Helicobacter pylori Exposure in Nausea and Vomiting of Pregnancy Increases Risk of Preterm Delivery

Background

Hyperemesis gravidarum (HG), a severe form of nausea and vomiting in pregnancy (NVP), is a leading indication for hospitalization in the first trimester. NVP and HG are associated with Helicobacter pylori (HP) infection in non-United States cohorts. How HP exposure and NVP interact to affect metabolic disturbance and pregnancy outcomes is not known.

Materials and Methods

We designed a retrospective cohort study relating HP and NVP to serum electrolyte laboratory results, preterm delivery, and infant birth weight. Single academic institution discovery and independent multi-institutional validation cohorts included pregnant subjects with an HP test result. Associations of HP, NVP, and pregnancy outcomes were assessed with odds ratio calculations, Student's t-tests, and multivariate logistic regression.

Results

Among subjects with positive HP test results, the prevalence of hyperemesis gravidarum (HG) was 0.025 (66 of 2671) and NVP was 0.27 (710 of 2671). Subjects with negative HP had prevalence of HG 0.015 (165 of 10,960) and NVP 0.22 (2392 of 10,960). History of HP exposure increased risk of NVP, including HG (odds ratio 1.3, 95% CI 1.1-1.4). Patients with HP exposure had lower serum potassium (mean difference 0.1 mEq/L) and bicarbonate (mean difference 0.3 mEq/L) during pregnancy than HP-negative patients (p < 0.01). Serum potassium was lowest in subjects with both NVP and HP exposure (mean 3.5 mEq/L [3.4-3.6], p < 0.0001). HP exposure alone carried increased risk for preterm delivery (OR 1.3 [1.1-1.4]). NVP alone increased risk of preterm delivery (OR 2.8 [2.5-3.1]) including second trimester delivery (OR 2.2 [1.7-2.8]). In multivariate analysis, HP exposure in the setting of NVP further increased risk of preterm delivery (adjusted OR 1.4 [1.0-1.9], p = 0.03).

Conclusions

H. pylori exposure and diagnosis of NVP are individually associated with metabolic disturbances and adverse pregnancy outcomes such as preterm labor and delivery, and their combination further increases risk in US populations.

540. Impact on Clinical Decision Making of Microbial Broad Range Metagenomic Cell-Free DNA at a Single Academic Medical Center, a Retrospective Study

Background

Broad-range metagenomic cell-free DNA testing (Karius®) can identify a variety of pathogens from a single blood sample to help in diagnosis of deep seated and bloodstream infections. Few studies have evaluated the impact of Karius testing on clinical decision making when compared to more conventional diagnostic methods.

Methods

We performed a retrospective cohort study of adult patients who had Karius tests at University of Iowa Hospitals and Clinics between 01/2020 and 10/2021. Chart review was conducted to obtain patient characteristics and clinical course including patient age, immunocompromising conditions, involvement of Infectious Disease (ID) consultant, reason for the test, and final diagnosis. Results of the Karius tests and conventional tests were compared for concordance. Clinical impact and change in management due to Karius testing were determined using previously established criteria outlined by Hogan et al.(Clin Infect Dis. 2021 Jan 27;72(2):239-245)

Results

Out of 26 patients who had Karius testing, 20 patients (77%) had an immunocompromising condition, the most common of which was hematologic malignancy (17 patients, 65%). Twenty-four patients (92%) had received a formal ID consultation prior to the test. The most common finding prior to testing was the presence of pulmonary infiltrates on imaging (20 patients, 77%). Karius testing was positive in 18/26 cases (69%). Organisms detected by Karius and conventional testing were concordant in 9/18 cases (50%). Karius test result had a positive clinical impact in 3 cases (12%), an indeterminant impact in 1 case (3%) and no impact in 22 cases (85%). Reasons for a positive impact are as follows: 1 case with initiation of antituberculosis therapy due to earlier diagnosis of tuberculosis, 1 case with de-escalation of antifungal therapy based on negative Karius results, and 1 case of clearance for urgent lung transplantation based on negative Karius results in the setting of mobile echo density on echocardiogram in the absence of other stigmata of endocarditis.

Conclusion

The impact of Karius testing on patient management appears limited. Further studies will be needed to identify patient populations or disease factors in which this testing have clinical impact.

Disclosures

All Authors: No reported disclosures.

Does Antimicrobial Prophylaxis in Patients with Specific Comorbidities Reduce the Risk of Infection after Simple Cystourethroscopy?

INTRODUCTION

We evaluated whether antimicrobial prophylaxis decreases rates of post-procedural infection (urinary tract infection or sepsis) after simple cystourethroscopy for patients with specific comorbidities.

METHODS

We utilized Epic® reporting software to conduct a retrospective review of all simple cystourethroscopy procedures performed by providers in our urology department from August 4, 2014 to December 31, 2019. Data collected included patient comorbidities, antimicrobial prophylaxis administration and incidence of post-procedural infection. Mixed effects logistic regression models were utilized to estimate the effects of antimicrobial prophylaxis and patient comorbidities on the odds of post-procedural infection.

RESULTS

Antimicrobial prophylaxis was given for 7,001 (78%) of 8,997 simple cystourethroscopy procedures. Overall, 83 (0.9%) post-procedural infections occurred. The estimated odds of post-procedural infection were lower when antimicrobial prophylaxis was given compared to those without prophylaxis (OR 0.51, 95% CI 0.35-0.76; p <0.01). The number needed to treat with antimicrobial prophylaxis to prevent 1 post-procedural infection was 100. None of the comorbidities evaluated showed significant benefit from antimicrobial prophylaxis for prevention of post-procedural infection.

CONCLUSIONS

Overall, the rate of post-procedural infection after simple office cystourethroscopy was low (0.9%). Though antimicrobial prophylaxis decreased the odds of post-procedural infection overall, the number needed to treat was high (100). Antibiotic prophylaxis was not shown to significantly reduce the risk of post-procedural infection in any of the comorbidity groups we evaluated. These findings suggest that the comorbidities evaluated in this study should not be used to recommend antibiotic prophylaxis for simple cystourethroscopy.

Practical Considerations for Implementation of SARS-CoV-2 Serological Testing in the Clinical Laboratory: Experience at an Academic Medical Center

Molecular techniques, especially reverse transcriptase polymerase chain reaction (RT-PCR), have been the gold standard for the diagnosis of acute severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Serological tests for SARS-CoV-2 have been widely used for serosurveys, epidemiology, and identification of potential convalescent plasma donors. However, the clinical role of serologic testing is still limited and evolving. In this report, we describe the experience of selecting, validating, and implementing SARS-CoV-2 serologic testing for clinical purposes at an academic medical center in a rural state. Successful implementation involved close collaboration between pathology, infectious diseases, and outpatient clinics. The most common clinician concerns were appropriateness/utility of testing, patient charges/insurance coverage, and assay specificity. In analyzing test utilization, serologic testing in the first month after go-live was almost entirely outpatient and appeared to be strongly driven by patient interest (including health care workers and others in high-risk occupations for exposure to SARS-CoV-2), with little evidence that the results impacted clinical decision-making. Test volumes for serology declined steadily through October 31, 2020, with inpatient ordering assuming a steadily higher percentage of the total. In a 5-month period, SARS-CoV-2 serology test volumes amounted to only 1.3% of that of reverse transcriptase polymerase chain reaction. Unlike reverse transcriptase polymerase chain reaction, supply chain challenges and reagent availability were not major issues for serology testing. We also discuss the most recent challenge of requirements for SARS-CoV-2 testing in international travel protocols. Overall, our experience at an academic medical center shows that SARS-CoV-2 serology testing assumed a limited clinical role.

Asymptomatic Pre-Operative COVID-19 Screening for Essential and Elective Surgeries: Early Results of Universal Screening at a Midwestern Academic Medical Center

BACKGROUND

During the novel Coronavirus 2019 (COVID-19) worldwide pandemic, viral testing has largely focused on patients presenting with fever and respiratory symptoms. Although Centers for Disease Control has reported 1,551,095 cases in the United States as of May 21, 2020, asymptomatic infection rates remain unknown within the U.S., especially in geographically disparate regions.

METHODS

On April 7, 2020 our hospital established universal SARS-CoV-2 screening using RT-PCR RNA detection from nasopharyngeal swabs from asymptomatic patients prior to essential and elective surgeries. This study included 1,997 asymptomatic patients undergoing surgical procedures and 1,797 admitted for medical management at a Midwestern academic hospital between April 7, 2020 and May 21, 2020.

RESULTS

As of May 21, asymptomatic testing for SARS-CoV-2 infection had been completed for 1,997 surgical patients and 1,797 non-surgical patients. Initial testing was positive in 26 patients, with an additional four positive tests occurring during repeat testing when greater than 48 hours had elapsed since initial testing. Overall asymptomatic infection rate was 0.79%. Asymptomatic infection rate was significantly lower in surgical patients (0.35% vs. 1.28%, p=0.001). Surgical patients tended to be older than non-surgical patients, although this was not statistically significant (51, IQR 27-65 vsx 46, IQR 28-64, p=0.057). Orthopedic surgery patients were significantly younger than those from other surgical services (42 vs. 53 yrs, p<0.001), however orthopedic and non-orthopedic surgical patients had similar asymptomatic infection rates (0.70% vs. 0.25%, p=0.173).

CONCLUSION

Among asymptomatic patients tested at a Midwestern academic medical center, 0.79% were infected with SARS-CoV-2 virus. These findings will help guide screening protocols at medical centers while providing essential and elective procedures during the COVID-19 pandemic. While the asymptomatic infection rate was low, this data substantiates the threat of asymptomatic infections and potential for community viral spread. These results may not be generalizable to large urban population centers or areas with high concentrations of COVID-19, each region must use available data to evaluate the risk-benefit ratio of universal testing vs universal contact precautions.Level of Evidence: IV.

Experience With Pretravel Testing for SARS-CoV-2 at an Academic Medical Center

International travel has been a significant factor in the coronavirus disease 2019 pandemic. Many countries and airlines have implemented travel restrictions to limit the spread of the causative agent, severe acute respiratory syndrome coronavirus-2. A common requirement has been a negative reverse-transcriptase polymerase chain reaction performed by a clinical laboratory within 48 to 72 hours of departure. A more recent travel mandate for severe acute respiratory syndrome coronavirus-2 immunoglobulin M serology testing was instituted by the Chinese government on October 29, 2020. Pretravel testing for severe acute respiratory syndrome coronavirus-2 raises complications in terms of cost, turnaround time, and follow-up of positive results. In this report, we describe the experience of a multidisciplinary collaboration to develop a workflow for pretravel severe acute respiratory syndrome coronavirus-2 reverse-transcriptase polymerase chain reaction and immunoglobulin M serology testing at an academic medical center. The workflow primarily involved self-payment by patients and preferred retrieval of results by the patient through the electronic health record patient portal (Epic MyChart). A total of 556 unique patients underwent pretravel reverse-transcriptase polymerase chain reaction testing, with 13 (2.4%) having one or more positive results, a rate similar to that for reverse-transcriptase polymerase chain reaction testing performed for other protocol-driven asymptomatic screening (eg, inpatient admissions, preprocedural) at our medical center. For 5 of 13 reverse-transcriptase polymerase chain reaction positive samples, the traveler had clinical history, prior reverse-transcriptase polymerase chain reaction positive, and high cycle thresholds values on pretravel testing consistent with remote infection and minimal transmission risk. Severe acute respiratory syndrome coronavirus-2 immunoglobulin M was performed on only 24 patients but resulted in 2 likely false positives. Overall, our experience at an academic medical center shows the challenge with pretravel severe acute respiratory syndrome coronavirus-2 testing.

The Postmortem Features of Mucormycosis

Mucormycosis is a rare and severe invasive fungal infection caused by ubiquitous fungi of the order Mucorales. Infection often occurs in immunocompromised hosts and includes cutaneous, pulmonary, gastrointestinal, rhinocerebral, and disseminated forms of disease. Although the clinical characteristics of mucormycosis are well established, infection can be difficult to diagnose antemortem, resulting in frequent postmortem diagnoses. Despite this, the gross appearance of mucormycosis at autopsy has not been well described. In the present report we illustrate the gross and histologic findings in four autopsy cases of mucormycosis, including one case of pulmonary disease and three cases of disseminated mucormycosis with cerebral, pulmonary, hepatic, renal, and gastrointestinal involvement. In all cases autopsy examination demonstrated characteristic hemorrhagic infarcts with a targetoid appearance in the affected organs. These findings are secondary to fungal angioinvasion with subsequent thrombosis and tissue necrosis. Mucormycosis should be suspected at autopsy when these characteristic infarcts are identified within the proper clinical context, and a high suspicion for atypical infections should be maintained postmortem in immunosuppressed patients.

Characteristics of Nontuberculous Mycobacterial Infections at a Midwestern Tertiary Hospital: A Retrospective Study of 365 Patients

Background

The prevalence of infections due to nontuberculous mycobacteria (NTM) is increasing worldwide, yet little is known about the epidemiology and pathophysiology of these ubiquitous environmental organisms. Pulmonary disease due to Mycobacterium avium complex is most prevalent, but many other NTM species can cause disease in virtually any organ system. As NTM becomes an increasingly common cause of morbidity and mortality, more information is needed about the epidemiology of NTM disease.

Methods

We conducted a retrospective chart review of all patients with cultures that grew NTM at a Midwestern tertiary hospital from 1996 to 2017. Information on demographics, medical history, clinical findings, treatment, and outcome was obtained from medical records of all NTM isolates. American Thoracic Society/Infectious Diseases Society of America criteria were used to define pulmonary NTM infections.

Results

We identified 1064 NTM isolates, 365 of which met criteria for NTM infection. Pulmonary cases predominated (185 of 365; 50.7%), followed by skin/soft tissue (56 of 365; 15.3%), disseminated (40 of 365; 11%), and lymphatic (28 of 365; 7.7%) disease. Mycobacterium avium complex was the most common species (184 of 365; 50.4%). Individuals aged >50 years were most affected (207 of 365; 56.7%). Common comorbidities included structural lung disease (116 of 365; 31.8%), use of immunosuppressive medications (78 of 365; 21.4%), malignancy (59 of 365; 16.2%), and human immunodeficiency virus (42 of 365; 11.5%).

Conclusions

This large cohort provides information on the demographics, risk factors, and disease course of patients with pulmonary and extrapulmonary NTM infections. Most patients had medical comorbidities that resulted in anatomic, genetic, or immunologic risk factors for NTM infection. Further population-based studies and increased disease surveillance are warranted to further characterize NTM infection prevalence and trends.

Data on the relationship of signal-to-cutoff ratio of two HIV antigen/antibody combination assays to subsequent confirmation of HIV-1 infection in a low-prevalence population

HIV-1/2 antigen/antibody (Ag/Ab) immunoassays that detect HIV-1 and HIV-2 antibodies and HIV-1 p24 antigen are commonly used in the diagnosis of HIV-1/HIV-2 infections in human plasma/serum. Samples from patients with positive screening results require confirmation by antibody differentiation and/or HIV PCR assays. HIV screening assays are commonly reported as positive or negative based on a signal-to-cutoff (S/CO) threshold. For some HIV screening assays, the strength of the S/CO value correlates with likelihood that confirmatory testing will be positive. The data in this article provide results from two HIV Ag/Ab combination assays (Abbott Architect HIV Ag/Ab Combo Assay, a 4^th generation combination assay; Bio-Rad Bioplex 2200 HIV Ag-Ab Assay, a 5^th generation assay). The data include 23,331 HIV screening results, S/CO ratios, antibody differentiation or Western blot results (for samples with positive HIV screens), HIV-1 PCR results (if performed), patient location at time of testing, age, and sex. Distribution of S/CO ratios for the Bio-Rad HIV screening assay data and the distribution of S/CO values for samples with positive screening results were analyzed.

Pollination and fruit set in two rewardless slipper orchids and their hybrids (Cypripedium, Orchidaceae): large yellow flowers outperform small white flowers in the northern tall grass prairie

Species with rewardless flowers often have low fruit to flower ratios, although wide temporal and spatial variation in fruiting success can occur. We compared floral phenotypes, insect visitors and fruiting success in four populations of the small white (Cypripedium candidum) and yellow (C. parviflorum) lady's slipper orchids and their hybrids near the northern extent of North America's tall grass prairie. Flower and fruit numbers were observed for two seasons on marked individuals (n = 1811). Floral traits were measured on 82-140 individuals per taxon and analysed in relation to fruiting success. All insects found inside flowers were collected, inspected for pollen smears and measured for comparison to floral features. Among orchid taxa, C. candidum had the smallest flowers, lowest number and variety of insect visitors, and lowest fruit to flower ratios. These measures were intermediate in hybrids and highest in C. parviflorum, despite low flower numbers in the latter. Within orchid taxa, fruit number was positively related to flower number, but fruit to flower ratios decreased slightly, as would be expected if pollinators left unrewarding patches. Potential pollinators included the dipteran Odontomyia pubescens and hymenopterans Andrena spp., Apis mellifera and Lasioglossum zonulum. Cypripedium parviflorum had a reproductive advantage over C. candidum across multiple populations and years. Hybrids showed segregation for floral traits, and hybrid fruiting success increased with a deeper intensity of yellow pigment and larger escape routes for floral visitors. These same attributes likely contributed to the relatively high fruit set in C. parviflorum in the study region.

1997. Real-World Impact of Accelerate Pheno Implementation with Antimicrobial Stewardship Intervention

Background

Accelerate Pheno® (AP) is a novel diagnostic system that provides rapid identification and antibiotic susceptibility results for most commonly isolated organisms within hours of blood culture (BC) positivity. There are little data on this technology’s real-world implementation with antimicrobial stewardship intervention and effect on optimal targeted therapy.

Methods

AP was implemented at UIHC in September 2018 and paired with antimicrobial stewardship team (AST) review. AST recommendations were provided in real time during weekday hours and through a retrospective review process for off-hours results. Microbiologic and clinical data were collected prospectively. Due to inconsistencies in instrument performance identified after the first month, two post-implementation periods (Group A = October 2018–January 2019; Group B = February 2019–mid-April 2019) were analyzed to assess quality improvement efforts during clinical roll-out.

Results

In the 6.5-month combined period, 690 unique BC samples were run on AP and reviewed by AST (417 in A; 273 in B). Performance of the technology improved, with 78.9% (329/417) of isolates in Grp A identified vs. 85.3% in Grp B (233/273). Percentage of runs with progression to antibiotic susceptibility improved from 76.1% to 92.3%. Over both time periods, AST intervened on 277 samples (Figure 1). Recommendations (bug-drug mismatch, de-escalation, dose optimization, and infectious disease consult) were accepted at a rate of 97.4%. Time from BC positivity to optimal therapy was 15.3 hours (Figure 2).

Conclusion

Implementation of AP with AST review resulted in rapid identification and antibiotic susceptibility results with early optimization of antimicrobial therapy. Highest impact was seen in the management of patients with resistant Gram-negative infections. Oversight of the implementation by a partnership of clinical microbiology and the antimicrobial stewardship team was critical in identifying real-time implementation issues and opportunities for quality improvement. Though real-world performance was slightly inferior to published trial data, the instrument’s exceedingly fast time to AS represents a significant advantage over other systems and enhances clinical care and patient safety particularly when paired with AST intervention.

Disclosures

All authors: No reported disclosures.

Burden and Characteristics of Unsolicited Emails from Medical/Scientific Journals, Conferences, and Webinars to Faculty and Trainees at an Academic Pathology Department

Background

Professionals and trainees in the medical and scientific fields may receive high e-mail volumes for conferences and journals. In this report, we analyze the amount and characteristics of unsolicited e-mails for journals, conferences, and webinars received by faculty and trainees in a pathology department at an academic medical center.

Methods

With informed consent, we analyzed 7 consecutive days of e-mails from faculty and trainees who voluntarily participated in the study and saved unsolicited e-mails from their institutional e-mail address (including junk e-mail folder) for medical/scientific journals, conferences, and webinars. All e-mails were examined for characteristics such as reply receipts, domain name, and spam likelihood. Journal e-mails were specifically analyzed for claims in the message body (for example, peer review, indexing in databases/resources, rapid publication) and actual inclusion in recognized journal databases/resources.

Results

A total of 17 faculty (4 assistant, 4 associate, and 9 full professors) and 9 trainees (5 medical students, 2 pathology residents, and 2 pathology fellows) completed the study. A total of 755 e-mails met study criteria (417 e-mails from 328 unique journals, 244 for conferences, and 94 for webinars). Overall, 44.4% of e-mails were flagged as potential spam by the institutional default settings, and 13.8% requested reply receipts. The highest burden of e-mails in 7 days was by associate and full professors (maximum 158 or approximately 8200 per year), although some trainees and assistant professors had over 30 e-mails in 7 days (approximately 1560 per year). Common characteristics of journal e-mails were mention of "peer review" in the message body and low rates of inclusion in recognized journal databases/resources, with 76.4% not found in any of 9 journal databases/resources. The location for conferences in e-mails included 31 different countries, with the most common being the United States (33.2%), Italy (9.8%), China (4.9%), United Kingdom (4.9%), and Canada (4.5%).

Conclusions

The present study in an academic pathology department shows a high burden of unsolicited e-mails for medical/scientific journals, conferences, and webinars, especially to associate and full professors. We also demonstrate that some pathology trainees and junior faculty are receiving an estimated 1500 unsolicited e-mails per year.

Cutaneous Infections Due to Nontuberculosis Mycobacterium: Recognition and Management

Nontuberculous mycobacteria (NTM) are a diverse group of organisms that are ubiquitous in the environment, and the incidence of cutaneous infections due to NTM has been steadily increasing. Cutaneous infections due to NTM can be difficult to diagnose, due to their wide spectrum of clinical presentations and histopathological findings that are often nonspecific. A variety of modalities including tissue culture and polymerase chain reaction (PCR) assays may be necessary to identify the organism. Treatment can also be challenging, as it can depend on multiple factors, including the causative organism, the patient's immunological status, and the extent of disease involvement. In this review, we discuss the common presentations of cutaneous NTM infections, diagnostic tools, and treatment recommendations. A multi-disciplinary approach that involves good communication between the clinician, the histopathologist, the microbiologist, and infectious disease specialists can help lead to successful diagnosis and management.

Angioinvasive fungal infections impacting the skin: Diagnosis, management, and complications

As discussed in the first article in this continuing medical education series, angioinvasive fungal infections pose a significant risk to immunocompromised and immunocompetent patients alike, with a potential for severe morbidity and high mortality. The first article in this series focused on the epidemiology and clinical presentation of these infections; this article discusses the diagnosis, management, and potential complications of these infections. The mainstay diagnostic tests (positive tissue culture with histologic confirmation) are often supplemented with serum biomarker assays and molecular testing (eg, quantitative polymerase chain reaction analysis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry) to ensure proper speciation. When an angioinvasive fungal infection is suspected or diagnosed, further workup for visceral involvement also is essential and may partially depend on the organism. Different fungal organisms have varied susceptibilities to antifungal agents, and knowledge on optimal treatment regimens is important to avoid the potential complications associated with undertreated or untreated fungal infections.

Implementation of a Mobile Clinical Decision Support Application to Augment Local Antimicrobial Stewardship

Background:

Medical applications for mobile devices allow clinicians to leverage microbiological data and standardized guidelines to treat patients with infectious diseases. We report the implementation of a mobile clinical decision support (CDS) application to augment local antimicrobial stewardship.

Methods:

We detail the implementation of our mobile CDS application over 20 months. Application utilization data were collected and evaluated using descriptive statistics to quantify the impact of our implementation.

Results:

Project initiation focused on engaging key stakeholders, developing a business case, and selecting a mobile platform. The preimplementation phase included content development, creation of a pathway for content approval within the hospital committee structure, engaging clinical leaders, and formatting the first version of the guide. Implementation involved a media campaign, staff education, and integration within the electronic medical record and hospital mobile devices. The postimplementation phase required ongoing quality improvement, revision of outdated content, and repeated staff education. The evaluation phase included a guide utilization analysis, reporting to hospital leadership, and sustainability and innovation planning. The mobile application was downloaded 3056 times and accessed 9259 times during the study period. The companion web viewer was accessed 8214 times.

Conclusions:

Successful implementation of a customizable mobile CDS tool enabled our team to expand beyond microbiological data to clinical diagnosis, treatment, and antimicrobial stewardship, broadening our influence on antimicrobial prescribing and incorporating utilization data to inspire new quality and safety initiatives. Further studies are needed to assess the impact on antimicrobial utilization, infection control measures, and patient care outcomes.

Implementation of Epic Beaker Anatomic Pathology at an Academic Medical Center

Background:

Beaker is a relatively new laboratory information system (LIS) offered by Epic Systems Corporation as part of its suite of health-care software and bundled with its electronic medical record, EpicCare. It is divided into two modules, Beaker anatomic pathology (Beaker AP) and Beaker Clinical Pathology. In this report, we describe our experience implementing Beaker AP version 2014 at an academic medical center with a go-live date of October 2015.

Methods:

This report covers preimplementation preparations and challenges beginning in September 2014, issues discovered soon after go-live in October 2015, and some post go-live optimizations using data from meetings, debriefings, and the project closure document.

Results:

We share specific issues that we encountered during implementation, including difficulties with the proposed frozen section workflow, developing a shared specimen source dictionary, and implementation of the standard Beaker workflow in large institution with trainees. We share specific strategies that we used to overcome these issues for a successful Beaker AP implementation. Several areas of the laboratory-required adaptation of the default Beaker build parameters to meet the needs of the workflow in a busy academic medical center. In a few areas, our laboratory was unable to use the Beaker functionality to support our workflow, and we have continued to use paper or have altered our workflow. In spite of several difficulties that required creative solutions before go-live, the implementation has been successful based on satisfaction surveys completed by pathologists and others who use the software. However, optimization of Beaker workflows has continued to be an ongoing process after go-live to the present time.

Conclusions:

The Beaker AP LIS can be successfully implemented at an academic medical center but requires significant forethought, creative adaptation, and continued shared management of the ongoing product by institutional and departmental information technology staff as well as laboratory managers to meet the needs of the laboratory.

Traditional versus reverse syphilis algorithms: A comparison at a large academic medical center

Objectives

An increasing number of institutions are transitioning from the traditional syphilis testing algorithm (initial screening with nontreponemal tests) to the ‘reverse’ algorithm (initial screening with treponemal tests such as syphilis IgG). The aim of this study was to evaluate the switch in syphilis algorithm at an academic medical center with a population with low syphilis prevalence.

Design and methods

We performed a six-year retrospective study at the University of Iowa Hospitals and Clinics, an academic medical center, comparing the traditional algorithm (n=12,612) with the reverse algorithm (n=10,453). False positives were considered to be positive screens with negative confirmatory testing.

Results

Using the traditional algorithm, 93 samples (0.7% of total) screened positive with RPR, with 40 of these samples having negative TP-PA testing (43% of positive screens, 0.3% of total). Using the reverse algorithm, 110 screened positive with syphilis IgG (1.1% of total), and 33 of these samples had both negative RPR and TP-PA (30% of positive screens, 0.3% of total). In both algorithms, higher RPR titers and syphilis IgG values were associated with increased probability of positive confirmation.

Conclusions

In this study at an academic medical center, the reverse algorithm had significantly more total positive screens than the traditional algorithm. Both algorithms produced equivalent rates of active infection. The quantitative difference in positives between the two algorithms are the category of patients who are syphilis IgG positive, RPR non-reactive, and TP-PA reactive. Specimens with higher RPR titers and syphilis IgG values are more likely to confirm positive.

Using Focused Laboratory Management and Quality Improvement Projects to Enhance Resident Training and Foster Scholarship

Training in patient safety, quality, and management is widely recognized as an important element of graduate medical education. These concepts have been intertwined in pathology graduate medical education for many years, although training programs face challenges in creating explicit learning opportunities in these fields. Tangibly involving pathology residents in management and quality improvement projects has the potential to teach and reinforce key concepts and further fulfill Accreditation Council for Graduate Medical Education goals for pursuing projects related to patient safety and quality improvement. In this report, we present our experience at a pathology residency program (University of Iowa) in engaging pathology residents in projects related to practical issues of laboratory management, process improvement, and informatics. In this program, at least 1 management/quality improvement project, typically performed during a clinical chemistry/management rotation, was required and ideally resulted in a journal publication. The residency program also initiated a monthly management/informatics series for pathology externs, residents, and fellows that covers a wide range of topics. Since 2010, all pathology residents at the University of Iowa have completed at least 1 management/quality improvement project. Many of the projects involved aspects of laboratory test utilization, with some projects focused on other areas such as human resources, informatics, or process improvement. Since 2012, 31 peer-reviewed journal articles involving effort from 26 residents have been published. Multiple projects resulted in changes in ongoing practice, particularly within the hospital electronic health record. Focused management/quality improvement projects involving pathology residents can result in both meaningful quality improvement and scholarly output.

Neonatal Enterovirus Infection: Case Series of Clinical Sepsis and Positive Cerebrospinal Fluid Polymerase Chain Reaction Test with Myocarditis and Cerebral White Matter Injury Complications

Objective We describe five neonates with enteroviral (EV) infection to demonstrate central nervous system (CNS) and cardiac complications and report successful treatment of myocarditis with immunoglobulin intravenous (IVIG) in two. Study Design Case series identified during three enteroviral seasons in one neonatal intensive care unit (NICU) by cerebral spinal fluid (CSF) reverse transcriptase polymerase chain reaction (PCR) testing for EV in neonates suspected to have sepsis, but with sterile bacterial cultures. Results Cases were identified in each of three sequential years in a NICU with 800 to 900 admissions/year. Two cases were likely acquired perinatally; all were symptomatic with lethargy and poor feeding by age 5 to 10 days. All had signs of sepsis and/or meningitis; one progressed to periventricular leukomalacia and encephalomalacia. Two recovered from myocarditis after treatment that included IVIG 3 to 5 g/kg. Conclusion Neonates who appear septic without bacterial etiology may have EV CNS infections that can be diagnosed rapidly by CSF PCR testing. Cases may be underdiagnosed in the early neonatal period if specific testing is not performed. Neonates with EV infection should be investigated for evidence of periventricular leukomalacia, screened for myocarditis, and considered for IVIG treatment.

Identification of Low-Level Vancomycin Resistance in Staphylococcus aureus in the Era of Informatics

Vancomycin-intermediateStaphylococcus aureus(VISA) and heteroresistant VISA (hVISA) are pathogens for which accurate antimicrobial susceptibility testing (AST) would rule out standard treatment with vancomycin. Unfortunately, AST for vancomycin is relatively slow and standard methods are unable to reliably detect VISA and hVISA. An article in this issue (C. A. Mather, B. J. Werth, S. Sivagnanam, D. J. SenGupta, and S. M. Butler-Wu, J Clin Microbiol 54:883-890, 2016, doi:http://dx.doi.org/10.1128/JCM.02428-15) describes a rapid whole-cell matrix-assisted laser desorption ionization-time of flight proxy susceptibility method that highlights current innovations and challenges with rapid AST, VISA/hVISA identification, and clinical bioinformatics.

Implementation of Epic Beaker Clinical Pathology at an academic medical center

BACKGROUND

Epic Beaker Clinical Pathology (CP) is a relatively new laboratory information system (LIS) operating within the Epic suite of software applications. To date, there have not been any publications describing implementation of Beaker CP. In this report, we describe our experience in implementing Beaker CP version 2012 at a state academic medical center with a go-live of August 2014 and a subsequent upgrade to Beaker version 2014 in May 2015. The implementation of Beaker CP was concurrent with implementations of Epic modules for revenue cycle, patient scheduling, and patient registration.

METHODS

Our analysis covers approximately 3 years of time (2 years preimplementation of Beaker CP and roughly 1 year after) using data summarized from pre- and post-implementation meetings, debriefings, and the closure document for the project.

RESULTS

We summarize positive aspects of, and key factors leading to, a successful implementation of Beaker CP. The early inclusion of subject matter experts in the design and validation of Beaker workflows was very helpful. Since Beaker CP does not directly interface with laboratory instrumentation, the clinical laboratories spent extensive preimplementation effort establishing middleware interfaces. Immediate challenges postimplementation included bar code scanning and nursing adaptation to Beaker CP specimen collection. The most substantial changes in laboratory workflow occurred with microbiology orders. This posed a considerable challenge with microbiology orders from the operating rooms and required intensive interventions in the weeks following go-live. In postimplementation surveys, pathology staff, informatics staff, and end-users expressed satisfaction with the new LIS.

CONCLUSIONS

Beaker CP can serve as an effective LIS for an academic medical center. Careful planning and preparation aid the transition to this LIS.

Use of a data warehouse at an academic medical center for clinical pathology quality improvement, education, and research

BACKGROUND

Pathology data contained within the electronic health record (EHR), and laboratory information system (LIS) of hospitals represents a potentially powerful resource to improve clinical care. However, existing reporting tools within commercial EHR and LIS software may not be able to efficiently and rapidly mine data for quality improvement and research applications.

MATERIALS AND METHODS

We present experience using a data warehouse produced collaboratively between an academic medical center and a private company. The data warehouse contains data from the EHR, LIS, admission/discharge/transfer system, and billing records and can be accessed using a self-service data access tool known as Starmaker. The Starmaker software allows users to use complex Boolean logic, include and exclude rules, unit conversion and reference scaling, and value aggregation using a straightforward visual interface. More complex queries can be achieved by users with experience with Structured Query Language. Queries can use biomedical ontologies such as Logical Observation Identifiers Names and Codes and Systematized Nomenclature of Medicine.

RESULT

We present examples of successful searches using Starmaker, falling mostly in the realm of microbiology and clinical chemistry/toxicology. The searches were ones that were either very difficult or basically infeasible using reporting tools within the EHR and LIS used in the medical center. One of the main strengths of Starmaker searches is rapid results, with typical searches covering 5 years taking only 1-2 min. A "Run Count" feature quickly outputs the number of cases meeting criteria, allowing for refinement of searches before downloading patient-identifiable data. The Starmaker tool is available to pathology residents and fellows, with some using this tool for quality improvement and scholarly projects.

CONCLUSION

A data warehouse has significant potential for improving utilization of clinical pathology testing. Software that can access data warehouse using a straightforward visual interface can be incorporated into pathology training programs.

Infection with a chlorophyllic eukaryote after a traumatic freshwater injury

Infections with chlorophyllic algae are uncommon. Invasive infection with Desmodesmus armatus developed in two patients independently after they each sustained a penetrating freshwater injury.

Treatment and prevention of urinary tract infection with orally active FimH inhibitors

Chronic and recurrent urinary tract infections pose a serious medical problem because there are few effective treatment options. Patients with chronic urinary tract infections are commonly treated with long-term prophylactic antibiotics that promote the development of antibiotic-resistant forms of uropathogenic Escherichia coli (UPEC), further complicating treatment. We developed small-molecular weight compounds termed mannosides that specifically inhibit the FimH type 1 pilus lectin of UPEC, which mediates bacterial colonization, invasion, and formation of recalcitrant intracellular bacterial communities in the bladder epithelium. Here, we optimized these compounds for oral bioavailability and demonstrated their fast-acting efficacy in treating chronic urinary tract infections in a preclinical murine model. These compounds also prevented infection in vivo when given prophylactically and strongly potentiated the activity of the current standard of care therapy, trimethoprim-sulfamethoxazole, against clinically resistant PBC-1 UPEC bacteria. These compounds have therapeutic efficacy after oral administration for the treatment of established urinary tract infections in vivo. Their unique mechanism of action-targeting the pilus tip adhesin FimH-circumvents the conventional requirement for drug penetration of the outer membrane, minimizing the potential for the development of resistance. The small-molecular weight compounds described herein promise to provide substantial benefit to women suffering from chronic and recurrent urinary tract infections.

Intra-individual variability in serum hepcidin precludes its use as a marker of iron status in hemodialysis patients

An accurate assessment of iron status in dialysis patients is important because both anemia and overtreatment with erythropoiesis-stimulating agents are associated with poor clinical outcomes. We have previously shown that both analytical and intra-individual (biological) variability in serum ferritin limits its utility as a proxy for iron stores in patients in this setting. As hepcidin is a direct regulator of iron status, its measurement might be useful for monitoring patients with iron dysregulation. We assessed short-term intra-individual variation of serum hepcidin in 28 patients with stable chronic kidney disease on hemodialysis. The intra-individual variability for serum hepcidin ranged from 9-79% during an initial 2-week to 12-85% over a 6-week period. The concentration of serum hepcidin was significantly correlated with serum C-reactive protein levels over the 6-week study period. Hence, significant intra-individual variability of hepcidin is likely dependent on short-term fluctuations in the inflammatory state. Thus, our results suggest that short-term measurement of serum hepcidin should not be used to guide clinical decisions regarding management of iron status in chronic hemodialysis patients.

The phylogenetic position of Carex section Phyllostachys and its implications for phylogeny and subgeneric circumscription in Carex (Cyperaceae)

Wide speculation surrounds the origin and phylogenetic relationships of the most highly reduced sections in the genus Carex. In order to gain a better understanding of phylogeny in Carex, the relationship of the reduced sect. Phyllostachys to 12 putatively related sections, representing all four subgenera (Primocarex, Indocarex, Carex, Vignea), was inferred from sequences of the ITS (internal transcribed spacer) region of nrDNA. Phylogenetic reconstructions identified two main clades: (1) a "compound" clade composed of sections from subg. Indocarex, Primocarex, and a portion of subg. Carex, and (2) a "reduced" clade consisting of sections from subg. Carex (Phyllostachys) and Primocarex (Filifoliae and Firmiculmes). Subgenus Indocarex was paraphyletic within the "compound" clade supporting classifications that have merged it within a wider subg. Indocarex/Carex/Primocarex line. Subgenus Primocarex was polyphyletic. This result was consistent with theories that extreme reduction has occurred along several different evolutionary lines in Carex. Phylogenetic theories inferred from the presence or abnormal growth of the rachilla were not supported by tree topologies. Difficult sectional circumscriptions, such as the separation of sections Laxiflorae and Careyanae, were strongly upheld by sequence data. The ITS region is an effective tool for defining sectional limits and for estimating relationships among sections in Carex, but does not provide enough phylogenetic information to fully resolve relationships below the sectional level.