Respiratory pathogens during the COVID-19 pandemic: Alterations in detection and seasonality in Nashville, Tennessee
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ABSTRACT:
SUBMITTER: Haddadin Z
PROVIDER: S-EPMC9348857 | biostudies-literature | 2022 Jan
REPOSITORIES: biostudies-literature
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Project description:Objective To survey the epidemiology of respiratory pathogens during the coronavirus disease 2019 (COVID-19) pandemic using multiplex polymerase chain reaction (PCR). Methods Specimens were assayed using multiplex nested PCR. Materials Specimens were obtained from outpatients who presented with symptoms of upper respiratory tract infection and asymptomatic outpatients who had contact with patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection at Tohoku Medical and Pharmaceutical University Hospital in Sendai, Japan, from November 1, 2020, to May 31, 2023. The analysis included multiple specimens collected from the same patients at different time-points. Data were collected from the electronic records after testing. Results This study included 8,335 patients (4,311 men) with a median age of 59 years old, and 11,741 total specimens were collected. At least 1 positive SARS-CoV-2 result was obtained for 1,710 (14.6%) specimens. Furthermore, 15 pathogens were identified in the positive specimens, and rhinovirus/enterovirus was detected more frequently than other viruses. We identified a larger number of SARS-CoV-2-positive specimens in patients ≥10 years old. In contrast, in patients 0-9 years old, we identified a larger number of specimens positive for rhinovirus/enterovirus than for other viruses. Conclusion In this study, we examined the epidemiology of circulating respiratory pathogens during the COVID-19 pandemic era.
| S-EPMC11239251 | biostudies-literature
Project description:Backgroundprevious worldwide reports indicated a substantial short-term reduction in various respiratory infections during the early phase of the SARS-CoV-2 pandemic.Aimsexploring the long-term impact of the COVID-19 pandemic on respiratory pathogens.Methodsretrospective analysis of bacterial and viral positivity rate in respiratory samples, between 1 January 2017-30 June 2022 in a tertiary hospital in Jerusalem, Israel.ResultsA decline in overall respiratory tests and positivity rate was observed in the first months of the pandemic. Respiratory isolations of Hemophilus influenza and Streptococcus pneumoniae were insignificantly affected and returned to their monthly average by November 2020, despite a parallel surge in COVID-19 activity, while Mycoplasma pneumoniae was almost eliminated from the respiratory pathogens scene. Each viral pathogen acted differently, with adenovirus affected only for few months. Human-metapneumovirus and respiratory-syncytial-virus had reduced activity for approximately a year, and influenza A virus resurged in November 2021 with the elimination of Influenza-B.ConclusionsAfter an immediate decline in non-SARS-CoV-2 respiratory infections, each pathogen has a different pattern during a 2-year follow-up. These patterns might be influenced by intrinsic factors of each pathogen and different risk reduction behaviors of the population. Since some of these measures will remain in the following years, we cannot predict the timing of return to pre-COVID-19 normalcy.
| S-EPMC9864990 | biostudies-literature
Project description:ObjectivesTo investigate whether the three nationwide coronavirus disease 2019 (COVID-19) lockdowns imposed in Israel during the full first pandemic year altered the traditional seasonality of pediatric respiratory healthcare utilization.MethodsMonth by month pediatric emergency department (ED) visits and hospitalizations for respiratory diagnoses during the first full COVID-19 year were compared to those recorded for the six consecutive years preceding the pandemic. Data were collected from the patients' electronic files by utilizing a data extraction platform (MDClone© ).ResultsA significant decline of 40% in respiratory ED visits and 54%-73% in respiratory hospitalizations during the first COVID-19 year compared with the pre-COVID-19 years were observed (p < 0.001 and p < 0.001, respectively). The rate of respiratory ED visits out of the total monthly visits, mostly for asthma, peaked during June 2020, compared with proceeding years (109 [5.9%] versus 88 [3.9%] visits; p < 0.001). This peak occurred 2 weeks after the lifting of the first lockdown, resembling the "back-to-school asthma" phenomenon of September.ConclusionsThis study demonstrates important changes in the seasonality of pediatric respiratory illnesses during the first COVID-19 year, including a new "back-from-lockdown" asthma peak. These dramatic changes along with the recent resurgence of respiratory diseases may indicate the beginnings of altered seasonality in pediatric pulmonary pathologies as collateral damage of the pandemic.
| S-EPMC9088630 | biostudies-literature
Project description:BackgroundSeasonal variation has been observed for various bacterial and viral infections. We aimed to further study seasonality of respiratory viruses and bacterial pathogens in relation to antibiotic use, as well as meteorological parameters.MethodsAn ecologic study of antibiotic exposure, meteorological parameters, detection of respiratory viruses and clinical isolates of Clostridioides difficile, Methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pneumoniae, and Escherichia coli and Klebsiella pneumoniae (grouped together as gram-negative bacteria; GNB) in Rhode Island from 2012 to 2016.ResultsPeak detection of C. difficile occurred 3 months after the peak in antibiotic prescriptions filled (OR = 1.24, 95% CI, 1.07-1.43; P = 0.006). Peak MRSA detection was noted 7 months after the peak in antibiotic prescriptions filled (OR = 1.69, 95% CI, 1.21-2.35; P = 0.003) and 10 months after the peak in respiratory virus detection (OR = 1.04, 95% CI, 1.01-1.06; P = 0.003). Peak GNB detection was noted 2 months after the peak mean monthly ambient temperature (OR = 1.69, 95% C.I., 1.20-2.39; P = 0.004). Peak detection of S. pneumoniae was noted at the same time as the peak in detection of respiratory viruses (OR = 1.01, 95% C.I., 1.00-1.01; P = 0.015).ConclusionsWe identified distinct seasonal variation in detection of respiratory viruses and bacterial pathogens. C. difficile seasonality may, in part, be related to antibiotic prescriptions filled; GNB seasonality may be related to ambient temperature and S. pneumoniae may be related to concurrent respiratory viral infections.
| S-EPMC6647268 | biostudies-literature
Project description:ObjectiveInfectious diseases are global health challenge, impacted the communities worldwide particularly in the midst of COVID-19 pandemic. The need of rapid and accurate automated systems for detecting pathogens of concern has always been critical. Ideally, such systems shall detect a large panel of pathogens simultaneously regardless of well-equipped facilities and highly trained operators, thus realizing on-site diagnosis for frontline healthcare providers and in critical locations such as borders and airports.Methods & resultsAvalon Automated Multiplex System, AAMST, is developed to automate a series of biochemistry protocols to detect nucleic acid sequences from multiple pathogens in one test. Automated processes include isolation of nucleic acids from unprocessed samples, reverse transcription and two rounds of amplifications. All procedures are carried out in a microfluidic cartridge performed by a desktop analyzer. The system was validated with reference controls and showed good agreement with their laboratory counterparts. In total 63 clinical samples, 13 positives including those from COVID-19 patients and 50 negative cases were detected, consistent with clinical diagnosis using conventional laboratory methods.ConclusionsThe proposed system has demonstrated promising utility. It would benefit the screening and diagnosis of COVID-19 and other infectious diseases in a simple, rapid and accurate fashion. Clinical and Translational Impact Statement- A rapid and multiplex diagnostic system proposed in this work can clinically help to control spread of COVID-19 and other infectious agents as it can provide timely diagnosis, isolation and treatment to patients. Using the system at remoted clinical sites can facilitate early clinical management and surveillance.
| S-EPMC10332469 | biostudies-literature
Project description:We aimed to investigate the epidemiological characteristics of non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory pathogens among patients with acute respiratory infections (ARIs) in Shijiazhuang, China, during the coronavirus disease 2019 (COVID-19) pandemic (January 2021--December 2022) and after the relaxation of COVID-19 restrictive measures (January 2022--December 2023). This retrospective study enrolled 6,633 ARIs patients who visited the Hebei General Hospital between 2021- and 2023. Nasopharyngeal swabs samples were collected for multiplex PCR detection of 13 common respiratory pathogens. Respiratory pathogens were detected in 31.58% of individuals diagnosed with ARIs, whileereas a co-infection with multiple pathogens was observed in 8.5% of the ARI patients. In the years 2021 and 2022, 326 (27.63%) and 283 (24.38%) respiratory pathogens were found to be positive, respectively, during the COVID-19 pandemic. However, in 2023, subsequent to the easing of COVID-19 restrictions, the positivity rate significantly rose to 34.62%, with 4,292 cases identified. The majority of positive cases over the last three3 years were concentrated in patients under 14 years old. The predominant pathogens identified were human rhinovirus (HRVs) (15.08%) in 2021, mycoplasma pneumonia (MP) (6.46%) in 2022, and influenza A virus (FluA) (11.35%) in 2023. Seasonal prevalence patterns of most pathogens were affected, except for parainfluenza virus (PIV). There was a simultaneous increase in the positive cases and positivity rates of FluA and adenovirus (ADV) Iin 2023, compared to 2021 and 2022. Additionally, the infection rates of respiratory syncytial virus (RSV), MP, and coronavirus (CoV) in 2023 either exceeded or were comparable to those in 2021 and 2022. Conversely, the positivity rates of PIV, RVs, metapneumovirus (MPV), and influenza B virus (FluB) were lower in 2023 compared to 2021 or 2022.ImportanceThe implementation of strict non-pharmaceutical interventions (NPIs) during the coronavirus disease 2019 (COVID-19) pandemic may lead to changes in the epidemiological features of respiratory pathogens, as well as the occurrence of immune debt, potentially causing a resurgence in respiratory pathogen activity following the easing of strict NPIs measures. There are limited reports on the epidemiological characteristics of respiratory pathogens among patients of all ages with acute respiratory infections (ARIs) during the COVID-19 pandemic and after the easing of COVID-19 restrictions. Our study investigated the epidemiology of 13 respiratory pathogens in Shijiazhuang, China, from January 2021 to December 2023. Thisese data isare crucial for the ongoing surveillance of epidemiological shifts in respiratory pathogens during and post the -COVID-19 pandemic, and serves as a scientific foundation for the prevention and management of ARIs.
| S-EPMC11537120 | biostudies-literature
Project description:ObjectiveTo determine if non-pharmaceutical interventions (NPIs) impacted on respiratory virus detections in Queensland, Australia, during the COVID-19 pandemic year of 2020.MethodsWe analysed weekly counts of influenza, human metapneumovirus, parainfluenza, respiratory syncytial virus, rhinovirus, and adenovirus available from a Queensland laboratory network for the year 2020. These were compared with averaged counts from 2015 to 2019.ResultsOverall, 686,199 tests were performed. The timing of NPI implementation was associated with a sharp and sustained decline in influenza, where during the typical annual influenza season (weeks 23-40) no cases were detected from 163,296 tests compared with an average of 26.1% (11,844/45,396) of tests positive in 2015-2019. Similar results were observed for human metapneumovirus and parainfluenza. Respiratory syncytial virus detections also declined but increased in weeks 48-52 (5.6%; 562/10,078) to exceed the 2015-2019 average (2.9%; 150/5,018). Rhinovirus detections increased after schools reopened, peaking in weeks 23-27 (57.4%; 36,228/63,115), exceeding the 2017-2019 detections during that period (21.9%; 8,365/38,072).ConclusionsNPIs implemented to control COVID-19 were associated with altered frequency and proportions of respiratory virus detections. Implications for public health: NPIs derived from influenza pandemic plans were associated with profound decreases in influenza detections during 2020.
| S-EPMC8652525 | biostudies-literature
Project description:ObjectiveEvaluate the association between provider-ordered viral testing and antibiotic treatment practices among children discharged from an ED or hospitalized with an acute respiratory infection (ARI).DesignActive, prospective ARI surveillance study from November 2017 to February 2020.SettingPediatric hospital and emergency department in Nashville, Tennessee.ParticipantsChildren 30 days to 17 years old seeking medical care for fever and/or respiratory symptoms.MethodsAntibiotics prescribed during the child's ED visit or administered during hospitalization were categorized into (1) None administered; (2) Narrow-spectrum; and (3) Broad-spectrum. Setting-specific models were built using unconditional polytomous logistic regression with robust sandwich estimators to estimate the adjusted odds ratios and 95% confidence intervals between provider-ordered viral testing (ie, tested versus not tested) and viral test result (ie, positive test versus not tested and negative test versus not tested) and three-level antibiotic administration.Results4,107 children were enrolled and tested, of which 2,616 (64%) were seen in the ED and 1,491 (36%) were hospitalized. In the ED, children who received a provider-ordered viral test had 25% decreased odds (aOR: 0.75; 95% CI: 0.54, 0.98) of receiving a narrow-spectrum antibiotic during their visit than those without testing. In the inpatient setting, children with a negative provider-ordered viral test had 57% increased odds (aOR: 1.57; 95% CI: 1.01, 2.44) of being administered a broad-spectrum antibiotic compared to children without testing.ConclusionsIn our study, the impact of provider-ordered viral testing on antibiotic practices differed by setting. Additional studies evaluating the influence of viral testing on antibiotic stewardship and antibiotic prescribing practices are needed.
| S-EPMC10945942 | biostudies-literature
Project description:Respiratory viruses, including coronaviruses, are known to have a high incidence of infection during winter, especially in temperate regions. Dry and cold conditions during winter are the major drivers for increased respiratory tract infections as they increase virus stability and transmission and weaken the host immune system. The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in China in December 2020 and swiftly spread across the globe causing substantial health and economic burdens. Several countries are battling with the second wave of the virus after a devastating first wave of spread, while some are still in the midst of their first wave. It remains unclear whether SARS-CoV-2 will eventually become seasonal or will continue to circulate year-round. In an attempt to address this question, we review the current knowledge regarding the seasonality of respiratory viruses including coronaviruses and the viral and host factors that govern their seasonal pattern. Moreover, we discuss the properties of SARS-CoV-2 and the potential impact of meteorological factors on its spread.
| S-EPMC7522168 | biostudies-literature
Project description:Surges in infections caused by respiratory pathogens have been documented in multiple settings after relaxation of pandemic restrictions. Antibodies to major antigens from respiratory syncytial virus and group A Streptococcus waned significantly in a longitudinal adult cohort throughout the pandemic. This waning may have contributed to the pathogen-surges that followed.
| S-EPMC11793024 | biostudies-literature