Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome

BACKGROUND : Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. METHODS : Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. RESULTS : Statistically significant differences were observed in alpha diversity when targeted metagenomics and ISPro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the ISPro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. CONCLUSIONS : It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.SUPPLEMENTARY MATERIAL: Table S1. Inclusion and exclusion criteria for COPD patients in this study. Table S2. Clinical characteristic of patients. Table S3. Comparison of the number of amplicons and operational taxonomic units for each sample for the targeted metagenomics and IS-Pro methods. Figure S1. Relative abundance of specific phyla in the sputum microbiome of COPD participants as detected by targeted metagenomics and IS-Pro methods (n = 23). The dots represent the different abundances of each sample, according to the different phyla. Phyla that are depicted with a single line on the y-axis were not present in any samples for that method. Figure S2. Bar plots showing the relative abundance of genera in the sputum microbiome of COPD participants as characterised by targeted metagenomics and IS-Pro methods (n = 23). The operational taxonomic units that could not be classified at a genus level are indicated as NA on the graph. Figure S3. The distribution of the unclassified operational taxonomic units (OTUs) at a class level of the sputum microbiome of COPD participants for targeted metagenomics and IS-Pro methods by phyla. At a class level, all the OTUs from targeted metagenomics could be classified.National Health Laboratory Service of South Africa (NHLS) Research Trusthttps://bmcmicrobiol.biomedcentral.comam2022Internal MedicineMedical Microbiolog

Factors associated with airway colonisation and invasion due to Klebsiella spp.

The clinical significance of a heavy growth of Klebsiella spp. in sputum was studied in 54 patients. All but 3 patients had significant factors potentially associated with respiratory tract colonisation or invasion. Risk factors identified for colonisation of the airway and for invasive disease were similar. Patients with commnunity-acquired Klebsiella infections were more likely to have underlying chronic respiratory diseases. Prior antibiotic use was a risk factor for nosocomial infections which occurred more conunonly with antibiotic-resistant organisms.The most commmon diagnoses were airway colonisation, acute community-acquired chest infections, and nosocomial chest infections. Primary acute conununity-acquired pneumonia was unconunon.The sensitivity and specificity of the sputum Gram stain (in the setting of positive sputum cultures) in suggesting the presence of invasive disease due to Klebsiella spp. were 42% and 69% respectively

South African Thoracic Society position statement on the management of non-cystic fibrosis bronchiectasis in adults: 2023

Background. Bronchiectasis is a chronic lung disorder that affects the lives of many South Africans. Post-tuberculosis (TB) bronchiectasis is an important complication of previous pulmonary TB and a common cause of bronchiectasis in South Africa (SA). No previous statements on the management of bronchiectasis in SA have been published. Objectives. To provide a position statement that will act as a template for the management of adult patients with bronchiectasis in SA. Methods. The South African Thoracic Society appointed an editorial committee to compile a position statement on the management of adult non-cystic fibrosis (CF) bronchiectasis in SA. Results. A position statement addressing the management of non-CF bronchiectasis in adults in SA was compiled. This position statement covers the epidemiology, aetiology, diagnosis, investigations and various aspects of management of adult patients with non-CF bronchiectasis in SA. Conclusion. Bronchiectasis has largely been a neglected lung condition, but new research has improved the outlook for patients. Collaboration between interprofessional team members in patient management is important. In SA, more research into the epidemiology of bronchiectasis, especially post-TB bronchiectasis and HIV-associated bronchiectasis, is required

Calcium efflux and influx in f-met-leu-phe (fMLP)-activated human neutrophils are chronologically distinct events

The kinetics of efflux of calcium mobilized from intracellular stores following activation of human neutrophils with the synthetic chemotactic tripeptide, fMLP (1 μm), as well as that of the subsequent store-operated influx of this cation, has been measured by radiometric procedures using 45Ca. These procedures enabled distinction between net efflux and influx of 45Ca. Preincubation of neutrophils in medium containing 45Ca as the sole source of Ca2+, followed by activation with fMLP, resulted in a rapid efflux of the cation, which coincided with its release from intracellular stores. Efflux terminated at ≈ 30 s after addition of fMLP to neutrophils and resulted in the loss of 42 ± 3% (P< 0.005) of cell-associated 45Ca. Net influx of 45Ca, which was insensitive to the voltage-dependent Ca2+ channel blockading agent, verapamil (20 μm), could only be detected at 30–60 s after the addition of fMLP to neutrophils, and proceeded for about 5 min, resulting in intracellular concentrations of Ca2+ which were 27 ± 3% (P< 0.05) higher than preactivation levels. These results demonstrate that the efflux of cytoplasmic Ca2+ mobilized from intracellular stores during activation of neutrophils by fMLP, and the subsequent influx of extracellular Ca2+ to replete these stores, are chronologically distinct events in fMLP-activated neutrophils

An unusual cause of an anterior mediastinal mass

Mesothelioma is a rare tumour and its radiological growth pattern varies. We report the case of a biopsy proven Malignant Pleural Mesothelioma (MPM) presenting as an anterior mediastinal mass in a platinum miner. The prognosis for this aggressive tumour remains poor, despite combination treatment modalities

Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable diferences for alpha and beta diversity measures between the disease states. However, a diference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the frst to report lung microbiome composition in COPD patients from Africa. In this small sample set, no diferences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.National Health Laboratory Service of South Africa (NHLS) Research Trusthttp://www.nature.com/srep/index.htmlpm2022Internal MedicineMedical Oncolog

Critical care admission of South African (SA) surgical patients: Results of the SA Surgical Outcomes Study

Background. Appropriate critical care admissions are an important component of surgical care. However, there are few data describing postoperative critical care admission in resource-limited low- and middle-income countries.Objective. To describe the demographics, organ failures, organ support and outcomes of non-cardiac surgical patients admitted to critical care units in South Africa (SA).Methods. The SA Surgical Outcomes Study (SASOS) was a 7-day national, multicentre, prospective, observational cohort study of all patients ≥16 years of age undergoing inpatient non-cardiac surgery between 19 and 26 May 2014 at 50 government-funded hospitals. All patients admitted to critical care units during this study were included for analysis.Results. Of the 3 927 SASOS patients, 255 (6.5%) were admitted to critical care units; of these admissions, 144 (56.5%) were planned, and 111 (43.5%) unplanned. The incidence of confirmed or strongly suspected infection at the time of admission was 35.4%, with a significantly higher incidence in unplanned admissions (49.1 v. 24.8%, p&lt;0.001). Unplanned admission cases were more frequently hypovolaemic, had septic shock, and required significantly more inotropic, ventilatory and renal support in the first 48 hours after admission. Overall mortality was 22.4%, with unplanned admissions having a significantly longer critical care length of stay and overall mortality (33.3 v. 13.9%, p&lt;0.001).Conclusion. The outcome of patients admitted to public sector critical care units in SA is strongly associated with unplanned admissions. Adequate ‘high care-dependency units’ for postoperative care of elective surgical patients could potentially decrease the burden on critical care resources in SA by 23%. This study was registered on ClinicalTrials.gov (NCT02141867)

Pulmonary Cryptococcosis Presenting as Endobronchial Lesions in a Patient under Corticosteroid Treatment

We report a case of pulmonary cryptococcosis in an immunocompromised patient who had focal endobronchial lesions. When we first examined her, she complained of a productive cough that had lasted for two months. Seventeen months prior to this examination, she had been diagnosed with Sjogren syndrome and Sweet syndrome. Since that diagnosis, her condition had been maintained with low-dose prednisolone. We performed a chest CT scan, which revealed a mass, 3 cm in diameter, in the upper lobe of her left lung. A bronchoscopic examination revealed 3 white, elevated lesions in the upper lobe bronchus of her left lung. After 40 days of treatment with fluconazole, the shadow of her lung mass decreased in size to that of a scarred lesion and her white, elevated bronchial lesions disappeared

Drug-resistant tuberculosis clinical trials: proposed core research definitions in adults.

Drug-resistant tuberculosis (DR-TB) is a growing public health problem, and for the first time in decades, new drugs for the treatment of this disease have been developed. These new drugs have prompted strengthened efforts in DR-TB clinical trials research, and there are now multiple ongoing and planned DR-TB clinical trials. To facilitate comparability and maximise policy impact, a common set of core research definitions is needed, and this paper presents a core set of efficacy and safety definitions as well as other important considerations in DR-TB clinical trials work. To elaborate these definitions, a search of clinical trials registries, published manuscripts and conference proceedings was undertaken to identify groups conducting trials of new regimens for the treatment of DR-TB. Individuals from these groups developed the core set of definitions presented here. Further work is needed to validate and assess the utility of these definitions but they represent an important first step to ensure there is comparability in clinical trials on multidrug-resistant TB

Safety of hospital discharge before return of bowel function after elective colorectal surgery

Background Ileus is common after colorectal surgery and is associated with an increased risk of postoperative complications. Identifying features of normal bowel recovery and the appropriateness for hospital discharge is challenging. This study explored the safety of hospital discharge before the return of bowel function. Methods A prospective, multicentre cohort study was undertaken across an international collaborative network. Adult patients undergoing elective colorectal resection between January and April 2018 were included. The main outcome of interest was readmission to hospital within 30 days of surgery. The impact of discharge timing according to the return of bowel function was explored using multivariable regression analysis. Other outcomes were postoperative complications within 30 days of surgery, measured using the Clavien-Dindo classification system. Results A total of 3288 patients were included in the analysis, of whom 301 (9 center dot 2 per cent) were discharged before the return of bowel function. The median duration of hospital stay for patients discharged before and after return of bowel function was 5 (i.q.r. 4-7) and 7 (6-8) days respectively (P &lt; 0 center dot 001). There were no significant differences in rates of readmission between these groups (6 center dot 6 versus 8 center dot 0 per cent; P = 0 center dot 499), and this remained the case after multivariable adjustment for baseline differences (odds ratio 0 center dot 90, 95 per cent c.i. 0 center dot 55 to 1 center dot 46; P = 0 center dot 659). Rates of postoperative complications were also similar in those discharged before versus after return of bowel function (minor: 34 center dot 7 versus 39 center dot 5 per cent; major 3 center dot 3 versus 3 center dot 4 per cent; P = 0 center dot 110). Conclusion Discharge before return of bowel function after elective colorectal surgery appears to be safe in appropriately selected patients