Preanalytical conditions can interfere with M. tuberculosis detection by PCR in respiratory samples

Detection of respiratory pathogenic bacterial nucleic acid detection by Loop-mediated Isothermal Amplification in patients with bacterial pulmonary infections

Objective

Nucleic acid testing can accurately and rapidly identify the presence of pathogenic bacteria. In this study, we analyzed respiratory pathogenic bacteria nucleic acids by LAMP (Loop-mediated isothermal amplification) to clarify the clinical application in patients with bacterial pulmonary infections.

Methods

Clinical data and specimens were collected from 99 patients with bacterial pulmonary infections from June 2021 to April 2023. We compared the differences between nucleic acid detection of LAMP and sputum culture. The correlation between inflammation manifestations of pulmonary imaging and the nucleic acid detection of LAMP was compared and analyzed. And the relationship between LAMP and blood inflammatory markers were analyzed.

Results

The positive rate of LAMP using sputum specimens was significantly higher than that of sputum culture (P < 0.05). Pathogenic bacteria in sputum samples are more likely to be detected by LAMP in patients with inflammatory on lung imaging examination. The coincidence rate of elevated PCT and CRP expression with positive LAMP results were 83.87 % and 88.71 %, respectively. Moreover, PCT, CRP and WBC were significantly higher in LAMP positive group than those in negative group (P < 0.05).

Conclusion

Nucleic acid testing of sputum specimens for pathogenic bacteria by LAMP on the basis of imaging examination can provide a rapid and accurate experimental basis for clinical diagnosis of bacterial pulmonary infections.

Diagnostic Performance of Different Laboratory Methods for the Detection of Extrapulmonary Tuberculosis

Accurate and appropriate extrapulmonary tuberculosis (EPTB) diagnosis remains challenging due to its paucibacillary nature, requirement of invasive collection procedures, and lack of sensitive tests. This study investigated the diagnostic performance of different methods for the diagnosis of EPTB. A total of 1340 EPTB specimens were collected from presumptive EPTB patients from four different hospitals between November 2015 and March 2017. The collected specimens were tested with AFB microscopy, culture, Xpert MTB/RIF assay (Xpert), and MTBDRplus assay. Among the 1340 EPTB specimens, 49 (3.66%), 141 (10.52%), 166 (12.39%), and 154 (11.49%) were positive in AFB microscopy, culture, Xpert MTB/RIF, and MTBDRplus assay, respectively. A total of 194 (14.9%) cases were found positive in at least one of these methods. Using culture as a reference standard, the sensitivity and specificity of AFB microscopy, Xpert MTB/RIF, and MTBDRplus assay were: 27.0%/99.1%, 83.7%/96.0%, and 79.4%/96.5%, respectively. Compared to the composite reference standard, the sensitivity of culture, AFB microscopy, Xpert MTB/RIF, and MTBDRplus assay was 72.7%, 25.3%, 85.6%, and 79.4%, respectively, with a specificity of 100% for all the methods. The Xpert MTB/RIF assay showed the highest sensitivity compared to other methods. Considering the short turnaround time and promising findings, Xpert MTB/RIF assay should be integrated into national TB guidelines as a routine diagnostic test.

Comparison of Analytical Sensitivity (Limit of Detection) of Xpert MTB/RIF and Xpert MTB/RIF Ultra for Non-Sputum Specimens

Tuberculosis (TB) is a significant public health threat and has remained a leading cause of death in many parts of the world. Rapid and accurate testing and timely diagnosis can improve treatment efficacy and reduce new exposures. The Cepheid Xpert® MTB/RIF tests have two marketed products (US-IVD and Ultra) that are widely accepted for diagnosis of TB but have not yet been approved for non-sputum specimens. Despite numerous studies in the literature, no data for the analytical sensitivity of these two products on the non-sputum samples are available to date. This is the first study that systematically determined the analytical sensitivities of both US-IVD and Ultra tests on cerebrospinal fluid (CSF), tissue, and bronchoalveolar lavage (BAL). The limits of detection (LoDs) on the US-IVD test for both Mycobacterium tuberculosis and rifampin resistance in CFU/mL, respectively, were as follows: CSF (3.3 and 4.6), tissue (15 and 23), and bronchoalveolar lavage (BAL) (45 and 60), and on the Ultra test: CSF (0.16 and 2.7), tissue (0.11 and 12), and BAL (0.65, and 7.5). Overall, the analytical sensitivities of the Ultra test were substantially better than US-IVD for all sample types tested. This study provided a foundation for using either the US-IVD or Ultra test for the early detection of both pulmonary and extrapulmonary (EP) TB. Furthermore, using Ultra could result in higher TB case detection rates in subjects with paucibacillary TB and EP TB, positively impacting WHO goals to eradicate TB.

Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS

Background

Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS).

Methods

A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis.

Results

A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSL_B and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSL_B and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples.

Conclusion

High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSL_B and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.

Tuberculous pleural effusion: diagnosis & management

Background: Tuberculosis (TB) is the world's leading cause of death from infectious disease. The World Health Organization (WHO) recognized 6.3 million new TB cases in 2017, 16% corresponding to extrapulmonary forms; pleural tuberculosis (PT) is the most common extrapulmonary form in adults. PT diagnosis is often challenging because the scarcity of bacilli in pleural fluid (PF), sometimes requiring invasive procedures to obtain pleural tissue for histological, microbiological or molecular examination. In regions of medium and high disease prevalence, adenosine deaminase (ADA), interferon gamma (IFN-γ) and interleukin 27 (IL-27) dosages are useful to establish presumptive diagnosis in patients with compatible clinical/radiological picture who present with lymphocytic pleural effusion. PT treatment is similar to the pulmonary TB treatment regimen recommended by WHO. Area covered: In this update, we present a PT review, including epidemiology, pathogenesis, clinical features, diagnosis, and therapy. Expert opinion: There is no PF test alone accurate for PT diagnosis, despite the evolution in clinical laboratory. ADA, IFN-γ and IL-27 are valuable laboratory biomarkers; however, IFN-γ and IL-27 are quite expensive. Molecular tests present low sensitivity in PF, being useful for diagnostic confirmation. Multidrug therapy remains the PT treatment choice. Advancing research in immunotherapy may bring benefits to PT patients.