scholarly journals Adjusting for time of infection or positive test when estimating the risk of a post-infection outcome in an epidemic

Author(s):  
Shaun R Seaman ◽  
Tommy Nyberg ◽  
Christopher E Overton ◽  
David Pascall ◽  
Anne M Presanis ◽  
...  

When comparing the risk of a post-infection binary outcome, e.g. hospitalisation, for two variants of an infectious pathogen, it is important to adjust for calendar time of infection to avoid the confounding that would occur if the relative incidence of the two variants and the variant-specific risks of the outcome both change over time. Infection time is typically unknown and time of positive test used instead. Likewise, time of positive test may be used instead of infection time when assessing how the risk of the binary outcome changes over calendar time. Here we show that if mean time from infection to positive test is correlated with the outcome, the risk conditional on positive test time depends on whether incidence of infection is increasing or decreasing over calendar time. This complicates interpretation of risk ratios adjusted for positive test time. We also propose a simple sensitivity analysis that indicates how these risk ratios may differ from the risk ratios adjusted for infection time.

2021 ◽  
Vol 8 ◽  
Author(s):  
Kirsten E. McLoughlin ◽  
Carolina N. Correia ◽  
John A. Browne ◽  
David A. Magee ◽  
Nicolas C. Nalpas ◽  
...  

Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.


Parasitology ◽  
2015 ◽  
Vol 142 (14) ◽  
pp. 1715-1721 ◽  
Author(s):  
LEILANE A. CHAVES ◽  
ANA LÚCIA R. GONÇALVES ◽  
FABIANA M. PAULA ◽  
NEIDE. M. SILVA ◽  
CLÁUDIO V. SILVA ◽  
...  

SUMMARYDefinitive diagnosis of strongyloidiasis in humans is typically achieved by detection of larvae in fecal samples. However, limitations on sensitivity of parasitological methods emphasize the need for more robust diagnostic methods. The aim of this study was to compare the diagnostic value of three methods: eggs per gram of feces (EPG), coproantigen detection by enzyme linked immunosorbent assay (ELISA), and DNA detection by conventional polymerase chain reaction (PCR). The assays were performed at 0 and 5, 8, 13, 21 and 39 days post-infection (dpi) using fecal samples from experimentally infected immunocompetent and immunosuppressed rats. In immunocompetent rats, eggs were detected in feces on days 5, 8 and 13 dpi; coproantigen detection and PCR amplification were successful at all post-infection time points (5, 8, 13, 21 and 39 dpi). In immunosuppressed rats, eggs were detected at 5, 8, 13 and 21; coproantigen detection and PCR amplification were successful at all post-infection time points. In conclusion, these results suggest that coproantigen detection and PCR may be more sensitive alternatives to traditional methods such as EPG for diagnosis of Strongyloides venezuelensis infection.


2021 ◽  
Author(s):  
Paul M McKeigue ◽  
David McAllister ◽  
Chris Robertson ◽  
Diane Stockton ◽  
Helen Colhoun

Background -- The objective of this study was to investigate how protection against COVID-19 conferred by previous infection is modified by vaccination. Methods -- In a cohort of all 152655 individuals in Scotland alive at 90 days after a positive test for SARS-CoV-2 (confirmed by cycle threshold < 30, or two tests) followed till 22 September 2021, rate ratios for reinfection were estimated with calendar time or tests as timescale. Findings -- Rates of detected and hospitalised reinfection with COVID-19 while unvaccinated were respectively 6.8 (95% CI 6.4 to 7.2) and 0.18 (95% CI 0.12 to 0.25) per 1000 person-months. These rates were respectively 68% and 74% lower than in a matched cohort of individuals who had not previously tested positive. Efficacy of two doses of vaccine in those with previous infection was estimated as as 84% (95 percent CI 81% to 86%) against detected reinfection and 71% (95 percent CI 29% to 88%) against hospitalised or fatal reinfection. The rate of detected reinfection after two doses of vaccine was 1.35 (95% CI 1.02 to 1.78) times higher in those vaccinated before first infection than in those unvaccinated at first infection. Interpretation -- The combination of natural infection and vaccination provides maximal protection against new infection with SARS-CoV-2: prior vaccination does not impair this protection.


1998 ◽  
Vol 331 (1) ◽  
pp. 331-339 ◽  
Author(s):  
William G. SINKINS ◽  
Mark ESTACION ◽  
William P. SCHILLING

TrpC1 appears to be a store-operated channel (SOC) when expressed in mammalian cells. In the present study, TrpC1 was expressed in Sf9 insect cells using the baculovirus expression system. Expression of TrpC1 caused an increase in basal cytosolic free Ca2+ concentration ([Ca2+]i) as a function of post-infection time. Basal Ba2+ influx, an index of plasmalemmal Ca2+ permeability, was also increased and was blocked by La3+. Although the thapsigargin-induced change in [Ca2+]i was greater in TrpC1-expressing cells than controls, Ba2+ influx was unaffected by thapsigargin. Whole-cell membrane currents recorded in TrpC1-expressing cells increased as a function of post-infection time and were (1) inwardly rectifying in symmetrical sodium gluconate solutions, (2) non-selective with respect to Na+, Ca2+ and Ba2+, and (3) blocked by La3+. Furthermore TrpC1 currents were unaffected by (1) thapsigargin, (2) dialysis of the cell with Ins(1,4,5)P3 or (3) dialysis of the cell with solutions containing high concentrations of the Ca2+ chelator, EGTA. These results suggest that TrpC1 forms non-selective cation channels that are constitutively active when expressed in Sf9 cells, but insensitive to depletion of the internal Ca2+ stores. Thus TrpC1 may be a subunit of a SOC which alone can form functional channels in Sf9 cells, but which requires additional subunits or cytoplasmic factors present in mammalian cells for expression of SOC activity.


2021 ◽  
pp. 112972982098737
Author(s):  
Teoh Sze Yong ◽  
Anushya A/P Vijayanathan ◽  
Eric Chung ◽  
Wei Lin Ng ◽  
Nur Adura Yaakup ◽  
...  

Objective: To compare catheter related blood stream infection (CRBSI) rate between cuffed tunnelled and non-cuffed tunnelled PICC. Methods: We prospectively followed 100 patients (50:50 cuffed and non-cuffed PICC) and compared CRBSI rate between these groups. Daily review and similar catheter care were performed until a PICC-related complication, completion of therapy, death or defined end-of-study date necessitate removal. CRBSI was confirmed in each case by demonstrating concordance between isolates colonizing the PICC at the time of infection and from peripheral blood cultures. Results: A total of 50 cuffed PICC were placed for 1864 catheter-days. Of these, 12 patients (24%) developed infection, for which 5 patients (10%) had a CRBSI for a rate of 2.7 per 1000 catheter-days. Another 50 tunnelled non-cuffed PICCs were placed for 2057 catheter-days. Of these, 7 patients (14%) developed infection, for which 3 patients (6%) had a CRBSI. for a rate of 1.5 per 1000 catheter-days. The mean time to development of infection is 24 days in cuffed and 19 days in non-cuffed groups. The mean duration of utilization was significantly longer in non-cuffed than in cuffed group (43 days in non-cuffed vs 37 days in cuffed group, p = 0.008). Conclusions: Cuffed PICC does not further reduce the rate of local or bloodstream infection. Tunnelled non-cuffed PICC is shown to be as effective if not better at reducing risk of CRBSI and providing longer catheter dwell time compared to cuffed PICC.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1452-1452
Author(s):  
Matthew R. Kovacs ◽  
Alejandro Lazo-Langner ◽  
Martha L Louzada ◽  
Michael J. Kovacs

Abstract Background. Lupus Anticoagulants (LA) and Antiphospholipid Antibodies (APLA) are known to be associated with both arterial and venous thromboembolism (VTE). The implications of positive test results often include indefinite anticoagulant therapy and thus accurately identifying these patients is important. Current guidelines for laboratory testing of both LA and APLA, require that initial positive results are confirmed by repeat testing at least 12 weeks after initial positivity to be considered diagnostic. Repeat testing is not routinely performed once a patient is deemed to be positive. If repeat testing is performed years after initial confirmation and is negative, the clinical implications of this are not certain and there are no criteria to determine which patients can safely be considered negative. We aimed to determine the proportion of patients with positive LA or APLA who remained positive at least 2 years after initial confirmation. Methods. We retrospectively reviewed a cohort of patients with positive LA and APLA evaluated at the Thrombosis Clinic of the London Health Sciences Centre (London, Ontario, Canada) between 1998 and 2016 and who had repeat LA/APLA tests done at least 2 years after the initial LA/APLA positive confirmation. LA testing was done as per the International Society on Thrombosis and Haemostasis criteria available at the time of testing, using dilute Russell viper venom time screening and confirmatory tests in all cases. APLA testing was done using commercial enzyme-linked immunosorbent assays (Louisville APL Diagnostics Inc. or Inova Diagnostics Inc.), according to the manufacturers' instructions. Results. We included 73 patients (39 [53.4%] female). The average age at diagnosis of LA or APLA was 49.3 years. The average follow-up was 103.1 months (range 24 to 218 months). At diagnosis, 57 (78%) patients had a VTE (26 deep vein thrombosis [DVT], 16 pulmonary embolism [PE], 17 both DVT and PE), 10 had a stroke or transient ischemic attack (TIA) and 3 myocardial infarction (MI). Warfarin was the most common long-term anticoagulant used (66 of 73 patients). Nine patients were treated with rivaroxaban, 5 with LMWH, and 1 patient was treated with edoxaban. A total of 4 patients did not require anticoagulant therapy. Eleven (15.1%) patients suffered a recurrent thrombotic event while on anticoagulant therapy, (5 DVT, 5 PE, 1 DVT and PE). Nine of the recurrent events occurred while the patient was being treated with warfarin. Four of the 40 female patients suffered at least one miscarriage. One patient died while being followed due to complications from renal failure. The mean time between the first positive test and the first confirmatory test was 8.9 months (range 3 to 132), whereas the mean time between the first confirmatory test and the first repeat test was 68.9 months (range 24 to 207). Thirty-seven (50.6%) patients were negative on the second repeat test. All of them remained on anticoagulants. Conclusion. Our results suggest that up to 50% of patients became negative for LA and/or APLA at least 2 years after initial positivity, particularly if only one type of test was positive at diagnosis. The clinical relevance of this result is not certain including implications about discontinuing anticoagulant therapy. Further research in this relevant matter is warranted. Table Table. Disclosures Lazo-Langner: Pfizer: Honoraria; Bayer: Honoraria; Daiichi Sankyo: Research Funding. Louzada:Pfizer: Honoraria; Janssen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Bayer: Honoraria. Kovacs:Daiichi Sankyo Pharma: Research Funding; LEO Pharma: Honoraria; Bayer: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding.


2022 ◽  
Vol 10 (1) ◽  
pp. 0-0

Software failure prediction is an important activity during agile software development as it can help managers to identify the failure modules. Thus, it can reduce the test time, cost and assign testing resources efficiently. RapidMiner Studio9.4 has been used to perform all the required steps from preparing the primary data to visualizing the results and evaluating the outputs, as well as verifying and improving them in a unified environment. Two datasets are used in this work, the results for the first one indicate that the percentage of failure to predict the time used in the test is for all 181 rows, for all test times recorded, is 3% for Mean time between failures (MTBF). Whereas, SVM achieved a 97% success in predicting compared to previous work whose results indicated that the use of Administrative Delay Time (ADT) achieved a statistically significant overall success rate of 93.5%. At the same time, the second dataset result indicates that the percentage of failure to predict the time used is 1.5% for MTBF, SVM achieved 98.5% prediction.


Author(s):  
Eric Tchetgen Tchetgen

AbstractThe risk ratio effect measure is often the main parameter of interest in epidemiologic studies with a binary outcome. In this paper, the author presents a simple and efficient two-stage approach to estimate the risk ratios directly, which does not directly rely on consistency for an estimate of the baseline risk. This latter property is a key advantage of the approach over existing methods, because, unlike these other methods, the proposed approach obviates the need to restrict the predicted risk probabilities to fall below one, in order to recover efficient inferences about risk ratios. An additional appeal of the approach is that it is easy to implement. Finally, when the primary interest is in the effect of a specific binary exposure, a simple doubly robust closed-form estimator is derived, for the multiplicative effect of the exposure. Specifically, we show how one can adjust for confounding by incorporating a working regression model for the propensity score so that the correct inferences about the multiplicative effect of the exposure are recovered if either this model is correct or a working model for the association between confounders and outcome risk is correct, but both do not necessarily hold.


Author(s):  
Joshua G Petrie ◽  
Latifa A Bazzi ◽  
Adrian B McDermott ◽  
Dean Follmann ◽  
Dominic Esposito ◽  
...  

Abstract Background We investigated frequency of reinfection with seasonal coronaviruses (HCoV) and serum antibody response following infection over 8 years in the Household Influenza Vaccine Evaluation cohort. Methods Households were followed annually for identification of acute respiratory illness with RT-PCR confirmed HCoV infection. Serum collected before and at two time points post infection were tested using a multiplex binding assay to quantify antibody to seasonal, SARS-CoV-1, and SARS-CoV-2 spike proteins and SARS-CoV-2 spike sub-domains and N protein. Results Of 3418 participants, 40% were followed for ≥3years. A total of 1004 HCoV infections were documented; 303 (30%) were reinfections of any HCoV type. The number of HCoV infections ranged from 1 to 13 per individual. The mean time to reinfection with the same type was estimated at 983 days for 229E, 578 days for HKU1, 615 days for OC43, and 711 days for NL63. Binding antibody levels to seasonal HCoVs were high, with little increase post-infection, and were maintained over time. Homologous, pre-infection antibody levels did not significantly correlate with odds of infection, and there was little cross response to SARS-CoV-2 proteins. Conclusions Reinfection with seasonal HCoVs is frequent. Binding anti-spike protein antibodies do not correlate with protection from seasonal HCoV infection.


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