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1.
PLoS One ; 17(11): e0277201, 2022.
Article in English | MEDLINE | ID: covidwho-2197029

ABSTRACT

OBJECTIVES: Respiratory tract infection (RTI) incidence varies between people, but little is known about why. The aim of this study is therefore to identify risk factors for acquiring RTIs. METHODS: We conducted a secondary analysis of 16,908 participants in the PRIMIT study, a pre-pandemic randomised trial showing handwashing reduced incidence of RTIs in the community. Data was analysed using multivariable logistic regression analyses of self-reported RTI acquisition. RESULTS: After controlling for handwashing, RTI in the previous year (1 to 2 RTIs: adjusted OR 1.96, 95% CI 1.79 to 2.13, p<0.001; 3 to 5 RTIs: aOR 3.89, 95% CI 3.49 to 4.33, p<0.001; ≥6 RTIs: OR 5.52, 95% CI 4.37 to 6.97, p<0.001); skin conditions that prevent handwashing (aOR 1.39, 95% CI 1.24 to 1.55, p<0.001); children under 16 years in the household (aOR 1.27, 95% CI 1.12, 1.43, p<0.001); chronic lung condition (aOR 1.16, 95% CI 1.02 to 1.32, p = 0.026); female sex (aOR 1.10, 95% CI 1.03 to 1.18, p = 0.005), and post-secondary education (aOR 1.09, 95% CI 1.02 to 1.17, p = 0.01) increased the likelihood of RTI. Those over the age of 65 years were less likely to develop an infection (aOR 0.89, 95% CI 0.82 to 0.97, p = 0.009). Household crowding and influenza vaccination do not influence RTI acquisition. A post-hoc exploratory analysis found no evidence these subgroups differentially benefited from handwashing. CONCLUSIONS: Previous RTIs, chronic lung conditions, skin conditions that prevent handwashing, and the presence of household children predispose to RTI acquisition. Further research is needed to understand how host and microbial factors explain the relationship between previous and future RTIs.


Subject(s)
Community-Acquired Infections , Respiratory Tract Infections , Aged , Child , Female , Humans , Community-Acquired Infections/epidemiology , Community-Acquired Infections/prevention & control , Crowding , Family Characteristics , Respiratory System , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control , Risk Factors
3.
BMC Pediatr ; 22(1): 452, 2022 Jul 27.
Article in English | MEDLINE | ID: covidwho-1965734

ABSTRACT

BACKGROUND: Pneumonia is a serious problem that threatens the health of newborns. This study aimed to investigate the clinical characteristics of hospitalized term and preterm infants with community-acquired viral pneumonia. METHODS: This was a retrospective analysis of cases of community-acquired viral pneumonia in the Neonatal Department. Nasopharyngeal aspirate (NPA) samples were collected for pathogen detection, and clinical data were collected. We analysed pathogenic species and clinical characteristics among these infants. RESULTS: RSV is the main virus in term infants, and parainfluenza virus (PIV) 3 is the main virus in preterm infants. Patients infected with PIV3 were more susceptible to coinfection with bacteria than those with respiratory syncytial virus (RSV) infection (p < 0.05). Preterm infants infected with PIV3 were more likely to be coinfected with bacteria than term infants (p < 0.05), mainly gram-negative bacteria (especially Klebsiella pneumonia). Term infants with bacterial infection were more prone to fever, cyanosis, moist rales, three concave signs, elevated C-reactive protein (CRP) levels, respiratory failure and the need for higher level of oxygen support and mechanical ventilation than those with simple viral infection (p < 0.05). The incidence of hyponatremia in neonatal community-acquired pneumonia (CAP) was high. CONCLUSIONS: RSV and PIV3 were the leading causes of neonatal viral CAP. PIV3 infection is the main cause of viral CAP in preterm infants, and these individuals are more likely to be coinfected with bacteria than term infants, mainly gram-negative bacteria. Term infants with CAP coinfected with bacteria were more likely to have greater disease severity than those with single viral infections.


Subject(s)
Community-Acquired Infections , Pneumonia, Viral , Respiratory Syncytial Virus Infections , Virus Diseases , Community-Acquired Infections/epidemiology , Humans , Infant , Infant, Newborn , Infant, Premature , Pneumonia, Viral/complications , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Respiratory Syncytial Virus Infections/complications , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Retrospective Studies
4.
JMIR Public Health Surveill ; 7(4): e24292, 2021 04 07.
Article in English | MEDLINE | ID: covidwho-2141292

ABSTRACT

BACKGROUND: Significant uncertainty has existed about the safety of reopening college and university campuses before the COVID-19 pandemic is better controlled. Moreover, little is known about the effects that on-campus students may have on local higher-risk communities. OBJECTIVE: We aimed to estimate the range of potential community and campus COVID-19 exposures, infections, and mortality under various university reopening plans and uncertainties. METHODS: We developed campus-only, community-only, and campus × community epidemic differential equations and agent-based models, with inputs estimated via published and grey literature, expert opinion, and parameter search algorithms. Campus opening plans (spanning fully open, hybrid, and fully virtual approaches) were identified from websites and publications. Additional student and community exposures, infections, and mortality over 16-week semesters were estimated under each scenario, with 10% trimmed medians, standard deviations, and probability intervals computed to omit extreme outliers. Sensitivity analyses were conducted to inform potential effective interventions. RESULTS: Predicted 16-week campus and additional community exposures, infections, and mortality for the base case with no precautions (or negligible compliance) varied significantly from their medians (4- to 10-fold). Over 5% of on-campus students were infected after a mean of 76 (SD 17) days, with the greatest increase (first inflection point) occurring on average on day 84 (SD 10.2 days) of the semester and with total additional community exposures, infections, and mortality ranging from 1-187, 13-820, and 1-21 per 10,000 residents, respectively. Reopening precautions reduced infections by 24%-26% and mortality by 36%-50% in both populations. Beyond campus and community reproductive numbers, sensitivity analysis indicated no dominant factors that interventions could primarily target to reduce the magnitude and variability in outcomes, suggesting the importance of comprehensive public health measures and surveillance. CONCLUSIONS: Community and campus COVID-19 exposures, infections, and mortality resulting from reopening campuses are highly unpredictable regardless of precautions. Public health implications include the need for effective surveillance and flexible campus operations.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Universities/organization & administration , COVID-19/mortality , Community-Acquired Infections/epidemiology , Humans , Models, Theoretical , Risk Assessment , Uncertainty , United States/epidemiology
5.
Front Immunol ; 13: 894170, 2022.
Article in English | MEDLINE | ID: covidwho-2141903

ABSTRACT

The metabolic characteristics of COVID-19 disease are still largely unknown. Here, 44 patients with COVID-19 (31 mild COVID-19 patients and 13 severe COVID-19 patients), 42 healthy controls (HC), and 42 patients with community-acquired pneumonia (CAP), were involved in the study to assess their serum metabolomic profiles. We used widely targeted metabolomics based on an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The differentially expressed metabolites in the plasma of mild and severe COVID-19 patients, CAP patients, and HC subjects were screened, and the main metabolic pathways involved were analyzed. Multiple mature machine learning algorithms confirmed that the metabolites performed excellently in discriminating COVID-19 groups from CAP and HC subjects, with an area under the curve (AUC) of 1. The specific dysregulation of AMP, dGMP, sn-glycero-3-phosphocholine, and carnitine was observed in the severe COVID-19 group. Moreover, random forest analysis suggested that these metabolites could discriminate between severe COVID-19 patients and mild COVID-19 patients, with an AUC of 0.921. This study may broaden our understanding of pathophysiological mechanisms of COVID-19 and may offer an experimental basis for developing novel treatment strategies against it.


Subject(s)
COVID-19 , Community-Acquired Infections , Pneumonia , Chromatography, High Pressure Liquid/methods , Chromatography, Liquid/methods , Humans , Metabolomics/methods , Tandem Mass Spectrometry/methods
6.
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
7.
Int J Infect Dis ; 111: 108-116, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-2113607

ABSTRACT

OBJECTIVES: To validate and recalibrate the CURB-65 and pneumonia severity index (PSI) in predicting 30-day mortality and critical care intervention (CCI) in a multiethnic population with COVID-19, along with evaluating both models in predicting CCI. METHODS: Retrospective data was collected for 1181 patients admitted to the largest hospital in Qatar with COVID-19 pneumonia. The area under the curve (AUC), calibration curves, and other metrics were bootstrapped to examine the performance of the models. Variables constituting the CURB-65 and PSI scores underwent further analysis using the Least Absolute Shrinkage and Selection Operator (LASSO) along with logistic regression to develop a model predicting CCI. Complex machine learning models were built for comparative analysis. RESULTS: The PSI performed better than CURB-65 in predicting 30-day mortality (AUC 0.83, 0.78 respectively), while CURB-65 outperformed PSI in predicting CCI (AUC 0.78, 0.70 respectively). The modified PSI/CURB-65 model (respiratory rate, oxygen saturation, hematocrit, age, sodium, and glucose) predicting CCI had excellent accuracy (AUC 0.823) and good calibration. CONCLUSIONS: Our study recalibrated, externally validated the PSI and CURB-65 for predicting 30-day mortality and CCI, and developed a model for predicting CCI. Our tool can potentially guide clinicians in Qatar to stratify patients with COVID-19 pneumonia.


Subject(s)
COVID-19 , Community-Acquired Infections , Pneumonia , Critical Care , Hospital Mortality , Humans , Pneumonia/diagnosis , Pneumonia/therapy , Prognosis , Retrospective Studies , SARS-CoV-2 , Severity of Illness Index
8.
Eur Rev Med Pharmacol Sci ; 26(21): 8172-8179, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2117927

ABSTRACT

OBJECTIVE: To compare the characteristics and outcomes of critically ill patients admitted to the intensive care unit (ICU) due to COVID-19 or influenza- associated pneumonia. PATIENTS AND METHODS: We conducted a two-center retrospective study on patients admitted to the ICU due to either COVID-19 associated pneumonia (CAP) or influenza-associated pneumonia (IAP). Baseline characteristics, therapy during hospitalization and clinical outcomes were assessed. RESULTS: Our study included 86 patients admitted to the ICU. Twenty-four patients (28%) had IAP and 62 patients (72%) had CAP. Those with IAP had more comorbidities of cardiac disease (p=0.005) and chronic obstructive lung disease (p=0.03) compared to those with CAP. Non-invasive ventilation was used significantly more in patients with IAP (p=0.001). The use of neuromuscular blockade was significantly higher in CAP patients (p=0.001). CAP patients had less favourable ventilation parameters. PEEP was significantly higher in those with CAP on the first day of admission (p=0.002). There was no difference in mortality (p=0.61) between the groups. CONCLUSIONS: Patients admission to the ICU with CAP had less comorbidity than those with IAP. Patients with CAP had poorer ventilatory parameters patterns, requiring more aggressive ventilation and ECMO support. The overall mortality did not differ significantly between the groups.


Subject(s)
COVID-19 , Community-Acquired Infections , Influenza, Human , Pneumonia , Humans , Retrospective Studies , Influenza, Human/epidemiology , Influenza, Human/therapy , COVID-19/therapy , Seasons , Intensive Care Units
9.
Probl Sotsialnoi Gig Zdravookhranenniiai Istor Med ; 30(s1): 1044-1049, 2022 Dec 15.
Article in Russian | MEDLINE | ID: covidwho-2117152

ABSTRACT

The review traces the evolution of the section on the use of antibacterial drugs in the temporary guidelines of the Ministry of Health for the treatment of a new coronavirus infection. Diagnostic approaches that play an important role in deciding on the need and duration of antibacterial therapy are presented. Routine use of fluoroquinolones should be restricted due to the adverse safety spectrum. According to existing data, the tactic of short courses of antibacterial therapy for community-acquired pneumonia are not inferior in effectiveness to longer courses. Unjustified prescribing of antibiotics increases the cost of medical care, promotes the selection of resistant pathogens and leads to adverse side effects. Timely updating of clinical recommendations, implementation of programs to control the appointment of antibacterial agents in medical organizations and strengthening the role of the clinical pharmacology service can reduce these adverse events.


Subject(s)
COVID-19 , Community-Acquired Infections , Pneumonia , Humans , COVID-19/drug therapy , Anti-Bacterial Agents/adverse effects , Community-Acquired Infections/drug therapy
10.
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
13.
BMC Pulm Med ; 22(1): 379, 2022 Oct 14.
Article in English | MEDLINE | ID: covidwho-2079411

ABSTRACT

BACKGROUND: Community-acquired pneumonia (CAP) is the most frequent infection diagnosis in hospitals. Antimicrobial therapy for CAP is depicted in clinical practice guidelines, but adherence data and effect of antibiotic stewardship measures are lacking. METHODS: A dedicated antibiotic team pointed out CAP as a potential target for antimicrobial stewardship (AMS) measures at a 1.000-bed, tertiary care, teaching university hospital in Norway from March until May for the years 2016 throughout 2021. The aim of the AMS program was to increase diagnostic and antimicrobial therapy adherence to national clinical practice guideline recommendations through multiple and continuous AMS efforts. Descriptive statistics were retrospectively used to delineate antimicrobial therapy for CAP. The primary outcomes were proportions that received narrow-spectrum beta-lactams, and broad-spectrum antimicrobial therapy. RESULTS: 1.112 CAP episodes were identified. The annual proportion that received narrow-spectrum beta-lactams increased from 56.1 to 74.4% (p = 0.045). Correspondingly, the annual proportion that received broad-spectrum antimicrobial therapy decreased from 34.1 to 17.1% (p = 0.002). Trends were affected by the coronavirus pandemic. Mortality and 30-day readmission rates remained unchanged. De-escalation strategies were frequently unutilized, and overall therapy duration exceeded clinical practice guideline recommendations substantially. Microbiologically confirmed CAP episodes increased from 33.7 to 56.2% during the study period. CONCLUSION: CAP is a suitable model condition that is sensitive to AMS measures. A continuous focus on improved microbiological diagnostics and antimicrobial therapy initiation is efficient in increasing adherence to guideline recommendations. There is an unmet need for better antimicrobial de-escalation strategies.


Subject(s)
Anti-Infective Agents , Community-Acquired Infections , Coronavirus , Pneumonia , Anti-Bacterial Agents/therapeutic use , Anti-Infective Agents/therapeutic use , Community-Acquired Infections/drug therapy , Humans , Pandemics , Pneumonia/drug therapy , Retrospective Studies , beta-Lactams/therapeutic use
14.
Eur Respir Rev ; 31(166)2022 Dec 31.
Article in English | MEDLINE | ID: covidwho-2079388

ABSTRACT

Lower respiratory infections include acute bronchitis, influenza, community-acquired pneumonia, acute exacerbation of COPD and acute exacerbation of bronchiectasis. They are a major cause of death worldwide and often affect the most vulnerable: children, elderly and the impoverished. In this paper, we review the clinical presentation, diagnosis, severity assessment and treatment of adult outpatients with lower respiratory infections. The paper is divided into sections on specific lower respiratory infections, but we also dedicate a section to COVID-19 given the importance of the ongoing pandemic. Lower respiratory infections are heterogeneous entities, carry different risks for adverse events, and require different management strategies. For instance, while patients with acute bronchitis are rarely admitted to hospital and generally do not require antimicrobials, approximately 40% of patients seen for community-acquired pneumonia require admission. Clinicians caring for patients with lower respiratory infections face several challenges, including an increasing population of patients with immunosuppression, potential need for diagnostic tests that may not be readily available, antibiotic resistance and social aspects that place these patients at higher risk. Management principles for patients with lower respiratory infections include knowledge of local surveillance data, strategic use of diagnostic tests according to surveillance data, and judicious use of antimicrobials.


Subject(s)
Anti-Infective Agents , Bronchitis , COVID-19 , Community-Acquired Infections , Pneumonia , Respiratory Tract Infections , Adult , Child , Humans , Aged , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/epidemiology , Community-Acquired Infections/diagnosis , Community-Acquired Infections/drug therapy , Community-Acquired Infections/epidemiology , Bronchitis/diagnosis , Bronchitis/drug therapy , Pneumonia/diagnosis , Acute Disease , Anti-Infective Agents/therapeutic use , Hospitals , Anti-Bacterial Agents/adverse effects
15.
Front Immunol ; 13: 983550, 2022.
Article in English | MEDLINE | ID: covidwho-2065515

ABSTRACT

The current COVID-19 pandemic has highlighted a need to further understand lung mucosal immunity to reduce the burden of community acquired pneumonia, including that caused by the SARS-CoV-2 virus. Local mucosal immunity provides the first line of defence against respiratory pathogens, however very little is known about the mechanisms involved, with a majority of literature on respiratory infections based on the examination of peripheral blood. The mortality for severe community acquired pneumonia has been rising annually, even prior to the current pandemic, highlighting a significant need to increase knowledge, understanding and research in this field. In this review we profile key mediators of lung mucosal immunity, the dysfunction that occurs in the diseased lung microenvironment including the imbalance of inflammatory mediators and dysbiosis of the local microbiome. A greater understanding of lung tissue-based immunity may lead to improved diagnostic and prognostic procedures and novel treatment strategies aimed at reducing the disease burden of community acquired pneumonia, avoiding the systemic manifestations of infection and excess morbidity and mortality.


Subject(s)
COVID-19 , Community-Acquired Infections , Humans , Immunity, Mucosal , Inflammation Mediators , Pandemics , SARS-CoV-2
16.
Expert Rev Anti Infect Ther ; 20(12): 1537-1550, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2062697

ABSTRACT

INTRODUCTION: Although viruses are an underestimated cause of community-acquired pneumonias (CAP) and hospital-acquired pneumonias (HAP)/ventilator-associated pneumonias (VAP) in intensive care unit (ICU) patients, they have an impact on morbidity and mortality. AREAS COVERED: In this perspective article, we discuss the available data regarding the management of severe influenza CAP and herpesviridae HAP/VAP. We review diagnostic and therapeutic strategies in order to give clear messages and address unsolved questions. EXPERT OPINION: Influenza CAP affects yearly thousands of people; however, robust data regarding antiviral treatment in the most critical forms are scarce. While efficacy of oseltamivir has been investigated in randomized controlled trials (RCT) in uncomplicated influenza, only observational data are available in ICU patients. Herpesviridae are an underestimated cause of HAP/VAP in ICU patients. Whilst incidence of herpesviridae identification in samples from lower respiratory tract of ICU patients is relatively high (from 20% to 50%), efforts should be made to differentiate local reactivation from true lung infection. Only few randomized controlled trials evaluated the efficacy of antiviral treatment in herpesviridae reactivation/infection in ICU patients and all were exploratory or negative. Further studies are needed to evaluate the impact of such treatment in specific populations.


Subject(s)
COVID-19 , Community-Acquired Infections , Healthcare-Associated Pneumonia , Influenza, Human , Pneumonia, Ventilator-Associated , Virus Diseases , Humans , Intensive Care Units , Community-Acquired Infections/drug therapy , Community-Acquired Infections/epidemiology , Antiviral Agents/therapeutic use
17.
BMC Infect Dis ; 22(1): 763, 2022 Sep 30.
Article in English | MEDLINE | ID: covidwho-2053867

ABSTRACT

BACKGROUND: The COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP). METHODS: This study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann-Whitney's U test was used to analyse continuous variables. Fisher's exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values. RESULTS: Admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort. CONCLUSION: During the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2.


Subject(s)
COVID-19 , Community-Acquired Infections , Pneumonia , Respiratory Tract Infections , COVID-19/epidemiology , Community-Acquired Infections/epidemiology , Humans , Pandemics , Pneumonia/epidemiology , Prospective Studies , Respiratory Tract Infections/epidemiology , SARS-CoV-2
18.
Lancet Microbe ; 3(7): e512-e520, 2022 07.
Article in English | MEDLINE | ID: covidwho-2050135

ABSTRACT

BACKGROUND: Chlamydia psittaci can infect a wide range of avian species, occasionally causing psittacosis (also known as parrot fever) in humans. Most human psittacosis cases are associated with close contact with pet birds or poultry. In December, 2020, an outbreak of severe community-acquired pneumonia of unknown aetiology was reported in a hospital in Shandong province, China, and some of the patients' close contacts had respiratory symptoms. Our aims were to determine the causative agent of this epidemic and whether there had been human-to-human transmission. METHODS: For this epidemiological and aetiological investigation study, we enrolled patients who had community-acquired pneumonia confirmed by chest CT at two local hospitals in Shandong Province in China. We collected sputum, bronchoalveolar lavage fluid, and nasopharyngeal swab samples from participants and detected pathogens by surveying for 22 target respiratory microbes using a commercial assay, followed by metagenomic next-generation sequencing, specific nested PCR, and qPCR tests. We excluded individuals who were C psittaci-negative on both tests. We recruited close contacts of the C psittaci-positive patients, and tested nasopharyngeal swabs from the close contacts and samples from ducks from the processing plant where these patients worked. We then integrated the epidemiological, clinical, and laboratory data to reveal the potential chain of transmission of C psittaci that characterised this outbreak. FINDINGS: Between Dec 4 and 29, 2020, we used metagenomic next-generation sequencing and different PCR-based approaches to test 12 inpatients with community-acquired pneumonia, of whom six (50%) were workers at a duck-meat processing plant and two (17%) were unemployed people, who were positive for C psittaci and enrolled in this study. We contacted 61 close contacts of the six patients who worked at the duck-meat processing plant, of whom 61 (100%) were enrolled and tested, and we determined that the community-acquired pneumonia outbreak was caused by C psittaci. Within the outbreak cluster, 17 (77%) of 22 participants had confirmed C psittaci infections and five (23%) of 22 participants were asymptomatic C psittaci carriers. The outbreak had begun with avian-to-human transmission, and was followed by secondary and tertiary human-to-human transmission, which included transmission by several asymptomatic carriers and by health-care workers. In addition, some of the participants with confirmed C psittaci infection had no identified source of infection, which suggested cryptic bacterial transmission. INTERPRETATION: Our study data might represent the first documented report of human-to-human transmission of C psittaci in China. Therefore, C psittaci has the potential to evolve human-to-human transmission via various routes, should be considered an elevated biosecurity and emergent risk, and be included as part of the routine diagnosis globally, especially for high-risk populations. FUNDING: Academic Promotion Programme of Shandong First Medical University, National Science and Technology Major Project, ARC Australian Laureate Fellowship.


Subject(s)
Chlamydophila psittaci , Community-Acquired Infections , Pneumonia , Psittacosis , Animals , Australia , Birds , China/epidemiology , Chlamydophila psittaci/genetics , Community-Acquired Infections/diagnosis , Humans , Pneumonia/diagnosis , Psittacosis/diagnosis
19.
Urol J ; 19(5): 386-391, 2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-2026216

ABSTRACT

PURPOSE: To evaluate whether there were any changes in the rates of urinary tract infection (UTI) and antibiotic resistance in pediatric patients during the pandemic period. MATERIALS AND METHODS: Urine culture samples collected due to suspected UTI were searched retrospectively from our hospital database, and the patients with growth in urine culture were identified. They were divided into 2 groups as Group A (before COVID-19, March 11, 2019- March 11, 2020) and Group B (COVID-19 period, March 11, 2020- March 11, 2021). Also, COVID-19 period was divided into 3 subgroups (March 2020- June 2020: first epidemic peak, July 2020 - November 2020: normalization process, December 2020- March 2021: second epidemic peak). We adjusted the patient age as <1, 1-6 and 7-18 years. Age, gender, microorganism strain types, and their antibiotic resistance patterns were compared between the 2 groups Results: This cross-sectional study included 250 eligible patients (Group A, n=182 and Group B, n=68) with a mean age of 10.91 ± 5.58 years. The male/female ratio was higher in Group B than in Group A (p = .004). Incidence of UTIs was lower in the curfew and restriction periods due to epidemic peaks than normalization process (p = .001). The proportion of E.coli decreased from 80.2% to 61.8% during the pandemic period when compared to pre-pandemic period (p = .001). Group B had lower rates of resistance to ampicillin, fosfomycin and nitrofurantoin for E.coli than Group A (p = .001, p = .012 and p = .001, respectively). Also, Group B had higher rate of uncommon microorganisms and lower rate of resistance to nitrofurantoin for E.coli than Group A in patients aged 7-18 years (p = .003 and p = .023, respectively). CONCLUSION: Our study demonstrates that the ongoing COVID-19 pandemic process has caused alterations in community-acquired UTIs in children. More hygienic lifestyle may be considered as the main factor in this change.


Subject(s)
COVID-19 , Community-Acquired Infections , Escherichia coli Infections , Urinary Tract Infections , Humans , Female , Male , Child , Child, Preschool , Adolescent , COVID-19/epidemiology , Pandemics , Nitrofurantoin , Escherichia coli Infections/epidemiology , Cross-Sectional Studies , Retrospective Studies , Microbial Sensitivity Tests , Anti-Bacterial Agents/therapeutic use , Urinary Tract Infections/drug therapy , Urinary Tract Infections/epidemiology , Community-Acquired Infections/epidemiology , Community-Acquired Infections/drug therapy , Escherichia coli
20.
Respir Res ; 23(1): 239, 2022 Sep 10.
Article in English | MEDLINE | ID: covidwho-2021290

ABSTRACT

INTRODUCTION: Despite improvements in medical science and public health, mortality of community-acquired pneumonia (CAP) has barely changed throughout the last 15 years. The current SARS-CoV-2 pandemic has once again highlighted the central importance of acute respiratory infections to human health. The "network of excellence on Community Acquired Pneumonia" (CAPNETZ) hosts the most comprehensive CAP database worldwide including more than 12,000 patients. CAPNETZ connects physicians, microbiologists, virologists, epidemiologists, and computer scientists throughout Europe. Our aim was to summarize the current situation in CAP research and identify the most pressing unmet needs in CAP research. METHODS: To identify areas of future CAP research, CAPNETZ followed a multiple-step procedure. First, research members of CAPNETZ were individually asked to identify unmet needs. Second, the top 100 experts in the field of CAP research were asked for their insights about the unmet needs in CAP (Delphi approach). Third, internal and external experts discussed unmet needs in CAP at a scientific retreat. RESULTS: Eleven topics for future CAP research were identified: detection of causative pathogens, next generation sequencing for antimicrobial treatment guidance, imaging diagnostics, biomarkers, risk stratification, antiviral and antibiotic treatment, adjunctive therapy, vaccines and prevention, systemic and local immune response, comorbidities, and long-term cardio-vascular complications. CONCLUSION: Pneumonia is a complex disease where the interplay between pathogens, immune system and comorbidities not only impose an immediate risk of mortality but also affect the patients' risk of developing comorbidities as well as mortality for up to a decade after pneumonia has resolved. Our review of unmet needs in CAP research has shown that there are still major shortcomings in our knowledge of CAP.


Subject(s)
COVID-19 , Community-Acquired Infections , Pneumonia , Anti-Bacterial Agents/therapeutic use , Community-Acquired Infections/diagnosis , Community-Acquired Infections/epidemiology , Community-Acquired Infections/therapy , Europe/epidemiology , Humans , Pneumonia/diagnosis , Pneumonia/epidemiology , Pneumonia/therapy , SARS-CoV-2
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