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Microbiology Spectrum Feb 2024In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections...
In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: ( = 7), ( = 2), ( = 2), and ( = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of () appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of () (aOR 5.31, 95% CI 1.29-26.6) and (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. , and appeared to be the possible causes of TB-like symptoms. () and / also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as and , one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches.
Topics: Humans; RNA, Ribosomal, 16S; Tuberculosis, Pulmonary; Mycobacterium tuberculosis; Rifampin; Sputum; Sensitivity and Specificity; Tuberculosis; Respiratory Tract Infections
PubMed: 38189296
DOI: 10.1128/spectrum.02931-23 -
Virulence Dec 2024is a major cause of chronic obstructive pulmonary disease. Toll-like receptor 2 (TLR2) plays an important role in the inflammatory response in host respiratory...
is a major cause of chronic obstructive pulmonary disease. Toll-like receptor 2 (TLR2) plays an important role in the inflammatory response in host respiratory epithelial cells. induces an inflammatory immune response in respiratory epithelial cells that is mostly dependent on TLR2. However, the mechanisms by which this pathogen adheres to and invades the respiratory epithelium are not well understood. The present study aimed to reveal the role of TLR2 in adhesion to and invasion into alveolar epithelial cells, using molecular techniques. Pretreatment with the TLR2 inhibitor TLR2-IN-C29 enhanced adhesion to A549 cells but reduced its invasion, whereas the agonist Pam3CSK4 reduced both adhesion and invasion into A549 cells. Similarly, 73-OR strain adhesion and invasion were significantly reduced in TLR2 A549 cells. Moreover, the lung clearance rate of the 73-OR strain was significantly higher in TLR2 C57/BL6J mice than in wild-type (WT) mice. Histological analysis showed that inflammatory responses were milder in TLR2 C57/BL6J mice than in WT mice, which was confirmed by a decrease in cytokine levels in TLR2 C57/BL6J mice. Overall, these results indicate that TLR2 promoted adhesion and invasion of A549 cells and lung tissues and mediated inflammatory responses in infected lungs. This study provides important insights into the development of potential therapeutic strategies against and TLR2-induced inflammatory responses.
Topics: Animals; Mice; Alveolar Epithelial Cells; Epithelial Cells; Lung; Moraxella catarrhalis; Toll-Like Receptor 2
PubMed: 38169345
DOI: 10.1080/21505594.2023.2298548 -
Frontiers in Public Health 2023This study aimed to investigate the etiology, clinical features, and outcomes of community-acquired pneumonia (CAP) in adults. Understanding the causative pathogens is...
OBJECTIVES
This study aimed to investigate the etiology, clinical features, and outcomes of community-acquired pneumonia (CAP) in adults. Understanding the causative pathogens is essential for effective treatment and prevention.
DESIGN
Between 2016-2018, 518 hospitalized adults with CAP and 241 controls without symptoms were prospectively enrolled. Urine samples were collected for pneumococcal urinary antigen tests and nasopharyngeal swabs for viral and bacterial analysis, combined with routine diagnostic care.
RESULTS
Among the included CAP patients, was the most common pathogen, detected in 28% of patients, followed by in 16%. Viruses were identified in 28%, and concurrent viruses and bacteria were detected in 15%. There was no difference in mortality, length of stay, or symptoms at hospitalization when comparing patients with bacterial, viral, or mixed etiologies. Among the control subjects without respiratory symptoms, , , or were detected in 5-7%, and viruses in 7%.
CONCLUSION
emerged as the predominant cause of CAP, followed closely by viruses and . Intriguingly, symptoms and outcome were similar regardless of etiology. These findings highlight the complexity of this respiratory infection and emphasize the importance of comprehensive diagnostic and treatment strategies.: ClinicalTrials.gov, identifier [NCT03606135].
Topics: Adult; Humans; Bacteriophages; Community-Acquired Infections; Hospitalization; Pneumonia, Bacterial; Respiratory Tract Infections; Streptococcus pneumoniae; Treatment Outcome; Case-Control Studies
PubMed: 38152664
DOI: 10.3389/fpubh.2023.1258981 -
Frontiers in Microbiology 2023The role of the microbiome in asthma is highlighted, considering its influence on immune responses and its connection to alterations in asthmatic patients. In this... (Review)
Review
The role of the microbiome in asthma is highlighted, considering its influence on immune responses and its connection to alterations in asthmatic patients. In this context, we review the variables influencing asthma phenotypes from a microbiome perspective and provide insights into the microbiome's role in asthma pathogenesis. Previous cohort studies in patients with asthma have shown that the presence of genera such as , and in the gut microbiome has been associated with protection against the disease. While, the presence of other genera such as , and in the respiratory microbiome has been implicated in asthma pathogenesis, indicating a potential link between microbial dysbiosis and the development of asthma. Furthermore, respiratory infections have been demonstrated to impact the composition of the upper respiratory tract microbiota, increasing susceptibility to bacterial diseases and potentially triggering asthma exacerbations. By understanding the interplay between the microbiome and asthma, valuable insights into disease mechanisms can be gained, potentially leading to the development of novel therapeutic approaches.
PubMed: 38146448
DOI: 10.3389/fmicb.2023.1295215 -
Revista Espanola de Quimioterapia :... Feb 2024
Topics: Child; Humans; Moraxella; Spain; Moraxella catarrhalis; Bacteremia; Hospitals
PubMed: 38116941
DOI: 10.37201/req/076.2023 -
Monaldi Archives For Chest Disease =... Dec 2023There is limited data available about allergic bronchopulmonary aspergillosis (ABPA) in Pakistan. The aim of the study was to describe the radiological and...
There is limited data available about allergic bronchopulmonary aspergillosis (ABPA) in Pakistan. The aim of the study was to describe the radiological and microbiological profile of ABPA patients presenting to the outpatient pulmonary clinic of a tertiary care hospital in Karachi, Pakistan. A retrospective study was conducted on ABPA patients who presented to the pulmonary outpatient clinic at Aga Khan University Hospital, Karachi, Pakistan, from January 2017 to December 2019. Data was collected on microbiology and radiology features on predesigned proforma. A total of 7759 asthmatic patients presented at the outpatient pulmonology clinic during the study period. Of the 245 patients labeled as ABPA, 167 fulfilled the inclusion criteria, and 91 (54.5%) were female (mean age 41.9±13.0 years). A high resolution computed tomography scan of the chest was available for 126 patients. Of these, 104 (82.5%) patients had bronchiectasis. Central bronchiectasis was noted in 98 (94.2%), mucus plugging in 71 (56.3%), and hyperinflation was seen in 30 (23.4%) patients. Microbiological testing was available in 103/167 (61.7%) patients. The most common bacterial pathogen was Pseudomonas aeruginosa 32 (31.1%), followed by Hemophilus influenzae 16 (15.5%), and Moraxella catarrhalis 7 (9.7%). Aspergillus fumigatus 17 (23.6%) was the most common mold, followed by Aspergillus flavus 16 (22.2%) and Aspergillus niger 11 (15.3%). Co-infection (bacterial and fungal) was found in 18 (17.45%) patients. Bronchiectasis was frequently observed in our cohort of patients with ABPA. Pseudomonas aeruginosa was found to be common among bacterial pathogens. Isolation of fungus is not uncommon in these patients.
PubMed: 38112637
DOI: 10.4081/monaldi.2023.2803 -
Veterinary Research Dec 2023Artificial intelligence (AI) was developed to distinguish cattle by their muzzle patterns and identify early cases of disease, including infectious bovine...
Artificial intelligence (AI) was developed to distinguish cattle by their muzzle patterns and identify early cases of disease, including infectious bovine keratoconjunctivitis (IBK). It was tested on 870 cattle in four locations, with 170 developing IBK. The AI identified 169 of the 170 cases prior to their identification by veterinarians, and another 17 cases that remained free of IBK signs (sensitivity = 99.4%, specificity = 97.6%). These results indicate the AI can detect emerging IBK cases by muzzle images very early in the disease process and be used as an intervention tool in the prevention of IBK outbreaks.
Topics: Cattle; Animals; Artificial Intelligence; Cattle Diseases; Keratoconjunctivitis; Moraxella
PubMed: 38102629
DOI: 10.1186/s13567-023-01255-w -
JPMA. the Journal of the Pakistan... Dec 2023To detect mutation in cases having haemoglobin A2 level >7% on high performance liquid chromatography.
OBJECTIVE
To detect mutation in cases having haemoglobin A2 level >7% on high performance liquid chromatography.
METHODS
The cross-sectional, descriptive study was conducted from July 2017 to December 2018 at the Department of Haematology and Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan, and comprised patients of either gender with haemoglobin A2 ≥7%. The samples were collected from different cities of Punjab in collaboration with the Punjab Thalassemia Prevention Programme, Lahore. The samples were subjected to complete blood count and high performance liquid chromatography using automated haematology analysers and variant-II beta thalassemia short programme, respectively. To analyse haemoglobin E mutations at the molecular level, polymerase chain reaction-restriction fragment length polymorphism (PCR_RFLP) was performed using a type IIS restriction endonuclease known as Mnl1 (derived from Moraxella nonliquefaciens) to cleave DNA at specific sites and the results were further confirmed on randomly selected samples using Sanger sequencing. Data was analysed using SPSS 25.
RESULTS
Of the 39 patients, 15(38.5%) were males and 24(61.5%) were females. The overall median age was 14 (23) years. There were 29 (74.4%) patients with thalassemia family history, and 22(56.4%) had a positive family history of transfusion related to thalassemia, while no patient had a family history of iron therapy. The median haemoglobin A, haemoglobin A2 and haemoglobin F levels were 72.2 (65.2-79.1) %, 26.6 (19.1-34.0) % and 0.9 (-0.8-2.6) %, respectively. After molecular investigation, HbAE mutation was found in 23(59%) patients, while wild type HbAA genotype was found in 16(41%). The heterozygous HbE mutation was present in 23(59%) patients.
CONCLUSIONS
Frequently missed/undiagnosed cases of haemoglobin E that co-elute with haemoglobin A2 in the same high performance liquid chromatography window were detected among those with haemoglobin A2 ≥7%.
Topics: Male; Female; Humans; Adolescent; Hemoglobin E; Hemoglobin A2; Cross-Sectional Studies; Genotype; beta-Thalassemia; Thalassemia; Mutation
PubMed: 38083912
DOI: 10.47391/JPMA.7138 -
Microbiology Resource Announcements Jan 2024sp. strain DOX410 was isolated from a systematic enrichment culture to investigate strains with 1,4-dioxane degradation potential. The genome of strain DOX410 consists...
sp. strain DOX410 was isolated from a systematic enrichment culture to investigate strains with 1,4-dioxane degradation potential. The genome of strain DOX410 consists of five complete contigs and contained genes related to degradation of the aromatic ring structure of 1,4-dioxane.
PubMed: 38054709
DOI: 10.1128/mra.00933-23 -
The Lancet. Microbe Jan 2024Deployment of non-pharmaceutical interventions such as face masking and physical distancing during the COVID-19 pandemic could have altered the transmission dynamics and... (Observational Study)
Observational Study
BACKGROUND
Deployment of non-pharmaceutical interventions such as face masking and physical distancing during the COVID-19 pandemic could have altered the transmission dynamics and carriage of respiratory organisms. We evaluated colonisation with Streptococcus pneumoniae and other upper respiratory tract bacterial colonisers before and during the COVID-19 pandemic.
METHODS
We did two cross-sectional surveys in Soweto, South Africa from July 3 to Dec 13, 2018 (pre-COVID-19 period) and from Aug 4, 2021, to March 31, 2022 (COVID-19 period) in healthy children (aged ≤60 months) who had recorded HIV status and had not received antibiotics in the 21 days before enrolment. At enrolment, we collected nasopharyngeal swab samples from child participants. Following nucleic acid extraction, nanofluidic quantitative PCR was used to screen all samples for 92 S pneumoniae serotypes and 14 other bacteria. The primary objective was to compare the prevalence and density of pneumococcal nasopharyngeal colonisation, overall and stratified by 13-valent pneumococcal conjugate vaccine (PCV13) serotypes and non-vaccine serotypes. Secondary study objectives included a comparison of serotype-specific pneumococcal colonisation and density, as well as colonisation by the 14 other bacteria in the COVID-19 versus pre-COVID-19 period. We used an adjusted multiple logistic and linear regression model to compare the colonisation prevalence and density between study periods.
FINDINGS
We analysed nasopharyngeal swabs from 1107 children (n=571 in the pre-COVID-19 period; n=536 in the COVID-19 period). We observed no change in overall pneumococcal colonisation between periods (274 [51%] of 536 in the COVID-19 period vs 282 [49%] of 571 in the pre-COVID-19 period; adjusted odds ratio [aOR] 1·03 [95% CI 0·95-1·12]). The prevalence of PCV13 serotypes was lower in the COVID-19 than in the pre-COVID-19 period (72 [13%] vs 106 [19%]; 0·87 [0·78-0·97]), whereas the prevalence of non-typeable S pneumoniae was higher (34 [6%] vs 63 [12%]; 1·30 [1·12-1·50]). The mean log density for overall pneumococcal colonisation was lower in the COVID-19 period than in the pre-COVID-19 period (3·96 [95% CI 3·85-4·07] vs 4·72 [4·63-4·80] log genome equivalents per mL; p<0·0001). A lower density of non-vaccine serotypes (3·63 [3·51-3·74] vs 4·08 [3·95-4·22] log genome equivalents per mL; p<0·0001) and non-typeable S pneumoniae (3·11 [2·94-3·29] vs 4·41 [4·06-4·75] log genome equivalents per mL; p<0·00001) was also observed in the COVID-19 period. There was no difference in the density of PCV13 serotypes between the periods. The prevalence of colonisation during the COVID-19 versus pre-COVID-19 period was lower for non-typeable Haemophilus influenzae (280 [49%] vs 165 [31%]; aOR 0·77 [95% CI 0·71-0·84]), Moraxella catarrhalis (328 [57%] vs 242 [45%]; 0·85 [0·79-0·92]), and Neisseria lactamica (51 [9%] vs 13 [2%]; 0·64 [0·52-0·78]), but higher for Acinetobacter baumannii (34 [6%] vs 102 [19%]; 1·55 [1·35-1·77]) and Staphylococcus aureus (29 [5%] vs 52 [10%]; 1·28 [1·10-1·50]).
INTERPRETATION
There were variable effects on the colonisation prevalence and density of bacterial organisms during the COVID-19 compared with the pre-COVID-19 period. The lower prevalence of PCV13 serotype together with other respiratory organisms including non-typeable H influenzae and M catarrhalis could have in part contributed to a decrease in all-cause lower respiratory tract infections observed in South Africa during the initial stage of the COVID-19 pandemic. The pathophysiological mechanism for the increase in A baumannii and S aureus colonisation warrants further investigation, as does the clinical relevance of these findings.
FUNDING
The Bill & Melinda Gates Foundation.
Topics: Child; Humans; South Africa; Cross-Sectional Studies; Pandemics; Carrier State; COVID-19; Streptococcus pneumoniae; Nasopharynx; Moraxella catarrhalis; Haemophilus influenzae; Staphylococcus aureus
PubMed: 38048806
DOI: 10.1016/S2666-5247(23)00260-4