Fluid Specimens Research Articles

Choroid plexus as a mediator of CNS inflammation in multiple sclerosis.

The pathophysiology of multiple sclerosis (MS) remains poorly understood despite decades of tremendous research efforts. Advances in neuroradiography coupled with availability of unbiased approaches including spatial transcriptomics, proteomics, metabolomics, and lipidomics that are compatible with brain and fluid specimens from patients raise hope that discovery of novel disease drivers is on the horizon. Once thought to be little more than salty bathwater, our modern understanding of cerebrospinal fluid (CSF) suggests the CSF as a compelling, critical regulator of brain function in health and disease. Recent studies in the field have reinvigorated interest in CSF as a medium to better understand MS and to deliver disease-modifying therapies. In turn, the choroid plexus, an epithelial tissue located within each brain ventricle that regulates CSF and forms a key blood-CSF barrier, is uniquely positioned to orchestrate neuroinflammation associated with MS. In this perspective review, we will discuss what is known about the choroid plexus as a conductor of immune responses and how it may propagate neuroinflammation associated with MS via the CSF.

Programmed DNA tile response system enabled accurate detection of ATP for clinical diagnosis

Adenosine triphosphate (ATP), as a crucial signaling molecule, is of high potential diagnosis value for multiple diseases. However, current technologies for ATP detection struggle to satisfy the harsh conditions required for biospecimen tests, existing several limitations for clinical practical application. In this study, the DNA tile response system was designed and constructed by integrating nucleic acid aptamer, hybrid chain reaction (HCR), and DNA tile self-assembly technology to achieve accurate detection of ATP in body fluid specimens. The DNA tile response system, possessing high-order structure characteristic, could remove HCR false-positive products and conquer the high noise background to enhance the detection sensitivity. Under the optimal reaction parameters, this system achieved the low limit of detection (LOD) of 189.23 nM over a wide linear range and splendid detection specificity faced with multiple interference terms. Furthermore, this system, possessing simple storage conditions, long-term detection stability, and superior anti-interference performance, was sufficient to satisfy the detection requirements for complicated biological specimens in multi-scenarios. Ultimately, the DNA tile response system showed excellent diagnostic efficiency that could easily distinguish urinary tract infection patients and healthy controls through ATP quantification, as well as hypertension patients and healthy ones. This system provides a high-potential rapid detection tool for early diagnosis and dynamic monitoring of urinary tract infections and hypertension, holding enormous potential for clinical translation due to the superiorities of simple operation, general applicability, and low instrument requirements.

The Cytological Diagnosis of a Malignant Effusion Is Independent of the Volume of Fluid Processed.

The relationship between pleural fluid volume and cytological diagnosis of malignancy has been often investigated with conflicting conclusions on whether or not a minimum fluid volume should be defined. The primary objective of this retrospective investigation is to evaluate the relationship between fluid volume and cytological diagnosis of malignancy. A total of 511 body fluid specimen reports received between January 2018 and December 2019 were examined to investigate the relationship between diagnosis of malignancy to volume and biochemical properties. Pleural fluid (n = 252) and peritoneal fluid (n = 250) specimens were binned into two volume groups (< 75 mL, ≥ 75 mL). Pericardial fluid specimens (n = 9) were excluded due to small sample size. Prevalence of malignancy for pleural and peritoneal fluids was 20.2% and 20.08%, respectively, with no significant difference between the two volume groups. Malignant pleural effusions were associated with a serum to fluid protein ratio > 0.5 and malignant peritoneal effusions were associated with a serum ascites albumin gradient (SAAG) < 1.1 g/dL. Our study did not find a significant difference in the diagnosis of malignancy between volumes ≥ 75 mL and < 75 mL in either pleural or peritoneal fluid. Fluid volume is, therefore, not an adequacy criterion for detecting malignancy in either pleural or peritoneal fluid. Our analysis on the biochemical properties of each malignant fluid type was supportive of current use of Light's criteria and SAAG for effusion fluid evaluation.

Maternal-Newborn ABO Blood Groups and Risk of Bacterial Infection in Newborns

Newborn immunity largely relies on maternal-fetal transfer of antibodies in utero. Incongruency in ABO blood groups between a mother and newborn may be associated with protection against serious infections, but data specific to newborn bacterial infections are lacking. To ascertain the association between maternal-newborn ABO blood group incongruence and lower risk of bacterial infection in newborns. This cohort study used linked patient-level datasets for all singleton live births between January 1, 2014, and December 31, 2020, in hospitals and health centers in Ontario, Canada. The cohort comprised maternal-newborn pairs with known ABO blood groups. Data analysis was conducted between February and May 2024. Maternal-newborn ABO blood group incongruence vs congruence. The primary outcome was a bacterial infection arising in newborns within 30 days of birth. Bacterial infection was cultured from either blood, cerebrospinal fluid, urine, or lung specimen. Secondary outcomes were a bacterial infection with 7 days and 90 days of birth. Modified Poisson regression generated adjusted relative risks (ARRs) and 95% CIs, adjusted for neonatal sex and preterm birth. A total of 138 207 maternal-newborn pairs (maternal mean [SD] age, 31.8 [5.1] years among those with ABO blood group incongruency and 31.5 [5.1] years among those with ABO blood group congruency; newborn mean [SD] gestational age, 38.5 [2.3] weeks among those with incongruency and 38.4 [2.5] weeks among those with congruency; 19 475 males [51.3%] with incongruency and 52 041 males [51.9%] with congruency) were analyzed. Of these pairs, 37 953 (27.5%) had ABO blood group incongruency and 100 254 (72.5%) had ABO blood group congruency. Within 30 days of birth, 328 (8.6 per 1000) newborns in the incongruent group and 1029 (10.3 per 1000) newborns in the congruent group experienced a bacterial infection, corresponding to an ARR of 0.91 (95% CI, 0.81-1.03). The ARRs for bacterial infection within 7 days and 90 days of birth were 0.89 (95% CI, 0.73-1.09) and 0.86 (95% CI, 0.78-0.94), respectively. This cohort study found no association between maternal-newborn ABO blood group incongruence and risk of bacterial infection in newborns within 30 and 7 days of birth. However, incongruence was associated with a decreased risk of bacterial infection within 90 days of birth.

Digital peroral pancreatoscopy to determine surgery for patients who have intraductal papillary mucinous neoplasms of the pancreas with mural nodules

Background and study aims: Since more than a few patients having intraductal papillary mucinous neoplasms of the pancreas (IPMNs) with mural nodules (MNs) are benign, clinical plans should be determined by using histocytological specimens especially for those patients with high-risk for surgery or with a small MN. Patients and methods: This study included 27 patients to evaluate the efficacy of peroral pancreatoscopy using a SpyGlass DS system (POPS-DS) for patients with MN-positive IPMN, mainly focusing on the ability of POPS-DS to detect malignancy. Results: Biopsy specimens obtained under POPS-DS guidance could be used for the histological evaluations of all patients with MNs in the main pancreatic duct and 67% of the patients with MNs in the branch ducts, whereas fluid specimens collected during POPS-DS could be used for histocytological evaluations for all patients. For the 13 patients who underwent surgery just after POPS-DS, the sensitivity, specificity, and accuracy of POPS-DS to detect malignancy were 89%, 100%, and 92%, respectively. For the 12 patients who underwent surveillance without surgery, the cumulative 3-year progression rates for 9 benign IPMNs and 3 malignant ones determined using POPS-DS were 0% and 100%, respectively. However, the sensitivity of POPS to detect IPMN epithelium in the resection margin was 20%. Only one patient developed procedure-related pancreatitis (mild). Conclusions: POPS-DS could be used to accurately detect malignancy for patients with MN-positive IPMN. Therefore, histocytological evaluations using POPS-DS can contribute to the selection of patients for whom surgery would be appropriate.

Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections

Preoperative identification of causal organism(s) is crucial for effective prosthetic joint infection treatment. Herein, we explore the clinical application of a novel metatranscriptomic (MT) workflow, CSI-Dx, to detect pathogens associated with prosthetic joint infection. MT provides insight into transcriptionally active microbes, overcoming limitations of culture-based and available molecular methods. This study included 340 human synovial fluid specimens subjected to CSI-Dx and traditional culture-based methods. Exploratory analyses were conducted to determine sensitivity and specificity of CSI-Dx for detecting clinically-relevant taxa. Our findings provide insights into the active microbial community composition of synovial fluid from arthroplasty patients and demonstrate the potential clinical utility of CSI-Dx for aiding prosthetic joint infection diagnosis. This approach offers potential for improved sensitivity and acceptable specificity compared to synovial fluid culture, enabling detection of culturable and non-culturable microorganisms. Furthermore, CSI-Dx provides valuable information on antimicrobial resistance gene expression. While further optimization is needed, integrating metatranscriptomic technologies like CSI-Dx into routine clinical practice can revolutionize prosthetic joint infection diagnosis by offering a comprehensive and active snapshot of associated pathogens.

Epidemiology of pneumococcal meningitis in sentinel hospital surveillance of Viet Nam, 2015–2018

BackgroundStreptococcus pneumoniae (S. pneumoniae), Haemophilus influenzae (H. influenzae), and Neisseria meningitidis (N. meningitidis) are leading causes of childhood bacterial meningitis and preventable by vaccines. The aim of this hospital-based sentinel surveillance is to describe the epidemiological characteristics of pneumococcal meningitis, including disease burden, and to provide baseline data on pneumococcal serotype distribution to support decision making for pneumococcal conjugate vaccine (PCV) introduction in Vietnam.MethodsSurveillance for probable bacterial meningitis in children 1–59 months of age is conducted in three tertiary level pediatric hospitals: one in Hanoi and two in Ho Chi Minh City. Cerebrospinal fluid (CSF) specimens were collected via lumbar puncture from children with suspected meningitis. Specimens were transferred immediately to the laboratory department of the respective hospital for cytology, biochemistry, and microbiology testing, including culture. PCR testing was conducted on CSF specimens for bacterial detection (S. pneumoniae, H. influenzae, and N. meningitidis) and pneumococcal serotyping.ResultsDuring 2015–2018, a total of 1,803 children with probable bacterial meningitis were detected; 1,780 had CSF specimens available for testing. Of 245 laboratory-confirmed positive cases, the majority were caused by S. pneumoniae (229,93.5%). Of those with S. pneumoniae detected, over 70% were caused by serotypes included in currently available PCV products; serotypes 6 A/6B (27.1%), 14 (19.7%), and 23 F (16.2%) were the most common serotypes. Children with laboratory-confirmed pneumococcal meningitis were more likely to live in Hanoi (p < 0.0001) and children 12–23 months of age were at greater odds (OR = 1.65, 95% CI: 1.11, 2.43; p = 0.006) of having confirmed pneumococcal meningitis compared to children < 12 months of age when compared to those without laboratory-confirmed bacterial meningitis. Additionally, children with confirmed pneumococcal meningitis were more likely to exhibit signs and symptoms consistent with clinical meningitis compared to negative laboratory-confirmed meningitis cases (p < 0.0001) and had a greater odds of death (OR = 6.18, 95% CI: 2.98, 12.86; p < 0.0001).ConclusionsPneumococcal meningitis contributes to a large burden of bacterial meningitis in Vietnamese children. A large proportion are caused by serotypes covered by PCVs currently available. Introduction of PCV into the routine immunization program could reduce the burden of pneumococcal meningitis in Viet Nam.

Clinical Utility of Broad Range PCR for Infectious Organisms

Abstract Broad range PCR is used to identify infectious organisms when bacterial, fungal, and mycobacterial cultures are negative despite clinical evidence of infection. We performed a 6-month retrospective chart review to assess the actionability of broad range PCR and identify opportunities to improve the utility of this referral test at our institution. One hundred eleven broad range PCR tests were ordered from July to December 2023. Seventy-five (67.6%) results did not affect patient management, 18 (16.2%) results affected patient management, and the treatment impact of 18 (16.2%) results is unknown because they were from outside consult cases. There were no instances in which antibiotic therapy was completely discontinued due to a negative broad range PCR result. Concurrent in-house microbiology testing yielded a positive result in 15 (13.5%) cases, of which 8 (53%) had a negative broad range PCR result and 2 (13.3%) had a conflicting broad range PCR result. Thirty-eight (34.2%) specimens were formalin fixed paraffin embedded tissue, 29 (26.1%) were fresh tissue, 13 (11.7%) were ESWABS, and the remaining 31 specimens were various fluid types (27.9%). While fresh tissue is the preferred specimen, broad range PCR detected an organism in 20 (53%) formalin fixed paraffin embedded tissue specimens, 11 (37.9%) fresh tissue specimens, 3 (23.1%) ESWAB specimens, and 2 (6.5%) fluid specimens (abscess aspirate and cerebrospinal fluid). Improvements in physician communication and laboratory workflow are necessary to improve the specimen quality and thus the utility of this referral test at our institution.

Streptococcus pneumoniae in Medical Districts of Burkina Faso: Serotype Distribution and Antibiotic Susceptibility during 2010 to 2012

Introduction: Streptococcus pneumoniae is a highly virulent pathogen. Despite the recent introduction of vaccines in the program of prevention in Burkina Faso, treatment by antibiotics has remained in use. The aim of this study was to determine the serotypes implied in invasive pneumococcal infections and their resistance to antibiotics used for routine treatment in Burkina Faso. Methods: From March 2010 to December 2012, a total of 6,102 cerebrospinal fluid (CSF) and pleural fluid (PF) specimens were collected in Burkina Faso. The specimens were analyzed by latex agglutination assay, culture, and real time polymerase chain reaction (rt-PCR) for species identification. Serotyping was performed by rt-PCR and minimum inhibitory concentrations were determined by the E-test. Results: Among 562 S. pneumoniae strains identified from 6,102 specimens, 440 isolates were serotyped by rt-PCR. Serotypes 1 and 5 were the most common (50%); however, 70 (15.9%) strains were not detected by rt-PCR methodology. Among patients of less than 20 years of age, serotype 1 was the most frequent strain identified (9.3% to 13.2%). Ampicillin and ceftriaxone were the most active antibiotics in vitro against the strains identified. The rate of S. pneumoniae strains susceptible to chloramphenicol was 83%. Serotypes 1 (7/49) and 5 (5/7) were non-susceptible to chloramphenicol. Conclusion: Serotypes 1 and 5 were the common serotypes identified. Conjugate vaccines introduced in Burkina Faso should take in account these valences, to decrease the incidence of pneumococcal infections efficiently.

Are the postmortem concentration changes of the synthetic cannabinoid cumyl-5F-P7AICA and its N-pentanoic acid metabolite dependent on the environmental conditions? – A systematic study following pulmonary administration to pigs

The number of fatal cases involving synthetic cannabinoids (SCs) is increasing. However, interpretation of postmortem (PM) toxicological findings is challenging, due to unknown PM intervals and possible redistribution processes or instabilities. Only sparse data on SCs are available. Therefore, a controlled pig study was performed to determine the PM stability of cumyl-5F-P7AICA under different environmental conditions. Ten pigs inhalatively received 200 µg/kg body weight cumyl-5F-P7AICA each. Six hours later, they were euthanized and biopsies of the main tissues and body fluids were taken. Animals were stored in air or water (n=5 each) and samples were repeatedly taken for three days. Quantification of cumyl-5F-P7AICA and its N-pentanoic acid metabolite (NPA) was performed using standard addition or a fully validated method (blood) followed by LC-MS/MS. Time-dependent concentration changes of cumyl-5F-P7AICA were observed in liver, bile fluid and muscle specimens at both conditions. Concentrations of NPA only changed considerably in duodenum content of animals stored in air. Environment-dependent concentrations changes were only observed for cumyl-5F-P7AICA in kidney and the NPA metabolite in duodenum content. Overall, cumyl-5F-P7AICA and its metabolite seem to be quite stable in PM specimens. Hence, also central blood might be analyzed, if no peripheral blood is available.

B-079 Characterization of an isoelectric focusing method for detection of IgG oligoclonal banding in paired cerebrospinal fluid and serum specimens

Abstract Background Qualitative assessment of IgG-specific oligoclonal banding (OCB) in paired serum and cerebrospinal fluid (CSF) samples is useful for evaluating inflammatory conditions of the central nervous system such as multiple sclerosis. Here we characterized the performance of an IgG-specific method using isoelectric focusing on agarose gel matrix for the detection of OCB in paired serum and CSF samples. Methods Specimens of 20 paired, simultaneously collected CSF and serum patient samples were tested on Sebia (Hydrasys 2 System) provided by the National Institutes of Health (NIH) Diagnostic Laboratories. We tested these paired samples using the Helena IgG IFE-20 kit (SPIFE® Touch) method and the results were read by two independent individuals blinded to each other’s assessments. The results were compared to the NIH results for agreement. Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) were calculated. Analytical sensitivity of the Helena assay was assessed via serial dilutions of a CSF OCB positive sample (total IgG 4.5 mg/dL). Results Figure 1 shows serum and CSF pairs for the control (A), two example positive OCB patients (B &amp; D) and a negative OCB patient (C). The Helena assay was concordant with Sebia for 11/12 positive OCB patients (PPA 91.6%) and 8/8 negative subjects (NPA 100%). 20-fold was the highest dilution that remained positive. Conclusions OCB detection using paired serum and CSF samples and isoelectric focusing electrophoresis is considered the preferred method. The Helena IgG IFE-20 assay is such a method and showed high PPA and NPA concordance with the Sebia System. Thus, the Helena OCB assay can be considered an accurate and analytically sensitive method for assessing OCB in serum and CSF.

Utility and performance of cell blocks in cerebrospinal fluid cytology: Experience at two teaching hospitals.

Cytology cell blocks (CBs) are not routinely made for cerebrospinal fluid (CSF) specimens. The goal of this study was to identify when CSF CB preparation improves diagnostic performance. Under institutional review board approval, a retrospective review of CSF cytology cases was conducted at a tertiary university-based hospital and an affiliated county hospital. Patient history, CSF volume, final diagnosis, use of stains, and whether the CB was contributory was determined from the cytopathology report. CSF nucleated cell count data was obtained from the medical record. A total of 69 CSF specimens with CBs from January 2006 to March 2023 were identified from 61 patients. The median CSF volume was 8mL (interquartile range, 4-13mL; range, 1-800mL), with immunohistochemical stains performed on 29 (42%) cases. Per cytology report, CB was contributory in 23 cases (33%), not contributory in 34 cases (49%), and not discussed in 12 cases (17%). The median volume was 8mL for cases in which CB was contributory, not contributory, or not discussed. There was no difference in average nucleated cell counts between cases in which CB was contributory versus not contributory (73.9 vs. 40.0, p=.175). CBs for CSF samples were contributory in a subset (33%) of cases. The authors were unable to identify any specific pre-analytic factors, including specimen volume and average nucleated cell counts, for cases in which CB was contributory. Further evaluation is needed to identify if there are scenarios in which CSF CBs should be routinely prepared.

Clinical, radiographic and biochemical assessment of proximal cavities restored with composite resin using incremental vs. bulk packing techniques: One-year randomized clinical trial

BackgroundBulk-fill resin composites may suffer from recurrent caries around compound proximal restorations in posterior teeth, especially at the proximo-gingival interface.Over 12 months, will the bulk fill technique affect the caries recurrence rate at gingival margins when compared to the conventional incremental packing technique? How early will the first clinical, radiographical, and biochemical evidence of caries recurrence occur?MethodsAfter randomization, in 30 patients with two compound (OM or OD) supragingival lesions, one tooth was restored using the bulk fill technique on one side (group 1) (n = 15). In contrast, the other tooth on the other side was restored utilizing the incremental layering technique (group 2) (n = 15). Both teeth received restorative material (X-tra fil, Voco, Cuxhaven, Germany). The FDI criteria were used to evaluate restorations. As for the periodontal assessment, the gingival index, plaque index, papillary bleeding scoring index and periodontal pocket depth were evaluated. The gingival crevicular fluid (GCF) specimens were gathered, and MMP-9 was extracted and quantitated by ELISA. A customized radiographic template was designed, and 3D printed digital bitewing radiographs were taken. Assessments were done clinically, radiographically and biochemically at baseline (1 week) and after 3, 6 and 12 months. Data was statistically analyzed.ResultsThe null hypothesis was accepted clinically; no statistically significant differences appeared between bulk and incrementally filled posterior restorations. As for the radiographic assessment, the null hypothesis was accepted except for increased periodontal ligament width at 3 months. The null hypothesis for the biochemical evaluation was rejected as there were significant changes in levels of MMP-9 at different testing times.Conclusions1. With similar results but less sensitivity and significant time saving, the bulk fill technique can be considered an efficient alternative to the incremental fill technique in restoring proximal cavities. 2. Early evidence of caries recurrence can be correlated to an increase in the MMP-9 level in gingival crevicular fluid, followed by an increase in radiographic periodontal ligament width measurement.Trial registrationAn ethical approval from the Research Ethics Committee at the Faculty of Dentistry, October 6 University, (Approval No. RECO6U/5-2022). The study was registered at the Pan African Clinical Trials Registry on 24/07/2023 with an identification number (PACTR202307573531455).

Demographic and pathogen characteristics of incident bacterial meningitis in infants in South Africa: A cohort study.

Bacterial meningitis is a major cause of death, with an approximate case fatality rate of 37% across all age groups in South Africa. This study aimed to describe the demographic and pathogen characteristics of incident meningitis in children aged <1 year in South Africa from 2014 through 2018, during a period when Haemophilus influenzae type b vaccine and pneumococcal conjugate vaccines (PCV) were both included in the expanded program on immunization (EPI). We conducted a cohort study of routine laboratory data in the National Health Laboratory Service Corporate Data Warehouse, which covers approximately 80% of the South African population. We defined a case of laboratory-confirmed bacterial meningitis as any person aged <1 year with meningitis diagnosed by culture and identification of a pathogen documented as being a common cause of meningitis in CSF. The cause-specific incidence risks were calculated by dividing the number of positive specimens in each age group and year by the corresponding mid-year population for children under 1 year old and those in the post-neonatal period (≥ 28 days to 365 days old). For children under 28 days old, the annual numbers of registered livebirths were used. We used Poisson regression to compare the incidence of meningitis by year. We identified 3575 (1.5%) cases of culture-confirmed bacterial meningitis from the 232,016 cerebrospinal fluid (CSF) specimens tested from 2014-2018. The highest number of cases were recorded in children aged <28 days (1873, 52.4%), male children (1800, 50.4%) as well as in the Gauteng Province (2014, 56.3%). Acinetobacter baumannii (14.9%), followed by Klebsiella pneumoniae (13.5%), and group B streptococcus (GBS) (10.7%), were the most common pathogens detected. Overall, A. baumannii had the highest incidence risk, occurring at 9.8 per 100,000 persons in children aged <1 year in 2018. Among neonates, A. baumannii peaked at 14.9 per 100,000 livebirths in 2018, while Streptococcus pneumoniae was most common in the post-neonatal period (≥ 28 days to 365 days old), peaking at 9.8 per 100,000 persons in 2014. There was an increase in the annual incidence of most pathogens over the study period. There was an increasing trend in the annual incidence of bacterial meningitis in infants caused by most pathogens, particularly A. baumannii, K. pneumoniae and GBS. In addition to increased uptake of vaccination, prevention measures to reduce nosocomial and mother-to-child transmission of bacteria could include antenatal screening for GBS in pregnant women, rigorous hygiene in the hospital environment as well as rational antibiotic use.

Cytomorphologic analysis of pulmonary neuroendocrine tumors – The physical effect of abrasion and aspiration on cytomorphology

Neuroendocrine tumors of the lung display characteristic cytomorphologic features allowing direct diagnosis. The specificity of these features in distinguishing subtypes of neuroendocrine tumors, and their differences among types of cytologic specimen poses as interpretative potential pitfalls. This study reviewed and compared bronchial, effusion fluid and fine-needle aspiration cytology specimens of neuroendocrine tumors of the lung to address these issues. Histology-proven cytology specimens of neuroendocrine tumors were reviewed for cytomorphological parameters focusing on reported specific neuroendocrine nuclear and background features. Totally, 46 cases (26 bronchial, 11 effusion and 9 aspirate specimens), corresponding to 37 small cell carcinomas, 7 neuroendocrine carcinomas and 2 carcinoids were reviewed. Nuclear moulding (n = 35/37, 95 %), naked nuclei (n = 33/37, 89 %) and marked nuclear irregularity (n = 32/37, 86 %) were the three most common features of small cell carcinoma. The only specific feature for small cell carcinoma was the lack of prominent nucleoli (p = 0.004). For pulmonary carcinoids, in addition to the above features, other features associated with neuroendocrine carcinoma reviewed including crush artifact and necrotic material were absent. Compared to bronchial and aspiration cytology, crush artifact (p < 0.001) and necrotic material (p = 0.014) were absent on effusion fluid specimens and naked nuclei were less frequently seen (p = 0.022), while prominent nucleoli were more often observed (p = 0.005). Nuclear moulding, irregularity and naked nuclei are common but not unique features to small cell carcinomas. Effusion fluid specimens have “cleaner” backgrounds while displaying greater nuclear atypia. The type of cytologic preparation/specimen is an important factor which must be considered during diagnostic interpretation.

Changes in cerebrospinal fluid proteins across the spectrum of untreated and treated chronic HIV-1 infection.

Using the Olink Explore 1536 platform, we measured 1,463 unique proteins in 303 cerebrospinal fluid (CSF) specimens from four clinical centers contributed by uninfected controls and 12 groups of people living with HIV-1 infection representing the spectrum of progressive untreated and treated chronic infection. We present three initial analyses of these measurements: an overview of the CSF protein features of the sample; correlations of the CSF proteins with CSF HIV-1 RNA and neurofilament light chain protein (NfL) concentrations; and comparison of CSF proteins in HIV-associated dementia (HAD) and neurosymptomatic CSF escape (NSE). These reveal a complex but coherent picture of CSF protein changes with highest concentrations of many proteins during CNS injury in the HAD and NSE groups and variable protein changes across the course of systemic HIV-1 progression that included two common patterns, designated as lymphoid and myeloid patterns, related to principal involvement of their underlying inflammatory cell lineages. Antiretroviral therapy reduced CSF protein perturbations, though not always to control levels. The dataset of these CSF protein measurements, along with background clinical information, is posted online. Extended studies of this unique dataset will supplement this report to provide more detailed characterization of the dynamic impact of HIV-1 infection on the CSF proteome across the spectrum of HIV-1 infection, advancing the mechanistic understanding of HIV-1-related CNS pathobiology.

Optimization of the Diagnosis of Central Nervous System Infections in Vietnamese Hospitals: Results From a Retrospective Multicenter Study.

Central nervous system infections pose significant health challenges, particularly in low- and middle-income countries, because of high morbidity and mortality rates. Rapid and accurate diagnosis is essential for effective treatment to prevent adverse outcomes. Traditional culture-based diagnostics are often slow and lack specificity. This study evaluates the BioFire FilmArray Meningitis/Encephalitis (FAME) Panel against standard diagnostics in Vietnam to assess its clinical impact and suitability for local epidemiology. We conducted a prospective study involving 330 patients with suspected central nervous system infections at 4 hospitals in northern Vietnam from July 2022 to April 2023. Cerebrospinal fluid samples were analyzed using routine culture methods and FAME. We compared pathogen detection rates and assessed the potential clinical impact of FAME results on patient management. Of the 330 cerebrospinal fluid specimens, 64 (19%) were positive by either conventional diagnostics (n = 48) and/or FAME (n = 33). The agreement between FAME and conventional diagnostics was 87%. Key pathogens Mycobacterium tuberculosis (n = 7), Klebsiella pneumoniae (n = 5), Streptococcus suis (n = 5), Epstein-Barr virus (n = 3), Acinetobacter baumannii (n = 1), and Trichosporon asahii (n = 1) were not detected by FAME. Classical meningitis parameter clinical symptoms, altered glucose, protein, and pleocytosis were good predictors of FAME positivity, indicating their utility in optimizing local diagnostic algorithms. FAME complements traditional diagnostics by offering rapid and broad pathogen detection, crucial for timely and appropriate therapy. However, its effectiveness varies with local epidemiology, and it should not replace conventional methods entirely. Tailoring diagnostic panels to regional pathogen prevalence is recommended to enhance diagnostic accuracy and clinical outcomes in low- and middle-income countries.

Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis

At present, the diagnosis of lower respiratory tract infections (LRTIs) is difficult, and there is an urgent need for better diagnostic methods. This study enrolled 136 patients from 2020 to 2021 and collected bronchoalveolar lavage fluid (BALF) specimens. We used metatranscriptome to analyze the lower respiratory tract microbiome (LRTM) and host immune response. The diversity of the LRTM in LRTIs significantly decreased, manifested by a decrease in the abundance of normal microbiota and an increase in the abundance of opportunistic pathogens. The upregulated differentially expressed genes (DEGs) in the LRTIs group were mainly enriched in infection immune response-related pathways. Klebsiella pneumoniae had the most significant increase in abundance in LRTIs, which was strongly correlated with host infection or inflammation genes TNFRSF1B, CSF3R, and IL6R. We combined LRTM and host transcriptome data to construct a machine-learning model with 12 screened features to discriminate LRTIs and non-LRTIs. The results showed that the model trained by Random Forest in the validate set had the best performance (ROC AUC: 0.937, 95% CI: 0.832–1). The independent external dataset showed an accuracy of 76.5% for this model. This study suggests that the model integrating LRTM and host transcriptome data can be an effective tool for LRTIs diagnosis.

1187P Molecular diagnosis of lung cancer via ctDNA and ctRNA detection on bronchoscopic fluid specimens from 31 patients: A retrospective analysis

1187P Molecular diagnosis of lung cancer via ctDNA and ctRNA detection on bronchoscopic fluid specimens from 31 patients: A retrospective analysis

Comparative analysis of metagenomic and targeted next-generation sequencing for pathogens diagnosis in bronchoalveolar lavage fluid specimens.

Although the emerging NGS-based assays, metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), have been extensively utilized for the identification of pathogens in pulmonary infections, there have been limited studies systematically evaluating differences in the efficacy of mNGS and multiplex PCR-based tNGS in bronchoalveolar lavage fluid (BALF) specimens. In this study, 85 suspected infectious BALF specimens were collected. Parallel mNGS and tNGS workflows to each sample were performed; then, we comparatively compared their consistency in detecting pathogens. The differential results for clinically key pathogens were confirmed using PCR. The microbial detection rates of BALF specimens by the mNGS and tNGS workflows were 95.18% (79/83) and 92.77% (77/83), respectively, with no significant difference. mNGS identified 55 different microorganisms, whereas tNGS detected 49 pathogens. The comparative analysis of mNGS and tNGS revealed that 86.75% (72/83) of the specimens were complete or partial concordance. Particularly, mNGS and tNGS differed significantly in detection rates for some of the human herpesviruses only, including Human gammaherpesvirus 4 (P<0.001), Human betaherpesvirus 7 (P<0.001), Human betaherpesvirus 5 (P<0.05) and Human betaherpesvirus 6 (P<0.01), in which tNGS always had higher detection rates. Orthogonal testing of clinically critical pathogens showed a total coincidence rate of 50% for mNGS and PCR, as well as for tNGS and PCR. Overall, the performance of mNGS and multiplex PCR-based tNGS assays was similar for bacteria and fungi, and tNGS may be superior to mNGS for the detection of DNA viruses. No significant differences were seen between the two NGS assays compared to PCR.