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Background Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections. However, their clinical utility is unclear. Methods We conducted a retrospective analysis of specimens that underwent 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) followed by Sanger sequencing at our institution from April 2017 through March 2019. Results A total of 566 specimens obtained from 460 patients were studied. Patients were considered clinically infected or noninfected based on final diagnosis and management. In 17% of patients, 16S rRNA PCR/sequencing was positive and in 5% of patients, this test led to an impact on clinical care. In comparison, bacterial cultures were positive in 21% of patients. Specimens with a positive Gram stain had 12 times greater odds of having a positive molecular result than those with a negative Gram stain (95% confidence interval for odds ratio, 5.2–31.4). Overall, PCR positivity was higher in cardiovascular specimens (37%) obtained from clinically infected patients, with bacterial cultures being more likely to be positive for musculoskeletal specimens (P Conclusion 16S rRNA PCR/sequencing can play a role in the diagnostic evaluation of patients with culture-negative infections, especially those with cardiovascular infections.

Introduction Bed bugs are hematophagous insects that can be problematic in some urban emergency departments. The objective was to determine if red blood cell (RBC) and coagulation indices of bed bug–infested emergency department (ED) patients differed from those of noninfested control patients. Methods A chart review from a single health system was performed for ED patients between February 1, 2011, and February 1, 2017. Bed bug–infested patients were matched to noninfested control patients on the basis of age, sex, and the presenting ED. Variables were analyzed with the t-test and Pearson χ2 test and were modeled with multivariable logistic regression. Results The study had 332 bed bug–infested patients and 4952 controls. Infested patients had lower hemoglobin (11.7 g/dL vs 12.8 g/dL), hematocrit (35.0% vs 37.9%), RBC counts (4.1 × 109/L vs 4.4 × 109/L), mean corpuscular volume (86.0 vs 87.5 fL/cell), and mean corpuscular hemoglobin concentrations (33.2 vs 33.7 g/dL) and higher RBC distribution width-coefficient of variation (RDW-CV) (15.2% vs 14.2%) than noninfested patients (all P ≤ .003). Infested patients were more likely to be anemic (59.5% vs 36.9%) and to have severe anemia (4.4% vs 0.7%) (P Conclusion Bed bug infestated patients in the ED are associated with anemia.

Formal medical and public health microbiology (MPHM) fellowship programs play a key role in preparing future clinical microbiology laboratory directors for their leadership and management responsibilities. Given the continually evolving MPHM field, fellowships must remain adaptable to changes in the field, providing trainees with the opportunity to engage with newly emerging diagnostic modalities, while continuing to emphasize the "bread and butter" techniques of clinical microbiology. This article discusses the key components of a fellowship program and provides recommendations for incorporating educational best practices.

Pathologists are responsible for rapidly providing a diagnosis on critical health issues. Challenging cases benefit from additional opinions of pathologist colleagues. In addition to on-site colleagues, there is an active worldwide community of pathologists on social media for complementary opinions. Such access to pathologists worldwide has the capacity to improve diagnostic accuracy and generate broader consensus on next steps in patient care. From Twitter we curate 13,626 images from 6,351 tweets from 25 pathologists from 13 countries. We supplement the Twitter data with 113,161 images from 1,074,484 PubMed articles. We develop machine learning and deep learning models to (i) accurately identify histopathology stains, (ii) discriminate between tissues, and (iii) differentiate disease states. Area Under Receiver Operating Characteristic is 0.805-0.996 for these tasks. We repurpose the disease classifier to search for similar disease states given an image and clinical covariates. We report precision@k=1 = 0.7618±0.0018 (chance 0.397±0.004, mean±stdev). The classifiers find texture and tissue are important clinico-visual features of disease. Deep features trained only on natural images (e.g. cats and dogs) substantially improved search performance, while pathology-specific deep features and cell nuclei features further improved search to a lesser extent. We implement a social media bot (@pathobot on Twitter) to use the trained classifiers to aid pathologists in obtaining real-time feedback on challenging cases. If a social media post containing pathology text and images mentions the bot, the bot generates quantitative predictions of disease state (normal/artifact/infection/injury/nontumor, pre-neoplastic/benign/ low-grade-malignant-potential, or malignant) and lists similar cases across social media and PubMed. Our project has become a globally distributed expert system that facilitates pathological diagnosis and brings expertise to underserved regions or hospitals with less expertise in a particular disease. This is the first pan-tissue pan-disease (i.e. from infection to malignancy) method for prediction and search on social media, and the first pathology study prospectively tested in public on social media. We will share data throughpathobotology.org. We expect our project to cultivate a more connected world of physicians and improve patient care worldwide.

Omadacycline, vancomycin, and rifampin, as well as rifampin combination therapies, were evaluated in an experimental rat model of methicillin-resistant Staphylococcus aureus (MRSA) osteomyelitis. All treatment groups had less MRSA recovered than saline-treated animals. The emergence of rifampin resistance was observed in 3 of 16 animals with rifampin monotherapy and none with rifampin combination therapy. After treatment, the median tibial bacterial loads were 6.04, 0.1, 4.81, and 5.24 log10 CFU/g for saline-, rifampin-, vancomycin-, and omadacycline-treated animals, respectively. Omadacycline or vancomycin administered with rifampin yielded no detectable MRSA. Omadacycline administered with rifampin deserves evaluation in humans as a potential treatment for osteomyelitis.

Bed bugs are common urban pests. Unlike many other blood-feeding human ectoparasites, bed bugs are not known to be vectors of human infectious diseases, but clinical and epidemiological studies to directly interrogate this link have been limited. Here, we aimed to determine whether bed bugs were associated with infectious diseases in a set of infested patients presenting to emergency departments (ED) in the greater Cleveland, OH area. We performed a retrospective case-control study involving 332 ED patients with bed bugs and 4,952 control patients, seen from February 1, 2011, through February 1, 2017. Cases and controls were matched by age, sex, and the presenting ED. Additionally, data were adjusted for ≥20 sociodemographic variables, triage data, and comorbidities in multivariable regression analyses. Seventeen laboratory values, ten different ED and inpatient diagnoses, chest radiographs, infectious disease consults, and blood cultures were examined. The odds of bed bug infestation were significantly higher for patients that had positive blood cultures, had blood cultures growing coagulase-negative Staphylococcus, were diagnosed with pneumonia, were diagnosed with cellulitis, received an infectious disease consult, received a chest radiograph, and had higher percentages of eosinophils in the blood (P < .05 for all). Additional investigations are needed to determine whether bed bugs directly contribute to disease by transmitting causative agents, whether bed bug exposure contributes secondarily contributes to infections, or whether these associations are better explained by other environmental and social determinants of health., Bacteremia; Cellulitis; Cimex lectularius; Coagulase-negative Staphylococcus; Eosinophil; Pneumonia

Cyclospora cayetanensis is an intestinal coccidian parasite transmitted to humans through the consumption of oocysts in fecally contaminated food and water. Infection is found worldwide and is highly endemic in tropical and subtropical regions with poor sanitation. Disease in developed countries is usually observed in travelers and in seasonal outbreaks associated with imported produce from endemic areas. Recently, summertime outbreaks in the United States have also been linked to locally grown produce. Cyclosporiasis causes a diarrheal illness which may be severe in infants, the elderly, and immunocompromised individuals. The increased adoption of highly sensitive molecular diagnostic tests, including commercially available multiplex panels for gastrointestinal pathogens, has facilitated the detection of infection and likely contributed to the increased reports of cases in developed countries. This manuscript reviews important aspects of the biology, epidemiology, and clinical manifestations of C. cayetanensis and provides an in-depth discussion of current laboratory diagnostic methods.

Rapid and accurate diagnostic testing is essential to bring the ongoing COVID-19 pandemic to an end. As the demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to increase amid supply shortages, many laboratories have investigated the use of sources other than nasopharyngeal (NP) swabs. Saliva and midturbinate (MT) nasal swabs are attractive alternatives, as they allow for self-collection and are well accepted by patients. Saliva also requires limited consumables. We compared the performance of health care provider-collected NP swabs, patient-collected MT swabs, and patient-collected saliva specimens for SARS-CoV-2 detection using a laboratory-developed PCR assay that had received Emergency Use Authorization by the FDA. Of 281 total evaluable samples, 33 (11.7%) NP swabs, 33 (11.7%) MT swabs, and 32 (11.4%) saliva specimens were positive for SARS-CoV-2 following resolution of discordant results. Compared to NP swabs, saliva exhibited a sensitivity of 90.9% (30/33) and specificity of 99.2% (246/248), while patient-collected MT swabs exhibited a sensitivity of 93.9% (31/33) and specificity of 99.2% (246/248). When comparing to the consensus standard, the sensitivity was found to be 100% (31/31) for both NP and MT swabs and 96.8% (30/31) for saliva specimens, while specificity was the same in both NP swabs and saliva specimens (98.8% [247/250]) and 99.2% (248/250) for MT swabs. Pretreatment of saliva with proteinase K and heating for 15 min prior to extraction reduced the invalid rate from 26.7% (52/195) to 0% (0/195). These data show that midturbinate nasal swabs and saliva are suitable sources for self-collection in individuals who require routine monitoring for SARS-CoV-2 infection.

Clinical microbiology laboratories play a crucial role in patient care using traditional and innovative diagnostics. Challenges faced by laboratories include emerging pathogens, rapidly evolving technologies, health care-acquired infections, antibiotic-resistant organisms, and diverse patient populations. Despite these challenges, many clinical microbiology laboratories in the United States are not directed by doctoral level microbiology-trained individuals with sufficient time dedicated to laboratory leadership. The manuscript highlights the need for medical microbiology laboratory directors with appropriate training and qualifications.

The rapidly spreading COVID-19 pandemic demanded immediate organizational pivots in departments of laboratory medicine and pathology, including development and implementation of severe acute respiratory syndrome coronavirus 2 diagnostics in the face of unprecedented supply chain shortages. Laboratory medicine and pathology educational programs were affected in numerous ways. Here, we overview the effects of COVID-19 on the large, academic Department of Laboratory Medicine and Pathology educational practice at Mayo Clinic, highlighting lessons learned for the post-pandemic era and planning for the possibility of a future pandemic.

Objectives Pathogenic free-living amebae (FLAs) cause skin, ocular, and central nervous system (CNS) infections with significant morbidity and mortality. Diagnosis of FLA infections by pathologic examination of tissue sections can be aided using molecular assays. This study investigated the performance characteristics of a multiplex real-time polymerase chain reaction (PCR) assay (FLA-PCR) for detection and differentiation of FLAs in clinical specimens. Methods FLA-PCR was performed on 39 human specimens comprising one cutaneous, 14 corneal, and 24 CNS formalin-fixed, paraffin-embedded (FFPE) tissues with a histopathologic diagnosis of FLA infection and four CNS FFPE tissues with inflammation but no evidence of FLAs. In addition, clinical specificity and assay limit of detection were determined. Results FLA detection sensitivities ranged from 79% to 84% in FFPE tissues. No cross-reactivity was observed. Conclusions While sensitivity is limited, FLA-PCR assay may serve as a useful adjunct for detection or confirmation of FLA infections in FFPE tissues.

Objective To describe the clinical features and epidemiology of leprosy in patients evaluated in a Midwestern dermatology clinic. Patients and Methods We performed a retrospective review of clinical and laboratory data from patients with leprosy who were evaluated in the Department of Dermatology at Mayo Clinic in Rochester, Minnesota, from January 1, 1994, through December 31, 2017. Results Nine patients, 7 male and 2 female, were identified, ranging in age from 15 to 63 years (mean age, 38 years). Six of the 9 patients (67%) were foreign-born: 3 from Oceania (2 from Micronesia and 1 from Guam), 1 from Southeast Asia (Indonesia), and 2 from Mexico. Three patients were born in the United States. All 9 patients presented with skin lesions (granulomatous histopathologic type), and 8 had neuropathy. Leprosy was multibacillary in 8 patients and paucibacillary in 1. Two patients experienced a type 1 treatment reaction, and 5 had type 2 reactions. Three of the 9 patients had speciation by polymerase chain reaction (Mycobacterium leprae in 2 and Mycobacterium lepromatosis in 1). Conclusion Despite its rarity in the United States, leprosy should be considered in the differential diagnosis when evaluating both foreign- and US-born patients with granulomatous dermatitis and peripheral neuropathy. Because M lepromatosis was not identified until 2008 and requires polymerase chain reaction for diagnosis, the incidence of this species among patients with leprosy diagnosed in earlier years is unknown.

Background Schistosomiasis is a parasitic disease that affects the health of hundreds of millions of people worldwide. Affordable diagnostic methods are necessary for developing countries to monitor schistosomiasis rates and treat infected individuals, particularly in, Madagascar, a country with the world’s fifth highest rate of schistosomiasis. # Methods We established the prevalence rate of schistosomiasis among the local population served by a clinic in rural northwestern Madagascar. Additionally, we compared different low-cost methods for schistosomiasis detection, including empirical diagnostic methods in use before this study. 500 patients were recruited in this study, of whom 380 received three tests—urine microscopy, point-of-care circulating cathodic antigen (POC-CCA) testing, and urinalysis to screen for *Schistosoma haematobium* and *Schistosoma mansoni*. # Results By combining these modalities, we recorded a schistosomiasis prevalence rate of 64.47%, which was significantly higher than the 4.84% of patients who were diagnosed and treated through previous empirical methods. # Conclusions Our results indicate that screening tests are a necessary component of schistosomiasis control programs. The clinic continued to use urinalysis strip testing and urine microscopy to detect schistosomiasis after this study and decided to discontinue the use of POC-CCA *S. mansoni* urine testing because of cost. Increased awareness of schistosomiasis resulting from this screening program led to the installation of multiple infrastructure projects in local communities to improve access to potable water, demonstrating community benefits of schistosomiasis screening that extend beyond the identification of infected individuals.

Background Echinococcus multilocularis is one of the most severe and lethal parasitic diseases of humans, most often reported in Europe and Asia. Only 1 previous case has been documented in the contiguous United States from Minnesota in 1977. European haplotypes have been identified in carnivores and domestic dogs as well as recently in patients in western and central Canada. Methods We used immunohistochemical testing with the monoclonal antibody Em2G11 and a species-specific enzyme-linked immunosorbent assay affinity-purified antigen Em2, as well as COX1 gene sequencing. Results Using pathology, immunohistochemical staining, specific immunodiagnostic testing, and COX1 gene sequencing, we were able to definitively identify E. multilocularis as the causative agent of our patient’s liver and lung lesions, which clustered most closely with the European haplotype. Conclusions We have identified the first case of a European haplotype E. multilocularis in the United States and the first case of this parasitic infection east of the Mississippi River. Given the identification of this haplotype in Canada, this appears to be an emerging infectious disease in North America.

A 25-year-old Caucasian American woman without significant medical history presented to the travel clinic with a 1-week history of worsening diarrhea and bloating. She had recently returned from an 8-month trip to Ethiopia, where she worked as a Peace Corps volunteer. While in Ethiopia, she resided

Shotgun metagenomic sequencing can detect nucleic acids from bacteria, fungi, viruses, and/or parasites in clinical specimens; however, little data exist to guide its optimal application to clinical practice. We retrospectively reviewed results of shotgun metagenomic sequencing testing requested on cerebrospinal fluid samples submitted to an outside reference laboratory from December 2017 through December 2019. Of the 53 samples from Mayo Clinic patients, 47 were requested by neurologists, with infectious diseases consultation in 23 cases. The majority of patients presented with difficult-to-diagnose subacute or chronic conditions. Positive results were reported for 9 (17%) Mayo Clinic patient samples, with 6 interpreted as likely contamination. Potential pathogens reported included bunyavirus, human herpesvirus 7, and enterovirus D-68, ultimately impacting care in two cases. Twenty-seven additional samples were submitted from Mayo Clinic Laboratories reference clients, with positive results reported for three (11%): two with potential pathogens (West Nile virus and Toxoplasma gondii) and one with Streptococcus species with other bacteria below the reporting threshold (considered to represent contamination). Of 68 negative results, 10 included comments on decreased sensitivity due to high DNA background (n = 5), high RNA background (n = 1), insufficient RNA read depth (n = 3), or quality control (QC) failure with an external RNA control (n = 1). The overall positive-result rate was 15% (12/80), with 58% (7/12) of these interpreted as being inconsistent with the patient’s clinical presentation. Overall, potential pathogens were found in a low percentage of cases, and positive results were often of unclear clinical significance. Testing was commonly employed in cases of diagnostic uncertainty and when immunotherapy was being considered.

Tick-borne diseases, due to a diversity of bacterial pathogens, represent a significant and increasing public health threat throughout the Northern Hemisphere. A high-throughput 16S V1-V2 rRNA gene-based metagenomics assay was developed and evaluated using13,000 residual samples from patients suspected of having tick-borne illness and1,000 controls. Taxonomic predictions for tick-borne bacteria were exceptionally accurate, as independently validated by secondary testing. Overall, 881 specimens were positive for bacterial tick-borne agents. Twelve tick-borne bacterial species were detected, including two novel pathogens, representing a 100% increase in the number of tick-borne bacteria identified compared to what was possible by initial PCR testing. In three blood specimens, two tick-borne bacteria were simultaneously detected. Seven bacteria, not known to be tick transmitted, were also confirmed to be unique to samples from persons suspected of having tick-borne illness. These results indicate that 16S V1-V2 metagenomics can greatly simplify diagnosis and accelerate the discovery of bacterial tick-borne pathogens.

Lyme disease (LD) is an increasing public health problem. Current laboratory testing is insensitive in early infection, the stage at which appropriate treatment is most effective in preventing disease sequelae. The Lyme Disease Biobank (LDB) collects samples from individuals with symptoms consistent with early LD presenting with or without erythema migrans (EM) or an annular, expanding skin lesion and uninfected individuals from areas of endemicity. Samples were collected from 550 participants (298 cases and 252 controls) according to institutional review board-approved protocols and shipped to a centralized biorepository., Lyme disease (LD) is an increasing public health problem. Current laboratory testing is insensitive in early infection, the stage at which appropriate treatment is most effective in preventing disease sequelae. The Lyme Disease Biobank (LDB) collects samples from individuals with symptoms consistent with early LD presenting with or without erythema migrans (EM) or an annular, expanding skin lesion and uninfected individuals from areas of endemicity. Samples were collected from 550 participants (298 cases and 252 controls) according to institutional review board-approved protocols and shipped to a centralized biorepository. Testing was performed to confirm the presence of tick-borne pathogens by real-time PCR, and a subset of samples was tested for Borrelia burgdorferi by culture. Serology was performed on all samples using the CDC’s standard two-tiered testing algorithm (STTTA) for LD. LD diagnosis was supported by laboratory testing in 82 cases, including positive results by use of the STTTA, PCR, or culture or positive results by two enzyme-linked immunosorbent assays for cases presenting with EM lesion sizes of >5 cm. The remaining 216 cases had negative laboratory testing results. For the controls, 43 were positive by at least one of the tiers and 6 were positive by use of the STTTA. The results obtained with this collection highlight and reinforce the known limitations of serologic testing in early LD, with only 29% of individuals presenting with EM lesion sizes of >5 cm yielding a positive result using the STTTA. Aliquots of whole blood, serum, and urine from clinically characterized patients with and without LD are available to investigators in academia and industry for evaluation or development of novel diagnostic assays for LD, to continue to improve upon currently available methods.

Background Tick-borne diseases are an important cause of human morbidity and mortality in the United States. The past several decades have witnessed an increase in both the number of recognized tick-borne pathogens and the number of tick-borne disease cases, whereas tick surveys have revealed substantial geographic expansions of tick populations throughout the country. Multiple laboratory testing options exist for diagnosis of tick-borne diseases, including serology, microscopy, and molecular-based methods. The preferred approach varies by the specific disease, locally available test options, and the stage of illness at patient presentation. Accurate and timely detection of tick-borne illness is of utmost importance, as prompt treatment is strongly linked to better outcomes. Content This review covers the clinical manifestations and preferred diagnostic approaches for important bacterial, viral, and parasitic tick-borne diseases in the United States, including Lyme disease, tick-borne relapsing fever, anaplasmosis, ehrlichiosis, spotted fever rickettsioses, and babesiosis. Infection with emerging pathogens such as Borrelia miyamotoi, Powassan virus, Heartland virus, Colorado tick fever virus, and Bourbon virus are also covered. Summary Our understanding of tick-borne diseases in the United States continues to improve with the detection of novel pathogens and development of new diagnostic modalities. While conventional diagnostic methods, including serology and microscopy, will play an ongoing role in the diagnosis of tick-borne diseases, implementation of advanced molecular diagnostics will further broaden our understanding of these diseases by facilitating detection of emerging pathogens and providing more accurate and timely diagnosis.

Background: Cutaneous myiasis is a self-limited skin infestation by developing fly larvae, with three clinical subtypes: furuncular, migratory, and wound myiasis. Furuncular myiasis is endemic throughout much of Africa; however, few reports are from the Horn of Africa. Clinical presentation: An 85-year-old woman in Somaliland presented with a 12-day history of multiple painful and pruritic nodules on the temple, arm, chest, breast, flank, and legs. The posterior of a larva was visible within several lesions. One larva was extracted from an arm nodule and identified as Cordylobia anthropophaga (tumbu fly) by morphologic examination. The patient was instructed to occlude the other nodules with petroleum jelly and return in 3 days. Instead, she visited a traditional healer who extracted the remaining larvae. Conclusions: We present a case of furuncular cutaneous myiasis due to Cordylobia anthropophaga. Treatment options for this infestation include occlusion with petroleum jelly to cause larvae to exit, surgical extraction, and oral ivermectin. Occlusion may not be acceptable for some patients. Extraction may cause significant inflammatory response if the larva is damaged during the process. To our knowledge, this is the first published report of myiasis in Somaliland, although it is probably underreported. Myiasis is a common dermatosis associated with travel to endemic areas. Furuncular myiasis can easily be misdiagnosed as furunculosis or cellulitis. Dermatologists must be familiar with the clinical features and management of this dermatosis. Keywords: myiasis, cutaneous myiasis, furuncular myiasis, tumbu fly, fly larvae, Somaliland

BACKGROUND: Tick-transmitted Borrelia species fall into two heterogeneous bacterial complexes comprised of multiple species, the relapsing fever (RF) group and the Borrelia burgdorferi sensu lato group, which are the causative agents of Lyme borreliosis (LB), the most common tickborne disease in the northern hemisphere. Geographic expansion of human LB in the United States and discovery of emerging Borrelia pathogens underscores the importance of surveillance for disease causing Borrelia. METHODS: De-identified clinical specimens, submitted by providers throughout the United States, for patients suspected of LB, anaplasmosis, ehrlichiosis, or babesiosis, were screened using a Borrelia genus level TaqMan PCR. Borrelia species and sequence types (STs) were characterized by multi-locus sequence typing (MLST) utilizing next generation sequencing. RESULTS: Among the 7,292 tested specimens tested, five different Borrelia species were identified: two causing LB, B. burgdorferi (n=25) and B. mayonii (n=9), and three RF borreliae, B. hermsii (n=1), B. miyamotoi (n=8), and Candidatus B. johnsonii (n=1), a species previously detected only in the bat tick, Carios kelleyi. ST diversity was greatest for B. burgdorferi positive specimens, with new STs identified primarily among synovial fluids. CONCLUSION: These results demonstrate broad PCR screening followed by MLST is a powerful surveillance tool for uncovering the spectrum of Borrelia species causing human disease, improving understanding of their geographic distribution, and investigating the correlation between B. burgdorferi STs and joint involvement. Detection of Candidatus B. johnsonii in a patient with suspected tickborne disease suggests this species may be a previously undetected cause of illness in humans with exposure to bat ticks.

Ehrlichioses and anaplasmosis have undergone dramatic increases in incidence, and the geographic ranges of their occurrence and vectors have also expanded. There is marked underreporting of these diseases owing to deficient physician awareness and knowledge of the illnesses as well as limited access to appropriate diagnostic tests. Human monocytic ehrlichiosis and anaplasmosis are life threatening diseases with estimated case fatality rates of 2.7 and 0.3%, respectively. However, knowledge of their full range of signs and symptoms is incomplete, and the incidence of subclinical infections is unknown. Currently available laboratory diagnostic methods are poorly utilized, and with the exception of nucleic acid amplification tests are not useful for diagnosis during the acute stage of illness when timely treatment is needed. The Ehrlichiosis and Anaplasmosis Subcommittee of the Tick-Borne Disease Working Group recommended active clinical surveillance to determine the true incidence, full clinical spectrum, and risk factors for severe illness, as well as standardized surveillance of ticks for these pathogens, and enhanced education of primary medical caregivers and the public regarding these diseases. The subcommittee identified the needs to develop sensitive, specific acute stage diagnostic tests for local clinical laboratories and point-of-care testing, to develop approaches for utilizing electronic medical records, data mining, and artificial intelligence for assisting early diagnosis and treatment, and to develop adjunctive therapies for severe disease.

Granulomatous inflammation is a histologic pattern of tissue reaction which appears following cell injury. Granulomatous inflammation is caused by a variety of conditions including infection, autoimmune, toxic, allergic, drug, and neoplastic conditions. The tissue reaction pattern narrows the pathologic and clinical differential diagnosis and subsequent clinical management. Common reaction patterns include necrotizing granulomas, non necrotizing granulomas, suppurative granulomas, diffuse granulomatous inflammation, and foreign body giant cell reaction. Prototypical examples of necrotizing granulomas are seen with mycobacterial infections and non-necrotizing granulomas with sarcoidosis. However, broad differential diagnoses exist within each category. Using a pattern based algorithmic approach, identification of the etiology becomes apparent when taken with clinical context.The pulmonary system is one of the most commonly affected sites to encounter granulomatous inflammation. Infectious causes of granuloma are most prevalent with mycobacteria and dimorphic fungi leading the differential diagnoses. Unlike the lung, skin can be affected by several routes, including direct inoculation, endogenous sources, and hematogenous spread. This broad basis of involvement introduces a variety of infectious agents, which can present as necrotizing or non-necrotizing granulomatous inflammation. Non-infectious etiologies require a thorough clinicopathologic review to narrow the scope of the pathogenesis which include: foreign body reaction, autoimmune, neoplastic, and drug related etiologies. Granulomatous inflammation of the kidney, often referred to as granulomatous interstitial nephritis (GIN) is unlike organ systems such as the skin or lungs. The differential diagnosis of GIN is more frequently due to drugs and sarcoidosis as compared to infections (fungal and mycobacterial).Herein we discuss the pathogenesis and histologic patterns seen in a variety of organ systems and clinical conditions. Keywords: Foreign-body, Granulomatous inflammation, Granuloma, Mycobacterial, Sarcoidal, Tuberculous

Tropheryma whipplei, the agent of Whipple disease, causes a rare bacterial disease that may be fatal if not treated. The classical form of the disease includes diarrhoea, weight loss, arthritis, endocarditis and neurological manifestations. Genotyping studies done in Europe, Africa and Asia showed high genetic diversity with no correlation between genotypes and clinical features, but contributed to a better understanding of the epidemiology of the disease. More than 70 genotypes have been described. No similar assessment of T. whipplei in the USA and the Caribbean has been performed. In this study, we describe genetic analysis of DNA from histopathological samples obtained from 30 patients from the Americas with Whipple disease and compare the genotypes with those previously identified. Complete genotypes were obtained from 18 patients (60%). Only 4 genotypes were previously described, and 14 were newly reported, confirming the diversity of T. whipplei strains.

A patient with asplenia and multiple red blood cell transfusions acquired babesiosis infection with Babesia divergens-like/MO-1 organisms and not Babesia microti, the common United States species. He had no known tick exposure. This is believed to be the first transfusion-transmitted case and the fifth documented case of B. divergens-like/MO-1 infection.

We report an asplenic patient who was infected with Babesia divergens–like/MO-1. The clinical course was complicated by multiorgan failure that required intubation and dialysis. The patient recovered after an exchange transfusion and antimicrobial drug therapy. Physicians should be alert for additional cases, particularly in asplenic persons.

The morphologic similarities of the microfilariae and their infrequency in clinical specimens in settings of endemicity present challenges to clinical laboratories in maintaining competence for accurate identification and differentiation. We present here a review of the primary filarial nematodes causing human infection, including an illustrated key, which we hope will improve the diagnostic capabilities of hematologists, microbiologists, medical technologists, and similarly qualified laboratorians.

Microsporidiosis is an emerging opportunistic infection in immunocompromised patients. We report a case of fatal disseminated Anncaliia algerae infection in a profoundly immunosuppressed pancreas and kidney transplant recipient.

Infectious colitis is a significant cause of morbidity and mortality worldwide and may be caused by a wide variety of bacteria, viruses, fungi, and parasites. This chapter discusses the clinical and pathologic manifestations of the primary agents infecting the colon that may be seen by the surgical pathologist: the diarrheagenic bacteria in the family Enterobacteriaceae (Escherichia coli, Aeromonas, Salmonella, Shigella, Campylobacter, and Yersinia species), Clostridioides (formerly Clostridium) difficile, Bradyspira spirochetes causing intestinal spirochetosis, Aspergillus species, members of the Mucorales, Cryptococcus neoformans/C. gattii, Histoplasma capsulatum, cytomegalovirus, human immunodeficiency virus, Entamoeba histolytica, Balantidioides coli, Schistosoma species, and Trichuris trichiura. Also covered are the histopathologic differential diagnosis and recommended ancillary tests.

In the United States, laboratories frequently offer multiple different assays for testing of cerebrospinal fluid (CSF) samples to provide laboratory support for the diagnosis of central nervous system Lyme disease (CNSLD). Often included among these diagnostic tests are the same enzyme immunoassays and immunoblots that are routinely used to detect the presence of antibodies to Borrelia burgdorferi in serum. However, performing these assays on CSF alone may yield positive results simply from passive diffusion of serum antibodies into the CSF. In addition, such tests are only U.S. Food and Drug Administration cleared and well validated for testing serum, not CSF. When performed using CSF, positive results from these assays do not establish the presence of intrathecal antibody production to B. burgdorferi and therefore should not be offered. The preferred test to detect intrathecal production of antibodies to B. burgdorferi is the antibody index assay, which corrects for passive diffusion of serum antibodies into CSF and requires testing of paired serum and CSF collected at approximately the same time. However, this assay also has limitations and should only be used to establish a diagnosis of CNSLD in conjunction with patient exposure history, clinical presentation, and other laboratory findings.

There is substantial evidence that stool culture and parasitological examinations are of minimal to no value after 3 days of hospitalization. We implemented and studied the impact of a clinical decision support tool (CDST) to decrease the number of unnecessary stool cultures (STCUL), ova/parasite (O&P) examinations, and Giardia/Cryptosporidium enzyme immunoassay screens (GC-EIA) performed for patients hospitalized >3 days. We studied the frequency of stool studies ordered before or on day 3 and after day 3 of hospitalization (i.e., categorical orders/total number of orders) before and after this intervention and denoted the numbers and types of microorganisms detected within those time frames. This intervention, which corresponded to a custom-programmed hard-stop alert tool in the Epic hospital information system, allowed providers to override the intervention by calling the laboratory, if testing was deemed medically necessary. Comparative statistics were employed to determine significance, and cost savings were estimated based on our internal costs. Before the intervention, 129/670 (19.25%) O&P examinations, 47/204 (23.04%) GC-EIA, and 249/1,229 (20.26%) STCUL were ordered after 3 days of hospitalization. After the intervention, 46/521 (8.83%) O&P examinations, 27/157 (17.20%) GC-EIA, and 106/1,028 (10.31%) STCUL were ordered after 3 days of hospitalization. The proportions of reductions in the number of tests performed after 3 days and the associated P values were 54.1% for O&P examinations (P < 0.0001), 22.58% for GC-EIA (P = 0.2807), and 49.1% for STCUL (P < 0.0001). This was estimated to have resulted in $8,108.84 of cost savings. The electronic CDST resulted in a substantial reduction in the number of evaluations of stool cultures and the number of parasitological examinations for patients hospitalized for more than 3 days and in a cost savings while retaining the ability of the clinician to obtain these tests if clinically indicated.