Identification Of Organisms Research Articles

BERT contextual embeddings for taxonomic classification of bacterial DNA sequences

Biological taxonomic classification is an important task needed for the identification and discovery of organisms, as well as the inference of their evolutionary relationships. The order and structure of biological sequence components has an essential and primary role in what the sequence’s identity and function is. In order to be able to efficiently differentiate between different bacterial categories, interactions and positions of the biological components in sequences must be known — which is an essential challenge in biological sequence classification. In this light, a considerable amount of recent research has been made to explore efficient representations of biological sequences such as spectral k-mer representation, one-hot encoding, Hilbert space curves and classical word embeddings such as Word2Vec. This paper identifies the taxonomic classification of bacterial 16S rRNA genes at five resolutions mapping hierarchical taxonomic ranks. A Bidirectional Encoder Representations from Transformers (BERT) model is pretrained using biological sequences, which to the best of our knowledge is the first time BERT has been trained with such sequences. A complete prediction model is then proposed – BioSeqBERT-CNN – that initially extracts contextual embeddings representations of DNA sequences using the pretrained BERT model. Extracted representations are further used for taxonomic classification through a Convolutional Neural Network (CNN). For boosting the deep learning classification performance, a data augmentation step is applied. Classification with the original dataset on the most fine-grained rank produced an accuracy of 93.5%, which surpasses that of recent works by 1.5–24.3%. Using data augmentation, an accuracy of 99.9% is achieved, which exceeds values of recent works by a minimum and maximum of 7.9% and 30.7%, respectively on the most fine-grained taxonomic rank. This exhibits promising performance promoting the study of using contextual embeddings to represent biological sequences, with Deep Learning networks.

Frequency of Inflammatory Diarrhoea (Faecal Leukocyte Count ≥ 5/Ml Or Faecal Cal-protetctin Positive) in young patients presenting with Acute Gastroenteritis

One of the common dilemma and the most important cause of child death below the age of 5 years in developing countries is acute gastroenteritis. Aim: To check the frequency of inflammatory diarrhoea (faecal leukocyte count ≥ 5/ml or faecal calprotetctin positive) in young patients presenting with acute gastroenteritis in hospital. Study design: Descriptive cross sectional study. Methodology: Patients (n=366) within the age range of 1 day to 6 years presenting to the OPD with the complaints of symptoms associated with acute gastroenteritis (diarrhoea with or without abdominal pain, vomiting and nausea) were included into the study. Patients demographic data were collected. Stool samples from the patients were obtained in sterile bottles and sent for Stool RE and CS examination. All this information was recorded on Performa. Data was analyzed using SPSS version 26. Results were presented as frequency and percentage. Age was presented as mean± SD. Results: Out of total 366 patients 178 (48.6%) were male and 188(51.4%) were female. Mean age of the patients presenting to the OPD/MRC was 826 days (2.2 years) ± 618 days, with a range 13 days to 2187 days (5.9 years). Frequency of inflammatory diarrhea was 193(52.7%) among patients presenting with acute gastroenteritis as compared to non inflammatory diarrhoea. Conclusion: It was concluded that frequency of inflammatory diarrhoea in young patients presenting with acute gastroenteritis is alarmingly high in our region. Various programs for the identification and eradication of causative factors and organisms should be carried out along with education of masses about this fatal condition. Keywords: Acute Gastroenteritis, Diarrhoea, Infectious Diarrhoea, Inflammatory Diarrhoea and Non-Inflammatory Diarrhoea,

Role of corneal biopsy in the management of infectious keratitis.

The aim of this study was to review the existing literature and investigate the role of microbiologic culture and histopathologic examination of corneal biopsies in the management of infectious keratitis. Corneal biopsy continues to be a significantly useful tool in the diagnosis and tailored management of infectious keratitis. Several techniques can be employed for tissue collection, handling and processing to optimize diagnostic yield and maximize safety, including emerging femtosecond laser-assisted biopsy. Corneal opacities represent a significant cause of global blindness, and infectious keratitis is the most common cause. Organism identification in progressive infectious keratitis is essential for proper management. However, microbiological culture alone has a high rate of false-negative results. Records from the Bascom Palmer Eye Institute were retrospectively searched for patients between 1 January 2015, and 31 December 2019, who underwent corneal biopsy, therapeutic keratoplasty or endothelial graft removal for infectious keratitis and had specimens bisected and submitted for evaluation with both microbiologic culture and histopathologic examination. Detection of bacteria, fungus and mycobacteria was not statistically different between culture and histopathology. Microbiology and histopathology are complementary methods for the identification of causative microorganisms in corneal specimens with presumed infectious keratitis.

Not All That Glitters Is Gold: Barcoding Effort Reveals Taxonomic Incongruences in Iconic Ross Sea Sea Stars

The Southern Ocean is one of the most exposed regions to climate-related changes on our planet. Better understanding of the current biodiversity and past speciation events, as well as implementation of conservation actions and accurate identification of organisms to species level in this unique environment, is fundamental. In this study, two species of sea stars, Odontaster roseus Janosik & Halanych, 2010 and Odontaster pearsei Janosik & Halanych, 2010, are reported for the first time from the Terra Nova Bay area (TNB, Ross Sea, Antarctica) by using a combination of molecular (DNA barcoding) and morphological (coloration and skeletal features) analyses. Molecular results agree with external morphological characters of the two identified species, making occurrence in the area unequivocal. The two species were recently described from the Antarctic Peninsula, and went unnoticed for a long time in TNB, possibly having been confused with O. meridionalis (E.A. Smith, 1876), with which they share a bright yellow coloration. This latter species seems to be absent in the Ross Sea. Thus, the past literature referring to O. meridionalis in the Ross Sea should be treated with caution as these “yellow morphs” could be one of the two recently described species or even orange–yellow morphs of the red-colored congeneric O. validus Koehler, 1906. This work highlights the paucity of knowledge even in purportedly well-studied areas and in iconic Antarctic organisms.

Impact of delayed processing of positive blood cultures on organism detection: a prospective multi-centre study

BackgroundBlood cultures remain the gold standard investigation for the diagnosis of bloodstream infections. In many locations, quality-assured processing of positive blood cultures is not possible. One solution is to incubate blood cultures locally, and then transport bottles that flag positive to a central reference laboratory for organism identification and antimicrobial susceptibility testing. However, the impact of delay between the bottle flagging positive and subsequent sub-culture on the viability of the isolate has received little attention.MethodsThis study evaluated the impact of delays to sub-culture (22 h to seven days) in three different temperature conditions (2–8 °C, 22–27 °C and 35 ± 2 °C) for bottles that had flagged positive in automated detection systems using a mixture of spiked and routine clinical specimens. Ninety spiked samples for five common bacterial causes of sepsis (Escherichia coli, Haemophilus influenzae, Staphylococcus aureus, Streptococcus agalactiae and Streptococcus pneumoniae) and 125 consecutive positive clinical blood cultures were evaluated at four laboratories located in Cambodia, Lao PDR and Thailand. In addition, the utility of transport swabs for preserving organism viability was investigated.ResultsAll organisms were recoverable from all sub-cultures in all temperature conditions with the exception of S. pneumoniae, which was less likely to be recoverable after longer delays (> 46–50 h), when stored in hotter temperatures (35 °C), and from BacT/ALERT when compared with BACTEC blood culture bottles. Storage of positive blood culture bottles in cooler temperatures (22–27 °C or below) and the use of Amies bacterial transport swabs helped preserve viability of S. pneumoniae.ConclusionsThese results have practical implications for the optimal workflow for blood culture bottles that have flagged positive in automated detection systems located remotely from a central processing laboratory, particularly in tropical resource-constrained contexts.

Identification and Frequency of Causative Organism in Oral Candidiasis in Early Childhood in Bangladesh

Identification and Frequency of Causative Organism in Oral Candidiasis in Early Childhood in Bangladesh

PRIMARY STERNAL OSTEOMYELITIS IN A CHILD: A CASE REPORT

TYPE: Case Report TOPIC: Pediatrics INTRODUCTION: Primary sternal osteomyelitis which develop without any contiguous focus of infection is a rare condition, that too in children. MRI and biopsy are required for diagnosis. Rarity of the condition often results in delayed diagnosis and treatment. CASE PRESENTATION: A 9 year old boy , who was otherwise normal, presented with high fever - 9 days, followed by painful limitation of movement of right upper limb.O/E- Sick and toxic child..Tender, firm swelling, 2 x 2cm ,over the sterno-chondral junction of 2nd and 3rd rib with signs of inflammation.Rest of physical examination WNL. Investigation revealed anemia, polymorphonuclear leucocytosis with elevated ESR and CRP. Cultures were sterile. USG revealed collection below Rt sternoclavicular joint which yielded a dry tap . CECT showed non enhancing collection with no cortical defect in sternum. MRI revealed T2 hyperintensity and T1 hypointensity showing diffusion restriction of sternum suggestive of bone marrow edema.CT-guided sternal biopsy confirmed sternal osteomyelitis. Patient responded to Meropenem and Vancomycin after nonresponse to Cloxacillin and cefotaxime.Treatment continued for 4 weeks and patient recovered completely. DISCUSSION: Primary sternal osteomyelitis is diagnosed after exclusion of other sources of infection. Close proximity to vital organs can complicate the condition. Early recognition, identification of the causal organism, and early initiation of culture-driven intravenous antibiotic therapy is crucial in determining outcome. Staphylococcus aureus,coagulase negative staphylococcus, group B streptococcus, and other streptococcus species are most commonly implicated organisms.Nearly half requires surgical debridement and resection. CONCLUSIONS: Early diagnosis and appropriate treatment results in complete recovery of sternal osteomyelitis DISCLOSURE: Nothing to declare. KEYWORD: sternal osteomyelitis

An Australian Algorithm to Guide the Surgical Management of Chronic Prosthetic Joint Infection: A Multi-Disciplinary Team Approach

AbstractChronic prosthetic joint infection (PJI) is a leading cause of failure for total joint arthroplasty. Historically, two-stage revision arthroplasty has been considered the gold standard approach to chronic PJI, however, emerging evidence suggests that one-stage revision arthroplasty may be underutilized. To our knowledge, there have been no previously published guidelines for the surgical management of chronic PJI in Australia, resulting in significant heterogeneity in management within and across centers. We aim to review contemporary concepts in the surgical management of PJI and develop an evidence-based algorithm to optimize the management of chronic hip and knee PJI, incorporating a multidisciplinary team (MDT) approach. A review was conducted to identify existing articles discussing surgical management of chronic PJI, specifically contraindications to one-stage revision arthroplasty. Absolute contraindications for one-stage revision include difficulty in treating organisms, significant soft tissue compromise, and concurrent sepsis. Relative contraindications include lack of preoperative identification of organism, presence of a sinus tract, fungal infections, significant bone loss, and immunocompromise. In determining the management of patients with a relative contraindication, MDT discussion with the consideration of patient's overall local, host, and microbiological profile is necessary. Using gathered evidence, absolute and relative contraindications for one-stage revision arthroplasty were developed into an algorithm. The algorithm is designed to assist our PJI MDT in making optimized decisions when choosing between a one-stage versus two-stage approach. Ongoing follow-up is underway to determine the effect of implementing this algorithm on patient outcomes, eradication rates, and revision rates within our center.

ELEVATIONS OF PROCALCITONIN AND D-DIMER IN PATIENTS WITH COVID-19 CORRELATE WITH VENTILATOR-ASSOCIATED PNEUMONIA IN THE SETTING OF VENTILATOR-ASSOCIATED EVENTS AND SPUTUM PRODUCTION

TYPE: Abstract TOPIC: Critical Care PURPOSE: It is undetermined whether trending of inflammatory markers in mechanically-ventilated COVID-19 patients is useful in identifying ventilator-associated pneumonia (VAP). The goal of this study is to determine if initial intubation, ventilator-associated events (VAE), or sputum collection was associated with elevations in inflammatory markers, procalcitonin, or positive cultures. METHODS: 287 patients were enrolled in this retrospective study. Data was analyzed into three cohorts: initial intubation, VAE, and sputum collection. Within each group, markers associated with each inciting event were compared to admission values RESULTS: The VAE cohort exhibited differences in WBC (14.1 vs 7.2, p=0.006), d-dimer (4144 vs 881, p<0.001), and CRP (10.4 vs 16, p=0.049). There were no significant differences in procalcitonin and ferritin. The sputum collection cohort revealed differences in WBC (16.8 vs 7.7, p<0.001), procalcitonin (2.95 vs 0.65, p=0.01), and CRP (10.2 vs 15.8, p=0.047). There were no significant differences in FiO2, PEEP, d-dimer, or ferritin. The VAE cohort identified a cultured organism 83% of the time, the initial intubation cohort 35%, and sputum collection cohort 38%. CONCLUSIONS: VAE was associated with a rise in d-dimer, while sputum culture collection was associated with elevated procalcitonin. Interestingly, VAE is suggestive of VAP with an identified organism 83% of the time. Furthermore, d-dimer was associated with VAE and positive organism identification. CLINICAL IMPLICATIONS: This data suggests a role for trending d-dimer and procalcitonin for identification of VAP in setting of a VAE or sputum collection. DISCLOSURE: Nothing to declare. KEYWORD: procalcitonin

P17 Quality assurance in bacterial identification and antimicrobial susceptibility testing results: an essential component of antimicrobial resistance surveillance

BackgroundAntimicrobial resistance (AMR) is a major threat to human health. Bacterial identification and antibiotic susceptibility testing play an essential role in patient care and control of antibiotic resistance mechanisms by indicating which antibiotics are most likely to treat an infection, reducing the empirical prescription of broad-spectrum antibiotics and avoiding the unnecessary prescription of antibiotics to reduce healthcare costs. AMR surveillance in Kenya has historically been focused on pathogens that cause significant mortality and morbidity such as diarrhoea illnesses and bacteraemia. Many private hospitals and a few public hospitals in Kenya have the capacity to conduct antimicrobial susceptibility testing; however, the available data are rarely verified for quality.MethodsThis study was conducted in five sentinel sites in Kenya. Clinical samples were processed in the sites as part of routine microbiology. Each sentinel site selected isolates as per the National AMR sample referral guide and sent them to the National Microbiology Reference Laboratory (NMRL) for quality assessment. Upon reception of isolates at NMRL, they were subcultured and subjected to organism identification testing using MALDI-TOF equipment. Antimicrobial susceptibility testing was performed using Vitek 2 compact. In case of any discrepancy on organism identification, correct antibiotic selection and resistance interpretation, the sites were informed.ResultsAntimicrobial susceptibility testing was conducted on Escherichia coli and Staphylococcus aureus, which were the most frequently isolated pathogens. High resistance to cephalosporins was observed with the E. coli isolates. Over 80% susceptibility of E. coli to amikacin, ampicillin, gentamicin, meropenem, nitrofurantoin and piperacillin/tazobactam was observed. This shows that the antibiotics can be used for empirical therapy in areas where there is no laboratory capacity for antibiotic susceptibility testing. Resistance to gentamicin of S. aureus isolates was found to be 10%, which shows that gentamicin still finds a role in controlling S. aureus infections. Penicillin resistance in S. aureus was 100%. High levels of resistance were observed with erythromycin (61%) and ampicillin (84%)ConclusionsThere is no site that scored 100% in pathogen identification and drug–bug combination. Continuous capacity building of AMR surveillance sites through mentorships to improve quality of data generated is of paramount importance. E. coli and S. aureus were the most frequently isolated pathogens. High levels of resistance were observed with erythromycin (61%) and ampicillin (84%), which calls for antibiotic stewardship programmes to educate on optimal antibiotic use.

The Smart Soil Organism Detector: An instrument and machine learning pipeline for soil species identification

Understanding the diversity of soil organisms is complicated by both scale and substrate. Every footprint we leave in the soil covers hundreds to millions of organisms yet we cannot see them without extremely laborious extraction and microsopy endeavors. Studying them is also challenging. Keeping them alive so that we can understand their lifecycles and ecological roles ranges from difficult to impossible. Functional and taxonomic identification of soil organisms, while possible, is also challenging. Here we present the Smart Soil Organism Detector, an instrument and machine learning pipeline that combines high-resolution imaging, multi-spectral sensing, large-bore flow cytometry, and machine learning to extract, isolate, count, identify, and separate soil organisms in a high-throughput, high-resolution, non-destructive, and reproducible manner. This system is not only capable of separating alive nematodes, dead nematodes, and nematode cuticles from soil with 100% out-of-sample accuracy, but also capable of identifying nematode strains (sub-species) with 95.5% out-of-sample accuracy and 99.4% specificity. Soil micro-arthropods were identified to class with 96.1% out-of-sample accuracy. Broadly applicable across soil taxa, the Smart SOD system is a tool for understanding global soil biodiversity.

Development and Validation of a Predictive Model for Failure of Medical Management in Spinal Epidural Abscesses.

The optimal management of spinal epidural abscesses (SEA) secondary to primary spinal infections has demonstrated large variability in the literature. Although some literature suggests a high rate of neurological deterioration, others suggest failure of medical management is uncommon. To develop a predictive model to evaluate the likelihood of failure of medical therapy in the setting of SEA. A retrospective review was conducted of all patients presenting with SEA from primary spinal infections. Patients presenting with MRI evidence of SEA without neurological deficits were included. Failure of medical management was defined as requiring surgical intervention over 72 hours after the initiation of antibiotics. A machine learning method (Risk-Calibrated Supersparse Linear Integer Model) was used to create a risk stratification score to identify patients at high risk for requiring surgical intervention. In total, 159 patients were identified as presenting with MRI findings of SEA without evidence of neurological deficit. Of these patients, 50 required delayed surgery compared with 109 whose infection were successfully treated with surgical intervention. The Spinal Epidural Abscess Predictive Score was created using a machine learning model with an area under the curve of 0.8043 with calibration error of 14.7%. Factors included active malignancy, spondylodiscitis, organism identification, blood cultures, and sex. The probability of failure of medical management ranged from <5% for a score of 2 or less and >95% for a score of 7 or more. The Spinal Epidural Abscess Predictive Score model is a quick and accurate tool to assist in clinical decision-making in SEA.

Learnings from a Cutibacterium acnes pseudo-outbreak in pediatric neurosurgical patients

Background:Cutibacterium acnes is normal skin flora as well as a common culture contaminant. It can cause infections in the setting of sterile implants, although clinical presentations can be subtle. Differentiating true infection from sample contamination is challenging and has implications for patient care. We describe an investigation of a cluster of 7 hospitalized pediatric patients with C. acnes isolated from anaerobic cultures of cerebrospinal fluid (CSF) over 3 weeks at a quaternary-care children’s hospital. Methods: An outbreak response was coordinated between the infection prevention and control (IPC), microbiology, and neurosurgery teams. We defined a case as a hospitalized patient with C. acnes isolated from a CSF culture beginning in November 2020. We reviewed charts of all cases and CSF culture collection on all case units, transport to and processing at the microbiology laboratory, and the IPC team measured adherence for all processes. Results: There were 8 positive cultures in 7 cases from November 10 to 27, 2020. The median case age was 2 months (range, 0–119). Cases occurred on 4 different units. All positive patients had at least 1 implanted neurosurgical device used for CSF drainage. There were no clear commonalities in surgeon responsible for device placement, hardware type placed, or staff collecting CSF samples. A standard protocol for CSF collection was followed for all cases. Overall, 3 patients cleared cultures without intervention, 2 received oral antibiotics, and 2 underwent surgical removal of their device. Specimen processing was unchanged, although due to supply issues, an alternative anaerobic culture media (Anaerobic Systems, Morgan Hills, CA) was used for 6 weeks, during which all cases were identified. Compared to routine media, the alternative is known to enhance organism detection. The company reported no concerns for media contamination or C. acnes outbreaks. Once routine media became available, CSF culture positivity for C. acnes returned to baseline (late November or early December) (Fig. 1). Conclusions: We identified a likely pseudo-outbreak related to temporary use of a more sensitive culture media. No direct patient harm was identified, although many had increased risk of harm by surgical intervention or prolonged length of stay. Technological advances may enhance organism identification but challenge existing paradigms of care. More studies are needed to better delineate the intersection of diagnostic advancements with patient care standards.Funding: NoneDisclosures: None

Diagnosing Onychomycosis: What's New?

An overview of the long-established methods of diagnosing onychomycosis (potassium hydroxide testing, fungal culture, and histopathological examination) is provided followed by an outline of other diagnostic methods currently in use or under development. These methods generally use one of two diagnostic techniques: visual identification of infection (fungal elements or onychomycosis signs) or organism identification (typing of fungal genus/species). Visual diagnosis (dermoscopy, optical coherence tomography, confocal microscopy, UV fluorescence excitation) provides clinical evidence of infection, but may be limited by lack of organism information when treatment decisions are needed. The organism identification methods (lateral flow techniques, polymerase chain reaction, MALDI-TOF mass spectroscopy and Raman spectroscopy) seek to provide faster and more reliable identification than standard fungal culture methods. Additionally, artificial intelligence methods are being applied to assist with visual identification, with good success. Despite being considered the ‘gold standard’ for diagnosis, clinicians are generally well aware that the established methods have many limitations for diagnosis. The new techniques seek to augment established methods, but also have advantages and disadvantages relative to their diagnostic use. It remains to be seen which of the newer methods will become more widely used for diagnosis of onychomycosis. Clinicians need to be aware of the limitations of diagnostic utility calculations as well, and look beyond the numbers to assess which techniques will provide the best options for patient assessment and management.

Применение нейронных сетей в системе распознавания промысловых гидробионтов в условиях повышенной флуктуации

The article focuses on using artificial neural networks for the recognition of commercial hydrobionts in conditions of increased fluctuation. Research has not been conducted in the field of recognition of aquaculture objects for reasons of solving the applied problems and achieving the required indicators. There is described the development of software for recognition of aquaculture objects based on the YOLOv5 model, as well as the proper methodology for the semi-automatic formation of effective visual training samples. There has been analyzed the model operation scheme and substantiated the importance of the training sample and its influence on the quality of pattern recognition by a neural network. Effective identification of aquatic organisms requires the methods for dividing it into zones according to various distinctive features and separating the required objects not only from the background, but also taking into account fluctuations above the water surface. There has been developed a method for eliminating fluctuations in order to increase the efficiency of recognition of aquatic organisms by a neural network. There is described the process of testing software for the detection of commercial hydrobionts trained on a sample by the proposed method. &#x0D; It has been inferred that the recognition rate directly depends not only on the quality of the training sample and the volume of images, but also on the technical characteristics of the electronic computer

Speed and safety of mass spectrometry for identification of Burkholderia pseudomallei directly from spiked blood cultures

Burkholderia pseudomallei is a bipolar Gram-negative bacillus and the causative agent of melioidosis; an infectious disease which commonly presents with bacteraemia. Data regarding direct from blood culture identification of B. pseudomallei using the Vitek mass spectrometer (MS) are limited. The authors aim to assess the safety and sensitivity of the Vitek MS for identification of B. pseudomallei from spiked positive blood culture samples. Safety was assessed by determining the ability of the standard MS α-cyano-4-hydroxycinnamic acid (CHCA) matrix solution to inactivate B. pseudomallei. Organism identification using the manufacturer's blood culture extraction method was compared to an in-house technique. Additionally, identification following abbreviated agar incubation of blood culture broth was performed. All 70 MS target spots were inactivated by the matrix solution. The manufacturer's blood culture extraction method identified 0/26 (0%) B. pseudomallei samples. An in-house method using the spun deposit from blood culture broth samples identified 38/38 (100%) B. pseudomallei samples. MS analysis of a blood culture broth drop on Chocolate agar following a 6 h incubation identified 30/32 (94%) samples. Decreased time to diagnosis of melioidosis bacteraemia is likely to improve patient outcomes. This study adds to the literature with regards to the utility of MALDI-TOF MS identification of B. pseudomallei both directly from positive blood culture broth and a subsequent 6 h plate incubation. The use of a standard matrix solution inactivates the organism, and use of the spun deposit from a positive blood culture broth is most effective for early identification of B. pseudomallei.

Diagnostic accuracy of the metagenomic next-generation sequencing (mNGS) for detection of bacterial meningoencephalitis: a systematic review and meta-analysis.

The early diagnosis of bacterial meningoencephalitis (BM/E) is difficult, and delay in diagnosis can cause complications leading to neurological impairment/death. In cases of unexplained BM/E, the metagenomic NGS (mNGS) offers an advantage over conventional methods, especially when a rare pathogen is implicated or the patient is on antibiotics. This study aims to evaluate and compare the diagnostic efficacy of mNGS for the diagnosis of BM/E using cerebrospinal fluid (CSF) specimens versus a composite reference standard (CRS). The electronic databases (Embase, PubMed, and Web of Science) were searched up to 15 June 2021. Studies such as cohort, case-control, prospective, or retrospective studies that assessed the diagnostic efficacy of mNGS in suspected bacterial meningitis/encephalitis cases were included. Ten studies met the inclusion criteria, including three retrospective and seven prospective studies. The sensitivity of mNGS for diagnosis of BM/E from CSF samples ranged from 33 (95% CI: 13-62) to 98% (95% CI: 76-99). The specificity of mNGS ranged from 67 (95% CI: 55-78) to 98% (95% CI: 95-99). The estimated AUC (area under curve) by hierarchical summary receiver operating characteristic (HSROC) of the studies being analyzed was 0.912. The meta-regression analysis demonstrated that the different types of studies (single-center vs. multi-center) had an effect on the specificity of mNGS for BM/E compared with CRS (90% vs. 96%, meta-regression P < 0.05). The current analysis revealed moderate diagnostic accuracy of mNGS. This approach can be helpful, especially in cases of undiagnosed BM/E by identification of organism and subsequently accelerating the patient management.

What is the Clinical Impact of a Multiplex Gastrointestinal Panel in Children?

Because pediatric gastroenteritis is often self-limited, guidelines do not routinely recommend routine stool testing, although early identification of organisms may lead to expeditious treatment and optimal infection control. Nucleic acid amplification multiplex diagnostic panels are highly sensitive and rapid, detecting the nucleic acid of bacteria, parasites, and viruses simultaneously. The objective of this study was to compare the results of stool testing in children pre- and post-introduction of a molecular multiplex gastrointestinal panel (GIP). This is a multicenter cross-sectional cohort study of inpatient and outpatient children who had stool testing performed in the Children’s Hospital Colorado microbiology laboratory between 2013 and 2017. The 2 years before the introduction of the GIP in November 2015 functioned as historical controls. Testing options in each era are described below: In total, 8720 patient encounters with 12 222 stool tests were assessed. Patients hospitalized with community-acquired diarrhea were used to evaluate primary...

Clinical Relevance of Xpert MRSA/SA in Guiding Therapeutic Decisions for Staphylococcal Infections: A Diagnostic Test Accuracy Analysis.

IntroductionRapid identification of the causal organism and antibiotic resistance is crucial for guiding targeted therapy in patients with suspected staphylococcal infection. A meta-analysis was carried out to evaluate the diagnostic relevance of Xpert™ MRSA/SA (Xpert) from clinical samples of various origins for limiting the use of unnecessary empirical methicillin-resistant Staphylococcus aureus (MRSA) therapy.MethodsFive databases, including the Cochrane Library, Scopus, PubMed, Web of Science, and Embase, were comprehensively inspected from inception to October 12, 2021. The pooled summary estimates were evaluated using a bivariate random-effects model.ResultsOur inclusion criteria were met by 49 publications containing 68 datasets out of 735 citations. A total of 21 studies (n = 4996) examined the accuracy of Xpert in detecting methicillin-sensitive S. aureus (MSSA), while 47 studies (n = 45,430) examined the accuracy of Xpert in detecting MRSA. As compared to MRSA, Xpert’s diagnostic performance for MSSA detection was markedly higher [sensitivity: 0.97 (0.96–0.98), specificity: 0.97 (0.97–0.98), area under curve (AUC): 0.99 (0.99–1.0)]. Xpert’s pooled sensitivity and specificity differed marginally across sample types, including screening of colonization, lower respiratory tract (LRT), osteoarticular, and bloodstream samples. Notably, the Xpert pooled specificity was consistently ≥ 92% against microbiological culture across all sample types. The diagnostic efficiency heterogeneity was not explained by a meta-regression and subgroup analysis of research design, sample conditions, and sampling methods (P > 0.05).ConclusionOur findings suggest that Xpert could be used as the favoured screening test for the early detection of staphylococcal infection in a variety of sample types, with the goal of guiding therapeutic decisions.Supplementary InformationThe online version contains supplementary material available at 10.1007/s40121-022-00632-w.

Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis.

Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host–pathogen interplay is well described, less is known about the pathogen’s role, including pathogen–pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.