major impact on the poultry industry worldwide. Live attenuated vaccines are widely available and are administered early in the life of commercial birds, often followed by one or more rounds of revaccination, generating conditions that can favour recombination between vaccines. Better understanding of the factors that contribute to the generation of recombinant ILTVs will inform the safer use of live attenuated herpesvirus vaccines. This study aimed to examine the parameters of infection that allow superinfection and may enable the generation of recombinant progeny in the natural host. In this study, 120 specific-pathogen free (SPF) chickens in 8 groups were inoculated with two genetically distinct live-attenuated ILTV vaccine strains with 1-4 days interval between the first and second vaccinations. After inoculation, viral genomes were detected in tracheal swabs in all groups, with lowest copies detected in swabs collected from the groups where the interval between inoculations was 4 days. Superinfection of the host was defined as the detection of the virus that was inoculated last, and this was detected in tracheal swabs from all groups. Virus could be isolated from swabs at a limited number of timepoints, and these further illustrated superinfection of the birds as recombinant viruses were detected among the progeny. This study has demonstrated superinfection at host level and shows recombination events occur under a very broad range of infection conditions. The occurrence of superinfection after unsynchronised infection with multiple viruses, and subsequent genomic recombination, highlight the importance of using only one type of vaccine per flock as the most effective way to limit recombination.
Topics: Animals; Chickens; Herpesviridae Infections; Herpesvirus 1, Gallid; Poultry Diseases; Recombination, Genetic; Superinfection; Vaccines, Attenuated; Viral Vaccines
PubMed: 33012604
DOI: 10.1016/j.vaccine.2020.09.064 -
Advanced Biomedical Research 2023Bacterial superinfections are one of the crucial challenges in patients with coronavirus disease 2019 (COVID-19) that are associated with a high mortality rate. The...
BACKGROUND
Bacterial superinfections are one of the crucial challenges in patients with coronavirus disease 2019 (COVID-19) that are associated with a high mortality rate. The current study was designed to assess bacterial superinfections and antibiotic management in COVID-19 patients admitted to intensive care unit (ICU).
MATERIAL AND METHODS
Seventy-three adult intubated patients with COVID-19 were included in a cross-sectional study. The lung aspirate samples were collected in two stages and assessed for bacterial growth by standard methods. Antimicrobial susceptibility testing was performed using the Kirby-Bauer method as recommended by the Clinical Laboratory Standard Institute guideline (2021 edition). Also, demographic and clinical data were collected. The statistical analysis was done by chisquare test and Student's -test, and a value <0.05 was considered significant.
RESULTS
Forty men and thirty-three women with a mean age of 64.78 ± 13.90 have included in our study. The mean length of hospitalization and stay in ICU were 18.77 ± 12.94 and 13.51 ± 9.83 days, respectively; 84.9% of cases died. Thirty-three patients had a bacterial superinfection mainly caused by spp and spp; 21.2% of piperacillin/tazobactam consumers' patients survived that; the differences were significant (p = 0.034). A significant relationship was seen between superinfection and length of hospital stay until intubation (p = 0.033).
CONCLUSION
Bacterial superinfection and mortality rates were relatively high in COVID-19 patients admitted to ICU. According to the results, using beta-lactam/beta-lactamase inhibitors antibiotics in hospitalized patients in ICU can effectively control superinfection.
PubMed: 37057242
DOI: 10.4103/abr.abr_82_22 -
Journal of Neuroinflammation Feb 2023Patients with COVID-19 can have a variety of neurological symptoms, but the active involvement of central nervous system (CNS) in COVID-19 remains unclear. While routine...
Patients with COVID-19 can have a variety of neurological symptoms, but the active involvement of central nervous system (CNS) in COVID-19 remains unclear. While routine cerebrospinal fluid (CSF) analyses in patients with neurological manifestations of COVID-19 generally show no or only mild inflammation, more detailed data on inflammatory mediators in the CSF of patients with COVID-19 are scarce. We studied the inflammatory response in paired CSF and serum samples of patients with COVID-19 (n = 38). Patients with herpes simplex virus encephalitis (HSVE, n = 10) and patients with non-inflammatory, non-neurodegenerative neurological diseases (n = 28) served as controls. We used proteomics, enzyme-linked immunoassays, and semiquantitative cytokine arrays to characterize inflammatory proteins. Autoantibody screening was performed with cell-based assays and native tissue staining. RNA sequencing of long-non-coding RNA and circular RNA was done to study the transcriptome. Proteomics on single protein level and subsequent pathway analysis showed similar yet strongly attenuated inflammatory changes in the CSF of COVID-19 patients compared to HSVE patients with, e.g., downregulation of the apolipoproteins and extracellular matrix proteins. Protein upregulation of the complement system, the serpin proteins pathways, and other proteins including glycoproteins alpha-2 and alpha-1 acid. Importantly, calculation of interleukin-6, interleukin-16, and CXCL10 CSF/serum indices suggest that these inflammatory mediators reach the CSF from the systemic circulation, rather than being produced within the CNS. Antibody screening revealed no pathological levels of known neuronal autoantibodies. When stratifying COVID-19 patients into those with and without bacterial superinfection as indicated by elevated procalcitonin levels, inflammatory markers were significantly (p < 0.01) higher in those with bacterial superinfection. RNA sequencing in the CSF revealed 101 linear RNAs comprising messenger RNAs, and two circRNAs being significantly differentially expressed in COVID-19 than in non-neuroinflammatory controls and neurodegenerative patients. Our findings may explain the absence of signs of intrathecal inflammation upon routine CSF testing despite the presence of SARS-CoV2 infection-associated neurological symptoms. The relevance of blood-derived mediators of inflammation in the CSF for neurological COVID-19 and post-COVID-19 symptoms deserves further investigation.
Topics: Humans; Proteome; RNA, Viral; Superinfection; COVID-19; SARS-CoV-2; Brain; Inflammation; Encephalitis, Herpes Simplex; Inflammation Mediators
PubMed: 36759861
DOI: 10.1186/s12974-023-02711-2 -
Pancreatology : Official Journal of the... Apr 2022SARS-CoV-2 can cause acute pancreatitis (AP) and SARS-CoV-2 superinfection can occur in patients with AP during prolonged hospitalisation. Our objective was to...
BACKGROUND
SARS-CoV-2 can cause acute pancreatitis (AP) and SARS-CoV-2 superinfection can occur in patients with AP during prolonged hospitalisation. Our objective was to characterize SARS-CoV-2 related AP and study the impact of SARS-CoV-2 superinfection on outcomes in AP.
METHODS
In this multicentre prospective study, all patients with AP and SARS-CoV-2 infection between August 2020 and February 2021 were divided into two groups: SARS-CoV-2-related AP and superadded SARS-CoV-2 infection in patients with AP. The two groups were compared with each other and the whole cohort was compared with a non-COVID AP cohort.
RESULTS
A total of 85 patients with SARS-CoV-2 and AP (SARS-CoV-2-related AP; n = 18 and AP with SARS-CoV-2 superadded infection; n = 67) were included during the study period. They had a higher mortality [28 (32.9%) vs. 44 (19.1%), aOR 2.8 (95% CI, 1.5-5.3)] than 230 propensity matched non-COVID AP patients. Mortality in SARS-CoV-2 and AP patients was due to critical COVID. SARS-CoV-2-related- AP (n = 18) had a higher but statistically insignificant mortality than SARS-CoV-2 superinfection in AP [8/18 (44.4%) vs 20/67 (29.8%), p = 0.24]. On multivariable analysis, infection with SARS-CoV-2 (aHR 2.3; 95% CI, 1.43.7) was a predictor of in-hospital mortality in addition to organ failure (OF) in patients with AP.
CONCLUSION
Patients with AP and SARS-CoV-2 infection had a higher mortality than matched non-COVID AP patients which was largely attributable to the severity of COVID-19. SARS-CoV-2 related AP had higher OF and in-hospital mortality.
Topics: Acute Disease; COVID-19; Humans; Pancreatitis, Chronic; Prospective Studies; SARS-CoV-2; Superinfection
PubMed: 35131169
DOI: 10.1016/j.pan.2022.01.008 -
Respiration; International Review of... 2022Findings from autopsies have provided evidence on systemic microvascular damage as one of the underlying mechanisms of Coronavirus disease 2019 (CO-VID-19). The aim of...
BACKGROUND
Findings from autopsies have provided evidence on systemic microvascular damage as one of the underlying mechanisms of Coronavirus disease 2019 (CO-VID-19). The aim of this study was to correlate autopsy-based cause of death in SARS-CoV-2, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive patients with chest imaging and severity grade of pulmonary and systemic morphological vascular pathology.
METHODS
Fifteen SARS-CoV-2 positive autopsies with clinically distinct presentations (age 22-89 years) were retrospectively analyzed with focus on vascular, thromboembolic, and ischemic changes in pulmonary and in extrapulmonary sites. Eight patients died due to COVID-19 associated respiratory failure with diffuse alveolar damage in various stages and/or multi-organ failure, whereas other reasons such as cardiac decompensation, complication of malignant tumors, or septic shock were the cause of death in 7 further patients. The severity of gross and histopathological changes was semi-quantitatively scored as 0 (absent), 1 (mild), and 3 (severe). Severity scores between the 2 groups were correlated with selected clinical parameters, initial chest imaging, autopsy-based cause of death, and compared using Pearson χ2 and Mann-Whitney U tests.
RESULTS
Severe pulmonary endotheliitis (p = 0.031, p = 0.029) and multi-organ involvement (p = 0.026, p = 0.006) correlated significantly with COVID-19 associated death. Pulmonary microthrombi showed limited statistical correlation, while tissue necrosis, gross pulmonary embolism, and bacterial superinfection did not differentiate the 2 study groups. Chest imaging at hospital admission did not differ either.
CONCLUSIONS
Extensive pulmonary endotheliitis and multi-organ involvement are characteristic autopsy features in fatal CO-VID-19 associated deaths. Thromboembolic and ischemic events and bacterial superinfections occur frequently in SARS-CoV-2 infection independently of outcome.
Topics: Adult; Aged; Aged, 80 and over; Autopsy; COVID-19; Cause of Death; Cohort Studies; Endothelium, Vascular; Female; Humans; Male; Middle Aged; Multiple Organ Failure; Pulmonary Alveoli; Respiratory Distress Syndrome; Vasculitis; Young Adult
PubMed: 34525475
DOI: 10.1159/000518914 -
Epidemiology and Infection Nov 2022Episodes of bacterial superinfections have been well identified for several respiratory viruses, notably influenza. In this retrospective study, we compared the...
Episodes of bacterial superinfections have been well identified for several respiratory viruses, notably influenza. In this retrospective study, we compared the frequency of superinfections in COVID-19 patients to those found in influenza-positive patients, and to controls without viral infection. We included 42 468 patients who had been diagnosed with COVID-19 and 266 261 subjects who had tested COVID-19 negative between 26 February 2020 and 1 May 2021. In addition, 4059 patients were included who had tested positive for the influenza virus between 1 January 2017 and 31 December 2019. Bacterial infections in COVID-19 patients were more frequently healthcare-associated, and acquired in ICUs, were associated with longer ICU stays, and occurred in older and male patients when compared to controls and to influenza patients ( < 0.0001 for all). The most common pathogens proved to be less frequent in COVID-19 patients, including fewer cases of bacteraemia involving ( < 0.0001) and ( = 0.027) when compared to controls. In respiratory specimens ( < 0.0001) was more frequent in controls, while ( < 0.0001) was more frequent in influenza patients. Likewise, species associated with nosocomial transmission, such as and , were more frequent among COVID-19 patients. Finally, we observed a high frequency of bacteraemia among COVID-19 patients, which were mainly ICU-acquired and associated with a longer timescale to acquisition.
Topics: Humans; Male; Aged; COVID-19; Superinfection; Retrospective Studies; Influenza, Human; Escherichia coli; Bacterial Infections; Hospitals; Bacteremia
PubMed: 36345840
DOI: 10.1017/S0950268822001704 -
Radiology Case Reports Jul 2022Infected endometriomas are rarely described in the literature with most cases being managed laparoscopically or open laparotomy. We present an infected endometrioma in a...
Infected endometriomas are rarely described in the literature with most cases being managed laparoscopically or open laparotomy. We present an infected endometrioma in a 48-year-old female with a history of extensive peritoneal adhesions in the setting of a contralateral tubo-ovarian abscess that was unresponsive to antibiotic therapy. Initially, the tubo-ovarian abscess was percutaneously drained, however, the patient did not clinically improve. The suspected infected endometrioma was then percutaneously drained which then led to clinical improvement. Typically, endometriomas are managed laparoscopically chiefly due to the risk of content spillage into the peritoneum, however, the case presented demonstrated that an ultrasound-guided transabdominal approach drainage can be feasible in a surgically complicated patient who was unresponsive to antibiotics in which a percutaneous approach was favored rather than a surgical approach.
PubMed: 35601388
DOI: 10.1016/j.radcr.2022.04.027 -
Viruses Nov 2020"Cross-protection", a nearly 100 years-old virological term, is suggested to be changed to "close protection". Evidence for the need of such change has accumulated over... (Review)
Review
"Cross-protection", a nearly 100 years-old virological term, is suggested to be changed to "close protection". Evidence for the need of such change has accumulated over the past six decades from the laboratory experiments and field tests conducted by plant pathologists and plant virologists working with different plant viruses, and, in particular, from research on (CTV). A direct confirmation of such close protection came with the finding that "pre-immunization" of citrus plants with the variants of the T36 strain of CTV but not with variants of other virus strains was providing protection against a fluorescent protein-tagged T36-based recombinant virus variant. Under natural conditions close protection is functional and is closely associated both with the conservation of the CTV genome sequence and prevention of superinfection by closely similar isolates. It is suggested that the mechanism is primarily directed to prevent the danger of virus population collapse that could be expected to result through quasispecies divergence of large RNA genomes of the CTV variants continuously replicating within long-living and highly voluminous fruit trees. This review article provides an overview of the CTV cross-protection research, along with a discussion of the phenomenon in the context of the CTV biology and genetics.
Topics: Citrus; Closterovirus; Cross Protection; Evolution, Molecular; Genome, Viral; Genomics; Host-Pathogen Interactions; Phenotype; Plant Diseases; Superinfection; Virus Replication
PubMed: 33256049
DOI: 10.3390/v12121353 -
Pediatric Pulmonology Apr 2020Acute respiratory infections are amongst the leading causes of childhood morbidity and mortality globally. Viruses are the predominant cause of such infections, but...
Acute respiratory infections are amongst the leading causes of childhood morbidity and mortality globally. Viruses are the predominant cause of such infections, but mixed etiologies with bacteria has for decades raised the question of the interplay between them in causality and determination of the outcome of such infections. In this review, we examine recent microbiological, biochemical, and immunological advances that contribute to elucidating the mechanisms by which infections by specific viruses enable bacterial infections in the airway, and exacerbate them. We analyze specific domains in which viruses play such facilitating role including enhancement of bacterial adhesion by unmasking cryptic receptors and upregulation of adhesion proteins, disruption of tight junction integrity favoring paracellular transmigration of bacteria and loss of epithelial barrier integrity, increased availability of nutrient, such as mucins and iron, alteration of innate and adaptive immune responses, and disabling defense against bacteria, and lastly, changes in airway microbiome that render the lung more vulnerable to pathogens. Separate exhaustive analysis of each domain focuses on individuals with cystic fibrosis (CF), in whom viruses may play a key role in paving the way for the primary injury that leads to permanence of bacterial pathogens, viruses may then serve as triggers for "CF exacerbations"; these constituting the signature and ultimately the outcome determinants of these patients.
Topics: Bacteria; Bacterial Infections; Child; Cystic Fibrosis; Humans; Lung; Microbiota; Mucins; Respiratory Tract Infections; Superinfection; Viruses
PubMed: 32084305
DOI: 10.1002/ppul.24699 -
Critical Care Explorations Jun 2021To describe the epidemiology of superinfections (occurring > 48 hr after hospital admission) and their impact on the ICU and 28-day mortality in patients with...
UNLABELLED
To describe the epidemiology of superinfections (occurring > 48 hr after hospital admission) and their impact on the ICU and 28-day mortality in patients with coronavirus disease 2019 with acute respiratory distress syndrome, requiring mechanical ventilation.
DESIGN
Retrospective analysis of prospectively collected observational data.
SETTING
University-affiliated adult ICU.
PATIENTS
Ninety-two coronavirus disease 2019 patients admitted to the ICU from February 21, 2020, to May 6, 2020.
INTERVENTIONS
None.
MEASUREMENTS AND MAIN RESULTS
The prevalence of superinfection at ICU admission was 21.7%, and 53 patients (57.6%) had at least one superinfection during ICU stay, with a total of 75 (82%) ventilator-associated pneumonia and 57 (62%) systemic infections. The most common pathogens responsible for ventilator-associated pneumonia were ( = 26, 34.7%) and ( = 14, 18.7%). Bloodstream infection occurred in 16 cases, including methicillin-resistant ( = 8, 14.0%), species ( = 6, 10.5%), and species ( = 2, 3.5%). Fungal infections occurred in 41 cases, including 36 probable (30 by , six by ) and five proven invasive candidiasis (three , two ). Presence of bacterial infections (odds ratio, 10.53; 95% CI, 2.31-63.42; = 0.005), age (odds ratio, 1.17; 95% CI, 1.07-1.31; = 0.001), and the highest Sequential Organ Failure Assessment score (odds ratio, 1.27; 95% CI, 1.06-1.63; = 0.032) were independently associated with ICU or 28-day mortality.
CONCLUSIONS
Prevalence of superinfections in coronavirus disease 2019 patients requiring mechanical ventilation was high in this series, and bacterial superinfections were independently associated with ICU or 28-day mortality (whichever comes first).
PubMed: 34136819
DOI: 10.1097/CCE.0000000000000430