Supplemental Data for: A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota v1 (protocols.io.yktfuwn)

Accurate and informative microbiological testing is essential for guiding diagnosis and management of pneumonia in patients who are critically ill. Sampling of tracheal aspirate (TA) is less invasive compared with mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach in patients who are mechanically ventilated, despite the historical belief that TA was suboptimal due to contamination from oral microbes. Advancements in metagenomic next-generation sequencing (mNGS) now permit assessment of airway microbiota without a need for culture and, as such, provide an opportunity to examine differences between mBAL and TA at a resolution previously unachievable. Here, we engaged shotgun mNGS to assess quantitatively the airway microbiome in matched mBAL and TA specimens from a prospective cohort of critically ill adults. We observed moderate differences between sample types across all subjects; however, we found significant compositional similarity in subjects with bacterial pneumonia, whose microbial communities were characterized by dominant pathogens. In contrast, in patients with noninfectious acute respiratory illnesses, significant differences were observed between sample types. Our findings suggest that TA sampling provides a similar assessment of airway microbiota as more invasive testing by mBAL in patients with pneumonia.

Download Full-text

Malassezia furfur in the tracheal aspirate of ventilated neonates – a prospective, longitudinal study

Zeitschrift für Geburtshilfe und Neonatologie ◽

10.1055/s-2005-871370 ◽

2005 ◽

Vol 209 (S 1) ◽

Author(s):

E Yilmaz ◽

B Müller-Edenborn ◽

R Mittal ◽

A Holzinger ◽

A Schulze ◽

...

Keyword(s):

Longitudinal Study ◽

Tracheal Aspirate ◽

Malassezia Furfur ◽

Prospective Longitudinal Study ◽

Prospective Longitudinal

Download Full-text

Pseudomonas laryngeal perichondritis: unexpected diagnosis

BMJ Case Reports ◽

10.1136/bcr-2020-237129 ◽

2020 ◽

Vol 13 (12) ◽

pp. e237129

Author(s):

Siti Salwa Zainal Abidin ◽

Thean Yean Kew ◽

Mawaddah Azman ◽

Marina Mat Baki

Keyword(s):

Diabetes Mellitus ◽

Pseudomonas Aeruginosa ◽

Vocal Fold ◽

Histopathological Examination ◽

Thyroid Cartilage ◽

Tracheal Aspirate ◽

Good Recovery ◽

Antituberculous Drug ◽

False Vocal ◽

Oral Ciprofloxacin

A 57-year-old male chronic smoker with underlying diabetes mellitus presented with dysphonia associated with cough, dysphagia and reduced effort tolerance of 3 months’ duration. Videoendoscope finding revealed bilateral polypoidal and erythematous true and false vocal fold with small glottic airway. The patient was initially treated as having tuberculous laryngitis and started on antituberculous drug. However, no improvement was observed. CT of the neck showed erosion of thyroid cartilage, which points to laryngeal carcinoma as a differential diagnosis. However, the erosion was more diffuse and appeared systemic in origin. The diagnosis of laryngeal perichondritis was made when the histopathological examination revealed features of inflammation, and the tracheal aspirate isolated Pseudomonas aeruginosa. The patient made a good recovery following treatment with oral ciprofloxacin.

Download Full-text

Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children

Journal of the Pediatric Infectious Diseases Society ◽

10.1093/jpids/piaa141 ◽

2021 ◽

Author(s):

Andrea Coleman ◽

Seweryn Bialasiewicz ◽

Robyn L Marsh ◽

Eva Grahn Håkansson ◽

Kyra Cottrell ◽

...

Keyword(s):

Healthy Children ◽

Upper Respiratory Tract ◽

Indigenous Australian ◽

Ionization Time ◽

Australian Aboriginal ◽

Flight Mass Spectrometry ◽

Upper Respiratory ◽

Corynebacterium Pseudodiphtheriticum ◽

Nasal Microbiota ◽

Respiratory Microbiota

Abstract Background We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health. Methods In total, 103 Indigenous Australian children aged 2–7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children’s ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis. Results Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P < .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P < .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children. Conclusions Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.

Download Full-text

Systems Biology and Bile Acid Signalling in Microbiome-Host Interactions in the Cystic Fibrosis Lung

Antibiotics ◽

10.3390/antibiotics10070766 ◽

2021 ◽

Vol 10 (7) ◽

pp. 766

Author(s):

David F. Woods ◽

Stephanie Flynn ◽

Jose A. Caparrós-Martín ◽

Stephen M. Stick ◽

F. Jerry Reen ◽

...

Keyword(s):

Cystic Fibrosis ◽

Bile Acids ◽

Host Response ◽

Signal Molecules ◽

Therapeutic Approaches ◽

Related Factors ◽

Host Interactions ◽

Important Host ◽

Respiratory Microbiota

The study of the respiratory microbiota has revealed that the lungs of healthy and diseased individuals harbour distinct microbial communities. Imbalances in these communities can contribute to the pathogenesis of lung disease. How these imbalances occur and establish is largely unknown. This review is focused on the genetically inherited condition of Cystic Fibrosis (CF). Understanding the microbial and host-related factors that govern the establishment of chronic CF lung inflammation and pathogen colonisation is essential. Specifically, dissecting the interplay in the inflammation–pathogen–host axis. Bile acids are important host derived and microbially modified signal molecules that have been detected in CF lungs. These bile acids are associated with inflammation and restructuring of the lung microbiota linked to chronicity. This community remodelling involves a switch in the lung microbiota from a high biodiversity/low pathogen state to a low biodiversity/pathogen-dominated state. Bile acids are particularly associated with the dominance of Proteobacterial pathogens. The ability of bile acids to impact directly on both the lung microbiota and the host response offers a unifying principle underpinning the pathogenesis of CF. The modulating role of bile acids in lung microbiota dysbiosis and inflammation could offer new potential targets for designing innovative therapeutic approaches for respiratory disease.

Download Full-text

267 Identification of interleukin 2 and 4 messenger RNA in bronchial alveolar lavage cells and allergen specific cell lines from atopic individuals

Journal of Allergy and Clinical Immunology ◽

10.1016/0091-6749(91)91550-d ◽

1991 ◽

Vol 87 (1) ◽

pp. 206 ◽

Cited By ~ 3

Author(s):

J DISHUK ◽

C WATSON ◽

L BORISH ◽

L ROSENWASSER

Keyword(s):

Cell Lines ◽

Messenger Rna ◽

Interleukin 2 ◽

Specific Cell ◽

Bronchial Alveolar Lavage

Download Full-text

Diversity of staphylococcal cassette chromosome mec structures in coagulase-negative staphylococci and relationship to drug resistance

Journal of Medical Microbiology ◽

10.1099/jmm.0.015800-0 ◽

2010 ◽

Vol 59 (3) ◽

pp. 323-329 ◽

Cited By ~ 25

Author(s):

Elvira Garza-González ◽

Daniel López ◽

Cesar Pezina ◽

Walter Muruet ◽

Virgilio Bocanegra-García ◽

...

Keyword(s):

Drug Resistance ◽

Tertiary Care ◽

Tracheal Aspirate ◽

Type I ◽

Care Hospital ◽

Coagulase Negative Staphylococci ◽

High Genetic Diversity ◽

Type Iii ◽

Broth Microdilution Method ◽

Staphylococcal Cassette Chromosome

The objective of this study was to determine the distribution of staphylococcal cassette chromosome mec (SCCmec) elements in meticillin-resistant coagulase-negative staphylococci (MR-CoNS) isolated from a tertiary-care hospital in Mexico and to examine the relationship to drug resistance. Fifty selected MR-CoNS isolates collected from catheters (n=15), blood (n=15), bone (n=9), bronchial lavage (n=2) and urine (n=2) and one isolate each from an abscess, cerebrospinal fluid, eye, pleural effusion, synovial fluid, tracheal aspirate and wound secretion were examined. Susceptibility testing was performed by the broth microdilution method. SCCmec types were determined by multiplex PCR and PFGE was carried out as described previously for Staphylococcus aureus. Among the MR-CoNS strains studied, the most frequently isolated species were Staphylococcus epidermidis (n=26) and Staphylococcus haemolyticus (n=13). Staphylococcus cohnii (n=5), Staphylococcus hominis (n=3), Staphylococcus sciuri (n=1), Staphylococcus pasteuri (n=1) and the recently described species Staphylococcus pettenkoferi (n=1) were also identified. The most frequent MR-CoNS genotype identified was SCCmec type IVa in S. epidermidis isolates, which also showed a high diversity in their PFGE patterns. A clone was found that amplified both SCCmec III and V elements in five isolates examined. The single MR S. pettenkoferi isolate harboured SCCmec type IVd and the single MR S. pasteuri isolate harboured SCCmec type I. The carriage of SCCmec type III was associated with resistance or intermediate resistance to meropenem (P <0.05). These results confirm the high prevalence of S. epidermidis SCCmec IVa and the high genetic diversity among MR-CoNS strains. As far as is known, this is the first report describing the newly identified S. pettenkoferi possessing SCCmec IVd and S. pasteuri harbouring SCCmec type I. MR-CoNS harbouring SCCmec type III were found to be more resistant to meropenem.

Download Full-text