scholarly journals Broad range detection of viral and bacterial pathogens in bronchoalveolar lavage fluid of children to identify the cause of lower respiratory tract infections

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Heping Wang ◽  
Jiali Gu ◽  
Xiaonan Li ◽  
Christa E. van der Gaast-de Jongh ◽  
Wenjian Wang ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Clinical Diagnosis ◽  
Pathogen Detection ◽  
Bacterial Pathogens ◽  
Clinical Diagnostics ◽  
Large Set ◽  
Detection Rates ◽  
Multiplex Qpcr ◽  
Accurate Treatment ◽  
Tract Infections

Abstract Background Knowledge on the etiology of LRTIs is essential for improvement of the clinical diagnosis and accurate treatment. Molecular detection methods were applied to identify a broad range of bacterial and viral pathogens in a large set of bronchial alveolar lavage (BAL) fluid samples. The patterns of detected pathogens were correlated to the clinical symptoms. Methods BAL fluid samples and clinical data were collected from 573 hospitalized children between 1 month and 14 years of age with LRTIs, enrolled from January to December 2018. Pathogens were detected using standardized clinical diagnostics, with a sensitive, high-throughput GeXP-based multiplex PCR and with multiplex qPCR. Data were analyzed to describe the correlation between the severity of respiratory tract disease and the pathogens identified. Results The pathogen detection rate with GeXP-based PCR and multiplex qPCR was significantly higher than by clinical routine diagnostics (76.09% VS 36.13%,χ2 = 8.191, P = 0.004). The most frequently detected pathogens in the BAL fluid were human adenovirus (HADV)(21.82%), Mycoplasma pneumoniae (20.24%), human rhinovirus (13.96%), Streptococcus pneumoniae (8.90%) and Haemophilus influenzae (8.90%). In 16.4% of the cases co-detection with two or three different pathogens was found. Viral detection rates declined with age, while atypical pathogen detection rates increased with age. Oxygen supply in the HADV and Influenza H1N1 infected patients was more frequent (49.43%) than in patients infected with other pathogens. Conclusion Broad range detection of viral and bacterial pathogens using molecular methods is a promising and implementable approach to improve clinical diagnosis and accurate treatment of LRTI in children.

scholarly journals Broad Range Detection of Viral and Bacterial Pathogens in Bronchoalveolar Lavage Fluid of Children to Identify the Cause of Lower Respiratory Tract Infections

2020 ◽  
Author(s):  
Heping Wang ◽  
Jiali Gu ◽  
Xiaonan Li ◽  
Christa E. van der Gaast de Jongh ◽  
Wenjian Wang ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Clinical Diagnosis ◽  
Pathogen Detection ◽  
Bacterial Pathogens ◽  
Clinical Diagnostics ◽  
Large Set ◽  
Detection Rates ◽  
Multiplex Qpcr ◽  
Accurate Treatment ◽  
Tract Infections

Abstract OBJECTIVES: Knowledge on the etiology of LRTIs is essential for improvement of the clinical diagnosis and accurate treatment. Molecular detection methods were applied to identify a broad range of bacterial and viral pathogens in a large set of bronchial alveolar lavage (BAL) fluid samples. The patterns of detected pathogens were correlated to the clinical symptoms.METHODS: BAL fluid samples and clinical data were collected from 573 hospitalized children between 1 month and 14 years of age with LRTIs, enrolled from January to December 2018. Pathogens were detected using standardized clinical diagnostics, with a sensitive, high-throughput GeXP-based multiplex PCR and with multiplex qPCR. Data were analyzed to describe the correlation between the severity of respiratory tract disease and the pathogens identified.RESULTS: The pathogen detection rate with GeXP-based PCR and multiplex qPCR was significantly higher than by clinical routine diagnostics (76.09% VS 36.13%,χ2 = 8.191, P=0.004). The most frequently detected pathogens in the BAL fluid were human adenovirus (HADV)(21.82%), Mycoplasma pneumoniae (20.24%), human rhinovirus (13.96%), Streptococcus pneumoniae (8.90%) and Haemophilus influenzae (8.90%). In 16.4 % of the cases co-infection with two or three different pathogens was found. Viral detection rates declined with age, while atypical pathogen detection rates increased with age. Oxygen supply in the HADV and Influenza H1N1 infected patients was more frequent (49.43%) than in patients infected with other pathogens.CONCLUSION: Broad range detection of viral and bacterial pathogens using molecular methods is a promising and implementable approach to improve clinical diagnosis and accurate treatment of LRTI in children.

scholarly journals The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life

2021 ◽  
Vol 9 (7) ◽  
pp. 1446
Author(s):  
Ivo Hoefnagels ◽  
Josephine van de Maat ◽  
Jeroen J.A. van Kampen ◽  
Annemarie van Rossum ◽  
Charlie Obihara ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Disease Severity ◽  
Lower Respiratory Tract ◽  
Influenza A ◽  
Pediatric Population ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Detection Rates ◽  
Tract Infections ◽  
Respiratory Microbiome

Lower respiratory tract infections (LRTIs) in children are common and, although often mild, a major cause of mortality and hospitalization. Recently, the respiratory microbiome has been associated with both susceptibility and severity of LRTI. In this current study, we combined respiratory microbiome, viral, and clinical data to find associations with the severity of LRTI. Nasopharyngeal aspirates of children aged one month to five years included in the STRAP study (Study to Reduce Antibiotic prescription in childhood Pneumonia), who presented at the emergency department (ED) with fever and cough or dyspnea, were sequenced with nanopore 16S-rRNA gene sequencing and subsequently analyzed with hierarchical clustering to identify respiratory microbiome profiles. Samples were also tested using a panel of 15 respiratory viruses and Mycoplasma pneumoniae, which were analyzed in two groups, according to their reported virulence. The primary outcome was hospitalization, as measure of disease severity. Nasopharyngeal samples were isolated from a total of 167 children. After quality filtering, microbiome results were available for 54 children and virology panels for 158 children. Six distinct genus-dominant microbiome profiles were identified, with Haemophilus-, Moraxella-, and Streptococcus-dominant profiles being the most prevalent. However, these profiles were not found to be significantly associated with hospitalization. At least one virus was detected in 139 (88%) children, of whom 32.4% had co-infections with multiple viruses. Viral co-infections were common for adenovirus, bocavirus, and enterovirus, and uncommon for human metapneumovirus (hMPV) and influenza A virus. The detection of enteroviruses was negatively associated with hospitalization. Virulence groups were not significantly associated with hospitalization. Our data underlines high detection rates and co-infection of viruses in children with respiratory symptoms and confirms the predominant presence of Haemophilus-, Streptococcus-, and Moraxella-dominant profiles in a symptomatic pediatric population at the ED. However, we could not assess significant associations between microbiome profiles and disease severity measures.

scholarly journals Burden of multidrug resistant respiratory pathogens in intensive care units of tertiary care hospital

2019 ◽  
Vol 10 (2) ◽  
pp. 14-19 ◽  
Author(s):  
Dharm Raj Bhatta ◽  
Deependra Hamal ◽  
Rajani Shrestha ◽  
Supram HS ◽  
Pushpanjali Joshi ◽  
...  
Keyword(s):  
Intensive Care ◽  
Respiratory Tract ◽  
Intensive Care Units ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Bacterial Pathogens ◽  
Multidrug Resistant ◽  
Lower Respiratory Tract Infections ◽  
Acinetobacter Species ◽  
Tract Infections

Background: Lower respiratory tract infections are one of the most common infections among the patients in Intensive Care Units (ICUs). Admission in ICUs and use of life supporting devices increase the risk of infection with multidrug resistant pathogens. Aims and Objectives: This study was aimed to determine the prevalence and antibiograms ofthe bacterial pathogens causing lower respiratory tract infectionsamong patients of ICUs. Materials and Methods: A total of 184 specimens from patients admitted in ICUswith lower respiratory tract infections were included in this study. Isolation, identification and antibiotic susceptibility testing of the isolates was performed by standard microbiological techniques. Carbapenamase detection was performed by modified Hodge test method.Detection of metallo beta lactamase (MBL) was tested by imipenem and imipenem/EDTA disc. Detection of Klebsiellapneumoniaecarbapenamase (KPC) was performed by imipenem and imipenem/phenyl boronic acid. Results: Out of 184 samples, 131 showed significant growth of bacterial pathogens. Acinetobacter species (42.6%), Staphylococcus aureus (16.9%) and Pseudomonasaeruginosa(13.9%)were the three most common isolates. Out of 22 imipenem resistant isolates of Acientobacter species, 9 were KPC producer, 4 were MBL producers and 3 isolates were positive for MBL and KPC both. Among the Acinetobacter species, 5.1% isolates were resistant to tigecycline and colistin. One isolate of Pseudomonas aeruginosa was positive for MBL. Conclusions:High prevalence of multidrug resistant bacteria in ICUs was recorded. Gram negative bacilli were predominantly associated with LRTI among ICU patients;Acinetobacterspecies being most common isolate. Detection of carbapenamase among the Acinetobacterand emergence of tigecycline resistancelimits the therapeutic options.Regular monitoring of such resistant isolates would be important for managing infection control in critical units.

scholarly journals Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping

2020 ◽  
Vol 19 (3) ◽  
pp. 518-528 ◽  
Author(s):  
Roger Karlsson ◽  
Annika Thorsell ◽  
Margarita Gomila ◽  
Francisco Salvà-Serra ◽  
Hedvig E. Jakobsson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Infectious Diseases ◽  
Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Clinical Laboratory ◽  
Bacterial Pathogens ◽  
Clinical Samples ◽  
Tandem Ms ◽  
Adequate Treatment ◽  
Tract Infections

Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.

scholarly journals Nasopharyngeal gene expression, a novel approach to study the course of respiratory syncytial virus infection

2014 ◽  
Vol 45 (3) ◽  
pp. 718-725 ◽  
Author(s):  
Corné H. van den Kieboom ◽  
Inge M.L. Ahout ◽  
Aldert Zomer ◽  
Kim H. Brand ◽  
Ronald de Groot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Respiratory Syncytial Virus ◽  
Respiratory Tract ◽  
Pathogen Detection ◽  
Severe Disease ◽  
Host Gene ◽  
Host Gene Expression ◽  
Rsv Infection ◽  
Syncytial Virus ◽  
Tract Infections

Respiratory syncytial virus (RSV) causes mild infections in the vast majority of children. However, in some cases, it causes severe disease, such as bronchiolitis and pneumonia. Development of severe RSV infection is determined by the host response. Therefore, the main aim of this study was to identify biomarkers associated with severe RSV infection.To identify biomarkers, nasopharyngeal gene expression was profiled by microarray studies, resulting in the selection of five genes: ubiquitin D, tetraspanin 8, mucin 13, β-microseminoprotein and chemokine ligand 7.These genes were validated by real-time quantitative PCR in an independent validation cohort, which confirmed significant differences in gene expression between mildly and severely infected and between recovery and acute patients.Nasopharyngeal aspirate samples are regularly taken when a viral respiratory tract infection is suspected. In this article, we describe a method to discriminate between mild and severe RSV infection based on differential host gene expression. The combination of pathogen detection and host gene expression analysis in nasopharyngeal aspirates will significantly improve the diagnosis and prognosis of respiratory tract infections.

scholarly journals Antibiotic Resistance Pattern of Bacteria Isolated from patients with upper respiratory tract infections; a four year study in Tripoli city

2018 ◽  
Author(s):  
Ahmed Atia ◽  
Najla Elyounsi ◽  
Ahmed Abired ◽  
Amal Wanis ◽  
Abdulsalam Ashour
Keyword(s):  
Antibiotic Resistance ◽  
Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Bacterial Pathogens ◽  
Health Concern ◽  
Resistance Pattern ◽  
Antibiotic Administration ◽  
Upper Respiratory Tract ◽  
Upper Respiratory ◽  
Tract Infections

1) Background: Respiratory tract infections (RTI) has been known to be a significant health concern for mortality and morbidity since many years. This study was aimed at determining the prevalence of bacterial pathogen causing upper respiratory tract (URTIs) and the susceptibility patterns to frequently used antibiotics among patients attending Abusetta hospital in Tripoli district; 2) Methods: A total of 1,110 throat swabs were collected between Jan, 2011 to December, 2014 and inoculated onto Blood agar, MacCkonkey agar and Chocolate agar then incubated at 37 oC for 24 hours. Bacterial pathogens were determined by bacteriological culture methods and antibiotic susceptibility of the isolates was identified following Clinical Laboratory Standard Institute guidelines (CLSI); 3) Results: Of the 1,110 respiratory samples tested, 71.1% (n = 789) of specimens were positive cultures with the dominant bacterial pathogens being streptococcus pneumonia 43.3% (n = 342), followed by pseudomonas aeruginosa 22.8% (n = 180), staphylococcus aurous 13.8% (n = 109), Escherichia Coli 6.9% (n = 55), Enterobacter spp 6.2% (n = 49), Citrobacter 4.5% (n = 36), and Klebsiella 2.2% (n = 18). Most isolates exhibited resistance against the commonly used antibiotics and to at least one antibiotic; and 4) Conclusions: The level of antibiotic resistance in this study is alarming and brings to light the timely and suitable diagnosis of the common bacteria causes of URTIs and proper antibiotic administration based on susceptibility test.

scholarly journals Clinical study of lower respiratory tract infections in children attending a tertiary care hospital

2017 ◽  
Vol 4 (5) ◽  
pp. 1733
Author(s):  
Venkata Krishna Munagala ◽  
Ramisetty M. Uma Mahesh ◽  
Jithendra Kandati ◽  
Munilakshmi Ponugoti
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Bacterial Pathogens ◽  
Tertiary Care ◽  
Care Hospital ◽  
Upper Respiratory Tract ◽  
Lower Respiratory Tract Infections ◽  
Cross Sectional ◽  
Tract Infections

Background: WHO estimated burden of respiratory tract infections in 2010, estimates four and half million deaths due to respiratory tract infections among children every year. In India, 1.2 million deaths have been reported among children due to RTI among 5.9 million deaths globally. Lower respiratory tract infections are most common causes of death than upper respiratory tract infections. Pneumonia and Bronchiolitis are most common types of LRTI in children. Pneumonia accounts for most of the deaths in children < 5 years of age. The present study was undertaken with an objective to know the various types of lower respiratory tract infections in children less than 12 years of age. The study also aims to know the various bacterial agents causing respiratory tract infections with their antibiotic susceptibility.Methods: Hospital based, prospective cross-sectional study was conducted for a period of one year and 375 children were enrolled. Demographic, clinical history and examination was done and signs and symptoms noted. All necessary investigations were performed and followed regularly for management and outcome.Results: Incidence of LRTI in the study was 9.76% with male preponderance (65.33%) and most common among children in 1-4 years age group. Ratio of males to females was 1.9:1. 73.6% of cases were in low socio-economic group, 35.2% were found with PEM-I grade and 18.13% had no immunization coverage. Cough and breathlessness were the major symptoms and respiratory distress and clubbing were major signs in the study. Bronchopneumonia was the commonest cause (38.7%) followed by bronchiolitis and Allergic bronchitis. 18.45 of cases had anemia and Leucocytosis was also present. Pulmonary infiltration was the major finding in the X-ray of chest. Streptococcus pneumoniae and Klebsiella pneumoniae were the common bacterial pathogens isolated.Conclusions: To conclude, our study clearly highlighted the various types of clinical presentations, risk factors and different types of LRTI in children <12 years of age. Understanding a clear knowledge of the etiology and bacterial pathogens clearly provides guidance for the physician in management and clinical outcome. 

scholarly journals In Vitro Activity of Lefamulin Against a Global Collection of Bacterial Pathogens Commonly Causing Community-Acquired Bacterial Pneumonia (CABP, SENTRY 2015)

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S373-S373 ◽  
Author(s):  
Susanne Paukner ◽  
Helio S Sader ◽  
Jennifer M Streit ◽  
Robert K Flamm ◽  
Steven P Gelone
Keyword(s):  
Respiratory Tract ◽  
Bacterial Pathogens ◽  
Bloodstream Infections ◽  
Vitro Activity ◽  
Asia Pacific ◽  
Respiratory Pathogens ◽  
In Vitro Activity ◽  
Tract Infections ◽  
Research Grant

Abstract Background CABP is the number one reason for death by infectious diseases worldwide and emerging resistance complicates its treatment. Lefamulin is the first semi-synthetic pleuromutilin antibiotic for IV and oral use in humans. It is currently in Phase 3 trials for the treatment of CABP in adults. Lefamulin effectively and selectively inhibits bacterial translation by binding to the peptidyl transferase center (PTC) via four H-bonds and other interactions at the A- and P-site resulting in an “induced fit.” This study investigated the activity of lefamulin and comparators against a contemporary set of bacterial pathogens associated with community-acquired respiratory infections collected worldwide. Methods Unique patients’ isolates (n = 2817) were collected globally in US (19.7%), Europe (36.9%), Latin America (5.7%) and Asia-Pacific region (37.6%) (30 countries, 116 sites) from adult and pediatric patients with respiratory tract infection (88.0%), bloodstream infections (5.5%) and other infections (2.4%). Lefamulin and comparators were tested by CLSI broth microdilution and susceptibility was determined using the CLSI (2017) breakpoints. Results LEF was the most potent compound tested, with 99.7% of all S. pneumoniae isolates being inhibited at a concentration of ≤0.25 mg/L (MIC50/90 values of 0.06/0.12 mg/L) and its activity was not affected by resistance to other antibiotic classes. S. pneumoniae isolates were largely susceptible to levofloxacin (99.1%) and ceftriaxone (96.5%), while 34.5%, 23.3% and 16.8% of isolates were resistant to macrolides, tetracycline and clindamycin, respectively. Lefamulin also showed potent activity against H. influenzae (MIC50/90 of 0.5/1 mg/L), including 22.0% of ß-lactamase producing strains, and M. catarrhalis (0.06/0.12 mg/L). Conclusion Lefamulin demonstrated potent in vitro activity against this global collection of contemporary respiratory pathogens and its activity was unchanged regardless of resistance phenotype to the other antibiotic classes including macrolides, ß-lactams, tetracyclines or fluoroquinolones. These data support the continued clinical development of lefamulin for the treatment of respiratory tract infections, including CABP. Disclosures S. Paukner, Nabriva Therapeutics: Employee and Shareholder, Salary; H. S. Sader, Nabriva Therapeutics: Research Contractor, Research grant; J. M. Streit, Nabriva Therapeutics: Research Contractor, Research grant; R. K. Flamm, Nabriva Therapeutics: Research Contractor, Research grant; S. P. Gelone, Nabriva Therapeutics: Employee and Shareholder, Salary

Sign in / Sign up

Export Citation Format

Share Document