Respiratory Samples Research Articles

Clinical and biologic profiles of patients with acute respiratory distress syndrome by prevalence of chronic obstructive pulmonary disease or emphysema; a cohort study

IntroductionAcute respiratory distress syndrome (ARDS) is characterized by diffuse lung injury. The impact of pre-existing chronic obstructive pulmonary disease (COPD) or emphysema on ARDS pathogenesis is not well characterized.MethodsSecondary analysis of ARDS patients enrolled in the Acute Lung Injury Registry and Biospecimen Repository at the University of Pittsburgh between June 2012 and September 2021. Patients were categorized into two mutually exclusive groups by the prevalence of COPD or emphysema at the time of ARDS diagnosis. The COPD/emphysema group comprised ARDS patients with radiological evidence of emphysema, chart diagnosis of COPD, or both. Demographics, lung mechanics, and clinical outcomes were obtained from the electronic medical record. Host-response biomarkers known to have validated associations with ARDS were previously measured in plasma and lower respiratory tract samples using a customized Luminex assay. Continuous and categorical variables were compared between groups with and without COPD/emphysema.Results217 patients with ARDS were included in the study, 57 (27%) had COPD/emphysema. Patients with COPD/emphysema were older (median 62 [interquartile range 55–69] versus 53 [41–64] years, p < 0.01), more likely to be male (62% vs. 44%, p = 0.02) and had a higher prevalence of congestive heart failure (25% vs. 4%, p < 0.01) compared to patients without COPD/emphysema. Baseline demographics, laboratory parameters, and mechanical ventilatory characteristics were otherwise similar between the two groups. No difference in 90-day mortality was observed between groups; however, patients with COPD/emphysema had shorter duration of intensive care unit (ICU) stay (median 10 [7–18] versus 16 [9–28] days, p = 0.04) and shorter duration of mechanical ventilation (median 7 [4–16] vs. 12 [6–20] days, p = 0.01). Host response biomarkers in serum and lower respiratory tract samples did not significantly differ between groups.ConclusionARDS patients with COPD or emphysema had similar respiratory mechanics, host response biomarker profiles, and mortality compared to those without COPD or emphysema but with a shorter median duration of mechanical ventilation and ICU length of stay. Future studies should address differences in clinical and biological responses by disease severity, and should investigate the impact of severity of COPD and emphysema on mechanical ventilation and targeted therapeutic strategies in ARDS.Clinical trial numberNot applicable

Accuracy of Xpert and alternative sampling methods to diagnose childhood pulmonary tuberculosis, a prospective cohort study

ObjectivesThe aim of the study was to estimate sensitivity and specificity of childhood pulmonary tuberculosis (CPTB) diagnostic tests, including Xpert and alternative samples such as nasopharyngeal aspirate and stool. We used latent class analysis to overcome the lack of gold standard. MethodsWe included 1165 children suspected of having CPTB in a prospective cohort study conducted in Ivory Coast, Madagascar, and Cameroon. We used Bayesian latent class analysis to evaluate the performance of multiple diagnostic tests for CPTB: smear microscopy, mycobacterial culture, and Xpert MTB/RIF carried out on different types of samples (sputum after 10 years of age, gastric aspirate before 10 of age, nasopharyngeal aspirate, stool), tuberculin skin test (TST), and chest X-ray. ResultsMedian age was 3.5 years (95% credible interval [1.3–8.2]). Smear microscopy was highly specific in all types of samples but lacked sensitivity (sputum 31% (95% credible interval [18–46]), gastric aspirate 36% [27–45], nasopharyngeal aspirate 24% [17–32], stool 24% [17–32]). Culture sensitivity was slightly higher in gastric (75% [65–83]) than nasopharyngeal aspirate (64% [54–72]). Xpert sensitivity was similar in gastric (69% [59–78]) and nasopharyngeal aspirate (66% [57–74]) but lower in sputum (58% [43–74]) and stools (53% [44–62]). Xpert was highly specific in all respiratory samples (sputum 96% [96–100], gastric aspirate 100% [99–100], nasopharyngeal aspirate 100% [99–100]). ConclusionsXpert performed on nasopharyngeal aspirate shows similar accuracy than culture. It was also similar to that in gastric aspirate. It highlights it’s an interesting CPTB diagnostic combination.

Pulmonary Aspergillosis: An Observation from a Tertiary Care Hospital of Western Uttar Pradesh

Background: Aspergillus is the most frequently occurring fungal infection in immunocompromised patients with a high mortality rate. Invasive pulmonary aspergillosis is the most serious entity on the spectrum of pulmonary aspergillosis. Limited studies on the occurrence of pulmonary aspergillosis from this geographical area prompted us to carry out this study. Materials and Methods: This hospital-based cross-sectional observational study was carried out in the Postgraduate Department of Microbiology of a tertiary care medical teaching hospital in western Uttar Pradesh for one year. A total of 1032 respiratory samples were subjected for isolation and identification of fungal pathogens by direct microscopic examination (KOH mount) and culture on Sabouraud dextrose agar. Results: The isolation rate of pulmonary aspergilli was 6.97%. The majority of the respiratory samples received were sputum 900 (87.2%) followed by bronchoalveolar lavage fluid 132 (12.7%). The pulmonary pathology was predominantly seen in the age group of 41–50 years (25%). Male patients (69%) were predominant. The majority of the samples (50%) were from the respiratory medicine ward followed by the respiratory medicine ICU (25%). Aspergillus fumigatus (58%) was the predominant species isolated followed by Aspergillus flavus (25%). Conclusion: Isolation of Aspergillus species from patients of pulmonary pathology needs to be correlated clinically to rule out colonization as they may need proper antifungal treatment. Indiscriminate use of antifungals may lead to the emergence of antifungal drug resistance.

The Clinical Application Value of a Novel Chip in the Detection of Pathogens in Adult Pneumonia: A Multi-Centre Prospective Study in China.

The detection of pathogenic microorganisms plays a significant role in the diagnosis and management of pneumonia that are responsible for a substantial number of deaths worldwide. However, conventional microbiological tests (CMT) have low accuracy and are time-consuming. In this study, we aim to evaluate the clinical value of Chips for Complicated Infection Detection (CCID) in detecting pneumonia pathogens. This study was conducted at nine hospitals in China from January 2021 to September 2022. Respiratory samples from adult pneumonia patients were collected from each patient. CMT and CCID were performed in parallel to identify the pathogens. A total of 245 patients were included, with 73% being elderly. CCID identified pathogenic microbes in 78.0% of patients and conventional microbiological tests (CMT) in 57.1% of the patients (p<0.001). The overall positive and negative percent agreements between CCID and CMT for pathogen detection were 90.07% and 38.46%, respectively. 38.8% of patients were diagnosed with mixed infections with at least two pathogens by CCID. Bacterial infections identified by CCID accounted for 60.0% of 245 patients, with the top 3 being Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterococcus faecium, respectively. K. pneumoniae was the most common pathogen in elderly patients, with a significantly higher prevalence compared to non-elderly patients (p = 0.0011). Among the 197 patients who had used antibiotics before sample collection, the positive rate of CCID was significantly higher than that of CMT (p < 0.001). This study indicates that compared to CMT, this novel chip has significant advantages in detecting pathogens in pneumonia patients, especially in the elderly.

Performance of stool-based molecular tests and processing methods for paediatric tuberculosis diagnosis: a systematic review and meta-analysis

There has been a global pursuit to improve the diagnosis of tuberculosis in young children by applying diagnostic methods on accessible biospecimens such as stool. We aimed to conduct a systematic review on the accuracy of stool-based molecular tests for tuberculosis diagnosis in children and to assess the impact of the available pre-processing methods and other design characteristics. In this systematic review and meta-analysis, we evaluated studies in children younger than 16years with presumptive tuberculosis that were published in English, Spanish, French, and Portuguese from Jan 1, 2000, to May3, 2024, in MEDLINE, Embase, and Embase Classic, comparing the molecular detection of Mycobacterium tuberculosis DNA in stool with microbiological tests on other samples or a clinical diagnosis. We did not exclude studies based on geographical location, sample size, or study design if they were reporting primary data. Two independent reviewers (LC-C and SM) screened titles, abstracts, and full-text articles for eligibility and extracted data on study characteristics, study population, and diagnostic performance. If information relevant to the main analysis was not reported in the article, the corresponding authors were contacted. Point estimates and 95% CIs were calculated for sensitivity and specificity for each study and for the different molecular tests (Xpert MTB/RIF, Xpert Ultra MTB/RIF [Cepheid, Sunnyvale, CA, USA], and other tests) versus a reference standard (culture only, any bacteriological confirmation, and tuberculosis case definition). Sensitivity and specificity were stratified by the stool processing method. We also quantified the additionality of stool Xpert Ultra tests for tuberculosis bacteriological confirmation. The protocol was registered with PROSPERO, CRD42022341514. A total of 4521records were identified through the database search, one record was identified from an article bibliography, and 67studies were retained for full-text reading. 39studies were included in the qualitative synthesis, 35of which were included in the meta-analyses. When using any bacteriological confirmation from a respiratory sample as the reference standard, stool Xpert sensitivity was 0·60 (95% CI 0·48-0·71), stool Xpert Ultra sensitivity was 0·73 (0·63-0·81), and sensitivity was 0·44 (0·29-0·60) for other in-house molecular methods combined. When using tuberculosis case definition as the reference standard, stool Xpert sensitivity was 0·23 (0·11-0·41), stool Xpert Ultra sensitivity was 0·38 (0·22-0·56), and sensitivity was 0·17 (0·09-0·23) for other in-house molecular methods. The addition of stool Xpert Ultra increased bacteriological confirmation of tuberculosis by 38·6% overall. Further, the utilisation of centrifuge-free simplified methods improved the sensitivity of stool Xpert Ultra when using any bacteriological confirmation as a reference standard (0·77 [0·66-0·85] for centrifuge-free methods vs 0·61[0·41-0·78] for non-centrifuge-free methods). This systematic review and meta-analysis supports the use of Xpert Ultra in stool samples as a diagnostic tool for paediatric tuberculosis diagnosis. Stool-based Xpert Ultra can contribute to increase the bacteriological confirmation in this population, even when respiratory specimens are also tested. The EDCTP2 programme supported by the EU via Stool4TB Project and the European Society of Pediatric Infectious Diseases.

Enteroviruses, Respiratory Syncytial Virus and Seasonal Coronaviruses in Influenza-like Illness Cases in Nepal

Acute respiratory infection is one of the leading causes of morbidity and mortality among children in low- and middle-income countries. Due to limited diagnostic capability, many respiratory pathogens causing influenza-like illness go undetected. This study aims to detect enterovirus, respiratory syncytial virus, seasonal coronavirus and respiratory pathogens other than influenza in patients with influenza-like illness. A total of 997 (54.3%) respiratory samples (collected in the years 2016–2018) were randomly selected from 1835 influenza-negative samples. The xTAG Respiratory Viral Panel (RVP) FAST v2 panel was used to detect respiratory pathogens including enterovirus/rhinovirus (EV/RV), respiratory syncytial virus (RSV) and seasonal coronavirus (HKU1, OC43, NL63 and 229E). A total of 78.7% (785/997) were positive for respiratory viruses. Of these viruses, EV/RV was detected in 36.3% (362/997), which is the highest number, followed by RSV in 13.7% (137/997). The seasonal coronaviruses HKU1 and OC43 (1.5%, 15/997), NL63 (1.2%, 12/997) and 229E (1%, 10/997) were also detected. The EV/RV-positive samples were sequenced, of which 16.7% (5/30) were confirmed as EVs and were identified as coxsackievirus (CV) types CVB5, CVB3, CV21 and CVB2. The findings of this study highlight the importance of strengthening influenza-like illness surveillance programs in the region by including other respiratory viruses in their scope besides seasonal human influenza viruses.

Performance of rapid antigen tests to detect SARS-CoV-2 variant diversity and correlation with viral culture positivity: implication for diagnostic development and future public health strategies.

Despite the availability of vaccines, COVID-19 continues to be a major health concern, and antigen-based rapid diagnostic tests (Ag-RDTs) are commonly used as point-of-care or at-home diagnostic tests. In this study, we evaluated the performance of two commercially available Ag-RDTs and a research Ag-RDT to detect multiple SARS-CoV-2 variants using upper respiratory tract swab samples from clinical COVID-19 cases. Furthermore, we determined whether Ag-RDT results correlated with culture positivity, a potential proxy of viral transmissibility. Our results have important implications to inform future testing and response strategies during periods of high COVID-19 transmission with new variants.

Contribution of Other Respiratory Viruses During Influenza Epidemic Activity in Catalonia, Spain, 2008–2020

Background: During seasonal influenza activity, circulation of other respiratory viruses (ORVs) may contribute to the increased disease burden that is attributed to influenza without laboratory confirmation. The objective of this study was to characterize and evaluate the magnitude of this contribution over 12 seasons of influenza using the Acute Respiratory Infection Sentinel Surveillance system in Catalonia (PIDIRAC). Methods: A retrospective descriptive study of isolations from respiratory samples obtained by the sentinel surveillance network of physicians was carried out from 2008 to 2020 in Catalonia, Spain. Information was collected on demographic variables (age, sex), influenza vaccination status, epidemic activity weeks each season, and influenza laboratory confirmation. Results: A total of 12,690 samples were collected, with 46% (5831) collected during peak influenza seasonal epidemic activity. In total, 49.6% of the sampled participants were male and 51.1% were aged &lt;15 years. Of these, 73.7% (4298) of samples were positive for at least one respiratory virus; 79.7% (3425 samples) were positive for the influenza virus (IV), with 3067 samples positive for one IV type, 8 samples showing coinfection with two types of IV, and 350 showing coinfection of IV with more than one virus. The distribution of influenza viruses was 64.2% IVA, 35.2% IVB, and 0.1% IVC. Of the other respiratory viruses identified, there was a high proportion of human rhinovirus (32.3%), followed by human adenovirus (24.3%) and respiratory syncytial virus (18; 7%). Four percent were coinfected with two or more viruses other than influenza. The distribution of coinfections with ORVs and influenza by age groups presents a significant difference in proportions for 0–4, 5–14, 15–64 and &gt;64 (21.5%, 10.8%, 8.2% and 7.6%: p &lt; 0.001). A lower ORVs coinfection ratio was observed in the influenza-vaccinated population (11.9% vs. 17.4% OR: 0.64 IC 95% 0.36–1.14). Conclusions: During the weeks of seasonal influenza epidemic activity, other respiratory viruses contribute substantially, either individually or through the coinfection of two or more viruses, to the morbidity attributed to influenza viruses as influenza-like illness (ILI). The contribution of these viruses is especially significant in the pediatric and elderly population. Identifying the epidemiology of most clinically relevant respiratory viruses will aid the development of models of infection and allow for the development of targeted treatments, particularly for populations most vulnerable to respiratory viruses-induced diseases.

Respiratory Carriage of Methicillin-Resistant Staphylococcus aureus-Encoding Gene in Hajj Pilgrims.

To assess the carriage of methicillin-resistant Staphylococcus aureus-encoding genes (MRSA) among French Hajj pilgrim cohorts. A prospective cohort study was conducted on pilgrims from Marseille during the 2014 to 2018 Hajj. Respiratory samples were collected before and after the pilgrimage. S. aureus and then MRSA-encoding genes were identified using real-time PCR. A total of 606 pilgrims were included with a sex ratio of 1:1.3 with a median age of 61 years (interquartile = 56-66 years, range = 21-88 years). A total of 511/606 (84.3%) pilgrims presented at least one respiratory symptom during their pilgrimage. Cough was the most frequent symptom occurring in 76.2% of pilgrims, followed by sore throat (57.6%), rhinitis (54.6%), and voice failure (36.3%). 87 (14.4%) were positive with S. aureus before travelling. On return, 130/606 (21.4%) participants were positive. The acquisition rate of S. aureus was 13.0% (79/606). The prevalence of MRSA pre- and post-travel and acquisition rate was 4.1% (25/606), 10.6% (62/606), and 8.2% (50/606), respectively. All MRSA were positive with mecA gene. No case was positive with mecC. Our study highlights the importance of surveillance and infection control measures during mass gatherings such as the Hajj to mitigate the spread of infectious pathogens, including antimicrobial-resistant bacteria like MRSA. Further research is warranted to elucidate the specific factors contributing to S. aureus and MRSA transmission during the pilgrimage and to inform targeted interventions aimed at reducing the burden of MRSA infection among pilgrims.

Epidemiology and genetic diversity of human respiratory syncytial virus in Belgium between 2011 and 2019

BackgroundHuman respiratory syncytial virus (HRSV) is worldwide one of the leading causes of acute respiratory tract infections in young children and the elderly population. Two distinct subtypes of HRSV (A and B) and a multitude of genotypes have been described. The laboratory of Clinical and Epidemiological Virology (KU Leuven/University Hospitals Leuven) has a long-standing history of HRSV surveillance in Belgium.MethodsIn this study, the seasonal circulation of HRSV in Belgium was monitored during 8 consecutive seasons prior to the SARS-CoV-2 pandemic (2011–2012 until 2018–2019). By use of a multiplex quantitative real time PCR panel, 27,386 respiratory samples were tested for HRSV. Further subtyping and sequencing of the HRSV positive samples was performed by PCR and Sanger sequencing. The prevalence and positivity rate were estimated in 4 distinct age groups and the circulating strains of each subtype were situated in a global context and in reference to the described genotypes in literature.ResultsHRSV circulated in Belgium in a yearly re-occurring pattern during the winter months and both HRSV subtypes co-circulated simultaneously. All HRSV-B strains contained the 60 nt duplication in the HVR2 region of the G gene. Strains of subtype HRSV-A with a 72 nt duplication in the HVR2 region were first observed during the 2011–2012 season and replaced all other circulating strains from 2014 to 2015 onwards.

Isavuconazole and Amphotericin B Synergic Antifungal Activity: In Vitro Evaluation on Pulmonary Aspergillosis Molds Isolates

Background/Objectives. Pulmonary aspergillosis is a severe respiratory infection caused by Aspergillus spp., whose resistance profiles and invasive attitude complicate therapeutical strategies. Several aspergillosis cases emerged as superinfections during the SARS-CoV-2 pandemic when isavuconazole and amphotericin B became essential antifungal alternatives. The main purpose of the present study was to investigate a possible synergic activity between these molecules against Aspergillus spp. isolated from respiratory samples. Methods. The gradient test method detected isavuconazole and amphotericin B MIC values, prompting an arrangement of their combination into an R.P.M.I. agar medium. According to Liofilchem s.r.l. instructions, the FIC index was used to establish synergy, additivity, indifference, or antagonism. Results. Among 36 Aspergillus spp. isolates, only A. fumigatus strains showed both synergy and additivity episodes. A. niger reported the highest antagonism percentage, while A. terreus revealed several indifference episodes. Conclusions. Isavuconazole and amphotericin B remain fundamental therapeutical alternatives, including a possible synergic effect against A. fumigatus. On the basis of this species-related difference, further studies will be essential to investigate different antifungal drug combinations against filamentous fungi isolates.

Difference between real world practice and clinical research: A comparison of oropharyngeal and nasopharyngeal sampling data in influenza

Oropharyngeal (OP) sampling is one of the most commonly used methods for respiratory sampling, but its positivity rate in real practice compared with that of nasopharyngeal (NP) sampling is not fully known. The differences between OP and NP in practice and between practice and the literature were compared. In total, 2323 positive results from 6708 patients were recorded in the laboratory test system, and 15,021 positive results from 31,333 patients were recorded in the national report. The positivity rate changed from 2.3 % to 38.11 % after the sampling method was changed from OP to NP in the same setting. The difference between OP and NP (calculated as (NP-OP)/NP) varies from −7.73–28.57 % in the literature and from 61.35–94.59 % in practice. Real-world practice is complicated and thus different from strictly quality-controlled studies.

Effects of COVID-19 pandemic on epidemiological features of viral respiratory tract infections in children: a single-centre study.

The epidemiology of respiratory infections may vary depending on factors such as climate changes, geographical features, and urbanization. Pandemics also change the epidemiological characteristics of not only the relevant infectious agent itself but also other infectious agents. This study aims to assess the impact of the COVID-19 pandemic on the epidemiology of viral respiratory infections in children. We retrospectively reviewed the medical records of children aged ≤18years with laboratory-confirmed viral respiratory infections other than COVID-19 from January 2018 to March 2023. Data on demographic characteristics, month and year of admission, and microbiological results were collected. During the study period, 1,829 respiratory samples were sent for polymerase chain reaction testing. Rhinovirus was identified in 24% of the patients, mixed infections in 21%, influenza virus in 20%, and respiratory syncytial virus in 12.5%. A 38.6% decrease in viral respiratory infections was observed in 2020, followed by a 188% increase in 2021. The respiratory syncytial virus was significantly more common in the post-pandemic period (13.8%) compared to the pre-pandemic period (8.1%), but no seasonal shift in respiratory syncytial virus infection was observed. There was also a yearly increase in influenza infections in the post-pandemic period compared to the pre-pandemic period. After the COVID-19 pandemic, the frequency of parainfluenza virus infections increased during the summer months, and this finding provides a new contribution to the existing literature.

Experience of microbiological monitoring of the respiratory tract microflora in patients with cystic fibrosis during therapy with the combination drug elexacaftor/tezacaftor/ivacaftor + ivacaftor

Bacterial complications of the respiratory tract are negative prognostic factors leading to a decrease in pulmonary function, duration, and quality of life of patients with cystic fibrosis. To date, a sufficient number of studies have not been accumulated to reliably prove or reject microbiological improvement during targeted therapy. The aim of the study was to collect continuous microbiological data from patients with cystic fibrosis in the Samara region receiving treatment with elexacaftor/tezacaftor/ivacaftor + ivacaftor from November-December 2021. The article presents eight clinical observations. At the time of therapy initiation, seven patients had chronic respiratory tract infection associated with Burkholderia cenocepacia ST 208, combined with chronic Pseudomonas aeruginosa infection in two of them. One patient had a chronic P. aeruginosa infection in association with Aspergillus fumigatus. Conclusion. An expansion of the species composition in the respiratory samples was demonstrated in all cases. The majority of patients showed microbiological improvement. Thus, biochemical and, as a result, microecological changes in the lungs against the normalization of chlorine channel function allow suggesting that key pathogens may be eradicated during the therapy with elexacaftor/tezacaftor/ivacaftor + ivacaftor.

Radio-Biological Confrontation in the Diagnosis of Invasive Aspergillosis: About Two Cases and Review of Literature

Invasive pulmonary aspergillosis due to Aspergillus fumigatus is an often serious mycosis, usually occurring in severely immunocompromised patients. It is accompanied by a high mortality rate due to its often difficult and late diagnosis. Diagnosis is based on early chest computed tomography and mycological examination of respiratory samples. Both patients had presented with acute respiratory distress, developing in a context of fever and deterioration of the general condition despite the initiation of broad-spectrum empirical treatment. In each of them, a chest CT scan was performed, objectifying atypical cavitary images not suggesting pulmonary aspergillosis. Cytobacteriological examination of sputum and search for Mycobacterium tuberculosis were negative. Serology for aspergillus antigens and a sample of bronchoalveolar lavage fluid for a mycological study were requested. Direct examination of bronchoalveolar lavage fluid was negative, but culture allowed the identification of Aspergillus fumigatus. Galactomannan testing was positive. Given these results, treatment with injectable voriconazole was initiated in our two cases. The evolution was marked by a clinical improvement of one patient and the death of the other patient. Invasive pulmonary aspergillosis is a major concern due to the frequency of its complications. Its diagnosis must be early to ensure adequate management for a better prognosis.

Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.

Probe-based nucleic acid enrichment represents an effective route to enhance the detection capacity of next-generation sequencing (NGS) in a set of clinically diverse and relevant microbial species. In this study, we assessed the effect of the enrichment-based sequencing on identifying respiratory infections using tiling RNA probes targeting 76 respiratory pathogens and sequenced using both Illumina and Oxford Nanopore platforms. Forty respiratory swab samples pre-tested for a panel of respiratory pathogens by qPCR were used to benchmark the sequencing data. We observed a general improvement in sensitivity after enrichment. The overall detection rate increased from 73 to 85% after probe capture detected by Illumina. Moreover, enrichment with probe sets boosted the frequency of unique pathogen reads by 34.6 and 37.8-fold for Illumina DNA and cDNA sequencing, respectively. This also resulted in significant improvements on genome coverage especially in viruses. Despite these advantages, we found that library pooling may cause reads mis-assignment, probably due to crosstalk issues arise from post-capture PCR and from pooled sequencing, thus increasing the risk of bleed-through signal. Taken together, an overall improvement in the breadth and depth of pathogen coverage is achieved using enrichment-based sequencing method. For future applications, automated library processing and pooling-free sequencing could enhance the precision and timeliness of probe enrichment-based clinical metagenomics.

A Retrospective Analysis of Broad-Range Microbial PCR-Sequencing Findings and Culture Results in 101 Bronchoalveolar Lavage Specimens

Abstract Introduction/Objective Pneumonia is a significant cause of illness and death, identifying its cause is challenging and critical for effective antibiotic treatment and for reducing the length of stay. Bronchoalveolar lavage is commonly performed to obtain high-quality lower respiratory tract samples. While traditional culture methods have been the standard for pathogen detection, microbial rRNA broad-range polymerase chain reaction (BR-PCR) has emerged as an alternative method. Methods/Case Report A retrospective analysis was conducted on 101 patients suspected of severe pulmonary infections at Oregon Health and Science University (OHSU). Results (if a Case Study enter NA) When important microbial etiology is considered, culture detected 26%, while BR- PCR detected 20%. Both methods proved effective in detecting common pathogens; however, culture demonstrated superiority in detecting fungal pathogens due to potential sampling biases associated with PCR. Furthermore, culture holds the advantages of being faster and more cost-effective, although it may fail to detect difficult to non-cultivable organisms, like Legionella spp. Culture is indispensable for susceptibility testing and strain typing purposes. More often than not, BR-PCR captures airway microbiota indiscriminately with minimal clinical significance, potentially confusing clinical interpretation. Conclusion Novel technologies like Biofire Pneumonia Panel (BPP), a multiplex PCR, have shown promise in the rapid detection of pneumonia pathogens including bacteria, viruses, and resistance genes (&amp;lt; 2 hours), complementing the traditional culture methods for microbiological diagnosis. Based on this analysis we recommend introducing BPP at OHSU.

Alterations in the Antimicrobial Resistance Profile of Acinetobacter baumannii Strains Isolated from Intensive Care Unit Patients: Five-Year Follow-up in Cappadocia

Background: This study aims to determine alterations in the antibiotic resistance status of Acinetobacter baumannii strains isolated from lower respiratory tract samples of patients in intensive care units over the years. Methods: In this comprehensive study, A. baumannii strains isolated from aspirate and sputum samples of patients hospitalized in intensive care units of a second-stage state hospital between January 2018 and December 2022 were meticulously and retrospectively investigated and analyzed for antimicrobial resistance. Results: The rate of aspirate and sputum samples in the study was 18.1% (754/4151); The positivity rate of cultures was 51.7% (390/754); The rate of those associated with A. baumannii was found to be 65.6% (256/390).. 90.2% of the isolates were isolated from the general intensive care unit (231/256). The rates of A. baumannii isolated from aspirate and sputum samples were 67.4% (213/316) and 58.1% (43/74), respectively. The carbapenem resistance rate in A. baumannii isolates grown in aspirate samples was 96.5%, fluoroquinolone resistance was 91.7%; The carbapenem resistance rate in sputum samples was 96.1% and fluoroquinolone resistance was 90.9%. The most effective antibiotics against A. baumannii strains isolated from both aspirate and sputum samples were colistin 100% (n=256), TMP/SXT 55.8% (143/256), tigecycline 50.3% (129/256), respectively. Conclusion: Our study reveals a concerning trend-a high frequency of multidrug-resistant A. baumannii isolates are being identified in the Central Anatolia region of our country. This high prevalence, which is a cause for immediate concern, underscores the urgent and immediate need for robust infection control measures to curb the spread of A. baumannii in hospitals.

Males are at higher risk of colonization and infection with multi-drug-resistant organisms than females

Global rise of multidrug-resistant organisms (MDRO) is alarming and antimicrobial resistance (AMR) poses a significant public health threat globally. Although certain risk factors are known including recent antimicrobial therapy, inappropriate use and hospitalization, the focus on gender-specific aspects in MDRO is scarce. Our aim was to show gender-specific differences in colonization and infections of multiple MDRO and their detection sites. For this multicentre, retrospective cohort study surveillance data between 2015 and 2020 was collected in 86 hospitals of the Helios group, Germany. The following multidrug-resistant bacteria were analysed according to sample site: MRSA, Enterococcus spp., Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa and Acinetobacter baumannii. Out of the 7,081,708 cases in the database, 187,656 patients were found to be colonized with MDRO (2.65%). A documented infection with MDRO was identified in 33,023 patients (0.466%), with the origin of infection known in 24,231 cases. Male gender was a risk factor for both infection and colonization of any MDRO (p< .001). Males exhibited a higher likelihood of MDRO detection in superficial skin/soft tissue, blood cultures (p < .001), and respiratory samples (p = .002). Additionally, gender-specific differences in MDRO detection site and pathogens were found with slightly higher proportion of MRSA infection in deep skin/soft tissue and respiratory samples for females. Our study reinforces the existing hypothesis that male gender is a risk factor for MDRO, supported by our large dataset. It highlights the need to acknowledge gender-specific MDRO susceptibility in clinical practice.

Evaluating the Efficacy of a Polymerase Chain Reaction Assay for Pneumocystis carinii Detection in Respiratory Samples

Abstract Introduction: Accurately identifying patients with pneumocystis pneumonia (PCP) presents considerable challenges, primarily relying on clinical suspicion. The manifestations of PCP lack specificity, encompassing symptoms such as cough, dyspnoea, fever, hypoxaemia, malaise and weight loss. Therefore, this study assesses the efficacy of a polymerase chain reaction (PCR) assay intended for use in clinical microbiology laboratories for the identification of Pneumocystis carinii from respiratory specimens. Materials and Methods: In this retrospective study, the medical records of patients aged 18 years and above were examined, focusing on those assessed using pneumocystis PCR-based tests. The study spanned from 2019 to 2022 in our tertiary care centre at Max Hospital, Saket. In this study, sputum and bronchoalveolar lavage (BAL) samples were proceeded for both staining and PCR for multi-copy mtLSU gene and single-copy dihydropteroate synthase polymorphisms (DHPS) fas gene of P. jirovecii. Results: In the analysis of 112 BAL specimens, 17 were identified as positive for P. carinii through both Grocott-Gomori’s Methenamine Silver Staining (GMS) staining and PCR. In addition, two BAL specimens were negative through GMS staining but showed positive results with PCR. On reviewing the clinical details of the patients associated with these two specimens, it was discovered that both individuals were under systemic steroid treatment, yet neither exhibited clinical signs of pneumocystis pneumonia (PCP). Consequently, these instances were classified as false positives by PCR. In comparison to GMS, the PCR assay demonstrated a sensitivity of 100% and specificity of 98% for detecting P. carinii in BAL specimens. Conclusions: The study underscores the necessity for individualised approaches, with each laboratory assessing the positive and negative predictive values based on their specific prevalence rates. In the ongoing pursuit of improving PCP diagnosis, PCR emerges as a promising screening tool that when used judiciously in conjunction with confirmatory measures, can enhance diagnostic precision in immunosuppressed populations.