Positive Specimens Research Articles

OGC O01 - Stomach Cancer Elective Surgery Morbidity and Mortality at 90-Days (HOLD Study): A Prospective, International Collaborative Cohort Study

Abstract Background Data on multinational 90-day mortality and morbidity rates after surgery for gastric cancer is limited in the literature. This study aimed to understand the 90-day mortality and morbidity outcomes according to GASTRODATA Registry for elective gastric cancer surgery patients and identify risk factors. Method We conducted an international prospective study on ≥18 years patients undergoing elective surgery for gastric cancer with curative intent from 01 April 2022 to 30 September 2022. Known metastatic disease, concurrent secondary cancers, gastrointestinal stromal tumour (GIST) and Siewert type I/II oesophagogastric junction malignancies were excluded. Univariate and multivariate logistic regression was used to identify variables associated to 90-day outcome. Results 380 collaborators from 47 countries submitted data on 1538 patients. Mean age was 64.2 years and 58.5% were males. 90-day morbidity rate was 38.2% (n=587) and mortality rate was 2.9% (n=45). Pre-operative higher CCI or ASA score, pre-operative weight loss >10%, and surgical determinants such as type of gastric resection, positive specimen margin, number of harvested lymph nodes, longer surgery duration and post operative pathological IV staging (p value<0.05) were identified as predictors of postoperative severe complications and mortality. Conclusion Elective gastric cancer surgery has a 90-day morbidity of 38.2% and 90-day mortality of 2.9%, globally. This study identified several factors associated with higher morbidity and exemplified the importance of a unified language on surgical morbidity, pre-habilitation and ongoing audits to enhance patient outcomes.

Single‐Center Survey of Prevalence of Viruses in Pediatric Liver Explants

ABSTRACTBackgroundAdenovirus has been implicated as a cause of acute liver failure (ALF) following a global outbreak of adenovirus‐associated ALF in 2021. To understand any association between viral infection and ALF, it is important to know the baseline prevalence of that virus in children undergoing liver transplant for acute and chronic liver disease (CLD). Our objective was to perform retrospective evaluation of prevalence of common hepatotropic viruses among children who underwent liver transplant at our center.MethodsWe studied 33 stored frozen hepatic explant samples (originally collected between 2004 and 2021 as part of a liver repository) which fell into three categories: ALF (n = 18), acute on chronic liver failure (ACLF, n = 7), and CLD (n = 8). DNA was extracted from the samples, and viral PCR testing was performed for adenovirus, EBV, CMV, and HHV‐6.ResultsAdenovirus was detected in a single case of indeterminate ALF transplanted in 2019. CMV was detected in two cases, and there were no EBV positive specimens in any group. HHV‐6 was more prevalent with 21 of 33 specimens testing positive including ALF, ACLF, and CLD cases.ConclusionThis retrospective study of common childhood virus prevalence in liver explants provides important baseline information for studying potential viral etiologies of ALF. We did not identify any clusters of infections. The most frequently occurring virus and only virus found in all categories was HHV‐6, underscoring the high prevalence in this heterogenous group. Adenovirus was identified in 1 out of 18 of ALF samples, but likely was not a hepatic pathogen.

Abstract 4115801: Assessing Prevalence of Cardiac Amyloidosis at the Time of Spinal Laminectomy for Spinal Stenosis

Introduction: Cardiac amyloidosis (CA) involves deposition of amyloid fibrils within cardiac myocardium, resulting in heart failure. Recent studies have shown an association between amyloid deposition in the ligamentum flavum (LF) and development of CA. Our study aims to investigate the prevalence of CA in patients identified with amyloid deposition in their LF at the time of spinal laminectomy for spinal stenosis, employing a comprehensive approach integrating multi-modality imaging and laboratory testing. Methods: This is a retrospective study of patients age >50 years old who underwent spinal laminectomy for non-congenital spinal stenosis or spondyloarthropathy. LF tissue samples obtained during surgery were examined histologically for amyloid deposition. Patients with positive findings underwent testing, including serum markers, echocardiography, and 99mtechnetium pyrophosphate (99mTcPYP) scintigraphy. Additionally, cardiac magnetic resonance imaging (cMRI) was obtained when clinically appropriate to assess for CA. Results: Among the 197 enrolled patients, 39 (19.3%) exhibited amyloid deposition in LF tissue. Patient demographics and clinical characteristics did not significantly differ between the positive and negative groups (Table 1). Of the 39 amyloid positive specimens, subtyping using mass spectrometry identified 1 (3%) light-chain, 28 (72%) transthyretin (TTR), and 10 (25%) were unable to be subtyped. Of the 28 TTR positive patients, 8 were of the wild type genotype. Furthermore, 18 of the 28 TTR patients underwent 99mTcPYP scintigraphy, of which none had cardiac uptake consistent with TTR amyloidosis; the other 10 declined work up. Of the 10 untyped patients, 6 had 99mTcPYP scintigraphy with none of the patients having cardiac uptake. Adjunctive cMRI in select positive patients showed findings inconsistent with amyloid deposition. Serum NT-proBNP, Troponin T, and serum pre-albumin levels were similar between groups. Conclusion: Amyloid deposition in LF tissue did not correlate with cardiac manifestations of amyloidosis at the time of surgery. Longitudinal investigation is ongoing to better understand the relationship between amyloid deposition in LF tissue and the development of CA over time.

Relationship Between HSV-1 Serostatus and HSV-2 IgG Confirmation Results using an Inhibition Assay

Abstract Background: Approximately 2% of HerpeSelect Herpes Simples Virus type 2 (HSV-2) IgG enzyme immunoassay (screen assay) sera positive samples do not confirm using an HSV-2 IgG inhibition assay. Of these, roughly 1.33% are confirmed negative and a small proportion (0.2%) are indeterminate due to inhibition observed with HSV-1 and HSV-2 lysate. The objective of this study was to assess the relationship between HSV-1 IgG serostatus and HSV-2 IgG confirmation results using the HSV-2 IgG inhibition assay. Methods: This study included consecutive HSV-2 IgG screen-positive specimens regardless of index value. Specimens were also tested for HSV-1 IgG. The HSV-2 IgG confirmation results from the inhibition assay were evaluated to assess the relationship between inhibition results and HSV-1 serostatus. Results: Of the 21,006 positive HSV-2 IgG specimens, 13,237 (63%) were also positive for HSV-1 IgG. The proportion of HSV-1 IgG-positive samples among inhibition-indeterminate samples (33/40, 83%) was higher than among inhibition-negative (167/279, 60%) and inhibition-positive (13,041/20,691, 63%) samples. Among HSV-1 IgG-positive samples, the median HSV-1 IgG index was also significantly higher for the inhibition-indeterminate group (median = 48.8) than for the inhibition-negative (median = 30.7) and inhibition-positive groups (median = 31.2) (P = 0.00013 and P = 3.1e-05, respectively). Conclusion: These findings suggest that HSV-2 IgG inhibition-indeterminate, but not inhibition-negative, results are associated with higher index values of HSV-1 IgG. Further studies are needed to understand other factors associated with inhibition-indeterminate results.

Determination of the mean duration of recent infection and false recency rate for the HIV triplex multiplex bead assay.

We developed the HIV Triplex multiplex bead assay to identify and serotype HIV infection with high sensitivity and specificity; and distinguish recent from long-term HIV-1 infections. It can facilitate accurate incidence estimation, while reducing the number of tests and blood collected, which is highly desirable for use in future studies and surveys. Using previously collected, treatment-naive longitudinal seroconversion HIV-1 positive panels and specimens from individuals infected for >12 months, we determined the assay's mean duration of recent infection (MDRI) and false-recency rate (FRR) respectively, at various mean fluorescent intensity (MFI) cutoffs. We tested seroconversion specimens (N = 814) from 142 individuals infected with HIV-1 subtypes B, C, or AE, and 1341 cross-sectional specimens from individuals infected >12 months. The MFI cutoffs of 1000 to 2000 were evaluated for recency classification, including an MFI of 1250 corresponding to the limiting antigen avidity enzyme immunoassay (LAg-EIA) cutoff of 1.5 normalized optical density for MDRI and FRR. We used four statistical methods: Methods 1 and 2 used the empirically balanced observation time approach. Method 2 MFI values were raised to power = 1.33, based on a repeated measures model to linearize the relationship between MFI and time points, whereas Method 1 was not linearized. Methods 3 and 4 employed quadratic and linear interpolations for each seroconversion panel. FRR was calculated by dividing the number of specimens misclassified as recent by the total number of specimens tested. MDRI values ranged from 135-146 days at MFI = 1000 to 229-279 days at MFI = 2000 by the 4 methods. FRR varied from 0.15%-1.27% with increasing MFI cutoff. At MFI = 1250, the average MDRI of 4 methods was 169 days and ranged from 159-183 with overlapping 95% CIs and FRR = 0.52%. The HIV Triplex assay demonstrates a longer dynamic range compared to current HIV recency assays with a low FRR for cutoffs examined. With a longer dynamic range and low FRR, the MDRI for recent infection can be extended as appropriate to detect more recent infections, increasing the value of incidence assays benefiting public health surveillance and future surveys.

Evaluation of autoimmune neurology testing clinical utility and stewardship initiatives

Abstract Testing for neural autoantibodies associated with autoimmune neurological diseases has an important role in clinical care. However, as they are niche tests for relatively rare diseases, they often have longer turn-around-times and more expensive costs than many other laboratory tests. In addition, due to the low yield of positive results, they often appear as attractive stewardship targets. Our objective was to review current utilization and ordering patterns and evaluate the impact of ongoing stewardship efforts to inform next steps regarding stewardship of these tests. Methods: Data on utilization and ordering patterns of autoimmune and paraneoplastic neural autoantibody panels from January 1 to December 31, 2023, was obtained from reference laboratory and electronic medical record (EMR) data. Additional data on best practice advisories from the most recent six months was obtained from the EMR. Results: Overall, we observed that providers tested 2270 patients both from our defined test menu (five total tests, ~89% of total orders) and through the miscellaneous route (12 total tests, ~11% of total orders), which allows providers to place orders for tests not currently on our menu. Just under one third of the orders were in cerebrospinal fluid (CSF) (n=725), while the remaining were for serum (n=1545). The percent positivity was generally higher in serum specimens, ranging from 0 to 50% per test (n=227 total positive specimens). The percent positivity in CSF specimens ranged from 0 to 40% per test (n=29 total positive specimens), which is generally consistent with previously published literature. Most of the orders were placed by neurology providers (56%). The best practice advisories (BPAs) currently in use are soft stops that target repeat tests in the same specimen type within thirty days of a previous order. Of note, these BPAs can only catch orders placed through the defined process. In six months, the BPA for repeat serum orders fired 104 times for 42 unique patients; the BPA for repeat CSF orders fired 96 times for 38 unique patients. The serum BPA resulted in elimination of the repeat order for 43% of patients (n=18), while the CSF BPA resulted in elimination of the repeat order for 24% of patients (n=9). We observed some situations in which the BPA appeared to be firing when previous orders were incorrectly collected and so not able to be sent out. Conclusion: Based on these data, we plan three main steps to continue to refine autoimmune neurology testing: 1) update our test menu to offer the most clinically useful orders through the defined route, 2) pilot review of tests ordered through the miscellaneous route, and 3) optimize BPAs to target situations with inappropriate utilization rather than technical issues.

Expression of interleukin-8 and integrin β3 predicts prognosis of patients with hepatocellular carcinoma after hepatectomy.

As important components in the tumor microenvironment, interleukin-8 (IL-8) and integrin β3 play a key role in the progression and metastasis of hepatocellular carcinoma (HCC). This study aimed to determine the expression of IL-8 and integrin β3 and their prognostic value in patients with HCC after hepatectomy. We investigated the expression of IL-8 and integrin β3, their clinical significance, as well as their correlation in the cancer tissue of 130 patients with HCC using immunohistochemistry. The prognostic value of IL-8 and integrin β3 was investigated through the follow-up of patients with HCC after hepatectomy. In HCC, IL-8 expression had a positive correlation with integrin β3 expression. Increased expressions of IL-8 and integrin β3 were indicators of tumor progression and poor prognosis in patients with HCC after hepatectomy. IL-8 positive specimens exhibited a higher proportion of macrovascular invasion, larger tumor size, poor differentiation, and advanced tumor-node-metastasis (TNM) stage (P < .05, respectively). Integrin β3 positive group exhibited a higher proportion of TNM III-staged tumors (P < .05). The results indicated that macrovascular invasion, advanced TNM stage, and integrin β3 expression were independent unfavorable prognostic factors in HCC after hepatectomy. Integrin β3 expression was proved to be an independent unfavorable prognostic factor in HCC after hepatectomy. Targeting integrin β3 might be a potential therapeutic approach in preventing tumor progression in HCC.

Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020.

BackgroundDespite the unprecedented measures implemented globally in early 2020 to prevent the spread of SARS-CoV-2, Sweden, as many other countries, experienced a severe first wave during the COVID-19 pandemic.AimWe investigated the introduction and spread of SARS-CoV-2 into Sweden.MethodsWe analysed stored respiratory specimens (n = 1,979), sampled 7 February-2 April 2020, by PCR for SARS-CoV-2 and sequenced PCR-positive specimens. Sequences generated from newly detected cases and stored positive specimens February-June 2020 (n = 954) were combined with sequences (Sweden: n = 730; other countries: n = 129,913) retrieved from other sources for Nextstrain clade assignment and phylogenetic analyses.ResultsTwelve previously unrecognised SARS-CoV-2 cases were identified: the earliest was sampled on 3 March, 1 week before recognised community transmission. We showed an early influx of clades 20A and 20B from Italy (201/328, 61% of cases exposed abroad) and clades 19A and 20C from Austria (61/328, 19%). Clade 20C dominated the first wave (20C: 908/1,684, 54%; 20B: 438/1,684, 26%; 20A: 263/1,684, 16%), and 800 of 1,684 (48%) Swedish sequences formed a country-specific 20C cluster defined by a spike mutation (G24368T). At the regional level, the proportion of clade 20C sequences correlated with an earlier weighted mean date of COVID-19 deaths.ConclusionCommunity transmission in Sweden started when mitigation efforts still focused on preventing influx. This created a transmission advantage for clade 20C, likely introduced from ongoing cryptic spread in Austria. Therefore, pandemic preparedness should have a comprehensive approach, including capacity for large-scale diagnostics to allow early detection of travel-related cases and community transmission.

Evaluation of the Seegene Allplex™ RV master assay for one-step simultaneous detection of eight respiratory viruses in nasopharyngeal specimens

BackgroundThe Seegene Allplex™ RV Master (RVM) assay is a one-step multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) system for detecting eight viral respiratory pathogens from nasopharyngeal swab, aspirate, and bronchoalveolar lavage specimens. The eight RVM targets are: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Influenza A (Flu A), Influenza B (Flu B), Human respiratory syncytial virus (RSV), adenovirus (AdV), rhinovirus (HRV), parainfluenza virus (PIV), and metapneumovirus (MPV). The assay is based on Seegene’s multiple detection temperature (MuDT) technology and provides cycle threshold (Ct) values for each of its viral targets upon PCR completion. ObjectiveWe aimed to evaluate the diagnostic performance of the RVM assay by calculating sensitivity, specificity, accuracy, Positive Predictive Value (PPV), Negative Predictive Value (NPV), Positive Percent Agreement (PPA), Negative Percent Agreement (NPA), and Overall Percent Agreement (OPA) compared to definite diagnosis and analogous reference assays. Study designDiagnostic sensitivity, specificity, accuracy, PPV, and NPV were calculated by comparing the results of the RVM assay to that of definite diagnosis assays; while PPA, NPA, and OPA were calculated by comparing results of the RVM assay to that of analogous reference products. Definite diagnosis and reference methods comprised whole genome sequencing and PCR genotyping, the Allplex™ SARS-CoV-2/FluA/FluB/RSV and Respiratory Panels 1, 2, and 3 assays (Seegene), and the Xpert® Xpress SARS-CoV-2/FluA/FluB/RSV Plus assay (Cepheid). Reproducibility of the RVM assay using fully-automated and semi-automated nucleic acid (NA) extraction workflows and as performed by independent operators was also assessed. In total, 249 positive respiratory specimens and at least 50 negative specimens for each target tested were used for this evaluation study. ResultsSensitivity, specificity, accuracy, PPV, NPV, PPA, NPA, and OPA ranged from 95.7 % to 100 % for detecting all eight targets tested on the RVM assay. Reproducibility PPA, NPA, and OPA between automated and semi-automated NA extraction workflows were all >97.9 %, while the reproducibility PPA, NPA and OPA between independent operators were all 100 %. ConclusionThese results demonstrate a high level of sensitivity, specificity, accuracy and diagnostic predictive value of the RVM assay and high agreement with comparable reference assays in identifying all eight of its targets. Taken together, our study underscores the diagnostic utility of the RVM assay in detecting eight viral respiratory pathogens.

Pathogenetic investigation of an outbreak of upper respiratory tract infection in a kindergarten in Baiyin City, Gansu Province

This study focuses on the cases(mainly characterized by respiratory symptoms such as cough, runny nose, fever, sore throat, and nasal congestion)of an outbreak of upper respiratory tract infections in a kindergarten in Jingyuan County, Baiyin City, Gansu Province, in May 2023. The epidemiological data were collected, and pharyngeal swab specimens were also obtained from the patients. The specimens of the research participants were subjected to respiratory multi-pathogen testing, and the positive specimens were further analyzed by sequencing the second hypervariable region (HRV2) of the G gene of respiratory syncytial virus (RSV) and constructing a phylogenetic tree. A total of 90 patients were collected, with an incidence rate of 22.84% (90/394), and the highest incidence was observed in the junior class group at 29.55%. Among the 17 pharyngeal swab specimens collected, 16 specimens were identified with the A subtype of respiratory syncytial virus. Sequencing analysis confirmed that it was the A subtype ON1 genotype. Based on the aforementioned testing results, it can be concluded that the current epidemic was primarily caused by infection with the A subtype of respiratory syncytial virus. Following the implementation of intervention measures, the epidemic has been effectively controlled.

Utilization of MALDI-TOF MS in the etiological diagnosis of deep-seated anaerobic bacterial infections

PurposeDeep-seated abscesses can be caused by a wide array of bacteria in various anatomical sites, the precise identification of which is crucial for implementing organism-specific treatments which can reduce morbidity and mortality. MALDI-TOF MS is a powerful proteomic method for the swift and accurate identification of anaerobic organisms. The aim of this study was to investigate deep-seated infections by MALDI-TOF MS (in comparison to VITEK®2 ANC ID card and phenotypic biochemical tests) and to determine the susceptibility pattern of identified microorganisms. Materials and methodsA total of 104 samples from patients suspected of deep-seated infections were aseptically collected and subjected to microscopy, aerobic/anaerobic cultures and subsequent identification via MALDI-TOF MS followed by antimicrobial susceptibility testing. Anaerobic bacteria were also identified using the VITEK-2 system and phenotypic biochemical tests. ResultsOut of the 104 samples tested, 41.3 % (43/104) showed positive results, predominantly in pus specimens (88 %). Mixed infections were found in 21 % of the positive cases. Of the 52 organisms identified from positive specimens, 19.2 % (10/52) were obligate anaerobes, with Bacteroides fragilis group being the most prevalent, followed by both Clostridium perfringens and Clostridium sporogenes respectively. Escherichia coli was observed to be the most common facultative anaerobic isolate. All obligate anaerobes were successfully identified to the species level via MALDI-TOF MS. In contrast, the VITEK®2 ANC ID card identified only 40 % (4/10) anaerobic bacteria to the species level. All obligate anaerobic organisms showed 100 % susceptibility to metronidazole, vancomycin and ertapenem. 25 % of the Bacteroides spp. and 50 % of Clostridium perfringens isolates were found to be resistant to clindamycin. ConclusionMALDI-TOF MS proves as a beneficial diagnostic tool for bacterial identification, eliminating the labour-intensive and time consuming conventional microbiological methods. Its accuracy of bacterial detection further helps in combating antibiotic resistance and improving patient outcomes in deep-seated infections.

B-263 Analytical Performance Evaluation of Eleven Drug of Abuse Assays on the Atellica CI Analyzer

Abstract Background The Atellica® CI Analyzer is an automated, high-throughput integrated chemistry and immunoassay analyzer utilizing both Atellica® CH and Atellica® IM Assays. This study evaluated the analytical performance of the Atellica CH Amphetamines (Amp), Barbiturates (Brb), Benzodiazepine (Bnz), Cannabinoids THC (Thc), Cocaine Metabolite (Coc), Ecstasy (Xtc), Methadone (Mdn), Opiates (Op), Oxycodone (OXY), Phencyclidine (Pcp), and Propoxyphene (Ppx) Assays on the Atellica CI Analyzer. Methods Precision and method comparison (MC) studies were used as performance indicators. Precision studies were performed according to CLSI EP05-A3 using quality control (QC) samples consisting of contrived human urine samples. One aliquot of each QC was tested in duplicate in two runs per day ≥2 hours apart on each analyzer for ≥ 20 days. Precision for each assay was evaluated with one reagent lot on one system. Method comparison studies were performed with three reagent lots according to CLSI EP12-A2. Individual native and contrived human urine samples were analyzed using the Atellica CH Amp, Barb, Bnz, Thc, Coc, Xtc, Mdn, Op, OXY, Pcp, and Ppx Assays on both the Atellica CH and Atellica CI Analyzers. The results were assessed based on analyte values used for distinguishing positive (value ≥cutoff) and negative (value &amp;lt;cutoff) specimens. Results As shown in table below, repeatability and within-lab %CVs based on manufacturer arbitrary units (mAU) were &amp;lt;0.8% and &amp;lt;3.2%, respectively or qualitative interpretation for each replicate remained unchanged for all 80 precision testing measurements (OXY, PcP). Qualitative accuracy assessed by concordance analysis demonstrated ≥95% agreement between the Atellica CI Analyzer and Atellica CH Analyzer. Conclusions Evaluation of the Atellica CH Amp, Barb, Bnz, Thc, Coc, Xtc, Mdn, Op, OXY, Pcp, and Ppx Assays using the Atellica CI Analyzer demonstrated acceptable precision and equivalent performance compared to the same assays on the Atellica CH Analyzer.

Evaluation of GeneXpert MTB/Rif Ultra assay performance on formalin-fixed paraffin-embedded tissues for Mycobacterium tuberculosis detection.

We evaluated the Xpert MTB/Rif Ultra assay performance for Mycobacterium tuberculosis (MTB) detection in formalin-fixed paraffin-embedded tissue (FFPET) compared to mycobacterial culture or laboratory-developed MTB PCR test (LDT). FFPET samples with histological features suggestive of tuberculosis from 2018 to 2023 were selected. Five hundred microlitres of tissue lysis buffer was added to FFPET scrolls and incubated at 75 °C for 5 min. After adding 50 µl of proteinase K and overnight incubation at 56 °C, sample aliquots were processed as per the manufacturer's instructions. MTB culture or LDT assay results were used as a reference for sensitivity and specificity calculations. Of 51 eligible FFPET, 32 were positive for MTB either by culture or LDT PCR on FFPET. Xpert MTB/Rif Ultra detected MTB in 23/32 positive specimens [71.9%, 95% confidence interval (CI) 54.6-84.4%]. Of nine discordant specimens, seven were MTB positive by culture and two were identified by LDT MTB PCR only, as no specimen was submitted for MTB culture. Of 19 negative samples, 100% specificity (95% CI 83.2-100.0%) was attained via Xpert MTB/Rif Ultra. Implementation of Xpert MTB/Rif Ultra on FFPET within clinical laboratories is promising, given its improved turnaround time compared to MTB culture and ability to detect MTB in cases where no tissue is available for culture.

Impact of direct identification of bacteria in blood culture–positive specimens by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry on physician selection of antimicrobial therapy

BackgroundRapid identification of the causative organism in blood stream infections is essential for early initiation of appropriate antimicrobial therapy. Direct identification of bacteria in positive blood culture bottles using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry is a promising application. A variety of direct identification methods have been reported; however, few studies have evaluated the impact of these methods on physician decision making regarding antimicrobial therapy. MethodsWe developed a simple method for direct bacterial identification and applied it to daily clinical practice to investigate the impact of direct identification of bacteria in positive blood culture bottles on physicians’ choice of antimicrobial agents for treatment. ResultsFrom January 2016 to December 2022, we attempted direct identification in 98 cases and successfully acquired identification results in 88 cases. In three cases, no empiric antimicrobial agents were initiated at the time of venipuncture for blood culture but later initiated based on the direct identification results. In the remaining 85 cases, empiric antimicrobial therapy was initiated at the time blood cultures were performed, and in 29 cases, empiric antimicrobial therapy was changed after direct identification. In 17 of these 29 cases, the antimicrobial therapy was changed based on the direct identification of bacterial genus/species, resulting in a change to an effective antimicrobial therapy before the antimicrobial susceptibility testing results were available. ConclusionsDirect identification of bacteria from positive blood culture bottles could contribute to earlier selection of or changes to antimicrobial therapies by attending physicians.

Investigation of suspected false positive norovirus results on a syndromic gastrointestinal multiplex molecular panel

BackgroundSuspected false positive norovirus results occurred after introduction of the BioFire® FilmArray® Gastrointestinal panel (BF-GIP) into 6 laboratory sites, in British Columbia, Canada. ObjectivesThe primary objective was to investigate suspected false positive results by performing additional molecular assays and whole genome sequencing (WGS). The second objective was to determine if melting curve review could predict false positive results. Study designFrom February 2023 to May 2024, the proportion of potential false positive norovirus results from the BF-GIP was calculated based on confirmatory testing using alternate molecular method. A subset of 65 norovirus BF-GIP positive specimens, including 35 negatives and 30 positives on additional molecular assays, underwent WGS. Melting curves appearances from 150 specimens were reviewed. ResultsOverall, 215/784 (27.4 %) BF-GIP norovirus results were suspected to be false positives. When using WGS, 64/65 results were in agreement with confirmatory testing. Notably, 35 specimens negative on confirmatory testing and suspected to be BF-GIP norovirus false positive results were undetectable by WGS. Melting curves did not accurately predict false positives, since 20/72 (27.8 %) had typical appearances upon review. ConclusionsBF-GIP produces false positive results for norovirus, which cannot be predicted by melting curve review.

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.

Effectiveness of selective antibiotics use in ESBL-related UTIs

BackgroundUrinary tract infections (UTIs) are the second most common infection, affecting 150 million people each year worldwide. Enterobacteriaceae species expressing extended-spectrum β-lactamases (ESBLs) are on the rise across the globe and are becoming a severe problem in the therapeutic management of clinical cases of urinary tract infection. Knowledge of the prevalence and antibiogram profile of such isolates is essential to develop an appropriate treatment methodology. This study aimed to investigate the prevalence of Enterobacteriaceae isolates exhibiting ESBL and their selective oral antibiogram profile at the district general hospital, Polonnaruwa.ResultsA total of 4386 urine specimens received to the Microbiology Laboratory during the study period. Among them, 1081 (24.6%) showed positive results for urine culture while 200/1081 specimens showed ESBL isolates. Out of the selected 200 specimen’s majority (67.5%) of samples received from the In-Patient Department. There were 200 patients and reported that 115 (57.5%) were females and 85 (42.5%) were males. The majority (51%) of the patients belong to the age group of 55–74 years. Among the ESBLs positive specimens, the majority 74.5% (n = 149) identified organisms were E. coli followed by Klebsiella spp.17.5% (n = 35), Enterobacteriaceae 7% (n = 14) and only1% (n = 2) isolate of Proteus spp. Mecillinam (87.92%) and Nitrofurantoin (83.2%) showed higher effectiveness against E. coli. Nitrofurantoin showed the highest effectiveness against Klebsiella spp. (40%), other Enterobacteriaceae spp. (100%). Proteus spp. showed 100% effectiveness and resistance respectively against Ciprofloxacin, Cotrimoxazole and Nitrofurantoin.ConclusionThe most predominant ESBLs producing uro-pathogen was the E. coli in the study setting and E. coli had higher sensitivity rate against Mecillinam. Among currently used oral antibiotics Nitrofurantoin was the best choice for UTIs caused by ESBL producers.

Epidemiology and genetic characterization of influenza viruses circulating in Bhutan in 2022.

Influenza (Flu) causes considerable morbidity and mortality globally, and in Bhutan, Flu viruses are a leading cause of acute respiratory infection and cause outbreaks during Flu seasons. In this study, we aim to analyze the epidemiology and the genetic characterization of Flu viruses circulated in Bhutan in 2022. Respiratory specimens were collected from patients who meet the case definition for influenza-like illness (ILI) and severe acute respiratory infection (SARI) from sentinel sites. Specimens were tested for Flu and SARS-CoV-2 viruses by RT-PCR using the Multiplex Assay. Selected positive specimens were utilized for Flu viral genome sequencing by next-generation sequencing. Descriptive analysis was performed on patient demographics to see the proportion of Flu-associated ILI and SARI. All data were analyzed using Epi Info7 and QGIS 3.16 software. A weekly average of 16.2 ILI cases per 1000 outpatient visits and 18 SARI cases per 1000 admitted cases were reported in 2022. The median age among ILI was 12 years (IQR: 5-28) and SARI was 6.2 (IQR: 2.5-15) years. Flu A(H3N2) (70.2%) subtype was the most predominant circulating strain. Flu A(H1N1)pdm09 and Flu B viruses belonged to subclades that were mismatched to the vaccine strains recommended for the 2021-2022 season but matched the vaccine strain for the 2022-2023 season with vaccine efficacy 85.14% and 88.07% respectively. Flu A(H3N2) virus belonged to two subclades which differed from the vaccine strains recommended in both the 2021-2022 and 2022-2023 seasons with vaccine efficacy 68.28%. Flu virus positivity rates were substantially elevated during the Flu season in 2022 compared to 2021. Flu A(H3N2) subtype was the most predominant circulating strain in the country and globally. Genetic characterization of the Flu viruses in Bhutan showed a close relatedness of high vaccine efficacy with the vaccine strain that WHO recommended for the 2022-23 season.

Evaluation of an in-house pan-Malassezia quantitative PCR in human clinical samples.

Althought Malassezia spp. have been involved in various pathologies, they are an integral part of the cutaneous, gut, oral, ears, nose and throat (ENT) mycobiota. Since Malassezia are difficult to grow in culture, unexhaustive molecular biology methods have been developed to detect them. The aim of the study was to evaluate an in-house pan-Malassezia quantitative polymerase chain reaction (panM-qPCR) on various clinical human samples and determine Malassezia burden in various human mycobiota. The panM-qPCR was designed to target the repeated 28S rDNA gene from all Malassezia species. We used the assay to quantify the Malassezia burden on 361 samples from 161 subjects (80 skin swabs from 10 healthy volunteers (HV), 13 samples from 2 seborrheic dermatitis patients (SD), 90 skin samples from 19 burned patients, 119 stool samples from 89 immunocompromised patients, 59 ENT samples from 41 patients). For HV, the amount of Malassezia was different according to the swabbed areas. Quantification cycle (Cq) in SD is lower than in HV. In burned patients, Cq was significantly lower compared to HV. In stool samples, 6.7% were positive for Malassezia spp. with a high Cq. For the ENT area, a higher proportion of positive specimens were detected in ear samples than in nose samples. Our findings emphasized the importance of qPCR, confirming elevated Malassezia spp. levels on individuals' faces and scalps, increased burden in SD patients and in severely burnt patients than in HV. The pan-MqPCR appears to be a promising tool for studying Malassezia in various human mycobiota.

A case report of human infection with avian influenza H10N3 with a complex respiratory disease history

BackgroundOn March 16th 2024, the first case of Human infection with avian influenza H10N3 since the end of the global COVID-19 Pandemic was reported in Kunming, China. To enhance comprehension of the source of infection and risk factors of the H10N3 virus infection, this case report summarizes the clinical features, epidemiological investigation, and laboratory test results. Provides recommendations for the prevention and control of Human infection with avian influenza H10N3.Case presentationA 51-year-old male with a history of COVID-19 infection and a smoking habit of 30 years, worked in livestock breeding and was exposed to sick and dead poultry before falling ill with fever and chills on 28th February 2024. A week later, he was diagnosed with severe pneumonia, influenza, and respiratory failure by the Third People's Hospital of Kunming(KM-TPH). He was discharged on 17th April and none of his 6 close contacts showed any symptoms of illness. Environmental samples taken from the epidemic spot revealed that peacock feces tested positive for avian influenza sub-type H9 and waterfowl specimens showed positive results for avian influenza sub-type H5. Gene sequencing conducted on positive specimens from the patient's respiratory tract by the Chinese Centre for Disease Control and Prevention (CCDC) showed a high degree of similarity (98.6–99.5%) with the strain responsible for the second global case of human infected with H10N3 (reported from Zhejiang, China 2022).ConclusionsAccording to the available epidemiological information, there is limited evidence to suggest that H10N3 viruses are excessively lethal. However, adaptive site mutations have been observed in the H10N3 isoform of mammals. While it is unlikely that the H10N3 virus will spread among humans, the possibility of additional cases cannot be entirely ruled out. Symptoms of human infection with H10N3 avian influenza are similar to those of common respiratory infections, which may result in them being overlooked during initial clinical consultations. Therefore, it is essential to improve surveillance of the H10 sub-type of avian influenza and to increase the awareness of hospital-related workers of cases of pneumonia of unknown origin.