scholarly journals Approach to Identifying Causative Pathogens of Community-Acquired Pneumonia in Children Using Culture, Molecular, and Serology Tests

2021 ◽  
Vol 9 ◽  
Author(s):  
Yan Mardian ◽  
Adhella Menur Naysilla ◽  
Dewi Lokida ◽  
Helmia Farida ◽  
Abu Tholib Aman ◽  
...  
Keyword(s):  
Bacterial Colonization ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Diagnostic Methods ◽  
Limiting Factor ◽  
Causative Pathogen ◽  
Chain Reaction ◽  
Prevalence Data ◽  
Polymerase Chain ◽  
Carriage Prevalence

Determining the causative pathogen(s) of community-acquired pneumonia (CAP) in children remains a challenge despite advances in diagnostic methods. Currently available guidelines generally recommend empiric antimicrobial therapy when the specific etiology is unknown. However, shifts in epidemiology, emergence of new pathogens, and increasing antimicrobial resistance underscore the importance of identifying causative pathogen(s). Although viral CAP among children is increasingly recognized, distinguishing viral from bacterial etiologies remains difficult. Obtaining high quality samples from infected lung tissue is typically the limiting factor. Additionally, interpretation of results from routinely collected specimens (blood, sputum, and nasopharyngeal swabs) is complicated by bacterial colonization and prolonged shedding of incidental respiratory viruses. Using current literature on assessment of CAP causes in children, we developed an approach for identifying the most likely causative pathogen(s) using blood and sputum culture, polymerase chain reaction (PCR), and paired serology. Our proposed rules do not rely on carriage prevalence data from controls. We herein share our perspective in order to help clinicians and researchers classify and manage childhood pneumonia.

Detection of respiratory viruses and Legionella spp. by real-time polymerase chain reaction in patients with community acquired pneumonia

2009 ◽  
Vol 41 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Bram M.W. Diederen ◽  
Menno M. Van Der Eerden ◽  
Fer Vlaspolder ◽  
Wim G. Boersma ◽  
Jan A.J.W. Kluytmans ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Respiratory viruses in adults hospitalised with Community-Acquired Pneumonia during the non-winter months in Melbourne: Routine diagnostic practice may miss large numbers of influenza and respiratory syncytial virus infections.

2019 ◽  
Vol 43 ◽  
Author(s):  
Lucy A Desmond ◽  
Melanie A Lloyd ◽  
Shelley A Ryan ◽  
Edward D Janus ◽  
Harin A Karunajeewa
Keyword(s):  
Polymerase Chain Reaction ◽  
Respiratory Syncytial Virus ◽  
Elderly Patients ◽  
Multiplex Pcr ◽  
Viral Infections ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Syncytial Virus

Background Community-Acquired Pneumonia (CAP) is one of the highest health burden conditions in Australia. Disease notifications and other data from routine diagnosis suffers from selection bias that may misrepresent the true contribution of various aetiological agents. However existing Australian prospective studies of CAP aetiology have either under-represented elderly patients, not utilised Polymerase Chain Reaction (PCR) diagnostics or been limited to winter months. We therefore sought to re-evaluate CAP aetiology by systematically applying multiplex PCR in a representative cohort of mostly elderly patients hospitalised in Melbourne during non-winter months and compare diagnostic results with those obtained under usual conditions of care. Methods Seventy two CAP inpatients were prospectively enrolled over 2 ten-week blocks during non-winter months in Melbourne in 2016-17. Nasopharyngeal and oropharyngeal swabs were obtained at admission and analysed by multiplex-PCR for 7 respiratory viruses and 5 atypical bacteria. Results Median age was 74 (interquartile range 67-80) years, with 38 (52.8%) males and 34 (47.2%) females. PCR was positive in 24 (33.3%), including 12 Picornavirus (50.5% of those with a virus), 4 RSV (16.7%) and 4 influenza A (16.7%). CAP-Sym questionnaire responses were similar in those with and without viral infections. Most (80%) pathogens detected by the study, including all 8 cases of influenza and RSV, were not otherwise detected by treating clinicians during hospital admission. Conclusion One third of patients admitted with CAP during non-winter months had PCR-detectable respiratory viral infections, including many cases of influenza and RSV that were missed by existing routine clinical diagnostic processes. Keywords: Lower Respiratory Tract Infection (LRTI), Community-Acquired Pneumonia (CAP) Polymerase Chain Reaction (PCR), Influenza, Respiratory Syncytial Virus

scholarly journals Respiratory virus monitoring in patients with community-acquired pneumonia during COVID-19 pandemic in Khabarovsk in 2020

2021 ◽  
pp. 21-27
Author(s):  
L. V. Butakova ◽  
E. Yu. Sapega ◽  
O. E. Trotsenko ◽  
L. A. Balakhontseva ◽  
E. N. Prisyazhnyuk ◽  
...  
Keyword(s):  
Virus Type ◽  
Respiratory Virus ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Parainfluenza Virus ◽  
Sample Collection ◽  
Chain Reaction ◽  
Khabarovsk Krai ◽  
Polymerase Chain ◽  
Type 3

Introduction. Emergence and spread of new coronavirus SARS-CoV-2 among population of the Khabarovsk krai influenced the growth of reported cases of community-acquired pneumonia in year 2020. Aim. To determine proportion of other respiratory viruses in development of viral pneumonia epidemic process in the Khabarovsk city in year 2020 during COVID-19 pandemic. Materials and methods. Sputum of 346 patients with community-acquired pneumonia that were hospitalized with suspected diagnosis of COVID-19 was analyzed during year 2020 in Khabarovsk city. Identification of viral agents was performed via real-time reverse-transcriptase polymerase chain reaction. Results. SARSCOV-2 RNA was identified in 183 (52.9%) out of 346 patients. Among other respiratory viruses parainfluenza virus type 3 and rhinoviruses were dominant mostly in SARS-CoV-2 negative examined people. It should be noted that etiology of pneumonia was identified only in 12.9% of all cases in this group (163 people). Co-infection with SARS-CoV-2 and other respiratory viruses such as parainfluenza virus type 3 virus, other coronaviruses and adenovirus was detected only in 2.2% of the cases. Conclusion. Low level of respiratory viruses detection in sputum can be caused by poor technique of sample collection in the hospital, disruption of storage and transportation conditions as well as development of secondary bacterial infection in certain patients. In order to evaluate influence of other respiratory viruses on the course of COVID-19 with underlying coinfection further investigation including analysis of patients’ clinical data is needed.

Comparison of Droplet Digital Polymerase Chain Reaction (ddPCR) and Real-Time Quantitative Polymerase Chain Reaction (qPCR) in Detecting Neonatal Invasive Fungal Infections

2021 ◽  
Vol 11 (3) ◽  
pp. 373-379
Author(s):  
Huitao Li ◽  
Xueyu Chen ◽  
Xiaomei Qiu ◽  
Weimin Huang ◽  
Chuanzhong Yang
Keyword(s):  
Polymerase Chain Reaction ◽  
Limit Of Detection ◽  
Quantitative Polymerase Chain Reaction ◽  
Diagnostic Methods ◽  
Chain Reaction ◽  
Fungal Isolation ◽  
Blood Samples ◽  
Fungal Strains ◽  
Polymerase Chain ◽  
Digital Polymerase Chain Reaction

Invasive fungal infection (IFI) is the leading cause of death in neonatal patients, yet the diagnosis of IFI remains a major challenge. At present, most IFI laboratory diagnostic methods are based on classical, but limited, methods such as fungal isolation and culture and histopathological examination. Recently, quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) technology have been adopted to quantify nucleic-acid identification. In this study, we established qPCR and ddPCR assays for IFI diagnosis and quantification. qPCR and ddPCR were carried out using identical primers and probe for the amplification of 18S rRNA. Assay results for three fungal strains were positive, whereas ten non-fungal strains had negative results, indicating 100% specificity for both ddPCR and qPCR methods. Genomic DNA of Candida albicans was tested after a serial dilution to compare the sensitivity of the two PCR methods. The limit of detection of ddPCR was 3.2 copies/L, which was a ten-fold increase compared with that of the qPCR method (32 copies/L). Blood samples from 127 patients with high-risk factors and clinical symptoms for IFI were collected from a NICU in Shenzhen, China, and analyzed using qPCR and ddPCR. Thirty-four blood samples from neonates had a proven or probable diagnosis of IFI, and 25 of these were positive by qPCR, whereas 30 were positive by ddPCR. Among the 93 blood samples from neonates who had a possible IFI or no IFI, 24 were positive using qPCR, and 7 were positive using ddPCR. In conclusion, ddPCR is a rapid and accurate pan-fungal detection method and provides a promising prospect for IFI clinical screening.

scholarly journals UTILITY OF ANTIGEN DETECTION TEST AND POLYMERASE CHAIN REACTION IN THE DIFFERENTIATION OF TUBERCULOUS AND NON-TUBERCULOUS MYCOBACTERIA

2017 ◽  
Vol 10 (6) ◽  
pp. 289
Author(s):  
Yogita Singh ◽  
Raji Vasanth ◽  
Shrikala Baliga ◽  
Dhanashree B
Keyword(s):  
Polymerase Chain Reaction ◽  
False Negative ◽  
Diagnostic Methods ◽  
Clinical Samples ◽  
Chain Reaction ◽  
College Hospital ◽  
Medical College ◽  
Negative Results ◽  
Polymerase Chain ◽  
Mycobacterium Spp

Objectives: Cultivation and identification of mycobacteria to species level remains difficult and time-consuming. Hence, easy and rapid diagnostic methods are necessary for the differentiation of Mycobacterium tuberculosis (MTB) from non-tuberculous mycobacteria (NTM). The present study aims to detect and differentiate MTB from NTM isolated from clinical samples by immunochromatographic test (ICT) and polymerase chain reaction (PCR). Methods: Over a period of 1 year, clinical samples (n=496) received from suspected cases of TB, at the Department of Microbiology, Kasturba Medical College Hospital, Mangalore were cultured to isolate Mycobacterium spp. Identification of all the isolates was done by conventional biochemical technique, ICT, and PCR. Results: Among the 496 samples processed, 49 (9.87%) were acid-fast bacilli smear positive and 59 (11.89%) samples showed the growth of Mycobacterium spp. Among these, 10 were rapid growers, 49 were slow-growing mycobacteria, out of which 30 were MTB as identified by conventional biochemical reaction. Out of 59 Mycobacterial isolates subjected to ICT for the detection of MPT 64 antigen, only 28 were identified as MTB. However, all the 30 isolates were correctly identified as MTB by PCR. Conclusion: Hence, PCR is essential for rapid differentiation of non-tuberculous Mycobacterium from MTB. False negative results seen with immunochromatographic MPT 64 antigen assay could be due to mutations within the mpt64 gene. Further studies are necessary to characterize these PCR-positive and immunochromatographic assay negative MTB isolates.

scholarly journals Comparative Study of Immune-Diagnostic Tools with Polymerase Chain Reaction in Sub-Clinical Leishmaniasis Isolates

2011 ◽  
Vol 12 (1) ◽  
pp. 34-39 ◽  
Author(s):  
Nazar M Abdalla
Keyword(s):  
Polymerase Chain Reaction ◽  
Skin Test ◽  
Diagnostic Methods ◽  
Diagnostic Tools ◽  
Enzyme Linked Immunosorbent Assay ◽  
Clinical Form ◽  
Chain Reaction ◽  
Leishmanin Skin Test ◽  
Wide Range ◽  
Polymerase Chain

Objective: This study aimed to identify cases of leishmaniasis in the Nuba Mountain area, which is situated in a unique geographical site located in the centre of Sudanese leishmania belt. Wide range of investigations are available for detection of leishmania cases, but still the most reliable and easy test used as screening and epidemiological tool in field studies needs to be evaluated. The most commonly used conventional diagnostic methods direct microscopy and culture have some drawbacks in diagnosing subclinical cases of leishmaniasis. Materials and methods: In this study, comparative properties of various immune-diagnostic tools with Polymerase Chain Reaction used in sub-clinical leishmaniasis isolates were explored. The immune-diagnostic tools involved in this study include- Leishmanin Skin Test (LST), Enzyme Linked Immunosorbent Assay (ELISA) and Direct Agglutination Test (DAT). The study was conducted in the Green Valley village (Rashad Province, South Kordofan State) with a population of 332. Most of the villagers presented with sub-clinical form of leishmaniasis with minor symptoms and signs without the features found in clinical form of visceral leishmaniasis such as fever, diarrhoea, epistaxis, enlarged lymph nodes, spleen and liver. In this study we collected demographic, clinical and epidemiological data using special questionnaire. Leishmanin skin test (LST), ELISA, DAT and PCR for parasite DNA detection were used. Result: The final positive cases detected by PCR were 32 out of 332 belong to L. donovani species. The final positive cases detected by LST were 51.2% of the total population under study, while 11 out of the 37 tested samples were positive by ELISA. All of the 332 villagers showed negative readings by DAT with exception of three individuals who were positive with very high titers. Conclusion: DNA etxtraction and amplification with primers can be a good screening tool in subclinical leishmaniasis isolates. Keyword: Sub-clinical; Leishmaniasis; Leishmanin Skin Test; ELISA; DAT; PCR. DOI: 10.3329/jom.v12i1.5422J Medicine 2011; 12 : 34-39

scholarly journals Concomitant Marked Decline in Prevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Other Respiratory Viruses Among Symptomatic Patients Following Public Health Interventions in Australia: Data from St Vincent’s Hospital and Associated Screening Clinics, Sydney, NSW

2020 ◽  
Author(s):  
Deborah Marriott ◽  
Rohan Beresford ◽  
Feras Mirdad ◽  
Damien Stark ◽  
Allan Glanville ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Respiratory Viruses ◽  
Health Interventions ◽  
Control Measures ◽  
Public Health Interventions ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Marked Decline ◽  
Polymerase Chain ◽  
Australian Hospital

Abstract Our Australian hospital tested almost 22 000 symptomatic people over 11 weeks for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a multiplex polymerase chain reaction (PCR) assay. Following travel bans and physical distancing, SARS-CoV-2 and other respiratory viruses diagnoses fell dramatically. Increasing rhinovirus diagnoses as social control measures were relaxed may indirectly indicate an elevated risk of coronavirus disease 2019 (COVID-19) resurgence.

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