1
|
Doxey AC, Abu Mazen N, Homm M, Chu V, Hunjan M, Lobb B, Lee S, Kurs-Lasky M, Williams JV, MacDonald W, Johnson M, Hirota JA, Shaikh N. Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection. Genome Med 2025; 17:22. [PMID: 40098147 PMCID: PMC11912616 DOI: 10.1186/s13073-025-01447-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 03/03/2025] [Indexed: 03/19/2025] Open
Abstract
BACKGROUND Acute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections (URIs) is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential to overcome several limitations of other methods. In addition, RNA-seq may reveal novel host-response biomarkers for development of future diagnostic assays that distinguish bacterial from viral infections. There are however no available RNA-seq datasets of pediatric AS that provide a comprehensive view of both pathogen etiology and host immune response. METHODS Here, we performed untargeted RNA-seq (metatranscriptomics) of nasopharyngeal samples from 221 children with AS and performed a comprehensive analysis of pathogen etiology and the impact of bacterial and viral infections on host immune responses. Accuracy of RNA-seq-based pathogen detection was evaluated by comparison with culture tests for three common bacterial pathogens and qRT-PCR tests for 12 respiratory viruses. Host gene expression patterns were explored to identify potential host responses that distinguish bacterial from viral infections. RESULTS RNA-seq-based pathogen detection showed high concordance with culture or qRT-PCR, showing 87%/81% sensitivity (sens) / specificity (spec) for detecting three AS-associated bacterial pathogens, and 86%/92% (sens/spec) for detecting 12 URI-associated viruses, respectively. RNA-seq also detected an additional 22 pathogens not tested for clinically and identified plausible pathogens in 11/19 (58%) of cases where no organism was detected by culture or qRT-PCR. We reconstructed genomes of 196 viruses across the samples including novel strains of coronaviruses, respiratory syncytial virus, and enterovirus D68, which provide useful genomic data for ongoing pathogen surveillance programs. By analyzing host gene expression, we identified host-response signatures that differentiate bacterial and viral infections, revealing hundreds of candidate gene biomarkers for future diagnostic assays. CONCLUSIONS Our study provides a one-of-kind dataset that profiles the interplay between pathogen infection and host responses in pediatric AS and URI. It reveals bacterial and viral-specific host responses that could enable new diagnostic approaches and demonstrates the potential of untargeted RNA-seq in diagnostic analysis of AS and URI.
Collapse
Affiliation(s)
- Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
- Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
- Faculty of Health Sciences, Department of Medicine, McMaster University, 1200 Main Street West, ON, Hamilton, L8N 3Z5, Canada.
| | - Nooran Abu Mazen
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Max Homm
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Vivian Chu
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Manjot Hunjan
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Briallen Lobb
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sojin Lee
- Division of General Academic Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224-1334, USA
| | - Marcia Kurs-Lasky
- Division of General Academic Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224-1334, USA
| | - John V Williams
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, 1218 Scaife Hall 3550 Terrace Street, Pittsburgh, PA, USA
| | - William MacDonald
- Division of General Academic Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224-1334, USA
| | - Monika Johnson
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, 1218 Scaife Hall 3550 Terrace Street, Pittsburgh, PA, USA
| | - Jeremy A Hirota
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Firestone Institute for Respiratory Health, St. Joseph's Hospital, 50 Charlton Avenue East, Hamilton, ON, L8N 4A6, Canada
- Department of Medicine, University of British Columbia, 2775 Laurel Street Vancouver, British Columbia, V5Z 1M9, Canada
- Faculty of Health Sciences, Department of Medicine, McMaster University, 1200 Main Street West, ON, Hamilton, L8N 3Z5, Canada
| | - Nader Shaikh
- Division of General Academic Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224-1334, USA.
| |
Collapse
|
2
|
Zhang W, Li L, Zhang Y, Dai J, Qiu C, Chen R, Shi F. Perturbations in the airway microbiome are associated with type 2 asthma phenotype and severity. Ann Allergy Asthma Immunol 2025; 134:296-305.e9. [PMID: 39549985 DOI: 10.1016/j.anai.2024.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/14/2024] [Accepted: 11/04/2024] [Indexed: 11/18/2024]
Abstract
BACKGROUND Airway microbiome has been linked to asthma heterogeneity, yet little is known about the associations between airway microbiota and type 2 (T2) asthma phenotype and severity. OBJECTIVE To determine the relationship of nasopharyngeal (NP) and induced sputum (IS) microbiota to the phenotypic features of T2 asthma. METHODS NP and IS samples from subjects with T2 mild-to-moderate asthma (n = 23), subjects with severe asthma (n = 21), and healthy controls (n = 16) were analyzed. Bacterial microbiota and functional profiles were compared. The correlation between microbial communities and clinical and inflammatory features was evaluated in individuals with asthma of 2 statuses. RESULTS Differences in NP and IS microbiota were associated with T2 asthma phenotype. Alterations in NP microbiota were more reflective of T2 inflammation and severity, with additional stratification of a subgroup characterized by significant elevations in T2 inflammatory biomarkers and reductions in bacterial richness and diversity (P < .05). Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, and Rhodococcus were identified as hub taxa within NP microbial network in T2 severe asthma, which were prevalent in the entire airway and involved in bacterial functions including inflammatory and steroid responses (P < .05). The composition and diversity of IS microbiota were complex, with Veillonella as the most altered genus, having an increase with increasing asthma severity. CONCLUSION Our work revealed the significant associations of microbiota perturbations throughout the entire respiratory tract to the extent of T2 inflammation, phenotype and severity in T2 asthma. The specific taxa identified invite further mechanistic investigations to unravel their possibility as biomarkers and therapeutic targets for T2 severe asthma.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Lifei Li
- Key Laboratory of Shenzhen Respiratory Diseases, Institute of Shenzhen Respiratory Diseases, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People's Republic of China
| | - Yu Zhang
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Junjie Dai
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Chen Qiu
- Key Laboratory of Shenzhen Respiratory Diseases, Institute of Shenzhen Respiratory Diseases, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People's Republic of China
| | - Rongchang Chen
- Key Laboratory of Shenzhen Respiratory Diseases, Institute of Shenzhen Respiratory Diseases, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People's Republic of China
| | - Fei Shi
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China.
| |
Collapse
|
3
|
AbuMazen N, Chu V, Hunjan M, Lobb B, Lee S, Kurs-Lasky M, Williams JV, MacDonald W, Johnson M, Hirota JA, Shaikh N, Doxey AC. Nasopharyngeal metatranscriptomics reveals host-pathogen signatures of pediatric sinusitis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.03.24303663. [PMID: 38496499 PMCID: PMC10942525 DOI: 10.1101/2024.03.03.24303663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Acute sinusitis (AS) is the fifth leading cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections in children is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential to overcome several limitations of other methods. However, the utility of sequencing-based approaches in analysis of AS has not been fully explored. Here, we performed RNA-seq of nasopharyngeal samples from 221 children with clinically diagnosed AS to characterize their pathogen and host-response profiles. Results from RNA-seq were compared with those obtained using culture for three common bacterial pathogens and qRT-PCR for 12 respiratory viruses. Metatranscriptomic pathogen detection showed high concordance with culture or qRT-PCR, showing 87%/81% sensitivity (sens) / specificity (spec) for detecting bacteria, and 86%/92% (sens/spec) for viruses, respectively. We also detected an additional 22 pathogens not tested for in the clinical panel, and identified plausible pathogens in 11/19 (58%) of cases where no organism was detected by culture or qRT-PCR. We assembled genomes of 205 viruses across the samples including novel strains of coronaviruses, respiratory syncytial virus (RSV), and enterovirus D68. By analyzing host gene expression, we identified host-response signatures that distinguished bacterial and viral infections and correlated with pathogen abundance. Ultimately, our study demonstrates the potential of untargeted metatranscriptomics for in depth analysis of the etiology of AS, comprehensive host-response profiling, and using these together to work towards optimized patient care.
Collapse
Affiliation(s)
- Nooran AbuMazen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, Ontario, Canada
| | - Vivian Chu
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, Ontario, Canada
| | - Manjot Hunjan
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, Ontario, Canada
| | - Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, Ontario, Canada
| | - Sojin Lee
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics
| | - Marcia Kurs-Lasky
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics
| | - John V. Williams
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William MacDonald
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics
| | - Monika Johnson
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jeremy A. Hirota
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph’s Hospital, Hamilton, Ontario, Canada
- University of British Columbia, Department of Medicine, Vancouver, British Columbia, Canada
- McMaster University, Department of Medicine, Hamilton, Ontario, Canada
| | - Nader Shaikh
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, Ontario, Canada
- Cheriton School of Computer Science, Waterloo, Ontario, Canada
- McMaster University, Department of Medicine, Hamilton, Ontario, Canada
| |
Collapse
|
4
|
Girma S, Bekele T, Leta S, Tegegne DT, Demissie T, Hadush B, Aragaw K, Tufa TB, Tolera TS, Tafess K. Evaluation of the effect of therapeutic durations on small ruminant bacterial pneumonia. BMC Vet Res 2024; 20:68. [PMID: 38395815 PMCID: PMC10893678 DOI: 10.1186/s12917-024-03917-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Sheep and goat production in Ethiopia is hindered by numerous substandard production systems and various diseases. Respiratory disease complexes (RDC) pose a significant threat to the productivity of these animals. Pneumonia is a common manifestation of respiratory disease complexes and often necessitates a prolonged course of antibiotic treatment. This study aimed to optimize and propose the ideal duration of therapy for pneumonia in sheep and goats. METHODS The study was conducted from February to June 2021 at the Veterinary Teaching Hospital of the College of Veterinary Medicine and Agriculture, Addis Ababa University. The study recruited 54 sheep and goats presented to the hospital for treatment with a confirmed RDC as determined based on clinical signs and bacteriological methods. The animals were randomly allocated to 5 groups each group receiving 10% oxytetracycline (Phenxyl, Phenix, Belgum) intramuscularly for a duration of 3, 4, 5, 6 and 7 consecutive days. The treatment outcomes were assessed by recording vital signs (body temperature, respiratory rate, heart rate, coughing, and nasal discharges), performing lung ultrasonography (L-USG) as well as collection of nasal swabs for bacterial isolation and molecular identification before and after completion of the treatment. An ordered logistic regression model with random effects was employed to determine the optimal therapeutic duration, taking into account the cumulative scores of the outcome variables across the different groups. RESULTS Among the 54 sheep and goats treated with 10% oxytetracycline, a total of 74.07% (95% CI, 60.35-85.04) achieved complete recovery, as confirmed through clinical, ultrasound, and bacteriological methods. In Group 1 (G1), out of 12 sheep and goats, 8 (83.0%) recovered completely; in Group 2 (G2), out of 11 animals, 9 (82.0%) recovered completely; in Group 3 (G3), out of 11 animals, 10 (93.0%) recovered completely; in Group 4 (G4), out of 9 animals, 9 (100.0%) recovered completely; and in Group 5 (G5), out of 11 animals, 10 (91.0%) recovered completely. Bacteriological examination of nasal swabs indicated involvement of M. hemolytica in 27 (50.00%) and P. multocida in 13 (24.07%) of pneumonic animals. Detection of specific marker genes confirmed only five of the presumptive M. hemolytica isolates, whilst no isolates tested positive for P. multocida. Post-treatment samples collected from recovered animals did not yield any M. hemolytica nor P. multocida. Based on results from clinical signs, L-USG, and bacterial infection variables, the group of sheep and goats treated for seven consecutive days (G5) showed the highest recovery score compared to the other groups, and there was a statistically significant difference (coefficient (β) = - 2.296, p = 0.021) in variable score between G5 and G1. These findings suggest that the administration of 10% oxytetracycline for a full course of seven consecutive days resulted in symptomatic and clinical recovery rates from respiratory disease in sheep and goats.
Collapse
Affiliation(s)
- Sisay Girma
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Tesfaye Bekele
- School of Veterinary Medicine, Wolaita Sodo University, Wolaita Sodo, Ethiopia
| | - Samson Leta
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Desiye Tesfaye Tegegne
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural Research Center, P.O. Box 249, Holeta, Ethiopia
| | - Tilaye Demissie
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Birhanu Hadush
- Department of Veterinary Clinical Medicine and Epidemiology, College of Veterinary Sciences, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Kassaye Aragaw
- Faculty of Veterinary Medicine, Hawassa University, P.O. Box 05, Hawassa, Ethiopia
| | - Takele Beyene Tufa
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Teshale Sori Tolera
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Ketema Tafess
- Institute of Pharmaceutical Sciences, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| |
Collapse
|
5
|
Shaikh N, Hoberman A, Shope TR, Jeong JH, Kurs-Lasky M, Martin JM, Bhatnagar S, Muniz GB, Block SL, Andrasko M, Lee MC, Rajakumar K, Wald ER. Identifying Children Likely to Benefit From Antibiotics for Acute Sinusitis: A Randomized Clinical Trial. JAMA 2023; 330:349-358. [PMID: 37490085 PMCID: PMC10370259 DOI: 10.1001/jama.2023.10854] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/01/2023] [Indexed: 07/26/2023]
Abstract
Importance The large overlap between symptoms of acute sinusitis and viral upper respiratory tract infection suggests that certain subgroups of children being diagnosed with acute sinusitis, and subsequently treated with antibiotics, derive little benefit from antibiotic use. Objective To assess if antibiotic therapy could be appropriately withheld in prespecified subgroups. Design, Setting, and Participants Randomized clinical trial including 515 children aged 2 to 11 years diagnosed with acute sinusitis based on clinical criteria. The trial was conducted between February 2016 and April 2022 at primary care offices affiliated with 6 US institutions and was designed to evaluate whether symptom burden differed in subgroups defined by nasopharyngeal Streptococcus pneumoniae, Haemophilus influenzae, or Moraxella catarrhalis on bacterial culture and by the presence of colored nasal discharge. Interventions Oral amoxicillin (90 mg/kg/d) and clavulanate (6.4 mg/kg/d) (n = 254) or placebo (n = 256) for 10 days. Main Outcomes and Measures The primary outcome was symptom burden based on daily symptom scores on a validated scale (range, 0-40) during the 10 days after diagnosis. Secondary outcomes included treatment failure, adverse events including clinically significant diarrhea, and resource use by families. Results Most of the 510 included children were aged 2 to 5 years (64%), male (54%), White (52%), and not Hispanic (89%). The mean symptom scores were significantly lower in children in the amoxicillin and clavulanate group (9.04 [95% CI, 8.71 to 9.37]) compared with those in the placebo group (10.60 [95% CI, 10.27 to 10.93]) (between-group difference, -1.69 [95% CI, -2.07 to -1.31]). The length of time to symptom resolution was significantly lower for children in the antibiotic group (7.0 days) than in the placebo group (9.0 days) (P = .003). Children without nasopharyngeal pathogens detected did not benefit from antibiotic treatment as much as those with pathogens detected; the between-group difference in mean symptom scores was -0.88 (95% CI, -1.63 to -0.12) in those without pathogens detected compared with -1.95 (95% CI, -2.40 to -1.51) in those with pathogens detected. Efficacy did not differ significantly according to whether colored nasal discharge was present (the between-group difference was -1.62 [95% CI, -2.09 to -1.16] for colored nasal discharge vs -1.70 [95% CI, -2.38 to -1.03] for clear nasal discharge; P = .52 for the interaction between treatment group and the presence of colored nasal discharge). Conclusions In children with acute sinusitis, antibiotic treatment had minimal benefit for those without nasopharyngeal bacterial pathogens on presentation, and its effects did not depend on the color of nasal discharge. Testing for specific bacteria on presentation may represent a strategy to reduce antibiotic use in this condition. Trial Registration ClinicalTrials.gov Identifier: NCT02554383.
Collapse
Affiliation(s)
- Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alejandro Hoberman
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Timothy R. Shope
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jong-Hyeon Jeong
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania
| | - Marcia Kurs-Lasky
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Judith M. Martin
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sonika Bhatnagar
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Gysella B. Muniz
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Melissa Andrasko
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Matthew C. Lee
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kumaravel Rajakumar
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ellen R. Wald
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison
| |
Collapse
|
6
|
Janeczek K, Emeryk A, Zimmer Ł, Poleszak E, Ordak M. Nasal carriage of
Staphylococcus aureus
in children with grass pollen‐induced allergic rhinitis and the effect of polyvalent mechanical bacterial lysate immunostimulation on carriage status: A randomized controlled trial. Immun Inflamm Dis 2022; 10:e584. [PMID: 34965026 PMCID: PMC8926494 DOI: 10.1002/iid3.584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022] Open
Abstract
Background Numerous studies indicate that Staphylococcus aureus (S. aureus) colonizing the nasal cavity plays a role in the pathogenesis of allergic rhinitis (AR). This bacterium is able to produce a variety of toxins with superantigenic properties that can exacerbate allergic inflammation. Objective The objective of the study was to evaluate the ability of polyvalent mechanical bacterial lysate (PMBL) to eliminate S. aureus nasal carriage in children with grass pollen‐induced AR. Methods This randomized, double‐blind, placebo‐controlled study included 80 children aged 5–17 years with seasonal AR (SAR). At the randomization visit and after 12 weeks of the study, a swab was taken from the region of the middle nasal meatus. Standard microbiology culture and identification techniques were used to analyze the swab contents. Results Nasal colonization by S. aureus was confirmed in 29 children (42%), with Moraxella catarrhalis in three participants (4.4%). Physiological flora was detected in 37 children. No statistically significant differences were observed between the two measurement points in both the PMBL and placebo groups with respect to the number of patients whose nasal swab cultures showed a growth of S. aureus (p = 1). Both groups also showed no significant changes in the mean number of S. aureus colonies in nasal swab cultures taken at baseline and after 12 weeks of the study (PMBL group p = .41; placebo group p = .16). Conclusion Almost every second child with SAR is S. aureus nasal carrier. Sublingual administration of PMBL in children with grass pollen‐induced AR did not affect S. aureus nasal colonization. Therefore, PMBL should not be used for the eradication of S. aureus from the nasal cavity.
Collapse
Affiliation(s)
- Kamil Janeczek
- Department of Pulmonary Diseases and Children Rheumatology Medical University of Lublin Lublin Poland
| | - Andrzej Emeryk
- Department of Pulmonary Diseases and Children Rheumatology Medical University of Lublin Lublin Poland
| | - Łukasz Zimmer
- Department of Applied and Social Pharmacy Medical University of Lublin Lublin Poland
| | - Ewa Poleszak
- Department of Applied and Social Pharmacy Medical University of Lublin Lublin Poland
| | - Michał Ordak
- Department of Pharmacodynamics Centre for Preclinical Research and Technology, Medical University of Warsaw Warsaw Poland
| |
Collapse
|
7
|
Lopez SMC, Shaikh N, Johnson M, Liu H, Martin JM, Williams JV. Viral Coinfection and Nasal Cytokines in Children With Clinically Diagnosed Acute Sinusitis. Front Pediatr 2022; 9:783665. [PMID: 35096705 PMCID: PMC8791629 DOI: 10.3389/fped.2021.783665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Children with no pathogenic bacteria in the nasopharynx are unlikely to have acute bacterial sinusitis. We evaluated whether information on clinical presentation, viral co-detection, and mucosal cytokine levels could be used to predict presence of bacteria in the nasopharynx. Method: We obtained nasopharyngeal (NP) swabs from children diagnosed with acute sinusitis. NP swabs were processed for bacterial culture, viral PCR testing, and cytokine expression. We examined whether results of the bacterial culture could be predicted based on the presence of clinical information, presence of viruses or mucosal cytokine levels. Results: We enrolled 174 children; 123 (71%) had a positive culture for potentially pathogenic bacteria and 51 (29%) had normal flora. 122/174 (70%) tested positive for one or more viruses. Compared to children with normal flora, children with pathogenic bacteria were more likely to have viruses (p < 0.01), but this relationship disappeared when we adjusted for age. Children with pathogenic bacteria in their nasopharynx and children with normal flora had similar levels of nasal cytokines. Conclusion: In children with clinically diagnosed acute sinusitis, clinical presentation, levels of nasal cytokines, and presence of viruses do not differentiate children with and without pathogenic bacteria in their nasopharynx.
Collapse
Affiliation(s)
- Santiago M. C. Lopez
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, United States
- Sanford Research, Environmental Influences on Health and Disease Group, Sioux Falls, SD, United States
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Monika Johnson
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Hui Liu
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Judith M. Martin
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
8
|
Mikkili I, Karlapudi AP, Venkateswarulu TC, Kodali VP, Macamdas DSS, Sreerama K. Potential of artificial intelligence to accelerate diagnosis and drug discovery for COVID-19. PeerJ 2021; 9:e12073. [PMID: 34707924 PMCID: PMC8500072 DOI: 10.7717/peerj.12073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/05/2021] [Indexed: 12/24/2022] Open
Abstract
The coronavirus disease (COVID-19) pandemic has caused havoc worldwide. The tests currently used to diagnose COVID-19 are based on real time reverse transcription polymerase chain reaction (RT-PCR), computed tomography medical imaging techniques and immunoassays. It takes 2 days to obtain results from the RT-PCR test and also shortage of test kits creating a requirement for alternate and rapid methods to accurately diagnose COVID-19. Application of artificial intelligence technologies such as the Internet of Things, machine learning tools and big data analysis to COVID-19 diagnosis could yield rapid and accurate results. The neural networks and machine learning tools can also be used to develop potential drug molecules. Pharmaceutical companies face challenges linked to the costs of drug molecules, research and development efforts, reduced efficiency of drugs, safety concerns and the conduct of clinical trials. In this review, relevant features of artificial intelligence and their potential applications in COVID-19 diagnosis and drug development are highlighted.
Collapse
Affiliation(s)
- Indira Mikkili
- Biotechnology, Vignan’s Foundation for Science, Technology & Research, Guntur, Andhra Pradesh, India
| | - Abraham Peele Karlapudi
- Biotechnology, Vignan’s Foundation for Science, Technology & Research, Guntur, Andhra Pradesh, India
| | - T. C. Venkateswarulu
- Biotechnology, Vignan’s Foundation for Science, Technology & Research, Guntur, Andhra Pradesh, India
| | | | | | - Krupanidhi Sreerama
- Biotechnology, Vignan’s Foundation for Science, Technology & Research, Guntur, Andhra Pradesh, India
| |
Collapse
|
9
|
Seroconversion and Skin Mucosal Parameters during Koi Herpesvirus Shedding in Common Carp, Cyprinus carpio. Int J Mol Sci 2020; 21:ijms21228482. [PMID: 33187217 PMCID: PMC7696817 DOI: 10.3390/ijms21228482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Seroconversion and the mucosal lysozyme G (lysG), complement 3 (c3), and immunoglobulins M (IgMsec) and Z2 (IgZ2) were measured for up to 900 degree days (DD) in skin swabs from common carp exposed to koi herpesvirus (KHV or CyHV-3) at either a non-permissive temperature (12 °C) or permissive temperatures (17 and 22 °C), and in survivors subjected to temperature increase to 22 °C 500 DD after the initial exposure. The survival rate at 22 °C varied from 100% in fish initially exposed at 12 °C, to 20% at 17 °C and 0% at 22 °C. Viral shedding episodes lasted for up to 29 days (493 DD) for fish clinically infected at 17 °C, and up to 57 days (684 DD) for asymptomatic fish held at 12 °C. Up-regulation of lysG transcripts was measured at 17 and 22 °C. Down-regulation of c3 and IgMsec transcripts was measured independent of the water temperature, followed by up-regulation after the temperature increase coinciding with seroconversion and clearance of KHV from the skin mucus. IgZ2 mRNA showed a negative correlation with IgM transcripts. KHV subversion of the complement system at the mucosal site coupled with poor immunoglobulin secretion during the viral replication might contribute to the long window of viral shedding, thus facilitating viral transmission.
Collapse
|
10
|
Gorzynski JE, De Jong HN, Amar D, Hughes CR, Ioannidis A, Bierman R, Liu D, Tanigawa Y, Kistler A, Kamm J, Kim J, Cappello L, Neff NF, Rubinacci S, Delaneau O, Shoura MJ, Seo K, Kirillova A, Raja A, Sutton S, Huang C, Sahoo MK, Mallempati KC, Montero-Martin G, Osoegawa K, Jimenez-Morales D, Watson N, Hammond N, Joshi R, Fernandez-Vina M, Christle JW, Wheeler MT, Febbo P, Farh K, Schroth G, Desouza F, Palacios J, Salzman J, Pinsky BA, Rivas MA, Bustamante CD, Ashley EA, Parikh VN. High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020. [PMID: 32766602 DOI: 10.1101/2020.07.27.20163147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.
Collapse
|
11
|
Fuellen G, Liesenfeld O, Kowald A, Barrantes I, Bastian M, Simm A, Jansen L, Tietz-Latza A, Quandt D, Franceschi C, Walter M. The preventive strategy for pandemics in the elderly is to collect in advance samples & data to counteract chronic inflammation (inflammaging). Ageing Res Rev 2020; 62:101091. [PMID: 32454090 PMCID: PMC7245683 DOI: 10.1016/j.arr.2020.101091] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022]
Abstract
Fighting the current COVID-19 pandemic, we must not forget to prepare for the next. Since elderly and frail people are at high risk, we wish to predict their vulnerability, and intervene if possible. For example, it would take little effort to take additional swabs or dried blood spots. Such minimally-invasive sampling, exemplified here during screening for potential COVID-19 infection, can yield the data to discover biomarkers to better handle this and the next respiratory disease pandemic. Longitudinal outcome data can then be combined with other epidemics and old-age health data, to discover the best biomarkers to predict (i) coping with infection & inflammation and thus hospitalization or intensive care, (ii) long-term health challenges, e.g. deterioration of lung function after intensive care, and (iii) treatment & vaccination response. Further, there are universal triggers of old-age morbidity & mortality, and the elimination of senescent cells improved health in pilot studies in idiopathic lung fibrosis & osteoarthritis patients alike. Biomarker studies are needed to test the hypothesis that resilience of the elderly during a pandemic can be improved by countering chronic inflammation and/or removing senescent cells. Our review suggests that more samples should be taken and saved systematically, following minimum standards, and data be made available, to maximize healthspan & minimize frailty, leading to savings in health care, gains in quality of life, and preparing us better for the next pandemic, all at the same time.
Collapse
|
12
|
Abstract
Pediatric chronic rhinosinusitis (CRS) remains an elusive diagnostic medical condition, largely based on imperfect diagnostic criteria, lack of controlled studies of therapy, lack of measure for resolution, and lack of information of pediatric sinus microbiome dysbiosis. The true prevalence of pediatric CRS is unknown, and symptoms often over-lap with other diagnoses. We review the unmet needs in pediatric CRS, to highlight potential research opportunities to improve understanding and therapy of the disease process.
Collapse
|