DNA Virome: Sequencing and Data Analysis of Viral Metagenome of Poultry Suffering from Respiratory Diseases

2018 ◽  
Vol 13 (03) ◽  
Author(s):  
Manisha R. Sajnani ◽  
D. Sudarsanam ◽  
Subhash J. Jakhesara ◽  
Siddhardha Solosanc, ◽  
Chaitanya G. Joshi ◽  
...  
Keyword(s):  
Respiratory Diseases ◽  
Respiratory Tract Infections ◽  
De Novo ◽  
Respiratory Infections ◽  
Economic Loss ◽  
Common Causes ◽  
Commercial Broiler ◽  
Poultry Flock ◽  
Tract Infections ◽  
Taking Action

Respiratory diseases are the most common causes of death in a poultry flock. Knowledge of the avian respiratory system is essential for developing a health monitoring plan for a poultry flock, recognizing problems that may occur, and taking action to correct them. Recently, respiratory diseases in commercial broiler chicken flocks have increased in India and no significant cause has been identified till date. Viral populations are predominant in respiratory tract infections and they cause severe economic loss through decreased productivity. We performed shotgun sequencing approach to understand viruses associated with or causing respiratory infections (RI) in broilers. We report high quality sequencing reads, de novo assembled sequences, taxonomical as well as functional classifications of virome of the infected broiler birds.

Frequency and pattern of respiratory diseases in children

2017 ◽  
Vol 4 (5) ◽  
pp. 1567
Author(s):  
Urooj Samoo ◽  
Shaista Ehsan ◽  
Farah Agha
Keyword(s):  
Respiratory Diseases ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
Tertiary Care ◽  
First Trimester ◽  
Cross Sectional Study ◽  
P Value ◽  
Cross Sectional ◽  
Pediatric Age Group ◽  
Tract Infections

Background: Respiratory tract infections are a major cause of   morbidity and mortality in children. Therefore, it is imperative that research studies be conducted to determine the pattern of respiratory diseases in the pediatric age group. Present study was done to determine the outcome, frequency and pattern of respiratory infections in children admitted in a tertiary care hospital.Methods: This prospective, cross-sectional study was conducted from September 2014 to February 2016. Data was analyzed on SPSS 20.0. P value of <0.05 was observed noteworthy.Results: A total of 286 children were admitted with respiratory diseases. Out of these there were 180 cases of Pneumonia. Peak occurrence of Pneumonia was observed in first trimester of the year.Conclusions: Efforts are required to devise strategies to decrease the burden of respiratory diseases in children.  

scholarly journals Infections Caused by RSV among Children and Adults during Two Epidemic Seasons

2011 ◽  
Vol 60 (3) ◽  
pp. 253-258 ◽  
Author(s):  
KATARZYNA PANCER ◽  
AGNIESZKA CIĄĆKA ◽  
WŁODZIMIERZ GUT ◽  
BOŻENA LIPKA ◽  
JUSTYNA MIERZEJEWSKA ◽  
...  
Keyword(s):  
Young Children ◽  
Respiratory Tract ◽  
Respiratory Diseases ◽  
Respiratory Tract Infections ◽  
Rt Pcr ◽  
Epidemic Season ◽  
Chronic Respiratory Diseases ◽  
Common Causes ◽  
Syncytial Virus ◽  
Tract Infections

Respiratory Syncytial Virus (RSV) is one of the most common causes of lower respiratory tract infections in young children, immunocompromised patients (children and adults), patients with chronic respiratory diseases and elderly people. Reinfections occur throughout the life, but the severity of disease decreased with subsequent infection. The aim of this study was to analyze the frequency of RSV infections in two selected subpopulations: young children (below 5 y.) and adults with chronic respiratory diseases (25-87 y.). Nasopharyngeal swabs (334) collected from October 2008 to March 2010 were examined. The presence of RSV genome was determined by RT-PCR and the presence of RSV antigen by quick immunochromatographic test. Positive results of RT-PCR were found in 45.2% of all swabs: 48.6% samples in 2008; 41.5% in 2009; 50.8% in 2010. The highest frequency of RSV-positive samples was in fall-winter months, but differences in RSV epidemic seasons were found. In the first season (2008-2009) an increased number of RSV infections was observed from November 2008, but in the second season--from January 2010. Generally, the frequency of RSV-positive RT-PCR among children was 53%, among adults 25%. The highest difference was observed in the first three-month period of 2010. RT-PCR positive samples were found in 68.5% of children and 5.9% of adults. However, the RSV antigen was found in 44.4% of samples collected from adults in this period. Our results indicate that the contribution of RSV infections during epidemic season of respiratory tract infections in Poland was really high among children and adults.

scholarly journals Ability of Microorganisms, Causing Respiratory Infections in Children, to Form Biofilms in vitro

2021 ◽  
Vol 6 (1) ◽  
pp. 177-183
Author(s):  
H. O. Isaieva ◽  
◽  
M. M. Mishyna ◽  
Y. A. Mozgova ◽  
M. O. Gonchar ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Respiratory Tract ◽  
Optical Density ◽  
Respiratory Diseases ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
Gram Positive ◽  
Gram Negative ◽  
Tract Infections

The purpose of the study was to detect ability to form biofilms by microorganisms that cause respiratory tract infections. Materials and methods. The study involved 97 strains of microorganisms. Microorganisms were isolated from children with respiratory tract infections. All strains, isolated from patients, were able to form biofilms. There were 44 strains of S. aureus (from patients with pneumonia – 13 strains, from patients with other respiratory diseases – 31), 34 strains of S. pneumoniae (pneumonia – 27 strains, other respiratory diseases – 7), 13 strains of K. pneumoniae (pneumonia – 6 strains, other respiratory diseases – 7), 6 strains of P. aeruginosa (pneumonia – 5 strains, other respiratory diseases – 1). Children were treated at the pulmonary department and intensive care unit in Kharkiv Regional Children's Clinical Hospital. Results and discussion. The optical density of primary biofilms formed by Gram-positive microorganisms was 1.33±0.24 Units of OD, and their secondary biofilms was 0.32±0.10 Units of OD. In patients with pneumonia optical density of primary biofilms of Gram-positive microorganisms was 1.48±0.21 Units of OD and of secondary biofilms was 0.30±0.08 Units of OD. Optical density of primary biofilms of Gram-positive microorganisms in patients with other respiratory infections was 1.18±0.15 Units of OD, of secondary biofilms was 0.35±0.12 Units of OD. The optical density of primary biofilms formed by Gram-negative microorganisms was 2.01±1.03 Units of OD, optical density of secondary biofilms was 1.06±0.42 Units of OD. In patients with pneumonia optical density of primary biofilms of Gram-negative microorganisms was 2.57±0.87 Units of OD, of secondary biofilms was 1.21±0.50 Units of OD. Optical density of primary biofilms of Gram-negative microorganisms in patients with other respiratory infections was 1.24±0.66 Units of OD, of secondary biofilms was 0.84±0.11 Units of OD. Conclusion. Gram-negative microorganisms in general formed more massive biofilms compared with Gram-positive microorganisms. Among all microorganisms P. aeruginosa formed the thickest primary and secondary biofilms. Strains of P. aeruginosa isolated from patients with pneumonia formed the thickest primary and secondary biofilms. Strains of S. aureus isolated from patients with other respiratory infections formed most massive primary biofilms, strains of K. pneumoniae formed the hardest secondary biofilms in this group

scholarly journals Human coronaviruses in persons with acute respiratory infections in Ghana

2020 ◽  
pp. 5-11
Author(s):  
Prince K Parbie ◽  
Julius AA Mingle ◽  
Michael Ntiri ◽  
Michael Adjabeng ◽  
Kofi Bonney ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
Severe Disease ◽  
Respiratory Illness ◽  
Economic Loss ◽  
Influenza Surveillance ◽  
Acute Respiratory Infections ◽  
Human Coronaviruses ◽  
Tract Infections

Background: Acute respiratory infections (ARI) remain a leading cause of morbidity, mortality, and economic loss globally. Until recently, human coronaviruses (HCoVs) have been mainly associated with mild respiratory tract infections. The 2003 outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV) and cases of Middle East respiratory syndrome coronavirus (MERS-CoV), since 2012, illustrate the potential of coronaviruses to cause severe disease. Objective: This study investigated the presence of human coronaviruses in acute respiratory illness in Ghana. Methods: As part of routine influenza surveillance, nasopharyngeal and oropharyngeal (NP/OP) swabs obtained from 200 patients (100 hospital inpatients and 100 outpatients) with Influenza-like-illness from sentinel health facilities in Ghana from January 2013 to March 2014, were screened for the presence of HCoVs at the National Influenza Center using real-time reverse transcriptase polymerase chain reaction assays. Results: Human CoVs were detected in 7(3.5%) out of 200 cases investigated: HCo V HKU1 in 3 patient, HCo V 229E in 2 patients, HCo V OC43 in 1patient, and HCo V NL63 in 1 patient. No co-infection with HCoV types was detected. Out of 7 patients with HCoV infections, 6 were aged 5 yr. or greater.Also, HCoVs were detected more frequently in outpatients (5/100) than in hospitalized patients (2/100) with acute respiratory tract infections, though statistically insignificant (p>0.005). None of the respiratory specimens tested were positive for MERS-CoV, indicating the absence of MERS-CoV infection in Ghana between January 2013 and March 2014. Conclusion: This work provides an important reference point for coronavirus infections in humans in Ghana noting the current concern on the 2019 novel coronavirus.

Lower respiratory tract infections in patients with comorbidities

2020 ◽  
Vol 1 (1) ◽  
pp. 29-34
Author(s):  
Leonid Dvoretsky ◽  
Keyword(s):  
Respiratory Diseases ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
Chronic Obstructive ◽  
Lower Respiratory Tract Infections ◽  
Obstructive Pulmonary Disease ◽  
Artery Disease ◽  
Tract Infections ◽  
Viral Respiratory Infections ◽  
Viral Respiratory

Comorbidities are an important factor of the various infectious respiratory diseases emergence, complications development and prognosis. The most frequent comorbidities affecting the course and outcome of respiratory infections are the following: cardiovascular disease (heart failure, various types of coronary artery disease, cerebrovascular disease), chronic obstructive pulmonary disease, diabetes mellitus, obesity. The paper reports data on the discussed comorbidities impact on the course and outcome of bacterial and viral respiratory infections, inter alia in patients with COVID-19.

scholarly journals Viral etiology and epidemiology of pediatric patients hospitalized for acute respiratory tract infections in Macao: a retrospective study from 2014 to 2017

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Cheng Lei ◽  
Lisong Yang ◽  
Cheong Tat Lou ◽  
Fan Yang ◽  
Kin Ian SiTou ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Pediatric Patients ◽  
Respiratory Infections ◽  
Upper Respiratory Tract ◽  
Viral Etiology ◽  
Upper Respiratory ◽  
Syncytial Virus ◽  
Tract Infections

Abstract Background Acute respiratory infections (ARIs) are among the leading causes of hospitalization in children. Understanding the local dominant viral etiologies is important to inform infection control practices and clinical management. This study aimed to investigate the viral etiology and epidemiology of respiratory infections among pediatric inpatients in Macao. Methods A retrospective study using electronic health records between 2014 and 2017 at Kiang Wu Hospital was performed. Nasopharyngeal swab specimens were obtained from hospitalized children aged 13 years or younger with respiratory tract diseases. xMAP multiplex assays were employed to detect respiratory agents including 10 respiratory viruses. Data were analyzed to describe the frequency and seasonality. Results Of the 4880 children enrolled in the study, 3767 (77.1%) were positive for at least one of the 13 viral pathogens tested, of which 2707 (55.5%) being male and 2635 (70.0%) under 2 years old. Among the positive results, there were 3091 (82.0%) single infections and 676 (18.0%) multiple infections. The predominant viruses included human rhinovirus/enterovirus (HRV/EV 27.4%), adenovirus (ADV, 15.8%), respiratory syncytial virus B (RSVB, 7.8%) and respiratory syncytial virus A (RSVA, 7.8%). The detection of viral infection was the most prevalent in autumn (960/1176, 81.6%), followed by spring (1095/1406, 77.9%), winter (768/992, 77.4%), and summer (944/1306, 72.3%), with HRV/EV and ADV being most commonly detected throughout the 4 years of study period. The detection rate of viral infection was highest among ARI patients presented with croup (123/141, 87.2%), followed by lower respiratory tract infection (1924/2356, 81.7%) and upper respiratory tract infection (1720/2383, 72.2%). FluA, FluB and ADV were positive factors for upper respiratory tract infections. On the other hand, infection with RSVA, RSVB, PIV3, PIV4, HMPV, and EV/RHV were positively associated with lower respiratory tract infections; and PIV1, PIV2, and PIV3 were positively associated with croup. Conclusions This is the first study in Macao to determine the viral etiology and epidemiology of pediatric patients hospitalized for ARIs. The study findings can contribute to the awareness of pathogen, appropriate preventative measure, accurate diagnosis, and proper clinical management of respiratory viral infections among children in Macao.

scholarly journals 2018 recommendations for the management of community acquired pneumonia

2018 ◽  
Vol 44 (5) ◽  
pp. 405-423 ◽  
Author(s):  
Ricardo de Amorim Corrêa ◽  
Andre Nathan Costa ◽  
Fernando Lundgren ◽  
Lessandra Michelin ◽  
Mara Rúbia Figueiredo ◽  
...  
Keyword(s):  
Cause Of Death ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
Scientific Evidence ◽  
Prognostic Score ◽  
Community Acquired Pneumonia ◽  
Lower Respiratory Tract Infections ◽  
Etiologic Agents ◽  
Tract Infections ◽  
Respiratory Microbiota

ABSTRACT Community-acquired pneumonia (CAP) is the leading cause of death worldwide. Despite the vast diversity of respiratory microbiota, Streptococcus pneumoniae remains the most prevalent pathogen among etiologic agents. Despite the significant decrease in the mortality rates for lower respiratory tract infections in recent decades, CAP ranks third as a cause of death in Brazil. Since the latest Guidelines on CAP from the Sociedade Brasileira de Pneumologia e Tisiologia (SBPT, Brazilian Thoracic Association) were published (2009), there have been major advances in the application of imaging tests, in etiologic investigation, in risk stratification at admission and prognostic score stratification, in the use of biomarkers, and in the recommendations for antibiotic therapy (and its duration) and prevention through vaccination. To review these topics, the SBPT Committee on Respiratory Infections summoned 13 members with recognized experience in CAP in Brazil who identified issues relevant to clinical practice that require updates given the publication of new epidemiological and scientific evidence. Twelve topics concerning diagnostic, prognostic, therapeutic, and preventive issues were developed. The topics were divided among the authors, who conducted a nonsystematic review of the literature, but giving priority to major publications in the specific areas, including original articles, review articles, and systematic reviews. All authors had the opportunity to review and comment on all questions, producing a single final document that was approved by consensus.

Medical Consultations After Typhoon Haiyan in a Field Hospital in the Philippines

2019 ◽  
Vol 14 (1) ◽  
pp. 34-38
Author(s):  
Julita Gil Cuesta ◽  
Joris Adriaan Frank van Loenhout ◽  
Maria Lourdes de Lara Banquesio ◽  
Masniza Mustaffa ◽  
Debarati Guha-Sapir
Keyword(s):  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
District Hospital ◽  
The Philippines ◽  
Upper Respiratory Tract ◽  
Field Hospital ◽  
Adult Men ◽  
Medical Consultations ◽  
Upper Respiratory ◽  
Tract Infections

ABSTRACTIntroduction and Objectives:Typhoon Haiyan partially destroyed the Ormoc District Hospital in the Philippines. A field hospital was established to replace its outpatient department for 5 weeks. We investigated the reasons for medical consultation in the field hospital.Methods:We described the consultations by sex, age, week, and diagnosis according to the Surveillance in Post-Extreme Emergencies and Disasters system. We compared the number and proportion of upper respiratory tract infections (URTIs) with a control season in 2014.Results:We included 6785 consultations, 55.9% from women. The majority of consultations were communicable diseases (88.2%) followed by noncommunicable (7.1%) and injuries (5.6%). Males suffered more often from injuries than women (66.0% vs 34.0%). Consultations due to injuries decreased from 10.0% in the first to 2.9% in the last week. The most frequent diagnosis over the study period was acute respiratory infections (ARIs) (73.1%), of which 83.0% were children. The number of daily URTIs was higher than in a similar 2014 period.Conclusions:ARI was the most prevalent diagnosis. We recommend ARI treatments being fully accessible after such a disaster. During the first week, injury prevention should focus on adult men. Studies after natural disasters should include control periods to better understand disease distribution, ultimately improving the prioritization in disasters.

scholarly journals Characterization of the microflora of ventilator-associated respiratory tract infections in patients with severe trauma

2015 ◽  
Vol 20 (1) ◽  
pp. 8-13
Author(s):  
O. A Orlova ◽  
V. G Akimkin
Keyword(s):  
Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
Severe Trauma ◽  
Surgical Intensive Care Unit ◽  
Surgical Intensive Care ◽  
Microbial Associations ◽  
Initial Severity ◽  
Tract Infections

Rationale The relevance of ventilator-associated respiratory tract infections in severe injury patients (SIP) is associated with both features of causative pathogens and the initial severity of the state of patients. Among causative pathogens nosocomial flora is dominant. Purpose - to perform an analysis of the microbiological monitoring of ventilator-associated respiratory tract infections in SIP. The analysis was based on the results of a prospective epidemiological, clinical, and instrumental study of 100 SIP with ventilator-associated respiratory tract infections, stayed in the surgical intensive care unit. The proportion of ventilator-associated respiratory infections in the structure of nosocomial infections in these patients is between 90 - 95%, at that there was revealed the prevalence of nosocomial pneumonia (61%). Ventilator-associated respiratory tract infection most commonly occurs during the first 10 days of mechanical ventilation. The prevailing flora was represented by Gram negative Acinetobacter baumamnnii (40.3 ± 2.1%) and Pseudomonas aeruginosa (38.4% ± 3.2%). Isolated microorganisms possessed multiple antibiotic resistance, with the greatest extent to aminoglycosides - 69.5%, fluoroquinolones - 40.3%, penicillin - 37.6%; cephalosporins (third generation) - 33.8%. There is noted marked preponderance of microbial associations compared with monocultures 57.1 ± 5.3%.

scholarly journals Usefulness of procalcitonin (PCT), C-reactive protein (CRP), and white blood cell (WBC) levels in the differential diagnosis of acute bacterial, viral, and mycoplasmal respiratory tract infections in children

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yang Li ◽  
Lanfang Min ◽  
Xin Zhang
Keyword(s):  
Differential Diagnosis ◽  
Respiratory Tract ◽  
Bacterial Infection ◽  
Bacterial Infections ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
Diagnostic Value ◽  
Significant Difference ◽  
Group A ◽  
Tract Infections

Abstract Background There is a lack of studies comparing PCT, CRP and WBC levels in the differential diagnosis of acute bacterial, viral, and mycoplasmal respiratory tract infections. It is necessary to explore the correlation between above markers and different types of ARTI. Methods 108 children with confirmed bacterial infection were regarded as group A, 116 children with virus infection were regarded as group B, and 122 children with mycoplasmal infection were regarded as group C. The levels of PCT, CRP and WBC of the three groups were detected and compared. Results The levels of PCT, CRP and WBC in group A were significantly higher than those in groups B and C (p < 0.05). The positive rate of combined detection of PCT, CRP and WBC was significant higher than that of single detection. There was no significant difference in PCT, CRP and WBC levels between the group of G+ bacterial infection and G− bacterial infection (p > 0.05). ROC curve results showed that the AUC of PCT, CRP and WBC for the diagnosis of bacterial respiratory infections were 0.65, 0.55, and 0.58, respectively. Conclusions PCT, CRP and WBC can be combined as effective indicators for the identification of acute bacterial or no-bacterial infections in children. The levels of PCT and CRP have higher differential diagnostic value than that of WBC in infection, and the combined examination of the three is more valuable in clinic.

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