Improve Pathogen Detection Research Articles

Enhanced pathogen identification among patients with clinically suspected meningitis.

Delayed or incorrect treatment of meningitis may result in adverse patient outcomes. However, laboratory testing in resource-limited settings is often limited to conventional diagnostic methods. We explored the utility of syndromic molecular assays for diagnosis. We tested cerebrospinal fluid (CSF) specimens collected from patients with clinically suspected meningitis submitted to a tertiary hospital laboratory in January 2021 - May 2021. Primary microbiological analysis (culture, Gram stain and cytochemical analysis) was performed as part of routine testing. Residual CSF specimens were tested using a bacterial triplex real-time polymerase chain reaction (PCR) assay and a syndromic multi-pathogen real-time PCR assay for the detection of up to 18 bacterial and viral pathogens. Pathogen detection was compared between conventional and molecular assays. A potential pathogen was detected in 6% (12/188) and 47% (89/188) of specimens on the triplex and the multi-pathogen assay, respectively. Epstein-Barr virus (49/188; 26%), human herpes virus 7 (22/188; 12%), herpes simplex virus 1 (13/188; 7%) and Streptococcus pneumoniae (10/188; 5%) were the leading pathogens detected on the syndromic multi-pathogen PCR. Further, using the multi-pathogen PCR assay, a potential pathogen was detected in 44% (73/166) of the specimens which were negative following routine testing. Overall, combining routine testing and molecular platforms significantly improved pathogen detection (p < 0.001); a potential pathogen was identified in 51% (95/188) of the specimens tested, compared to 12% (22/188) using routine methods alone. The use of molecular tests improved pathogen detection by 39% when paired with routine methods. Multi-pathogen molecular testing is useful for rapidly diagnosing meningitis cases.

Streptococcus salivarius pneumonia-associated pneumomediastinum: a case report and literature review

BackgroundStreptococcus salivarius is an opportunistic pathogen, and there have been no reported cases of Streptococcus salivarius pneumonia to date. Pneumomediastinum is usually secondary to tracheal or esophageal injury and is very rare as a complication of pneumonia. We report a case of Streptococcus salivarius pneumonia complicated by pneumomediastinum, aiming to enhance clinicians’ awareness of rare pathogens and uncommon complications in pneumonia.Case presentationThe patient, a 36-year-old male, presented with a persistent cough and sputum production for one week, accompanied by a sore throat that had developed just one day prior. Chest computed tomography (CT) disclosed pneumomediastinum alongside obstructive atelectasis in the left lower lobe. Streptococcus salivarius infection was conclusively identified through bronchoalveolar lavage metagenomic next-generation sequencing (mNGS), as well as smear and culture analyses. The patient was administered intravenous amoxicillin-clavulanate potassium for a duration of seven days as part of the anti-infection regimen. Given the stability of the patient’s respiratory and circulatory systems, a tube drainage procedure was deemed unnecessary. Post-treatment, the patient’s clinical symptoms notably improved. A subsequent chest CT scan revealed the re-expansion of the left lower lung and near-complete resolution of pneumomediastinum.ConclusionThere are numerous pathogens that can cause pneumonia. While focusing on common pathogens, it is important not to overlook rare ones. When considering infections from rare pathogens, it is recommended to promptly perform a bronchoscopy and submit bronchoalveolar lavage fluid for mNGS to improve pathogen detection rates. During the diagnosis and treatment of pneumonia, it is crucial to be vigilant for rare complications. When a patient presents with symptoms such as dyspnea or subcutaneous emphysema, it is advisable to immediately perform a chest CT scan to rule out pneumomediastinum.

Subtracting the background by reducing cell-free DNA’s confounding effects on Mycobacterium tuberculosis quantitation and the sputum microbiome

DNA characterisation in people with tuberculosis (TB) is critical for diagnostic and microbiome evaluations. However, extracellular DNA, more frequent in people on chemotherapy, confounds results. We evaluated whether nucleic acid dyes [propidium monoazide (PMA), PEMAX] and DNaseI could reduce this. PCR [16S Mycobacterium tuberculosis complex (Mtb) qPCR, Xpert MTB/RIF] was done on dilution series of untreated and treated (PMA, PEMAX, DNaseI) Mtb. Separately, 16S rRNA gene qPCR and sequencing were done on untreated and treated sputa before (Cohort A: 11 TB-negatives, 9 TB-positives; Cohort B: 19 TB-positives, PEMAX only) and 24-weeks after chemotherapy (Cohort B). PMA and PEMAX reduced PCR-detected Mtb DNA for dilution series and Cohort A sputum versus untreated controls, suggesting non-intact Mtb is present before treatment-start. PEMAX enabled sequencing-based Mycobacterium-detection in 7/12 (58%) TB-positive sputa where no such reads otherwise occurred. In Cohort A, PMA- and PEMAX-treated versus untreated sputa had decreased α- and increased β-diversities. In Cohort B, β-diversity differences between timepoints were only detected with PEMAX. DNaseI had negligible effects. PMA and PEMAX (but not DNaseI) reduced extracellular DNA in PCR and improved pathogen detection by sequencing. PEMAX additionally detected chemotherapy-associated taxonomic changes that would otherwise be missed. Dyes enhance microbiome evaluations especially during chemotherapy.

MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.

Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets-MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples.

Microbial aetiology of community-acquired pneumonia in hospitalised adults: A prospective study utilising comprehensive molecular testing

ObjectivesThis study aimed to describe the microbial aetiology of community-acquired pneumonia (CAP) in adults admitted to a tertiary care hospital and assess the impact of syndromic polymerase chain reaction (PCR) panels on pathogen detection. MethodsConducted at Haukeland University Hospital, Norway, from September 2020 to April 2023, this prospective study enrolled adults with suspected CAP. We analysed lower respiratory tract samples using both standard-of-care tests and the BIOFIRE® FILMARRAY® Pneumonia Plus Panel (FAP plus). The added value of FAP Plus in enhancing the detection of clinically relevant pathogens, alongside standard-of-care diagnostics, was assessed. ResultsOf the 3238 patients screened, 640 met the inclusion criteria, with 384 confirmed to have CAP at discharge. In these patients, pathogens with proven or probable clinical significance were identified in 312 (81.3%) patients. Haemophilus influenzae was the most prevalent pathogen, found in 118 patients (30.7%), followed by SARS-CoV-2 in 74 (19.3%), and Streptococcus pneumoniae in 64 (16.7%). Respiratory viruses were detected in 186 (48.4%) patients. The use of FAP plus improved the pathogen detection rate from 62.8% with standard-of-care methods to 81.3%. ConclusionsPathogens were identified in 81% of CAP patients, with Haemophilus influenzae and respiratory viruses being the most frequently detected pathogens. The addition of the FAP plus panel, markedly improved pathogen detection rates compared to standard-of-care diagnostics alone.

Microbiological Spectrum of Osteoarticular Infections and Their Management in Mongolian Children.

Introduction. Osteoarticular infections (OI) in children cause considerable morbidity with associated long-lasting sequelae. Comprehensive clinical and microbiological data in Mongolian children are missing. Objectives. To generate epidemiological, clinical and microbiological data on osteoarticular infections (OI) in Mongolian children after the introduction of a standardized management protocol. Methods. A prospective study was done between 2019 and 2022 at the only tertiary pediatric hospital in Mongolia. Results. Forty-two children presented with septic arthritis (SA), 6 with osteomyelitis (OM) and 23 with combined SA and OM. Newborns and young infants (≤3 months) comprised 38.%. A causative organism was identified in 38 children: Staphylococcus aureus (n = 31), Klebsiella spp (n = 3), Enterobacter spp (n = 2), Enterobacter spp + Klebsiella spp (n = 1) and Candida albicans (n = 1). Five children (7%) had sequelae. Mongolian children with OI were younger compared to other cohorts. Conclusion. A standardized protocol for the management of OI in children was taken up well by the patients and treating staff leading to improved pathogen detection, facilitating antimicrobial stewardship in the future.

Fracture related Infection - Challenges in definition and diagnosis

In the field of orthopedics and trauma surgery, the rise of periprosthetic joint infections following joint replacement and fracture-related infections (FRI) has become a growing concern. The recent establishment of a definitive definition for FRI aimed to standardize diagnosis and treatment approaches while considering unique aspects of implant-associated infections in the presence of concomitant bone fractures.Diagnosing FRI can be challenging due to the varied clinical symptoms, and confirmatory criteria may not always be evident, necessitating additional diagnostic measures. Blood markers like leukocyte count, C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR) have limited specificity. Although novel biomarkers such as D-dimer and interleukin-6 (IL-6) show potential, they require further investigation. The use of microbiological diagnostics with tissue samples and sonication has improved pathogen detection. Cross-sectional imaging techniques like CT scans and MRI scans help evaluate bone status, soft tissue infiltration, and abscesses. Nuclear medicine techniques are accurate but may not always be practical in routine clinical practice.Histopathological interpretation for FRI remains less standardized compared to periprosthetic joint infections (PJI). FRI diagnosis requires the identification of visible microorganisms in deep tissue specimens and the quantification of polymorphonuclear neutrophils (PMNs).The defined concept of FRI has opened doors for better diagnostic and treatment approaches. However, challenges persist, especially in preoperative diagnosis, particularly for cases with unclear clinical presentations. Future endeavors aimed at optimizing diagnostic procedures and establishing a histopathological classification for FRI could lead to improved treatment recommendations and outcomes.

A Phi29-based unbiased exponential amplification and genotyping approach improves pathogen detection in tick samples.

Ticks are vectors for many infectious diseases, such as spotted fever group (SFG) rickettsioses and borreliosis, and are valuable in the study of pathogen ecology. Ticks have several growth stages that vary considerably in size; therefore, in most cases, DNA extracted from ticks is insufficient for subsequent studies, particularly for multiple pathogen screening and genotyping. Unbiased amplification of DNA from tick samples before analysis is a major requirement for subsequent ecological surveys and other studies. Phi29 DNA polymerase, an enzyme that exhibits strand displacement activity, can exponentially amplify DNA randomly, generating large quantities of DNA. In the present study, we developed a Phi29-based unbiased exponential amplification (PEA) assay to obtain sufficient tick DNA for genetic analysis. By using tick-borne pathogen detection and genotyping as a model, we tested and evaluated the feasibility of the assay. DNA was extracted from single ticks and subjected to PEA. The results showed that tick DNA could be amplified up to 105 fold. The amplified products were successfully used for pathogen screening and genotyping. Rickettsia was successfully detected and genotyped in samples with amplified DNA from single ticks. Furthermore, we identified a new genotype of Rickettsia from ticks collected from Dandong city, Liaoning province, Northeast China. This PEA assay is universal and can be extended to other applications where the quantity of DNA is greatly limited.

A diagnostic test of real-time PCR detection in the diagnosis of clinical bloodstream infection

Blood culture remains the standard for diagnosing bloodstream infections, but it is difficult to identify bacteria directly and timeliness. The real-time polymerase chain reaction (PCR) has the potential to fill this diagnostic gap. This study intends to explore the sensitivity and specificity of PCR in detecting bloodstream infection pathogens and to compare it with routine blood culture to explore its clinical application value. A total of 126 patients with bloodstream infections collected from various clinical departments of The First Hospital of Hebei Medical University. The patient's sample was divided into two parts. The one for multiplex PCR detection was performed using the Pathogeno Elite Multiplex PCR kit. Another blood culture was a fully automatic blood culture system from Autobio company. Among the 126 patients, a total of 17 pathogens were detected by PCR and blood culture both methods. PCR detected a total of 43 positive samples and 83 negative samples. Five samples were positive with blood culture, and 81 were negative. The negative predictive value of PCR was 0.98, with a sensitivity of 0.71 and a specificity of 0.68. A total of 38 specimens were positive for PCR but negative for blood culture, and 2 samples were positive for blood culture but negative for PCR. The top 5 pathogens with PCR detection were Epstein-Barr virus (27 cases), Human herpes virus 5 (9 cases), Klebsiella pneumoniae (5 cases), Staphylococcus (5 cases), and Stenotrophomonas maltophilia (4 cases). PCR detection can rapidly identify more pathogens and even multi-pathogen infections. Therefore, PCR testing may improve pathogen detection in patients with suspected bloodstream infections, enabling targeted treatment of patients.

Clinical value of bacterial culture in sinus tract in the diagnosis of fracture-related infection

Objectives: This study compared the results of bacterial culture from operation versus sinus tract samples in patients with fracture-related infection (FRI), and examined the ability of bacterial culture in sinus tract to identify pathogenic bacteria. Methods: A retrospective analysis of 53 patients with FRI from June 2016 to June 2021 was done. Common infection sites were femur, tibiofibular, hip joint, and ankle. Samples collected in sinus tract and during the operation were sent for bacterial culture. Results were summarized and compared, respectively, with pathogenic bacteria. Results: In sinus tract bacterial culture, bacteria were found in 75.6% of culture samples. The top 3 bacteria presented were: Staphylococcus aureus (32.26%), Staphylococcus epidermis (12.90%), and Pseudomonas aeruginosa (8.06%). Bacterial culture from the sinus tract matched the result of intraoperative samples 67.30% of the time, while 51.50% matched the pathogenic bacteria. Conclusion: Bacterial culture of sinus tract samples is not recommended as the basis for identifying pathogenic bacteria. Stopping antibiotic 2 weeks before operation, taking multiple samples at different sites, and sending multiple samples for bacterial culture are good ways to improve pathogen detection rate.

The Retrospective on Atypical Brucella Species Leads to Novel Definitions.

The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively.

Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia.

BackgroundThe diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming.ObjectivesTo evaluate the clinical performance of a rapid nanopore-sequencing based metagenomics test for diagnosis of bacterial pathogens in common LRIs through a large-scale prospective study.MethodsWe enrolled 292 hospitalized patients suspected to have LRIs between November 2018 and June 2019 in a single-center, prospective cohort study. Rapid clinical metagenomics test was performed on-site, and the results were compared with those of routine microbiology tests.Results171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRIs. The turnaround time (from sample registration to result) for the rapid metagenomics test was 6.4 ± 1.4 hours, compared to 94.8 ± 34.9 hours for routine culture. Compared with culture and real-time PCR validation tests, rapid metagenomics achieved 96.6% sensitivity and 88.0% specificity and identified pathogens in 63 out of 161 (39.1%) culture-negative samples. Correlation between enriched anaerobes and lung abscess was observed by Gene Set Enrichment Analysis. Moreover, 38 anaerobic species failed in culture was identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture.ConclusionsRapid clinical metagenomics test improved pathogen detection yield in the diagnosis of LRI. Empirical antimicrobial therapy could be de-escalated if rapid metagenomics test results were hypothetically applied to clinical management.

Real-time gastrointestinal infection surveillance through a cloud-based network of clinical laboratories.

Acute gastrointestinal infection (AGI) represents a significant public health concern. To control and treat AGI, it is critical to quickly and accurately identify its causes. The use of novel multiplex molecular assays for pathogen detection and identification provides a unique opportunity to improve pathogen detection, and better understand risk factors and burden associated with AGI in the community. In this study, de-identified results from BioFire® FilmArray® Gastrointestinal (GI) Panel were obtained from January 01, 2016 to October 31, 2018 through BioFire® Syndromic Trends (Trend), a cloud database. Data was analyzed to describe the occurrence of pathogens causing AGI across United States sites and the relative rankings of pathogens monitored by FoodNet, a CDC surveillance system were compared. During the period of the study, the number of tests performed increased 10-fold and overall, 42.6% were positive for one or more pathogens. Seventy percent of the detections were bacteria, 25% viruses, and 4% parasites. Clostridium difficile, enteropathogenic Escherichia coli (EPEC) and norovirus were the most frequently detected pathogens. Seasonality was observed for several pathogens including astrovirus, rotavirus, and norovirus, EPEC, and Campylobacter. The co-detection rate was 10.2%. Enterotoxigenic E. coli (ETEC), Plesiomonas shigelloides, enteroaggregative E. coli (EAEC), and Entamoeba histolytica were detected with another pathogen over 60% of the time, while less than 30% of C. difficile and Cyclospora cayetanensis were detected with another pathogen. Positive correlations among co-detections were found between Shigella/Enteroinvasive E. coli with E. histolytica, and ETEC with EAEC. Overall, the relative ranking of detections for the eight GI pathogens monitored by FoodNet and BioFire Trend were similar for five of them. AGI data from BioFire Trend is available in near real-time and represents a rich data source for the study of disease burden and GI pathogen circulation in the community, especially for those pathogens not often targeted by surveillance.

Diversity of the Genomes and Neurotoxins of Strains of Clostridium botulinum Group I and Clostridium sporogenes Associated with Foodborne, Infant and Wound Botulism.

Clostridium botulinum Group I and Clostridium sporogenes are closely related bacteria responsible for foodborne, infant and wound botulism. A comparative genomic study with 556 highly diverse strains of C. botulinum Group I and C. sporogenes (including 417 newly sequenced strains) has been carried out to characterise the genetic diversity and spread of these bacteria and their neurotoxin genes. Core genome single-nucleotide polymorphism (SNP) analysis revealed two major lineages; C. botulinum Group I (most strains possessed botulinum neurotoxin gene(s) of types A, B and/or F) and C. sporogenes (some strains possessed a type B botulinum neurotoxin gene). Both lineages contained strains responsible for foodborne, infant and wound botulism. A new C. sporogenes cluster was identified that included five strains with a gene encoding botulinum neurotoxin sub-type B1. There was significant evidence of horizontal transfer of botulinum neurotoxin genes between distantly related bacteria. Population structure/diversity have been characterised, and novel associations discovered between whole genome lineage, botulinum neurotoxin sub-type variant, epidemiological links to foodborne, infant and wound botulism, and geographic origin. The impact of genomic and physiological variability on the botulism risk has been assessed. The genome sequences are a valuable resource for future research (e.g., pathogen biology, evolution of C. botulinum and its neurotoxin genes, improved pathogen detection and discrimination), and support enhanced risk assessments and the prevention of botulism.

Improved Pathogen Detection in Neonatal Sepsis to Boost Antibiotic Stewardship

Improved Pathogen Detection in Neonatal Sepsis to Boost Antibiotic Stewardship

High Accuracy of Second Generation Unyvero ITI Automated Multiplex PCR Analysis of Joint Fluid Aspirate in Low-Grade Prosthetic Hip and Knee Joint Infections

Aims and Objectives:A major obstacle for the treatment of prosthetic joint infections (PJIs) is the identification of the organism causing it. While the diagnostic criteria ruling PJIs in or out have become ever more accurate, detecting the causative pathogen(s) still relies mostly on conventional culture. The aim of this study was to evaluate the diagnostic potential of a second generation multiplex PCR assay (Unyvero ITI G2, Curetis AG, Holzgerlingen, Germany) used on synovial fluid specimens.Materials and Methods:Prospectively collected frozen joint fluid specimens from 26 patients undergoing arthroplasty revision surgery of the hip or knee for any reason were tested as per the manufacturer’s protocol. The sensitivity and specificity were calculated using the Chi-squared-test and a combination of the serum CRP level, leukocyte count, erythrocyte sedimentation rate, joint fluid culture, tissue biopsy culture, and tissue biopsy histology served as gold standard.Results:Of the 26 cases included in the study, 15 were infected and 11 aseptic. Conventional joint fluid culture showed a sensitivity 0.67 and a specificity of 0.91. Joint fluid multiplex PCR yielded a sensitivity of 0.8 and a specificity of 1.0.Conclusion:This is the first study to assess the second generation Unyvero ITI cartridge on joint fluid aspirate for the detection of prosthetic joint infection. In our setting, the method achieved a higher diagnostic accuracy than conventional culture. We conclude that, to improve pathogen detection before revision surgery, this method represents a valuable tool.

Improved pre-operative diagnostic accuracy for low-grade prosthetic joint infections using second-generation multiplex Polymerase chain reaction on joint fluid aspirate

BackgroundA major obstacle for the treatment of prosthetic joint infection (PJI) is the identification of the underlying causative organism. While the diagnostic criteria ruling PJI in or out have become ever more accurate, the detection of the causative pathogen(s) still relies mostly on conventional and time-consuming microbial culture. The aim of this study was to evaluate the diagnostic potential of a second-generation multiplex PCR assay (Unyvero ITI G2, Curetis AG, Holzgerlingen, Germany) used on synovial fluid specimens. Our hypothesis was that the method would yield a higher diagnostic accuracy in the pre-operative workup than synovial fluid culture. Thus, a more precise classification of septic and aseptic prosthesis failure could be achieved before revision surgery.MethodsProspectively collected frozen joint fluid specimens from 26 patients undergoing arthroplasty revision surgery of the hip or knee were tested as per the manufacturer’s protocol. Sensitivities, specificities, positive and negative predictive values as well as positive and negative likelihood ratios with corresponding confidence intervals were estimated using the statistical software R. A combination of the serum C-reactive protein (CRP) level, leukocyte count, erythrocyte sedimentation rate, joint fluid culture, tissue biopsy culture, and tissue biopsy histology served as the gold standard.ResultsOf the 26 patients included in the study, 15 were infected and 11 were aseptic. Conventional joint fluid culture showed a sensitivity of 0.67 and a specificity of 0.91. Joint fluid multiplex PCR yielded a sensitivity of 0.8 and a specificity of 1.0.ConclusionsUsing the second-generation Unyvero ITI cartridge on joint fluid aspirate for the detection of prosthetic joint infection, we were able to achieve a higher diagnostic accuracy than with conventional culture. We conclude that to improve pathogen detection before revision surgery, this method represents a valuable and practicable tool.

Implementation of Case-Based Surveillance and Real-time Polymerase Chain Reaction to Monitor Bacterial Meningitis Pathogens in Chad.

BackgroundMeningococcal serogroup A conjugate vaccine (MACV) was introduced in Chad during 2011–2012. Meningitis surveillance has been conducted nationwide since 2003, with case-based surveillance (CBS) in select districts from 2012. In 2016, the MenAfriNet consortium supported Chad to implement CBS in 4 additional districts and real-time polymerase chain reaction (rt-PCR) at the national reference laboratory (NRL) to improve pathogen detection. We describe analysis of bacterial meningitis cases during 3 periods: pre-MACV (2010–2012), pre-MenAfriNet (2013–2015), and post-MenAfriNet (2016–2018).MethodsNational surveillance targeted meningitis cases caused by Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae. Cerebrospinal fluid specimens, inoculated trans-isolate media, and/or isolates from suspected meningitis cases were tested via culture, latex, and/or rt-PCR; confirmed bacterial meningitis was defined by a positive result on any test. We calculated proportion of suspected cases with a specimen received by period, and proportion of specimens with a bacterial meningitis pathogen identified, by period, pathogen, and test.ResultsThe NRL received specimens for 6.8% (876/12813), 46.4% (316/681), and 79.1% (787/995) of suspected meningitis cases in 2010–2012, 2013–2015, and 2016–2018, respectively, with a bacterial meningitis pathogen detected in 33.6% (294/876), 27.8% (88/316), and 33.2% (261/787) of tested specimens. The number of N. meningitidis serogroup A (NmA) among confirmed bacterial meningitis cases decreased from 254 (86.4%) during 2010–2012 to 2 (2.3%) during 2013–2015, with zero NmA cases detected after 2014. In contrast, proportional and absolute increases were seen between 2010–2012, 2013–2015, and 2016–2018 in cases caused by S. pneumoniae (5.1% [15/294], 65.9% [58/88], and 52.1% [136/261]), NmX (0.7% [2/294], 1.1% [1/88], and 22.2% [58/261]), and Hib (0.3% [1/294], 11.4% [10/88], and 14.9% [39/261]). Of specimens received at the NRL, proportions tested during the 3 periods were 47.7% (418), 53.2% (168), and 9.0% (71) by latex; 81.4% (713), 98.4% (311), and 93.9% (739) by culture; and 0.0% (0), 0.0% (0), and 90.5% (712) by rt-PCR, respectively. During the post-MenAfriNet period (2016–2018), 86.1% (678) of confirmed cases were tested by both culture and rt-PCR, with 12.5% (85) and 32.4% (220) positive by culture and rt-PCR, respectively.ConclusionsCBS implementation was associated with increased specimen referral. Increased detection of non-NmA cases could reflect changes in incidence or increased sensitivity of case detection with rt-PCR. Continued surveillance with the use of rt-PCR to monitor changing epidemiology could inform the development of effective vaccination strategies.

1489. Clinical Utility and Patterns of the use of the Gastrointestinal PCR Panel Over a 2-Year Period at a University Hospital

BackgroundUp to 80% of cases of acute infectious gastroenteritis do not have an identifiable etiologic agent. Molecular syndromic diagnostic panels, such as the Biofire® Filmarray® gastrointestinal (GI) panel, can improve pathogen detection, including frequent causes of community-onset diarrhea. There are little data about the real-world use and test characteristics of the GI panel in the clinical setting. The objective of this study was to evaluate the patterns of use and clinical utility of the GI panel.MethodsWe conducted a retrospective cohort study of adults (age >18 years) admitted to the University of Colorado Hospital for whom a GI Panel was ordered from October 1, 2015 to August 31, 2017. Primary outcomes included patient demographics and co-morbidities, time since admission to test order, and cumulative test results. Descriptive statistics were utilized to summarize the frequencies of the primary outcome measures.Results1684 panels were ordered and completed during the study period compared with 1379 stand-alone C. difficile PCRs. Seventeen of the 22 components of the panel had been validated by our lab prior to the study period; therefore, results were only available for these pathogens. Most GI panels (78%) were ordered in the first 48 hours of admission, with 6% ordered between 48 and 72 hours after admission, and 16% >72 hours after admission. The GI panel yielded an organism 34% of the time. The most frequently identified organism was C. difficile (18.5%) followed by Norovirus (5.2%) and Enteropathogenic E. coli (5.1%).ConclusionOver a 2-year period at a University hospital, the GI panel only had a positive result in 20% of patients tested. Although most of the tests were ordered in the first 48 hours after admission, 22% were ordered after 48 hours, after which etiologies of hospital-onset diarrhea are expected to be more common. Among all GI Panel tests ordered, C. difficile was the most common organism identified, followed by Norovirus. Each of these organisms has an accurate and less costly alternative test. Stand-alone testing for C. difficile and Norovirus should be considered prior to the GI Panel for patients admitted to the hospital, particularly when admitted >48 hours.Disclosures All authors: No reported disclosures.

Use of Diagnostic Metagenomics in the Clinical Microbiology Laboratory

Next Generation Sequencing (NGS)-based assays have recently entered the realm of the clinical microbiology laboratory9s capacity, providing an exciting potential for improvement in infectious disease detection and identification. There are many diagnostic applications of NGS, such as targeted or amplicon NGS and metagenomic NGS (mNGS). mNGS has received the most attention for diagnostics due to its unbiased nature and hypothesis free testing approach. While mNGS may have improved pathogen detection compared to conventional culture-based testing, and has shown clinically utility in some specific cases, the application of this technology is still investigational and many barriers and limitations remain to be overcome. This review will cover both the advantages and limitations of mNGS, and addresses the need for and incorporation of new technologist skillsets in the clinical microbiology laboratory to successfully implement mNGS diagnostics.