Viral Polymerase Chain Reaction Testing Research Articles

Antibiotic Use and Respiratory Viral PCR Testing Among Pediatric Patients With Nosocomial Fever.

Objective Pediatric patients admitted to the hospital often develop fevers during their inpatient stay, and many children are empirically started on antibiotics. The utility of respiratory viral panel (RVP) polymerase chain reaction (PCR) testing in the evaluation of nosocomial fevers in admitted patients is unclear. We sought to evaluate whether RVP testing is associated with the use of antibiotics among inpatient pediatric patients. Patients and methods We conducted a retrospective chart review of children admitted from November 2015 to June 2018. We included all patients who developed fever 48 hours or more after admission to the hospital and who were not already receiving treatment for a presumed infection (on antibiotics). Results Among 671 patients, there were 833 inpatient febrile episodes. The mean age of children was 6.3 years old, and 57.1% were boys. Out of 99 RVP samples analyzed, 22 were positive (22.2%). Antibiotics were started in 27.8%while 33.5% of patients were already on antibiotics. On multivariate logistic regression, having an RVP sent was significantly associated with increased initiation of antibiotics (aOR 95% CI 1.18-14.18, p=0.03). Furthermore, those with a positive RVP had a shorter course of antibiotics compared to those with a negative RVP (mean 6.8 vs 11.3 days, p=0.019). Conclusions Children with positive RVP had decreased antibiotic exposure compared to those with negative RVP results. RVP testing may be used to promote antibiotic stewardship among hospitalized children.

CRYPTOGENIC ORGANIZING PNEUMONIA: A DIAGNOSTIC DILEMMA IN A WORLD DOMINATED BY COVID-19 PNEUMONIA

CRYPTOGENIC ORGANIZING PNEUMONIA: A DIAGNOSTIC DILEMMA IN A WORLD DOMINATED BY COVID-19 PNEUMONIA

SARS-CoV-2 symptomatic reinfection among patients with primary antibody deficiency

SARS-CoV-2 symptomatic reinfection among patients with primary antibody deficiency

Discord between presence of follicular conjunctivitis and Chlamydia trachomatis infection in a single Torres Strait Island community: a cross‐sectional survey

ObjectiveRecent surveys identified trachomatous inflammation – follicular (TF) at endemic levels in the Torres Strait Islands; however, local health staff do not report trachomatous trichiasis (TT) in adults. We undertook a cross‐sectional survey involving eye examination and microbiological testing to better understand this disconnect. MethodsWe examined 169 of 207 (82%) residents and collected ocular swabs for polymerase chain reaction (PCR) testing for Chlamydia trachomatis. Other viral PCR tests and bacterial culture were also performed. ResultsTF prevalence in children aged 5–9 years was 23% (7/30). No ocular C. trachomatis was identified by PCR. For the 72 participants (43%) with follicles, bacterial culture was positive for 11 (15%) individuals. No individual had trachomatous trichiasis. ConclusionsFollicular conjunctivitis consistent with TF was prevalent but ocular C. trachomatis and cicatricial trachoma were absent. Non‐chlamydial infections or environmental causes of follicular conjunctivitis may be causing TF in this community. Implications for public healthIn similar settings, reliance on simplified clinical assessment alone may lead to an overestimation of the public health problem posed by trachoma. Consideration should be given to incorporating C. trachomatis PCR, and in certain settings, a detailed clinical exam could be performed by an experienced ophthalmologist during prevalence surveys.

Clinical Decision Making During the COVID-19 Pandemic.

The authors apply principles for translating imprecision in diagnostic and therapeutic information into clinical decisions to address 3 ongoing areas of uncertainty related to diagnosis, treatment, and prevention of COVID-19. They briefly review the current state of knowledge, highlight the level of uncertainty, and then suggest a pathway forward for clinical decision making during the pandemic.

Mitigation of in-hospital risk of coronavirus disease 2019: Experience from a haematology-oncology and stem cell transplant setting.

. Coronavirus disease 2019 (Covid-19) was first described in December 2019 and has evolved into an ongoing global pandemic. Cancer patients on chemotherapy are immunocompromised and are at the highest risk of Covid-19-related complications. We describe our experience with the management of haematology-oncology and stem cell transplant (SCT) patients receiving curative chemotherapy in a hospital with a high influx of Covid-19 patients. . We did a prospective observational study at a 99-bedded cancer centre of a tertiary care teaching hospital from April 2020 to September 2020. Preventive measures taken were categorized as follows: (i) staff: screening, mandatory use of personal protective equipment (PPE), risk stratification of potential exposure and testing and isolation as needed; (ii) patients: mandatory viral polymerase chain reaction testing, segregation of positive and untested patients and testing of family members; and (iii) environment: mandatory regular cleaning, visitor restriction, telemedicine services and reassignment of priority to clinic visits. Treatment of the underlying conditions was continued with added precautions. . A total of 54 patients were included in the analysis, including 48 with haematological malignancies and 6 for stem cell therapy. Preventive measures were universally applied, and chemotherapy with a curative intent was initiated as per protocol. Three patients were detected to have Covid-19 infection before admission and one after the institution of chemotherapy. Nine patients died after the first cycle of chemotherapy, 2 due to severe Covid-19-related illness and 7 due to complications of chemotherapy or disease progression. . In the wake of the Covid-19 pandemic, treatment for haematological malignancies must continue while balancing the risk of Covid-19 infections. Our report emphasizes the effectiveness of measures such as hand hygiene, social isolation, patient segregation, use of masks and PPE and universal pre-treatment testing for Covid-19 in reducing the risk of infection in a high-risk clinical setting.

Do I Need Proof of the Culprit? Decreasing Respiratory Viral Testing in Critically Ill Patients.

A 2-year-old, previously healthy boy with an upper respiratory infection presents to the emergency department with acute-onset stridor and respiratory distress. He quickly improves with intramuscular dexamethasone and initiation of heliox via high-flow nasal cannula. He is admitted to the PICU for respiratory insufficiency, requiring heliox, and high risk of respiratory failure. Before calling the PICU team for admission, the emergency department resident sends a respiratory viral polymerase chain reaction (PCR) panel. When her attending questions its necessity, she answers, “They [PICU admitting team] will ask for it. They always want to know which bug it is.” Historically, at our institution, respiratory viral PCR panels were commonly ordered for patients with more severe disease requiring PICU admission to find the culprit virus. Local practice had evolved to sending respiratory viral PCR tests for the majority of PICU patients with respiratory complaints, even before admission. Since its introduction, respiratory viral PCR panel–testing proponents have advocated its use to reduce unnecessary health care resource use.1–3 However, studies in which authors evaluate the clinical impact of respiratory viral PCR panel testing have varied in their results and lacked consistent evidence to support changes in management or outcomes, including antibiotic administration, chest radiographic imaging, hospital admission, and hospital length of stay.3–7 In addition, commonly held beliefs include the need to test for isolation and cohort practices or to identify treatable viruses. The Choosing Wisely guidelines of the American Society for Clinical Pathology recommend against routine, broad respiratory viral …

Impact of respiratory viral polymerase chain reaction testing on de-escalation of antibiotic therapy in children who require chronic positive pressure ventilation.

Children who require chronic positive pressure ventilation (CPPV) are frequently hospitalized with acute respiratory infections. Although respiratory viral testing is often performed, it is unclear how positive results impact antibiotic use. We sought to assess the impact of respiratory viral testing on antibiotic use in hospitalized children on CPPV. This retrospective cohort study included hospitalized children on CPPV who had respiratory viral polymerase chain reaction (RVP) testing on admission. Primary exposure was a positive RVP result; primary outcome was antibiotic de-escalation, defined as discontinuation of antibiotics or narrowing of antimicrobial spectra. To determine the independent association of positive RVP and antibiotic de-escalation, a generalized linear mixed effect model was used to account for within patient clustering and confounders defined a priori (blood and respiratory cultures, leukocytosis, bandemia, chest radiograph findings, aspiration risk, and recent admission). A total of 200 admissions representing 118 patients were included. A viral pathogen was identified in 46.5% (93/200) of admissions; rhinovirus was most frequently identified (61.5% of positive RVPs). Antibiotic de-escalation occurred in 33% of admissions (35.5% of RVP-positive admissions vs 30.8% of RVP-negative admissions; P = .49). In adjusted analysis, there was no association between positive RVP and antibiotics de-escalation (adjusted OR: 0.86; 95% confidence interval: 0.32-2.26). This single center cohort study suggests that respiratory viral testing may not impact antibiotic prescribing for hospitalized children on CPPV. There is need for improved stewardship of both diagnostic testing and antimicrobial use in this population.

New York City Innocence Lost: Cardiology in the COVID-19 Pandemic.

New York City Innocence Lost: Cardiology in the COVID-19 Pandemic.

Follow-up and Clinical Outcomes of Human Immunodeficiency Virus (HIV)-Exposed Infants in A Low-Prevalence Setting in A Multidisciplinary Model of Care in Australia: The Children's HIV Exposure Study 1.

Prevention of mother-to-child transmission (PMTCT) of human immunodeficiency virus (HIV) is effective, but outcome information beyond the postnatal period in low-prevalence settings is scarce. A multidisciplinary model of care (MOC) was developed to ensure PMTCT. Our aims in this study were to assess how well HIV-exposed infants are followed up through this MOC and to determine infant outcomes to age 18 months. This was a multicenter, prospective study of infants exposed to HIV during pregnancy, born 1 September 2009-31 August 2016 in Victoria, Australia. There were 129 live births from 127 pregnancies. There were no episodes of HIV transmission. Sixteen (13%) infants were born prematurely, 15 (12%) had low birthweight, and 6 (5%) had a congenital anomaly. There were 122 (95%) infants with an HIV polymerase chain reaction (PCR) within 2 weeks of birth. The proportion in the MOC reduced from 95% at 2 weeks postnatally to 75% by 18 months. Eighty-eight percent cared for within the MOC had 2 viral PCR tests completed after stopping antiretroviral prophylaxis compared with 22% of those outside of the MOC. By 18 months, 84/126 (67%) children attended follow-up, with higher rates within the MOC than outside (76% vs 6%; odds ratio, 46; 95% confidence interval, 6 to 365; P < .001). HIV-exposed, uninfected infants in this low-prevalence setting had good prospective follow-up through this MOC to 3 months. The decrease in follow-up by 18 months could be addressed in several ways, including expanding the MOC and providing better links to regional/rural services.

The clinical impact of pneumocystis and viral PCR testing on bronchoalveolar lavage in immunosuppressed patients.

IntroductionPulmonary infiltrates in immunosuppressed patients are common. Yields from bronchoscopy with bronchoalveolar lavage (BAL) has been reported to be between 31 and 65%. The clinical impact of pneumocystis and viral Polymerase chain reaction (PCR) testing on BAL has not been extensively evaluated in a mixed immunosuppressed patient population.MethodsWe performed a retrospective chart review of immunosuppressed adults with pulmonary infiltrates who underwent BAL at the University of Rochester Medical Center. Only one BAL per patient was included. We compared the rate of positive PCR testing to conventional testing. We then investigated factors associated with positive PCR testing. Finally, we assessed for changes in antimicrobial therapy after bronchoscopy.ResultsThree hundred and fifty-nine patients underwent BAL with 249 patients having pneumocystis PCR testing and 142 having viral PCR testing. Pneumocystis identification occurred in 43 patients and viral species identification occurred in 56 patients. PCR testing increased pneumocystis identification compared to microscopy, 14% vs. 5%, p = 0.01, and viral identification compared to culture, 25% vs. 6%, p = 0.0001. Of the patients with positive pneumocystis PCR testing 49% had antibiotics stopped, 66% were started on anti-pneumocystis therapy, and only 6% did not receive treatment. There was no difference in the number of patients with antibiotics stopped based on viral PCR testing results.DiscussionPCR testing increases BAL yield in immunosuppressed patients compared to conventional testing. Pneumocystis identified by PCR only may cause a self-limited infection and may not require antimicrobial therapy. PCR testing should be included in the evaluation of pulmonary infiltrates in immunosuppressed patients.

Systemic steroid treatment of acute bronchiolitis: A retrospective study

Purpose: Previous studies have reported that clinical efficacy of steroid therapy for acute bronchiolitis is controversial. However, since it is still frequently used in clinical practice, we sought to re-evaluate its effectiveness. Methods: This study included 277 children with acute bronchiolitis who were admitted to Kyungpook National University Children’s Hospital from March 2013 to July 2016. Erythrocyte sedimentation rates, C-reactive protein (CRP) levels, and viral polymerase chain reaction testing results were obtained, and respiratory rate (RR) was measured periodically. Forty-eight patients were treated with an intravenous (IV) steroid (17.3%, IV group) and 19 patients were treated with a per oral (PO) steroid medication (6.9%, PO group). The remaining 210 patients were steroid-free patients (74.2%, nonsteroid group). Results: RR and CRP levels were higher in the IV group, along with a longer hospitalization period and duration of wheezing. The rate of change from the fastest initial RR to the mean RR on the first treatment day was greatest in the IV group; this finding was sta tistically significant after controlling for initial RR (16.06% in the IV group, 3.94% in the PO group, 4.90% in the nonsteroid group; P<0.01). Conclusion: There was a trend of IV steroid treatment toward more severe bronchiolitis. A significant reduction in RR on the first day of steroid treatment was observed in IV steroid-treated patients. IV steroid therapy may play a positive role in initial RR stabilization for severe bronchiolitis. (Allergy Asthma Respir Dis 2017;5:326-330)

Viruses are frequently present as the infecting agent in acute exacerbations of chronic obstructive pulmonary disease in patients presenting to hospital.

BackgroundViral causes of acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are well recognised but only recently have rapid tests become available.AimsTo identify respiratory viruses in the general population and those associated with hospitalisation in AECOPD using polymerase chain reaction (PCR) on nasopharyngeal aspirate (NPA), and the relationship between symptoms, viral detection and inflammatory markers.MethodsA review of viruses detected in the general population in a health district between August 2014 and July 2015, using multiplex PCR for viruses from NPA samples. In addition, a single hospital, retrospective audit of patients admitted with suspected AECOPD was conducted.ResultsOf the 8811 NPA tested, 5599 (64%) were positive for at least one virus and 2069 of these were obtained from adults. In adults, the most common viruses identified were Influenza A (31%), Rhinovirus (27%) and respiratory syncytial virus A/B (10%). Most patients with AECOPD (102 of 153) had NPA sent for viral PCR testing and 59 (58%) were positive. The most common viruses identified were Influenza A (31%), Rhinovirus (24%) and respiratory syncytial virus A/B (17%) with co‐infecting bacteria cultured in 22 sputum samples. Patients with influenza‐like symptoms were more likely to have a positive viral PCR than those without symptoms (P < 0.004). The median C‐reactive protein on admission was lower in the virus‐infected than uninfected AECOPD (28 vs 60 mg/L, P < 0.026).ConclusionThe spectrum of viruses detected in patients with AECOPD is similar to that of the general population. Viruses are more likely to be identified in patients with AECOPD who present with influenza‐like symptoms and a low C‐reactive protein.

High Frequency of Detection by PCR of Viral Nucleic Acid in The Blood of Infants Presenting with Clinical Myocarditis.

Specific viruses are associated with pediatric myocarditis, but the prevalence of viral DNAemia detected by blood polymerase chain reaction (PCR) is unknown. We evaluated the prevalence of known cardiotropic viruses (enterovirus, adenovirus, human herpesvirus 6, and parvovirus B19) in children with clinical myocarditis (n = 21). Results were compared to pediatric controls with similar viral PCR testing. The majority of positive PCR (89 %) was noted in children ≤12 months of age at diagnosis compared to older children. Infant myocarditis patients (8/10) had increased the prevalence of PCR positivity compared to infant pediatric controls (4/114) (p < 0.0001). Other than age, patient characteristics at diagnosis were similar between PCR-positive and PCR-negative patients. Both PCR-negative myocarditis infants had clinical recovery at follow-up. Of the PCR-positive myocarditis infants, 4 had clinical recovery, 2 developed chronic cardiomyopathy, 1 underwent heart transplant, and 1 died. Infants with clinical myocarditis have a high rate of blood viral positivity, which is higher compared to older children with myocarditis and healthy infant controls. Age-related differences in PCR positivity may be due to differences in host and/or virus characteristics. Our findings suggest that viral blood PCR may be a useful diagnostic tool and identify patients who would potentially benefit from virus-specific therapy.

Concurrent Respiratory Viruses and Kawasaki Disease.

The diagnosis of Kawasaki disease (KD) remains challenging without a definitive diagnostic test and currently is guided by using clinical patient characteristics and supported by laboratory data. The role of respiratory viruses in the pathogenesis of KD is not fully understood. Charts of patients with KD admitted to Children's Hospital Colorado from January 2009 to May 2013 were retrospectively reviewed. Patients with KD who had a nasopharyngeal wash submitted for multiplex polymerase chain reaction (PCR) viral testing were included. Clinical characteristics, laboratory data, and outcomes of patients with and without positive respiratory viral PCR results were compared. Of 222 patients with KD admitted to the hospital, 192 (86%) had a respiratory viral PCR test performed on or shortly after admission. Ninety-three (41.9%) of the 192 patients with KD had a positive respiratory viral PCR, and the majority were positive for rhinovirus/enterovirus. No statistically significant differences were found in the clinical characteristics and laboratory values between the groups with and without positive respiratory viral PCR findings. Both groups had the same frequency of upper respiratory and gastrointestinal symptoms and had the same incidence of admission to the PICU, intravenous immunoglobulin-resistant disease, and coronary artery lesions. No differences in clinical presentations or outcomes in children with KD stratified according to positive or negative respiratory viral PCR testing were observed. A positive respiratory viral PCR or presence of respiratory symptoms at the time of presentation should not be used to exclude a diagnosis of KD.

Multiplex Viral Polymerase Chain Reaction Testing Using the FilmArray Device Compared With Direct Fluorescent Antibody Testing

Advances in fluidics, electronics, and instrument design have enabled automation of complex molecular assays. The FilmArray Respiratory Panel (RP) is one such assay; it allows for rapid detection of multiple viral and bacterial respiratory targets via nested polymerase chain reaction (PCR), with all components contained within a single pouch. We performed a detailed comparison of workflow between the FilmArray RP and direct fluorescent antibody (DFA) staining. The FilmArray RP proved to be more efficient, with as few as 91 total touches needed and as little as 4 minutes 52 seconds hands-on time. This compares with as many as 502 total touches and 12 minutes 45 seconds hands-on time for DFA staining. FilmArray RP detected a greater number of organisms (20 viruses and bacteria vs 7 viruses for DFA staining) and required less training compared with DFA staining. The ease of use of the FilmArray RP makes this molecular assay amenable to operation 24 hours a day, 7 days a week in routine laboratory and point-of-care settings.

552

Introduction: Human rhinoviruses (HRVs) cause nearly half of all acute respiratory illness, which tend to be mild in nature. Recent evidence suggests that HRVs may be an important cause of lower respiratory tract infection. The recent availability of respiratory viral polymerase chain reaction testing has improved our ability to identify and survey infectious agents like HRVs. We investigated the impact of HRVs on morbidity and mortality outcomes in children with severe viral respiratory infection. Methods: This was a retrospective cohort study of all patients admitted to the intensive care unit (ICU) at three urban academic tertiary care children's hospitals with laboratory-confirmed HRV respiratory infection between January 2010 and June 2011. We captured demographic and clinical data and analyzed associated morbidity and mortality outcomes. Results: There were 519 patients included in our analysis. The median patient age was 2.7 years. The median hospital and ICU lengths of stay were 4 days and 2 days, respectively. 34% of patients had a history of asthma and 26% of patients had a chronic medical condition other than asthma. 32% of patients required mechanical ventilation. Twelve patients (2.3%) did not survive to discharge. The rate of viral co-infection was low (12.5%) and was not associated with mortality. Predisposing factors associated with increased mortality included immunocompromised state (p<0.001), neuromuscular disease (p=0.013), severity of illness score (p<0.001) and bacterial co-infection (p=0.005). Controlling for bacterial co-infection and severity of illness, immunocompromised state and neuromuscular disease each independently increased mortality [OR=22, p<0.001 and OR=15, p=0.002, respectively]. Conclusions: Analysis of our results suggests that there is substantial morbidity and mortality associated with severe respiratory infection due to HRVs in children. Immunocompromised state and neuromuscular disease independently increase mortality. The burden of illness from HRVs on the ICU in terms of resource utilization may be considerable.

HIV infection in severely malnourished children in Kumasi, Ghana: a cross-sectional prospective study

BackgroundThe Human Immunodeficiency Virus (HIV) epidemic has adversely affected the nutritional status and mortality of children in Africa. This study assessed the disease burden, predictive clinical features and outcomes for children with severe acute malnutrition (SAM) and concomitant HIV infection.MethodsThis was a cross-sectional prospective study of children with SAM aged between 3 months and 13 years admitted to the nutritional rehabilitation unit (NRU) of Komfo Anokye Teaching Hospital. Socio-demographic, anthropometric and clinical data were documented and HIV serostatus established with 2 rapid HIV antibody tests and Enzyme-linked immunosorbent assay, if indicated. HIV viral polymerase chain reaction testing was not available at the time of the study. Logistic regression analyses were used to identify significant clinical predictors of HIV seropositivity.ResultsSixty-seven (27.2%, 95% CI = 21.8-33.3%) of the 246 study children had positive HIV antibody results. Uptake of provider-initiated HIV testing and counselling was 100%. Amongst children aged 18 months and over, the HIV seroprevalence was 28.3% (30/106). HIV seropositivity was strongly associated with prolonged fever, cough and diarrhoea; oral thrush, generalised lymphadenopathy and pulmonary tuberculosis (p value < 0.001 for all parameters). The presence of ≥ 3 of the first 5 aforementioned parameters was highly specific (98.3-100%) for HIV seropositivity in study children. HIV seropositivity was also significantly associated with cough, vomiting, lethargy/altered consciousness, skin rash and hepatomegaly (p value < 0.05 for all parameters). Overall mortality rate was 17.5%, with HIV seropositive children having a significantly higher mortality rate (37.8% versus 10.1%; p value < 0.001) and a lower rate of weight gain (2.4 g/kg/day versus 7.0 g/kg/day; p value < 0.001).ConclusionsHIV testing was well accepted by parents/carers and should be offered in all NRUs. There was a high HIV seroprevalence among children with SAM and a significantly poorer outcome in mortality and weight gain. Some clinical features were identified to be predictive of HIV seropositivity and could be useful as indicators to prompt further investigation and/or referral in resource limited settings where HIV test kits are unavailable. This would aid in the early detection and comprehensive management of the HIV seropositive child with SAM.

Interpretation of positive molecular tests of common viruses in the cerebrospinal fluid

Many central nervous system infections are historically difficult to diagnose. Polymerase chain reaction (PCR) has revolutionized the diagnosis of these infections because of their high sensitivity despite the lack of data on clinical usefulness. We conducted a retrospective study that included patients with positive cerebrospinal fluid (CSF) PCR for herpes simplex virus, varicella-zoster virus, JC virus, cytomegalovirus (CMV), and Epstein-Barr virus (EBV) between January 2009 and December 2011. The positive results were grouped into definite, likely, and possible true positives and likely false-positive categories based on pre-specified definitions specific to each virus. Of 1663 CSF viral PCR tests, 88 were positive (5%). The combined positive predictive value (PPV) was 58%. The PPVs were least for CMV and EBV at 29 and 37%, respectively. A positive CSF viral PCR result has to be interpreted with caution due to several false-positive results.

Virus isolation, polymerase chain reaction and in vitro antibody production for the diagnosis of pediatric human immunodeficiency virus infection

Viral culture (VC), polymerase chain reaction (PCR) and in vitro antibody production (IVAP) by peripheral blood mononuclear cells were compared for the early diagnosis of HIV-1 infection in 46 infants born to HIV-1 seropositive mothers. The ten children considered infected on the basis of clinical signs and persistence of anti-HIV-1 antibodies had at least one positive viral culture and seven were always positive in both PCR and IVAP tests. PCR and IVAP tests were occasionally negative in three infected children. Among 30 healthy children who became seronegative and were always negative for viral culture, 22 (73.3%) were also repeatedly negative in PCR and IVAP. We report 6 cases of children classified as P2A at the term of this study but who had lost anti-HIV-1 antibodies. They presented at least one positive viral culture and occasional positive PCR and/or IVAP results. The results indicate that the combination of viral culture, PCR and IVAP tests improves the early diagnosis of pediatric HIV infection.