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2.
Front Immunol ; 13: 909011, 2022.
Article in English | MEDLINE | ID: covidwho-2198834

ABSTRACT

Coronavirus disease-2019 (COVID-19), caused by SARS-CoV-2, is an infectious disease that poses severe threats to global public health and significant economic losses. The COVID-19 global burden is rapidly increasing, with over 246.53 million COVID-19 cases and 49.97 million deaths reported in the WHO 2021 report. People with compromised immunity, such as tuberculosis (TB) patients, are highly exposed to severe COVID-19. Both COVID-19 and TB diseases spread primarily through respiratory droplets from an infected person to a healthy person, which may cause pneumonia and cytokine storms, leading to severe respiratory disorders. The COVID-19-TB coinfection could be fatal, exacerbating the current COVID-19 pandemic apart from cellular immune deficiency, coagulation activation, myocardial infarction, and other organ dysfunction. This study aimed to assess the pathogenesis of SARS-CoV-2-Mycobacterium tuberculosis coinfections. We provide a brief overview of COVID19-TB coinfection and discuss SARS-CoV-2 host cellular receptors and pathogenesis. In addition, we discuss M. tuberculosis host cellular receptors and pathogenesis. Moreover, we highlight the impact of SARS-CoV-2 on TB patients and the pathological pathways that connect SARS-CoV-2 and M. tuberculosis infection. Further, we discuss the impact of BCG vaccination on SARS-CoV-2 cases coinfected with M. tuberculosis, as well as the diagnostic challenges associated with the coinfection.


Subject(s)
COVID-19 , Coinfection , Mycobacterium tuberculosis , Tuberculosis , Humans , Pandemics , SARS-CoV-2 , Tuberculosis/epidemiology
3.
Med Mycol J ; 63(3): 59-64, 2022.
Article in English | MEDLINE | ID: covidwho-2198582

ABSTRACT

Acute invasive fungal rhinosinusitis is a rare infection primarily affecting patients with co-morbidities like immunosuppression and poorly controlled diabetes. Mucormycosis is increasingly being reported in patients with SARS-CoV-2 (COVID-19). However, reports of coinfection of aspergillosis and mucormycosis involving nose, paranasal sinuses, orbit, and brain are rare in literature. We aimed to evaluate the patient demographics, clinical presentation, and management of cases presenting with mixed infection. We carried out retrospective analysis of 12 patients with confirmed diagnosis of mixed invasive fungal infections post-COVID-19 disease out of 70 cases of COVID-19-associated mucormycosis (CAM) presenting to a tertiary-level hospital in North India from May to June 2021. All patients had diabetes mellitus; the mean age was 48 years. The common presenting features were headache, nasal congestion, palatal ulcer, and vision loss accompanied by facial pain and swelling. Two patients developed cerebral abscess during the course of treatment; three patients had concurrent COVID-19 pneumonia. All patients received systemic liposomal amphotericin B and serial surgical debridements. The overall mortality rate was 16.7%. Our study demonstrates that mucormycosis and aspergillosis are angioinvasive mycoses that are clinically and radiologically identical. KOH direct mount of clinical sample showing septate hyphae should be extensively searched for aseptate hyphae after digestion and clearing of the tissue. A high index of suspicion of mixed infection post-COVID-19 and early initiation of liposomal amphotericin B followed by prompt surgical intervention can reduce the overall morbidity and mortality among patients with this condition.


Subject(s)
Aspergillosis , COVID-19 , Coinfection , Invasive Fungal Infections , Mucormycosis , Sinusitis , Antifungal Agents/therapeutic use , Aspergillosis/microbiology , COVID-19/complications , Coinfection/complications , Coinfection/drug therapy , Coinfection/microbiology , Humans , Invasive Fungal Infections/drug therapy , Middle Aged , Mucormycosis/complications , Mucormycosis/diagnosis , Retrospective Studies , SARS-CoV-2 , Sinusitis/complications , Sinusitis/microbiology , Tertiary Care Centers
4.
Cochrane Database Syst Rev ; 6: CD015209, 2022 06 13.
Article in English | MEDLINE | ID: covidwho-2172307

ABSTRACT

BACKGROUND: With potential antiviral and anti-inflammatory properties, Janus kinase (JAK) inhibitors represent a potential treatment for symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. They may modulate the exuberant immune response to SARS-CoV-2 infection. Furthermore, a direct antiviral effect has been described. An understanding of the current evidence regarding the efficacy and safety of JAK inhibitors as a treatment for coronavirus disease 2019 (COVID-19) is required. OBJECTIVES: To assess the effects of systemic JAK inhibitors plus standard of care compared to standard of care alone (plus/minus placebo) on clinical outcomes in individuals (outpatient or in-hospital) with any severity of COVID-19, and to maintain the currency of the evidence using a living systematic review approach. SEARCH METHODS: We searched the Cochrane COVID-19 Study Register (comprising MEDLINE, Embase, ClinicalTrials.gov, World Health Organization (WHO) International Clinical Trials Registry Platform, medRxiv, and Cochrane Central Register of Controlled Trials), Web of Science, WHO COVID-19 Global literature on coronavirus disease, and the US Department of Veterans Affairs Evidence Synthesis Program (VA ESP) Covid-19 Evidence Reviews to identify studies up to February 2022. We monitor newly published randomised controlled trials (RCTs) weekly using the Cochrane COVID-19 Study Register, and have incorporated all new trials from this source until the first week of April 2022. SELECTION CRITERIA: We included RCTs that compared systemic JAK inhibitors plus standard of care to standard of care alone (plus/minus placebo) for the treatment of individuals with COVID-19. We used the WHO definitions of illness severity for COVID-19. DATA COLLECTION AND ANALYSIS: We assessed risk of bias of primary outcomes using Cochrane's Risk of Bias 2 (RoB 2) tool. We used GRADE to rate the certainty of evidence for the following primary outcomes: all-cause mortality (up to day 28), all-cause mortality (up to day 60), improvement in clinical status: alive and without need for in-hospital medical care (up to day 28), worsening of clinical status: new need for invasive mechanical ventilation or death (up to day 28), adverse events (any grade), serious adverse events, secondary infections. MAIN RESULTS: We included six RCTs with 11,145 participants investigating systemic JAK inhibitors plus standard of care compared to standard of care alone (plus/minus placebo). Standard of care followed local protocols and included the application of glucocorticoids (five studies reported their use in a range of 70% to 95% of their participants; one study restricted glucocorticoid use to non-COVID-19 specific indications), antibiotic agents, anticoagulants, and antiviral agents, as well as non-pharmaceutical procedures. At study entry, about 65% of participants required low-flow oxygen, about 23% required high-flow oxygen or non-invasive ventilation, about 8% did not need any respiratory support, and only about 4% were intubated. We also identified 13 ongoing studies, and 9 studies that are completed or terminated and where classification is pending. Individuals with moderate to severe disease Four studies investigated the single agent baricitinib (10,815 participants), one tofacitinib (289 participants), and one ruxolitinib (41 participants). Systemic JAK inhibitors probably decrease all-cause mortality at up to day 28 (95 of 1000 participants in the intervention group versus 131 of 1000 participants in the control group; risk ratio (RR) 0.72, 95% confidence interval (CI) 0.57 to 0.91; 6 studies, 11,145 participants; moderate-certainty evidence), and decrease all-cause mortality at up to day 60 (125 of 1000 participants in the intervention group versus 181 of 1000 participants in the control group; RR 0.69, 95% CI 0.56 to 0.86; 2 studies, 1626 participants; high-certainty evidence). Systemic JAK inhibitors probably make little or no difference in improvement in clinical status (discharged alive or hospitalised, but no longer requiring ongoing medical care) (801 of 1000 participants in the intervention group versus 778 of 1000 participants in the control group; RR 1.03, 95% CI 1.00 to 1.06; 4 studies, 10,802 participants; moderate-certainty evidence). They probably decrease the risk of worsening of clinical status (new need for invasive mechanical ventilation or death at day 28) (154 of 1000 participants in the intervention group versus 172 of 1000 participants in the control group; RR 0.90, 95% CI 0.82 to 0.98; 2 studies, 9417 participants; moderate-certainty evidence). Systemic JAK inhibitors probably make little or no difference in the rate of adverse events (any grade) (427 of 1000 participants in the intervention group versus 441 of 1000 participants in the control group; RR 0.97, 95% CI 0.88 to 1.08; 3 studies, 1885 participants; moderate-certainty evidence), and probably decrease the occurrence of serious adverse events (160 of 1000 participants in the intervention group versus 202 of 1000 participants in the control group; RR 0.79, 95% CI 0.68 to 0.92; 4 studies, 2901 participants; moderate-certainty evidence). JAK inhibitors may make little or no difference to the rate of secondary infection (111 of 1000 participants in the intervention group versus 113 of 1000 participants in the control group; RR 0.98, 95% CI 0.89 to 1.09; 4 studies, 10,041 participants; low-certainty evidence). Subgroup analysis by severity of COVID-19 disease or type of JAK inhibitor did not identify specific subgroups which benefit more or less from systemic JAK inhibitors. Individuals with asymptomatic or mild disease We did not identify any trial for this population. AUTHORS' CONCLUSIONS: In hospitalised individuals with moderate to severe COVID-19, moderate-certainty evidence shows that systemic JAK inhibitors probably decrease all-cause mortality. Baricitinib was the most often evaluated JAK inhibitor. Moderate-certainty evidence suggests that they probably make little or no difference in improvement in clinical status. Moderate-certainty evidence indicates that systemic JAK inhibitors probably decrease the risk of worsening of clinical status and make little or no difference in the rate of adverse events of any grade, whilst they probably decrease the occurrence of serious adverse events. Based on low-certainty evidence, JAK inhibitors may make little or no difference in the rate of secondary infection. Subgroup analysis by severity of COVID-19 or type of agent failed to identify specific subgroups which benefit more or less from systemic JAK inhibitors. Currently, there is no evidence on the efficacy and safety of systemic JAK inhibitors for individuals with asymptomatic or mild disease (non-hospitalised individuals).


Subject(s)
COVID-19 , Coinfection , Janus Kinase Inhibitors , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Humans , Janus Kinase Inhibitors/therapeutic use , Oxygen , Randomized Controlled Trials as Topic , SARS-CoV-2 , United States
5.
researchsquare; 2023.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-2482226.v1

ABSTRACT

The rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/ µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 hours. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.


Subject(s)
Coinfection
6.
BMC Public Health ; 22(1): 1167, 2022 06 11.
Article in English | MEDLINE | ID: covidwho-1885294

ABSTRACT

BACKGROUND: Lower respiratory tract infections are among the main causes of death. Although there are many respiratory viruses, diagnostic efforts are focused mainly on influenza. The Respiratory Viruses Network (RespVir) collects infection data, primarily from German university hospitals, for a high diversity of infections by respiratory pathogens. In this study, we computationally analysed a subset of the RespVir database, covering 217,150 samples tested for 17 different viral pathogens in the time span from 2010 to 2019. METHODS: We calculated the prevalence of 17 respiratory viruses, analysed their seasonality patterns using information-theoretic measures and agglomerative clustering, and analysed their propensity for dual infection using a new metric dubbed average coinfection exclusion score (ACES). RESULTS: After initial data pre-processing, we retained 206,814 samples, corresponding to 1,408,657 performed tests. We found that Influenza viruses were reported for almost the half of all infections and that they exhibited the highest degree of seasonality. Coinfections of viruses are frequent; the most prevalent coinfection was rhinovirus/bocavirus and most of the virus pairs had a positive ACES indicating a tendency to exclude each other regarding infection. CONCLUSIONS: The analysis of respiratory viruses dynamics in monoinfection and coinfection contributes to the prevention, diagnostic, treatment, and development of new therapeutics. Data obtained from multiplex testing is fundamental for this analysis and should be prioritized over single pathogen testing.


Subject(s)
Coinfection , Respiratory Tract Infections , Virus Diseases , Viruses , Coinfection/epidemiology , Humans , Infant , Rhinovirus , Virus Diseases/epidemiology
7.
JMIR Public Health Surveill ; 7(4): e27433, 2021 04 28.
Article in English | MEDLINE | ID: covidwho-2141323

ABSTRACT

BACKGROUND: Sentinel surveillance of influenza-like illness (ILI) in Egypt started in 2000 at 8 sentinel sites geographically distributed all over the country. In response to the COVID-19 pandemic, SARS-CoV-2 was added to the panel of viral testing by polymerase chain reaction for the first 2 patients with ILI seen at one of the sentinel sites. We report the first SARS-CoV-2 and influenza A(H1N1) virus co-infection with mild symptoms detected through routine ILI surveillance in Egypt. OBJECTIVE: This report aims to describe how the case was identified and the demographic and clinical characteristics and outcomes of the patient. METHODS: The case was identified by Central Public Health Laboratory staff, who contacted the ILI sentinel surveillance officer at the Ministry of Health. The case patient was contacted through a telephone call. Detailed information about the patient's clinical picture, course of disease, and outcome was obtained. The contacts of the patient were investigated for acute respiratory symptoms, disease confirmation, and outcomes. RESULTS: Among 510 specimens collected from patients with ILI symptoms from October 2019 to August 2020, 61 (12.0%) were COVID-19-positive and 29 (5.7%) tested positive for influenza, including 15 (51.7%) A(H1N1), 11 (38.0%) A(H3N2), and 3 (10.3%) influenza B specimens. A 21-year-old woman was confirmed to have SARS-CoV-2 and influenza A(H1N1) virus coinfection. She had a high fever of 40.2 °C and mild respiratory symptoms that resolved within 2 days with symptomatic treatment. All five of her family contacts had mild respiratory symptoms 2-3 days after exposure to the confirmed case, and their symptoms resolved without treatment or investigation. CONCLUSIONS: This case highlights the possible occurrence of SARS-CoV-2/influenza A(H1N1) coinfection in younger and healthy people, who may resolve the infection rapidly. We emphasize the usefulness of the surveillance system for detection of viral causative agents of ILI and recommend broadening of the testing panel, especially if it can guide case management.


Subject(s)
COVID-19/diagnosis , Coinfection , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza, Human/diagnosis , SARS-CoV-2/isolation & purification , Sentinel Surveillance , COVID-19/epidemiology , Egypt/epidemiology , Female , Humans , Influenza, Human/epidemiology , Young Adult
8.
AIDS ; 35(10): 1704-1706, 2021 08 01.
Article in English | MEDLINE | ID: covidwho-2135810

ABSTRACT

Hepatitis delta virus (HDV) is a highly pathogenic virus which can cause rapidly progressive liver disease in individuals with chronic hepatitis B virus and for which treatment options are limited. The incidence of sexually transmitted HDV infection is unknown. Here we report the case of a HDV seronegative man with pre-existent HIV/hepatitis B virus, taking effective tenofovir-containing antiretroviral therapy, who experienced a significant acute transaminitis with HDV antibody seroconversion and viraemia and no other identifiable cause.


Subject(s)
Coinfection , HIV Infections , Hepatitis B, Chronic , Hepatitis B , Hepatitis D , Superinfection , HIV Infections/complications , HIV Infections/drug therapy , Hepatitis B/complications , Hepatitis B virus , Hepatitis B, Chronic/complications , Hepatitis D/complications , Hepatitis D/diagnosis , Hepatitis Delta Virus , Humans , Male
9.
BMC Infect Dis ; 22(1): 891, 2022 Nov 28.
Article in English | MEDLINE | ID: covidwho-2139180

ABSTRACT

BACKGROUND: The impact of corticosteroids on patients with severe coronavirus disease 2019 (COVID-19)/chronic hepatitis B virus (HBV) co-infection is currently unknown. We aimed to investigate the association of corticosteroids on these patients. METHODS: This retrospective multicenter study screened 5447 confirmed COVID-19 patients hospitalized between Jan 1, 2020 to Apr 18, 2020 in seven centers in China, where the prevalence of chronic HBV infection is moderate to high. Severe patients who had chronic HBV and acute SARS-cov-2 infection were potentially eligible. The diagnosis of chronic HBV infection was based on positive testing for hepatitis B surface antigen (HBsAg) or HBV DNA during hospitalization and a medical history of chronic HBV infection. Severe patients (meeting one of following criteria: respiratory rate > 30 breaths/min; severe respiratory distress; or SpO2 ≤ 93% on room air; or oxygen index < 300 mmHg) with COVID-19/HBV co-infection were identified. The bias of confounding variables on corticosteroids effects was minimized using multivariable logistic regression model and inverse probability of treatment weighting (IPTW) based on propensity score. RESULTS: The prevalence of HBV co-infection in COVID-19 patients was 4.1%. There were 105 patients with severe COVID-19/HBV co-infections (median age 62 years, 57.1% male). Fifty-five patients received corticosteroid treatment and 50 patients did not. In the multivariable analysis, corticosteroid therapy (OR, 6.32, 95% CI 1.17-34.24, P = 0.033) was identified as an independent risk factor for 28-day mortality. With IPTW analysis, corticosteroid treatment was associated with delayed SARS-CoV-2 viral RNA clearance (OR, 2.95, 95% CI 1.63-5.32, P < 0.001), increased risk of 28-day and in-hospital mortality (OR, 4.90, 95% CI 1.68-14.28, P = 0.004; OR, 5.64, 95% CI 1.95-16.30, P = 0.001, respectively), and acute liver injury (OR, 4.50, 95% CI 2.57-7.85, P < 0.001). Methylprednisolone dose per day and cumulative dose in non-survivors were significantly higher than in survivors. CONCLUSIONS: In patients with severe COVID-19/HBV co-infection, corticosteroid treatment may be associated with increased risk of 28-day and in-hospital mortality.


Subject(s)
COVID-19 , Coinfection , Hepatitis B, Chronic , Hepatitis B , Humans , Male , Middle Aged , Female , SARS-CoV-2 , Hepatitis B, Chronic/complications , Hepatitis B, Chronic/drug therapy , COVID-19/drug therapy , Coinfection/drug therapy , Coinfection/epidemiology , Hepatitis B virus , Adrenal Cortex Hormones/therapeutic use , Hepatitis B Surface Antigens
10.
J Investig Med High Impact Case Rep ; 10: 23247096221140250, 2022.
Article in English | MEDLINE | ID: covidwho-2139082

ABSTRACT

Unvaccinated patients with comorbidities that impair the immune function, such as type 2 diabetes mellitus, are more likely to develop severe COVID-19. The COVID-19-associated acute respiratory distress syndrome has raised new concerns in intensive care units globally owing to the presence of secondary fungal infections. We report the case of a 71-year-old man from Ecuador with a history of type 2 diabetes mellitus, severe COVID-19 pneumonia, and lung cavitation associated with triple infections with Trichosporon asahii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The patient with a history of high blood pressure and type 2 diabetes was admitted to our hospital from a private care center with a diagnosis of COVID-19-associated acute respiratory distress syndrome. On arrival, the patient presented with signs of hypoxemic respiratory failure. During his stay at another hospital, he had received tocilizumab and corticosteroid therapy. Therefore, intubation was performed and mechanical ventilation was initiated. The patient developed a septic shock and renal failure with a glomerular filtration rate of 27.5 mL/min/1.73 m2; therefore, two hemodiafiltration sessions were started. The bronchoalveolar lavage revealed erythematous lesions in the bronchial tree and abundant purulent secretions and erosions in the bronchial mucosa, with a cavitary lesion in the right bronchial tree. The bronchoalveolar lavage samples were used to isolate Trichosporon asahii, Klebsiella pneumoniae, and Pseudomonas aeruginosa carbapenemase class A. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) Biotyper mass spectrometry and polymerase chain reaction (PCR) molecular identification were performed. This case report suggested that patients with severe COVID-19 pneumonia, with or without comorbidities, are more susceptible to opportunistic infections.


Subject(s)
COVID-19 , Coinfection , Diabetes Mellitus, Type 2 , Respiratory Distress Syndrome , Male , Humans , Aged , Klebsiella pneumoniae , Pseudomonas aeruginosa , COVID-19/complications , Diabetes Mellitus, Type 2/complications , Ecuador , Lung
11.
Semin Respir Crit Care Med ; 43(6): 924-935, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2133782

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic upended our approach to imaging community-acquired pneumonia, and this will alter our diagnostic algorithms for years to come. In light of these changes, it is worthwhile to consider several postpandemic scenarios of community-acquired pneumonia: (1) patient with pneumonia and recent positive COVID-19 testing; (2) patient with air space opacities and history of prior COVID-19 pneumonia (weeks earlier); (3) multifocal pneumonia with negative or unknown COVID-19 status; and (4) lobar or sublobar pneumonia with negative or unknown COVID-19 status. In the setting of positive COVID-19 testing and typical radiologic findings, the diagnosis of COVID-19 pneumonia is generally secure. The diagnosis prompts vigilance for thromboembolic disease acutely and, in severely ill patients, for invasive fungal disease. Persistent or recurrent air space opacities following COVID-19 infection may more often represent organizing pneumonia than secondary infection. When COVID-19 status is unknown or negative, widespread airway-centric disease suggests infection with mycoplasma, Haemophilus influenzae, or several respiratory viruses. Necrotizing pneumonia favors infection with pneumococcus, Staphylococcus, Klebsiella, and anaerobes. Lobar or sublobar pneumonia will continue to suggest the diagnosis of pneumococcus or consideration of other pathogens in the setting of local outbreaks. A positive COVID-19 test accompanied by these imaging patterns may suggest coinfection with one of the above pathogens, or when the prevalence of COVID-19 is very low, a false positive COVID-19 test. Clinicians may still proceed with testing for COVID-19 when radiologic patterns are atypical for COVID-19, dependent on the patient's exposure history and the local epidemiology of the virus.


Subject(s)
COVID-19 , Coinfection , Community-Acquired Infections , Pneumonia , Humans , COVID-19/epidemiology , COVID-19 Testing , Community-Acquired Infections/diagnosis , Community-Acquired Infections/epidemiology , Pneumonia/diagnosis , Pneumonia/epidemiology , Pandemics , Streptococcus pneumoniae
13.
medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.12.15.22282988

ABSTRACT

BackgroundThe COVID-19 pandemic and the associated containment measures had a substantial impact on pathogens causing pneumonia in adults. The objective of this study was to determine the etiology of hospitalized community-acquired pneumonia (CAP) among adults in Germany in 2021, the second year of the COVID-19 pandemic. MethodsSince January 2021, this on-going, prospective, population-based surveillances study enrolled adult patients with clinically and radiographically confirmed CAP at three hospitals in Thuringia, Germany, serving a population of approximately 280,000. Urine samples were collected from patients and tested for S. pneumoniae using the pneumococcal urinary antigen test (PUAT, BinaxNOW S. pneumoniae) and the proprietary serotype-specific urinary antigen detection (UAD) assays. Nasopharyngeal swabs were tested for 10 respiratory viruses by PCR. ResultsA total of 797 patients were enrolled, of whom 760 were included in the analysis. The median age of patients with CAP was 67 years; in-hospital case-fatality rate was 8.4%. A respiratory pathogen was detected in 553 (72.8%) patients. The most common pathogen was SARS-CoV-2 (n=498, 68.2%), followed by S. pneumoniae (n=40, 6.4%). Serotypes contained in the 13-valent, 15-valent and 20-valent pneumococcal conjugate vaccine were detected in 42.5%, 45.0%, and 70.0% of the pneumococcal CAP cases. Between the first and second half of 2021, the proportion of CAP cases associated with S. pneumoniae increased from 1.1% to 5.6% in patients aged 18-59 years and from 2.5% to 12.4% in those aged [≥]60 years; coinfection of SARS-CoV-2 and S. pneumoniae among COVID-19 patients increased from 0.7% (2/283 cases) to 6.0% (13/215) in patients aged [≥]18 years, and from 1.0% (2/195) to 8.7% (11/127) in those aged [≥]60 years. ConclusionIn Germany, the proportion of CAP cases associated with S. pneumoniae rebounded to a near-pandemic level in the second half of 2021 and many pneumococcal infections occurred in patients with COVID-19. Vaccination uptake against respiratory pathogens, including S. pneumoniae, should be strengthened.


Subject(s)
Pneumonia , COVID-19 , Pneumococcal Infections , Coinfection , Pneumonia, Pneumococcal
14.
biorxiv; 2022.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2022.12.15.520197

ABSTRACT

Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients. Rapid diagnostic tests are tools with a paramount impact both on improving patient care. Particularly in the case of respiratory infections, it is of great importance to quickly confirm/exclude the involvement of pathogens. The COVID-19 pandemic has been associated with changes in respiratory virus infections worldwide, which have differed between virus types. In this paper, we systematically searched the percentage of coinfection of various respiratory viruses in COVID-19-positive samples. We included patients of all ages, in all settings. The main outcome was the proportion of patients with viral coinfection. By describing the differences in changes between viral species across different geographies over the course of the COVID-19 pandemic, we may better understand the complex factors involved in the community cocirculation of respiratory viruses.


Subject(s)
COVID-19 , Coinfection , Respiratory Tract Infections
15.
Int J Infect Dis ; 111: 31-36, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-2113701

ABSTRACT

BACKGROUND: Correlation between coronavirus disease 2019 (COVID-19) and superinfections has been investigated, but remains to be fully assessed. This multi-centre study reports the impact of the pandemic on bloodstream infections (BSIs). METHODS: This study included all patients with BSIs admitted to four Italian hospitals between 1 January and 30 June 2020. Clinical, demographic and microbiologic data were compared with data for patients hospitalized during the same period in 2019. RESULTS: Among 26,012 patients admitted between 1 January and 30 June 2020, 1182 had COVID-19. Among the patients with COVID-19, 107 BSIs were observed, with an incidence rate of 8.19 episodes per 1000 patient-days. The incidence of BSI was significantly higher in these patients compared with patients without COVID-19 (2.72/1000 patient-days) and patients admitted in 2019 (2.76/1000 patient-days). In comparison with patients without COVID-19, BSI onset in patients with COVID-19 was delayed during the course of hospitalization (16.0 vs 5 days, respectively). Thirty-day mortality among patients with COVID-19 was 40.2%, which was significantly higher compared with patients without COVID-19 (23.7%). BSIs in patients with COVID-19 were frequently caused by multi-drug-resistant pathogens, which were often centre-dependent. CONCLUSIONS: BSIs are a common secondary infection in patients with COVID-19, characterized by increased risk during hospitalization and potentially burdened with high mortality.


Subject(s)
COVID-19 , Coinfection , Sepsis , Humans , Italy/epidemiology , SARS-CoV-2 , Sepsis/epidemiology
16.
Sci Rep ; 12(1): 19443, 2022 Nov 14.
Article in English | MEDLINE | ID: covidwho-2119409

ABSTRACT

Porcine deltacoronavirus (PDCoV) and porcine epidemic diarrhea virus (PEDV) infect the small intestine and cause swine enteric coronavirus disease. The mucosal innate immune system is the first line of defense against viral infection. The modulatory effect of PDCoV and PEDV coinfection on antiviral signaling cascades of the intestinal mucosa has not been reported. Here, we investigate the gene expression levels of pattern recognition receptors, downstream inflammatory signaling pathway molecules, and associated cytokines on the intestinal mucosa of neonatal piglets either infected with a single- or co-infected with PDCoV and PEDV using real-time PCR. The results demonstrate that single-PEDV regulates the noncanonical NF-κB signaling pathway through RIG-I regulation. In contrast, single-PDCoV and PDCoV/PEDV coinfection regulate proinflammatory and regulatory cytokines through TRAF6-mediated canonical NF-κB and IRF7 signaling pathways through TLRs. Although PDCoV/PEDV coinfection demonstrated an earlier modulatory effect in these signaling pathways, the regulation of proinflammatory and regulatory cytokines was observed simultaneously during single viral infection. These results suggested that PDCoV/PEDV coinfection may have synergistic effects that lead to enhanced viral evasion of the mucosal innate immune response.


Subject(s)
Coinfection , Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Swine , Porcine epidemic diarrhea virus/genetics , NF-kappa B , TNF Receptor-Associated Factor 6/genetics , Signal Transduction , Cytokines , Diarrhea
17.
BMC Public Health ; 22(1): 2061, 2022 11 10.
Article in English | MEDLINE | ID: covidwho-2116697

ABSTRACT

BACKGROUND: Data are lacking regarding the risk of viral SARS-CoV-2 transmission during a large indoor sporting event involving fans utilizing a controlled environment. We sought to describe case characteristics, mitigation protocols used, variants detected, and secondary infections detected during the 2021 National Collegiate Athletic Association (NCAA) Men's Basketball Tournament involving collegiate athletes from across the U.S. METHODS: This retrospective cohort study used data collected from March 16 to April 3, 2021, as part of a closed environment which required daily reverse transcription-polymerase chain reaction (RT-PCR) testing, social distancing, universal masking, and limited contact between tiers of participants. Nearly 3000 players, staff, and vendors participated in indoor, unmasked activities that involved direct exposure between cases and noninfected individuals. The main outcome of interest was transmission of SARS-CoV-2 virus, as measured by the number of new infections and variant(s) detected among positive cases. Secondary infections were identified through contact tracing by public health officials. RESULTS: Out of 2660 participants, 15 individuals (0.56%) screened positive for SARS-CoV-2. Four cases involved players or officials, and all cases were detected before any individual played in or officiated a game. Secondary transmissions all occurred outside the controlled environment. Among those disqualified from the tournament (4 cases; 26.7%), all individuals tested positive for the Iota variant (B.1.526). All other cases involved the Alpha variant (B.1.1.7). Nearly all teams (N = 58; 85.3%) reported that some individuals had received at least one dose of a vaccine. Overall, 17.9% of participants either had at least one dose of the vaccine or possessed documented infection within 90 days of the tournament. CONCLUSION: In this retrospective cohort study of the 2021 NCAA Men's Basketball Tournament closed environment, only a few cases were detected, and they were discovered in advance of potential exposure. These findings support the U.S. Centers for Disease Control and Prevention (CDC) guidelines for large indoor sporting events during the COVID-19 pandemic.


Subject(s)
Athletic Injuries , Basketball , COVID-19 , Coinfection , Male , Humans , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/prevention & control , Athletic Injuries/epidemiology , Retrospective Studies , Pandemics/prevention & control , Students , Incidence
18.
Saudi Med J ; 43(9): 1000-1006, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2111186

ABSTRACT

OBJECTIVES: To investigate the seroprevalence of the community-acquired bacterial that causes atypical pneumonia among confirmed severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) patients. METHODS: In this cohort study, we retrospectively investigated the seroprevalence of Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella pneumophila among randomly selected 189 confirmed COVID-19 patients at their time of hospital presentation via commercial immunoglobulin M (IgM) antibodies against these bacteria. We also carried out quantitative measurements of procalcitonin in patients' serum. RESULTS: The seropositivity for L. pneumophila was 12.6%, with significant distribution among patientsolder than 50 years (χ2 test, p=0.009), while those of M. pneumoniae was 6.3% and C. pneumoniae was 2.1%, indicating an overall co-infection rate of 21% among COVID-19 patients. No significant difference (χ2 test, p=0.628) in the distribution of bacterial co-infections existed between male and female patients. Procalcitonin positivity was confirmed amongst 5% of co-infected patients. CONCLUSION: Our study documented the seroprevalence of community-acquired bacteria co-infection among COVID-19 patients. In this study, procalcitonin was an inconclusive biomarker for non-severe bacterial co-infections among COVID-19 patients. Consideration and proper detection of community-acquired bacterial co-infection may minimize misdiagnosis during the current pandemic and positively reflect disease management and prognosis.


Subject(s)
COVID-19 , Coinfection , Community-Acquired Infections , Pneumonia, Bacterial , Adult , COVID-19/epidemiology , Cohort Studies , Coinfection/epidemiology , Community-Acquired Infections/diagnosis , Community-Acquired Infections/epidemiology , Female , Humans , Immunoglobulin M , Male , Mycoplasma pneumoniae , Pneumonia, Bacterial/epidemiology , Pneumonia, Bacterial/microbiology , Procalcitonin , Retrospective Studies , SARS-CoV-2 , Saudi Arabia/epidemiology , Seroepidemiologic Studies
19.
researchsquare; 2022.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-2373067.v1

ABSTRACT

Co-infection with COVID-19 and TB frequently results in fever, coughing, hypotension, a changed blood cell count, raised liver enzymes, and decreased hemoglobin. On May 19, 2022, a retired black African woman in her 59s arrived at the emergency room with a tuberculosis diagnosis. She had no recent travel history and was COVID-19-infected. Five days prior to her admission, her sons, who worked in the medical field, were found to be infected with the COVID-19 infection. The patient arrived at the emergency room with weak muscles, a fever, a productive cough, a sore throat, a lack of appetite, a headache, night sweats, and shortness of breath that had lasted for a day. On chest auscultation, there were reduced breath sounds in the right middle and upper lungs. A Mycobacterium tuberculosis infection without rifampicin resistance was detected in a sputum sample using the GeneXpert Mycobacterium tuberculosis and rifampicin tests. After 36 hours, a throat swab polymerase chain reaction test produced positive findings, confirming the presence of the COVID-19 infection. The patient required continuous oxygen at a rate of four liters per minute via a nasal cannula for the first five days while in the hospital, and she is still taking her anti-tubercular medications. In order to combat hospital-acquired infections, she was given therapy with broad-spectrum antibiotics consisting of 500 mg of azithromycin given once a day for five days and 1 g of intravenous ceftriaxone administered daily for five days.


Subject(s)
Infections , Tuberculosis, Pulmonary , COVID-19 , Coinfection , Headache , Tuberculosis , Dyspnea , Fever , Hypotension
20.
J Clin Virol ; 157: 105300, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2105314

ABSTRACT

BACKGROUND: Viral conjunctivitis (pink eye) can be highly contagious and is of public health importance. There remains significant debate whether SARS-CoV-2 can present as a primary conjunctivitis. The aim of this study was to identify pathogens associated with outpatient infectious conjunctivitis during the COVID-19 Delta surge. METHODS: This prospective study was conducted in the spring and summer months of 2021. 106 patients with acute conjunctivitis who presented to the Aravind Eye Center in Madurai, India were included. One anterior nasal swab and one conjunctival swab of each eye were obtained for each enrolled patient. Samples were subsequently processed for unbiased metagenomic RNA deep sequencing (RNA-seq). Outcomes included clinical findings and codetection of other pathogens with SARS-CoV-2 in patients with conjunctivitis. RESULTS: Among the 13 patients identified with human coronavirus RNA fragments in their swabs, 6 patients had SARS-CoV-2 infection, 5 patients had coinfections of SARS-CoV-2 and human adenovirus (HAdV), 1 patient had a coinfection with human coronavirus OC43 and HAdV, and 1 patient had a coinfection of Vittaforma corneae and SARS-CoV-2. 30% had bilateral disease and symptoms on presentation. Petechial hemorrhage was noted in 33% of patients with SARS-CoV-2 infection. No patients with SARS-CoV-2 or SARS-CoV-2 and HAdV infections had subepithelial infiltrates on presentation. All patients denied systemic symptoms. CONCLUSIONS: Among the patients presented with conjunctivitis associated with human coronavirus infection, over 50% of the patients had co-infections with other circulating pathogens, suggesting the public-health importance of broad pathogen testing and surveillance in the outpatient conjunctivitis population.


Subject(s)
COVID-19 , Coinfection , Conjunctivitis , Humans , SARS-CoV-2 , Coinfection/epidemiology , Outpatients , Prospective Studies , India/epidemiology , RNA
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