<b><i>Background:</i></b> Variable responses to hypothermic neuroprotection are related to the clinical heterogeneity of encephalopathic babies; hence better disease stratification may facilitate the development of individualized neuroprotective therapies. <b><i>Objectives:</i></b> We examined if whole blood gene expression analysis can identify specific transcriptome profiles in neonatal encephalopathy. <b><i>Material and Methods:</i></b> We performed next-generation sequencing on whole blood RNA from 12 babies with neonatal encephalopathy and 6 time-matched healthy term babies. Genes significantly differentially expressed between encephalopathic and control babies were identified. This set of genes was then compared to the host RNA response in septic neonates and subjected to pathway analysis. <b><i>Results:</i></b> We identified 950 statistically significant genes discriminating perfectly between healthy controls and neonatal encephalopathy. The major pathways in neonatal encephalopathy were axonal guidance signaling (<i>p</i> = 0.0009), granulocyte adhesion and diapedesis (<i>p</i> = 0.003), IL-12 signaling and production in macrophages (<i>p</i> = 0.003), and hypoxia-inducible factor 1α signaling (<i>p</i> = 0.004). There were only 137 genes in common between neonatal encephalopathy and bacterial sepsis sets. <b><i>Conclusion:</i></b> Babies with neonatal encephalopathy have striking differences in gene expression profiles compared with healthy control and septic babies. Gene expression profiles may be useful for disease stratification and for developing personalized neuroprotective therapies.
Transcriptome analyses have increased our understanding of the molecular mechanisms underlying human diseases. Most approaches aim to identify significant genes by comparing their expression values between healthy subjects and a group of patients with a certain disease. Given that studies normally contain few samples, the heterogeneity among individuals caused by environmental factors or undetected illnesses can impact gene expression analyses. We present a systematic analysis of sample heterogeneity in a variety of gene expression studies relating to inflammatory and infectious diseases and show that novel immunological insights may arise once heterogeneity is addressed. The perturbation score of samples is quantified using nonperturbed subjects (i.e., healthy subjects) as a reference group. Such a score allows us to detect outlying samples and subgroups of diseased patients and even assess the molecular perturbation of single cells infected with viruses. We also show how removal of outlying samples can improve the "signal" of the disease and impact detection of differentially expressed genes. The method is made available via the mdp Bioconductor R package and as a user-friendly webtool, webMDP, available at http://mdp.sysbio.tools.
from baseline, 1.8 [0.8]; from 1 year, -0.003 [0.6]).Adjusted mean between-group difference in change from baseline was -0.03 (95% CI, -0.25 to 0.19; P = .79)and from 1 year was -0.03 (95% CI, -0.23 to 0.17; P = .76).No between-group differences were found in the secondary outcomes (Table 2).Discussion | To our knowledge, this is the first randomized trial to evaluate long-term outcomes of CTS surgery.After a mean follow-up of 12.8 years after CTS surgery, there were no significant differences between open and endoscopic carpal tunnel release.The large symptom and functional improvements and high level of patient satisfaction achieved with surgery were durable and few patients had undergone further surgery.Study limitations include a single institution in Sweden and unknown generalizability.Our long-term follow-up was limited to patient-reported outcomes, which are central in CTS and were consistent across several measures with established reliability and validity.The results should help clinicians and patients in making treatment decisions.
A low procalcitonin (PCT) concentration facilitates exclusion of bacterial co-infections in COVID-19, but high costs associated with PCT measurements preclude universal adoption. Changes in inflammatory markers, including C-reactive protein (CRP), can be concordant, and predicting low PCT concentrations may avoid costs of redundant tests and support more cost-effective deployment of this diagnostic biomarker.To explore whether, in COVID-19, low PCT values could be predicted by the presence of low CRP concentrations.Unselected cohort of 224 COVID-19 patients admitted to hospital that underwent daily PCT and CRP measurements as standard care. Both 0.25 ng/mL and 0.5 ng/mL were used as cut-offs for positive PCT test results. Geometric mean was used to define high and low CRP values at each timepoint assessed.Admission PCT was <0.25 ng/mL in 160/224 (71.4%), 0.25-0.5 ng/mL in 27 (12.0%) and >0.5 ng/mL in 37 (16.5%). Elevated PCT was associated with increased risk of death (P = 0.0004) and was more commonly associated with microbiological evidence of bacterial co-infection (P < 0.0001). For high CRP values, significant heterogeneity in PCT measurements was observed, with maximal positive predictive value of 50% even for a PCT cut-off of 0.25 ng/mL. In contrast, low CRP was strongly predictive of low PCT concentrations, particularly <0.5 ng/mL, with a negative predictive value of 97.6% at time of hospital admission and 100% 48 hours into hospital stay.CRP-guided PCT testing algorithms can reduce unnecessary PCT measurement and costs, supporting antimicrobial stewardship strategies in COVID-19.
COVID-19 is infrequently complicated by bacterial co-infection, but antibiotic prescriptions are common. We used community-acquired pneumonia (CAP) as a benchmark to define the processes that occur in bacterial pulmonary infections, testing the hypothesis that baseline inflammatory markers and their response to antibiotic therapy could distinguish bacterial co-infection from COVID-19.Retrospective cohort study of CAP (lobar consolidation on chest radiograph) and COVID-19 (PCR detection of SARS-CoV-2) patients admitted to Royal Free Hospital (RFH) and Barnet Hospital (BH), serving as independent discovery and validation cohorts. All CAP and >90% COVID-19 patients received antibiotics on hospital admission.We identified 106 CAP and 619 COVID-19 patients at RFH. Compared with COVID-19, CAP was characterized by elevated baseline white cell count (WCC) [median 12.48 (IQR 8.2-15.3) versus 6.78 (IQR 5.2-9.5) ×106 cells/mL, P < 0.0001], C-reactive protein (CRP) [median 133.5 (IQR 65-221) versus 86.0 (IQR 42-160) mg/L, P < 0.0001], and greater reduction in CRP 48-72 h into admission [median ΔCRP -33 (IQR -112 to +3.5) versus +14 (IQR -15.5 to +70.5) mg/L, P < 0.0001]. These observations were recapitulated in the independent validation cohort at BH (169 CAP and 181 COVID-19 patients). A multivariate logistic regression model incorporating WCC and ΔCRP discriminated CAP from COVID-19 with AUC 0.88 (95% CI 0.83-0.94). Baseline WCC >8.2 × 106 cells/mL or falling CRP identified 94% of CAP cases, and excluded bacterial co-infection in 46% of COVID-19 patients.We propose that in COVID-19, absence of both elevated baseline WCC and antibiotic-related decrease in CRP can exclude bacterial co-infection and facilitate antibiotic stewardship efforts.
In this Journal, Rossotti and colleagues provided early data on tocilizumab utility in COVID-191Rossotti R. Travi G. Ughi N. et al.Safety and efficacy of anti-il6-receptor tocilizumab use in severe and critical patients affected by coronavirus disease 2019: a comparative analysis.J Infect. 2020; 81: e11-e17https://doi.org/10.1016/j.jinf.2020.07.008Abstract Full Text Full Text PDF PubMed Scopus (88) Google Scholar, later confirmed in randomised studies2RECOVERY Collaborative GroupTocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.Lancet. 2021; 397: 1637-1645https://doi.org/10.1016/S0140-6736(21)00676-0Abstract Full Text Full Text PDF PubMed Scopus (1192) Google Scholar. Tocilizumab-mediated inhibition of IL-6 signalling can decrease CRP concentrations1Rossotti R. Travi G. Ughi N. et al.Safety and efficacy of anti-il6-receptor tocilizumab use in severe and critical patients affected by coronavirus disease 2019: a comparative analysis.J Infect. 2020; 81: e11-e17https://doi.org/10.1016/j.jinf.2020.07.008Abstract Full Text Full Text PDF PubMed Scopus (88) Google Scholar, potentially confounding the diagnosis of bacterial co-infections in COVID-19 that occur more frequently following longer hospital stays and admissions to the intensive care unit (ICU)3Langford B.J. So M. Raybardhan S. et al.Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis.Clin Microbiol Infect. 2020; 26: 1622-1629https://doi.org/10.1016/j.cmi.2020.07.016Abstract Full Text Full Text PDF PubMed Scopus (916) Google Scholar, 4Russell C.D. Fairfield C.J. Drake T.M. et al.Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study.Lancet Microbe. June 2021; https://doi.org/10.1016/S2666-5247(21)00090-2Abstract Full Text Full Text PDF PubMed Scopus (196) Google Scholar, 5Mason C.Y. Kanitkar T. Richardson C.J. et al.Exclusion of bacterial co-infection in COVID-19 using baseline inflammatory markers and their response to antibiotics.J Antimicrob Chemother. January 2021; https://doi.org/10.1093/jac/dkaa563Crossref PubMed Scopus (31) Google Scholar. In inflammatory arthritides, serial tocilizumab dosing variably attenuates CRP responses following bacterial infections6Lang V.R. Englbrecht M. Rech J. et al.Risk of infections in rheumatoid arthritis patients treated with tocilizumab.Rheumatology (Oxford). 2012; 51: 852-857https://doi.org/10.1093/rheumatology/ker223Crossref PubMed Scopus (92) Google Scholar, but the effect following single-dose use in COVID-19 is not defined2RECOVERY Collaborative GroupTocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial.Lancet. 2021; 397: 1637-1645https://doi.org/10.1016/S0140-6736(21)00676-0Abstract Full Text Full Text PDF PubMed Scopus (1192) Google Scholar,7Bell L.C.K. Meydan C. Kim J. et al.Transcriptional response modules characterize IL-1β and IL-6 activity in COVID-19.iScience. 2021; 24101896https://doi.org/10.1016/j.isci.2020.101896Abstract Full Text Full Text PDF PubMed Scopus (26) Google Scholar. In a small COVID-19 cohort with blood stream infections (BSIs) that had received tocilizumab, CRP was reduced but remained detectable at the time of BSI diagnosis8Giacobbe D.R. Battaglini D. Ball L. et al.Bloodstream infections in critically ill patients with COVID-19.Eur J Clin Invest. 2020; 50: e13319https://doi.org/10.1111/eci.13319Crossref PubMed Scopus (194) Google Scholar. However, CRP kinetics related to BSI were not assessed, and thus the utility of CRP to guide antibiotic prescribing in this context remains unknown5Mason C.Y. Kanitkar T. Richardson C.J. et al.Exclusion of bacterial co-infection in COVID-19 using baseline inflammatory markers and their response to antibiotics.J Antimicrob Chemother. January 2021; https://doi.org/10.1093/jac/dkaa563Crossref PubMed Scopus (31) Google Scholar,9Seaton R.A. Gibbons C.L. Cooper L. et al.Survey of antibiotic and antifungal prescribing in patients with suspected and confirmed COVID-19 in Scottish hospitals.J Infect. 2020; 81: 952-960https://doi.org/10.1016/j.jinf.2020.09.024Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar. We addressed this question by testing the hypothesis that a single dose of tocilizumab for COVID-19 retained CRP responses to bacterial infections, as modelled by BSIs. We identified patients admitted to Royal Free Hospital (RFH) between 01/03/2020 and 01/02/2021, aged >18 years and diagnosed with COVID-19 by RT-PCR detection of SARS-CoV-2 from nasopharyngeal swabs. Tocilizumab use originated from routine clinical care delivery or randomised clinical trials after unblinding. COVID-19 associated BSIs were defined by isolation in blood cultures of any bacteria, excluding coagulase negative staphylococci, between 14 days prior to and 60 days after COVID-19 diagnosis. We excluded patients that developed BSIs prior to receiving tocilizumab. To assess dynamic CRP responses, we included only patients with blood parameter measurements performed at least 3 days prior to the onset of BSIs. Clinical, laboratory and drug data extraction, and statistical analyses were performed as previously described5Mason C.Y. Kanitkar T. Richardson C.J. et al.Exclusion of bacterial co-infection in COVID-19 using baseline inflammatory markers and their response to antibiotics.J Antimicrob Chemother. January 2021; https://doi.org/10.1093/jac/dkaa563Crossref PubMed Scopus (31) Google Scholar. The study was approved by the Research and Innovation Group at RFH, which stated that as this was a retrospective review of routine clinical data, formal ethics approval was not required. Within the COVID-19 patients that met our inclusion criteria, 107 had received tocilizumab, 17 of whom then developed a BSI during their hospital admission (Table 1). A separate cohort of 55 COVID-19 patients developed a BSI but had not received tocilizumab (Table 1). Tocilizumab use preceding BSIs was more commonly associated with ICU admission, but the BSI organisms were comparable between the groups (Table 1). In the first week after tocilizumab administration we observed a rapid fall in CRP (Fig. 1A), but not for total white cell, neutrophil or lymphocyte counts (Fig. 1A & fig S1). The CRP reduction following tocilizumab was short lived, with CRP concentrations rising within 21 days of tocilizumab receipt (Fig. 1A). To exclude confounding by bacterial co-infection, a sensitivity analysis on 90 patients that did not develop a BSI following tocilizumab also showed an early reduction followed by a rebound in CRP (fig S2A). A similar pattern was evident in patients that developed a BSI, although CRP concentrations showed less attenuation and greater heterogeneity within the 21-day period since tocilizumab administration (fig S2B).Table 1Baseline demographics and clinical characteristics for patients included in the study.No BSI & received tocilizumab(n = 90)BSI & received tocilizumab(n = 17)BSI & did not receive tocilizumab(n = 55)p value*relates to statistical comparison between COVID-19 patients who did or did not receive tocilizumab prior to the onset of BSI. Mann–Whitney test was used to compare age, Fisher's exact test was used to compare gender and microbiology results, and Chi-square test was used to compare ethnicity and Charlson co-morbidities.Age, years, median (range)63 (28–90)61 (50–78)63 (31–100)p = 0.383Gender, n (%)MaleFemale56 (62)34 (38)9 (53)8 (47)38 (69)17 (31)p = 0.253Ethnicity, n (%)WhiteBlackAsianMixedOther33 (42)7 (9)15 (19)2 (3)21 (27)4 (31)3 (23)4 (31)1 (8)1 (8)27 (55)7 (14)7 (14)0 (0)8 (16)p = 0.101Charlson co-morbidity score, n (%)0123+57 (63)25 (28)6 (7)2 (2)4 (24)11 (65)1 (6)1 (6)27 (49)17 (31)7 (13)4 (7)p = 0.095ICU admission, n (%)YesNo52 (58)38 (42)17 (100)0 (0)39 (72)15 (28)p = 0.015Corticosteroid use, n (%)YesNo79 (89)10 (11)15 (88)2 (12)35 (65)19 (35)p = 0.076BSI organism, n (%)Gram-negative bacilliEnterococcus sp.Staphylococcus aureusOtherN/A10 (40)2 (8)4 (16)1 (4)32 (62)12 (23)7 (13)1 (2)p = 0.507BSI = blood stream infection. relates to statistical comparison between COVID-19 patients who did or did not receive tocilizumab prior to the onset of BSI. Mann–Whitney test was used to compare age, Fisher's exact test was used to compare gender and microbiology results, and Chi-square test was used to compare ethnicity and Charlson co-morbidities. Open table in a new tab BSI = blood stream infection. To test the hypothesis that CRP would rise following a BSI independent of prior tocilizumab administration, we compared CRP responses in 17 patients that had received tocilizumab prior to a BSI with 55 patients who had not received tocilizumab. Strikingly, in both cohorts, BSIs resulted in clear CRP elevations (Figs. 1B & 1C). We calculated the change in CRP across the time of BSI onset to quantitatively compare this CRP rise. As blood samples were not collected daily in all patients, we derived paired sampling by calculating maximal CRP values 2 or 3 days prior to BSI-detecting blood culture collection and maximal CRP up to 2 days after BSI. This approach revealed an increase in CRP following BSI in 76.5% and 75.0% of patients that had or had not received tocilizumab respectively (Fig. 1D). Moreover, there was no difference in CRP increase between the groups (median CRP change +88 mg/L vs +76 mg/L respectively, p = 0.67 by Mann-Whitney test). As patients developed BSIs at varying times following receipt of tocilizumab, we tested the hypothesis that BSI-induced CRP increment would be proportional to the time interval between tocilizumab administration and BSI onset. However, in the 17 patients that both received tocilizumab and subsequently developed a BSI, no relationship was observed between the length of the tocilizumab-BSI interval and the change in CRP (r = 0.1069, p = 0.6811 by Rank-spearman correlation) (Fig. 1E). By inhibiting IL-6 signalling, tocilizumab may impact CRP-guided antibiotic prescribing decisions5Mason C.Y. Kanitkar T. Richardson C.J. et al.Exclusion of bacterial co-infection in COVID-19 using baseline inflammatory markers and their response to antibiotics.J Antimicrob Chemother. January 2021; https://doi.org/10.1093/jac/dkaa563Crossref PubMed Scopus (31) Google Scholar,9Seaton R.A. Gibbons C.L. Cooper L. et al.Survey of antibiotic and antifungal prescribing in patients with suspected and confirmed COVID-19 in Scottish hospitals.J Infect. 2020; 81: 952-960https://doi.org/10.1016/j.jinf.2020.09.024Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar. However, we demonstrate that prior administration of a single dose of tocilizumab does not attenuate CRP responses following a BSI, retaining the utility of this biomarker to diagnose bacterial co-infections associated with COVID-19. These findings have important implications for tocilizumab-treated COVID-19 patients: first, clinically-indicated antibiotic prescriptions are unlikely to be delayed, and second, low CRP levels alone are not an indication for continued prescription of unnecessary antibiotics, supporting stewardship efforts. Nevertheless, BSI onset did not initiate CRP elevations in all patients, irrespective of prior tocilizumab use, emphasising that CRP is only one contributor to diagnosing incipient bacterial infections. Despite preserved CRP responses to BSI, tocilizumab transiently reduced baseline CRP levels, mostly recovering within 21 days. Furthermore, BSI-associated CRP increments were unrelated to time since tocilizumab, indicating that single tocilizumab dosing may not completely neutralise IL-6 responses10Spencer S. Köstel Bal S. Egner W. et al.Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses.J Exp Med. 2019; 216: 1986-1998https://doi.org/10.1084/jem.20190344Crossref PubMed Scopus (136) Google Scholar, although a role for IL-6-independent CRP stimuli cannot be excluded. Measuring IL-6 signalling activity in vivo may predict attenuation of CRP responses and also inform the need for further tocilizumab dosing in COVID-197Bell L.C.K. Meydan C. Kim J. et al.Transcriptional response modules characterize IL-1β and IL-6 activity in COVID-19.iScience. 2021; 24101896https://doi.org/10.1016/j.isci.2020.101896Abstract Full Text Full Text PDF PubMed Scopus (26) Google Scholar. Our study was limited by its single-centre and retrospective nature, constraining patient numbers and negating correction for potential confounders. Nevertheless, increased frequency of corticosteroid use in tocilizumab recipients could have further attenuated CRP responses, counter to our observations. BSIs provided a standardised definition for bacterial infections, but limited extrapolation to non-BSI settings, an area of required future work to confirm the generalisability of our findings. In conclusion, we show that tocilizumab use in severe COVID-19 preserves elevations in CRP concentration following the onset of a confirmed bacterial co-infection, as modelled by BSIs. Use of tocilizumab should not negate judicious, CRP-guided use of antibiotics in COVID-19. EQW, IB, SB and GP conceived the study. EQW, CB, AN, BOF, JP, ML, SY, SH, DM, MS and GP collected and analysed the data. EQW, SB and GP drafted the manuscript. All authors reviewed and approved the final version of the manuscript. We declare that all authors have no conflicts of interest No external funding supported this work.
Abstract Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK 1 . Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children.
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