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1.
Genome Med ; 14(1): 18, 2022 02 21.
Article in English | MEDLINE | ID: covidwho-1688773

ABSTRACT

BACKGROUND: Measuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. However, there is little information to indicate how the performance of various published signatures compare to one another. METHODS: This systematic comparison of host gene expression signatures evaluated the performance of 28 signatures, validating them in 4589 subjects from 51 publicly available datasets. Thirteen COVID-specific datasets with 1416 subjects were included in a separate analysis. Individual signature performance was evaluated using the area under the receiving operating characteristic curve (AUC) value. Overall signature performance was evaluated using median AUCs and accuracies. RESULTS: Signature performance varied widely, with median AUCs ranging from 0.55 to 0.96 for bacterial classification and 0.69-0.97 for viral classification. Signature size varied (1-398 genes), with smaller signatures generally performing more poorly (P < 0.04). Viral infection was easier to diagnose than bacterial infection (84% vs. 79% overall accuracy, respectively; P < .001). Host gene expression classifiers performed more poorly in some pediatric populations (3 months-1 year and 2-11 years) compared to the adult population for both bacterial infection (73% and 70% vs. 82%, respectively; P < .001) and viral infection (80% and 79% vs. 88%, respectively; P < .001). We did not observe classification differences based on illness severity as defined by ICU admission for bacterial or viral infections. The median AUC across all signatures for COVID-19 classification was 0.80 compared to 0.83 for viral classification in the same datasets. CONCLUSIONS: In this systematic comparison of 28 host gene expression signatures, we observed differences based on a signature's size and characteristics of the validation population, including age and infection type. However, populations used for signature discovery did not impact performance, underscoring the redundancy among many of these signatures. Furthermore, differential performance in specific populations may only be observable through this type of large-scale validation.


Subject(s)
Bacterial Infections/diagnosis , Datasets as Topic/statistics & numerical data , Host-Pathogen Interactions/genetics , Transcriptome , Virus Diseases/diagnosis , Adult , Bacterial Infections/epidemiology , Bacterial Infections/genetics , Biomarkers/analysis , COVID-19/diagnosis , COVID-19/genetics , Child , Cohort Studies , Diagnosis, Differential , Gene Expression Profiling/statistics & numerical data , Genetic Association Studies/statistics & numerical data , Humans , Publications/statistics & numerical data , SARS-CoV-2/pathogenicity , Validation Studies as Topic , Virus Diseases/epidemiology , Virus Diseases/genetics
2.
West J Emerg Med ; 23(5): 754-759, 2022 Aug 10.
Article in English | MEDLINE | ID: covidwho-2056168

ABSTRACT

INTRODUCTION: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the coronavirus disease 2019 (COVID-19) pandemic that drastically impacted the United States. The evidence was not clear on how SARS-CoV-2 infection impacted children, given the high prevalence of SAR-CoV-2 infection. Febrile infants less than 60 days old are an ongoing challenge to risk-stratify for serious bacterial infection (SBI), including urinary tract infection (UTI), bacteremia, and meningitis. We hypothesized there would be a lower rate of SBI in SARS-CoV-2 positive febrile infants compared to those SARS-CoV-2 negative. METHODS: This was a retrospective chart review with a nested, age-matched, case-control study performed from March 2020-June 2021. Infants less than 60 days old presenting with fever were assigned groups based on SARS-CoV-2 infection. Blood, urine, and cerebrospinal fluid cultures were used as the gold standard to diagnose SBI. We compared overall rate of SBI as well as individual rates of SBI between each group. We performed a subgroup analysis evaluating the age group 29-60 days old. RESULTS: A total of 164 subjects met criteria for analysis: 30 COVID-19 positive and 134 COVID-19 negative subjects. Rate of SBI was 17.9% (95% confidence interval [CI]: 11.8-25.5%) in the COVID-19 negative group compared to 0% (95% CI: 0.0%-11.1%) in the COVID-19 group, which demonstrated statistical significance (p = 0.008). In the age-matched data, we found statistical significance for any SBI (p = <0.001). For individual rates of SBI, we found statistical significance for UTI (p = <0.001) and bacteremia (p = <0.001). The 29-60 days-old subgroup analysis did not achieve statistical significance (p = 0.11). CONCLUSION: This study demonstrated the utility of including SARS-CoV-2 infection as part of the risk stratification of febrile infants less than 60 days old. While overall there is a low incidence of bacteremia and meningitis in this age group, these results can contribute to existing literature and potentially help decrease invasive testing and exposure to broad-spectrum antibiotics.


Subject(s)
Bacteremia , Bacterial Infections , COVID-19 , Meningitis , Urinary Tract Infections , Anti-Bacterial Agents , Bacteremia/epidemiology , Bacteremia/microbiology , Bacterial Infections/diagnosis , Bacterial Infections/epidemiology , Bacterial Infections/microbiology , Case-Control Studies , Child , Fever/diagnosis , Humans , Infant , Infant, Newborn , Meningitis/complications , Meningitis/microbiology , Retrospective Studies , SARS-CoV-2 , Urinary Tract Infections/diagnosis , Urinary Tract Infections/epidemiology
3.
Acta Med Indones ; 54(2): 161-169, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1929381

ABSTRACT

BACKGROUND: Data on secondary bacterial infection in patients with COVID-19 in Indonesia are still limited, while the use of empirical antibiotics continues to increase. This study aims to determine the secondary bacterial infection rate in hospitalized COVID-19 patients and factors related to secondary bacterial infection. METHODS: This is a retrospective cohort study on hospitalized COVID-19 patients undergoing treatment at Cipto Mangunkusumo Hospital from March 2020 to September 2020. Secondary bacterial infection is defined as the identification of a bacterial pathogen from a microbiological examination. RESULTS: From a total of 255 subjects, secondary infection was identified in 14.5%. Predictors of secondary infection were early symptoms of shortness of breath (OR 5.31, 95% CI 1.3 - 21.5), decreased consciousness (OR 4.81, 95% CI 1.77 - 13.0), length of stay > 12 days (OR 8.2, 95% CI 2.9 - 23.3), and central venous catheter placement (OR 3.0, 95% CI 1.1 - 8.0) The most common pathogen of secondary bacterial infection is Acinetobacter sp. (n=9; 28%). Empirical antibiotics were administered to 82.4% of subjects with predominant use of macrolides (n=141; 32.4%). CONCLUSION: The secondary bacterial infection rate in COVID-19 was 14.5% and is associated with dyspnea, decreased consciousness, length of stay >12 days, and central venous catheter placement. The use of antibiotics in COVID-19 reaches 82.4% and requires special attention to prevent the occurrence of antibiotic resistance.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Anti-Bacterial Agents/therapeutic use , Bacteria , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Coinfection/drug therapy , Humans , Retrospective Studies , Tertiary Care Centers
4.
J Infect ; 85(4): 374-381, 2022 10.
Article in English | MEDLINE | ID: covidwho-1914623

ABSTRACT

BACKGROUND: Procalcitonin (PCT) and C-Reactive Protein (CRP) are useful biomarkers to differentiate bacterial from viral or fungal infections, although the association between them and co-infection or mortality in COVID-19 remains unclear. METHODS: The study represents a retrospective cohort study of patients admitted for COVID-19 pneumonia to 84 ICUs from ten countries between (March 2020-January 2021). Primary outcome was to determine whether PCT or CRP at admission could predict community-acquired bacterial respiratory co-infection (BC) and its added clinical value by determining the best discriminating cut-off values. Secondary outcome was to investigate its association with mortality. To evaluate the main outcome, a binary logistic regression was performed. The area under the curve evaluated diagnostic performance for BC prediction. RESULTS: 4635 patients were included, 7.6% fulfilled BC diagnosis. PCT (0.25[IQR 0.1-0.7] versus 0.20[IQR 0.1-0.5]ng/mL, p<0.001) and CRP (14.8[IQR 8.2-23.8] versus 13.3 [7-21.7]mg/dL, p=0.01) were higher in BC group. Neither PCT nor CRP were independently associated with BC and both had a poor ability to predict BC (AUC for PCT 0.56, for CRP 0.54). Baseline values of PCT<0.3ng/mL, could be helpful to rule out BC (negative predictive value 91.1%) and PCT≥0.50ng/mL was associated with ICU mortality (OR 1.5,p<0.001). CONCLUSIONS: These biomarkers at ICU admission led to a poor ability to predict BC among patients with COVID-19 pneumonia. Baseline values of PCT<0.3ng/mL may be useful to rule out BC, providing clinicians a valuable tool to guide antibiotic stewardship and allowing the unjustified overuse of antibiotics observed during the pandemic, additionally PCT≥0.50ng/mL might predict worsening outcomes.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Procalcitonin , Respiratory Tract Infections , Bacterial Infections/diagnosis , Biomarkers , C-Reactive Protein/analysis , COVID-19/diagnosis , Coinfection/diagnosis , Humans , Predictive Value of Tests , ROC Curve , Retrospective Studies
5.
J Paediatr Child Health ; 58(9): 1623-1628, 2022 09.
Article in English | MEDLINE | ID: covidwho-1901788

ABSTRACT

AIM: This study aimed to evaluate the usefulness and accuracy of the delta neutrophil index (DNI), an index expressing the number of immature granulocytes as a proportion of the total, as an inflammatory marker in predicting serious bacterial infections (SBIs). METHODS: Paediatric patients admitted to our hospital with fever were divided into four groups: SBI, non-SBI, COVID-19 and control group. White blood cell count, absolute neutrophil count, C-reactive protein and the DNI were recorded, and their accuracy in predicting SBI was evaluated. RESULTS: Mean DNI was 4.96 ± 8.38 in the SBI group (150 patients), 0.67 ± 1.68 in the non-SBI group (397 patients), 0.29 ± 0.99 in the COVID-19 group (112 patients) and 0.14 ± 0.21 in the control group (102 patients). The DNI was significantly higher in the SBI group compared with the non-SBI (P < 0.001); the non-SBI group also had higher levels than the COVID-19 group (P = 0.005). One percent increase in the DNI increased the SBI rate 1.36 times (odds ratio 1.36 (95% confidence interval 1.23-1.49), P < 0.001). Based on the determined cut-off value (>2.5%), the DNI (odds ratio 6.27 (95% confidence interval 3.85-10.21), P < 0.001) significantly predicted SBIs with 90.4% specificity and 47.7% sensitivity. CONCLUSIONS: SBIs in childrenare associated with an increase in DNI levels. Compared to other biomarkers, the DNI had higher specificity in predicting SBIs. The DNI may also be usefulin differentiating bacterial and non-bacterial infections in individualclinical syndromes. Currently, there is no evidence that serum DNI aids indifferentiating COVID-19 and upper respiratory tract infection.


Subject(s)
Bacterial Infections , COVID-19 , Bacterial Infections/diagnosis , Biomarkers , COVID-19/diagnosis , Child , Humans , Leukocyte Count , Neutrophils , Retrospective Studies
7.
Infection ; 50(5): 1243-1253, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1821023

ABSTRACT

OBJECTIVE: The aim of our study was to build a predictive model able to stratify the risk of bacterial co-infection at hospitalization in patients with COVID-19. METHODS: Multicenter observational study of adult patients hospitalized from February to December 2020 with confirmed COVID-19 diagnosis. Endpoint was microbiologically documented bacterial co-infection diagnosed within 72 h from hospitalization. The cohort was randomly split into derivation and validation cohort. To investigate risk factors for co-infection univariable and multivariable logistic regression analyses were performed. Predictive risk score was obtained assigning a point value corresponding to ß-coefficients to the variables in the multivariable model. ROC analysis in the validation cohort was used to estimate prediction accuracy. RESULTS: Overall, 1733 patients were analyzed: 61.4% males, median age 69 years (IQR 57-80), median Charlson 3 (IQR 2-6). Co-infection was diagnosed in 110 (6.3%) patients. Empirical antibiotics were started in 64.2 and 59.5% of patients with and without co-infection (p = 0.35). At multivariable analysis in the derivation cohort: WBC ≥ 7.7/mm3, PCT ≥ 0.2 ng/mL, and Charlson index ≥ 5 were risk factors for bacterial co-infection. A point was assigned to each variable obtaining a predictive score ranging from 0 to 5. In the validation cohort, ROC analysis showed AUC of 0.83 (95%CI 0.75-0.90). The optimal cut-point was ≥2 with sensitivity 70.0%, specificity 75.9%, positive predictive value 16.0% and negative predictive value 97.5%. According to individual risk score, patients were classified at low (point 0), intermediate (point 1), and high risk (point ≥ 2). CURB-65 ≥ 2 was further proposed to identify patients at intermediate risk who would benefit from early antibiotic coverage. CONCLUSIONS: Our score may be useful in stratifying bacterial co-infection risk in COVID-19 hospitalized patients, optimizing diagnostic testing and antibiotic use.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Adult , Aged , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/diagnosis , Bacterial Infections/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Cohort Studies , Coinfection/diagnosis , Coinfection/epidemiology , Female , Hospitalization , Humans , Male , Retrospective Studies
8.
Diagn Microbiol Infect Dis ; 103(4): 115721, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1819473

ABSTRACT

Our objectives were to evaluate the role of procalcitonin in identifying bacterial co-infections in hospitalized COVID-19 patients and quantify antibiotic prescribing during the 2020 pandemic surge. Hospitalized COVID-19 patients with both a procalcitonin test and blood or respiratory culture sent on admission were included in this retrospective study. Confirmed co-infection was determined by an infectious diseases specialist. In total, 819 patients were included; 335 (41%) had an elevated procalcitonin (>0.5 ng/mL) and of these, 42 (13%) had an initial bacterial co-infection. Positive predictive value of elevated procalcitonin for co-infection was 13% while the negative predictive value was 94%. Ninety-six percent of patients with an elevated procalcitonin received antibiotics (median 6 days of therapy), compared to 82% with low procalcitonin (median 4 days of therapy) (adjusted OR:3.3, P < 0.001). We observed elevated initial procalcitonin in many COVID patients without concurrent bacterial co-infections which potentially contributed to antibiotic over-prescribing.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Procalcitonin , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Biomarkers , COVID-19/complications , Calcitonin , Calcitonin Gene-Related Peptide , Coinfection/epidemiology , Humans , Procalcitonin/analysis , Retrospective Studies
9.
Crit Care ; 25(1): 281, 2021 08 05.
Article in English | MEDLINE | ID: covidwho-1770564

ABSTRACT

BACKGROUND: Procalcitonin (PCT) and C-reactive protein (CRP) were previously shown to have value for the detection of secondary infections in critically ill COVID-19 patients. However, since the introduction of immunomodulatory therapy, the value of these biomarkers is unclear. We investigated PCT and CRP kinetics in critically ill COVID-19 patients treated with dexamethasone with or without tocilizumab, and assessed the value of these biomarkers to detect secondary bacterial infections. METHODS: In this prospective study, 190 critically ill COVID-19 patients were divided into three treatment groups: no dexamethasone, no tocilizumab (D-T-), dexamethasone, no tocilizumab (D+T-), and dexamethasone and tocilizumab (D+T+). Serial data of PCT and CRP were aligned on the last day of dexamethasone treatment, and kinetics of these biomarkers were analyzed between 6 days prior to cessation of dexamethasone and 10 days afterwards. Furthermore, the D+T- and D+T+ groups were subdivided into secondary infection and no-secondary infection groups to analyze differences in PCT and CRP kinetics and calculate detection accuracy of these biomarkers for the occurrence of a secondary infection. RESULTS: Following cessation of dexamethasone, there was a rebound in PCT and CRP levels, most pronounced in the D+T- group. Upon occurrence of a secondary infection, no significant increase in PCT and CRP levels was observed in the D+T- group (p = 0.052 and p = 0.08, respectively). Although PCT levels increased significantly in patients of the D+T+ group who developed a secondary infection (p = 0.0003), this rise was only apparent from day 2 post-infection onwards. CRP levels remained suppressed in the D+T+ group. Receiver operating curve analysis of PCT and CRP levels yielded area under the curves of 0.52 and 0.55, respectively, which are both markedly lower than those found in the group of COVID-19 patients not treated with immunomodulatory drugs (0.80 and 0.76, respectively, with p values for differences between groups of 0.001 and 0.02, respectively). CONCLUSIONS: Cessation of dexamethasone in critically ill COVID-19 patients results in a rebound increase in PCT and CRP levels unrelated to the occurrence of secondary bacterial infections. Furthermore, immunomodulatory treatment with dexamethasone and tocilizumab considerably reduces the value of PCT and CRP for detection of secondary infections in COVID-19 patients.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , Bacterial Infections/diagnosis , COVID-19/drug therapy , Coinfection/diagnosis , Dexamethasone/therapeutic use , Aged , C-Reactive Protein/analysis , COVID-19/complications , Critical Illness , Female , Humans , Male , Middle Aged , Netherlands , Procalcitonin/analysis , Prospective Studies
11.
Infect Dis Now ; 52(4): 208-213, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1561203

ABSTRACT

OBJECTIVES: During the COVID-19 pandemic, antibiotic use was very common. However, bacterial co-/secondary infections with coronaviruses remain largely unknown in standard wards. We aimed to investigate the characteristics of pulmonary bacterial infections associated with COVID-19 in hospitalized patients. METHODS: A retrospective monocentric observational study was conducted in Bichat hospital, France, between February 26 and April 22, 2020. All patients hospitalized in standard wards with COVID-19 (positive nasopharyngeal PCR and/or typical aspect on CT-scan) and diagnosed with pulmonary bacterial infection (positive bacteriological samples) were included. Bacteriological and clinical data were collected from the microbiology laboratories and patient's medical records. RESULTS: Twenty-three bacteriological samples from 22 patients were positive out of 2075 screened samples (1.1%) from 784 patients (2.8%). Bacterial infection occurred within a median of 10 days after COVID-19 onset. Diagnosis of pulmonary bacterial infection was suspected on increase of oxygen requirements (20/22), productive cough or modification of sputum aspect (17/22), or fever (10/22). Positive samples included 13 sputum cultures, one FilmArray® assay on sputum samples, one bronchoalveolar lavage, six blood cultures, and two pneumococcal urinary antigen tests. The most frequent bacteria were Pseudomonas aeruginosa (6/23), Staphylococcus aureus (5/23), Streptococcus pneumoniae (4/23), Enterococcus faecalis (3/23), and Klebsiella aerogenes (3/23). No Legionella urinary antigen test was positive. Four out of 496 nasopharyngeal PCR tests (0.8%) were positive for intracellular bacteria (two Bordetella pertussis and two Mycoplasma pneumonia). CONCLUSIONS: Pulmonary bacterial secondary infections and co-infections with SARS-CoV-2 are uncommon. Antibiotic use should remain limited in the management of COVID-19.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Adult , Anti-Bacterial Agents/therapeutic use , Bacteria , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , COVID-19/epidemiology , Coinfection/drug therapy , Coinfection/epidemiology , Hospitals , Humans , Pandemics , Retrospective Studies , SARS-CoV-2
12.
Int J Nanomedicine ; 16: 6575-6591, 2021.
Article in English | MEDLINE | ID: covidwho-1533527

ABSTRACT

Public awareness of infectious diseases has increased in recent months, not only due to the current COVID-19 outbreak but also because of antimicrobial resistance (AMR) being declared a top-10 global health threat by the World Health Organization (WHO) in 2019. These global issues have spiked the realization that new and more efficient methods and approaches are urgently required to efficiently combat and overcome the failures in the diagnosis and therapy of infectious disease. This holds true not only for current diseases, but we should also have enough readiness to fight the unforeseen diseases so as to avoid future pandemics. A paradigm shift is needed, not only in infection treatment, but also diagnostic practices, to overcome the potential failures associated with early diagnosis stages, leading to unnecessary and inefficient treatments, while simultaneously promoting AMR. With the development of nanotechnology, nanomaterials fabricated as multifunctional nano-platforms for antibacterial therapeutics, diagnostics, or both (known as "theranostics") have attracted increasing attention. In the research field of nanomedicine, mesoporous silica nanoparticles (MSN) with a tailored structure, large surface area, high loading capacity, abundant chemical versatility, and acceptable biocompatibility, have shown great potential to integrate the desired functions for diagnosis of bacterial infections. The focus of this review is to present the advances in mesoporous materials in the form of nanoparticles (NPs) or composites that can easily and flexibly accommodate dual or multifunctional capabilities of separation, identification and tracking performed during the diagnosis of infectious diseases together with the inspiring NP designs in diagnosis of bacterial infections.


Subject(s)
Bacterial Infections , COVID-19 , Nanoparticles , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Humans , Porosity , SARS-CoV-2 , Silicon Dioxide
13.
Am J Trop Med Hyg ; 105(6): 1519-1520, 2021 10 29.
Article in English | MEDLINE | ID: covidwho-1497591

ABSTRACT

In this study, we described the proportion of COVID-19 patients started on antibiotics empirically and the work-ups performed to diagnose bacterial superinfection. We used a retrospective cohort study design involving medical records of symptomatic, hospitalized COVID-19 patients who were admitted to these centers. A total of 481 patients were included, with a median age of 41.0 years (interquartile range, 28-58.5 years). A total of 72.1% (N = 347) of COVID-19 patients received antibiotics, either before or during admission. This is troublesome because none of the patients' bacterial culture or inflammatory markers, such as the erythrocyte sedimentation rate or C-reactive protein, were evaluated, and only 73 (15.2%) underwent radiological investigations. Therefore, national COVID-19 guidelines should emphasize the rational use of antibiotics for the treatment of COVID-19, a primarily viral disease. Integrating antimicrobial stewardship into the COVID-19 response and expanding microbiological capacities in low-income countries are indispensable. Otherwise, we risk one pandemic aggravating another.


Subject(s)
Anti-Bacterial Agents/administration & dosage , COVID-19/drug therapy , SARS-CoV-2 , Adult , Antimicrobial Stewardship , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , Cohort Studies , Ethiopia/epidemiology , Female , Humans , Male , Middle Aged , Practice Guidelines as Topic , Retrospective Studies , Superinfection/diagnosis , Superinfection/drug therapy
14.
Acc Chem Res ; 54(21): 3991-4000, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1483068

ABSTRACT

The modern healthcare system faces an unrelenting threat from microorganisms, as evidenced by global outbreaks of new viral diseases, emerging antimicrobial resistance, and the rising incidence of healthcare-associated infections (HAIs). An effective response to these threats requires rapid and accurate diagnostic tests that can identify causative pathogens at the point of care (POC). Such tests could eliminate diagnostic uncertainties, facilitating patient triaging, minimizing the empiric use of antimicrobial drugs, and enabling targeted treatments. Current standard methods, however, often fail to meet the needs of rapid diagnosis in POC settings. Culture-based assays entail long processing times and require specialized laboratory infrastructure; nucleic acid (NA) tests are often limited to centralized hospitals due to assay complexity and high costs. Here we discuss two new POC tests developed in our groups to enable the rapid diagnosis of infection. The first is nanoPCR that takes advantages of core-shell magnetoplasmonic nanoparticles (MPNs): (i) Au shell significantly accelerates thermocycling via volumetric, plasmonic light-to-heat conversion and (ii) a magnetic core enables sensitive in situ fluorescent detection via magnetic clearing. By adopting a Ferris wheel module, the system expedites multisamples in parallel with a minimal setup. When applied to COVID-19 diagnosis, nanoPCR detected SARS-CoV-2 RNA down to 3.2 copy/µL within 17 min. In particular, nanoPCR diagnostics accurately identified COVID-19 cases in clinical samples (n = 150), validating its clinical applicability. The second is a polarization anisotropy diagnostic (PAD) system that exploits the principle of fluorescence polarization (FP) as a detection modality. Fluorescent probes were designed to alter their molecular weight upon recognizing target NAs. This event modulates the probes' tumbling rate (Brownian motion), which leads to changes in FP. The approach is robust against environmental noise and benefits from the ratiometric nature of the signal readout. We applied PAD to detect clinically relevant HAI bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus). The PAD assay demonstrated detection sensitivity down to the single bacterium level and determined both drug resistance and virulence status. In summary, these new tests have the potential to become powerful tools for rapid diagnosis in the infectious disease space. They do not require highly skilled personnel or labor-intensive analyses, and the assays are quick and cost-effective. These attributes will make nanoPCR and PAD well-aligned with a POC workflow to aid physicians to initiate prompt and informed patient treatment.


Subject(s)
Bacterial Infections/diagnosis , COVID-19 Testing , COVID-19/diagnosis , Fluorescence Polarization , Nanotechnology , Polymerase Chain Reaction , Fluorescent Dyes/chemistry , Humans , Point-of-Care Systems , RNA, Viral/genetics , SARS-CoV-2/genetics
15.
Diagn Microbiol Infect Dis ; 102(2): 115576, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1474473

ABSTRACT

The frequencies of 19 respiratory pathogens other than SARS-CoV-2 were assessed in 6,"?>235 Brazilian individuals tested for COVID-19. Overall, only 83 individuals who tested positive for SARS-CoV-2 had codetection of other pathogens. Individuals infected with Rhinovirus/Enterovirus, Human Coronavirus (HCoV)-HKU1, HCoV-NL63, HPIV-4, Influenza A (-H1N1 and other subtypes), Influenza B, Human Respiratory Syncytial Virus and Human Metapneumovirus were less likely to test positive for SARS-CoV-2. Infection with Streptococcys pyogenes, Chlamydophila pneumoniae, Mycoplasma pneumoniae, and Bordetella pertussis were more frequent in individuals who tested negative for SARS-CoV-2, but without significancy. We found 150 individuals infected with ≥2 pathogens other than SARS-CoV-2, only 3 out of whom tested positive for COVID-19. The codetection frequency was low in individuals diagnosed with COVID-19. Other viral infections may provide a cross-reactive, protective immune response against SARS-CoV-2. Screening for bacterial respiratory infections upon COVID-19 testing is important to drive suitable therapeutic approaches and avoid unnecessary antibiotic prescription.


Subject(s)
Bacterial Infections/diagnosis , COVID-19 Testing , COVID-19/diagnosis , Respiratory Tract Infections/diagnosis , SARS-CoV-2/isolation & purification , Adult , Brazil , Cross Reactions , Female , Humans , Male , Mass Screening , Middle Aged , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology
16.
BMC Pulm Med ; 21(1): 308, 2021 Sep 28.
Article in English | MEDLINE | ID: covidwho-1439539

ABSTRACT

BACKGROUND: Whether procalcitonin (PCT) or C-reactive protein (CRP) combined with certain clinical characteristics can better distinguish viral from bacterial infections remains unclear. The aim of the study was to assess the ability of PCT or CRP combined with clinical characteristics to distinguish between viral and bacterial infections in hospitalized non-intensive care unit (ICU) adults with lower respiratory tract infection (LRTI). METHODS: This was a post-hoc analysis of a randomized clinical trial previously conducted among LRTI patients. The ability of PCT, CRP and PCT or CRP combined with clinical symptoms to discriminate between viral and bacterial infection were assessed by portraying receiver operating characteristic (ROC) curves among patients with only a viral or a typical bacterial infection. RESULTS: In total, 209 infected patients (viral 69%, bacterial 31%) were included in the study. When using CRP or PCT to discriminate between viral and bacterial LRTI, the optimal cut-off points were 22 mg/L and 0.18 ng/mL, respectively. When the optimal cut-off for CRP (≤ 22 mg/L) or PCT (≤ 0.18 ng/mL) combined with rhinorrhea was used to discriminate viral from bacterial LRTI, the AUCs were 0.81 (95% CI: 0.75-0.87) and 0.80 (95% CI: 0.74-0.86), which was statistically significantly better than when CRP or PCT used alone (p < 0.001). When CRP ≤ 22 mg/L, PCT ≤ 0.18 ng/mL and rhinorrhea were combined, the AUC was 0.86 (95% CI: 0.80-0.91), which was statistically significantly higher than when CRP (≤ 22 mg/L) or PCT (≤ 0.18 ng/mL) was combined with rhinorrhea (p = 0.011 and p = 0.021). CONCLUSIONS: Either CRP ≤ 22 mg/L or PCT ≤ 0.18 ng/mL combined with rhinorrhea could help distinguish viral from bacterial infections in hospitalized non-ICU adults with LRTI. When rhinorrhea was combined together, discrimination ability was further improved.


Subject(s)
C-Reactive Protein/metabolism , Procalcitonin/blood , Respiratory Tract Infections/microbiology , Rhinorrhea/complications , Virus Diseases/diagnosis , Aged , Area Under Curve , Bacterial Infections/diagnosis , Female , Hospitalization , Humans , Male , Middle Aged , ROC Curve , Respiratory Tract Infections/blood , Retrospective Studies , Virus Diseases/blood
17.
Crit Care Med ; 49(10): 1664-1673, 2021 10 01.
Article in English | MEDLINE | ID: covidwho-1452743

ABSTRACT

OBJECTIVES: The rapid diagnosis of acute infections and sepsis remains a serious challenge. As a result of limitations in current diagnostics, guidelines recommend early antimicrobials for suspected sepsis patients to improve outcomes at a cost to antimicrobial stewardship. We aimed to develop and prospectively validate a new, 29-messenger RNA blood-based host-response classifier Inflammatix Bacterial Viral Non-Infected version 2 (IMX-BVN-2) to determine the likelihood of bacterial and viral infections. DESIGN: Prospective observational study. SETTING: Emergency Department, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany. PATIENTS: Three hundred twelve adult patients presenting to the emergency department with suspected acute infections or sepsis with at least one vital sign change. INTERVENTIONS: None (observational study only). MEASUREMENTS AND MAIN RESULTS: Gene expression levels from extracted whole blood RNA was quantified on a NanoString nCounter SPRINT (NanoString Technologies, Seattle, WA). Two predicted probability scores for the presence of bacterial and viral infection were calculated using the IMX-BVN-2 neural network classifier, which was trained on an independent development set. The IMX-BVN-2 bacterial score showed an area under the receiver operating curve for adjudicated bacterial versus ruled out bacterial infection of 0.90 (95% CI, 0.85-0.95) compared with 0.89 (95% CI, 0.84-0.94) for procalcitonin with procalcitonin being used in the adjudication. The IMX-BVN-2 viral score area under the receiver operating curve for adjudicated versus ruled out viral infection was 0.83 (95% CI, 0.77-0.89). CONCLUSIONS: IMX-BVN-2 demonstrated accuracy for detecting both viral infections and bacterial infections. This shows the potential of host-response tests as a novel and practical approach for determining the causes of infections, which could improve patient outcomes while upholding antimicrobial stewardship.


Subject(s)
Bacterial Infections/diagnosis , RNA, Messenger/analysis , Virus Diseases/diagnosis , Aged , Aged, 80 and over , Area Under Curve , Bacterial Infections/blood , Bacterial Infections/physiopathology , Berlin , Biomarkers/analysis , Biomarkers/blood , Emergency Service, Hospital/organization & administration , Emergency Service, Hospital/statistics & numerical data , Female , Humans , Male , Middle Aged , Prospective Studies , RNA, Messenger/blood , ROC Curve , Virus Diseases/blood , Virus Diseases/physiopathology
19.
Crit Rev Clin Lab Sci ; 59(1): 54-65, 2022 01.
Article in English | MEDLINE | ID: covidwho-1406434

ABSTRACT

Procalcitonin (PCT) is useful for differentiating between viral and bacterial infections and for reducing the unnecessary use of antibiotics. As the rise of antimicrobial resistance reaches "alarming" levels according to the World Health Organization, the importance of using biomarkers, such as PCT to limit unnecessary antibiotic exposure has further increased. Randomized trials in patients with respiratory tract infections have shown that PCT has prognostic implications and its use, embedded in stewardship protocols, leads to reductions in the use of antibiotics in different clinical settings without compromising clinical outcomes. However, available data are heterogeneous and recent trials found no significant benefit. Still, from these trials, we have learned several key considerations for the optimal use of PCT, which depend on the clinical setting, severity of presentation, and pretest probability for bacterial infection. For patients with respiratory infections and sepsis, PCT can be used to determine whether to initiate antimicrobial therapy in low-risk settings and, together with clinical data, whether to discontinue antimicrobial therapy in certain high-risk settings. There is also increasing evidence regarding PCT-guided therapy in patients with coronavirus disease 2019 (COVID-19). This review provides an up-to-date overview of the use of PCT in different clinical settings and diseases, including a discussion about its potential to improve the care of patients with COVID-19.


Subject(s)
Bacterial Infections , COVID-19 , Sepsis , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Biomarkers , Humans , Procalcitonin , SARS-CoV-2 , Sepsis/drug therapy
20.
Arch Dis Child ; 107(3): e3, 2022 03.
Article in English | MEDLINE | ID: covidwho-1388470

ABSTRACT

OBJECTIVE: Features of multisystem inflammatory syndrome in children (MIS-C) overlap with other febrile illnesses, hindering prompt and accurate diagnosis. The objectives of this study were to identify clinical and laboratory findings that distinguished MIS-C from febrile illnesses in which MIS-C was considered but ultimately excluded, and to examine the diseases that most often mimicked MIS-C in a tertiary medical centre. STUDY DESIGN: We identified all children hospitalised with fever who were evaluated for MIS-C at our centre and compared clinical signs and symptoms, SARS-CoV-2 status and laboratory studies between those with and without MIS-C. Multivariable logistic LASSO (least absolute shrinkage and selection operator) regression was used to identify the most discriminative presenting features of MIS-C. RESULTS: We identified 50 confirmed MIS-C cases (MIS-C+) and 68 children evaluated for, but ultimately not diagnosed with, MIS-C (MIS-C-). In univariable analysis, conjunctivitis, abdominal pain, fatigue, hypoxaemia, tachypnoea and hypotension at presentation were significantly more common among MIS-C+ patients. MIS-C+ and MIS-C- patients had similar elevations in C-reactive protein (CRP), but were differentiated by thrombocytopenia, lymphopenia, and elevated ferritin, neutrophil/lymphocyte ratio, BNP and troponin. In multivariable analysis, predictors of MIS-C included age, neutrophil/lymphocyte ratio, platelets, conjunctivitis, oral mucosa changes, abdominal pain and hypotension. CONCLUSIONS: Among hospitalised children undergoing evaluation for MIS-C, children with MIS-C were older, more likely to present with conjunctivitis, oral mucosa changes, abdominal pain and hypotension, and had higher neutrophil/lymphocyte ratios and lower platelet counts. These data may be helpful for discrimination of MIS-C from other febrile illnesses, including bacterial lymphadenitis and acute viral infection, with overlapping features.


Subject(s)
COVID-19/complications , Systemic Inflammatory Response Syndrome/diagnosis , Abdominal Pain/etiology , Adolescent , Age of Onset , Bacterial Infections/diagnosis , C-Reactive Protein/metabolism , COVID-19/blood , COVID-19/diagnosis , COVID-19/pathology , Child , Child, Preschool , Conjunctivitis/etiology , Diagnosis, Differential , Female , Humans , Hypotension/etiology , Leukocyte Count , Lymphadenitis/diagnosis , Lymphocyte Count , Male , Mouth Mucosa/pathology , Neutrophils , Platelet Count , Retrospective Studies , Systemic Inflammatory Response Syndrome/blood , Systemic Inflammatory Response Syndrome/complications , Systemic Inflammatory Response Syndrome/pathology , Urinary Tract Infections/diagnosis , Virus Diseases/diagnosis
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