Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by experts in both adult and pediatric laboratory and clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including arboviral Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also addressed. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.

Tau and Aβ42 in lavage fluid of pneumonia patients are associated with end-organ dysfunction: A prospective exploratory study

BACKGROUND

Bacterial pneumonia and sepsis are both common causes of end-organ dysfunction, especially in immunocompromised and critically ill patients. Pre-clinical data demonstrate that bacterial pneumonia and sepsis elicit the production of cytotoxic tau and amyloids from pulmonary endothelial cells, which cause lung and brain injury in naïve animal subjects, independent of the primary infection. The contribution of infection-elicited cytotoxic tau and amyloids to end-organ dysfunction has not been examined in the clinical setting. We hypothesized that cytotoxic tau and amyloids are present in the bronchoalveolar lavage fluid of critically ill patients with bacterial pneumonia and that these tau/amyloids are associated with end-organ dysfunction.

METHODS

Bacterial culture-positive and culture-negative mechanically ventilated patients were recruited into a prospective, exploratory observational study. Levels of tau and Aβ42 in, and cytotoxicity of, the bronchoalveolar lavage fluid were measured. Cytotoxic tau and amyloid concentrations were examined in comparison with patient clinical characteristics, including measures of end-organ dysfunction.

RESULTS

Tau and Aβ42 were increased in culture-positive patients (n = 49) compared to culture-negative patients (n = 50), independent of the causative bacterial organism. The mean age of patients was 52.1 ± 16.72 years old in the culture-positive group and 52.78 ± 18.18 years old in the culture-negative group. Males comprised 65.3% of the culture-positive group and 56% of the culture-negative group. Caucasian culture-positive patients had increased tau, boiled tau, and Aβ42 compared to both Caucasian and minority culture-negative patients. The increase in cytotoxins was most evident in males of all ages, and their presence was associated with end-organ dysfunction.

CONCLUSIONS

Bacterial infection promotes the generation of cytotoxic tau and Aβ42 within the lung, and these cytotoxins contribute to end-organ dysfunction among critically ill patients. This work illuminates an unappreciated mechanism of injury in critical illness.

Differential activation of programmed cell death in patients with severe SARS-CoV-2 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe lower airway disease and death in a subset of patients. Knowledge on the relative contribution of programmed cell death (PCD) to lung pathology is limited to few human autopsy studies with small sample size/scope, in vitro cell culture, and experimental model systems. In this study, we sought to identify, localize, and quantify activation of apoptosis, ferroptosis, pyroptosis, and necroptosis in FFPE lung tissues from patients that died from severe SARS-CoV-2 infection (n = 28) relative to uninfected controls (n = 13). Immunofluorescence (IF) staining, whole-slide imaging, and Image J software was used to localize and quantify expression of SARS-CoV-2 nucleoprotein and the following PCD protein markers: cleaved Caspase-3, pMLKL, cleaved Gasdermin D, and CD71, respectively. IF showed differential activation of each PCD pathway in infected lungs and dichotomous staining for SARS-CoV-2 nucleoprotein enabling distinction between high (n = 9) vs low viral burden (n = 19). No differences were observed in apoptosis and ferroptosis in SARS-CoV-2 infected lungs relative to uninfected controls. However, both pyroptosis and necroptosis were significantly increased in SARS-CoV-2-infected lungs. Increased pyroptosis was observed in SARS-CoV-2 infected lungs, irrespective of viral burden, suggesting an inflammation-driven mechanism. In contrast, necroptosis exhibited a very strong positive correlation with viral burden (R2 = 0.9925), suggesting a direct SARS-CoV-2 mediated effect. These data indicate a possible novel mechanism for viral-mediated necroptosis and a potential role for both lytic programmed cell death pathways, necroptosis and pyroptosis, in mediating infection outcome.

Priorities and Progress in Gram-positive Bacterial Infection Research by the Antibacterial Resistance Leadership Group: A Narrative Review

The Antibacterial Resistance Leadership Group (ARLG) has prioritized infections caused by gram-positive bacteria as one of its core areas of emphasis. The ARLG Gram-positive Committee has focused on studies responding to 3 main identified research priorities: (1) investigation of strategies or therapies for infections predominantly caused by gram-positive bacteria, (2) evaluation of the efficacy of novel agents for infections caused by methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci, and (3) optimization of dosing and duration of antimicrobial agents for gram-positive infections. Herein, we summarize ARLG accomplishments in gram-positive bacterial infection research, including studies aiming to (1) inform optimal vancomycin dosing, (2) determine the role of dalbavancin in MRSA bloodstream infection, (3) characterize enterococcal bloodstream infections, (4) demonstrate the benefits of short-course therapy for pediatric community-acquired pneumonia, (5) develop quality of life measures for use in clinical trials, and (6) advance understanding of the microbiome. Future studies will incorporate innovative methodologies with a focus on interventional clinical trials that have the potential to change clinical practice for difficult-to-treat infections, such as MRSA bloodstream infections.

Interferon-dependent signaling is critical for viral clearance in airway neutrophils

Neutrophilic inflammation characterizes several respiratory viral infections, including COVID-19-related acute respiratory distress syndrome, although its contribution to disease pathogenesis remains poorly understood. Blood and airway immune cells from 52 patients with severe COVID-19 were phenotyped by flow cytometry. Samples and clinical data were collected at 2 separate time points to assess changes during ICU stay. Blockade of type I interferon and interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) signaling was performed in vitro to determine their contribution to viral clearance in A2 neutrophils. We identified 2 neutrophil subpopulations (A1 and A2) in the airway compartment, where loss of the A2 subset correlated with increased viral burden and reduced 30-day survival. A2 neutrophils exhibited a discrete antiviral response with an increased interferon signature. Blockade of type I interferon attenuated viral clearance in A2 neutrophils and downregulated IFIT3 and key catabolic genes, demonstrating direct antiviral neutrophil function. Knockdown of IFIT3 in A2 neutrophils led to loss of IRF3 phosphorylation, with consequent reduced viral catabolism, providing the first discrete mechanism to our knowledge of type I interferon signaling in neutrophils. The identification of this neutrophil phenotype and its association with severe COVID-19 outcomes emphasizes its likely importance in other respiratory viral infections and potential for new therapeutic approaches in viral illness.

Immunity to pathogenic fungi in the eye

Fusarium, Aspergillus and Candida are important fungal pathogens that cause visual impairment and blindness in the USA and worldwide. This review will summarize the epidemiology and clinical features of corneal infections and discuss the immune and inflammatory responses that play an important role in clinical disease. In addition, we describe fungal virulence factors that are required for survival in infected corneas, and the activities of neutrophils in fungal killing, tissue damage and cytokine production.

Mucociliary transport deficiency and disease progression in Syrian hamsters with SARS-CoV-2 infection

Substantial clinical evidence supports the notion that ciliary function in the airways is important in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, the extent or nature of impairment of mucociliary transport (MCT) in in vivo models remains unknown. We hypothesize that SARS-CoV-2 infection results in MCT deficiency in the airways of golden Syrian hamsters that precedes pathological injury in lung parenchyma. Micro-optical coherence tomography was used to quantitate functional changes in the MCT apparatus. Both genomic and subgenomic viral RNA pathological and physiological changes were monitored in parallel. We show that SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 days postinfection (dpi) in hamsters, principally due to 79% diminished airway coverage of motile cilia. Correlating quantitation of physiological, virological, and pathological changes reveals steadily descending infection from the upper airways to lower airways to lung parenchyma within 7 dpi. Our results indicate that functional deficits of the MCT apparatus are a key aspect of COVID-19 pathogenesis, may extend viral retention, and could pose a risk factor for secondary infection. Clinically, monitoring abnormal ciliated cell function may indicate disease progression. Therapies directed toward the MCT apparatus deserve further investigation.

Coronary Stent Abscess in the Setting of Arteriovenous Graft Infection following COVID-19: An Autopsy Case Report

While rare, coronary stent infections present with significant mortality-with most infections and further complications occurring within months of percutaneous coronary intervention (PCI). Here, we discuss a post-COVID-19 patient who presented approximately one year after PCI for declotting of an arteriovenous graft (AVG). Upon admission, the patient was found to be bacteremic with multilobar pneumonia and an infection of the AVG. Empiric antibiotics were started, and blood cultures were subsequently positive for MRSA. Removal of the AVG was unsuccessful, and two days after admission, the patient passed. Autopsy revealed a perivascular abscess in the RCA near the origin of the stent with a ground section of the RCA with stent revealing abundant calcific atherosclerosis and marked necrosis of the artery wall. The cause of death was determined to be sepsis complicating coronary artery disease and chronic renal failure.

359. The Clinical Utility of the GenMark Dx ePlex® Fungal Blood Culture Identification Panel

Background

The GenMark ePlex® Fungal Blood Culture Identification (BCID) Panel utilizes electrowetting technology to detect 15 most common causes of fungemia. Rapid identification of fungal species and innate resistance patterns enable improved antifungal stewardship.

Methods

In this prospective study, aliquots of the initial diagnostic blood culture bottle with fungal organisms detected on Gram Stain (n=61) received standard of care (SOC) fungal identification in two study periods. MALDI-TOF MS was utilized in both phases. BCID-FP results were not reported to treating clinicians during the pre-implementation phase. After 35 isolates, BCID-FP results became part of the SOC for all bloodstream infections (implementation phase) with results available to providers. Chart reviews were performed to assess risk factors for candidemia and evaluate the potential then actual impact of the BCID-FP on the time to organism identification, treatment, and patient outcomes.

Results

A total of 61 patients were included in the final analysis, 35 in the pre-implementation phase and 26 in the post-implementation phase (Table 1). C. albicans was most common, followed by C. glabrata and C. parapsilosis. The cohort includes two cases of Cryptococcus as well as two rare yeasts unable to be identified by BCID-FP and requiring the state lab identification (Table 2). Overall outcomes and differences between groups are seen in Table 3. The BCID-FP identified species 1.4 days faster compared to SOC methods across all patients, 1.12 days in the pre-implementation phase vs. 1.81 days in the post-implementation phase. In 32 patients (52%), the BCID-FP allowed for an earlier change in antifungal therapy for species with known low risk of fluconazole resistance.

Conclusion

The BCID-FP enabled earlier fungal identification compared to SOC identification. Earlier identification allows for earlier antifungal stewardship as well as better empiric therapy for non-Candida­ fungal pathogens. Empiric therapy rates were low with high mortality rates, indicative of an ongoing need for improving the care of patients with fungemia.

Disclosures

Todd P. McCarty, MD, GenMark Dx: Grant/Research Support|GenMark Dx: Honoraria Sixto M. Leal, Jr., MD, PhD, GenMark Dx: Grant/Research Support|GenMark Dx: Honoraria.

186. Klebsiella aerogenes: Are there implications to taxonomic accuracy?

Background

With advances in genomics, microbiologists can accurately rename existing bacteria which may cause confusion among clinicians familiar with prior names. Limited investigation is available on the clinical impact of these name changes. University of Alabama at Birmingham Hospital microbiology updated Klebsiella aerogenes in the electronic medical record (EMR) to "Klebsiella (Enterobacter) aerogenes" to reflect change in nomenclature. Therapy selection differs between Klebsiella pneumoniae and Enterobacter spp. due to differences in Ambler Class C (AmpC) beta-lactamase production. Our Antimicrobial Stewardship Program previously implemented selective and cascaded susceptibility reporting for E. aerogenes to guide antibiotic selection which remained after nomenclature change. The goal of this study is to determine if the change led to inappropriate antibiotic use.

Methods

We reviewed blood culture data from May 2016-2020 which grew Enterobacter aerogenes or Klebsiella "Enterobacter" aerogenes. We excluded polymicrobial blood cultures, patients aged 18 and under, and patients who died within 48 hours of drawing blood cultures. Appropriate therapy was defined as an antibiotic with reported susceptibility with consideration of AmpC induction for a duration appropriate to clinical syndrome with minimum of 7 days. We recorded patient demographics, nature of therapy, and clinical outcomes. We performed comparative analysis with descriptive statistics to compare the two groups.

Results

There were 38 patients with K. aerogenes bacteremia, 21 patients prior to name change and 17 afterwards. None were ESBL. Cefepime was most often used directed inpatient therapy while oral ciprofloxacin was the most common outpatient regimen with no use of ceftriaxone. Prior to name change, there was one case (4.76%) that did not receive targeted AmpC therapy while there were two afterwards (11.8%), one of which decided by the ID consult team. Table 1

Demographics (Data presented as No. (%)) Table 2

Microbiology and Outcomes (Data presented as No. (%)) Table 3

Antimicrobial Selection. One patient that received 72 hours of appropriate therapy but died prior to completion of therapy. This was labeled labelled as appropriate therapy.

Conclusion

Care must be taken when taxonomic changes of clinically relevant bacteria may potentially affect optimization of antibiotics. As the ID consultants, we must be aware of these name changes and provide up to date recommendations. Cascade reporting and documentation in the EMR may be helpful to reduce morbidity related to changes in nomenclature.

Disclosures

Sixto M. Leal, Jr., MD, PhD, GenMark Dx: Grant/Research Support|GenMark Dx: Honoraria.

A single intranasal administration of AdCOVID protects against SARS-CoV-2 infection in the upper and lower respiratory tracts

The coronavirus disease 2019 (COVID-19) pandemic has illustrated the critical need for effective prophylactic vaccination to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Intranasal vaccination is an attractive approach for preventing COVID-19 as the nasal mucosa is the site of initial SARS-CoV-2 entry and viral replication prior to aspiration into the lungs. We previously demonstrated that a single intranasal administration of a candidate adenovirus type 5-vectored vaccine encoding the receptor-binding domain of the SARS-CoV-2 spike protein (AdCOVID) induced robust immunity in both the airway mucosa and periphery, and completely protected K18-hACE2 mice from lethal SARS-CoV-2 challenge. Here we show that a single intranasal administration of AdCOVID limits viral replication in the nasal cavity of K18-hACE2 mice. AdCOVID also induces sterilizing immunity in the lungs of mice as reflected by the absence of infectious virus. Finally, AdCOVID prevents SARS-CoV-2 induced pathological damage in the lungs of mice. These data show that AdCOVID not only limits viral replication in the respiratory tract, but it also prevents virus-induced inflammation and immunopathology following SARS-CoV-2 infection.

COVID-19 Vaccination and Remdesivir are Associated With Protection From New or Increased Levels of Donor-Specific Antibodies Among Kidney Transplant Recipients Hospitalized With COVID-19

Alloimmune responses in kidney transplant (KT) patients previously hospitalized with COVID-19 are understudied. We analyzed a cohort of 112 kidney transplant recipients who were hospitalized following a positive SARS-CoV-2 test result during the first 20 months of the COVID-19 pandemic. We found a cumulative incidence of 17% for the development of new donor-specific antibodies (DSA) or increased levels of pre-existing DSA in hospitalized SARS-CoV-2-infected KT patients. This risk extended 8 months post-infection. These changes in DSA status were associated with late allograft dysfunction. Risk factors for new or increased DSA responses in this KT patient cohort included the presence of circulating DSA pre-COVID-19 diagnosis and time post-transplantation. COVID-19 vaccination prior to infection and remdesivir administration during infection were each associated with decreased likelihood of developing a new or increased DSA response. These data show that new or enhanced DSA responses frequently occur among KT patients requiring admission with COVID-19 and suggest that surveillance, vaccination, and antiviral therapies may be important tools to prevent alloimmunity in these individuals.

COVID-19 Causes Ciliary Dysfunction as Demonstrated by Human Intranasal Micro-Optical Coherence Tomography Imaging

Severe acute respiratory syndrome coronavirus (SARS-CoV-2), causative agent of coronavirus disease 2019 (COVID-19), binds via ACE2 receptors, highly expressed in ciliated cells of the nasal epithelium. Micro-optical coherence tomography (μOCT) is a minimally invasive intranasal imaging technique that can determine cellular and functional dynamics of respiratory epithelia at 1-μm resolution, enabling real time visualization and quantification of epithelial anatomy, ciliary motion, and mucus transport. We hypothesized that respiratory epithelial cell dysfunction in COVID-19 will manifest as reduced ciliated cell function and mucociliary abnormalities, features readily visualized by μOCT. Symptomatic outpatients with SARS-CoV-2 aged ≥ 18 years were recruited within 14 days of symptom onset. Data was interpreted for subjects with COVID-19 (n=13) in comparison to healthy controls (n=8). Significant reduction in functional cilia, diminished ciliary beat frequency, and abnormal ciliary activity were evident. Other abnormalities included denuded epithelium, presence of mucus rafts, and increased inflammatory cells. Our results indicate that subjects with mild but symptomatic COVID-19 exhibit functional abnormalities of the respiratory mucosa underscoring the importance of mucociliary health in viral illness and disease transmission. Ciliary imaging enables investigation of early pathogenic mechanisms of COVID-19 and may be useful for evaluating disease progression and therapeutic response.

Graphical abstract

Meta-analysis of the robustness of COVID-19 diagnostic kit performance during the early pandemic

BACKGROUND

Accurate detection of SARS-CoV-2 is necessary to mitigate the COVID-19 pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19.

METHODS

We reviewed 85 studies (21 530 patients), published from five regions of the world, to highlight issues involved in the diagnosis of COVID-19 in the early phase of the pandemic. All relevant articles, published up to 31 May 2020, in PubMed, BioRiXv, MedRiXv and Google Scholar, were included. We evaluated the qualitative (9749 patients) and quantitative (10 355 patients) performance of RT-PCR and serologic diagnostic tests for real-world samples, and assessed the concordance (5538 patients) between test performance in meta-analyses. Synthesis of results was done using random effects modelling and bias was evaluated according to QUADAS-2 guidelines.

RESULTS

The RT-PCR tests exhibited heterogeneity in the primers and reagents used. Of 1957 positive RT-PCR COVID-19 participants, 1585 had positive serum antibody (IgM±IgG) tests (sensitivity 0.81, 95% CI 0.66 to 0.90). While 3509 of 3581 participants RT-PCR negative for COVID-19 were found negative by serology testing (specificity 0.98, 95% CI 0.94 to 0.99). The chemiluminescent immunoassay exhibited the highest sensitivity, followed by ELISA and lateral flow immunoassays. Serology tests had higher sensitivity and specificity for laboratory approval than for real-world reporting data.

DISCUSSION

The robustness of the assays/platforms is influenced by variability in sampling and reagents. Serological testing complements and may minimise false negative RT-PCR results. Lack of standardised assay protocols in the early phase of pandemic might have contributed to the spread of COVID-19.

Mucociliary Transport Deficiency and Disease Progression in Syrian Hamsters with SARS-CoV-2 Infection

Substantial clinical evidence supports the notion that ciliary function in the airways plays an important role in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, consequent impaired mucociliary transport (MCT) remains unknown for the intact MCT apparatus from an in vivo model of disease. Using golden Syrian hamsters, a common animal model that recapitulates human COVID-19, we quantitatively followed the time course of physiological, virological, and pathological changes upon SARS-CoV-2 infection, as well as the deficiency of the MCT apparatus using micro-optical coherence tomography, a novel method to visualize and simultaneously quantitate multiple aspects of the functional microanatomy of intact airways. Corresponding to progressive weight loss up to 7 days post-infection (dpi), viral detection and histopathological analysis in both the trachea and lung revealed steadily descending infection from the upper airways, as the main target of viral invasion, to lower airways and parenchymal lung, which are likely injured through indirect mechanisms. SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 dpi, largely due to diminished motile ciliation coverage, but not airway surface liquid depth, periciliary liquid depth, or cilia beat frequency of residual motile cilia. Further analysis indicated that the fewer motile cilia combined with abnormal ciliary motion of residual cilia contributed to the delayed MCT. The time course of physiological, virological, and pathological progression suggest that functional deficits of the MCT apparatus predispose to COVID-19 pathogenesis by extending viral retention and may be a risk factor for secondary infection. As a consequence, therapies directed towards the MCT apparatus deserve further investigation as a treatment modality.

200. Prospective Evaluation of the GenMark Dx ePlex® Blood Culture Identification Gram Positive Panel

Background

The ePlex BCID Gram-Positive (GP) panel utilizes electrowetting technology to detect the most common causes of GP bacteremia (20 targets) and 4 antimicrobial resistance genes in positive blood culture bottles. Rapid detection of intrinsic vancomycin resistance and acquired resistance genes (mecA, mecC, vanA, vanB) enables early optimization of antimicrobial therapy whereas early detection of common contaminants decreases unnecessary antibiotic utilization and hospitalizations.

Methods

In this prospective study, we evaluated the performance of the BCID-GP panel compared to traditional standard of care culture and susceptibility testing with organism identification using the BioMerieux Vitek MS Matrix Assisted Laser Desorption Ionization (MALDI) Time of Flight mass spectrometry. Samples submitted for standard of care testing in Biomerieux BacT/Alert resin FA/FN blood culture bottles on the BacT/Alert VIRTUO automated blood culture system with GP bacteria on direct exam (n=100) were included.

Results

All GP bacteria were represented on the BCID-GP panel, most tests 97/100 (97%) yielded valid results, 53 common skin contaminants (50 coagulase negative staphylococci (CNS), 2 Bacillus, 1 Corynebacterium) were identified, and 7/7 coinfections with Gram negative (GN) bacteria were detected by the Pan GN target and identified by the BCID-GN panel. Discordant analyses revealed a positive percent agreement (PPA) of 96/97 (99%) with 1 false negative CNS and a negative percent agreement (NPA) of 92/97 (94.8%) with 5 false positives for either S. epidermidis or Corynebacterium. Detection of vanA yielded a PPA of 4/4 and NPA of 9/9. mecA gene detection exhibited a PPA of 14/14 and NPA of 14/14 for S. aureus and a PPA of 31/32 (97%) and NPA of 16/16 for coagulase negative staphylococci with 1 false negative methicillin resistant S. epidermidis.

Conclusion

Detection of acquired vancomycin resistance (n=4) and absence of mecA gene detection in Staphylococcus species (n=30) represent opportunities for early optimization of antimicrobial therapy in 34/100 (34%) of samples. The BCID-GP panel provides rapid accurate detection of resistant isolates and common contaminants enabling high quality data driven optimization of antimicrobial therapy.

Disclosures

Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark (Grant/Research Support, Other Financial or Material Support, Honoraria for Research Presentation)T2 Biosystems (Consultant) Sixto M. Leal, Jr., MD, PhD, Abnova (Grant/Research Support)AltImmune (Grant/Research Support)Amplyx Pharmaceuticals (Grant/Research Support)Astellas Pharmaceuticals (Grant/Research Support)CNINE Dx (Grant/Research Support)GenMark Diagnostics (Grant/Research Support, Other Financial or Material Support, Honoraria- Research Presentation)IHMA (Grant/Research Support)IMMY Dx (Grant/Research Support)JMI/Sentry (Grant/Research Support)mFluiDx Dx (Grant/Research Support)SpeeDx Dx (Grant/Research Support)Tetraphase Pharmaceuticals (Grant/Research Support)

214. Prospective Evaluation of the GenMark Dx ePlex® Blood Culture Identification Gram Negative Panel

Background

The ePlex BCID Gram-Negative (GN) panel utilizes electrowetting technology to detect the most common causes of GN bacteremia (21 targets) and 6 antimicrobial resistance genes from positive blood culture bottles. Rapid detection of extended spectrum β-lactamases (ESBL; CTX-M), carbapenemases (KPC, NDM, IMP, VIM, OXA 23/48), and highly resistant bacteria such as Stenotrophomonas maltophilia enables early optimization of antimicrobial therapy.

Methods

In this prospective study, we evaluated the performance of the BCID-GN panel compared to traditional standard of care culture and susceptibility testing with organism identification using the BioMerieux Vitek MS Matrix Assisted Laser Desorption Ionization (MALDI) Time of Flight mass spectrometry. Samples submitted for standard of care testing in Biomerieux BacT/Alert resin FA/FN blood culture bottles on the BacT/Alert VIRTUO automated blood culture system with GN bacteria on direct exam (n=108) were included.

Results

All but two GN bacteria identified by MALDI were represented on the BCID-GN Panel (106/108, 98.1%) and most tests (107/108, 99.1%) yielded valid results. Discordant analyses revealed a positive percent agreement (PPA) of 102/105 (97.2%) with 3 false negatives (2 pan-susceptible Enterobacterales, 1 ESBL E.coli) and a negative percent agreement (NPA) of 105/105 (100%). Consistent with alternative resistance mechanisms, only 8/12 (66.7%) of Enterobacterales with resistance to 3rd generation cephalosporins harbored the CTX-M gene. In contrast, 8/8 (100%) of isolates from samples harboring the CTX-M gene were resistant to 3rd generation cephalosporins.

Conclusion

Detection of 1 S. maltophilia, 1 Acinetobacter baumannii expressing OXA 23/48, and 8 Enterobacterales expressing CTX-M represent opportunities for early optimization of antimicrobial therapy in 10/108 (9.3%) of samples. The BCID-GN Panel provides rapid accurate detection of resistant gram negative bacteria enabling high quality data driven optimization of antimicrobial therapy.

Disclosures

Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark (Grant/Research Support, Other Financial or Material Support, Honoraria for Research Presentation)T2 Biosystems (Consultant) Sixto M. Leal, Jr., MD, PhD, Abnova (Grant/Research Support)AltImmune (Grant/Research Support)Amplyx Pharmaceuticals (Grant/Research Support)Astellas Pharmaceuticals (Grant/Research Support)CNINE Dx (Grant/Research Support)GenMark Diagnostics (Grant/Research Support, Other Financial or Material Support, Honoraria- Research Presentation)IHMA (Grant/Research Support)IMMY Dx (Grant/Research Support)JMI/Sentry (Grant/Research Support)mFluiDx Dx (Grant/Research Support)SpeeDx Dx (Grant/Research Support)Tetraphase Pharmaceuticals (Grant/Research Support)

1022. Evaluating the Impact of GenMark Dx ePlex® Blood Culture Identification (BCID) on Gram-negative Bloodstream Infections

Background

The GenMark Dx ePlex BCID Gram-Negative (GN) panel utilizes electrowetting technology to detect the most common causes of GN bacteremia (21 targets) and 6 antimicrobial resistance (AMR) genes from positive blood culture (BC) bottles. Rapid detection of extended spectrum β-lactamases (ESBL: CTX-M & carbapenemases: KPC, NDM, IMP, VIM, OXA 23/48), and highly resistant bacteria such as S. maltophilia should enable early optimization of antimicrobial therapy.

Methods

In this prospective study, aliquots of positive BC bottles with GN bacteria detected on Gram stain (GS) (n=108) received standard of care (SOC) culture and antimicrobial susceptibility testing (AST). Additionally, samples were evaluated with the BCID-GN panel but only SOC results were reported in the EMR and available to inform clinical decisions. Chart reviews were performed to evaluate the impact of the BCID-GN panel on the time to organism identification, AST results, and optimization of antimicrobial therapy.

Results

A total of 108 patients are included in the analysis (Table 1). Escherichia coli was the most common bacteria identified followed by Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter species (Table 2). There were 11 (10.2%) polymicrobial bacteremias. Repeat BCs were obtained in 68 (63%) patients of which 13 (19%) were persistently positive. Eight (7%) patients had evidence of additional gram-positive (GP) pathogens. Organism identification occurred 26.7 hours faster than culture. In conjunction with GS, negative pan-GP marker data could have helped providers make the decision to remove GP antibiotic coverage in 63 (58%) patients. Narrowing from empiric meropenem could have occurred in 5 patients. Of 10 individuals infected with resistant isolates (1 S. maltophilia, 1 OXA 23/48, and 8 CTX-M) empiric therapy was ineffective in 4 (40%) cases. Optimization of antimicrobial therapy for 9 (8.3%) patients could have occurred an average of 52.4 hours earlier than standard methods.

Table 1. Patient demographics and co-morbidities.

Table 2. Gram-negative bacteria frequency.

Conclusion

The BCID-GN panel enabled earlier time to optimal treatment of highly resistant bacteria as well as multiple opportunities for narrowing gram negative spectrum and a higher degree of certainty in cessation of broad-spectrum gram-positive antibiotics

Disclosures

Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark (Grant/Research Support, Other Financial or Material Support, Honoraria for Research Presentation)T2 Biosystems (Consultant) Sixto M. Leal, Jr., MD, PhD, Abnova (Grant/Research Support)AltImmune (Grant/Research Support)Amplyx Pharmaceuticals (Grant/Research Support)Astellas Pharmaceuticals (Grant/Research Support)CNINE Dx (Grant/Research Support)GenMark Diagnostics (Grant/Research Support, Other Financial or Material Support, Honoraria- Research Presentation)IHMA (Grant/Research Support)IMMY Dx (Grant/Research Support)JMI/Sentry (Grant/Research Support)mFluiDx Dx (Grant/Research Support)SpeeDx Dx (Grant/Research Support)Tetraphase Pharmaceuticals (Grant/Research Support)

1027. Earlier Is Better: Progress Toward Decreased Time to Optimal Therapy and Improved Antibiotic Stewardship for Gram-positive Bloodstream Infections Through Use of GenMark Dx ePlex system

Background

The ePlex BCID Gram-Positive (GP) panel utilizes electrowetting technology to detect the most common causes of GP bacteremia (20 targets) and 4 antimicrobial resistance (AMR) genes in positive blood culture (BC) bottles. Rapid detection of intrinsic vancomycin resistance and acquired resistance genes (mecA, mecC, vanA, vanB) enables early optimization of antimicrobial therapy whereas early detection of common contaminants is expected to decrease unnecessary antibiotic utilization and hospitalizations.

Methods

In this prospective study, aliquots of BC bottles with GP bacteria detected on Gram stain (GS) (n=101) received standard of care (SOC) culture and antimicrobial susceptibility testing (AST). Additionally, samples were evaluated with the BCID-GP panel but only SOC results were reported in the EMR and available to inform clinical decisions. Patients were excluded if the sample was a subsequent culture in a persistent episode of bacteremia (n=17) or if the assay failed (n=4). Chart review was performed to evaluate the expected impact of the BCID-GP panel on the time to organism identification, AST results, and optimization of antimicrobial therapy.

Results

A total of 80 patients were included in the final analysis (Table 1). S. epidermidis was the most common bacteria identified, followed by S. aureus, and other coagulase-negative staphylococci. Thirty-nine patients with staphylococci (48.8%) had the mecA gene detected and 2 patients with E. faecium had the vanA gene detected. The BCID-GP panel saved a mean of 24.4 hours (h) to identification and 48.3h to susceptibility testing compared to standard methods across all patients. In 38 patients (47.5%), the BCID-GP panel result could have enabled an earlier change in antibiotic therapy. Table 2 highlights opportunities to optimize antimicrobial therapy 53.4h earlier for 16 (20%) patients with organisms expressing AMR genes, 29.2h earlier for 8 (10%) patients infected with organisms, such as streptococci, with very low resistance rates, and to stop antimicrobial therapy 42.9h earlier for 14 (17.5%) patients with contaminated blood cultures.

Conclusion

The BCID-GP panel could have enabled earlier optimization or stopping of antibiotics in many patients with significant time savings compared to standard laboratory methods.

Disclosures

Todd P. McCarty, MD, Cidara (Grant/Research Support)GenMark (Grant/Research Support, Other Financial or Material Support, Honoraria for Research Presentation)T2 Biosystems (Consultant) Sixto M. Leal, Jr., MD, PhD, Abnova (Grant/Research Support)AltImmune (Grant/Research Support)Amplyx Pharmaceuticals (Grant/Research Support)Astellas Pharmaceuticals (Grant/Research Support)CNINE Dx (Grant/Research Support)GenMark Diagnostics (Grant/Research Support, Other Financial or Material Support, Honoraria- Research Presentation)IHMA (Grant/Research Support)IMMY Dx (Grant/Research Support)JMI/Sentry (Grant/Research Support)mFluiDx Dx (Grant/Research Support)SpeeDx Dx (Grant/Research Support)Tetraphase Pharmaceuticals (Grant/Research Support)

Diagnosis of Clostridioides difficile infection by analysis of volatile organic compounds in breath, plasma, and stool: A cross-sectional proof-of-concept study

Clostridioides difficile infection (CDI) is an important infectious cause of antibiotic-associated diarrhea, with significant morbidity and mortality. Current diagnostic algorithms are based on identifying toxin by enzyme immunoassay (EIA) and toxin gene by real-time polymerase chain reaction (PCR) in patients with diarrhea. EIA’s sensitivity is poor, and PCR, although highly sensitive and specific, cannot differentiate infection from colonization. An ideal test that incorporates microbial factors, host factors, and host-microbe interaction might characterize true infection, and assess prognosis and recurrence. The study of volatile organic compounds (VOCs) has the potential to be an ideal diagnostic test. The presence of VOCs accounts for the characteristic odor of stool in CDI but their presence in breath and plasma has not been studied yet. A cross-sectional proof-of-concept study analyzing VOCs using selected ion flow tube mass spectrometry (SIFT-MS) was done on breath, stool, and plasma of patients with clinical features and positive PCR for CDI (cases) and compared with patients with clinical features but a negative PCR (control). Our results showed that VOC patterns in breath, stool, and plasma, had good accuracy [area under the receiver operating characteristic curve (ROC) 93%, 86%, and 91%, respectively] for identifying patients with CDI.

Predictors of Nonseroconversion after SARS-CoV-2 Infection

Not all persons recovering from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection develop SARS-CoV-2–specific antibodies. We show that nonseroconversion is associated with younger age and higher reverse transcription PCR cycle threshold values and identify SARS-CoV-2 viral loads in the nasopharynx as a major correlate of the systemic antibody response.

Meta-Analysis of Robustness of COVID-19 Diagnostic Kits During Early Pandemic

BACKGROUND

Accurate detection of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is necessary to mitigate the coronavirus disease-19 (COVID-19) pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19.

METHODS

We reviewed 85 studies (21,530 patients), published from five regions of the world, to highlight issues involved in the diagnosis of COVID-19 in the early phase of the pandemic, following the standards outlined in the PRISMA statement. All relevant articles, published up to May 31, 2020, in PubMed, BioRiXv, MedRiXv, and Google Scholar, were included. We evaluated the qualitative (9749 patients) and quantitative (10,355 patients) performance of RT-PCR and serologic diagnostic tests for real-world samples, and assessed the concordance (5,538 patients) between methods in meta-analyses.

RESULTS

The RT-PCR tests exhibited heterogeneity in the primers and reagents used. Of 1,957 positive RT-PCR COVID-19 participants, 1,585 had positive serum antibody (IgM +/- IgG) tests (sensitivity 0.81, 95%CI 0.66-.90). While 3,509 of 3581 participants RT-PCR negative for COVID-19 were found negative by serology testing (specificity 0.98, 95%CI 0.94-0.99). The chemiluminescent immunoassay exhibited the highest sensitivity, followed by ELISA and lateral flow immunoassays. Serology tests had higher sensitivity and specificity for laboratory-approval than for real-world reporting data.

CONCLUSIONS

The robustness of the assays/platforms is influenced by variability in sampling and reagents. Serological testing complements and may minimize false negative RT-PCR results. Lack of standardized assay protocols in the early phase of pandemic might have contributed to the spread of COVID-19.

Decreasing High Risk Exposures for Healthcare-workers through Universal Masking and Universal SARS-CoV-2 Testing upon entry to a Tertiary Care Facility

We describe the impact of universal masking and universal testing at admission on high risk exposures to SARS-CoV-2 for healthcare workers. Universal masking decreased the rate per patient day of high risk exposures by 68%, and universal testing further decreased those exposures by 77%.

Disseminated Metacestode Versteria Species Infection in Woman, Pennsylvania, USA1

A patient in Pennsylvania, USA, with common variable immunodeficiency sought care for fever, cough, and abdominal pain. Imaging revealed lesions involving multiple organs. Liver resection demonstrated necrotizing granulomas, recognizable tegument, and calcareous corpuscles indicative of an invasive cestode infection. Sequencing revealed 98% identity to a Versteria species of cestode found in mink.

258. False Negative Rate of T2Candida Assay in Blood Culture Positive Candidemia

Background

The T2Candida (T2C) assay is an FDA-approved, non-culture-based rapid diagnostic that utilizes PCR and magnetic resonance technology to detect candidemia in a whole blood specimen. T2C can detect the 5 most common pathogenic species: C. albicans, C. tropicalis, C. parapsilosis, C. krusei, and C. glabrata. The sensitivity of T2C is reported to be 88–94%, varying by the species, based on the original clinical trial from 2015. Only 6 patients with candidemia were included in the study, so it was supplemented with samples spiked with known quantities of Candida spp. In this study, we sought to evaluate the sensitivity of T2C with routine usage in a tertiary-care academic hospital.

Methods

All patients with a blood culture (BC) positive for Candida spp. during the years 2016 through 2018 were identified. Repeat positive cultures of the same species within 30 days of the initial culture were excluded. We then reviewed the medical records of those patients with a T2C collected ±12 hours from the time of the BC collection. Data collection included demographics, time to antifungal therapy, time to culture reported positive, impact of false negative T2C on antifungal therapy, and 30-day mortality.

Results

There were 281 episodes of candidemia (designated as a positive blood culture) in the study period. Forty-four of these episodes had a T2C collected within the specified timeframe (Figure 1). Overall, there were 17 false-negative T2C, reflecting a sensitivity of 61% (27/44). Excluding species not detected by T2C, the sensitivity was 71% (21/38). Of the false-negative group, antifungal therapy was impacted in 8 patients: delayed initiation in 6 patients (1–4 days) and treatment interruption in 2 patients (1 dose each). Demographics, time to treatment, time to culture positivity, and 30-day mortality were similar in the two groups (Table 1).

Conclusion

In spite of the test being readily available and increasingly used, only 44/281 (16%) of patients with a positive BC had a T2C ordered concurrently. Our experience shows a much lower sensitivity than the clinical trial, in part due to species not detected by T2C. Considering only those organisms on the T2C panel, the false-negative rate was 29%. Impact on treatment was limited to half of the false-negative patients with no difference in mortality.

Disclosures

All authors: No reported disclosures.

248. Thirty-Day Mortality Among Patients with Candidemia Diagnosed by T2Candida Assay Alone: Influence of Risk Factors and Candida Species

Background

Candidemia is a common cause of healthcare-associated bloodstream infection with high mortality rates despite antifungal therapy. Risk factors include prolonged ICU stay, immunosuppression, and exposure to broad-spectrum antibiotics. Blood cultures (BC) remain the gold standard for diagnosis but lack sensitivity and can take days to result. T2Candida (T2C) is a rapid diagnostic test utilizing PCR and magnetic resonance technology to detect five Candida species in whole blood in less than 6 hours. In this study we examined characteristics of patients with positive T2C assays in the absence of positive BC including risk factors and 30-day mortality rates.

Methods

We conducted a retrospective analysis of positive T2C cases at UAB Medical Center from 2016 to 2018 with either negative or no BC. For each patient we determined if clinical signs (e.g., hypotension, leukocytosis) and risk factors for candidemia were present at the time of collection. Our primary outcome of interest was 30-day mortality. Data were compared by multivariate analysis.

Results

A total of 173 patients with T2C positivity alone were included in the analysis. The most common risk factor was the use of broad-spectrum antibiotics followed by CVC (Table 1). The mean number of risk factors per patient was 3.6 (Figure 1). Overall 30-day mortality was 41%. Patients with a T2C result of C. albicans/C. tropicalis were almost 2.5 times more likely to die at 30 days (aOR 2.401, CI 1.159–4.974) compared with those with other positive results. Increasing number of risk factors (aOR 1.457, CI 1.126–1.886) and increasing age (aOR 1.052, CI 1.026–1.079) were significantly associated with increased odds of death at 30 days (Table 2).

Conclusion

In this study we demonstrate a significant association between increasing number of risk factors, older age, and A/T result with higher odds of 30-day mortality among patients with T2C positivity alone. While concern for false-positives exists when using T2C, our data suggest that this is an acutely ill population which warrants early and aggressive antifungal therapy. The lower limit of detection of T2C (1 cfu/mL) as compared with BC may explain lack of paired positive cultures in these patients despite clinical signs of and risk factors for candidemia.

Disclosures

All authors: No reported disclosures.

Mycoplasma pneumoniae Carriage With De Novo Macrolide-Resistance and Breakthrough Pneumonia

Mycoplasma pneumoniae pneumonia is prevalent in children and can be followed by upper airway carriage for months. Treatment of M pneumoniae pneumonia with macrolides is widespread and can lead to the development of macrolide resistance. The clinical consequences of chronic M pneumoniae carriage are unknown. In this article, we describe a child with acute lymphoblastic leukemia who developed macrolide-susceptible M pneumoniae pneumonia confirmed by nasopharyngeal secretions polymerase chain reaction and culture with good response to azithromycin. Five months later, the patient developed another M pneumoniae pneumonia that was diagnosed with positive macrolide-resistant M pneumoniae polymerase chain reaction and culture from the bronchoalveolar lavage. The child responded well to fluoroquinolones and eventually was discharged from the hospital. The M pneumoniae recovered from the second pneumonia is a novel strain and is genetically identical to the M pneumoniae that caused the first pneumonia, apart from the macrolide-resistance 23S ribosomal RNA gene. Both isolates are identical in both P1 (subtype 2 with a novel variant, 2bv) and multiple-locus variable number tandem repeat analysis type (53662). This is indicative of chronic M pneumoniae carriage with de novo macrolide-resistance mutation and subsequent breakthrough pneumonia that is reported for the first time here. Children with immunosuppression may be at increased risk of life-threatening macrolide-resistant pneumonia after M pneumoniae carriage. Further studies are required to evaluate the impact of this phenomenon. This will then guide strategies to limit the associated morbidity, such as testing for macrolide resistance, treatment of M pneumoniae pneumonia in high-risk children with bactericidal antibiotics (such as fluoroquinolones), and possibly eradication protocols of M pneumoniae carriage to prevent subsequent life-threatening infections.

Aspergillus fumigatus corneal infection is regulated by chitin synthases and by neutrophil-derived acidic mammalian chitinase

Aspergillus fumigatus is an important cause of pulmonary and systemic infections in immune compromised individuals, and of corneal ulcers and blindness in immune competent patients. To examine the role of chitin synthases in Aspergillus corneal infection, we analyzed Aspergillus mutants of chitin synthase family 1 and family 2, and found that compared with the parent strain, the quadruple mutants from both families were more readily killed by neutrophils in vitro, and that both also exhibited impaired hyphal growth in the cornea. Further, inhibition of chitin synthases using Nikkomycin Z enhanced neutrophil killing in vitro and in vivo in a murine model of A. fumigatus corneal infection. Acidic mammalian chitinase (AMCase) is mostly produced by macrophages in asthmatic lungs; however, we now demonstrate that neutrophils are a major source of AMCase, which inhibits hyphal growth. In A. fumigatus corneal infection, neutrophils are the major source of AMCase, and addition of AMCase inhibitors or adoptive transfer of neutrophils from AMCase^-/- mice resulted in impaired hyphal killing. Together, these findings identify chitin synthases as important fungal virulence factors and neutrophil-derived AMCase as an essential mediator of host defense.

Current and Emerging Molecular Tests for Human Papillomavirus-Related Neoplasia in the Genomic Era

Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelial cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential. During oncogenesis, HPV interferes with cell cycle regulation and incites DNA damage responses that thwart apoptosis and enable mutations to accumulate. Such mutations are an adverse effect of innate and adaptive antiviral immune responses that up-regulate DNA-editing enzymes, with natural selection of cells having a chromosomally integrated viral genome lacking expression of viral proteins targeted by the immune system. Infected cancers share a similar mutation signature, reflecting the effect of apolipoprotein B mRNA-editing catalytic polypeptide enzyme DNA-editing enzymes. It is feasible that genomic tests for characteristic mutations or methylation signatures, along with tests for dysregulated HPV gene expression, add value in predicting behavior of premalignant lesions. Furthermore, these tumor markers in cell-free DNA of plasma or body fluids may one day assist in early detection or monitoring cancer burden during treatment.

Targeted genomic enrichment and massively parallel sequencing identifies novel nonsyndromic hearing impairment pathogenic variants in Cameroonian families

In sub-Saharan Africa GJB2-related nonsyndromic hearing impairment (NSHI) is rare. Ten Cameroonian families was studied using a platform (OtoSCOPE®) with 116 genes. In seven of 10 families (70%), 12 pathogenic variants were identified in six genes. Five of the 12 (41.6%) variants are novel. These results confirm the efficiency of comprehensive genetic testing in defining the causes of NSHI in sub-Saharan Africa.

Pathogenic FBN1 variants in familial thoracic aortic aneurysms and dissections

Marfan syndrome (MFS) due to mutations in FBN1 is a known cause of thoracic aortic aneurysms and acute aortic dissections (TAAD) associated with pleiotropic manifestations. Genetic predisposition to TAAD can also be inherited in families in the absence of syndromic features, termed familial TAAD (FTAAD), and several causative genes have been identified to date. FBN1 mutations can also be identified in FTAAD families, but the frequency of these mutations has not been established. We performed exome sequencing of 183 FTAAD families and identified pathogenic FBN1 variants in five (2.7%) of these families. We also identified eight additional FBN1 rare variants that could not be unequivocally classified as disease-causing in six families. FBN1 sequencing should be considered in individuals with FTAAD even without significant systemic features of MFS.

Guidelines for investigating causality of sequence variants in human disease

The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development.

Aspergillus and Fusarium corneal infections are regulated by Th17 cells and IL-17-producing neutrophils

Fusarium and Aspergillus species of mold are major causes of corneal infections in the United States and worldwide, resulting in severe visual impairment and blindness. As there is evidence for T cell responses to these pathogenic fungi in infected individuals, we examined the role of IL-17A (IL-17) and IFN-γ in murine models of fungal keratitis. We found that C57BL/6 mice given intratracheal or s.c. immunization of conidia prior to corneal infection exhibited enhanced fungal killing and lower corneal opacity compared with unimmunized mice. Protective immunity was associated with temporal recruitment of IL-17-producing neutrophils and Th17 and Th1 cells and dependent on production of IL-17 but not IFN-γ. Protection was also impaired in neutrophil-depleted and Rag2(-/-) mice. Together, the results of these studies identify an essential role for IL-17-producing neutrophils and Th17 cells in regulating the growth of fungal hyphae and the severity of corneal disease.

Mgat2 ablation in the myeloid lineage leads to defective glycoantigen T cell responses

N-linked glycosylation is a central regulatory factor that influences the immune system in varied and profound ways, including leukocyte homing, T cell receptor signaling and others. Moreover, N-glycan branching has been demonstrated to change as a function of infection and inflammation. Our previous findings suggest that complex-type N-glycans on the class II major histocompatibility complex play an important role in antigen selection within antigen presenting cells (APCs) such that highly branched N-glycans promote polysaccharide (glycoantigen, GlyAg) presentation following Toll-like receptor 2 (TLR2)-dependent antigen processing. In order to explore the impact of N-glycan branching on the myeloid-derived APC population without the confounding problems of altering the branching of lymphocytes and non-hematopoietic cells, we created a novel myeloid-specific knockout of the β-1,2-N-acetylglucosaminyltransferase II (Mgat2) enzyme. Using this novel mouse, we found that the reduction in multi-antennary N-glycans characteristic of Mgat2 ablation had no impact on GlyAg-mediated TLR2 signaling. Likewise, no deficits in antigen uptake or cellular homing to lymph nodes were found. However, we discovered that Mgat2 ablation prevented GlyAg presentation and T cell activation in vitro and in vivo without apparent alterations in protein antigen response or myeloid-mediated protection from infection. These findings demonstrate that GlyAg presentation can be regulated by the N-glycan branching pattern of APCs, thereby establishing an in vivo model where the T cell-dependent activity of GlyAgs can be experimentally distinguished from GlyAg-mediated stimulation of the innate response through TLR2.

The RodA hydrophobin on Aspergillus fumigatus spores masks dectin-1- and dectin-2-dependent responses and enhances fungal survival in vivo

Aspergillus and Fusarium species are important causes of fungal infections worldwide. Airborne spores (conidia) of these filamentous fungi express a surface protein that confers hydrophobicity (hydrophobin) and covers cell wall components that would otherwise induce a host immune cell response. Using a mutant Aspergillus fumigatus strain (ΔrodA) that does not express the RodA hydrophobin, and Aspergillus and Fusarium conidia from clinical isolates that were treated with hydrofluoric acid (which removes the A. fumigatus RodA protein), we observed increased surface exposure of β1,3-glucan and α-mannose on Aspergillus and Fusarium conidia. We also found that ΔrodA and hydrofluoric acid-treated conidia stimulate significantly higher NF-κB p65 nuclear translocation and cytokine production by macrophages from C57BL/6, but not from Dectin-1(-/-) or Dectin-2(-/-) mice. Using a murine model of A. fumigatus corneal infection, we showed that ΔrodA conidia induced significantly higher cytokine production, neutrophil infiltration, and more rapid fungal clearance from C57BL/6 corneas compared with the parent G10 strain, which was dependent on Dectin-1 and Dectin-2. Together, these findings identify the hydrophobin RodA as a virulence factor that masks Dectin-1 and Dectin-2 recognition of conidia, resulting in impaired neutrophil recruitment to the cornea and increased fungal survival and clinical disease.

Host response and bacterial virulence factor expression in Pseudomonas aeruginosa and Streptococcus pneumoniae corneal ulcers

P. aeruginosa and S. pneumoniae are major bacterial causes of corneal ulcers in industrialized and in developing countries. The current study examined host innate immune responses at the site of infection, and also expression of bacterial virulence factors in clinical isolates from patients in south India. Corneal ulcer material was obtained from 49 patients with confirmed P. aeruginosa and 27 patients with S. pneumoniae, and gene expression of Toll Like Receptors (TLR), cytokines and inflammasome proteins was measured by quantitative PCR. Expression of P. aeruginosa type III secretion exotoxins and S. pneumoniae pneumolysin was detected by western blot analysis. We found that neutrophils comprised >90% cells in corneal ulcers, and that there was elevated expression of TLR2, TLR4, TLR5 and TLR9, the NLRP3 and NLRC4 inflammasomes and the ASC adaptor molecule. IL-1α IL-1β and IFN-γ expression was also elevated; however, there was no significant difference in expression of any of these genes between corneal ulcers from P. aeruginosa and S. pneumoniae infected patients. We also show that 41/49 (84%) of P. aeruginosa clinical isolates expressed ExoS and ExoT, whereas 5/49 (10%) of isolates expressed ExoS, ExoT and ExoU with only 2/49 isolates expressing ExoT and ExoU. In contrast, all 27 S. pneumoniae clinical isolates produced pneumolysin. Taken together, these findings demonstrate that ExoS/T expressing P. aeruginosa and pneumolysin expressing S. pneumoniae predominate in bacterial keratitis. While P. aeruginosa strains expressing both ExoU and ExoS are usually rare, these strains actually outnumbered strains expressing only ExoU in the current study. Further, as neutrophils are the predominant cell type in these corneal ulcers, they are the likely source of cytokines and of the increased TLR and inflammasome expression.

Fungal antioxidant pathways promote survival against neutrophils during infection

Filamentous fungi are a common cause of blindness and visual impairment worldwide. Using both murine model systems and in vitro human neutrophils, we found that NADPH oxidase produced by neutrophils was essential to control the growth of Aspergillus and Fusarium fungi in the cornea. We demonstrated that neutrophil oxidant production and antifungal activity are dependent on CD18, but not on the β-glucan receptor dectin-1. We used mutant A. fumigatus strains to show that the reactive oxygen species-sensing transcription factor Yap1, superoxide dismutases, and the Yap1-regulated thioredoxin antioxidant pathway are each required for protection against neutrophil-mediated oxidation of hyphae as well as optimal survival of fungal hyphae in vivo. We also demonstrated that thioredoxin inhibition using the anticancer drug PX-12 increased the sensitivity of fungal hyphae to both H2O2- and neutrophil-mediated killing in vitro. Additionally, topical application of PX-12 significantly enhanced neutrophil-mediated fungal killing in infected mouse corneas. Cumulatively, our data reveal critical host oxidative and fungal anti-oxidative mediators that regulate hyphal survival during infection. Further, these findings also indicate that targeting fungal anti-oxidative defenses via PX-12 may represent an efficacious strategy for treating fungal infections.

The role of cytokines and pathogen recognition molecules in fungal keratitis - Insights from human disease and animal models

Fungal infections of the cornea are an important cause of blindness and visual impairment worldwide, with contact lens wear being the main risk factor in the USA and other industrialized countries, and traumatic injury being the main risk factor in developing countries. In this review, we highlight recent advances in the understanding of the host response to Aspergillus and Fusarium species in infected human corneal tissue and in mouse models of fungal keratitis.

Expression of innate and adaptive immune mediators in human corneal tissue infected with Aspergillus or fusarium

BACKGROUND

Filamentous fungi of the genera Aspergillus and Fusarium are major causes of corneal ulcers in the United States and in the developing world and result in significant visual impairment and blindness.

METHODS

RNA was extracted from 110 patients with corneal ulcers in southern India within 1 week of infection with either Fusarium solani or Aspergillus flavus, and gene expression was determined by quantitative polymerase chain reaction. Posttransplant corneas from later stage disease (>2 weeks after infection) were also examined.

RESULTS

Expression of Dectin-1, Toll-like receptor 2 (TLR2), TLR4, TLR9, and NOD-like receptor protein (NLRP)3 messenger RNA was elevated >1000-fold compared with uninfected donor corneas, whereas Dectin-2 was constitutively expressed in uninfected corneas. Furthermore, interleukin 1β (IL-1β) expression was elevated >1000-fold, whereas IL-1α expression was not increased. Expression of IL-8, IL-17, and tumor necrosis factor α was also elevated. CD3(+)and CD4(+) T cells were detected in infected posttransplant corneas. Expression of IL-17 and interferon γ was elevated but not that of IL-4. There were no significant differences in the host response between Aspergillus- and Fusarium-infected corneas at any time point.

CONCLUSIONS

There is a common innate and adaptive immune response to these filamentous fungi, which includes the generation of T-helper 1 and T-helper 17 cells.

Novel TMPRSS3 variants in Pakistani families with autosomal recessive non-syndromic hearing impairment

Mutations in the TMPRSS3 gene are known to cause autosomal recessive non-syndromic hearing impairment (ARNSHI). After undergoing a genome scan, 10 consanguineous Pakistani families with ARNSHI were found to have significant or suggestive evidence of linkage to the TMPRSS3 region. In order to elucidate if the TMPRSS3 gene is responsible for ARNSHI in these families, the gene was sequenced using DNA samples from these families. Six TMPRSS3 variants were found to cosegregate in 10 families. None of these variants were detected in 500 control chromosomes. Four novel variants, three of which are missense [c.310G>A (p.Glu104Lys), c.767C>T (p.Ala256Val) and c.1273T>C (p.Cys425Arg)] and one nonsense [c.310G>T (p.Glu104Stop)], were identified. The pathogenicity of novel missense variants was investigated through bioinformatics analyses. Additionally, the previously reported deletion c.208delC (p.His70ThrfsX19) was identified in one family and the known mutation c.1219T>C (p.Cys407Arg) was found in five families, which makes c.1219T>C (p.Cys407Arg) as the most common TMPRSS3 mutation within the Pakistani population. Identification of these novel variants lends support to the importance of elements within the low-density lipoprotein receptor A (LDLRA) and serine protease domains in structural stability, ligand binding and proteolytic activity for proper TMPRSS3 function within the inner ear.

A novel g.-1258G>A mutation in a conserved putative regulatory element of PAX9 is associated with autosomal dominant molar hypodontia

Mutations in the transcription factor PAX9 which plays a critical role in the switching of odontogenic potential from the epithelium to the mesenchyme during tooth development cause autosomal dominant non-syndromic hypodontia primarily affecting molars. Linkage analysis on a family segregating autosomal dominant molar hypodontia with markers flanking and within PAX9 yielded a maximum multipoint LOD score of 3.6. No sequence variants were detected in the coding or 5'- and 3'-untranslated regions (UTRs) of PAX9. However, we identified a novel g.-1258G>A sequence variant in all affected individuals of the family but not in the unaffected family members or in 3088 control chromosomes. This mutation is within a putative 5'-regulatory sequence upstream of PAX9 highly conserved in primates, somewhat conserved in ungulates and carnivores but not conserved in rodents. Bioinformatics analysis of the sequence determined that there was no abolition or creation of a putative binding site for known transcription factors. Based on our previous findings that haploinsufficiency for PAX9 leads to hypodontia, we postulate that the g.-1258G>A variant reduces the expression of PAX9 which underlies the hypodontia phenotype in this family.

Distinct roles for Dectin-1 and TLR4 in the pathogenesis of Aspergillus fumigatus keratitis

Aspergillus species are a major worldwide cause of corneal ulcers, resulting in visual impairment and blindness in immunocompetent individuals. To enhance our understanding of the pathogenesis of Aspergillus keratitis, we developed a murine model in which red fluorescent protein (RFP)-expressing A. fumigatus (Af293.1RFP) conidia are injected into the corneal stroma, and disease progression and fungal survival are tracked over time. Using Mafia mice in which c-fms expressing macrophages and dendritic cells can be induced to undergo apoptosis, we demonstrated that the presence of resident corneal macrophages is essential for production of IL-1beta and CXCL1/KC, and for recruitment of neutrophils and mononuclear cells into the corneal stroma. We found that beta-glucan was highly expressed on germinating conidia and hyphae in the cornea stroma, and that both Dectin-1 and phospho-Syk were up-regulated in infected corneas. Additionally, we show that infected Dectin-1(-/-) corneas have impaired IL-1beta and CXCL1/KC production, resulting in diminished cellular infiltration and fungal clearance compared with control mice, especially during infection with clinical isolates expressing high beta-glucan. In contrast to Dectin 1(-/-) mice, cellular infiltration into infected TLR2(-/-), TLR4(-/-), and MD-2(-/-) mice corneas was unimpaired, indicating no role for these receptors in cell recruitment; however, fungal killing was significantly reduced in TLR4(-/-) mice, but not TLR2(-/-) or MD-2(-/-) mice. We also found that TRIF(-/-) and TIRAP(-/-) mice exhibited no fungal-killing defects, but that MyD88(-/-) and IL-1R1(-/-) mice were unable to regulate fungal growth. In conclusion, these data are consistent with a model in which beta-glucan on A.fumigatus germinating conidia activates Dectin-1 on corneal macrophages to produce IL-1beta, and CXCL1, which together with IL-1R1/MyD88-dependent activation, results in recruitment of neutrophils to the corneal stroma and TLR4-dependent fungal killing.

VAMP8/endobrevin is overexpressed in hyperreactive human platelets: suggested role for platelet microRNA

BACKGROUND

Variation in platelet reactivity contributes to disorders of hemostasis and thrombosis, but the molecular mechanisms are not well understood.

OBJECTIVES

To discover associations between interindividual platelet variability and the responsible platelet genes, and to begin to define the molecular mechanisms altering platelet gene expression.

SUBJECTS/METHODS

Two hundred and eighty-eight healthy subjects were phenotyped for platelet responsiveness. Platelet RNA from subjects demonstrating hyperreactivity (n=18) and hyporeactivity (n=11) was used to screen the human transcriptome.

RESULTS

Distinctly different mRNA profiles were observed between subjects with differing platelet reactivity. Increased levels of mRNA for VAMP8/endobrevin, a critical v-SNARE involved in platelet granule secretion, were associated with platelet hyperreactivity (Q=0.0275). Validation studies of microarray results showed 4.8-fold higher mean VAMP8 mRNA levels in hyperreactive than hyporeactive platelets (P=0.0023). VAMP8 protein levels varied 13-fold among platelets from these normal subjects, and were 2.5-fold higher in hyperreactive platelets (P=0.05). Among our cohort of 288 subjects, a VAMP8 single-nucleotide polymorphism (rs1010) was associated with platelet reactivity in an age-dependent manner (P<0.003). MicroRNA-96 was predicted to bind to the 3'-untranslated regionof VAMP8 mRNA and was detected in platelets. Overexpression of microRNA-96 in VAMP8-expressing cell lines caused a dose-dependent decrease in VAMP8 protein and mRNA, suggesting a role in VAMP8 mRNA degradation.

CONCLUSIONS

These findings support a role for VAMP8/endobrevin in the heterogeneity of platelet reactivity, and suggest a role for microRNA-96 in the regulation of VAMP8 expression.

Homeopathic practice in Intensive Care Units: objective semiology, symptom selection and a series of sepsis cases

Homeopathy has been used for more than two hundred years to treat chronic disease using various approaches in a wide range of diseases. However, for acute disease and critical illness, application has been limited by inadequate training of homeopathic physicians and the small number of pertinent clinical studies. In view of the difficulty of practising homeopathy in Intensive Care Units (ICU), a protocol was developed to facilitate description of objective homeopathic symptoms with a ranking of symptoms appropriate for these situations (Protocol for Objective Homeopathic Semiology). Examples of favorable results with individualized homeopathic treatments for a series of cases of Systemic Inflammatory Response Syndrome (sepsis) are described.