Diagnostic Accuracy of Cerebrospinal Fluid Multiplex Polymerase Chain Reaction Panel Testing in Patients With Suspected Central Nervous System Infections: A Multi-Center Study in the United Arab Emirates.

Background Delays in diagnosis and treatment of central nervous system (CNS) infections can lead to significant morbidity and mortality among children and adults. Prior antibiotic treatment is a major hurdle to accurate diagnosis due to falsely negative cerebrospinal fluid (CSF) cultures in partially treated patients. Increasingly, molecular diagnostic methods using multiplex polymerase chain reaction (mPCR) testing on CSF samples are being utilized in clinical practice for timely and accurate diagnosis. However, there is no data regarding the diagnostic accuracy or clinical impact of CSF mPCR testing in the Middle East region. We sought to compare the diagnostic accuracy of an automated mPCR CSF panel with routine CSF culture, the current gold standard, in the United Arab Emirates (UAE).  Methods This single-gated, multi-center, diagnostic accuracy study included patients from birth onwards who were admitted to any of the three participating hospitals with an initial diagnosis of meningitis or encephalitis, between January 2017 and March 2021, and had CSF samples collected for mPCR and culture. Sociodemographic, clinical, and molecular data were collected for all. Results A total of 353 CSF samples were collected from patients from 0-90 years old hospitalized for suspected CNS infection. Children constituted 51% of the study population, and males were slightly over-represented (55.2%). Pathogens were detected by mPCR in 78 (22%) CSF samples, of which 19 (24%) were bacteria and 59 (76%) were viruses. No fungal pathogens were detected. Enteroviruses were the most prevalent CNS pathogen among our cohort (40%), followed by herpes simplex virus type 2 (HSV-2) (12.5%). Children constituted 69% of positive samples for enterovirus, while HSV-2 was exclusively detected among adults. Using CSF culture as the diagnostic gold standard, the mPCR panel demonstrated high specificity (100%) and sensitivity (96.3%) in diagnosing CNS infection among all age groups. mPCR testing demonstrated a high overall percentage of agreement (OPA) with CSF culture (98.9%). Patients with bacterial meningitis had a significantly longer hospitalization (p=0.004) and duration of antibiotic therapy (p=0.001) compared to those with viral meningitis. Three CSF samples were negative on mPCR testing but positive on culture. These pathogens included: methicillin-sensitive Staphylococcus aureus(MSSA), Bacillus cereus, and Mycobacterium Tuberculosis (MTB). In addition, 13 patients had negative CSF cultures but tested positive on CSF mPCR. These pathogens included Streptococcus pneumoniae (seven patients), Haemophilus influenzae (three patients), Streptococcus agalactiae (two patients), and Escherichia coli (one patient). All discordant results were confirmed by reviewing the patient's clinical presentation, CSF analysis, clinical course, and final diagnosis. Conclusion CSF mPCR panel is a highly sensitive and specific diagnostic tool for the diagnosis of CNS infections among all age groups in the UAE. Routine use of CSF mPCR panels can decrease healthcare costs by reducing the length of stay and can also aid antibiotic stewardship efforts by reducing antibiotic overuse in patients with viral CSF infections. CSF culture and mPCR complement each other by identifying CNS pathogens in patients with prior antibiotic exposure who would otherwise be missed if relying on CSF culture alone. However, concomitant CSF culture samples should be sent to avoid missing unusual CNS pathogens.

ADVANCING THE UNDERSTANDING OF CLINICAL SEPSIS USING GENE EXPRESSION-DRIVEN MACHINE LEARNING TO IMPROVE PATIENT OUTCOMES.

ABSTRACT: Sepsis remains a major challenge that necessitates improved approaches to enhance patient outcomes. This study explored the potential of machine learning (ML) techniques to bridge the gap between clinical data and gene expression information to better predict and understand sepsis. We discuss the application of ML algorithms, including neural networks, deep learning, and ensemble methods, to address key evidence gaps and overcome the challenges in sepsis research. The lack of a clear definition of sepsis is highlighted as a major hurdle, but ML models offer a workaround by focusing on endpoint prediction. We emphasize the significance of gene transcript information and its use in ML models to provide insights into sepsis pathophysiology and biomarker identification. Temporal analysis and integration of gene expression data further enhance the accuracy and predictive capabilities of ML models for sepsis. Although challenges such as interpretability and bias exist, ML research offers exciting prospects for addressing critical clinical problems, improving sepsis management, and advancing precision medicine approaches. Collaborative efforts between clinicians and data scientists are essential for the successful implementation and translation of ML models into clinical practice. Machine learning has the potential to revolutionize our understanding of sepsis and significantly improve patient outcomes. Further research and collaboration between clinicians and data scientists are needed to fully understand the potential of ML in sepsis management.

Seasonal Prevalence of Respiratory Pathogens Among Children in the United Arab Emirates: A Multicenter Cross-Sectional Study in the Pre-COVID-19 Era.

Background Viral respiratory infections in children pose a significant burden on healthcare facilities globally. In the United Arab Emirates (UAE) these account for 15% of all healthcare encounters among children. However, the seasonal prevalence and molecular epidemiology of respiratory viral infections in the UAE remains unknown. We sought to determine trends in seasonal viral prevalence in order to monitor disease activity and optimize the timing of Respiratory Syncytial Virus (RSV) prophylaxis among high-risk infants in the UAE. Methods This cross-sectional multicenter study included children 0-18 years of age who presented to a large private healthcare group in Dubai, UAE, and had upper respiratory samples collected for multiplex polymerase chain reaction (mPCR) testing between January 1st and December 31st, 2019. Sociodemographic, clinical, and molecular data were examined for children who tested positive for any pathogen on the mPCR panel. Results A total of three thousand and ninety-eight infants and children had mPCR assays performed during the study period, of which 2427 (78.3%) were positive for any respiratory pathogen. The median age of our sample population was 39 months and 56.8% were male. Emergency room was the most common site (34.7%) of sample collection and the vast majority of children presented with fever (85.3%). Rhinovirus/enterovirus was the most prevalent viral infection (45%) throughout the year and peaked in September, followed by Influenza (20.2%), and RSV (17.1%). RSV season, defined as an infection prevalence of >10%, occurred from August to December with a peak in October. Adenovirus (15.6%) infections peaked in June and accounted for 43% of hospitalizations in our study (p<0.05). Viral co-infections with RSV and rhinovirus/enterovirus were most common and observed in 19.9 % of children. Conclusion Rhinovirus/enterovirus is the most prevalent viral pathogen throughout the calendar year among the pediatric population in the UAE. RSV season begins earlier than reported in other countries regionally, hence RSV prophylaxis should be initiated in August to optimize protection among high-risk infants.

A TRANSCRIPTOMIC APPRECIATION OF CHILDHOOD MENINGOCOCCAL AND POLYMICROBIAL SEPSIS FROM A PRO-INFLAMMATORY AND TRAJECTORIAL PERSPECTIVE, A ROLE FOR VASCULAR ENDOTHELIAL GROWTH FACTOR A AND B MODULATION?

ABSTRACT: This study investigated the temporal dynamics of childhood sepsis by analyzing gene expression changes associated with proinflammatory processes. Five datasets, including four meningococcal sepsis shock (MSS) datasets (two temporal and two longitudinal) and one polymicrobial sepsis dataset, were selected to track temporal changes in gene expression. Hierarchical clustering revealed three temporal phases: early, intermediate, and late, providing a framework for understanding sepsis progression. Principal component analysis supported the identification of gene expression trajectories. Differential gene analysis highlighted consistent upregulation of vascular endothelial growth factor A (VEGF-A) and nuclear factor κB1 (NFKB1), genes involved in inflammation, across the sepsis datasets. NFKB1 gene expression also showed temporal changes in the MSS datasets. In the postmortem dataset comparing MSS cases to controls, VEGF-A was upregulated and VEGF-B downregulated. Renal tissue exhibited higher VEGF-A expression compared with other tissues. Similar VEGF-A upregulation and VEGF-B downregulation patterns were observed in the cross-sectional MSS datasets and the polymicrobial sepsis dataset. Hexagonal plots confirmed VEGF-R (VEGF receptor)-VEGF-R2 signaling pathway enrichment in the MSS cross-sectional studies. The polymicrobial sepsis dataset also showed enrichment of the VEGF pathway in septic shock day 3 and sepsis day 3 samples compared with controls. These findings provide unique insights into the dynamic nature of sepsis from a transcriptomic perspective and suggest potential implications for biomarker development. Future research should focus on larger-scale temporal transcriptomic studies with appropriate control groups and validate the identified gene combination as a potential biomarker panel for sepsis.

A Rare Case of Primary Mycobacterium tuberculosis Myositis of the Thigh in an Immunocompetent Infant.

Mycobacterium tuberculosis (MTB) infection is a serious health condition that affects individuals of all age groups. Although MTB infections are more common in immunocompromised patients, they are frequently diagnosed in healthy individuals without apparent risk factors. Extrapulmonary infection is an uncommon manifestation of MTB infection, especially infection of the musculoskeletal system. Here, we present a rare case of a five-month-old immunocompetent infant who presented with a progressively enlarging swelling of the thigh without any other symptoms. After further evaluation, a diagnosis of primary MTB myositis of the thigh was made, which was treated successfully with first-line anti-tuberculosis therapy for nine months. This case report highlights the need to consider MTB infection in infants and children with unusual clinical findings. Due to its nonspecific symptoms and difficulty in diagnosis, clinicians need to maintain a high index of clinical suspicion for MTB infection, even in infants without risk factors for exposure.

High diagnostic accuracy of automated rapid Strep A test reduces antibiotic prescriptions for children in the United Arab Emirates.

BACKGROUND: Diagnosis of Group A Streptococcus (GAS) pharyngitis in children is hindered by variable sensitivity of clinical criteria and rapid Strep A tests (SAT), resulting in reliance on throat cultures as the gold standard for diagnosis. Delays while awaiting culture reports result in unnecessary antibiotic prescriptions among children, contributing to the spread of antimicrobial resistance (AMR). METHODS: Diagnostic accuracy study of an automated SAT (A-SAT) in children up to 16 years of age presenting to an emergency room with signs and symptoms of pharyngitis between March and June 2019. Paired throat swabs for A-SAT and culture were collected. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for A-SAT were calculated. RESULTS: Two hundred and ninety-one children were included in this study. 168 (57.7%) were boys and the mean age was 4.2 years. A-SAT was positive in 94 (32.3%) and throat culture was positive in 90 (30.9%) children. A-SAT and throat culture results showed a high level of consistency in our cohort. Only 6 (2%) children had inconsistent results, demonstrating that the A-SAT has a high sensitivity (98.9%), specificity (97.5%), PPV (94.7%) and NPV (99.5%) for the diagnosis of GAS pharyngitis in children. Only 92 (32%) children were prescribed antibiotics while the vast majority (68%) were not. CONCLUSIONS: A-SAT is a quick and reliable test with diagnostic accuracy comparable to throat culture. Its widespread clinical use can help limit antibiotic prescriptions to children presenting with pharyngitis, thus limiting the spread of AMR.

Diagnostic accuracy of QuickVue® Dipstick Strep A test and its effect on antibiotic prescribing in children in the United Arab Emirates.

BACKGROUND: Unnecessary antibiotic prescription to patients with upper respiratory tract infections (URTIs) has led to the increase in antibiotics resistant bacteria rates. In this study, we evaluated the diagnostic accuracy of QuickVue® Dipstick Strep A test (QV-SAT) in children presenting with acute pharyngotonsillitis and its effect on antibiotic prescribing. METHODS: A single-gated diagnostic accuracy study of children with fever, runny nose, and tonsillitis presenting to a paediatric clinic between March 2016 and September 2018. Paired throat swabs for QV-SAT and culture were collected. None of the children received antibiotics prior to sample collection. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the test were calculated. RESULTS: Two hundred four children were included in this study. 111 (54.4%) were boys and 146 (71.6%) were under the age of 5 years. QV-SAT was positive in 44 (21.6%) and throat culture was positive for Group A ß- haemolytic Streptococcus (GAS) in 42 (20.6%) of the children. The results of QV-SAT were highly consistent with culture results: only 2 (0.9%) children with negative results had a positive throat culture. The sensitivity of the QV-SAT in the identification of GAS infection was 100% (95% CI 91.6%, 100%) and the NPV was 100% (95% CI 99.9%, 100%). Only 42 children ( 20.6%) were given antibiotics, while 162 (79.4%) were not. CONCLUSION: The QV-SAT is a quick and reliable test that can help dramatically reduce antibiotic prescriptions to children presenting with fever and acute pharyngotonsillitis.

Persistent antibodies to HPV virus-like particles following natural infection are protective against subsequent cervicovaginal infection with related and unrelated HPV.

Whether persistent human papillomavirus (HPV) IgG antibodies following natural infection are protective against subsequent infection is unknown. In a cohort of 508 college women followed for 3 y, persistent seropositivity was defined as the presence of type-specific HPV virus-like particle (VLP) antibodies at > or = 2 consecutive visits 1 y apart. Protection from incident infection with any HPV was conferred by persistent antibodies to HPV16 (p = 0.02), HPV31 (p < 0.001), HPV33 (p = 0.03), HPV35 (p = 0.002), HPV52 (p = 0.007), HPV45 (p = 0.003), and HPV53 (p = 0.01). The risk of incident infection with species-specific HPV types was also decreased in women with persistent antibodies to any HPV type in that group, suggesting that exposure to HPV with persistent development of antibody response can be protective, and may explain the decreased efficacy of HPV vaccine in women with prior exposure.

Elevated levels of vitamin B12 and folate in vertically infected children with HIV-1.

OBJECTIVE: Neurologic and hematologic abnormalities are common in HIV-infected children and may be related to concomitant deficiencies in serum B12 and folate, which are highly prevalent in HIV-infected adults. We sought to determine the prevalence of B12 and folate deficiencies in HIV-infected children in the United States. METHODS: Cross-sectional information on demographics, folate and B12 levels, hematological parameters, concurrent CD4%, HIV-viral load and antiretroviral regimens were abstracted from the medical records of 103 vertically infected children followed in an outpatient pediatric HIV clinic in the Bronx, during 2001-2002. RESULTS: Mean age was 10 years (+/-4.4 years), 46% were male, 53% African-American and 46% Hispanic. Nineteen percent had significant immunologic suppression and 18 children had AIDS. All were receiving combination antiretroviral therapy and 66% were on a protease inhibitor-based regimen. Sixteen were taking cotrimoxazole prophylaxis. None were taking multivitamins or manifested clinical evidence of gastrointestinal malabsorption. All patients had serum folate or B12 levels within or above the normal range. Children with elevated B12 were significantly more likely to be younger (P = 0.0002) and have higher mean folate levels (P = 0.0004) compared with children with normal serum B12. In a multivariate logistic regression analysis, factors independently associated with elevated levels of vitamin B12 included: elevated serum folate [odds ratio (OR): 3.2; P = 0.01], nonnucleoside reverse transcriptase inhibitor use (OR: 0.38; P = 0.05) and female sex (OR: 0.67; P = 0.42) CONCLUSION: Folate and B12 deficiencies are uncommon in HIV-infected children in the United States, suggesting that routine supplementation with B12 and folate is not indicated without confirmation of micronutrient deficiency.

Predictors of seropositivity to human papillomavirus type 53: one of the most prevalent high risk-related cervical human papillomaviruses.

Persistent cervicovaginal infection with high-risk types of HPV is the major risk factor for subsequent cervical neoplasia. HPV53, part of the alpha 6 species group along with HPV types 30, 56, and 66, is one of the most prevalent high risk-related HPV types, yet little is known about the molecular basis of its benign behavior. We generated and utilized HPV53 virus-like particles (VLPs) to investigate risk factors for its seroprevalence in a population of young college women. Seropositivity to HPV53 VLPs was determined using a polymer-based ELISA to measure IgG reactive antibodies. Cervicovaginal cells were collected for HPV DNA detection and typing by MY09/11 PCR. A questionnaire queried for HPV risk factors to estimate odds ratios (ORs). Prevalence of cervicovaginal HPV DNA was 26% (n = 148); 3% of women (n = 17) had HPV53 DNA and 7% (n = 40) were seropositive to HPV53. Seroprevalence of IgG to HPV53 VLPs in women with cervicovaginal HPV53, HPV53-related types (HPV30, 55, and 66), other HPV types, and no HPV was 41%, 11%, 7%, and 6%, respectively (p(trend) < 0.001). Risk factors independently associated with HPV53 VLP seropositivity included use of oral contraceptive pills (OCPs) (OR: 4; 95% CI: 1.8, 9), having >or=2 regular partners in the last 6 months (OR: 2.5; 95 % CI: 1.1, 5.8), having a regular male partner with >or=4 lifetime sex partners (OR: 2.6; 95% CI: 1.1 6), seropositivity to HPV16 (OR: 6.7; 95% CI: 3.1, 14.5), and isolation of HPV53 DNA from cervicovaginal lavage (OR: 17.3; 95% CI: 5.3, 55.9). In conclusion, host serological responses to HPV53 VLPs are strongly type-specific, and subjects' risk for HPV53 seropositivity is independently associated with sexual behavior and OCP use.

The importance of testing whole stool for Shiga toxin: a clinical and microbiological perspective.

This case report emphasizes the importance of testing whole stool for the presence of Shiga toxin; especially in light of clinical suspicion, or whenever a grossly bloody stool specimen is received in the lab. Since organisms other than Escherichia coli O157:H7 can elaborate Shiga toxin, a negative stool culture for the usual enteric pathogens does not rule out the possibility of a Shiga toxin-mediated pathology in the appropriate clinical setting. The presence of this toxin in stool influences a physician's approach towards the patient's antimicrobial management.

Expression of G protein alpha subunits in the lateral wall of the rat cochlea.

Expression of five G protein alpha subunits was investigated in the rat cochlea by reverse transcription-polymerase chain reaction (RT-PCR) in order to understand their role in the cochlear signal transduction mechanisms. Immunohistochemical techniques were employed to study their distribution in the lateral wall of the cochlea. Total RNA was extracted with guanidine thiocyanate from cochleas and brains of 14-21-day-old rats. The extract was treated with DNase to degrade genomic DNA. After RT, the resulting cDNA was amplified by PCR using primers specific for the nucleotide sequences representing alpha subunits of heterotrimeric G proteins. The results indicated that mRNA for all five alpha subunits was expressed in the brain and cochlear samples. For immunohistochemical localization, temporal bones of 6-week-old rats were fixed in 4% paraformaldehyde and 0.1% glutaraldehyde and processed for embedding in paraffin wax. The dewaxed, midmodiolar sections of the cochlea were incubated with subunit-specific polyclonal antibodies. The pattern of immunoreactivity varied for the five G protein alpha subunits studied in the stria vascularis and spiral ligament. The significance of these findings and the role of G protein alpha subunits in cochlear fluid homeostasis are discussed.