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Purpose: Bronchoalveolar lavage is commonly used in clinical practice for unresolved pneumonia. However, bronchoalveolar lavage is not suitable for all patients as it is an invasive procedure and can worsen oxygenation. The diagnostic value of bronchial wash and sputum has been debated extensively over the years. In this study, we aim to compare the diagnostic value in several pathogens of bronchoalveolar lavage and bronchial wash, and secondarily bronchoalveolar lavage and sputum. Methods: We retrospectively included all adult patients in our hospital who underwent bronchoalveolar lavage, bronchial wash, and where sputum sampling was done between January 1st of 2018 and December 31st of 2021. The intraclass correlation coefficient was computed for the three tests. Results: In total, 308 patients were included. We found a level of correlation of 0.819 and 0.865, respectively, between bronchoalveolar lavage and bronchial wash for two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. For Stenotrophomonas maltophilia and Aspergillus fumigatus, we found an intraclass correlation coefficient of 0.568 and 0.624, respectively. Between bronchoalveolar lavage and sputum, we found varying levels of agreement. Conclusion: Our study shows reasonably well agreement levels between bronchoalveolar lavage and bronchial wash, suggesting that bronchial wash could potentially be an alternative to bronchoalveolar lavage. [ABSTRACT FROM AUTHOR]

Background Nontoxigenic Corynebacterium diphtheriae , often associated with wounds, can rarely cause infective endocarditis (IE). Five patients with C. diphtheriae IE were identified within 12 months at a Seattle-based hospital system. We reviewed prior C. diphtheriae –positive cultures to determine if detections had increased over time and evaluated epidemiologic trends. Methods We conducted a formal electronic health record search to identify all patients aged ≥18 years with C. diphtheriae detected in a clinical specimen (ie, wound, blood, sputum) between 1 September 2020 and 1 April 2023. We collected patient demographics, housing status, comorbidities, substance-use history, and level of medical care required at detection. We extracted laboratory data on susceptibilities of C. diphtheriae isolates and on other pathogens detected at the time of C. diphtheriae identification. Results Between 1 September 2020 and 1 April 2023, 44 patients (median age, 44 years) had a C. diphtheriae– positive clinical culture, with most detections occurring after March 2022. Patients were predominantly male (75%), White (66%), unstably housed (77%), and had a lifetime history of injecting drugs (75%). Most C. diphtheriae –positive cultures were polymicrobial, including wound cultures from 36 (82%) patients and blood cultures from 6 (14%) patients, not mutually exclusive. Thirty-four patients (77%), including all 5 patients with C. diphtheriae IE, required hospital admission for C. diphtheriae or a related condition. Of the 5 patients with IE, 3 died of IE and 1 from COVID-19. Conclusions Findings suggest a high-morbidity outbreak disproportionately affecting patients who use substances and are unstably housed. [ABSTRACT FROM AUTHOR]

Background: Drug-resistant tuberculosis (DR-TB) is difficult to treat, and its timely diagnosis is an important factor in successful treatment outcomes. Modern technology has made it possible to diagnose DR-TB more quickly than before when it took a long time to identify the presence of resistance Mycobacterium. Objective: To evaluate the efficacy of the Xpert MTB/XDR to test the susceptibility of MTB towards anti-TB drugs by using sputum samples from infected people. Methodology: A cross-sectional study was conducted at the Programmatic Management of Drug-Resistant TB Unit (PMDT), Lady Reading Hospital, Peshawar, from March 2021 to March 2023. This study included samples from patients identified as rifampicin-resistant patients. The Xpert® MTB/XDR test's diagnosis accuracy was compared to that of the MGIT960, the reference drug susceptibility testing (DST) techniques, and the Hain Genotype® MTBDR plus and MDRsl assays (LPA). Results: The present study included 180 patients. These patients were divided into three groups for study purposes based on technique used, i.e., Pre-LPA or DST, Post-LPA, and Ten color Xpert MTB/XDR, and followed up for their culture conversion. Gene-Xpert MTB/RIF showed 93% of cases were positive, and on DST all cases showed positive results. For drug resistance in DST, LPA, and Gene-Xpert MTB/XDR, 61.1% of patients were resistant to three first-line drugs, and 11.1% were resistant to the second line. The overall median time from the identification of patients suspected of MDR-TB to the initiation of treatment in DST was 93 days. In LPA it was 25 and 5 days by Ten color Gene Xpert MTB/XDR. Conclusion: This study concludes that based on the timely initiation of treatment and culture conversion reports, DST and LPA are less efficient than the Ten-color Gene Xpert MTB/XDR assay. [ABSTRACT FROM AUTHOR]

Introduction In high-burden settings, low-complexity screening tests for tuberculosis (TB) could expand the reach of community-based case-finding efforts. The potential costs and cost-effectiveness of approaches incorporating these tests are poorly understood. Methods We developed a microsimulation model assessing 3 approaches to community-based case-finding in hypothetical populations (India-, South Africa-, The Philippines-, Uganda-, and Vietnam-like settings) with TB prevalence 4 times that of national estimates: (1) screening with a point-of-care C-reactive protein (CRP) test, (2) screening with a more sensitive "Hypothetical Screening test" (95% sensitive for Xpert Ultra-positive TB, 70% specificity; equipment/labor costs similar to Xpert Ultra, but using a $2 cartridge) followed by sputum Xpert Ultra if positive, or (3) testing all individuals with sputum Xpert Ultra. Costs are expressed in 2023 US dollars and include treatment costs. Results Universal Xpert Ultra was estimated to cost a mean $4.0 million (95% uncertainty range: $3.5 to $4.6 million) and avert 3200 (2600 to 3900) TB-related disability-adjusted life years (DALYs) per 100 000 people screened ($670 [The Philippines] to $2000 [Vietnam] per DALY averted). CRP was projected to cost $550 (The Philippines) to $1500 (Vietnam) per DALY averted but with 44% fewer DALYs averted. The Hypothetical Screening test showed minimal benefit compared to universal Xpert Ultra, but if specificity were improved to 95% and per-test cost to $4.5 (all-inclusive), this strategy could cost $390 (The Philippines) to $940 (Vietnam) per DALY averted. Conclusions Screening tests can meaningfully improve the cost-effectiveness of community-based case-finding for TB but only if they are sensitive, specific, and inexpensive. [ABSTRACT FROM AUTHOR]

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Introduction: The association between Mycobacterium tuberculosis and the Human Immunodeficiency Virus can accelerate the deterioration of immunological functions. The risks are even more accentuated in the situation of a Non-tuberculous Mycobacterium and Mycobacterium tuberculosis co-infection. Case presentation: We present the case of a 59-year-old male patient, who was admitted at the hospital with non-specific symptoms. Further investigations reveal a remarkable particularity about the case: The infection with Mycobacterium tuberculosis was urogenital, whereas the one with Non-tuberculous mycobacteria was pulmonary. Conclusion: Both Mycobacterium tuberculosis and Non-tuberculous strains can exist within the same infection, posing great difficulties for diagnosis, as well as the treatment scheme. [ABSTRACT FROM AUTHOR]

Background and Aim: Proteus vulgaris, a Gram-negative bacterium, is a common cause of human infections, particularly urinary tract infections (UTIs). This study aimed to assess the multidrug resistance patterns of Proteus vulgarisisolated from diverse clinical samples, shedding light on its impact on healthcare-associated infections. Materials and Methods: In this cross-sectional study, 300 clinical samples were collected, including 100 urine samples, 50 wound samples, 50 vaginal samples, 50 blood cultures, and 50 sputum samples. All samples were selected in the same number (50:50), except the urine samples (100) because the urine samples in this study were more available in the collection from the study patients, which gave more advanced UTIs. Phenotypic and molecular techniques were employed to identify and characterize these bacteria, focusing on detecting resistance genes such as UreC and blaCTX-M. Results: Among the 300 clinical samples, 150 yielded positive cultures for Proteus species. These isolates were obtained from various clinical samples, including 48% from urine, 32% from wounds, 10% from vagina, 8% from blood, and 2% from sputum. Of the 100 P. vulgaris isolates, 88% harbored resistance genes on chromosomal DNA and plasmids. Specifically, 75% carried the UreC gene, and 50% carried the blaCTX-M gene. The highest prevalence of these resistant genes was observed in urine and wound pus samples. Conclusion: This study revealed a concerning prevalence of highly resistant multidrug-resistant (MDR) P. vulgaris isolates, particularly in female urinary tract infections. The genomic presence of the UreC gene, which encodes the urease enzyme, and the blaCTX-M gene, which confers resistance to cefotaxime, underscores the urgency of effective antimicrobial strategies in combating these infections. [ABSTRACT FROM AUTHOR]

Background: Intensive care units (ICU) are multidisciplinary departments where patients with life-threatening diseases, major surgical interventions, respiratory failure, coma condition, hemodynamic insufficiency, and ≥1 organ failure are admitted for relevant diagnoses and treatment. The present study sought to investigate pathogens causing infections in patients admitted to our respiratory ICU and their antibiotic resistance patterns. Materials and Methods: The antibiogram results and clinical data of all patient samples submitted between January 1, 2008, and December 31, 2010, were retrospectively reviewed. Ethics committee approval was obtained from Dicle University Faculty of Medicine. Results: In total, 248 patients with 561 culture results were included in the study. Microbial growth was detected in the following samples: blood, 336 (59.9%); deep tracheal aspirate, 104 (18.6%); urine, 89 (15.9%); wound drain, 12 (2.1%); central venous catheter liquid, 7 (1.3%); phlegm, 10 (1.8%); Foley tip liquid, 1 (0.2%); and pleural effusion, and 1 (0.2%). Rapid growth was most frequently noted in the cultures of coagulase-negative staphylococci (25.3%), Acinetobacter spp. (23.1%), and Escherichia coli (12.6%). Conclusions: the present study revealed microorganisms' resistance profiles similar to those of other relevant studies. The study provides important insights into the selection of empiric antibiotic therapy for patients admitted in intensive care unit. [ABSTRACT FROM AUTHOR]

Background Tuberculosis (TB) is well-known for causing wasting. Patients on treatment gain weight and weight loss is associated with unfavorable treatment outcomes. There is limited description of weight loss and its predictors during intensive treatment phase. The objective of this study was to assess the predictors of weight loss during intensive phase and to see if there is any association exists with sputum conversion at the end of intensive phase of treatment. Methods Data collected as a part of the prospective TB cohort (Regional Prospective Observational Research for TB India Phase 1) conducted in Pondicherry, Cuddalore and Viluppuram districts of Tamil Nadu were used for this study. Sputum smear and body weight comparison were made in the baseline and at the end of second month of treatment. Results In all, 726 participants had weight measurements at the two time points and 18.7% had weight loss; mean weight lost being 2.3 kg (SD 3.05). Mean weight loss was more among males (2.4 kg, SD 3.2), diabetics (2.8 kg, SD 3.9) and alcoholics (2.1 kg, SD 2.4). Alcohol consumption was the only predictor of weight loss after adjusting for age, diabetes, marital status and BMI (aRR 1.52, P 0.02). Weight loss was not associated with sputum conversion at the end of second month. Conclusions Alcohol use emerged as the major predictor for weight loss during intensive phase. [ABSTRACT FROM AUTHOR]

Background In people with human immunodeficiency virus (PWH), the World Health Organization–recommended tuberculosis (TB) 4-symptom screen (W4SS) targeting those who need molecular rapid testing may be suboptimal. We assessed the performance of different TB screening approaches in severely immunosuppressed PWH enrolled in the guided-treatment group of the STATIS trial (NCT02057796). Methods Ambulatory PWH with no overt evidence of TB and CD4 count <100 cells/µL were screened for TB prior to antiretroviral therapy (ART) initiation with W4SS, chest radiograph (CXR), urine lipoarabinomannan (LAM) test, and sputum Xpert MTB/RIF (Xpert). Correctly and wrongly identified cases by screening approaches were assessed overall and by CD4 count threshold (≤50 and 51–99 cells/µL). Results Of 525 enrolled participants (median CD4 count, 28 cells/µL), 48 (9.9%) were diagnosed with TB at enrollment. Among participants with a negative W4SS, 16% had either a positive Xpert, a CXR suggestive of TB, or a positive urine LAM test. The combination of sputum Xpert and urine LAM test was associated with the highest proportion of participants correctly identified as TB (95.8%) and non-TB cases (95.4%), with proportions equally high among participants with CD4 counts above or below 50 cells/µL. Restricting the use of sputum Xpert, urine LAM test, or CXR to participants with a positive W4SS reduced the proportion of wrongly and correctly identified cases. Conclusions There is a clear benefit to perform both sputum Xpert and urine LAM tests as TB screening in all severely immunosuppressed PWH prior to ART initiation, not only in those with a positive W4SS. Clinical Trials Registration. NCT02057796. [ABSTRACT FROM AUTHOR]

Background: Bronchiectasis is a serious, debilitating condition warranting specialist care. Aims: To determine if care provided in a tertiary hospital general respiratory clinic was guideline concordant and to validate the Bronchiectasis Severity Index (BSI) in the Australian context. Methods: A single‐centre ambispective study was conducted. The first stage involved a retrospective medical record audit between 1 January 2015 and 31 December 2016. All aspects of bronchiectasis management were reviewed. In the second prospective phase the cohort was followed for 4 years to determine survival and the validity of the BSI determined. Results: A total of 145 patients was included, with mean age of 65 years (standard deviation = 16.6). The aetiology of bronchiectasis was explicitly documented for 58 (40%) patients, with potential causes identified in another 37 patients. Post‐infectious aetiologies were described in 62 (43%) patients. Most patients had lung function testing (n = 142; 97%) and sputum culture results (n = 120; 83%). Long‐term antibiotics were prescribed to 49 (34%) patients. Only patients culturing Pseudomonas spp. were prescribed inhaled antibiotics. Documentation regarding essential management recommendations was low, including airway clearance (46%), pneumococcal vaccination (27%) and written action plans (32%). Severe disease was common, with more than one‐third (34–48%) having BSI scores >9. One‐fifth (21%) of the cohort died during the 4‐year follow‐up period. The BSI was significantly associated with mortality risk (odds ratio 7.7; 95% confidence interval = 3.1–19.3; P < 0.001). Conclusion: Our cohort had a high proportion of patients with severe disease and significant mortality; some, but not all, aspects of recommended care were delivered. [ABSTRACT FROM AUTHOR]

Background We report the yield of targeted universal tuberculosis (TB) testing of clinic attendees in high-risk groups. Methods Clinic attendees in primary healthcare facilities in South Africa with one of the following risk factors underwent sputum testing for TB: human immunodeficiency virus (HIV), contact with a TB patient in the past year, and having had TB in the past 2 years. A single sample was collected for Xpert-Ultra (Xpert) and culture. We report the proportion positive for Mycobacterium tuberculosis. Data were analyzed descriptively. The unadjusted clinical and demographic factors' relative risk of TB detected by culture or Xpert were calculated and concordance between Xpert and culture is described. Results A total of 30 513 participants had a TB test result. Median age was 39 years, and 11 553 (38%) were men. The majority (n = 21734, 71%) had HIV, 12 492 (41%) reported close contact with a TB patient, and 1573 (5%) reported prior TB. Overall, 8.3% were positive for M. tuberculosis by culture and/or Xpert compared with 6.0% with trace-positive results excluded. In asymptomatic participants, the yield was 6.7% and 10.1% in symptomatic participants (with trace-positives excluded). Only 10% of trace-positive results were culture-positive. We found that 55% of clinic attendees with a sputum result positive for M. tuberculosis did not have a positive TB symptom screen. Conclusions A high proportion of clinic attendees with specific risk factors (HIV, close TB contact, history of TB) test positive for M. tuberculosis when universal testing is implemented. [ABSTRACT FROM AUTHOR]

The introduction of two novel drugs, bedaquiline and delamanid, has given hope for better and shorter treatments of drug-resistant tuberculosis. A systematic review was conducted to evaluate the efficacy and safety of concomitant bedaquiline and delamanid administration. Pooled estimates of World Health Organization–defined favorable treatment outcome and significant QTc-interval prolongation (QTc ≥500 ms or ≥60 ms increase from baseline) were calculated using a random-effects model. Thirteen studies including a total of 1031 individuals with multidrug-resistant/rifampicin-resistant tuberculosis who received bedaquiline and delamanid were included. The pooled estimate of favorable treatment outcome was 73.1% (95% confidence interval [CI]: 64.3–81.8%). Sputum culture conversion at 6 months ranged from 61% to 95%. Overall, the pooled proportion of QTc-prolongation was 7.8% (95% CI: 4.1–11.6%) and few cardiac events were reported (0.8%; n = 6/798). Rates of sputum culture conversion and favorable treatment outcome were high in patients treated concomitantly with bedaquiline and delamanid, and the treatment seemed tolerable with low rates of clinically significant cardiac toxicity. [ABSTRACT FROM AUTHOR]

Background Rapid tuberculosis (TB) drug susceptibility testing (DST) is crucial. Genotype MTBDR sl is a widely deployed World Health Organization (WHO)–endorsed assay. Programmatic performance data, including non-actionable results from smear-negative sputum, are scarce. Methods Sputa from Xpert MTB/RIF individuals (n = 951) were routinely-tested using Genotype MTBDR plus and MTBDR sl (both version 2). Phenotypic DST was the second-line drug reference standard. Discrepant results underwent Sanger sequencing. Findings 89% (849 of 951) of individuals were culture-positive (56%, 476 of 849 smear-negative). MTBDR plus had at least 1 nonactionable result (control and/or TB-detection bands absent or invalid, precluding resistance reporting) in 19% (92 of 476) of smear-negatives; for MTBDR sl , 40% (171 of 427) were nonactionable (28%, 120 of 427 false-negative TB; 17%, 51 of 427 indeterminate). In smear-negatives, MTBDR sl sensitivity for fluoroquinolones was 84% (95% confidence interval, 67%–93), 81% (54%–95%) for second-line injectable drugs, and 57% (28%–82%) for both. Specificities were 93% (89%–98%), 88% (81%–93%), and 97% (91%–99%), respectively. Twenty-three percent (172 of 746) of Xpert rifampicin-resistant specimens were MTBDR plus isoniazid-susceptible. Days-to-second-line-susceptibility reporting with the programmatic advent of MTBDR sl improved (6 [5–7] vs 37 [35–46]; P <.001). Conclusions MTBDR sl did not generate a result in 4 of 10 smear-negatives, resulting in substantial missed resistance. However, if MTBDR sl generates an actionable result, that is accurate in ruling-in resistance. Isoniazid DST remains crucial. This study provides real-world, direct, second-line susceptibility testing performance data on non-actionable results (that, if unaccounted for, cause an overestimation of test utility), accuracy, and care cascade impact. [ABSTRACT FROM AUTHOR]

Background Recognizing pulmonary involvement in tuberculosis (TB) patients is necessary to prevent TB transmission. We describe frequency and characteristics of patients with extrapulmonary TB (EPTB), normal chest radiographs, and positive sputum culture. Methods We analyzed data of patients ≥15 years of age with EPTB reported to the California TB registry during 2011–2017 with cultured sputum and normal chest radiographs using generalized linear modeling to estimate prevalence ratios associated with positive sputum culture. Demographic, behavioral, clinical characteristics, and testing were compared for patients with positive and negative sputum culture. Results Of 1635 patients with EPTB and normal chest radiographs, 937 (57%) had sputum culture performed, and 127 (13%) patients had positive results for Mycobacterium tuberculosis complex. Patients with positive results were more likely to: be male, experience homelessness, use substances, have HIV, and have >1 disease site. Among 85 patients with HIV co-infection, 54% had positive culture results compared with 9.5% among 852 patients without HIV co-infection. Patients with EPTB in more than 1 site were also more likely to have a positive sputum culture. Conclusions Culturing sputum from patients with EPTB identified pulmonary cases not detected by chest radiograph, particularly among patients with HIV or >1 disease site. [ABSTRACT FROM AUTHOR]

Background Microbiologic diagnosis of childhood tuberculosis may be difficult. Oral swab specimens are a potential noninvasive alternative to sputum specimens for diagnosis. Methods This was a prospective diagnostic accuracy study of oral swab specimens (buccal and tongue) for pulmonary tuberculosis diagnosis in children (aged ≤ 15 years) in 2 South African hospital sites. Children with cough of any duration as well as a positive tuberculin skin test result, tuberculosis contact, loss of weight, or chest radiograph suggestive of pulmonary tuberculosis were enrolled. Two induced sputum specimens were tested with Xpert MTB/RIF (or Xpert MTB/RIF Ultra) assay and liquid culture. Oral swab specimens were obtained before sputum specimens, frozen, and later tested with Xpert MTB/RIF Ultra. Children were classified as microbiologically confirmed tuberculosis, unconfirmed tuberculosis (receipt of tuberculosis treatment), or unlikely tuberculosis according to National Institutes of Health consensus definitions based on sputum microbiologic results. Results Among 291 participants (median age [interquartile range], 32 [14–73] months), 57 (20%) had human immunodeficiency virus (HIV), and 87 (30%) were malnourished; 90 (31%) had confirmed pulmonary tuberculosis (rifampicin resistant in 6 [7%]), 157 (54%), unconfirmed pulmonary tuberculosis, and 44 (15%), unlikely tuberculosis. A single oral swab specimen was obtained from 126 (43%) of the participants (tongue in 96 and buccal in 30) and 2 swab specimens from 165 (57%) (tongue in 110 and buccal in 55). Sensitivity was low (22% [95% confidence interval, 15%–32%]) for all swab specimens combined (with confirmed pulmonary tuberculosis as reference), but specificity was high (100% [91%–100%]). The highest sensitivity was 33% (95% confidence interval, 15%–58%) among participants with HIV. The overall yield was 6.9% with 1 oral swab specimen and 7.2% with 2. Conclusions Use of the Xpert MTB/RIF Ultra assay with oral swab specimens provides poor yield for microbiologic pulmonary tuberculosis confirmation in children. [ABSTRACT FROM AUTHOR]

BACKGROUND: Clinical diagnosis of ICU-acquired pneumonia after cardiothoracic surgery is challenging. Johanson criteria (chest radiograph infiltrate, purulent tracheal secretions, fever, and leukocytosis) fail in half the cases. A high Clinical Pulmonary Infection Score (CPIS) and ≥ 2-point increase in Sequential Organ Failure Assessment (SOFA) score (SOFA ↑ ≥ 2) may improve diagnosis. The aim of the study was to evaluate whether CPIS or SOFA ↑ ≥ 2 contributes to predict ICU-acquired pneumonia in subjects after cardiothoracic surgery. METHODS: We used a prospective observational design. Spiegelhalter-Knill-Jones scoring systems including CPIS or SOFA ↑ ≥ 2, together with other clinical and laboratory variables, were developed in a derivation cohort. A positive quantitative pulmonary sample culture was required to confirm ICU-acquired pneumonia. Area under the receiver operating characteristic curve (AUROC) was computed for each of the 2 scoring systems. The best system was evaluated in a validation cohort. RESULTS: Derivation and validation cohorts included 172 and 108 subjects, with 410 and 216 suspected ICU-acquired pneumonia episodes, respectively. AUROC was 0.53 ± 0.03 for CPIS (P = .29) and 0.54 ± 0.03 for SOFA ↑ ≥ 2 (P = .29). Adding purulent tracheal secretions and leukocytosis to SOFA↑ ≥ 2 (SOFA model) increased AUROC to 0.65 ± 0.03 (P < .001). Adding catecholamine use to CPIS (CPIS model) increased AUROC only slightly, to 0.57 ± 0.03. The probabilities predicted by the SOFA model were reliable, especially when high or low. CONCLUSIONS: A clinical scoring system including at least SOFA ↑ ≥ 2 increase barely improved ICU-acquired pneumonia prediction in subjects after cardiothoracic surgery. [ABSTRACT FROM AUTHOR]

Background: The role of the sputum microbiome in chronic obstructive pulmonary disease (COPD) progression remains elusive. As the advent of the new culture-independent microbial sequencing technique makes it possible to disclose the complex microbiome community of the respiratory tract. The aim of this study was to use metagenomic next-generation sequencing (mNGS) to confirm whether there are differences in sputum microbiome of COPD between different exacerbation frequencies and lung function.Methods: Thirty-nine COPD patients were divided into a frequent exacerbators (FE) group (n = 20) and a non-frequent exacerbators (NFE) (n = 19) group according to their exacerbation history, or a mild group (FEV1/pre ≥ 50%, n = 20) and a severe group (FEV1/pre < 50%, n = 19) according to the lung function. Sputum was collected during their stable phase, followed by DNA extraction, untargeted metagenomic next-generation sequencing (mNGS) and bioinformatic analysis.Results: mNGS identified 3355 bacteria, 71 viruses and 22 fungi at the specie level. It was found that Shannon index and Simpson index in FE group was lower than that in NFE group (p = 0.005, 0.008, respectively) but similar between mild and severe groups. Out of top 10 bacteria taxa, Veillonella, Fusobacterium and Prevotella jejuni had a higher abundance in NFE group, Rothia had a higher abundance in mild group. Linear discriminant analysis revealed that many bacterial taxa were more abundant in NFE group, and they mostly belonged to Actinobacteria, Bacteroidetes and Fusobacteria phyla. Frequency of exacerbations was also found to be negatively correlated with alpha diversity (with Shannon index, r = - 0.423, p = 0.009; with Simpson index, r = - 0.482, p = 0.002). No significant correlation was observed between alpha diversity and FEV1/pre.Conclusions: Microbiome diversity in FE group was lower than that in NFE group. There was a significant difference in microbiome taxa abundance between FE and NFE groups, or mild and severe groups. These findings demonstrated that sputum microbiome community dysbiosis was associated with different exacerbation frequencies and lung function in stable COPD. [ABSTRACT FROM AUTHOR]

Background: Currently, the microbial etiology of community-acquired pneumonia in children remains challenging. While Gram stain and sputum culture are commonly used to detect bacterial pathogens, it is unclear whether these approaches can predict single pathogen from bronchoalveolar lavage fluid (BALF) culture.Methods: A retrospective study involving 287 children hospitalized for pneumonia was conducted. Sputum specimens were collected on admission; and BALF specimens were collected within 24 h after admission. Taking BALF culture as the reference standard, the sensitivity and specificity of Sputum Gram stain (SGS), sputum culture, and BALF Gram stain (BGS) were calculated. The agreement between these approaches and BALF culture was compared using kappa statistics.Results: For SGS, the specificity was 23%. The overall sensitivity was 70%, including 87% for Gram-positive (G+) cocci, 56% for Gram-negative (G-) cocci, and 50% for G-bacilli. For sputum culture, the specificity was 70%. The overall sensitivity was 64%, including 71% for Streptococcus pneumoniae, 71% for Moraxella catarrhalis, and 64% for Haemophilus influenzae. For BGS, the specificity was 71%. The overall sensitivity was 60%, including 77% for G+cocci, 38% for G-cocci, and 44% for G-bacilli. While SGS had poor agreement with BALF culture, both sputum culture and BGS had moderate agreement with BALF culture.Conclusions: Both sputum culture and BGS are helpful in predicting single bacterial pathogen from BALF culture among children with community-acquired pneumonia. Sputum cultures and BGS can provide early clues for BALF pathogen when BALF culture results are pending or bronchoscopy is not performed. [ABSTRACT FROM AUTHOR]

Background Intrapulmonary pharmacokinetics may better explain response to tuberculosis (TB) treatment than plasma pharmacokinetics. We explored these relationships by modeling bacillary clearance in sputum in adult patients on first-line treatment in Malawi. Methods Bacillary elimination rates (BER) were estimated using linear mixed-effects modelling of serial time-to-positivity in mycobacterial growth indicator tubes for sputum collected during the intensive phase of treatment (weeks 0–8) for microbiologically confirmed TB. Population pharmacokinetic models used plasma and intrapulmonary drug levels at 8 and 16 weeks. Pharmacokinetic-pharmacodynamic relationships were investigated using individual-level measures of drug exposure (area-under-the-concentration-time-curve [AUC] and C max) for rifampicin, isoniazid, pyrazinamide, and ethambutol, in plasma, epithelial lining fluid, and alveolar cells as covariates in the bacillary elimination models. Results Among 157 participants (58% human immunodeficiency virus [HIV] coinfected), drug exposure in plasma or alveolar cells was not associated with sputum bacillary clearance. Higher peak concentrations (C max) or exposure (AUC) to rifampicin or isoniazid in epithelial lining fluid was associated with more rapid bacillary elimination and shorter time to sputum negativity. More extensive disease on baseline chest radiograph was associated with slower bacillary elimination. Clinical outcome was captured in 133 participants, with 15 (11%) unfavorable outcomes recorded (recurrent TB, failed treatment, or death). No relationship between BER and late clinical outcome was identified. Conclusions Greater intrapulmonary drug exposure to rifampicin or isoniazid in the epithelial lining fluid was associated with more rapid bacillary clearance. Higher doses of rifampicin and isoniazid may result in sustained high intrapulmonary drug exposure, rapid bacillary clearance, shorter treatment duration and better treatment outcomes. [ABSTRACT FROM AUTHOR]

Objective. This study is aimed at investigating the pattern of change occurring in respiratory pathogens before and after the outbreak of COVID-19, a type of viral pneumonia for which a pandemic was declared (March 2020). The results were analyzed by gender and age to identify the association between personal hygiene and prevention of infection by respiratory pathogens. Methods. A retrospective analysis was performed on 39,814 sputum, bronchial aspirate, and transtracheal aspirate samples obtained from 15,398 patients visiting a university hospital, located in Chungcheongnam-do, South Korea, between January 2018 and December 2021. From 4,454 patients whose samples were culture positive for bacteria, 6,389 strains were isolated and further cultured. Results. The mean age of the outpatients with respiratory pathogens was 66.2 years, and the comparison of the culture test results by gender showed that 64.9% (2,892/4,454) were male and 35.1% (1,562/4,454) were female. Compared to the pre-COVID-19 pandemic period, the number of outpatients with a request for respiratory microbial cultures after the onset of the pandemic was reduced by 20.7% and the number of outpatients with a positive culture result was reduced by 23.0%. The number of respiratory samples received was reduced by 6.7% after the pandemic, while the sample positive rate was reduced by 18.3%. Among the isolated microbial strains, there was a significant decrease of 43.1% for the Acinetobacter baumannii complex, 60.5% for Streptococcus pneumoniae, 67.2% for Haemophilus influenzae, and 78.1% for Moraxella catarrhalis when compared with pre-COVID-19 levels. The distribution of respiratory microbial strains by age group showed that the highest percentage of isolated strains was in patients in their 70s. Conclusions. The improvements in personal hygiene due to the COVID-19 pandemic exerted a substantial influence on the pattern of change in other common respiratory microorganisms, which highlights the importance of personal hygiene management in the prevention of respiratory infections. [ABSTRACT FROM AUTHOR]

Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory illness in older adults. A major cause of COPD-related morbidity and mortality is acute exacerbation of COPD (AECOPD). Bacteria in the lungs play a role in exacerbation development, and the most common pathogen is non-typeable Haemophilus influenzae (NTHi). A vaccine to prevent AECOPD containing NTHi surface antigens was tested in a clinical trial. This study measured IgG and IgA against NTHi vaccine antigens in sputum. Sputum samples from 40 COPD patients vaccinated with the NTHi vaccine were collected at baseline and 30 days after the second dose. IgG and IgA antibodies against the target antigens and albumin were analyzed in the sputum. We compared antibody signals before and after vaccination, analyzed correlation with disease severity and between sputum and serum samples, and assessed transudation. Antigen-specific IgG were absent before vaccination and present with high titers after vaccination. Antigen-specific IgA before and after vaccination were low but significantly different for two antigens. IgG correlated between sputum and serum, and between sputum and disease severity. Sputum albumin was higher in patients with severe COPD than in those with moderate COPD, suggesting changes in transudation played a role. We demonstrated that immunization with the NTHi vaccine induces antigen-specific antibodies in sputum. The correlation between IgG from sputum and serum and the presence of albumin in the sputum of severe COPD patients suggested transudation of antibodies from the serum to the lungs, although local IgG production could not be excluded. Clinical Trial Registration : NCT02075541.

Background: Particulate matter (PM) and air pollution have been suggested to be associated with chronic obstructive pulmonary disease (COPD), contributing significantly to global respiratory disease-related mortality. This study aimed to investigate whether seasonal exposure to PM influences dysbiosis in the respiratory microbiota of patients with COPD., Methods: Sputum samples were collected four times over 1 year from 102 patients with COPD, and 16S rRNA sequencing was performed. The dynamics of the airway microbiota were analyzed depending on PM exposure levels and season., Results: The PM-low exposure group had higher α-diversity compared to the PM-high exposure group, particularly noted in spring. Some bacterial groups, including seven species such as Treponema socranskii, were more abundant in the low exposure group. Additionally, the bacterial community structure in summer significantly differed from that in other seasons, with significantly increased α-diversity in this season. The difference in the airway microbiome due to PM exposure was prominent in patients with moderate COPD., Conclusions: PM exposure may influence changes in the sputum microbiome depending on exposure levels and seasonal variations. Our results suggest that airway microbiomes could vary with PM exposure according to seasonal trends., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Bacterial infections of the lower airways are the main cause of mortality and morbidity in cystic fibrosis. The most frequently isolated pathogens are S. aureus and P. aeruginosa; bacterial co-infections are frequently observed. The aim of this review is to provide, in the current context, the indications regarding the best antibiotic strategy to adopt in subjects affected by CF infected with the most common pathogens. We selected relevant publications (guidelines, systematic reviews and clinical studies published so far on these topics) and we analysed the sampling methods used and antibiotic strategies adopted. Oropharyngeal sampling methods are considered less sensitive for pathogen detection than sputum. In non-expectorating people, induced sputum is considered equivalent to two-lobe bronchoalveolar lavage, which is considered invasive. Antibiotic treatment against the main pathogens can consist in eradication treatment in the early stages of infection, chronic suppressive therapy and treatment of the pulmonary exacerbations. This scheme is valid for P. aeruginosa but remains to be demonstrated for the other pathogens. For S. aureus, no evidence-based therapeutic strategies on how to treat the different stages of bacterial infection have been established with certainty. With regard to the treatment of the other classic pathogens (B. cepacia complex, A. xylosoxidans and S. maltophilia), no evidence-based indications exist and decision is left to the clinician. The recent introduction of highly effective modulators on the CFTR protein, in addition to the favourable effects described in regulatory trials, has led to a reduction in bacterial isolations; the real effect of which in clinical practice has still to be assessed on the basis of scientific data. CONCLUSIONS: The reliability of culture examination depends on sampling methods, and expectorated sputum continues to be the best method as it is simple and non-invasive. P. aeruginosa is the pathogen for which antibiotic strategies for the various stages of infection appear best established, and the efficacy of early eradication treatment and chronic suppressive therapy have been underlined in clinical trials and systematic reviews. The recent introduction of modulators into clinical practice, despite their widely described efficacy, has not yet led to suggestions for changes in antibiotic strategies against the pathogens most frequently isolated., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Objective: To study the characteristics of the airway microbiome co-occurrence network in patients with type 2 and non-type 2 asthma. Methods: In a prospective study based on a cohort of asthma patients, respiratory induced sputum samples were collected from 55 asthma patients [25 males and 30 females, with a median age of 47.7 years (age range 34.3-63.0 years)] admitted to the Department of Respiratory and Critical Care, Beijing Chaoyang Hospital, Capital Medical University and 12 healthy controls from the Physical Examination Centre of Beijing Chaoyang Hospital, Capital Medical University, from May 2021 to May 2022. According to the level of exhaled breath nitric oxide (FeNO), the asthma patients were divided into 22 cases in the high FeNO group (FeNO≥40 ppb, i.e. , type 2 asthma group) and 33 cases in the low FeNO group (FeNO<40 ppb, i.e., non-type 2 asthma group). All induced sputum samples were subjected to second-generation macrogenomic sequencing and bioinformatic analyses of microbial community diversity, compositional characteristics, symbiotic network characteristics and metabolic function prediction. The Kruskal-Wallis rank sum test was used for between-group comparisons, and the linear discriminant analysis (LEfSe) method was used to compare the differences in flora composition between groups. The R language was used for microbial network analysis. In addition, PICRUSt was used to predict the metabolic-functional characteristics of the microbial communities. Results: The microbial communities in the healthy control group had a lower proportion of p&#95;Firmicutes and p&#95;Proteobacteria than asthma patients, 29% and 21%, respectively; 37% and 33% in the low FeNO group and 42% and 26% in the high FeNO group. The microbial network in the low FeNO group had 64 pairs of edges forming 16 communities, and about 75% of the nodes had eigenvector centrality values between 0 and 0.05, and 25% of the nodes had eigenvector centrality values between 0.10 and 0.45. There were four layers of κ-nucleosynthesis, and about 42% of the vertices were in the centre of the two layers. The microbial network of the high-FeNO group had 80 pairs of edges forming 18 clusters, and 81% of the nodes had eigenvector centrality values between 0 and 0.05, and 19% of the nodes had eigenvector centrality values between 0.10 and 0.35. The κ-nucleus decomposition had eight layers, and 21% of the vertices were located in the centre's two layers. The main functional differences between the low and high FeNO groups were shown in metabolic pathways (including sugar, lipid, amino acid, and energy metabolism), drug resistance, biofilm transport, signalling, intercellular communication, and cellular repair. Conclusions: Compared with non-type 2 asthmatics, type 2 asthmatics had a higher alpha diversity of respiratory microbiota, lower levels of microorganisms in the p&#95;Proteobacteria , and a more aggregated microbial network. There was a significant difference in the predicted metabolic function of the two endotypes of asthmatics.

Identifying pathogens, resistance-conferring mutations, and strain types through targeted amplicon sequencing is an important tool. However, due to the limitations of short read sequencing, many applications require the division of limited clinical samples. Here, we present stilPCR (single-tube Illumina long read PCR), which allows the generation of hemi-nested amplicons in a single tube, with Illumina indexes and adapters, effectively increasing the Illumina read length without increasing the input requirements of reagents or sample. We have successfully utilized stilPCR on clinical sputum from tuberculosis patients to detect drug resistance mutations., Competing Interests: RJN, DB, SD, and SC are Cepheid employees. Other authors have no competing interests. Our affiliation with Cepheid does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Limberis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: In rural Nepal, poor road and transport networks and few testing laboratories impede tuberculosis diagnosis. A drone transport system was established to transport sputum samples to laboratories with advanced molecular diagnostic machines - GeneXpert MTB/RIF. This study explored the perceptions of using drones for tuberculosis diagnosis among community stakeholders, female community health volunteers, and healthcare providers from communities with drones implemented and without drone programs., Methods: In December 2019, we conducted focus group discussions in two drone-implemented and three without drone programs. We purposively selected 40 participants: Female community health volunteers (n=16), community stakeholders (n=18), and healthcare providers (n=6). Focus group discussions employed semi-structured questions, which were audio-recorded, transcribed, and translated into English. Codebook thematic analysis was performed and charted using three levels of the socioecological model: individual, community, and health system., Results: We identified four themes (i) Trust in drones underpins successful use for tuberculosis diagnosis; (ii) Drone-based sample transport optimised connectivity and accessibility for people with tuberculosis and healthcare providers; (iii) Drones create opportunities to improve community and health system, and (iv) External factors impede the use of drones to facilitate tuberculosis diagnosis. The study reported, at an individual level, people's trust in drones mainly through community-based events. For local healthcare providers, drones reduce transport time, opportunity costs, and immediate cash costs of transport. At the community level, drone use creates opportunities to increase the skills of local people as drone pilots. At the health system level, drone transport increases efficient sputum sample delivery and provides opportunities to transport medicines and other biomedical samples. Perceived challenges of using drones were adverse weather, limitations in skilled human resources, and financial resources to operate drones sustainably., Conclusions: Healthcare providers, female community health volunteers, and community stakeholders reported high levels of trust in drones and perceived their use for tuberculosis diagnosis and care to substantially benefit people with tuberculosis and providers in rural Nepal. There was a high level of demand for application to other healthcare services and wider geographical coverage, demonstrating drones as a potential tool for enhancing access to healthcare in geographically remote communities., Competing Interests: Declarations. Ethics approval and consent to participate: The approval for the use of drones for sputum sample transportation was received from twelve government Ministries and Departments policy and guidelines. The study received ethical approval from the Nepal Health Research Council (Approval number: 251–2019). The study provided a participant information sheet detailing the description of the study, objectives, risks and benefits of participating in the study, funding agencies, and their ability to withdraw at any point of time during the study period. All participants provided written informed consent. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Early diagnosis of Mycobacterium tuberculosis (MTB) infection is of great significance for the clinical management of tuberculosis (TB). We first explored the efficacy of single-molecule nanopore DNA sequencing in the early diagnosis of suspected TB patients and analyzed the advantages in differentiating and diagnosing MTB and non-tuberculous Mycobacteria (NTM)., Methods: In this cohort study, we reviewed the clinical data of suspected TB patients admitted from December 1, 2021, through April 15, 2022. All patients underwent 3 - 6 times acid-fast bacilli smear examinations of sputum, all of which were negative. To make a definitive diagnosis, we extracted specimens from the patients and performed specimen culture, Xpert MTB/Rif assay, and single-molecule nanopore DNA sequencing. The efficacy of different diagnostic methods in diagnosing suspected TB patients was compared using "Diagnostic Criteria for Pulmonary Tuberculosis" (WS288-2017) as the gold standard., Results: Among the 25 patients, 15 were infected with MTB, 5 were infected with NTM, 1 had mixed MTB and NTM infection, and 4 were negative. The accuracy of single-molecule nanopore DNA sequencing in diagnosing mycobacterial infection (MTB + NTM) was 92.0%, with a sensitivity of 90.5% and a specificity of 100%; the accuracy of diagnosing MTB infection was also 92.0%, with a sensitivity of 87.5% and a specificity of 100%. Single-molecule nanopore DNA sequencing showed an accuracy of 100% in differentiating MTB and NTM. However, the diagnostic accuracy and sensitivity of specimen culture and Xpert MTB/Rif assay were relatively low (≤ 52%) compared to "specimen culture + Xpert MTB/Rif assay". The diagnostic efficacy of single-molecule nanopore DNA sequencing was not affected by the source of tissue samples, while specimen culture and Xpert MTB/Rif assay could not diagnose mycobacterial infection using extrapulmonary specimens., Conclusions: As a third-generation sequencing technology, single-molecule nanopore DNA sequencing has significant application value in diagnosing suspected TB patients. Compared to traditional diagnostic methods, such as specimen culture and Xpert MTB/Rif assay, single-molecule nanopore DNA sequencing exhibits high diagnostic efficacy, low error rate, and convenient detection.

The sensitivity of Xpert MTB/RIF (Xpert) pooled testing is limited for diagnosing patients with paucibacillary tuberculosis (TB). We assessed whether pooled testing with Xpert MTB/RIF Ultra (Ultra) can be a sensitive and effective approach for mass TB screening. Conserved, frozen sputum samples, previously confirmed as positive or negative for Mycobacterium tuberculosis by individual Xpert assays, were mixed in pools of 4, 8, and 16 and then tested using Ultra. Each pool contained a single positive sample with varying mycobacterial loads. We then simulated TB screening at prevalence ranges of 0.2-1.0 % and calculated the cartridges required per case detected at different pool sizes. The overall sensitivity of Ultra pooled testing was high (88.9 %, 75.9-96.3). Sensitivity was greater in pools in which the positive sample had a high mycobacterial load compared to those with scant bacilli. As prevalence increased, the optimal pool size and benefits of pooled testing declined, but a pool size of 8 resulted in at least 80 % cartridge savings with the highest simulated prevalence. Sputum pooling using Ultra could be a sensitive and effective strategy for TB screening. However, broad TB screening in communities with limited resources will require new, lower-cost, high-throughput screening tools, perhaps based on non-sputum specimens., Competing Interests: Declaration of competing interest We report there are no competing interests to declare. Cepheid donated the Xpert MTB/RIF Ultra and Xpert MTB/RIF cartridges and a GeneXpert instrument in honor of the Investigator Initiated Study (no. Cepheid-IIS-2023-002)., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Objectives: This study aimed to evaluate the efficacy of inhaled cationic antibiotics, including tobramycin (TOB) and colistin (CST), using an in vitro alginate bead model that simulates Pseudomonas aeruginosa lung biofilms., Methods: Bioluminescent P. aeruginosa were encapsulated within alginate beads and dispersed in either Mueller-Hinton broth (MHB) or artificial sputum medium (ASM). The impact of bead size and culture medium on TOB and CST efficacy was assessed by monitoring bioluminescence kinetics, followed by colony-forming unit (CFU/mL) measurements. Antibiotic efficacy was quantified using a Hill inhibitory model to analyze variations in CFU/mL in response to TOB and CST concentrations., Results: The TOB EC 50 was found to be 8-fold higher when P. aeruginosa was encapsulated in larger beads (1200 μm) compared to smaller beads (60 μm). TOB efficacy further decreased twofold when larger beads were dispersed in ASM. In contrast, CST demonstrated superior efficacy, being four times more potent than TOB, with corresponding EC 50 values of 20.5 ± 2.8 times MIC and 78.4 ± 10.2 times MIC, respectively. No change in MICs was observed for either antibiotic, even after exposing bacteria to 200 times the MIC., Conclusions: This P. aeruginosa biofilm model highlights how alginate and mucus modulated the efficacy of TOB and CST, and suggested the superior efficacy of CST in eradicating pulmonary biofilms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Isoniazid is an early bactericidal anti-tuberculosis (TB) agent and isoniazid mono-resistance TB is the most prevalent drug-resistant TB worldwide. Concerns exist regarding whether resistance to isoniazid would lead to delayed culture conversion and worst outcomes. From January 2008 to November 2017, adult culture-positive pulmonary TB patients receiving isoniazid, rifampicin, pyrazinamide, and ethambutol were identified through Taiwan Center for Disease Control database and were followed until the end of 2017. Primary outcomes included time to sputum culture conversion (SCC) within two months. Secondary outcomes included death and unfavourable outcomes at the end of 2nd month. A total of 37,193 drug-susceptible and 2,832 isoniazid monoresistant pulmonary TB patients were identified. Compared with no resistance, isoniazid monoresistance was not associated with a delayed SCC (HR: 0.99, 95% CI: 0.94─1.05, p  = 0.8145), a higher risk of 2-month mortality (HR: 1.19, 95% CI: 0.92─1.53, p  = 0.1884), and unfavourable outcomes at 2nd month (OR: 1.05, 95% CI: 0.97─1.14, p  = 0.2427). Isoniazid monoresistance was associated with delayed SCC (HR: 0.90, 95% CI: 0.83─0.98, p  = 0.0099) and a higher risk of unfavourable outcomes (OR:1.18, 95% CI: 1.05─1.32, p  = 0.0053) in patients aged between 20 and 65, and delayed SCC in patients without underlying comorbidities (HR: 0.90, 95% CI: 0.81─0.98, p  = 0.0237). Isoniazid mono-resistant TB had a comparable outcome with drug-susceptible TB at the end of the intensive phase. Healthy, and non-elderly patients were more likely to had culture persistence, raising concerns about disease transmission in these subgroups and warranting early molecular testing for isoniazid resistance.

Purpose: The diagnosis of pulmonary cryptococcosis (PC) remains challenging, particularly in patients presenting with lobar or patchy consolidation on chest radiographs. Biopsies are sometimes performed for histopathologic examination and microbiological culture to differentiate infections, including PC, from lung cancers. However, to date, the clinical value of small biopsy samples and their reasonable processing methods for detecting Cryptococcus are rarely evaluated. Furthermore, the cryptococcal antigen (CrAg) test has been widely used in cryptococcosis diagnosis due to its high specificity. This 6-year retrospective study aimed to assess the efficacy of four tests commonly used for detecting Cryptococcus in the diagnosis of pulmonary cryptococcosis, and reveal that the combination of 2 or 3 methods would raise diagnosis sensitivity., Methods: The results of CrAg test, histopathologic examination and routine cryptococcal culture of sputum/bronchoalveolar lavage fluid (BALF) were collected from hospitalized patients between June 2019 to May 2024. Additionally, the results of 4 above-mentioned methods were analyzed to compare their effectiveness in PC diagnosis., Results: Among 1508 patients whose biopsy specimens were sent for pathogen detection, 63 PC cases were diagnosed, and 24 C. neoformans strains were cultivated using the Myco/F Lytic culture, which was more than those by sputum/BALF culture (9 strains). CrAg was positive in 82.5% (52/63) PC patients and remained the most sensitive method. The combination of CrAg and biopsy culture will increase the overall diagnostic yield to 95.2% (60/63)., Conclusions: In summary, for those having biopsy tissue collected, the combination of CrAg and biopsy culture using Myco/F could effectively identify most PC cases., Competing Interests: Declarations. Ethical Statement: The institutional review boards at the China-Japan Friendship Hospital approved the human subjects study protocol with approval number 2024-KY-158. Conflicts of interest: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Tuberculosis (TB) is a bacterial infection that usually affects the lungs, although it can also affect other parts of the body. Vitamin D deficiency and response to treatment have been demonstrated in patients with active TB in several studies, but not in MDR-TB patients, which is a new observation in the present study., Objective: To study the time to initial sputum culture conversion and to associate baseline vitamin D levels and response to treatment in patients with PTB Cat I and MDR-TB., Methods: A total of 897 North Indian participants were recruited and divided into three groups: treatment-naïve PTB Cat I, MDR-TB, and healthy controls. Serum biochemistry, including 25-hydroxyvitamin D and calcium, was measured in all participants with PTB, Cat I, and MDR-TB., Results: PTB Cat I patients had high bacillary load grading at baseline compared to 2 nd month followed by 6 th month of treatment. More severe chest radiographic features, such as cavitation and the presence of bilateral disease at baseline. Mean sputum smear conversion times were 0.95 ± 0.7 months and culture conversion to negative occurred at a mean time of 0.8 ± 0.7 in PTB Cat I patients compared to MDR-TB patients on average sputum smear and time of 2.4 ± 3 months. Significantly lower mean serum 25-hyroxyvitamin D concentration was found in the 6 th month than in the 2 nd month and baseline in PTB Cat I., Conclusion: Low serum vitamin D deficiency was observed in both groups during treatment and is one of the important factors responsible for susceptibility to TB in both groups; however, its significance is uncertain. Patients with continuous positive sputum for multidrug-resistant tuberculosis (MDR-TB) had a worse prognosis than those with sputum bacteriology conversion. Two months into a treatment regimen, sputum smear conversions may be a useful indicator of an MDR-TB patient's prognosis.

The GenoType CMdirect Ver 1.0 and GenoType Mycobacterium Common Mycobacteria Ver 2.0-line probe assays were utilized to identify nontuberculous mycobacteria (NTM) from decontaminated sputum in a GeneXpert MTB/RIF Ultra negative cohort. A preliminary NTM prevalence of 1.7 % was observed, with a 100 % specificity. The high specificity advocates the CMdirect as a possible rule-in test for NTM disease., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: The respiratory microbiota plays a crucial role in the development of tuberculosis (TB). While existing research has underscored imbalances in the respiratory microbiota of adult patients with TB, information regarding the lower respiratory tract (LRT) microbiota in pediatric patients with TB remains scarce., Methods: We employed 16S rRNA gene sequencing technology to investigate the LRT microbial communities of 85 children of different ages with active TB of different severities, 33 children with infectious diseases other than TB, and 48 sex- and age-matched healthy children., Results: A marked imbalance in the respiratory microbiota was observed in children with TB, highlighted by reduced alpha diversity and a distinct microbial community structure. Comparative analysis indicated that patients with severe TB exhibited lower Neisseria levels than those with non-severe TB (1.01% vs. 3.93%, respectively; p = .02). Streptococcus and Gemella levels were lower in bacteriologically confirmed TB cases compared with clinically diagnosed cases, and higher in healthy children younger than 10 years old than in the older group. Spearman correlation analysis demonstrated significant associations between the microbiota of the LRT and cytokine concentrations in the sputum of children with TB (e.g., an inverse correlation between Veillonella and interleukin-17A)., Conclusions: TB induced significant dysbiosis in the LRT microbiota of children that was associated with disease severity and the immunological response in the respiratory tract. Our findings may offer a deeper understanding of the role of the respiratory microbiome in TB pathogenesis and progression., (© 2024 Wiley Periodicals LLC.)

Objectives: Predicting progression of nontuberculous mycobacterial lung disease (NTM-LD) remains challenging. This study evaluated whether sputum bacterial microbiome diversity can be the biomarker and provide novel insights into related phenotypes and treatment timing., Methods: We analyzed 126 sputum microbiomes of 126 patients with newly diagnosed NTM-LD due to Mycobacterium avium complex, M. abscessus complex, and M. kansasii between May 2020 and December 2021. Patients were followed for 2 years to determine their disease progression status. We identified consistently representative genera that differentiated the progressor and nonprogressor by using six methodologies. These genera were used to construct a prediction model using random forest with five-fold cross validation., Results: Disease progression occurred in 49 (38.6%) patients. Compared with nonprogressors, α-diversity was lower in the progressors. Significant compositional differences existed in the β-diversity between groups (P = 0.001). The prediction model for NTM-LD progression constructed using seven genera (Burkholderia, Pseudomonas, Sphingomonas, Candidatus Saccharibacteria, Phocaeicola, Pelomonas, and Phascolarctobacterium) with significantly differential abundance achieved an area under curve of 0.871., Conclusion: Identification of the composition of sputum bacterial microbiome facilitates prediction of the course of NTM-LD, and maybe used to develop precision treatment involving modulating the respiratory microbiome composition to ameliorate NTM-LD., Competing Interests: Declarations of competing interest All authors have no conflicts of interest relevant to this study to declare., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Purpose: Some patients with pulmonary tuberculosis (PTB) do not display typical clinical features, leading to delays in diagnosis and treatment., Methods: We retrospectively analyzed PTB patients admitted to the Second Affiliated Hospital of Chongqing Medical University between 2017 and 2020. They are divided into pathological group (diagnosed through pathological biopsy) and control group (diagnosed via sputum or lavage fluid). Clinical data of both groups were compared. Based on radiographic features, the pathological group was further divided into the inflammation group, peripheral nodule group, and central occupancy group. We then statistically analyzed the computed tomography (CT) signs, bronchoscopic manifestations and results of pathological biopsy for each subgroup., Results: The pathological group consisted of 75 patients, while the control group had 338 patients. Multivariate logistic regression analysis showed that the pathological group had more diabetes (OR = 3.266, 95% CI = 1.609-6.630, P = 0.001), lower ESR (OR = 0.984, 95% CI = 0.971-0.998, P = 0.022), and lower CRP (OR = 0.990, 95% CI = 0.980-0.999, P = 0.036). In the three subgroups, the exudative lesions in the inflammation group were mostly located in atypical areas of PTB. The lobulation sign and spiculation sign were frequently observed in the peripheral nodule group. All presented with significant hilar mediastinal lymphadenopathy in the central occupancy group. In the pathological group, bronchoscopic manifestations typically included mucosal edema and bronchial stenosis., Conclusion: Diabetes is an independent risk factor for atypical PTB. Expression of erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) in atypical PTB is low. Radiologically, it is most easily misdiagnosed when presented as peripheral solid nodules or masses, so a biopsy is recommended., Competing Interests: Declaration of competing interest The authors have no competing interests to declare., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Escalating cases of multidrug-resistant tuberculosis (MDR-TB) pose a major challenge to global TB control efforts, necessitating innovative diagnostics to empower decentralized detection of gene mutations associated with resistance to rifampicin (RIF) and isoniazid (INH) in Mycobacterium tuberculosis (M. tuberculosis) in resource-constrained settings., Methods: Combining multiplex fluorescent PCR and Multiple Probes Melting Analysis, we identified mutations in the rpoB, katG, ahpC and inhA genes from sputum specimens. We first constructed a reference plasmid library comprising 40 prevalent mutations in the target genes' resistance determining regions and promoters, serving as positive controls. Our assay utilizes a four-tube asymmetric PCR method with specifically designed molecular beacon probes, enabling simultaneous detection of all 40 mutations. We evaluated the assay's effectiveness using DNA isolated from 50 clinically confirmed M. tuberculosis sputum specimens, comparing our results with those obtained from Sanger sequencing and retrospective validation involving bacteriological culture and phenotypic drug susceptibility testing (pDST). We also included the commercial Xpert MTB/RIF assay for accuracy comparison., Results: Our data demonstrated remarkable sensitivity in detecting resistance to RIF and INH, achieving values of 93.33% and 95.24%, respectively, with a specificity of 100%. The concordance between our assay and pDST was 98.00%. Furthermore, the accuracy of our assay was comparable to both Sanger sequencing and the Xpert assay. Importantly, our assay boasts a 4.2-h turnaround time and costs only $10 per test, making it an optimal choice for peripheral healthcare settings., Conclusion: These findings highlight our assay's potential as a promising tool for rapidly, accurately, and affordably detecting MDR-TB., Competing Interests: Declarations. Conflict of interest: All authors declare no competing interests as defined by Springer, or other interests that might be perceived to influence the results and/or discussion reported in this paper. Ethical approval, consent to participate and biosafety statement: This study received institutional approval from the Research Ethics Committee of Chaoshan Hospital (Approval number: CREA-CSH2021-003), affiliated with Jinan University First Affiliated Hospital, and the Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China. This approval was in line with the Helsinki declaration as revised in 2013 and its later amendments. All participants provided written informed consent to the collection, the storage and the use of biological samples for scientific analysis before participating in the study. To ensure ethical compliance, data pertinent to disease control were collected and subsequently anonymized for analysis. All experimental protocols of this study were performed following national technical specification for TB prevention and control., (© 2024. Springer-Verlag GmbH Germany, part of Springer Nature.)

Bacterial aerobic respiration may determine the outcome of antibiotic treatment in experimental settings, but the clinical relevance of bacterial aerobic respiration for the outcome of antibiotic treatment has not been tested. Therefore, we hypothesized that bacterial aerobic respiration is higher in sputum from patients with acute lower respiratory tract infections (aLRTI), than in sputum from patients with chronic LRTI (cLRTI), where the bacteria persist despite antibiotic treatment. The bacterial aerobic respiration was determined according to the dynamics of the oxygen (O 2 ) concentration in sputum from aLRTI patients (n = 52). This result was evaluated by comparison to previously published data from patients with cLRTI. O 2 consumption resulting in anoxic zones was more frequent in sputum with detected bacterial pathogens. The bacterial aerobic respiration in aLRTI sputum approximated 55% of the total O 2 consumption, which was significantly higher than previously published for cLRTI. The bacterial aerobic respiration in sputum was higher in aLRTI patients than previously seen in cLRTI patients, indicating the presence of bacteria with a sensitive physiology in aLRTI. These variations in bacterial physiology between aLRTI patients and cLRTI patients may contribute the huge difference in treatment success between the two patient groups., (© 2024 The Authors. APMIS published by John Wiley & Sons Ltd on behalf of Scandinavian Societies for Pathology, Medical Microbiology and Immunology.)

Background: India relies primarily on direct smear microscopy for tuberculosis (TB) diagnosis. However, the low sensitivity of smear microscopy emphasizes the need to improve its performance. We recently described the development of 'TB Detect ' kit which showed improved performance over direct smear microscopy at National Reference Laboratories (NRLs) in India., Methods: The present study was aimed to assess the operational feasibility of 'TB Detect ' microscopy in field settings. This was evaluated by (i) assessing the performance of 'TB Detect ' microscopy vs. LED-fluorescence microscopy (LED-FM) on consecutive presumptive pulmonary TB patients ( n  = 5300) who attended Designated Microscopy Centres (DMCs, n  = 13) under 4 NRLs at Bhubaneswar, Bhopal, Chennai, and New Delhi, and (ii) obtaining feedback from Scientists ( n  = 10) and laboratory technicians ( n  = 42) using semi-structured questionnaires under the following parameters: feasibility of initiation of 'TB Detect' microscopy in DMCs, sample preparation and testing, training, time-to-result, logistics, and troubleshooting. A scoring questionnaire was also used to assess 'TB Detect ' microscopy vs . LED-FM and statistical significance of the scores was calculated using paired t -test., Results: The overall positivity of 'TB Detect ' microscopy was 10.32% (547/5300) vs. 8.96% (475/5300) of LED-FM at all sites and the increment in positivity was significant ( p  = 0.019). In addition, 'TB Detect ' microscopy yielded an increment in smear grade status over LED-FM ( p  = 0.043). The feedback from the study-in-charge and kit users indicated that 'TB Detect ' microscopy was easily adapted in point-of-care settings. An analysis of scoring feedback suggested that it was easy to perform and observe in comparison to LED-FM ( p  < 0.005)., Conclusions: This study established the feasibility of 'TB Detect ' microscopy in field settings.

Lack of appropriate early diagnostic tools for drug-resistant tuberculosis (DR-TB) and their incomplete drug susceptibility testing (DST) profiling is concerning for TB disease control. Existing methods, such as phenotypic DST (pDST), are time-consuming, while Xpert MTB/RIF (Xpert) and line probe assay (LPA) are limited to detecting resistance to few drugs. Targeted next-generation sequencing (tNGS) has been recently approved by WHO as an alternative approach for rapid and comprehensive DST. We aimed to investigate the performance and feasibility of tNGS for detecting DR-TB directly from clinical samples in Bangladesh. pDST, LPA and tNGS were performed among 264 sputum samples, either rifampicin-resistant (RR) or rifampicin-sensitive (RS) TB cases confirmed by Xpert assay. Resistotypes of tNGS were compared with pDST, LPA and composite reference standard (CRS, resistant if either pDST or LPA showed a resistant result). tNGS results revealed higher sensitivities for rifampicin (RIF) (99.3%), isoniazid (INH) (96.3%), fluoroquinolones (FQs) (94.4%), and aminoglycosides (AMGs) (100%) but comparatively lower for ethambutol (76.6%), streptomycin (68.7%), ethionamide (56.0%) and pyrazinamide (50.7%) when compared with pDST. The sensitivities of tNGS for INH, RIF, FQs and AMGs were 93.0%, 96.6%, 90.9%, and 100%, respectively and the specificities ranged from 91.3 to 100% when compared with CRS. This proof of concept study, conducted in a high-burden setting demonstrated that tNGS is a valuable tool for identifying DR-TB directly from the clinical specimens. Its feasibility in our laboratory suggests potential implementation and moving tNGS from research settings into clinical settings.

Half of acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are caused by bacterial infection, but self-management plans (SMPs) generally advocate use of antibiotics and steroids for all events. We report findings from a qualitative study exploring the acceptability of a sputum colour chart and SMP to guide patient use of antibiotics and steroids (commonly termed a 'rescue pack'). Qualitative interviews were conducted with healthcare professionals (HCPs) and patients from the Colour COPD trial - a randomised controlled trial of usual care (SMP alone) versus usual care plus sputum colour chart to manage AECOPD across England and sampled to promote maximum variation. Interviews were audio-recorded, transcribed clean verbatim, then analysed thematically, using an adapted Framework approach. Expert patients contributed to the patient data analysis. Fourteen HCPs and 39 patients were interviewed from primary and secondary care. Three overarching themes were identified. (1) Handling tensions: the tension between stewardship of antimicrobials and need to reduce risk of serious illness. (2) Clinical and embodied legacies: established clinical practices of infection control and patient's own experiences of managing their condition over time have focused on early intervention for AECOPD. (3) Changing self-management practices: opportunities for changing practices through negotiating change between HCP and patient. In conclusion, while, in principle, the assessment of sputum colour using a chart to manage AECOPD was acceptable to both patients and HCPs, in practice, it is unlikely to have significant impact on well-established clinical practices for infection control and patient habits of self-management., Competing Interests: Competing interests: MM declares no financial or non-financial competing interests. All other authors received funding for their contributions to this study, they declare no non-financial competing interests., (© 2024. The Author(s).)

Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended., Competing Interests: Competing interests: The authors declare no competing interests. Ethical approval: All ethical regulations relevant to human research participants were followed. Ethical approval for this study was obtained by the Institutional Review Board of Mass General Brigham (Protocol #2018P002934, 2019P002868 and 2020P001761)., (© 2024. The Author(s).)

Tuberculosis is a highly infectious bacterial disease caused by Mycobacterium tuberculosis . The spread of this agent has caused serious health problems worldwide, and the rapid and accurate detection of M. tuberculosis is essential for controlling the spread of infection and for preventing the emergence of multidrug-resistant strains. In this study, the trans cleavage ability of CRISPR-Cas12a against single-stranded DNA was combined with hybridization chain reaction and chemiluminescent signal to establish an imaging sensor for the hypersensitive detection of M. tuberculosis DNA. We observed linear relationships between the concentration of M. tuberculosis DNA and the output signal over the ranges of 10 to 200 pM and 200 to 800 pM DNA. The equations of the standard curves were y = 56.08 x + 3303, with R 2 = 0.9916 for the lower range and y = 15.69 x + 10 685, with R 2 = 0.9929 for the higher range. The limit of detection was as low as 0.83 pM for genomic DNA, and a plasmid containing an M. tuberculosis -specific sequence was detected at 1 copy per μL. A detection accuracy of 100% was achieved in the analysis of DNA isolated from sputum of hospitalized tuberculosis patients. The sensitivity and specificity of the proposed sensor is combined with a long shelf-life and a low cost of materials. This study introduces a new method for tuberculosis detection and broadens the application of CRISPR-Cas12a-based sensors in clinical diagnosis.

Introduction: The TriAD study will assess the Xpert MTB/XDR (Xpert XDR; Cepheid) assay to detect tuberculosis (TB) drug resistance in sputum testing positive for TB to rapidly triage and treat patients with a short all-oral treatment regimen., Methods and Analysis: In this study, approximately 4800 Xpert MTB/RIF or Ultra MTB-positive patients (irrespective of rifampicin (RIF) resistance (RR) status) from several clinical sites across South Africa, Nigeria and Ethiopia will be enrolled over 18-24 months and followed-up for approximately 6 months post-TB treatment completion. Participants will be enrolled into one of two cohorts based on Xpert MTB/RIF and Xpert XDR results: Mycobacterium tuberculosis ( M.tb ) positive participants with RR in Cohort 1 (n=880) and M.tb positive RIF susceptible TB patients with isoniazid mono-resistance irrespective of presence of resistance to fluoroquinolones, second-line injectable drugs or ethionamide in Cohort 2 (n=400). Cohort 1 will be compared with historical cohorts from each implementing sites. The primary study outcomes include time to initiation of an appropriate treatment regimen by resistance profile and the proportion of patients with favourable treatment outcomes compared with historical cohorts from each of the implementing sites. Secondary outcomes include feasibility, acceptability and cost-effectiveness of this approach to inform policies and guidelines for programmatic implementation of this triage and treat model for drug-resistant tuberculosis management. Utility of the tuberculosis molecular bacterial load assay (TB-MBLA) for real-time treatment response assessment will also be evaluated., Ethics and Dissemination: The University of KwaZulu-Natal Biomedical Research Ethics Committee (BREC) and local research committees have provided ethical review and approval (BREC/00002654/2021, HREC 210805, NHREC/01/01/2007 and EPHI-IRB-459-2022). The South African Health Products Regulatory Authority (SAHPRA) have granted regulatory approval for the TRiAD Study (SAHPRA MD20211001). Trial results will be disseminated through conference presentations, peer-reviewed publications and the clinical trial registry., Trial Registration Number: Clinicaltrials.gov; Trial registration number: NCT05175794; South African National Clinical Trials Register (SANCTR DOH-27-012022-4720)., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY. Published by BMJ.)

Objectives: Patients with coronavirus disease 2019 (COVID-19) are at increased risk of opportunistic fungal infections. This study aims to identify fungal pathogens among COVID positive and negative patients, assess their antifungal susceptibility and evaluate biofilm forming ability of Candida spp. A cross-sectional study was conducted among sputum samples from 135 COVID positive and 101 COVID negative cases. Fungal pathogens were identified by conventional culture methods. Antifungal susceptibility test of Candida isolates was done by disc diffusion method and biofilm production by microtiter plate method., Results: The prevalence of fungal pathogens among COVID-positive and negative cases was 6.70% and 22.77% respectively. In COVID positive cases, Candida albicans (33.33%) was predominantly followed by Aspergillus flavus 2(22.22%) and Candida tropicalis, Mucor spp. and Aspergillus fumigatus. In COVID negative cases, Candida albicans (69.60%) prevailed followed by Trichosporon spp., Candida parapsilosis, Mucor and Alternaria. Age and gender were not associated with fungal infection. Most Candida spp. were susceptible to miconazole but resistant to ketoconazole. To the best of our knowledge, this study represents the first report from Nepal on critical and high priority fungal pathogens categorized by WHO. With fungal infections on the rise, enhanced clinical vigilanceand antifungal susceptibility testing are warranted., Competing Interests: Declarations. Ethics approval and consent to participate: This study was performed in accordance with the Declaration of Helsiki. Ethical approval of this study was obtained from the Institutional Review Committee (IRC) of the Institute of Science and Technology, Tribhuvan University (Ref. No.: IRC-IOST-22–0052). At the time of enrolment, written informed consent was taken from the patients or their legal guardians on behalf of the patients in case of participants under 16 years of age. Participants, parents or guardians were assured about the non-disclosure of information collected from them and were also informed about the use of data for analysis and using the results for improving patient care activities as well as publication without disclosing the name or identity of cases. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

The triple combination elexacaftor-tezacaftor-ivacaftor (ETI) has provided unprecedented clinical benefits for people with cystic fibrosis (pwCF) and drastically transformed the outcome of this disease. We aimed to describe the evolution of lung bacterial colonization in 198 French adult pwCF taking into account the use of concomitantly respiratory treatment. We collected sputum cultures produced during the entire follow-up period starting 3 years before and ending 1 year after ETI initiation. All sputum cultures were centralized and analyzed at our bacteriological laboratory. Clinical data included pulmonary function, respiratory treatments, physiotherapy, number of IV antibiotics treatment, as well as inpatient stays. We observed a significant decrease in colonization prevalence by any CF pathogen after one year of treatment with ETI (p < 0.001). This decrease was confirmed for Pseudomonas aeruginosa, MRSA and MSSA, Stenotrophomonas maltophilia, Achromobacter spp. and nontuberculous mycobacteria (NTM). The maximal density of bacteria documented in sputum cultures decreased from 2.10 7 CFU/ml to 1.10 6 CFU/ml after one year of ETI. We also found a decrease in prevalence of Pseudomonas aeruginosa chronic colonization and in the density of Pseudomonas aeruginosa after one year of ETI. These results confirm the decrease in prevalence and bacterial density of lung colonisation for most of the CF pathogens, including Achromobacter spp, Stenotrophomonas maltophilia concomitantly to the clinical improvement. Further studies are needed to better understand the underlying mechanisms of these microbiological changes., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: To improve tuberculosis case-finding, rapid, non-sputum triage tests need to be developed according to the World Health Organization target product profile (TPP) (>90% sensitivity, >70% specificity). We prospectively evaluated and compared artificial intelligence-based, computer-aided detection software, CAD4TBv7, and C-reactive protein assay (CRP) as triage tests at health facilities in Lesotho and South Africa., Methods: Adults (≥18 years) presenting with ≥1 of the 4 cardinal tuberculosis symptoms were consecutively recruited between February 2021 and April 2022. After informed consent, each participant underwent a digital chest X-ray for CAD4TBv7 and a CRP test. Participants provided 1 sputum sample for Xpert MTB/RIF Ultra and Xpert MTB/RIF and 1 for liquid culture. Additionally, an expert radiologist read the chest X-rays via teleradiology. For primary analysis, a composite microbiological reference standard (ie, positive culture or Xpert Ultra) was used., Results: We enrolled 1392 participants, 48% were people with HIV and 24% had previously tuberculosis. The receiver operating characteristic curve for CAD4TBv7 and CRP showed an area under the curve of .87 (95% CI: .84-.91) and .80 (95% CI: .76-.84), respectively. At thresholds corresponding to 90% sensitivity, specificity was 68.2% (95% CI: 65.4-71.0%) and 38.2% (95% CI: 35.3-41.1%) for CAD4TBv7 and CRP, respectively. CAD4TBv7 detected tuberculosis as well as an expert radiologist. CAD4TBv7 almost met the TPP criteria for tuberculosis triage., Conclusions: CAD4TBv7 is accurate as a triage test for patients with tuberculosis symptoms from areas with a high tuberculosis and HIV burden. The role of CRP in tuberculosis triage requires further research., Clinical Trials Registration: Clinicaltrials.gov identifier: NCT04666311., Competing Interests: Potential conflicts of interest. B. v. G. reports that his group received royalties from Delft Imaging Systems and that he holds shares in Thirona. K. R., B. v. G., A. v. H., A. S., K. M., L. L., T. Z., B. K. M. J., S. B., T. M., and M. K. report support related to this work from the European and Developing Countries Clinical Trials Partnership 2 (EDCTP2). K. R. reports grants unrelated to this work from EDCTP2 and Horizon 2020, as well as unpaid participation on a data safety monitoring board or scientific advisory board for evaluation of new TB diagnostics. S. B. reports a grant unrelated to this work from the National Institutes of Health (NIH) and travel support from MSD. T. M. reports travel support from MSD. N. D. L. reports support for travel from ViiV Healthcare and Gilead Sciences Sarl as well as for attending a board meeting from ViiV Healthcare and Pharming. S. B. and T. M. report travel support from MSD. The other authors report no potential conflict of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Background: Concerted efforts aim to reduce the burden of 6 months of anti-tuberculous treatment for tuberculosis (TB). Treatment cessation at 8 weeks is effective for most but incurs increased risk of disease relapse. We tested the hypothesis that blood RNA signatures or C-reactive protein (CRP) measurements discriminate 8-week sputum culture status, as a prerequisite for a biomarker to stratify risk of relapse following treatment cessation at this time-point., Methods: We identified blood RNA signatures of TB disease or cure by systematic review. We evaluated these signatures and CRP measurements in a pulmonary TB cohort, pre-treatment, at 2 and 8 weeks of treatment, and sustained cure after treatment completion. We tested biomarker discrimination of 8-week sputum culture status using area under the receiver operating characteristic curve (AUROC) analysis and, secondarily, assessed correlation of biomarker scores with time to culture positivity at 8 weeks of treatment., Results: 12 blood RNA signatures were reproduced in the dataset from 44 individuals with sputum culture-positive pulmonary TB. These normalised over time from TB treatment initiation. 11 out of 44 cases with blood RNA, CRP and sputum culture results were sputum culture-positive at 8 weeks of treatment. None of the contemporary blood RNA signatures discriminated sputum culture status at this time-point or correlated with bacterial load. CRP achieved modest discrimination with AUROC 0.69 (95% CI 0.52-0.87)., Conclusions: Selected TB blood RNA signatures and CRP do not provide biomarkers of microbiological clearance to support TB treatment cessation at 8 weeks. Resolution of blood transcriptional host responses in sputum culture-positive individuals suggests Mycobacterium tuberculosis may colonise the respiratory tract without triggering a detectable immune response., Competing Interests: Conflict of interest: C.J. Calderwood reports support for the present study from the National Institute for Health Research (Academic Clinical Fellowship), grants from the Wellcome Trust (225466/Z/22/Z), and support for attending meetings from the British Thoracic Society (Travel Award 2023). B. Oguti reports support for the present study from the National Institute for Health Research (Academic Clinical Fellowship, awarded via University College London). J.K. Roe reports patents held in relation to blood transcriptomic biomarkers of tuberculosis. R. Gupta reports support for the present study from the National Institute for Health Research (personal fellowship award). A.R. Martineau reports support for the present study from the British Lung Foundation, and patents held in relation to blood transcriptomic biomarkers of tuberculosis. M. Noursadeghi reports support for the present study from the Wellcome Trust and NIHR Biomedical Research Centre at University College London Hospitals NHS Trust, and patents held in relation to blood transcriptomic biomarkers of tuberculosis. The remaining authors have no potential conflicts of interest to disclose., (Copyright ©The authors 2024.)

During the coronavirus disease 2019 (COVID-19) pandemic, the exploration of microecology has been essential for elucidating the intricacies of infection mechanisms and the recovery of afflicted individuals. To decipher the interplay of microorganisms between the intestinal and respiratory tracts, we collected sputum and throat swabs and feces from COVID-19 patients and explored the mutual migration among intestinal and respiratory microorganisms. Using next-generation sequencing (NGS) technology, we investigated intestinal and respiratory microorganism intermigration in two patients with severe COVID-19 during their hospitalization. Notably, we observed an expedited recovery of microecological equilibrium in one patient harboring Mycobacterium avium. Comparative analyses between 32 healthy controls and 110 COVID-19 patients with different disease severities revealed alterations in predominant microorganisms inhabiting the respiratory and intestinal tracts of COVID-19 patients. Among the alterations, intestinal Bacteroides vulgatus (BV) was identified as a noteworthy microorganism that exhibited marked enrichment in patients with severe COVID-19. BV, when highly abundant, may inhibit the transitional growth of Escherichia coli/Enterococcus, indirectly prevent the overgrowth of salivary streptococci, and maintain lung/intestinal microecology stability. In summary, this study elucidates the bidirectional microbial intermigration between the intestinal and respiratory tracts in COVID-19 patients. These findings are expected to provide new ideas for the treatment and management of COVID-19, underscoring the essential role of microecology in infectious diseases. Nevertheless, a systematic study of the roles of BV in recovery from infection is required to gain a deeper understanding of the mechanisms of microbial migration., Competing Interests: Competing interests The authors declare no competing interests. Ethics statement This study conformed to the provisions of the Helsinki Declaration of 1975 (as revised in 2008) concerning human rights and was approved by the ethics committee at the First Affiliated Hospital of Guangzhou Medical University, China (ethical approval number: 2020-36). All patients provided written informed consent and volunteered to participate in the scientific research., (© 2024. The Author(s).)