A Prospective Clinical Study to EvaluAte the AbiliTy of the CloudCath System to Detect Peritonitis During In-Home Peritoneal Dialysis (CATCH)

Introduction

Peritonitis is the leading complication of peritoneal dialysis (PD). Patients are instructed to seek care promptly for signs (cloudy effluent) or symptoms (abdominal pain), and earlier treatment improves outcomes. The CloudCath Peritoneal Dialysis Drain Set Monitoring (CloudCath) system monitors turbidity in dialysis effluent and sends notifications of changes signaling possible peritonitis.

Methods

We conducted this single-arm, open-label, multicenter study of CloudCath system use during PD. We deactivated system notifications to participants and investigators, who followed standard-of-care for peritonitis signs and symptoms. Effectiveness endpoints measured time between CloudCath system notifications and peritonitis events using International Society of Peritoneal Dialysis (ISPD) criteria.

Results

Two hundred forty-three participants used the CloudCath system for 178.8 patient-years. Of 71 potential peritonitis events, 51 events (0.29 per patient-year) met ISPD white blood cell (WBC) count criteria. The system triggered notifications for 41 of 51 events (80.4%), with a median lead time of 2.6 days (10%-90% range, -1.0 to 15.7; P < 0.0001). Excluding 6 peritonitis events that occurred when the system was not in use, the system triggered notifications for 41 of 45 events (91.1%), with a median lead time of 3.0 days (10%-90% range, -0.5 to 18.8; P < 0.0001). Of the 0.78 notifications per patient-year, the majority were peritonitis events or nonperitonitis events such as exit site and tunnel infections or catheter/cycler issues.

Conclusion

The CloudCath system detected peritonitis events during PD several days earlier than the current standard-of-care and has the capacity to send notifications that could expedite peritonitis diagnosis and treatment.

The 8th International RASopathies Symposium: Expanding research and care practice through global collaboration and advocacy

Germline pathogenic variants in the RAS/mitogen-activated protein kinase (MAPK) signaling pathway are the molecular cause of RASopathies, a group of clinically overlapping genetic syndromes. RASopathies constitute a wide clinical spectrum characterized by distinct facial features, short stature, predisposition to cancer, and variable anomalies in nearly all the major body systems. With increasing global recognition of these conditions, the 8th International RASopathies Symposium spotlighted global perspectives on clinical care and research, including strategies for building international collaborations and developing diverse patient cohorts in anticipation of interventional trials. This biannual meeting, organized by RASopathies Network, was held in a hybrid virtual/in-person format. The agenda featured emerging discoveries and case findings as well as progress in preclinical and therapeutic pipelines. Stakeholders including basic scientists, clinician-scientists, practitioners, industry representatives, patients, and family advocates gathered to discuss cutting edge science, recognize current gaps in knowledge, and hear from people with RASopathies about the experience of daily living. Presentations by RASopathy self-advocates and early-stage investigators were featured throughout the program to encourage a sustainable, diverse, long-term research and advocacy partnership focused on improving health and bringing treatments to people with RASopathies.

Effectiveness of Self-Collected, Ambient Temperature-Preserved Nasal Swabs Compared to Samples Collected by Trained Staff for Genotyping of Respiratory Viruses by Shotgun RNA Sequencing: Comparative Study

BACKGROUND

The SARS-CoV-2 pandemic has underscored the need for field specimen collection and transport to diagnostic and public health laboratories. Self-collected nasal swabs transported without dependency on a cold chain have the potential to remove critical barriers to testing, expand testing capacity, and reduce opportunities for exposure of health professionals in the context of a pandemic.

OBJECTIVE

We compared nasal swab collection by study participants from themselves and their children at home to collection by trained research staff.

METHODS

Each adult participant collected 1 nasal swab, sampling both nares with the single swab, after which they collected 1 nasal swab from 1 child. After all the participant samples were collected for the household, the research staff member collected a separate single duplicate sample from each individual. Immediately after the sample collection, the adult participants completed a questionnaire about the acceptability of the sampling procedures. Swabs were placed in temperature-stable preservative and respiratory viruses were detected by shotgun RNA sequencing, enabling viral genome analysis.

RESULTS

In total, 21 households participated in the study, each with 1 adult and 1 child, yielding 42 individuals with paired samples. Study participants reported that self-collection was acceptable. Agreement between identified respiratory viruses in both swabs by RNA sequencing demonstrated that adequate collection technique was achieved by brief instructions.

CONCLUSIONS

Our results support the feasibility of a scalable and convenient means for the identification of respiratory viruses and implementation in pandemic preparedness for novel respiratory pathogens.

Performance characteristics of a prototype dialysate turbidity monitoring system to detect peritonitis in patients receiving peritoneal dialysis

BACKGROUND

The risk of peritonitis has limited wider adoption of peritoneal dialysis (PD) in the United States. We developed a prototype bedside dialysate turbidity monitoring system, aiming to improve diagnostic accuracy relative to conventional approaches which depend on visual inspection and reporting of insensitive and non-specific symptoms.

METHODS

The prototype system was tested in a single-centre, proof-of-principle clinical study in patients receiving intermittent PD. We obtained multiple effluent dialysate samples from each consenting participant. We compared turbidity measurements with diagnostic criteria endorsed by the International Society of Peritoneal Dialysis (ISPD).

RESULTS

Overall, we analysed 983 specimens from 65 patients, including 105 samples from patients with peritonitis and 878 samples from patients without peritonitis. An operating point derived from a previous in vitro study yielded an unadjusted sensitivity and specificity of 95.2% and 91.5%, respectively. The majority of samples that did not meet ISPD diagnostic criteria were either cases detected before criteria were met or were related to active peritonitis treatment and resolution.

CONCLUSION

This proof-of-principle study demonstrates the feasibility and diagnostic accuracy of a prototype dialysate turbidity monitoring system for peritonitis surveillance.

Novel Approach to Improve the Identification of the Bleeding Phenotype in Noonan Syndrome and Related RASopathies

OBJECTIVES

To characterize bleeding phenotype in Noonan Syndrome, to test the utility of following national guidelines in detecting this phenotype, to evaluate thromboelastography (TEG) as a diagnostic tool and to evaluate the cohort for genotype-phenotype correlations.

STUDY DESIGN

Participants with a clinical diagnosis NS or related RASopathy were enrolled in a cohort study. Study procedures included clinical bleeding assessment, coagulation testing per guidelines and hematology consultation. TEG was completed in a subset and genetic testing was conducted for those without a molecular diagnosis. International Society of Haemostasis and Thrombosis Bleeding Assessment Tool (ISTH-BAT) scores were calculated with hematology consultation. Bleeding phenotype was defined as abnormal bleeding score.

RESULTS

Twenty participants enrolled; 12completed clinical and laboratory evaluation, five of whom met the definition for bleeding phenotype. Four of the five participants with a bleeding phenotype had platelet aggregation defects and at least one additional coagulation defect. TEG was performed in nine participants, four with bleeding phenotype and five without, and results were normal in all cases. No genotype-phenotype correlation was found.

CONCLUSION

Five of 20 participants had a bleeding phenotype identified. Based on available data we do not recommend incorporating TEG into clinical practice for NS patients. Platelet aggregation defects were the most common abnormalities, which would not be detected on Tier 1 testing of current guidelines, therefore we propose a new algorithm.

670. Precision Metagenomic (PM) Sequencing Outperforms Conventional Urine Culture in Detecting Clinically Relevant Microorganisms

Background

Morbidity from urinary tract infection (UTI) is high. Urine culture is the reference method for UTI diagnosis. Its diagnostic yield is limited as prior antibiotic use prevents growth of established uropathogens, many emerging uropathogens do not grow under routine culture conditions, and results interpretation can be subjective. Faster, more comprehensive diagnostics could help manage recurrent and/or drug-resistant infections. We evaluated the diagnostic yield of a precision metagenomic (PM) workflow for pathogen detection & antimicrobial resistance (AMR) characterization directly from urine.

Methods

Residual urine samples from symptomatic adults evaluated by culture & susceptibility were identified by a combination of consecutive & stratified random sampling (n=480; 79% culture positive). DNA was extracted with modifications to the Quick-DNA Urine Kit (Zymo). Libraries were generated with Illumina DNA Prep with Enrichment for clinically relevant targets (191 pathogens, 1976 AMR markers) with the Explify Urinary ID/AMR Panel (UPIP, IDbyDNA). Enriched libraries were sequenced on the NextSeq550 (Illumina) and data analyzed with the Explify UPIP Data Analysis Solution (IDbyDNA).

Results

For bacterial uropathogens, 94% positive agreement was observed between this PM workflow and culture. PM detected fastidious and/or anaerobic potential uropathogens in 30% and 7% of samples reported as culture-negative or positive for other bacteria, respectively. Total agreement between AMR marker detection and phenotypic resistance was 78%. Notably, PM predicted phenotypes of ESBL E. coli and K. pneumoniae (10/10), MRSA (9/9), and vancomycin-resistant E. faecium (4/5). PM also detected pathogens associated with sexually-transmitted infection (C. trachomatis, HSV) and bacterial vaginosis (G. vaginalis). PM produced complete results within 24-36 hours of sample receipt (vs culture & susceptibility: 42-72 hrs).

Conclusion

The sensitivity of PM for uropathogen detection was noninferior to culture (Δ = 0.05; Nam RMLE; p < 0.0005). PM predicted antimicrobial resistance phenotypes for common uropathogens and identified potential pathogens not detected by conventional culture. Future studies should assess the impact of PM-guided management on clinical outcomes.

Disclosures

Rita C. Stinnett, PhD, MHS, IDbyDNA (Employee) Marta Mangifesta, PhD, IDbyDNA (Employee) Anagha Kadam, PhD, IDbyDNA (Employee) Heng Xie, PhD, IDbyDNA (Employee) Stacie Stauffer, BS, IDbyDNA (Employee) Jamie Lemon, PhD, D(ABMM), IDbyDNA (Employee) Benjamin Briggs, MD, PhD, IDbyDNA (Employee) Lauge Farnaes, MD, PhD, Cardea Bio (Advisor or Review Panel member)IDbyDNA (Employee) Robert Schlaberg, MD, MPH, IDbyDNA (Consultant, Shareholder, Co-founder)

Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections

BACKGROUND

Osteoarticular infections (OAIs) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children.

METHODS

This was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children's hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon's discretion per standard care (fluid or tissue) and based on imaging and operative findings. We compared mNGS to culture and usual care testing (culture and polymerase chain reaction [PCR]) from the same site.

RESULTS

We recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In 4 subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS.

CONCLUSIONS

In this single-site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.

Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections

Background

Pediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is important, both in terms of guiding therapeutic management and in characterizing prognosis. Usual care testing by culture and polymerase chain reaction is often unable to identify a pathogen. We examined the systematic application of metagenomic next-generation sequencing (mNGS) for detecting organisms and transcriptomic analysis of cerebrospinal fluid (CSF) in children with central nervous system (CNS) infections.

Methods

We conducted a prospective multisite study that aimed to enroll all children with a CSF pleocytosis and suspected CNS infection admitted to 1 of 3 tertiary pediatric hospitals during the study timeframe. After usual care testing had been performed, the remaining CSF was sent for mNGS and transcriptomic analysis.

Results

We screened 221 and enrolled 70 subjects over a 12-month recruitment period. A putative organism was isolated from CSF in 25 (35.7%) subjects by any diagnostic modality. Metagenomic next-generation sequencing of the CSF samples identified a pathogen in 20 (28.6%) subjects, which were also all identified by usual care testing. The median time to result was 38 hours.

Conclusions

Metagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections.

Cost Efficacy of Rapid Whole Genome Sequencing in the Pediatric Intensive Care Unit

The diagnostic and clinical utility of rapid whole genome sequencing (rWGS) for critically ill children in the intensive care unit (ICU) has been substantiated by multiple studies, but comprehensive cost-effectiveness evaluation of rWGS in the ICU outside of the neonatal age group is lacking. In this study, we examined cost data retrospectively for a cohort of 38 children in a regional pediatric ICU (PICU) who received rWGS. We identified seven of 17 patients who received molecular diagnoses by rWGS and had resultant changes in clinical management with sufficient clarity to permit cost and quality adjusted life years (QALY) modeling. Cost of PICU care was estimated to be reduced by $184,846 and a total of 12.1 QALYs were gained among these seven patients. The total cost of rWGS for patients and families for the entire cohort (38 probands) was $239,400. Thus, the net cost of rWGS was $54,554, representing $4,509 per QALY gained. This quantitative, retrospective examination of healthcare utilization associated with rWGS-informed medicine interventions in the PICU revealed approximately one-third of a QALY gained per patient tested at a cost per QALY that was approximately one-tenth of that typically sought for cost-effective new medical interventions. This evidence suggests that performance of rWGS as a first-tier test in selected PICU children with diseases of unknown etiology is associated with acceptable cost-per-QALY gained.

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA from body fluids to identify pathogens. The performance of mNGS testing of 182 body fluids from 160 patients with acute illness was evaluated using two sequencing platforms in comparison to microbiological testing using culture, 16S bacterial PCR and/or 28S-internal transcribed ribosomal gene spacer (28S-ITS) fungal PCR. Test sensitivity and specificity of detection were 79 and 91% for bacteria and 91 and 89% for fungi, respectively, by Illumina sequencing; and 75 and 81% for bacteria and 91 and 100% for fungi, respectively, by nanopore sequencing. In a case series of 12 patients with culture/PCR-negative body fluids but for whom an infectious diagnosis was ultimately established, seven (58%) were mNGS positive. Real-time computational analysis enabled pathogen identification by nanopore sequencing in a median 50-min sequencing and 6-h sample-to-answer time. Rapid mNGS testing is a promising tool for diagnosis of unknown infections from body fluids.

Partially automated whole-genome sequencing reanalysis of previously undiagnosed pediatric patients can efficiently yield new diagnoses

To investigate the diagnostic and clinical utility of a partially automated reanalysis pipeline, forty-eight cases of seriously ill children with suspected genetic disease who did not receive a diagnosis upon initial manual analysis of whole-genome sequencing (WGS) were reanalyzed at least 1 year later. Clinical natural language processing (CNLP) of medical records provided automated, updated patient phenotypes, and an automated analysis system delivered limited lists of possible diagnostic variants for each case. CNLP identified a median of 79 new clinical features per patient at least 1 year later. Compared to a standard manual reanalysis pipeline, the partially automated pipeline reduced the number of variants to be analyzed by 90% (range: 74%-96%). In 2 cases, diagnoses were made upon reinterpretation, representing an incremental diagnostic yield of 4.2% (2/48, 95% CI: 0.5–14.3%). Four additional cases were flagged with a possible diagnosis to be considered during subsequent reanalysis. Separately, copy number analysis led to diagnoses in two cases. Ongoing discovery of new disease genes and refined variant classification necessitate periodic reanalysis of negative WGS cases. The clinical features of patients sequenced as infants evolve rapidly with age. Partially automated reanalysis, including automated re-phenotyping through CNLP, has the potential to identify molecular diagnoses with reduced expert labor intensity.

Abstract B21: Childhood Cancer Molecular Map (C2M2) to define medulloblastoma heterogeneity and predict treatment response

Background: Medulloblastoma is a heterogenous group of tumors that collectively are the most common malignant brain tumor of childhood. Advances in treatment are required as one third of patients die from the disease, and those who survive suffer severe long-term side effects from therapy. The ability to sequence entire genome, methylome, and transcriptome of tumors provides the opportunity to identify underlying drivers of malignancy, predict treatment response, and develop novel therapies. A lack of reproducibility when comparing identified genetic mutations with treatment response is challenging because a single genetic change does not reflect the cellular state of a cancer cell in its entirety, which is expressing a multitude of genes. Computational methods allow for the creation of mapping systems that may more accurately describe the cellular state and thereby predict treatment response.

Objective: We used Childhood Cancer Molecular Map (C2M2) to define medulloblastoma heterogeneity and predict treatment response using patient-derived xenografts (PDX).

Methods: RNA transcription abundance from medulloblastoma samples published by Cho et al. were used to create C2M2. This was accomplished by analyzing the distribution of transcriptional abundance for each gene across all samples in order to select the genes that display the most asymmetric and non-Gaussian behavior. This delineated a “context score” for each gene, emphasizing those over- and underexpressed, allowing for the creation of a unique signature to model cellular states. The medulloblastoma samples from Cho et al. were then plotted onto the map based upon their RNA transcriptional abundance signatures, creating clusters of similar cellular states. Likewise, RNA transcription abundance from 20 PDX samples, for which drug response was known, was then mapped.

Results: C2M2 identified ten cellular states for medulloblastoma by which to define patient samples: SHH DNA repair, SHH glutamate signaling, SHH RNA repair, WNT, Photoreceptor and MYC (in which Group 3 medulloblastoma falls), Neuronal migration, Neuronal MAPK activation and Axonal (in which Group 4 medulloblastoma falls), and Homeobox activation. PDX samples for which drug response was known clustered similarly onto the map.

Conclusion: C2M2 using RNA transcriptional abundance from medulloblastoma samples could be used to predict drug response.

Citation Format: Huwate Yeerna, Benjamin Briggs, Jessica Rusert, Lukas Chavez, Jill Mesirov, Robert Wechsler-Reya, Pablo Tamayo. Childhood Cancer Molecular Map (C2M2) to define medulloblastoma heterogeneity and predict treatment response [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B21.

The Evaluation of Hematologic Screening and Perioperative Management in Patients with Noonan Syndrome: A Retrospective Chart Review

OBJECTIVES

To assess the potential impact of using screening recommendations for bleeding disorders in patients with Noonan syndrome on perioperative bleeding complications.

STUDY DESIGN

We performed a retrospective, single-site cohort study; patients were identified by query of the electronic medical record. All patients with a clinical diagnosis of Noonan syndrome over a 10-year period were included. Data on surgeries, hematologic evaluation, bleeding symptoms, and bleeding complications were extracted. Surgeries were graded as major or minor.

RESULTS

We identified 101 patients with Noonan syndrome, 70 of whom required surgery for a total of 164 procedures. Nine patients (9/70; 12.8%) had bleeding complications, occurring in those without comprehensive testing or perioperative intervention and undergoing major or dental surgery. Based on these findings, the risk of a bleeding complication for patients with Noonan syndrome who did not have comprehensive testing or perioperative intervention was 6.2% (95% CI 2.3%-10.1%), indicating the number needed to treat or screen would be 16 to prevent 1 bleeding complication (95% CI 9.9-43.9). The majority of patients had either no or incomplete evaluation (59 of 101; 58.4%).

CONCLUSIONS

With proper evaluation and management, the bleeding risk in patients with Noonan syndrome can be minimized. Efforts are needed to address the knowledge and implementation gap in this evaluation.

Pan-viral serology implicates enteroviruses in acute flaccid myelitis

Since 2012, the United States has experienced a biennial spike in pediatric acute flaccid myelitis (AFM).^1–6 Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF).² We interrogated CSF from children with AFM (n=42) and pediatric other neurologic disease controls (n=58) for intrathecal anti-viral antibodies using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). We also performed metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n=20 cases), both unbiased and with targeted enrichment for EVs. Using VirScan, the only viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n=29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n=22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology identified frequently high levels of CSF EV-specific antibodies in AFM compared to controls, providing further evidence for a causal role of non-polio EVs in AFM.

Biallelic loss of GNAS in a patient with pediatric medulloblastoma

Genome sequencing was performed on matched normal and tumor tissue from a 6.5-yr-old boy with a diagnosis of recurrent medulloblastoma. A pathogenic heterozygous c.432+1G>A canonical splice donor site variant in GNAS was detected on analysis of blood DNA. Analysis of tumor DNA showed the same splice variant along with copy-neutral loss of heterozygosity on Chromosome 20 encompassing GNAS, consistent with predicted biallelic loss of GNAS in the tumor specimen. This case strengthens the evidence implicating GNAS as a tumor-suppressor gene in medulloblastoma and highlights a scenario in which therapeutics targeting the cAMP pathway may be of great utility.

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

BACKGROUND

Metagenomic next-generation sequencing (NGS) of cerebrospinal fluid (CSF) has the potential to identify a broad range of pathogens in a single test.

METHODS

In a 1-year, multicenter, prospective study, we investigated the usefulness of metagenomic NGS of CSF for the diagnosis of infectious meningitis and encephalitis in hospitalized patients. All positive tests for pathogens on metagenomic NGS were confirmed by orthogonal laboratory testing. Physician feedback was elicited by teleconferences with a clinical microbial sequencing board and by surveys. Clinical effect was evaluated by retrospective chart review.

RESULTS

We enrolled 204 pediatric and adult patients at eight hospitals. Patients were severely ill: 48.5% had been admitted to the intensive care unit, and the 30-day mortality among all study patients was 11.3%. A total of 58 infections of the nervous system were diagnosed in 57 patients (27.9%). Among these 58 infections, metagenomic NGS identified 13 (22%) that were not identified by clinical testing at the source hospital. Among the remaining 45 infections (78%), metagenomic NGS made concurrent diagnoses in 19. Of the 26 infections not identified by metagenomic NGS, 11 were diagnosed by serologic testing only, 7 were diagnosed from tissue samples other than CSF, and 8 were negative on metagenomic NGS owing to low titers of pathogens in CSF. A total of 8 of 13 diagnoses made solely by metagenomic NGS had a likely clinical effect, with 7 of 13 guiding treatment.

CONCLUSIONS

Routine microbiologic testing is often insufficient to detect all neuroinvasive pathogens. In this study, metagenomic NGS of CSF obtained from patients with meningitis or encephalitis improved diagnosis of neurologic infections and provided actionable information in some cases. (Funded by the National Institutes of Health and others; PDAID ClinicalTrials.gov number, NCT02910037.).

Novel Factor XIII variant identified through whole-genome sequencing in a child with intracranial hemorrhage

Pediatric stroke can be either hemorrhagic or ischemic, with ∼5% of hemorrhagic strokes being caused by genetic coagulopathies. We report an 8 mo old presenting with a hemorrhagic stroke caused by severe Factor XIII deficiency (OMIM # 613225) in whom rapid whole-genome sequencing identified a novel variant in the F13A1 gene c.1352_1353delAT (p.His451ArgfsTer29).

2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases

Background

Recent studies have demonstrated the utility of metagenomic next-generation sequencing (mNGS) and RNA gene expression sequencing (RNA-Seq) for identifying causes of infections. Although these approaches have been largely tested to date using established sequencing platforms such as the Illumina HiSeq, the use of nanopore sequencing on the MinION sequencer (Oxford Nanopore Technologies) is attractive given rapid library preparation and real-time analysis of sequencing data resulting in accelerated sample-to-answer turnaround times.

Methods

We have developed a rapid molecular concatemerization library approach to increase the throughput of the nanopore sequencer analysis for metagenomic and RNA-Seq approaches. We have also developed a pipeline (SURPIrt, “Sequence-based ultra-rapid pathogen identification, real-time”) that allows for real-time, simultaneous metagenomic and transcriptomic analyses on the same sample.

Results

With the use of molecular concatemerization library approach, we show that metagenomic and transcriptomic data generated on the MinION are comparable to those on the Illumina platform, yet can be collected and analyzed in significantly less time (6 hours vs. 2–3 days).

Conclusion

Here we demonstrate simultaneous metagenomic and RNA-Seq analyses on a nanopore-based sequencing platform with real-time analysis of results. We foresee that this approach could be leveraged into a rapid screening test for diagnosis of infectious diseases in both hospital and field settings.

Disclosures

All authors: No reported disclosures.

Tularemia-induced erythema multiforme minor in an 11-year-old girl

Tularemia is a rare and potentially life-threatening infection caused by the highly infectious gram-negative coccobacillus Francisella tularensis. We present the case of an 11-year old girl who presented with erythema multiforme minor in the setting of an indolent but progressive soft tissue infection and was found to have tularemia. We review the role of dermatologists in identifying the features of and complications associated with this rare zoonosis and discuss the potential effect of climate change on its incidence.