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Objectives Our academic health care institution was the victim of a cyberattack that led to a complete shutdown of major patient care, operational, and communication systems, including our electronic health record (EHR), laboratory information system, pharmacy, scheduling, billing and coding, imaging software, internet, hospital shared computer drives, payroll, and digital communications. The EHR remained down for 25 days, significantly affecting our clinical pathology (CP) laboratory operations. Methods During the downtime, our CP laboratory incorporated manual interventions for patient specimen testing, recruited additional staff for reporting results, and employed multiple communication modalities to support patient care. The crisis required a swift response, employing innovative approaches to mitigate patient harm; regular, multidisciplinary engagement; and consistent, broad-reaching communications. CP leadership worked with hospital administration, staff, and our referral clients to provide the timely laboratory results needed for acute patient care. Results During this downtime, the laboratory lacked accurate information about the number of patient samples diverted to other laboratories, the number of specimens processed, and the number of test results reported. Conclusions This paper focuses on the approaches the CP division took to develop and maintain downtime operations. Laboratories should consider these strategies in preparation for a prolonged downtime.

Background Antimicrobial resistance (AMR) is a pressing global challenge detected by antimicrobial susceptibility testing (AST) performed by clinical laboratories. AST results are interpreted using clinical breakpoints, which are updated to enable accurate detection of new and emerging AMR. Laboratories that do not apply up-to-date breakpoints impede global efforts to address the AMR crisis, but the extent of this practice is poorly understood. Methods A total of 1490 clinical laboratories participating in a College of American Pathologists proficiency testing survey for bacterial cultures were queried to determine use of obsolete breakpoints. Results Between 37.9% and 70.5% of US laboratories reported using obsolete breakpoints for the antimicrobials that were queried. In contrast, only 17.7%–43.7% of international laboratories reported using obsolete breakpoints (P Conclusions These data demonstrate a significant gap in the ability to detect AMR in the US, and to a lesser extent internationally. Improved application of current breakpoints by clinical laboratories will require combined action from regulatory agencies, laboratory accreditation groups, and device manufacturers.

The U.S. Food & Drug Administration (FDA) regulates the marketing of manufacturers’ in vitro diagnostic tests (IVDs), including assays for the detection of SARS-CoV-2. The U.S. government’s Clinical Laboratory Improvement Amendments (CLIA) of 1988 regulates the studies that a clinical diagnostic laboratory needs to perform for an IVD before placing it into use. Until recently, the FDA has authorized the marketing of SARS-CoV-2 IVDs exclusively through the Emergency Use Authorization (EUA) pathway. The regulatory landscape continues to evolve, and IVDs will eventually be required to pass through conventional non-EUA FDA review pathways once the emergency declaration is terminated, in order to continue to be marketed as an IVD in the United States. When FDA regulatory status of an IVD changes or is anticipated to change, the laboratory should review manufacturer information and previously performed internal verification studies to determine what, if any, additional studies are needed before implementing the non-EUA version of the IVD in accordance with CLIA regulations. Herein, the College of American Pathologists’ Microbiology Committee provides guidance for how to approach regulatory considerations when an IVD is converted from EUA to non-EUA status.

On behalf of the Microbiology Committee of the College of American Pathologists (CAP), we respond to the recent commentary by Kirby and colleagues on the topic of bringing in new antimicrobial susceptibility testing ([1][1]). The authors state that “there is a lack of clarity regarding

Testing during the COVID-19 pandemic has been crucial to public health surveillance and clinical care. Supply chain constraints—spanning limitations in testing kits, reagents, pipet tips, and swabs availability—have challenged the ability to scale COVID-19 testing. During the early months, sample collection kits shortages constrained planned testing expansions. In response, the University of Vermont Medical Center, University of Vermont College of Medicine, Vermont Department of Health Laboratory, Aspenti Health, and providers across Vermont including 16 area hospitals partnered to surmount these barriers. The primary objectives were to increase supply availability and manage utilization. Within the first month of Vermont’s stay-at-home order, the University of Vermont Medical Center laboratory partnered with College of Medicine to create in-house collection kits, producing 5000 per week. University of Vermont Medical Center reassigned 4 phlebotomists, laboratory educators, and other laboratory staff, who had reduced workloads, to participate (requiring a total of 5.3-7.6 full-time equivalent (FTE) during the period of study). By August, automation at a local commercial laboratory produced 22,000 vials of media in one week (reducing the required personnel by 1.2 FTE). A multisite, cross-institutional approach was used to manage specimen collection kit utilization across Vermont. Hospital laboratory directors, managers, and providers agreed to order only as needed to avoid supply stockpiles and supported operational constraints through ongoing validations and kit assembly. Throughout this pandemic, Vermont has ranked highly in number of tests per million people, demonstrating the value of local collaboration to surmount obstacles during disease outbreaks and the importance of creative allocation of resources to address statewide needs.

Erythrocyte sedimentation rate (ESR) and C reactive protein (CRP) are commonly ordered in clinical practice to evaluate for inflammation. CRP is a more sensitive and specific test for detecting acute phase inflammation, and the American Society for Clinical Pathology recommends ordering CRP rather than ESR to detect acute phase inflammation in patients with undiagnosed conditions. We sought to understand CRP and ESR ordering practices and reduce unnecessary use of ESR testing at our academic medical centre. We surveyed physician leaders in clinical areas with high utilisation of ESR testing to understand the drivers of potential overutilisation of these tests. Based on survey responses, we designed an intervention focused on education, clinical decision support within the electronic medical record and quarterly audit and feedback. We evaluated appropriateness of ESR ordering before and after the intervention via structured chart audit. Comparison of monthly rates of ESR tests during the preintervention and postintervention periods was conducted using interrupted time series analysis. Clinical habit and ease of test ordering were identified as key drivers of ESR overuse. Compared with the preintervention period, we observed a 33% reduction in the number of ESR tests per month and a 25% reduction in combined CRP and ESR tests per month during the postintervention period. This reduction corresponded to an annual avoidance of 2633 ESR tests with a corresponding estimated direct cost avoidance of $23 701 annually. Although the rate of ESR testing decreased, there was no significant improvement in the clinical appropriateness of residual ESR test ordering following the intervention. A multifaceted intervention was associated with significant decreases in unnecessary ESR tests and concurrent ESR and CRP tests at our academic medical centre. Despite these reductions, there are continued opportunities to reduce inappropriate ESR testing.

Clostridium difficile is a major contributor to morbidity and mortality in the United States. Methods for identifying the organism in stool include molecular platforms, enzyme immunoassays (EIAs) for toxin, and culture. Controversy persists over whether molecular tests are too sensitive at identifying C. difficile , and there are questions about how additional laboratory information could inform clinical management and reduce over treatment. The aim of this study was to assess whether clinical factors are related to the toxin status of patients and whether information about toxin status could potentially inform clinical management of patients. A total of 201 PCR-positive C. difficile stool samples from adult patients at our institution underwent EIA toxin testing. Clinical and laboratory data were collected, and the percentage of PCR-positive/EIA-positive (PCR + /EIA + ) patients and PCR + and EIA-negative (PCR + /EIA − ) patients was calculated. Of the 201 samples, 47% were EIA positive and 53% were EIA negative. Although PCR + /EIA + patients were more likely to have had a prior C. difficile infection ( P = 0.015), there was no statistical difference between the additional data collected that correlated with a positive EIA result. We were unable to show that patients with an EIA + result had worse clinical parameters than those with EIA − results and concluded that establishing a testing algorithm that included both PCR and EIA testing would not change the clinical management of patients at our hospital.

An increasing spectrum and number of opportunistic fungal pathogens have been reported to cause disease in humans over the past decade. Disseminated phaeohyphomycoses caused by rare dematiaceous molds in immunocompromised patients have a high mortality rate and are increasingly reported in the literature. Early diagnosis of disseminated phaehyphomycosis is critical especially in neutropenic patients but can be hindered by the low sensitivity of fungal blood cultures and low clinical suspicion. Cutaneous manifestations are often the earliest sign of disease and conducting a thorough skin exam in febrile neutropenic patients can lead to more rapid diagnosis and initiation of treatment. PCR amplification and sequencing of mold RNA extracted from paraffin-embedded tissue can be useful for diagnosing rare fungal infections when negative fungal cultures preclude morphologic diagnosis. Effective treatment for disseminated phaehyphomycosis is lacking and there is a need to report experiences with the use of newer antifungals.

Objectives: Traditional microbial identification methods are based on morphology (both micro- and macroscopic) and biochemical tests that require long incubation periods and a good deal of technologist hands-on time. In addition, many of these methods have some degree of subjectivity. In comparison, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identifies microorganisms from colonies grown on solid media within minutes using very few reagents. Methods: A case-based approach was used to review the strengths and weaknesses of MALDI-TOF MS in clinical microbiology laboratories. Results: MALDI-TOF MS has been proven to be an accurate and reliable method for organism identification including bacteria, yeast, molds, and mycobacteria. It is rapid, with results often 24 hours earlier than traditional methods, and inexpensive. There are no FDA-approved systems available currently. Susceptibility data are still reliant on conventional methods. There are genetically similar organisms that cannot be discriminated reliably with this method. Conclusions: MALDI-TOF MS is an exciting, innovative method for organism identification in the clinical microbiology laboratory.

Introduction This module uses team-based learning (TBL) to help medical students understand and apply basic concepts of diagnostic testing such as sensitivity, specificity, and predictive values. The module was designed to occupy a single 2-hour session early in an undergraduate medical curriculum. Development of this activity was motivated by our experiences with learners at a variety of levels who continued to struggle with application and interpretation of test characteristics in clinical settings despite being proficient with the basic calculations. TBL was chosen as a format because of its focus on applications and the growing evidence base for its effectiveness in medical education. Methods The session was implemented early in the first course of our medical curriculum, with students who had been introduced previously to basic principles of statistics as well as calculations of test characteristics. Teams of five to seven members were maintained throughout the year. Individual sessions included preparatory material (reading and learning objectives) with which students became familiar in advance, individual and group readiness tests taken at the beginning of the session, and a brief review of any challenging concepts from these tests. After a short break, students spent the bulk of the session working in teams on more complex applications, with each application question followed by simultaneous reporting of answers and faculty-facilitated whole-class discussion. Results This session was implemented for the first time in 2014 and was well received by first-year medical students. Both the overall session and the specific applications were rated as useful or very useful by 76% and 87% of students, respectively. Faculty facilitators were pleased with the levels of engagement and understanding apparent during the session, and students scored a mean of 85.6% on related exam questions. Discussion We made minor revisions to clarify the wording of several questions and plan to implement the session as described here in the coming year, with timing adjusted in response to student feedback to quicken the pace of applications.

An increasing spectrum and number of opportunistic fungal pathogens have been reported to cause disease in humans over the past decade. Disseminated phaeohyphomycoses caused by rare dematiaceous molds in immunocompromised patients have a high mortality rate and are increasingly reported in the literature. Early diagnosis of disseminated phaehyphomycosis is critical especially in neutropenic patients but can be hindered by the low sensitivity of fungal blood cultures and low clinical suspicion. Cutaneous manifestations are often the earliest sign of disease and conducting a thorough skin exam in febrile neutropenic patients can lead to more rapid diagnosis and initiation of treatment. PCR amplification and sequencing of mold RNA extracted from paraffin-embedded tissue can be useful for diagnosing rare fungal infections when negative fungal cultures preclude morphologic diagnosis. Effective treatment for disseminated phaehyphomycosis is lacking and there is a need to report experiences with the use of newer antifungals.

Rapid identification of pathogens from blood cultures can decrease lengths of stay and improve patient outcomes. We evaluated the accuracy of the Verigene Gram-positive blood culture (BC-GP) nucleic acid test for investigational use only (Nanosphere, Inc., Northbrook, IL) for the identification of Gram-positive bacteria from blood cultures. The detection of resistance genes ( mecA in Staphylococcus aureus and Staphylococcus epidermidis and vanA or vanB in Enterococcus faecium and Enterococcus faecalis ) by the BC-GP assay also was assessed. A total of 186 positive blood cultures (in BacT/Alert FA bottles) with Gram-positive cocci observed with Gram staining were analyzed using the BC-GP assay. The BC-GP results were compared with the identification and susceptibility profiles obtained with routine methods in the clinical laboratory. Discordant results were arbitrated with additional biochemical, cefoxitin disk, and repeat BC-GP testing. The initial BC-GP organism identification was concordant with routine method results for 94.6% of the blood cultures. Only 40% of the Streptococcus pneumoniae identifications were correct. The detection of the mecA gene for 69 blood cultures with only S. aureus or S. epidermidis was concordant with susceptibility testing results. For 3 of 6 cultures with multiple Staphylococcus spp., mecA detection was reported but was correlated with oxacillin resistance in a species other than S. aureus or S. epidermidis . The detection of vanA agreed with susceptibility testing results for 45 of 46 cultures with E. faecalis or E. faecium . Comparison of the mean times to results for each organism group showed that BC-GP results were available 31 to 42 h earlier than phenotypic identifications and 41 to 50 h earlier than susceptibility results.

There are a growing number of cases detailing acute hepatic necrosis in patients taking black cohosh (Cimicifuga racemosa), an over-the-counter herbal supplement for management of menopausal symptoms. Our aim is to illustrate two cases of liver injury following the use of black cohosh characterized by histopathological features mimicking autoimmune hepatitis. Both patients reported black cohosh use for at least six months and had no evidence of another cause of liver disease. Their liver biopsies showed a component of centrilobular necrosis consistent with severe drug-induced liver injury. In addition, the biopsies showed characteristics of autoimmune-like liver injury with an interface hepatitis dominated by plasma cells. Although serum markers for autoimmune hepatitis were not particularly elevated, both patients responded to corticosteroids, supporting an immune-mediated component to the liver injury. Liver injury following the use of black cohosh should be included in the list of differential diagnoses for chronic hepatitis with features mimicking autoimmune hepatitis.

MHC class I-restricted CD8+ T cells play an important role in controlling HIV and SIV replication. In SIV-infected Indian rhesus macaques (Macaca mulatta), comprehensive CD8+ T cell epitope identification has only been undertaken for two alleles, Mamu-A*01 and Mamu-B*17. As a result, these two molecules account for virtually all known MHC class I-restricted SIV-derived CD8+ T cell epitopes. SIV pathogenesis research and vaccine testing have intensified the demand for epitopes restricted by additional MHC class I alleles due to the shortage of Mamu-A*01+ animals. Mamu-A*02 is a high frequency allele present in over 20% of macaques. In this study, we characterized the peptide binding of Mamu-A*02 using a panel of single amino acid substitution analogues and a library of 497 unrelated peptides. Of 230 SIVmac239 peptides that fit the Mamu-A*02 peptide-binding motif, 75 peptides bound Mamu-A*02 with IC50 values of ≤500 nM. We assessed the antigenicity of these 75 peptides using an IFN-γ ELISPOT assay with freshly isolated PBMC from eight Mamu-A*02+ SIV-infected macaques and identified 17 new epitopes for Mamu-A*02. The synthesis of five Mamu-A*02 tetramers demonstrated the discrepancy between tetramer binding and IFN-γ secretion by SIV-specific CD8+ T cells during chronic SIV infection. Bulk sequencing determined that 2 of the 17 epitopes accumulated amino acid replacements in SIV-infected macaques by the chronic phase of infection, suggestive of CD8+ T cell escape in vivo. This work enhances the use of the SIV-infected macaque model for HIV and increases our understanding of the breadth of CD8+ T cell responses in SIV infection.