A Hierarchical Genotyping Framework Using DNA Melting Temperatures Applied to Adenovirus Species Typing.

Known genetic variation, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. Increased taxonomic detail may be used by clinicians and public health decision-makers to observe circulation patterns, monitor for outbreaks, and inform testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of assay design and sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays to increase classification accuracy. An illustrative hierarchical classification model for human adenovirus (HAdV) species was developed and demonstrated ~95% cross-validated accuracy on a labeled dataset. The model was then applied to a near-real-time surveillance dataset in which deidentified adenovirus detected patient test data from 2018 through 2021 were classified into one of six adenovirus species. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence.

Stream Dissolved Organic Matter in Permafrost Regions Shows Surprising Compositional Similarities but Negative Priming and Nutrient Effects.

Permafrost degradation is delivering bioavailable dissolved organic matter (DOM) and inorganic nutrients to surface water networks. While these permafrost subsidies represent a small portion of total fluvial DOM and nutrient fluxes, they could influence food webs and net ecosystem carbon balance via priming or nutrient effects that destabilize background DOM. We investigated how addition of biolabile carbon (acetate) and inorganic nutrients (nitrogen and phosphorus) affected DOM decomposition with 28-day incubations. We incubated late-summer stream water from 23 locations nested in seven northern or high-altitude regions in Asia, Europe, and North America. DOM loss ranged from 3% to 52%, showing a variety of longitudinal patterns within stream networks. DOM optical properties varied widely, but DOM showed compositional similarity based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. Addition of acetate and nutrients decreased bulk DOM mineralization (i.e., negative priming), with more negative effects on biodegradable DOM but neutral or positive effects on stable DOM. Unexpectedly, acetate and nutrients triggered breakdown of colored DOM (CDOM), with median decreases of 1.6% in the control and 22% in the amended treatment. Additionally, the uptake of added acetate was strongly limited by nutrient availability across sites. These findings suggest that biolabile DOM and nutrients released from degrading permafrost may decrease background DOM mineralization but alter stoichiometry and light conditions in receiving waterbodies. We conclude that priming and nutrient effects are coupled in northern aquatic ecosystems and that quantifying two-way interactions between DOM properties and environmental conditions could resolve conflicting observations about the drivers of DOM in permafrost zone waterways.

Clinical Impact of the BIOFIRE Blood Culture Identification 2 Panel in Adult Patients with Bloodstream Infection: A Multicentre Observational Study in the United Arab Emirates.

Rapid pathogen identification is key to the proper management of patients with bloodstream infections (BSIs), especially in the intensive care setting. This multicentre study compared the time to pathogen identification results in 185 patients admitted to intensive care with a confirmed BSI, using conventional methods (n = 99 patients) and upon implementation of the BIOFIRE® Blood Culture Identification 2 (BCID2) Panel, a rapid molecular test allowing for the simultaneous identification of 43 BSI-related nucleic acids targets (n = 86 patients). The median time to result informing optimal antibiotic therapy was significantly shorter following the implementation of the BCID2 Panel (92 vs. 28 h pre vs. post BCID2 implementation; p < 0.0001). BCID2 usage in addition to conventional methods led to the identification of at least one pathogen in 98.8% patients vs. 87.9% using conventional methods alone (p = 0.003) and was associated with a lower 30-day mortality (17.3% vs. 31.6%, respectively; p = 0.019). This study at three intensive care units in the United Arab Emirates therefore demonstrates that, in addition to conventional microbiological methods and an effective antimicrobial stewardship program, the BCID2 Panel could improve the clinical outcome of patients admitted to the intensive care unit with a confirmed BSI.

Multiplex PCR Detection of Respiratory Tract Infections in SARS-CoV-2-Negative Patients Admitted to the Emergency Department: an International Multicenter Study during the COVID-19 Pandemic.

Respiratory tract infection (RTI) is a common cause of visits to the hospital emergency department. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), nonpharmaceutical intervention has influenced the rates of circulating respiratory viruses. In this study, we sought to detect RTI etiological agents other than SARS-CoV-2 in emergency department patients from 13 countries in Europe, the Middle East, and Africa from December 2020 to March 2021. We sought to measure the impact of patient characteristics and national-level behavioral restrictions on the positivity rate for RTI agents. Using the BioFire Respiratory Panel 2.0 Plus, 1,334 nasopharyngeal swabs from patients with RTI symptoms who were negative for SARS-CoV-2 were tested. The rate of positivity for viral or bacterial targets was 36.3%. Regarding viral targets, human rhinovirus or enterovirus was the most prevalent (56.5%), followed by human coronaviruses (11.0%) and adenoviruses (9.9%). Interestingly, age stratification showed that the positivity rate was significantly higher in the children's group than in the adults' group (68.8% versus 28.2%). In particular, human rhinovirus or enterovirus, the respiratory syncytial virus, and other viruses, such as the human metapneumovirus, were more frequently detected in children than in adults. A logistic regression model was also used to determine an association between the rate of positivity for viral agents with each country's behavioral restrictions or with patients' age and sex. Despite the impact of behavioral restrictions, various RTI pathogens were actively circulating, particularly in children, across the 13 countries. IMPORTANCE As SARS-CoV-2 has dominated the diagnostic strategies for RTIs during the current COVID-19 pandemic situation, our data provide evidence that a variety of RTI pathogens may be circulating in each of the 13 countries included in the study. It is now plausible that the COVID-19 pandemic will one day move forward to endemicity. Our study illustrates the potential utility of detecting respiratory pathogens other than SARS-CoV-2 in patients who are admitted to the emergency department for RTI symptoms. Knowing if a symptomatic patient is solely infected by an RTI pathogen or coinfected with SARS-CoV-2 may drive timely and appropriate clinical decision-making, especially in the emergency department setting.

The Effects of Social Distancing Policies on Non-SARS-CoV-2 Respiratory Pathogens.

BACKGROUND: The initial focus of the US public health response to coronavirus disease 2019 (COVID-19) was the implementation of numerous social distancing policies. While COVID-19 was the impetus for imposing these policies, it is not the only respiratory disease affected by their implementation. This study aimed to assess the impact of social distancing policies on non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory pathogens typically circulating across multiple US states. METHODS: Linear mixed-effect models were implemented to explore the effects of 5 social distancing policies on non-SARS-CoV-2 respiratory pathogens across 9 states from January 1 through May 1, 2020. The observed 2020 pathogen detection rates were compared week by week with historical rates to determine when the detection rates were different. RESULTS: Model results indicate that several social distancing policies were associated with a reduction in total detection rate, by nearly 15%. Policies were associated with decreases in pathogen circulation of human rhinovirus/enterovirus and human metapneumovirus, as well as influenza A, which typically decrease after winter. Parainfluenza viruses failed to circulate at historical levels during the spring. The total detection rate in April 2020 was 35% less than the historical average. Many of the pathogens driving this difference fell below the historical detection rate ranges within 2 weeks of initial policy implementation. CONCLUSIONS: This analysis investigated the effect of multiple social distancing policies implemented to reduce transmission of SARS-CoV-2 on non-SARS-CoV-2 respiratory pathogens. These findings suggest that social distancing policies may be used as an impactful public health tool to reduce communicable respiratory illness.