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Scientific Reports Oct 2023Composition of pulmonary microbiome of patients with severe pneumonia is poorly known. The aim of this work was to analyse the lung microbiome of patients admitted...
Composition of pulmonary microbiome of patients with severe pneumonia is poorly known. The aim of this work was to analyse the lung microbiome of patients admitted to the intensive care unit (ICU) with severe community acquired pneumonia (CAP) between 2019 and 2021 in comparison with a control group of 6 patients undergoing digestive surgery. As a second objective, the diagnostic capabilities of metagenomics was also studied in a small group of selected patients. The lung microbiome of patients with viral (5 with Influenza A and 8 with SARS-CoV-2) pneumonia at admission showed a similar diversity as the control group (p = 0.140 and p = 0.213 respectively). Contrarily, the group of 12 patients with pneumococcal pneumonia showed a significant lower Simpson´s index (p = 0.002). In the control group (n = 6) Proteobacteria (36.6%), Firmicutes (24.2%) and Actinobacteria (23.0%) were the predominant phyla. In SARS-CoV-2 patients (n = 8), there was a predominance of Proteobacteria (mean 41.6%) (Moraxella and Pelomonas at the genus level), Actinobacteria (24.6%) (Microbacterium) and Firmicutes (22.8%) mainly Streptococcus, Staphylococcus and Veillonella. In patients with Influenza A pneumonia (n = 5) there was a predominance of Firmicutes (35.1%) mainly Streptococcus followed by Proteobacteria (29.2%) (Moraxella, Acinetobacter and Pelomonas). In the group of pneumococcal pneumonia (n = 12) two phyla predominated: Firmicutes (53.1%) (Streptococcus) and Proteobacteria (36.5%) (Haemophilus). In the 7 patients with non-pneumococcal bacterial pneumonia Haemophilus influenzae (n = 2), Legionella pneumophila (n = 2), Klebsiella pneumoniae, Streptococcus pyogenes and Leptospira were detected by metagenomics, confirming the diagnosis done using conventional microbiological techniques. The diversity of the respiratory microbiome in patients with severe viral pneumonia at ICU admission was similar to that of the control group. Contrarily, patients with pneumococcal pneumonia showed a lower grade of diversity. At initial stages of SARS-CoV-2 infection, no important alterations in the pulmonary microbiome were observed. The analysis of bacterial microbiome showed promising results as a diagnostic tool.
Topics: Humans; Pneumonia, Pneumococcal; Influenza, Human; Critical Illness; COVID-19; SARS-CoV-2; Lung; Bacteria; Microbiota; Pneumonia, Viral; Firmicutes; Proteobacteria; Community-Acquired Infections
PubMed: 37853062
DOI: 10.1038/s41598-023-45007-4 -
BioRxiv : the Preprint Server For... Sep 2023Associative connections have previously been identified between nasopharyngeal infections and infant mortality. The nasopharyngeal microbiome may potentially influence...
INTRODUCTION
Associative connections have previously been identified between nasopharyngeal infections and infant mortality. The nasopharyngeal microbiome may potentially influence the severity of these infections.
METHODS
We conducted an analysis of a longitudinal prospective cohort study of 1,981 infants who underwent nasopharyngeal sampling from 1 week through 14 weeks of age at 2-3-week intervals. In all, 27 microbiome samples from 9 of the infants in the cohort who developed fatal acute febrile illness (fAFI) were analyzed in pooled comparisons with 69 samples from 10 healthy comparator infants. We completed 16S rRNA amplicon gene sequencing all infant NP samples and characterized the maturation of the infant NP microbiome among the fAFI(+) and fAFI(-) infant cohorts.
RESULTS
Beta diversity measures of fAFI(-) infants were markedly higher than those of fAFI(+) infants. The fAFI(+) infant NP microbiome was marked by higher abundances of , and , with low relative presence of , and .
CONCLUSIONS
Our results suggest that nasopharyngeal microbiome dysbiosis precedes fAFI in young infants. Early dysbiosis, involving microbes such as , may play a role in the causal pathway leading to fAFI or could be a marker of other pathogenic forces that directly lead to fAFI.
PubMed: 37808661
DOI: 10.1101/2023.09.27.559805 -
Frontiers in Microbiology 2023Bovine respiratory disease (BRD) is a significant health problem in beef cattle production, resulting in considerable economic losses due to mortalities, cost of...
BACKGROUND
Bovine respiratory disease (BRD) is a significant health problem in beef cattle production, resulting in considerable economic losses due to mortalities, cost of treatment, and reduced feed efficiency. The onset of BRD is multifactorial, with numerous stressors being implicated, including transportation from farms to feedlots. In relation to animal welfare, regulations or practices may require mandatory rest times during transportation. Despite this, there is limited information on how transportation and rest stops affect the respiratory microbiota.
RESULTS
This study evaluated the effect of cattle source (ranch-direct or auction market-derived) and rest stop duration (0 or 8 h of rest) on the upper respiratory tract microbiota and its relationship to stress response indicators (blood cortisol and haptoglobin) of recently weaned cattle transported for 36 h. The community structure of bacteria was altered by feedlot placement. When cattle were off-loaded for a rest, several key bacterial genera associated with BRD (, , ) were increased for most sampling times after feedlot placement for the ranch-direct cattle group, compared to animals given no rest stop. Similarly, more sampling time points had elevated levels of BRD-associated genera when auction market cattle were compared to ranch-direct. When evaluated across time and treatments several genera including were positively correlated with blood cortisol concentrations.
CONCLUSION
This is the first study to assess the effect of rest during transportation and cattle source on the respiratory microbiota in weaned beef calves. The results suggest that rest stops and auction market placement may be risk factors for BRD, based solely on increased abundance of BRD-associated genera in the upper respiratory tract. However, it was not possible to link these microbiota to disease outcome, due to low incidence of BRD in the study populations. Larger scale studies are needed to further define how transportation variables impact cattle health.
PubMed: 37808284
DOI: 10.3389/fmicb.2023.1192763 -
Respiratory Research Oct 2023Chronic obstructive pulmonary disease (COPD) is a lung disease characterised by airflow-limiting inflammation and mucus production. Acute exacerbations are a major cause... (Observational Study)
Observational Study
BACKGROUND
Chronic obstructive pulmonary disease (COPD) is a lung disease characterised by airflow-limiting inflammation and mucus production. Acute exacerbations are a major cause of COPD-related morbidity and mortality and are mostly associated with bacterial or viral infections. A vaccine targeting non-typeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat), the main bacteria associated with exacerbations, was tested in a Phase 2 trial. We assessed "ex-vivo" expression of vaccine candidate and housekeeping genes pd, pe, pilA, gapA, ompP6 of NTHi, and uspA2, parE, polA of Mcat in sputum samples of COPD patients and determined whether expression of the vaccine candidate genes pd, pe, pilA (NTHi) and uspA2 (Mcat) differed between stable and exacerbation samples.
METHODS
A single-centre, prospective, observational cohort study was conducted where 123 COPD patients were seen on enrolment, followed monthly for 2 years, and reviewed after onset of acute exacerbations. We selected 69 patients with sputum samples positive for NTHi or Mcat by PCR during at least one stable and one exacerbation visit. mRNA was isolated from the sputum, and expression of NTHi and Mcat genes was analysed with RT-PCR. Statistical analyses compared mRNA concentrations between stable and exacerbation samples and in relationship to COPD severity and exacerbation frequency.
RESULTS
The vaccine candidate genes were variably expressed in sputum samples, suggesting they are expressed in the lung. Absolute and relative expression of all NTHi vaccine candidate genes and Mcat uspA2 were similar between exacerbation and stable samples. Expression of pd and pilA was slightly associated with the number of exacerbations in the year before enrolment, and uspA2 with the disease severity status at enrolment.
CONCLUSIONS
The NTHi-Mcat vaccine candidate genes were expressed in sputum samples, and each gene had a specific level of expression. No statistically significant differences in gene expression were detectable between stable and exacerbation samples. However, the history of COPD exacerbations was slightly associated with the expression of pd, pilA and uspA2. Trial registration NCT01360398 ( https://www.
CLINICALTRIALS
gov ).
Topics: Humans; Sputum; Prospective Studies; Pulmonary Disease, Chronic Obstructive; Haemophilus Vaccines; Moraxella catarrhalis; Haemophilus influenzae; RNA, Messenger; RNA
PubMed: 37798723
DOI: 10.1186/s12931-023-02525-z -
Journal of Veterinary Research Sep 2023Universally, in microbiological diagnostics the detection of live bacteria is essential. Rapid identification of pathogens enables appropriate remedial measures to be...
INTRODUCTION
Universally, in microbiological diagnostics the detection of live bacteria is essential. Rapid identification of pathogens enables appropriate remedial measures to be taken. The identification of many bacteria simultaneously facilitates the determination of the characteristics of the accompanying microbiota and/or the microbiological complexity of a given environment.
MATERIAL AND METHODS
The effectiveness of the VITEK2 Compact automated microbial identification system and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), analytical profile index (API) and Remel RapID tests were compared in identification of bacteria isolated from the alpaca gastrointestinal tract.
RESULTS
Most isolates were Gram-positive, such as and and , , and ; ; ; ; ; , , and (the last only isolated manually by API Coryne and the VITEK2 system and (CBC) card). was misidentified by MALDI-TOF MS as (currently ). Gram-positive and Gram-variable were also isolated. Gram-negative , , and ; ; subsp. ; and ; , and ; subsp. ; ; ; ; ; and were also found. The yeasts and were also present.
CONCLUSION
MALDI-TOF MS enabled the identification of pathogens and opportunistic pathogens from the alpaca gut which may represent a high risk to human and animal health.
PubMed: 37786852
DOI: 10.2478/jvetres-2023-0051 -
The Journal of Allergy and Clinical... Feb 2023Eosinophilic, noneosinophilic, or mixed granulocytic inflammations are the hallmarks of asthma heterogeneity. Depending on the priming of lung immune and structural... (Review)
Review
Eosinophilic, noneosinophilic, or mixed granulocytic inflammations are the hallmarks of asthma heterogeneity. Depending on the priming of lung immune and structural cells, subjects with asthma might generate immune responses that are T2-prone or T17-prone immune response. Bacterial infections caused by , , or spp. induce the secretion of IL-17, which in turn recruit neutrophils into the airways. Clinical studies and experimental models of asthma indicated that neutrophil infiltration induces a specific phenotype of asthma, characterized by an impaired response to corticosteroid treatment. The understanding of pathways that regulate the T17-neutrophils axis is critical to delineate and develop host-directed therapies that might control asthma and its exacerbation episodes that course with infectious comorbidities. In this review, we outline clinical and experimental studies on the role of airway epithelial cells, S100A9, and high mobility group box 1, which act in concert with the IL-17-neutrophil axis activated by bacterial infections, and are related with asthma that is difficult to treat. Furthermore, we report critically our view in the light of these findings in an attempt to stimulate further investigations and development of immunotherapies for the control of severe asthma.
PubMed: 37780109
DOI: 10.1016/j.jacig.2022.08.003 -
ACS Omega Sep 2023The chloroform extract of exhibited high antibacterial and antifungal activities against 12 bacterial and 4 fungal strains; therefore, it was subjected to...
The chloroform extract of exhibited high antibacterial and antifungal activities against 12 bacterial and 4 fungal strains; therefore, it was subjected to bioassay-guided isolation to afford six compounds (-). The structures were determined via one- and two-dimensional nuclear magnetic spectroscopy and high-resolution electrospray ionization mass spectrometry experiments. The compounds were identified as furanonaphthoquinones [majoranaquinone (), 2,3-dimethylnaphtho[2,3-]furan-4,9-dione ()], diterpenes [19-hydroxyabieta-8,11,13-trien-7-one (), 13,14-seco-13-oxo-19-hydroxyabieta-8-en-14-al ()], and flavonoids [sterubin () and majoranin ()]. Compounds and were first obtained from a natural source and compounds and were previously undescribed. Majoranaquinone () exhibited a high antibacterial effect against 4 , 1 , and 1 strains (MIC values between 7.8 μM and 1 mM). In the efflux pump inhibition assay, majoranaquinone () showed substantial activity in ATCC 25922 strain. Furthermore, was found to be an effective biofilm formation inhibitor on ATCC 25922 and K-12 AG100 bacteria. Our findings proved that bioactivities of majoranaquinone () significantly exceed those of the essential oil constituents; therefore, it should also be considered when assessing the antimicrobial effects of .
PubMed: 37780020
DOI: 10.1021/acsomega.3c03982 -
Microbiology Spectrum Sep 2023This prospective study assessed the value of initial microscopy evaluation of sputum samples submitted for rapid syndromic PCR-based testing. Bacterial detections by the...
This prospective study assessed the value of initial microscopy evaluation of sputum samples submitted for rapid syndromic PCR-based testing. Bacterial detections by the BioFire FilmArray Pneumonia Panel in 126 high- and 108 low-quality sputum samples, based on initial microscopy evaluation in samples from patients with lower respiratory tract infections were compared. We found that high-quality samples had a higher proportion of bacterial detections compared to low-quality samples ( = 0.013). This included a higher proportion of detections of bacteria deemed clinically relevant by predefined criteria (70% and 55%, = 0.016), as well as a higher proportion of detections of (36% and 20%, = 0.010). High-quality samples also had more detections of bacteria with high semi-quantitative values. The study found no significant difference between high- and low-quality samples in the proportions of samples with a single species of bacteria detected, samples with a bacteria treated by the clinician, samples with detection of a proven etiology of community-acquired pneumonia by predefined criteria, the number of bacterial species detected, or the detection of , , or . The results showed that 40% (95% CI 35%-47%) of the bacterial detections would have been missed if only high-quality samples were analyzed. This included 41% (27%-56%) of detections of , 33% (23%-45%) of detections of , 42% (28%-58%) of detections of , and 37% (23%-54%) of detections of . These findings suggest that all sputum samples submitted for rapid syndromic PCR testing should be analyzed, regardless of initial microscopy quality assessment. (This study has been registered at ClinicalTrials.gov under registration no. NCT04660084.) IMPORTANCE Microscopic quality assessment of sputum samples was originally designed for sputum culture, and its applicability in today's workflow, which includes syndromic PCR testing, may differ. Addressing this crucial gap, our study emphasizes the need to optimize the use and workflow of syndromic PCR panels, like the BioFire FilmArray Pneumonia plus (FAP plus), in microbiology laboratories. These advanced PCR-based tests offer rapid and comprehensive pathogen detection for respiratory infections, yet their full potential remains uncertain. By comparing bacterial detections in high- and low-quality sputum samples, we underscore the importance of including low-quality samples in testing. Our findings reveal a significant proportion of potentially clinically relevant bacterial detections that would have been missed if only high-quality samples were analyzed. These insights support the efficient implementation of syndromic PCR panels, ultimately enhancing patient care and outcomes.
PubMed: 37772853
DOI: 10.1128/spectrum.03002-23 -
ACS Omega Sep 2023The need for highly sensitive, low-cost, and timely diagnostic technologies at the point of care is increasing. Surface-enhanced Raman spectroscopy (SERS) is a...
The need for highly sensitive, low-cost, and timely diagnostic technologies at the point of care is increasing. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique that is an advantageous technique to address this need, as it can rapidly detect analytes in small or dilute samples with improved sensitivity compared to conventional Raman spectroscopy. Despite the many advantages of SERS, one drawback of the technique is poor reproducibility due to variable interactions between nanoparticles and target analytes. To overcome this limitation, coupling SERS with the coffee ring effect has been implemented to concentrate and localize analyte-nanoparticle conjugates for improved signal reproducibility. However, current coffee ring platforms require laborious fabrication steps. Herein, we present a low-cost, two-step fabrication process for coffee ring-assisted SERS, utilizing wax-printed nitrocellulose paper. The platform was designed to produce a highly hydrophobic paper substrate that supports the coffee ring effect and tested using gold nanoparticles for SERS sensing. The nanoparticle concentration and solvent were varied to determine the effect of solution composition on ring formation and center clearance. The SERS signal was validated using 4-mercaptobenzoic acid (MBA) and tested with bacteria to ensure functionality for chemical and biological applications. The limit of detection using MBA is 41.56 nM, and the biochemical components of the bacterial cell wall were enhanced with low spectral variability. The developed platform is advantageous due to ease of fabrication and use, representing the next step toward implementing low-cost coffee ring-assisted SERS for point-of-care sensing.
PubMed: 37744797
DOI: 10.1021/acsomega.3c03690 -
Scientific Reports Sep 2023Silver-doped Cobalt Ferrite nanoparticles AgCoFeO with concentrations (x = 0, 0.05, 0.1, 0.15) have been prepared using a hydrothermal technique. The XRD pattern...
Silver-doped Cobalt Ferrite nanoparticles AgCoFeO with concentrations (x = 0, 0.05, 0.1, 0.15) have been prepared using a hydrothermal technique. The XRD pattern confirms the formation of the spinel phase of CoFeO and the presence of Ag ions in the spinel structure. The spinel phase AgCoFeO nanoparticles are confirmed by FTIR analysis by the major bands formed at 874 and 651 cm, which represent the tetrahedral and octahedral sites. The analysis of optical properties reveals an increase in band gap energy with increasing concentration of the dopant. The energy band gap values depicted for prepared nanoparticles with concentrations x = 0, 0.05, 0.1, 0.15 are 3.58 eV, 3.08 eV, 2.93 eV, and 2.84 eV respectively. Replacement of the Co ion with the nonmagnetic Ag ion causes a change in saturation magnetization, with Ms values of 48.36, 29.06, 40.69, and 45.85 emu/g being recorded. The CoFeO and Ag CoFeO nanoparticles were found to be effective against the Acinetobacter Lwoffii and Moraxella species, with a high inhibition zone value of x = 0.15 and 8 × 8 cm against bacteria. It is suggested that, by the above results, the synthesized material is suitable for memory storage devices and antibacterial activity.
PubMed: 37735178
DOI: 10.1038/s41598-023-41729-7