Whole-Blood PCR Preferred for Timely Diagnosis of Neuroinvasive West Nile Virus Infections: Lessons From the 2021 Arizona Outbreak

Background

In 2021, the state of Arizona experienced the largest focal outbreak of West Nile virus (WNV) in US history. Timely and accurate diagnostic testing remains a challenge for WNV due to transient viremia and limited immunoassay specificity. Recent studies have identified whole blood (WB) and urine as more sensitive specimen types for the detection of WNV RNA.

Methods

We evaluated ordering practices, test performance, and patient characteristics of probable and confirmed cases. In total, we identified 190 probable and proven cases, including 127 patients (66.8%) with neuroinvasive disease.

Results

Among all cases, only 29.5% had WNV polymerase chain reaction (PCR) testing ordered on WB, of which 80.3% resulted as positive, including 7 cases in which WNV serologic testing was negative and 5 cases for which serologic testing was not ordered. In comparison, only 23.7% of cases that had cerebrospinal fluid (CSF) PCR ordered had a positive result, including 3 cases that were negative by PCR on WB. In contrast, WNV PCR on WB detected 12 neuroinvasive cases that were CSF PCR negative. WNV PCR testing in urine was only ordered on 2 patients, both of whom were positive. Crossing cycle threshold (Ct) values were not significantly different between WB and CSF specimen types, nor was there a correlation between Ct value and days from symptom onset at the time of sample collection; all specimen types and time points had Ct values, with 98% above 30. WB was positive by WNV PCR in several patients for >7 days (range, 7-25 days) after symptom onset, as was the CSF PCR.

Conclusions

Taken together, these findings indicate that WNV PCR testing on WB may be the best initial test for timely diagnosis of WNV infection, irrespective of clinical manifestation; however, if negative in patients with suspected neuroinvasive disease, WNV PCR testing on CSF should be ordered.

Two lateral flow assays for detection of anti-coccidioidal antibodies show similar performance to immunodiffusion in dogs with coccidioidomycosis

OBJECTIVE

To compare 2 point-of-care lateral flow assays (LFAs) with immunodiffusion (ID) IgG results for anti-coccidioidal antibody detection in dogs with coccidioidomycosis. A further aim was to compare the quantifiable output of 1 of the LFAs to ID antibody titers.

SAMPLE

Serum banked from 73 client-owned dogs diagnosed with pulmonary or disseminated coccidioidomycosis.

METHODS

ID was used to determine antibody presence and titer against a coccidioidal antigen preparation. All sera were subsequently tested on an LFA based on recombinant chitinase 1 (CTS1) and the commercially available sōna LFA. LFA results were analyzed and compared to ID IgG results and clinical diagnosis.

RESULTS

All assays showed similar sensitivities in detecting anti-coccidioidal antibodies (83.6% to 89.0%). When compared with ID IgG, the CTS1 LFA had a positive percent agreement of 100%, while the sōna LFA had a positive percent agreement of 91.4%. Since the CTS1 LFA is semiquantitative, we were able to compare test line densities with ID titers and found a strong correlation between the 2 assays (Spearman ρ = 0.82).

CLINICAL RELEVANCE

This is the first side-by-side evaluation of a commercially available LFA (sōna) and a newer more rapid anti-CTS1 antibody LFA using serum from dogs with coccidioidomycosis. Both LFAs tested have similar sensitivity to ID IgG results. The CTS1 LFA can be read after 10 minutes and is semiquantitative, while the sōna LFA is read after 30 minutes, and the results are subject to interpretation. Accurate and fast detection of anti-coccidioidal antibodies allows clinicians to initiate appropriate treatment without diagnostic delay.

Development of a rapid lateral flow assay for detection of anti-coccidioidal antibodies

Coccidioides spp. are dimorphic fungi that are capable of infecting human and non-human mammals and can cause diverse manifestations of coccidioidomycosis or Valley fever (VF). In combination with clinical symptoms and radiographic findings, antibody-based diagnostic tests are often used to diagnose and monitor patients with VF. Chitinase 1 (CTS1) has previously been identified as the seroreactive antigen used in these diagnostic assays to detect anticoccidial IgG. Here, an indirect enzyme-linked immunosorbent assay to detect IgG to CTS1 demonstrated 165 of 178 (92.7%) patients with a positive result by immunodiffusion (ID) and/or complement fixation (CF) had antibodies to the single antigen CTS1. We then developed a rapid antibody lateral flow assay (LFA) to detect anti-CTS1 antibodies. Out of 143 samples tested, the LFA showed 92.9% positive percent agreement [95% confidence interval (CI), 84.3%-96.9%] and 97.7% negative percent agreement (95% CI, 87.9%-99.6%) with ID and CF assays. Serum or plasma from canines, macaques, and dolphins was also tested by the CTS1 LFA. Test line densities of the CTS1 LFA correlated in a linear manner with the reported CF and ID titers for human and non-human samples, respectively. This 10-min point-of-care test for the rapid detection of anti-coccidioidal antibodies could help to inform healthcare providers in real-time, potentially improving the efficiency of healthcare delivery.

Burkholderia pseudomallei Laboratory Exposure, Arizona, USA

We describe an incidental Burkholderia pseudomallei laboratory exposure in Arizona, USA. Because melioidosis cases are increasing in the United States and B. pseudomallei reservoirs have been discovered in the Gulf Coast Region, US laboratory staff could be at increased risk for B. pseudomallei exposure.

A Sample of the Future: Digital Health and Near-Patient Testing

We, a nurse and a laboratory director, share our experience supporting a research study that employed a digital health application and a rapid test for severe acute respiratory syndrome coronavirus 2 and the implications of this approach for health care delivery.

Clinical Laboratory Utility of a Humanized Antibody in Commercially Available Enzyme Immunoassays for Coccidioidomycosis

Coccidioidomycosis, also called valley fever (VF), is a fungal infection with endemicity in desert regions of the western United States as well as certain arid regions of Central and South America. Laboratory-based diagnosis of VF often relies on the composite results from three serologic-based diagnostics, complement fixation, immunodiffusion, and enzyme immunoassay (EIA). EIA is commonly performed in clinical laboratories because results can be obtained in a few hours. Two commercially available EIAs, IMMY clarus Coccidioides antibody and Meridian Premier Coccidioides, look for the presence of anticoccidioidal IgG and IgM in patient sera that are diluted 1:441. Per regulatory requirements, this dilution step must be verified with a dilution step control despite not being provided as a reagent in either FDA-approved EIA kit. Therefore, clinical laboratories collect and reuse patient sera in subsequent tests that had a positive result in a previous test. This is a nonstandard process, reinforcing the need for a consistent and reliable dilution control. Here, we evaluate the performance of a humanized IgG and IgM antibody as a dilution control in both EIA kits. Both humanized IgG and IgM work well in each EIA and meet the appropriate threshold for positivity. IMPORTANCE In southwestern and western regions of the United States, at least half a million diagnostic tests for coccidioidomycosis (valley fever) are run annually. Enzyme immunoassays (EIAs) are blood tests which require precise dilution of patient serum prior to testing. To ensure patient serum is properly diluted, there is a regulatory requirement to ensure the dilution step is accurate. Two FDA-approved EIAs used to aid in the diagnosis of coccidioidomycosis do not contain controls for this dilution step, leaving clinical laboratories with the only option of using previously positive patient sera, which may not react in a reliable or predictable manner. Here, we evaluate a humanized monoclonal antibody against a coccidioidal antigen and its utility as a dilution control in both available commercial EIAs. The use of a humanized monoclonal antibody provides a standardized and well-characterized dilution control for use in serological assays that aid in diagnosis of coccidioidomycosis.

Humanization and expression of IgG and IgM antibodies in plants as potential diagnostic reagents for Valley Fever

Monoclonal antibodies (mAbs) are important proteins used in many life science applications, from diagnostics to therapeutics. High demand for mAbs for different applications urges the development of rapid and reliable recombinant production platforms. Plants provide a quick and inexpensive system for producing recombinant mAbs. Moreover, when paired with an established platform for mAb discovery, plants can easily be tailored to produce mAbs of different isotypes against the same target. Here, we demonstrate that a hybridoma-generated mouse mAb against chitinase 1 (CTS1), an antigen from Coccidioides spp., can be biologically engineered for use with serologic diagnostic test kits for coccidioidomycosis (Valley Fever) using plant expression. The original mouse IgG was modified and recombinantly produced in glycoengineered Nicotiana benthamiana plants via transient expression as IgG and IgM isotypes with human kappa, gamma, and mu constant regions. The two mAb isotypes produced in plants were shown to maintain target antigen recognition to CTS1 using similar reagents as the Food and Drug Administration (FDA)-approved Valley Fever diagnostic kits. As none of the currently approved kits provide antibody dilution controls, humanization of antibodies that bind to CTS1, a major component of the diagnostic antigen preparation, may provide a solution to the lack of consistently reactive antibody controls for Valley Fever diagnosis. Furthermore, our work provides a foundation for reproducible and consistent production of recombinant mAbs engineered to have a specific isotype for use in diagnostic assays.

Rapid Detection of Urinary Tract Infection in 10 min by Tracking Multiple Phenotypic Features in a 30 s Large-Volume Scattering Video of Urine Microscopy

Rapid point-of-care (POC) diagnosis of bacterial infection diseases provides clinical benefits of prompt initiation of antimicrobial therapy and reduction of the overuse/misuse of unnecessary antibiotics for nonbacterial infections. We present here a POC compatible method for rapid bacterial infection detection in 10 min. We use a large-volume solution scattering imaging (LVSi) system with low magnifications (1-2×) to visualize bacteria in clinical samples, thus eliminating the need for culture-based isolation and enrichment. We tracked multiple intrinsic phenotypic features of individual cells in a short video. By clustering these features with a simple machine learning algorithm, we can differentiate Escherichia coli from similar-sized polystyrene beads, distinguish bacteria with different shapes, and distinguish E. coli from urine particles. We applied the method to detect urinary tract infections in 104 patient urine samples with a 30 s LVSi video, and the results showed 92.3% accuracy compared with the clinical culture results. This technology provides opportunities for rapid bacterial infection diagnosis at POC settings.

Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections

Surgical site infections (SSI) are a significant burden to patients and health care systems. We evaluated the use of Nanopore sequencing (NS) to rapidly detect microbial species and antimicrobial resistance (AMR) genes present in intraoperative bile aspirates. Bile aspirates from 42 patients undergoing pancreatic head resection were included. Three methods of DNA extraction using mechanical cell lysis or protease cell lysis were compared to determine the optimum method of DNA extraction. The impact of host DNA depletion, sequence run duration, and use of different AMR gene databases was also assessed. To determine clinical value, NS results were compared to standard culture (SC) results. NS identified microbial species in all culture positive samples. Mechanical lysis improved NS detection of cultured species from 60% to 76%, enabled detection of fungal species, and increased AMR predictions. Host DNA depletion improved detection of streptococcal species and AMR correlation with SC. Selection of AMR database influenced the number of AMR hits and resistance profile of 13 antibiotics. AMR prediction using CARD and ResFinder 4.1 correctly predicted 79% and 81% of the bile antibiogram, respectively. Sequence run duration positively correlated with detection of AMR genes. A minimum of 6 h was required to characterize the biliary microbes, resulting in a turnaround time of 14 h. Rapid identification of microbial species and AMR genes can be achieved by NS. NS results correlated with SC, suggesting that NS may be useful in guiding early antimicrobial therapy postsurgery. IMPORTANCE Surgical site infections (SSI) are a significant burden to patients and health care systems. They increase mortality rates, length of hospital stays, and associated health care costs. To reduce the risk of SSI, surgical patients are administered broad-spectrum antibiotics that are later adapted to target microbial species detected at the site of surgical incision. Use of broad-spectrum antibiotics can be harmful to the patient. We wanted to develop a rapid method of detecting microbial species and their antimicrobial resistance phenotypes. We developed a method of detecting microbial species and predicting resistance phenotypes using Nanopore sequencing. Results generated using Nanopore sequencing were similar to current methods of detection but were obtained in a significantly shorter amount of time. This suggests that Nanopore sequencing could be used to tailor antibiotics in surgical patients and reduce use of broad-spectrum antibiotics.

Development of a rapid point-of-care test that measures neutralizing antibodies to SARS-CoV-2

BACKGROUND

After receiving a COVID-19 vaccine, most recipients want to know if they are protected from infection and for how long. Since neutralizing antibodies are a correlate of protection, we developed a lateral flow assay (LFA) that measures levels of neutralizing antibodies from a drop of blood. The LFA is based on the principle that neutralizing antibodies block binding of the receptor-binding domain (RBD) to angiotensin-converting enzyme 2 (ACE2).

METHODS

The ability of the LFA was assessed to correctly measure neutralization of sera, plasma or whole blood from patients with COVID-19 using SARS-CoV-2 microneutralization assays. We also determined if the LFA distinguished patients with seasonal respiratory viruses from patients with COVID-19. To demonstrate the usefulness of the LFA, we tested previously infected and non-infected COVID-19 vaccine recipients at baseline and after first and second vaccine doses.

RESULTS

The LFA compared favorably with SARS-CoV-2 microneutralization assays with an area under the ROC curve of 98%. Sera obtained from patients with seasonal coronaviruses did not show neutralizing activity in the LFA. After a single mRNA vaccine dose, 87% of previously infected individuals demonstrated high levels of neutralizing antibodies. However, if individuals were not previously infected, only 24% demonstrated high levels of neutralizing antibodies after one vaccine dose. A second dose boosted neutralizing antibody levels just 8% higher in previously infected individuals, but over 63% higher in non-infected individuals.

CONCLUSIONS

A rapid, semi-quantitative, highly portable and inexpensive neutralizing antibody test might be useful for monitoring rise and fall in vaccine-induced neutralizing antibodies to COVID-19.

Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV-2 Viral Antigen and to Study Host Response

SARS-CoV-2 infection has become a major public health burden and affects many organs including lungs, kidneys, the liver, and the brain. Although the virus is readily detected and diagnosed using nasopharyngeal swabs by reverse transcriptase polymerase chain reaction (RT-PCR), detection of its presence in body fluids is fraught with difficulties. A number of published studies have failed to detect viral RNA by RT-PCR methods in urine. Although microbial identification in clinical microbiology using mass spectrometry is undertaken after culture, here we undertook a mass spectrometry-based approach that employed an enrichment step to capture and detect SARS-CoV-2 nucleocapsid protein directly from urine of COVID-19 patients without any culture. We detected SARS-CoV-2 nucleocapsid protein-derived peptides from 13 out of 39 urine samples. Further, a subset of COVID-19 positive and COVID-19 negative urine samples validated by mass spectrometry were used for the quantitative proteomics analysis. Proteins with increased abundance in urine of SARS-CoV-2 positive individuals were enriched in the acute phase response, regulation of complement system, and immune response. Notably, a number of renal proteins such as podocin (NPHS2), an amino acid transporter (SLC36A2), and sodium/glucose cotransporter 5 (SLC5A10), which are intimately involved in normal kidney function, were decreased in the urine of COVID-19 patients. Overall, the detection of viral antigens in urine using mass spectrometry and alterations of the urinary proteome could provide insights into understanding the pathogenesis of COVID-19.

Development of a Quantitative Antigen Assay to Detect Coccidioidal Chitinase-1 (CTS1) in Human Serum

Background

Coccidioidomycosis is often diagnosed with a collection of tests that rely on the patient's ability to mount an immune response to the fungus (antibody-based diagnostics), making diagnosis of this infection challenging. Here we present an antigen-based assay that detects and quantifies coccidioidal chitinase-1 (CTS1) in human serum.

Methods

An inhibition-based enzyme-linked immunoassay (ELISA) was developed that utilizes a monoclonal antibody specific for coccidioidal CTS1. CTS1 was quantified in commercial antigen preparations using recombinant CTS1 as a standard. Sera from 192 individuals from an endemic area were tested, which included 78 patients (40.6%) with proven or probable coccidioidomycosis.

Results

The quantity of CTS1 in diagnostic commercial antigen preparations from different suppliers varied. CTS1 antigenemia was detected in 87.2% of patients with proven or probable coccidioidomycosis. Specificity was determined to be 96.94% using serum from individuals who reside in the Phoenix, Arizona area who did not have coccidioidomycosis. Levels of CTS1 correlated with low- and high-titer serology from patients with a coccidioidomycosis diagnosis.

Conclusions

Since the CTS1 inhibition ELISA described in this report does not depend on the host immune response, it is a promising diagnostic tool to aid in diagnosis and disease monitoring of coccidioidomycosis.

Effectiveness of Physical Distancing: Staying 6 Feet Over to Put Respiratory Viruses 6 Feet Under

Community transmission of severe acute respiratory illness Coronavirus-2 (SARS-CoV-2) in Arizona was noted in March 2020. It was our hypothesis that the associated implementation of physical distancing and masking led to a decline in circulation and detection of common respiratory viruses. Nasopharyngeal swabs processed with the Biofire, Film Array respiratory panel at Mayo Clinic Arizona were reviewed from January 1, 2017, to July 31, 2020. A total of 13,324 nasopharyngeal swabs were analyzed. Between April and July 2017- 2019 (Period A) a mean of 262 tests were performed monthly, falling to 128 for the corresponding months of 2020 (Period B). A reduction in the monthly mean number of positive tests (Period A 71.5; Period B 2.8) and mean positivity rate (Period A 25.04%; Period B 2.07%) was observed. Rhinovirus/enterovirus was the most prevalent virus, with a monthly mean of 21.6 cases (30.2% of positives) for Period A and 2 cases (72.7% of positives) for Period B. Positivity for a second virus occurred in a mean of 2.1 positive tests (3.3%) in Period A but was absent in Period B. Implementation of distancing and masking coincides with a marked reduction in respiratory virus detection and likely circulation. Data from the fall/winter of 2020 will help clarify the potential role for distancing and masking as a mitigation strategy, not only for SARS-CoV-2 but also in the seasonal battle against common respiratory viruses.

Carbo-loading in Coccidioides spp.: A quantitative analysis of CAZyme abundance and resulting glycan populations

Coccidioides spp. are important pneumonia-causing pathogens of the American southwest, but little is known about their glycobiology and how their glycosylations differ from other pneumonia-causing fungi. There is mounting preliminary evidence to suggest genus or even species-specific glycosylations in the fungal kingdom due to the presence of unique carbohydrate-active enzymes (CAZymes) in fungal genomes (Deshpande et al. 2008, Glycobiology, 18(8), 626-637; Karkowska-Kuleta and Kozik 2015, Acta Biochim Pol., 62(3), 339-351). If Coccidioides spp.-specific glycans can be identified, it may be possible to exploit these differences to develop more specific diagnostic approaches and more effective therapeutics. Herein, we i) mined Coccidioides spp. and other pathogenic fungal genomes to identify CAZymes specific for Coccidioides spp., ii) proteomically determined the Coccidioides spp. "CAZome" produced in vivo and in vitro, and iii) utilized glycomics to differentiate Coccidioides genus-specific N-glycans from other pathogenic fungi. As far as we are aware, this is the first proteomic and glycomic comparison of the N-glycomes and CAZomes of different fungal genera during infection in human hosts.

Retrospective clinical evaluation of 4 lateral flow assays for the detection of SARS-CoV-2 IgG

In a Clinical Laboratory Improvement Amendments laboratory setting, we evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG detection with 4 lateral flow immunoassays [LFIAs; 2 iterations from BTNX Inc. (n = 457) and 1 each from ACON Laboratories (n = 200) and SD BIOSENSOR (n = 155)]. In a cohort of primarily hospitalized, reverse-transcription polymerase chain reaction-confirmed coronavirus disease 2019 cases, sensitivity at ≥14 days from symptom onset was: BTNX kit 1, 95%; BTNX kit 2, 91%; ACON, 95%; and SD, 92%. All assays showed good concordance with the Abbott SARS-CoV-2 IgG assay at ≥14 days from symptom onset: BTNX kit 1, 99%; BTNX kit 2, 94%; ACON, 99%; and SD, 100%. Specificity, measured using specimens collected prior to SARS-CoV-2 circulation in the United States and "cross-reactivity challenge" specimens, was 98% for BTNX kit 1 and ACON and 100% for BTNX kit 2 and SD. These results suggest that LFIAs may provide adequate results for rapid detection of SARS-CoV-2.

Is There an Optimal Cutoff for Aspiration Fluid Volume in the Diagnosis of Periprosthetic Joint Infection?

BACKGROUND

The diagnosis of periprosthetic joint infection is often challenging in the setting of low aspiration volumes, or in the presence of infection with a slow-growing organism. We sought to determine if an optimal threshold of aspiration fluid volume exists when cultures from the preoperative aspiration are compared to intraoperative cultures.

METHODS

All revision total hip and knee arthroplasty procedures over 5 years at our institution were reviewed. Cases were excluded if they underwent joint lavage during aspiration, had an antibiotic spacer in place, were suspected of adverse local tissue reaction to metal debris, did not have an accurate aspiration volume recorded, or if there were no aspiration or operative cultures available. Receiver operating characteristic curves were used to evaluate aspiration volume for identifying cases with identical aspiration and culture results.

RESULTS

A total of 857 revision cases were reviewed, among which 294 met inclusion criteria. There were 45 cases (15.3%) with discordant aspiration and operative cultures. The mean aspiration volume for identical cases was significantly higher than for discordant cases (19.1 vs 10.2 mL, P = .02). The proportion of slow-growing organisms was significantly greater among discordant compared to identical operative cultures (52.4% for discordant cases vs 8.2% for identical cases, P < .001). The optimal cutoff value for predicting identical cultures was 3.5 mL for typical organisms and 12.5 mL for slow-growing organisms.

CONCLUSION

Aspiration cultures are more likely to correlate with intraoperative cultures with higher aspiration volumes, and the optimal aspiration volume is higher for slow-growing organisms.

Comparison of two FDA-cleared EIA assays for the detection of Coccidioides antibodies against a composite clinical standard

Coccidioidomycosis is a disease endemic to the southwestern United States, parts of Mexico, and Central and South America. Diagnosis of the disease is commonly delayed because of the lack of prompt testing and the dearth of reliable diagnostic tests. Culture and nucleic acid testing require a specimen, yet the typical patient presents with a dry cough and no sputum. Serologic methods depend on an effective antibody response by the patient, but antibody production may be unreliable or delayed until several weeks after initial symptom onset. Most published reports of serologic assays compare them to traditional serologic tests such as complement fixation and immunodiffusion. We sought to characterize the performance of two commercially available serologic tests, Meridian Premier and IMMY Omega, against a composite clinical reference standard to determine the sensitivity and specificity of these tests in detecting whether antibody is likely present in clinical specimens. The composite reference standard included symptoms, radiologic findings, and serologic results from complement fixation and immunodiffusion. For the Meridian test, sensitivity and specificity respectively were 69.4% and 95.4% for immunoglobulin G (Ig G) and 57.1% and 70.4% for immunoglobulin M (IgM). For the IMMY assay, sensitivity and specificity respectively were 53.1% and 96.7% for IgG and 34.7% and 85.5% for IgM.

Evaluation of Virex® II 256 and Virex® Tb as Disinfectants of the Dimorphic Fungi Coccidioides immitis and Coccidioides posadasii

To date, limited published data exists regarding the efficacy of commonly used disinfectants in inactivating the Risk Group 3 dimorphic fungal pathogens, Coccidioides immitis and Coccidioides posadasii. Newer generation quaternary ammonium compounds, like Virex® II 256 and Virex® Tb, have not been previously evaluated. Herein, these disinfectants are evaluated against 10% bleach and 70% ethanol, for their ability to inactivate 5×10⁷ arthroconidial spores of C. immitis RS or C. posadasii strain Silveira within 2, 5, 10 or 20 minutes contact time in aqueous solution. Evidence is provided that both Virex® II 256 and Virex® Tb are highly effective alternatives to 10% bleach or 70% ethanol for the disinfection of 5×10⁷ arthroconidia of Coccidioides spp. within 2 minutes of contact time. 70% ethanol was seen as less effective in killing C.immitis RS arthroconidia and both 70% ethanol and 10% bleach were seen as less effective than the other disinfectants in killing C. posadasii strain Silveira, as longer contact times were required to completely inactivate the same number of arthroconidia.

Is It Actionable? An Evaluation of the Rapid PCR-Based Blood Culture Identification Panel on the Management of Gram-Positive and Gram-Negative Blood Stream Infections

Background

There is growing interest in the use of rapid blood culture identification (BCID) in antimicrobial stewardship programs (ASPs). Although many studies have looked at its clinical and economic utility, its comparative utility in gram-positive and gram-negative blood stream infections (BSIs) has not been as well characterized.

Methods

The study was a quasi-experimental retrospective study at the Mayo Clinic in Phoenix, Arizona. All adult patients with positive blood cultures before BCID implementation (June 2015 to December 2015) and after BCID implementation (June 2016 to December 2016) were included. The outcomes of interest included time to first appropriate antibiotic escalation, time to first appropriate antibiotic de-escalation, time to organism identification, length of stay, infectious diseases consultation, discharge disposition, and in-hospital mortality.

Results

In total, 203 patients were included in this study. There was a significant difference in the time to organism identification between the pre- and post-BCID cohorts (27.1 hours vs 3.3 hours, P < .0001). BCID did not significantly reduce the time to first appropriate antimicrobial escalation or de-escalation for either gram-positive BSIs (GP-BSIs) or gram-negative BSIs (GN-BSIs). Providers were more likely to escalate antimicrobial therapy in GP-BSIs after gram stain and more likely to de-escalate therapy in GN-BSIs after susceptibilities. Although there were no significant differences in changes in antimicrobial therapy for organism identification by BCID vs traditional methods, more than one-quarter of providers (28.1%) made changes after organism identification. There were no differences in hospital length of stay or in-hospital mortality comparing pre- vs post-BCID.

Conclusions

Although BCID significantly reduced the time to identification for both GP-BSIs and GN-BSIs, BCID did not reduce the time to first appropriate antimicrobial escalation and de-escalation.

Single dose versus multiple doses of rituximab for preemptive therapy of Epstein-Barr virus reactivation after hematopoietic cell transplantation

Epstein-Barr virus (EBV) reactivation is an unresolved medical issue after allogeneic hematopoietic stem cell transplantation (HSCT). Rituximab treatment is recommended for EBV reactivation after HSCT but the number of doses of rituximab to use is unclear. In this study, risk factors and outcomes of patients who needed 1 dose vs >1 doses of preemptive rituximab to clear EBV viremia were compared. A higher viral load was more likely to be associated with higher doses of rituximab. Patients whose EBV viremia cleared with 1 dose of rituximab were more likely to have a preceding reduction of immunosuppression. Overall survival (OS) in these 2 cohorts was not different (18.7 vs 26.6 months, respectively, p = .96). Since rituximab can have side effects and is fairly costly, a predictive model to determine the number of rituximab doses using viral load would be a useful and cost-effective manner to utilize rituximab for this indication.

Phenotypic Antimicrobial Susceptibility Testing with Deep Learning Video Microscopy

Timely determination of antimicrobial susceptibility for a bacterial infection enables precision prescription, shortens treatment time, and helps minimize the spread of antibiotic resistant infections. Current antimicrobial susceptibility testing (AST) methods often take several days and thus impede these clinical and health benefits. Here, we present an AST method by imaging freely moving bacterial cells in urine in real time and analyzing the videos with a deep learning algorithm. The deep learning algorithm determines if an antibiotic inhibits a bacterial cell by learning multiple phenotypic features of the cell without the need for defining and quantifying each feature. We apply the method to urinary tract infection, a common infection that affects millions of people, to determine the minimum inhibitory concentration of pathogens from human urine specimens spiked with lab strain E. coli (ATCC 43888) and an E. coli strain isolated from a clinical urine sample for different antibiotics within 30 min and validate the results with the gold standard broth macrodilution method. The deep learning video microscopy-based AST holds great potential to contribute to the solution of increasing drug-resistant infections.

Prospective study of the feasibility of point-of-care testing strategy for carbapenem-resistant organism detection

BACKGROUND/AIMS

 In an investigator-initiated, prospective study, we evaluated the feasibility of a five-gene sequence point-of-care (POC) testing strategy (Xpert CARBA-R Assay, Cepheid Inc., Sunnyvale, CA, USA), compared to reference laboratory PCR (48 - 72 hours turnaround time, two gene sequences), in patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and in a hospital outbreak investigation.

METHODS

 After informed consent, patients undergoing ERCP (September 2015 - April 2016, n = 191) at Mayo Clinic and potential hospital contacts (n = 9) of an index carbapenem-resistant organism (CRO)-positive inpatient were included. Two rectal swabs, one each for reference and POC assays were obtained. The Xpert CARBA-R Assay enables qualitative rapid detection of five beta-lactamase gene sequences associated with carbapenem-non-susceptibility in Gram-negative bacteria. Feasibility parameters (specimen processing and assay run time, ease of use) and percent agreement between the tests were calculated using JMP Pro11 (SAS Corp, Cary, NC, USA).

RESULTS

 Mean age was 62 ± 15 years; 108 (54 %) were male. Both tests were successfully performed in all patients. The POC test was rated by endoscopy nurses as easy/very easy to conduct in 193 patients (97 %); median assay run time and median time for specimen collection and processing were 55 minutes (interquartile range IQR: 53 - 55 minutes) and 3 minutes (IQR: 3 - 6 minutes), respectively. In 200/201 (99.5 %) tests, there was agreement between the POC and reference PCR.

CONCLUSIONS

 The more comprehensive POC CRO testing of patients in the endoscopy suite is feasible and results are available in < 1 hour. This strategy may enable rapid risk stratification of duodenoscope exposure to CRO and potentially improve operational efficiency and decrease costs.

Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira

The aims of this study are to provide protein-based evidence upon which to reannotate the genome of Coccidiodes posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira are analyzed using a GeLC-MS/MS method. Acquired spectra are processed with a proteogenomics workflow comprising a Silveira proteome database, a six-frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs. This study provides evidence for 837 genes expressed at the protein level, of which 169 proteins (20.2%) are putative proteins and 103 (12.3%) are not annotated in the Silveira genome. Additionally, 275 novel peptides are derived from intragenic regions of the genome and 13 from intergenic regions, resulting in 172 gene refinements. Additionally, we are the first group to report translationally active retrotransposon elements in a Coccidioides spp. Our study reveals that the currently annotated genome of C. posadasii str. Silveira needs refinement, which is likely to be the case for many nonmodel organisms.

Neuroinvasive St. Louis Encephalitis Virus Infection in Solid Organ Transplant Recipients

In summer 2015, three unrelated solid organ transplant recipients in Phoenix, Arizona, had meningoencephalitis suggestive of West Nile virus (WNV) infection. Testing was inconclusive but was later confirmed as St. Louis encephalitis (SLE). We retrospectively reviewed clinical manifestations, treatment, and outcomes of these transplant recipients. Common symptoms were fever, rigors, diarrhea, headache, and confusion. One patient died 3 days after hospitalization. Therapy for the other two patients was initiated with interferon α-2b (IFN) and intravenous IgG (IVIG; IFN plus IVIG in combination). Both patients tested positive for WNV by serologic assay, but SLE virus (SLEV) infection was later confirmed by plaque reduction neutralization test at a reference laboratory. Clinical improvement was observed within 72 h after initiation of IFN plus IVIG. SLEV has been an uncommon cause of neuroinvasive disease in the United States. Accurate, timely diagnosis is hindered because of clinical presentation similar to neuroinvasive WNV and SLE, serologic cross-reactivity, and lack of a commercially available serologic assay for SLEV. There is currently no approved therapy for flaviviral neuroinvasive disease. Anecdotal reports indicate varying success with IFN, IVIG, or IFN plus IVIG in WNV neuroinvasive disease. The same regimen might be of value for immunocompromised persons with neuroinvasive SLEV infection.

Microbiologic yield of bronchoalveolar lavage specimens from stem cell transplant recipients

PURPOSE

Stem cell transplant (SCT) recipients commonly undergo bronchoalveolar lavage (BAL) collection as an infectious pulmonary work-up. Previous studies report the utility and overall diagnostic yield of fiberoptic bronchoscopy with BAL in this vulnerable population, though none focused purely on microbiologic yield or made comparisons with less invasive means of pathogen detection. We sought to determine and elaborate on the microbiologic yield of BAL in SCT recipients, assess a correlation between BAL studies and less invasive means of pathogen detection, and assess the utility of repeating a BAL within 30 days.

METHODS

Between January 1, 2009, and July 31, 2013, we reviewed medical records of 125 SCT recipients who underwent 179 BALs. In addition to demographic information and details pertaining to their SCT, a comprehensive review of their microbiologic data was performed and recorded.

RESULTS

Our study showed an overall BAL microbiologic yield of 40%, despite 92% of patients receiving broad-spectrum antimicrobial therapy at the time of the BAL procedure.

CONCLUSIONS

Although an initial BAL sample in this population provides crucial microbiologic information, repeating the procedure within 30 days may have minimal additional microbiologic yield. BAL continues to be an essential diagnostic tool in SCT recipients undergoing an infectious pulmonary work-up.

Current and emerging techniques for antibiotic susceptibility tests

Infectious diseases caused by bacterial pathogens are a worldwide burden. Serious bacterial infection-related complications, such as sepsis, affect over a million people every year with mortality rates ranging from 30% to 50%. Crucial clinical microbiology laboratory responsibilities associated with patient management and treatment include isolating and identifying the causative bacterium and performing antibiotic susceptibility tests (ASTs), which are labor-intensive, complex, imprecise, and slow (taking days, depending on the growth rate of the pathogen). Considering the life-threatening condition of a septic patient and the increasing prevalence of antibiotic-resistant bacteria in hospitals, rapid and automated diagnostic tools are needed. This review summarizes the existing commercial AST methods and discusses some of the promising emerging AST tools that will empower humans to win the evolutionary war between microbial genes and human wits.

Total and Lectin-Binding Proteome of Spherulin from Coccidioides posadasii

Coccidioides is a virulent dimorphic fungus that causes coccidioidomycosis (valley fever) in mammals, including humans. Although the genome has been sequenced, a proteomic analysis does not exist. To address this gap in proteomic knowledge, we generated the proteome of spherulin (a well-studied lysate of fungal spherules) and identified 1390 proteins. Some of the proteins included glycosylation enzymes, which led us to hypothesize that fungal glycosylation patterns may be different from those of mammals and could be exploited to detect Coccidioides in tissues. We performed lectin-based immunohistochemistry on formalin-fixed paraffin-embedded human patients' lung tissues. GSL-II (Griffonia simplificonia lectin II) and sWGA (succinylated wheat germ agglutinin) lectins bound specifically to endospores and spherules in infected lungs. To identify lectin-binding glycoproteins in spherulin, we performed lectin-affinity chromatography, followed by LC-MS/MS. A total of 195 glycoproteins from spherulin bound to GSL-II, 224 glycoproteins bound to sWGA, and 145 glycoproteins bound to both lectins. This is the first report of the specific reactivity of GSL-II and sWGA lectins to Coccidioides endospores and spherules in infected human tissues and the first listing of the Coccidioidal proteome from spherulin using sequences present in three Coccidioides databases: RefSeq, SwissProt, and The Broad Institute's Coccidioides Genome project.

Gastric lap-band infection due to Mycobacterium abscessus presenting as new-onset ascites in a cirrhotic patient

Nontuberculous mycobacteria are ubiquitous environmental organisms that are infrequently implicated as pathogens. Peritoneal infection with nontuberculous mycobacteria is rare and published reports are most commonly associated with peritoneal dialysis. This study describes a case of a 41-year-old woman with cirrhosis who had Mycobacterium abscessus peritonitis and an abdominal abscess resulting from infection of a remotely placed gastric band (Lap-Band; Apollo Endosurgery, Inc).

Histopathology of Disseminated Mycobacterium bovis Infection Complicating Intravesical BCG Immunotherapy for Urothelial Carcinoma

Intravesical instillation of Bacillus Calmette-Guérin (BCG) is a mainstay of adjunctive therapy for superficial bladder cancer. Disseminated BCG infection ("BCG-osis") after this therapy is rare and potentially life-threatening; only isolated case reports detail the histopathologic findings thereof, few of which had a diagnosis confirmed by molecular testing. We report 3 additional cases of BCG-osis complicating BCG therapy, all confirmed by cultures and molecular assays, including the first cases of wedge biopsy-confirmed BCG pneumonia and BCG olecranon bursitis. When suggested by a relevant clinical history, recognition of randomly distributed granulomas in any organ should prompt consideration of BCG-osis and liberal performance of AFB stains, aided by targeted molecular assays. Physicians should maintain a high index of suspicion when miliary infiltrates arise after intravesical BCG instillation, and close multidisciplinary communication is essential. Pathologist awareness of this rare cause of granulomatous inflammation aids recognition of BCG-osis and facilitates prompt initiation of antimycobacterial therapy.

Atypical Shigella boydii 13 encodes virulence factors seen in attaching and effacing Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that causes watery diarrhea and hemorrhagic colitis. In this study, we identified StcE, a secreted zinc metalloprotease that contributes to intimate adherence of EHEC to host cells, in culture supernatants of atypical Shigella boydii 13 (Shigella B13) strains. Further examination of the Shigella B13 strains revealed that this cluster of pathogens does not invade but forms pedestals on HEp-2 cells similar to EHEC and enteropathogenic E. coli. This study also demonstrates that atypical Shigella B13 strains are more closely related to attaching and effacing E. coli and that their evolution recapitulates the progression from ancestral E. coli to EHEC.

Characterization of the StcE protease activity of Escherichia coli O157:H7

The StcE zinc metalloprotease is secreted by enterohemorrhagic Escherichia coli (EHEC) O157:H7 and contributes to intimate adherence of this bacterium to host cells, a process essential for mammalian colonization. StcE has also been shown to localize the inflammatory regulator C1 esterase inhibitor (C1-INH) to cell membranes. We tried to more fully characterize StcE activity to better understand its role in EHEC pathogenesis. StcE was active at pH 6.1 to 9.0, in the presence of NaCl concentrations ranging from 0 to 600 mM, and at 4 degrees C to 55 degrees C. Interestingly, antisera against StcE or C1-INH did not eliminate StcE cleavage of C1-INH. Treatment of StcE with the proteases trypsin, chymotrypsin, human neutrophil elastase, and Pseudomonas aeruginosa elastase did not eliminate StcE activity against C1-INH. After StcE was kept at 23 degrees C for 65 days, it exhibited full proteolytic activity, and it retained 30% of its original activity after incubation for 8 days at 37 degrees C. Together, these results show the StcE protease is a stable enzyme that is probably active in the environment of the colon. Additionally, k(cat)/K(m) data showed that StcE proteolytic activity was 2.5-fold more efficient with the secreted mucin MUC7 than with the complement regulator C1-INH. This evidence supports a model which includes two roles for StcE during infection, in which StcE acts first as a mucinase and then as an anti-inflammatory agent by localizing C1-INH to cell membranes.

Inhibition of plasma kallikrein by C1-inhibitor: role of endothelial cells and the amino-terminal domain of C1-inhibitor

Activation of plasma prekallikein and generation of bradykinin are responsible for the angioedema attacks observed with C1-inhibitor deficiency. Heterozygous individuals with <50% levels of active C1-inhibitor are susceptible to angioedema attacks indicating a critical need for C1-inhibitor to be present at maximum levels to prevent unwanted prekallikrein activation. Studies with purified proteins do not adequately explain this observation. Therefore to investigate why reduction of C1-inhibitor to levels seen in angioedema patients results in excessive kallikrein generation we examined the effect of endothelial cells on the inhibition of kallikrein by C1-inhibitor. Surprisingly, it was found that a C1-inhibitor concentration of greater than 1 microM was needed to inhibit 3 nM kallikrein. We propose that this apparent protection from inhibition was mediated by kallikrein binding to the cells via the heavy chain in a high molecular weight kininogen and zinc independent manner. Protection of kallikrein from inhibition was not observed when C1-inhibitor truncated in the amino-terminal domain by the StcE metalloproteinase was used, which suggests a novel function for this unique domain. The requirement for high concentrations of C1-inhibitor to fully inhibit kallikrein is consistent with the fact that reduced levels of C1-inhibitor result in the kallikrein activation seen in angioedema.

The StcE protease contributes to intimate adherence of enterohemorrhagic Escherichia coli O157:H7 to host cells

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a diarrheal pathogen that causes attaching and effacing (A/E) lesions on intestinal epithelial cells. Strains of the O157 serogroup carry the large virulence plasmid pO157, which encodes the etp type II secretion system that secretes the genetically linked zinc metalloprotease StcE. The Ler regulator controls expression of many genes involved in A/E lesion formation, as well as StcE, suggesting StcE may be important at a similar time during colonization. Our laboratory has previously demonstrated that StcE cleaves C1-esterase inhibitor, a regulator of multiple inflammation pathways. Here we report two new substrates for StcE, mucin 7 and glycoprotein 340, and that purified StcE reduces the viscosity of human saliva. We tested the hypothesis that StcE contributes to intimate adherence of EHEC to host cells by cleavage of glycoproteins from the cell surface. The fluorescent actin stain (FAS) test was used to observe the intimate adherence represented by fluorescently stained bacteria colocalized with regions of bundled actin formed on HEp-2 cells. An E. coli O157:H7 strain with a stcE gene deletion was not affected in its ability to generally adhere to HEp-2 cells, but it did score threefold lower on the FAS test than wild-type or complemented strains. Addition of exogenous recombinant StcE increased intimate adherence of the mutant to wild-type levels. Thus, StcE may help block host clearance of E. coli O157:H7 by destruction of some classes of glycoproteins, and it contributes to intimate adherence of E. coli O157:H7 to the HEp-2 cell surface.

StcE, a metalloprotease secreted by Escherichia coli O157:H7, specifically cleaves C1 esterase inhibitor

Escherichia coli O157:H7 causes diarrhoea, haemorrhagic colitis, and the haemolytic uraemic syndrome. We have identified a protein of previously unknown function encoded on the pO157 virulence plasmid of E. coli O157:H7, which is the first described protease that specifically cleaves C1 esterase inhibitor (C1-INH), a member of the serine protease inhibitor family. The protein, named StcE for secreted protease of C1 esterase inhibitor from EHEC (formerly Tagn), cleaves C1-INH to produce (unique) approximately 60-65 kDa fragments. StcE does not digest other serine protease inhibitors, extracellular matrix proteins or universal protease targets. We also observed that StcE causes the aggregation of cultured human T cells but not macrophage-like cells or B cells. Substitution of aspartic acid for glutamic acid at StcE position 435 within the consensus metalloprotease active site ablates its abilities to digest C1-INH and to aggregate T cells. StcE is secreted by the etp type II secretion pathway encoded on pO157, and extracellular StcE levels are positively regulated by the LEE-encoded regulator, Ler. StcE antigen and activity were detected in the faeces of a child with an E. coli O157:H7 infection, demonstrating the expression of StcE during human disease. Cleavage of C1-INH by StcE could plausibly cause localized pro-inflammatory and coagulation responses resulting in tissue damage, intestinal oedema and thrombotic abnormalities.