bluuebunny/crossref_metadata_2025 huggingface dataset:
Lab Wisely in Canada: Enhancing and highlighting the role of all clinical laboratory professionals in reducing harm and waste
Authors: VanSpronsen A , Nielsen C , Djukic B , Villatoro V
Published: October 2021

Introduction/Objective

Stewardship initiatives are a key strategy for addressing inappropriate utilization of clinical laboratory resources. These approaches require engagement of multiple types of stakeholders. Some professional groups are historically underrepresented, such as those who perform specimen collection, testing, and quality processes. A specific campaign is needed to engage these groups and highlight their expertise.

Methods/Case Report

We surveyed Medical Laboratory Technologists and Medical Laboratory Assistants to understand the barriers they face to participating in laboratory stewardship initiatives. These survey findings helped shape tools and resources that we created for new campaign called Lab Wisely. We also identified that one-third of existing Choosing Wisely Canada recommendations relate to laboratory testing. We categorized and tagged each recommendation to create a publicly-available searchable database which was placed on the campaign website (LabWisely.ca).

Results (if a Case Study enter NA)

NA

Conclusion

Laboratory testing is featured in a significant proportion of all Choosing Wisely Canada recommendations, supporting the idea that the clinical laboratory should be heavily involved in reducing medical overuse in healthcare. In our survey, we found that laboratory professionals face time and workload constraints, but feel a professional responsibility for ensuring appropriate resource use by all users. There was also a lack of ‘know- how’ around tangible ways to become involved. The Lab Wisely website has become a one-stop-shop for highlighting the role of technical and scientific professionals in laboratory stewardship and providing concrete tools that can be used to develop capacity in these groups. Every level of staff can and should be involved in improving the utilization of clinical laboratory services.
What Makes Our Medical Laboratory Workforce Unique?
Authors: Arora K , Sharma G
Published: October 2021

Introduction/Objective

A career in the medical laboratory requires advanced education and technical training. To assist both employers and employees, several government organizations conduct demographic, education, and wage surveys for the general U.S. labor market. Through its workforce surveys, the American Society of Clinical Pathology (ASCP) does the same for the medical laboratory professions. Our aim was to compare the findings of these surveys and identify similarities and dissimilarities between the general labor pool and the medical laboratory workforce.

Methods/Case Report

Since the 2021 ASCP Wage survey is currently open, we reviewed the findings described in ASCP’s 2019 Wage Survey of Medical Laboratories in the United States (Am J Clin Pathol 2021;155:649-673) with the publicly available information (for 2019) on demographics, educational attainment, and average hourly earnings available on the websites of U.S. Bureau of Labor Statistics (www.bls.gov) as well as United States Census (www.census.gov).

Results (if a Case Study enter NA)

In 2019, the male: female ratio was 52.9:47.1 in general labor pool and 19.1:80.9 in the medical laboratory workforce. The average age of a worker in the general labor pool was 41.9 years and was 42 years in the medical laboratory workforce. The average hourly earnings were $27.99/hour in the general labor pool and ranged from $16.64/hour (phlebotomists) to $53.95/hour (pathologists assistants) in the medical laboratory workforce, with the MLS/MT/CLS earning $30.02/hour to $52.53/hour. While 33.1% adults in the U.S. have attained a bachelor’s degree or above, 73.79% have attained this in the medical laboratory workforce.

Conclusion

Compared to the general labor pool, the medical laboratory workforce is a highly educated workforce and has a higher participation by women. The average worker age and average hourly wage are comparable. We encourage laboratorians to participate in ASCP surveys since such surveys reveal data that can drive better prospects for the medical laboratory workforce.
Standardizing Instructions for Ice and Cold Pack Use Can Mitigate Summer Temperatures on Two Commercially Available Outdoor Courier Lockboxes
Authors: Hart S A , Wiencek J R
Published: October 2021

Introduction/Objective

Clinical and Laboratory Standards Institute document GP44 recommends samples avoid temperatures >22°C during sample transport and storage. Outdoor courier lockboxes used in external sample transport can experience extreme temperatures (>40°C) in the summer. Ice (frozen at -20°C) and cold (refrigerated at 4-8°C) packs can be used to reduce internal lockbox temperatures during hot summer days. Unfortunately, there are no universally accepted instructions to maintain internal lockbox temperatures during these conditions. Therefore, our goal was to elucidate the impact of placing ice and cold packs at two specific time points to mitigate external summer temperatures in two commercially available outdoor courier lockboxes used at our institution.

Methods/Case Report

Two pairs of uniquely manufactured courier lockboxes (steel vs. urethane polymer) were placed outside in direct sunlight in Nashville, Tennessee during the second week of June 2021. Ambient outdoor and lockbox temperatures were monitored using data loggers during a four-day cycle. Each type of lockbox design had a control with no ice or cold packs. These controls were then compared to each experimental, paired lockbox with four ice packs placed at 8am and replaced with four cold packs at 4pm.

Results (if a Case Study enter NA)

The mean ambient outdoor temperature over these four days was 27.7°C (range: 22.2-39.8°C). Temperatures within the steel and urethane polymer lockboxes without ice or cold packs was 28.3°C (range: 22.4-40.8°C) and 31.6°C (range: 23.8-41.0°C), respectively. The addition of four ice packs at 8am and replaced with four cold packs at 4pm reduced temperatures in the steel box to 24.3°C (range: 17.4-27.9°C) whereas in the urethane polymer box temperatures were reduced to 13.4°C (range: 6.6-18.1°C).

Conclusion

Temperatures inside outdoor lockboxes can increase in summer commonly above the outdoor ambient temperature. Standardizing instructions for ice and cold packs can reduce internal outdoor courier lockbox temperatures during summer months, especially in urethane polymer lockboxes.
Diagnostic utility of flow cytometric immunophenotyping in cerebrospinal fluid specimen
Authors: Naiyer N , Lin H
Published: October 2021

Introduction/Objective

Flow cytometric immunophenotyping (FCI) of cerebrospinal fluids (CSF) has increasingly been used for diagnosing and monitoring hematologic malignancies. We reviewed CSF specimens sent for flow cytometry evaluation to identify the utility and limitations of FCI.

Methods/Case Report

We performed a retrospective review on CSF specimens received from July to October 2020. Samples were sent with requisition for unexplained neurologic signs or symptoms, to determine CNS involvement of neoplasm, or to stage a neoplasm. We reviewed specimen volume and cell count of flow cytometry samples and electronic medical records for possible diagnosis at time of specimen submission, final diagnosis, and concurrent cytology diagnosis.

Results (if a Case Study enter NA)

A total of 104 CSF samples from 59 patients were processed by the Flow Cytometry Laboratory during the review period. Of the 104 samples, 66% were from patients with a prior history of a hematologic malignancy, of which 20% had abnormal findings by FCI and cytomorphology. FCI was noncontributory for the cases in which patient did not have a previously diagnosed hematologic malignancy and underwent lumbar puncture for neurological abnormalities (n = 34). Concurrent cytology results were available in all but one case. Atypical or reactive findings by cytomorphology were seen in 21 cases (20%), for which flow cytometry studies showed no diagnostic immunophenotype in 12 cases. Abnormal FCI results occurred in 5 cases with history of hematologic malignancies, while concurrent cytomorphologic reports were negative.

Conclusion

Our findings suggest that CSF flow cytometry has low utility for screening patients with undifferentiated neurologic symptoms or without a prior hematologic malignancy history. Use as a screening tool for cases without clinical suspicion of hematolymphoid neoplasm is debatable. Flow cytometric and cytomorphologic analysis should be performed concurrently. While flow cytometric analysis in CSF may have higher sensitivity in hematologic malignancies, cytomorphology appears more favorable in identifying atypia or reactive conditions.
Rare presentation of primary hepatic marginal zone B-cell lymphoma and membranous glomerulopathy in a 3-year-old boy
Authors: Alkashash A M , Saxena R , Poulos C , Phillips C L , Nassiri M , Hains D
Published: October 2021

Introduction/Objective

Primary hepatic marginal zone B-cell lymphoma (MZL) is a rare entity that has been described with chronic inflammatory disorders such as chronic viral hepatitides B and C and primary biliary cholangitis. We report MZL in a 3-year-old African-American boy that was discovered incidentally at autopsy.

Methods/Case Report

The patient first came to medical attention at 9-months of age with bilateral periorbital edema that progressed to generalized edema of the[PL1] face, extremities, and abdomen. Laboratory testing showed nephrotic syndrome with massive proteinuria (50-60 g/day). A percutaneous renal biopsy specimen showed membranous glomerulopathy with PLA2R detected by immunofluorescence, and granular IgG deposition along tubular basement membranes. Serum was negative for anti-PLA2R antibodies. The patient suffered recurrent upper respiratory tract infections requiring several intensive care hospitalizations. At 3 years of age, he was transported unresponsive and pulseless to the emergency department where he was pronounced dead. A brother with the infantile nephrotic syndrome had died from sepsis at 2 years of age. Suspicion of abuse led to an autopsy by the medical examiner, who discovered nodular masses in the right and left liver lobes, which histologically showed a serpiginous infiltrate of small B-lymphocytes positive for CD20, CD43 admixed with plasmacytoid cells with kappa light chain restriction. There were no extrahepatic tumors. Transmission electron microscopy of glomeruli showed membranous glomerulopathy. Kidneys showed dense reactive interstitial lymphocytic infiltrate with germinal centers

Results (if a Case Study enter NA)

NA

Conclusion

To our knowledge, this is the first reported case of MZL presenting in a pediatric patient with membranous glomerulopathy. Both diagnoses are associated with autoimmune diseases and persistent, chronic inflammation. Recurrent infections in this patient suggest an immunoregulatory disorder, setting the stage for chronic inflammation, as seen in the kidney, with progression to MZL in the liver.
Hepatic Hyaline Arteriolosclerosis in Patients with Chronic Hyperglycemia
Authors: Kilpatrick M , Lewin D
Published: October 2021

Introduction/Objective

Hyaline arteriolosclerosis is a common feature of diabetic microangiopathy. It results from hyperglycemia-induced endothelial cell dysfunction and can be found in many sites including the retina, kidney, and skin. This histologic finding is important because studies have shown that in the kidney it is an independent risk factor for cardiovascular complications. To our knowledge, an association between hyperglycemia and hyaline arteriolosclerosis in the liver has not be studied. We aimed to investigate whether chronic hyperglycemia is associated with this histologic finding in liver arterioles.

Methods/Case Report

The first 50 liver biopsies performed at our institution starting January 1, 2020 were scanned into a digital pathology system (Philips, Cambridge, MA). For each biopsy, the patient’s highest recorded hemoglobin A1c (HbA1c) up to one year from the date of biopsy was recorded. The biopsies were then grouped into two groups: those from patients with a HbA1c greater than 6.5%, and those with a HbA1c value less than 6.5 %. Next, the digested periodic acid Schiff (DPAS) intensity of the arteriolar vessels in each biopsy was graded 0 to 3 by a single pathology resident who was blinded to its corresponding HbA1c group. Grade 0 to 1 was considered negative staining. Grade 2 to 3 was considered positive staining and indicative of hyaline arteriolosclerosis. By the end of the data collection, each case had been given a staining category and a HbA1c group. A 2 x 2 contingency table was constructed.

Results (if a Case Study enter NA)

37 of 50 patients had a recorded HbA1c meeting the study criteria. Of these 37 patients, 11 had an HbA1c greater than 6.5 % while 26 had an HbA1c less than 6.5%. Seven of the 11 biopsies from patients with an elevated HbA1c showed positive staining. Six of the 26 biopsies from patients with an HbA1c less than 6.5% showed positive staining.

Conclusion

We hypothesized that patients living with hyperglycemia may be more likely to exhibit hepatic hyaline arteriolosclerosis. A chi-squared test of independence was performed to examine the association between a liver biopsy’s HbA1c group and staining category. The relation between these variables was significant at p = < .05, χ 2 (2, N= 36) = 5.57, p = .0182, indicating liver biopsies with a HbA1c greater than 6.5 % are more likely to have this histologic finding. Future studies are needed to characterize diabetic hepatopathy, and its relatedness to macrovascular complications.
Porto-Sinusoidal Vascular Disease and Focal Nodular Hyperplasia-like Nodules in a Patient with Neurofibromatosis and Non-Cirrhotic Portal Hypertension
Authors: Alkashash A M , Khan S , Saxena R , Nephew L , Kubal C
Published: October 2021

Introduction/Objective

Non-cirrhotic portal hypertension (NCPH) is uncommon. The underlying pathophysiology appears to lie at the level of intrahepatic portal veins and sinusoids, hence the term “porto-sinusoidal vascular disease” (PSVD). We report a rare case of PSVD with focal nodular hyperplasia (FNH)-like nodules in a patient with neurofibromatosis type 2 (NF2).

Methods/Case Report

A 57-year-old male with NF2 and type 2 diabetes, presented with a large variceal bleed requiring blood transfusion and subsequent transjugular intrahepatic portosystemic shunt (TIPS). Imaging showed a nodular liver, presumed to be cirrhosis due to non-alcoholic liver disease. Liver biopsy was not done. Thereafter, he had several episodes of hepatic encephalopathy and TIPS was downsized to prevent recurrences. The patient required liver transplantation for intractable portal hypertension and severe hepatic encephalopathy; his liver synthetic function was near normal and MELD was 11. Portal vein was patent. The explanted liver was micronodular, soft and weighed 946 grams. Unencapsulated nodules, a few mm to 1 cm in size, were present. Microscopically, there was diffuse nodularity in the absence of bridging fibrosis. Thin, incomplete curvilinear fibrous septa were present. There were aberrant veins, hypervascular portal tracts, herniated portal veins and rare occluded portal veins. Trichrome and reticulin stains confirmed architectural abnormalities including nodularity, lack of bridging fibrosis and approximation of portal tracts. Immunohistochemistry for glutamine synthetase accentuated architectural distortion and revealed nodules with FNH-like geographic areas of staining.

Results (if a Case Study enter NA)

NA

Conclusion

This is a rare case of NCPH due to PSVD in a patient with NF2. Microscopy suggested incomplete septal cirrhosis (ISC), a pattern associated with both PSVD and regression of fibrosis in a cirrhotic liver. Isolated portal hypertension without loss of synthetic function favors primary PSVD over regression of fibrosis. FNH-like nodules are consistent with regenerative changes caused by localized abnormalities of blood flow.
Comparison of Saliva and Nasopharyngeal Swabs for SARS-CoV-2 Detection in an Emergency Department and Ambulatory Testing Locations
Authors: Attaway C , El-Sharkawy Navarro F , Richard-Greenblatt M , Herlihy S , Gentile C , Glaser L , Morris B , Abella B , Collman R
Published: October 2021

Introduction/Objective

Nasopharyngeal (NP) swabs have been the traditional specimen source used for testing for respiratory viruses. However, at the start of the COVID-19 pandemic, several studies suggested that saliva could also be used as a specimen source for testing for SARS-CoV-2. Despite potential benefits, there was limited data on the characteristics of this specimen type and few commercial assays with FDA emergency use authorization allowed saliva as a specimen source. In order to explore the feasibility and validate using saliva as a specimen source for ambulatory and emergency department patients we designed a study to compare saliva to NP swabs for SARS-CoV-2 testing.

Methods/Case Report

Specimens were collected in the emergency department and ambulatory testing sites between May 6, 2020-July 7, 2020. Nasopharyngeal swabs were collected as part of routine clinical practice and patients were given written instructions to self-collect 1mL of saliva into a sterile specimen cup with or without a straw. SARS-CoV-2 testing was performed in parallel with both specimen types using the TaqPath COVID-19 Combo Kit (Thermo Fisher Waltham, MA). Saliva was diluted 1:1 in saline prior to testing. Specimens were transported to the lab at 4C and frozen at -80C prior to testing.

Results (if a Case Study enter NA)

Seventy-four patients had both an NP swab and saliva tested in this study. Thirty of the 74 patients (41%) were unable to produce the full 1mL of saliva requested, but all samples had sufficient volume for testing after dilution. There were 34 positive samples obtained with an 82% positive agreement between the NP swabs and saliva. In 6 cases, the NP swab was positive, and the paired saliva was negative. In 1 case, only the saliva was positive. The average Ct of the positive NP swabs with a paired negative saliva sample was 39.6. There was only a single invalid test for one of the saliva samples.

Conclusion

Saliva was a straightforward sample to collect and test for SARS-CoV-2. Challenges included obtaining sufficient sample and a less predictable matrix that required dilution to ensure proper pipeting. In this study, NP swabs were more sensitive for detection of SARS-CoV-2. Paired saliva was more often negative in patients shedding small amounts of SARS-CoV-2 based on a high Ct of the positive NP sample.
Correlation Of Pcr Ct Values With Symptom Onset Across Diagnostic Platforms For Sars-Cov-2
Authors: Zia S Q , Mehrotra H , Tibbetts R J , Samuel L
Published: October 2021

Introduction/Objective

Following the definition of SARS-CoV2 outbreak as a pandemic by WHO, FDA gave EUA approval to the CDC real time polymerase chain reaction (PCR) assay and soon to other vendors to increase test availability. Most of testing platforms are PCR based, which test for multiple gene targets. We aimed to compare distribution of crossing threshold (cT) values of Diasorin (DIA), NeuMoDX (NDX) and Cepheid GenXpert (GX) for symptomatic and asymptomatic patients and assess performance of individual gene targets within the assays. We also correlated cT values with time from symptom onset.

Methods/Case Report

Retrospective review of medical and laboratory records of patients who tested positive for SARS-CoV2 between 08/01/2020 and 10/10/2020 on DIA, NDX, and GX platforms.

Results (if a Case Study enter NA)

We included 212 patients in our study. Days since symptom onset included 1 to 16 days. For DIA, mean Ct values for 46 symptomatic patients were 21.75 (S gene) and 22.74 (ORF1 gene); whereas 23.49 (S gene) and 25.49 (ORF1 gene) for 12 asymptomatic patients. Similarly, on NDX mean was 22.21 (N gene) and 23.13 (NSP2 gene) for 69 symptomatic, though 28.09 (N gene) and 28.61 (NSP2 gene) for 35 asymptomatic patients. GX manifested mean Ct value of 27.13 (E gene) and 31.22 (N2 gene) for 19 symptomatic; while 33.85 (E gene) and 36.42 (N2 gene) for 31 asymptomatic patients. Correlation coefficient for cT values versus days since symptom onset are DIA (r2 0.19), NDX (r2 0.22), and GX (r2 0.02).

Conclusion

The difference in cT values was statistically significant for symptomatic versus asymptomatic patients. There was positive correlation between days since symptom onset and cT values for DIA and NDX but not for GX, which may be due to difference in population tested in these platforms. These observations may be used to predict viral load and thus infectivity of patients who test positive for SARS-CoV2.
Novel discovery of Extended Spectrum β-lactamase (ESBL) Pluralibacter gergoviae in acute urinary tract infection and urolithiasis
Authors: Coate E , Merchen T , Cybulski R , Collier R , Mc Gann P , Mills E
Published: October 2021

Introduction/Objective

This case study describes the diagnosis, treatment, whole genome sequencing (WGS) and antibiotic resistance characterization from the ESBL-producing Pluralibacter gergoviae, a multi-drug resistant organism (MDRO) with a previously-documented presence in foodstuffs and cosmetics.

Methods/Case Report

A 39-year-old Hispanic American woman was admitted to the emergency department (ED) for fever, suprapubic tenderness, and pyuria. Three days prior to admission, patient underwent elective bilateral lithotripsy for retained nephrolithiasis. Seven days prior to ED admission, patient had an “Orgasm Shot” (O-Shot) which consists of platelet rich plasma that is drawn from the patient and injected into her vulvar area and around her clitoris to increase stimulation potential during orgasm. The patient was started on broad spectrum antibiotics, receiving Vancomycin and Ceftriaxone 1 gram 1 gram IV every 12 hours, intravenously. Urine cultures yielded two organisms, including a lactose fermenting as well as a non-lactose fermenting Gram negative rod. Mass spectrometry-based identification was successful in identifying the non-lactose fermenting colony as Pseudomonas aeruginosa, which also identified from a blood culture collected from the patient upon presentation to the ED. The lactose fermenting colony resulted in no identification by mass spectrometry but was identified using biochemical methods as Pluralibacter gergoviae, a recently-reclassified taxonomy previously identified as Enterobacter gergoviae. The P. gergoviae isolate was submitted to the Multidrug-Resistant Organism Repository (MRSN) at Walter Reed Army Institute of Research (WARIR) for WGS on Illumina Miseq. Sequencing and phenotypic/ genotypic data on isolate confirmed this as an ESBL P. gergoviae organism.

Results (if a Case Study enter NA)

NA

Conclusion

Summary data on possible epidemiological associations, antibiotic susceptibility testing, antibiotic resistance genes identified, and information on the antibiotic resistance plasmids will be presented. These findings from the WGS data, antibiotic susceptibilities will provide a lessons-learned for other clinical microbiology labs on how to identify unusual organisms such as P. gergoviae.
A rare case of Pneumocystis jirovecii and cytomegalovirus coinfection in the small bowel
Authors: Broder K , Geller R L , Del Rio C , Bhamidipati D
Published: October 2021

Introduction/Objective

Infection with Pneumocystis jirovecii remains a common cause of pneumonia in patients with Acquired Immune Deficiency Syndrome (AIDS). Extrapulmonary manifestations, however, are exceedingly rare. We describe a rare case of coinfection of the small bowel by Pneumocystis jirovecii and cytomegalovirus (CMV).

Methods/Case Report

A 48-year-old female with a history of HIV/AIDS, remote history of Pneumocystis jirovecii pneumonia, and previous non-compliance with HAART, presented to the emergency department with right lower quadrant abdominal pain, fever, and chills for 1 week. Her recent medical history included a hospital admission 1 month prior for community-acquired pneumonia with CD4 count and viral load of 12 cells/mcl and >680,000 copies/mL, respectively; upon discharge she restarted HAART. When she presented to the emergency department in our case, she demonstrated leukocytosis (14.3 K/mcl), tachycardia (131 bpm), and hypotension (87/58 mmHg). An abdominal CT scan showed free air with concern for perforated viscus and multi-station lymphadenopathy with gastrohepatic and retrocaval nodes >2 cm. A chest x-ray showed nodular and cavitary lesions, stable from prior imaging. The differential diagnoses in an AIDS patient with a gastrointestinal mass includes Kaposi’s sarcoma, lymphoproliferative process, or infection. The surgeons were concerned for tuberculosis as well, due to the hospital’s patient population, her bulky lymphadenopathy, and immune-compromised status. An exploratory laparotomy was performed and found jejunal perforations, mesenteric lymphadenopathy, and 3L of fluid in the abdomen. Pathology received 4 soft lymph nodes and a 57 cm segment of thickened small bowel with purulent perforation but no discrete mass. Microscopic examination showed a perforating pseudotumor and acute serositis extending to the margins of the specimen. Lymph node flow cytometry was negative for clonal populations. GMS stains highlighted innumerable “crushed-ping-pong-ball”-like fungal forms consistent with Pneumocystis in the jejunum and all 4 lymph nodes. A CMV immunohistochemical stain highlighted infected cells with nuclear enlargement and nuclear inclusions in the jejunum.

Results (if a Case Study enter NA)

NA

Conclusion

Extrapulmonary Pneumocystis infection is rare but clinicians, pathologists, and microbiologists must keep it in the differential of HIV patients, especially those who are not controlled on antiretroviral therapy.
Public health risk of Giardia and Cryptosporidium infection from urban wildlife
Authors: Leu-Burke G , Charoonsophonsak T , Madsen J
Published: October 2021

Introduction/Objective

The dedication of large areas in Anchorage for urban park environments encouraged increased interaction between migrating Canadian geese, approximately 1500 moose and humans. Urban wildlife inhabiting public establishments such as parking lots, creeks, playgrounds, and suburban backyards results in significant environmental fecal contamination. Previous studies found varying potential for zoonotic transmission of parasites through direct fecal contact or water contamination. With a significant number of vulnerable unsheltered individuals in Anchorage using public green belts, there is risk of asymptomatic, under diagnosed, parasitic infection due to exposure to fecal contamination.

Methods/Case Report

To assess environmental risk of parasitic zoonosis from urban wildlife, we surveyed fourteen high impact exposure areas including waterways and green spaces throughout Anchorage with ground collection of 106 fecal samples from moose (n=76) and geese (n=30). Using standard rapid antigen immunoassay detection method, we identified preserved samples for the presence of Cryptosporidium or Giardia.

Results (if a Case Study enter NA)

Overall evaluation of fecal samples found 23.6% positive for parasitic colonization in 87% of collection sites. Giardia was identified in 10.4% and Cryptosporidium in 13.2%. Comparative evaluation of each species found geese with a higher percentage of Cryptosporidium isolated (30%) when compared to moose (6%). Giardia was predominately found in moose (13%) with very few geese colonized.

Conclusion

Considering the high population of outdoor enthusiasts and a significant number of unsheltered individuals in Anchorage, discovering nearly a quarter of urban moose and geese colonized with Giardia and/or Cryptosporidium identifies a significant public health risk. Often using creeks and lagoons as their water source Anchorage’s vulnerable population includes a large number of immunocompromised HIV positive individuals in which parasitic infection, especially Cryptosporidium, can cause overall poor health and reduced quality of life. Therefore, active surveillance of parasitic colonization in urban wildlife is essential and continued evaluation necessary to determine public health risk.
Bacillus cereus Bacteremia: An Unusual Case Following Food Poisoning
Authors: Sabri A , Cavalieri S , Ahmad F , Martin S , Abushattal A
Published: October 2021

Introduction/Objective

Bacillus cereus is a spore-forming, gram-positive rod, well known for causing food poisoning. In addition, this bacterium often presents as a contaminant of blood cultures. Differentiating true bacteremia from contamination of blood samples is important as it has treatment implications. Early recognition is necessary, as it can cause septic shock if untreated. We present a challenging case of food poisoning with concomitant bacteremia in a young patient with a history of diabetes mellitus (DM), celiac disease, and new-onset chronic kidney disease (CKD).

Methods/Case Report

A 23-year-old adult male with a history of DM, new-onset CKD, and celiac disease presented with nausea, intermittent vomiting, and lower abdominal pain for 2 weeks. On initial evaluation, he had normal blood pressure but tachypnea and tachycardia. Physical examination was significant for left lower quadrant and flank tenderness. The symptoms were persistent and progressed to point that he could not tolerate meals due to vomiting. Two weeks earlier, he presented with similar complaints along with dysuria and was treated for suspected urinary tract infection with Co-trimoxazole. This time, further workup revealed normal white blood cell count (11.8 k/µL) with 81% neutrophils, elevated creatinine (3.56 mg/dL), blood urea nitrogen (49 mg/dL), and procalcitonin (0.39 ng/mL), with abnormal urinalysis showing increased turbidity, pyuria, and nitrituria. He was started on ceftriaxone, fluids, antiemetics and was admitted to the hospital for further management. The urine culture had no bacterial growth. Two sets of peripheral blood cultures (different sites at different times) had gram-positive rods which eventually turned out to be B. cereus, identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Levofloxacin was started, and he reported improvement in nausea and vomiting by the next day of admission and was discharged.

Results (if a Case Study enter NA)

NA

Conclusion

Differentiating true B. cereus bacteremia from blood sample contamination is important. Additionally, no symptoms are specific for B. cereus-associated food poisoning, and the presence of risk factors doesn’t always favor this entity over other entities, hence adding difficulty to the diagnosis. A high index of suspicion is needed, as early intervention can prevent the development of life-threatening complications.
Practical Approach to the Pathologic Diagnosis of Mixed Filamentous Fungal Infections in Burn Wounds: A Case Series
Authors: Pyden A D , Solomon I , Laga Canales A
Published: October 2021

Introduction/Objective

Opportunistic infections by fungi are a major source of morbidity and mortality in patients suffering from extensive burn wounds. Here we review a series of cases of infections by multiple fungi in burn wounds as diagnosed by histopathology and outline the key features for the pathologist to include in the report.

Methods/Case Report

Biopsies from patients with more than one fungal species identified in the laboratory in a concurrent culture or by PCR were included in this study. Three cases are presented with multiple fungi identified. Each case had yeast and at least one different hyaline mold species present on pathology; two cases additionally had mucormycetes present, with angioinvasion in one case. All organisms requiried microbiologic cultures and variably required molecular testing for full identification.

Results (if a Case Study enter NA)

N/A

Conclusion

Pathologists should be aware of the possibility of infection by multiple fungal species in burn wounds. Fungal morphology in tissue sections should allow for detection and distinction of mucormyctes and other hyaline molds. Histopathologic correlation with culture and/or PCR results is essential to distinguish potential contaminants from true infection.
Utility of Next Generation Sequencing in the Workup and Diagnosis of Myeloproliferative neoplasm in the Peripheral Blood: A single institution experience
Authors: Lynn T , Campbell A , Ding Y
Published: October 2021

Introduction/Objective

In patients with suspicion of Myeloproliferative neoplasm (MPN) and negative for BCR-ABL1, NCCN guideline currently recommends two molecular workup pathways in peripheral blood: 1) a multi-step reflex mutation testing algorithm including JAK2 V617F, CALR, MPL, JAK2 exon12 or 2) a multigene Next Generation Sequencing (NGS) panel that includes at least JAK2, CALR and MPL genes. Here we report the clinical utilization and impact of a NGS based MPN diagnosis assay.

Methods/Case Report

Total of 690 consecutive cases at Geisinger between 2019 and 2021 were included in this study. Patient’s CBC showed chronic cytosis in either single or multi-lineage myelopoiesis and was clinically suspicious for MPNs. For BCR-ABL1 negative cases, NGS based MPN diagnostic assay was performed, which include the four disease defining genes recommended by NCCN guideline: JAK2, CALR, MPL, CSF3R as well as three additional genes NRAS, PPM1D and TP53. Variants are classified in to four tiers based on their level of clinical significance.

Results (if a Case Study enter NA)

Among all cases tested, 25 out of 690 cases (3.6%) were positive for BCR-ABL1 transcript. 20.9% (139 out of 665 BCR-ABL1 negative cases) had at least one variant detected, which included 73 variants in Tier I category (11.0%), 6 variants in Tier II (0.9%), 57 variants in Tier III (8.6%) and 3 variants in Tier IV(0.5%). Among all disease defining mutations, JAK2 V617F was the most commonly detected mutation (59 cases and 8.8%), followed by CALR indel mutations (13 cases and 2.0%). In addition, double variants were detected in total 7 cases (1.0%).

Conclusion

Comparing to the conventional multi-step sequential workup for MPN diagnosis, the multi-gene NGS panel provides a cost-effective and time- saving solution. When detected concurrently with the disease defining mutations, NRAS, PPM1D and TP53 could provide not only additional prognostic information but also may suggest pending progression in myeloproliferative neoplasms.
In Egyptian Patients with Hepatocellular Carcinoma the role of MicroRNA-215
Authors: Ali H A
Published: October 2021

Introduction/Objective

MicroRNAs (miRNAs) are a class of evolutionarily conserved small non-coding RNAs which are make a contribution in the regulation of gene expression and protein translation, and they play vital roles in differentiation, cell growth, and the development of diverse types of cancers.

Methods/Case Report

Our research was done in hepatology and gastroenterology department at the National Liver Institute, Menoufia University. It included 135 patients and 60 healthy subjects serving as control group. We have 3 groups:

Group I (Control)

This group included 60 apparently healthy individuals. They were 32 males and 28 females, whose ages ranged from 39 to 67 years old (mean ±SD= 51.67 ± 6.40 years).

Group II (Cirrhosis)

This group included 75 patients with liver cirrhosis due to chronic HCV infection. They were 41 males and 34 females whose ages ranged from 41 to 68 years old (mean ±SD= 54±6.73 years).

Group III (HCC)

Sixty patients with HCC were included. They were 35 males and 25 females, whose ages ranged from 41 to 70 years old (mean ±SD= 53.97±6.15 years).

Laboratory Investigations

Complete blood count (CBC), Liver tests: aspartate transaminase (AST) and alanine transaminase (ALT), serum albumin, total and direct bilirubin, alkaline phosphatase and INR were measured. Serum creatinine was also measured. The analysis of serum alpha fetoprotein (AFP) (ng/ml) was done. Chronic HCV infection was diagnosed by detection of HCV antibody and HCV RNA by real time PCR. Anti-HCV antibody was detected by means of a third generation enzyme immunoassay. Quantification of HCV RNA level was performed by means of COBAS Taqman 84 (Roche) real time HCV RNA Assay with lower detection limit 15 IU/ml.

Results (if a Case Study enter NA)

In control group, miRNA-215 ranged from 1.60 to 21.30 with a median value of 6.89. In cirrhotic patients group, it ranged from 0.70 to 14.65 with a median value of 2.85. In patients with HCC group, it ranged from 0.03 to 10.95 with a median value of 0.52 (pg/ml). MiRNA-215 and AFA mean levels showed a statistically significant difference (p <0.001) between the three studied groups.

Conclusion

In conclusion, MicroRNA-215 was proved to be significantly lower in HCC patients compared to cirrhotic patients and control group. This marker might be used as a potential serologic marker for HCC and a complementary diagnostic tool in monitoring cirrhotic patients for detection of HCC.
Co-treatment of Garlic-Oils Extract, Dially-thiosulphate, and Histone Deacetylases Inhibitors (HDACI) Synergistically Inhibited Cell Proliferation and induced Apoptosis in Hepatocellular carcinoma cell lines
Authors: Fyala A S , Sultan A S
Published: October 2021

Introduction/Objective

Hepatocellular carcinoma (HCC) is the most common cause of cancer-deaths worldwide. Garlic (Allium Sativum), is a natural-medicinal herb which has anti-fungal, anti-bacterial, anti-inflammatory, anti-virus, and antiproliferative activities. Garlic-oil soluble-sulfur-compounds, diallyl-thiosulphate, (DT) are more effective than water-soluble-compounds in protection against cancer due to its capacity to induce apoptosis and revise anti- multidrug-resistance. Histone deacetylases inhibitors (HDACIs) are inhibitors of anti-cancer agents that play a role in inducing death, differentiation, apoptosis induction, and cell-cycle arrest in different cancer-types. The present studying aims to investigate the anti-proliferative effect of organosulfur-oil DT extract of garlic by possible modulation of HDACIs role on HCC cell-lines.

Methods/Case Report

Two HDACIs, suberanilohydroxamic acid (SAHA) and trichostatinA (TSA), were used to investigate their role on proliferation of two HCC cell-lines, HepG2 and Hep3B, respectively. Cell proliferation was examined by Wst-1 assay, apoptosis induction signaling pathways, cell-cycle analysis, and western-blot analysis of the major oncogenic signaling pathways in the two tested cell-lines.

Results (if a Case Study enter NA)

Our data showed that DT significantly inhibited the cell-proliferation and induced cell-cycle arrest at G2/M phase in both HCC cell-lines. In addition, co-treatment of DT and HDACIs for 48h enhanced the cell inhibitory effect and induced apoptosis by up-regulation of p53, p21, and Bax protein expression and down- regulation of Bcl-2 and cyclin-D1 protein expression compared to control or each treatment alone. Furthermore, the data showed that DT significantly increased caspases-3 activity in Hep-G2 cell-line than that of Hep3B cell-line in a dose dependent-time compared to the control. Apoptosis induction was consistent with up-regulated caspase-3 activity, and HepG2 cells, but not Hep3B cells, showed a significant increase in response to co-treatment of DT with SAHA compared to co-treatment with TSA.

Conclusion

The data of the present study demonstrated that DT, non-toxicity compound, might be a new modulator for HDACIs effects, which in turn might be a promising prospective agent for HCC treatment.
Multiplex Fragment analysis detects all COVID-19 variants of concern
Authors: SoRelle J A , Clark A , Wang Z , Park J
Published: October 2021

Introduction/Objective

The majority of tracking methods have employed whole genome sequencing, which can be very expensive and time consuming. An alternative method has been to use genotyping of specific mutations to identify variants. However, tracking SARS-CoV-2 variants by targeted methods has been a moving target. Most methods only multiplex four targets per reaction, but we have multiplexed 8 targets in a single tube using fragment analysis.

Methods/Case Report

Fluorescently labeled primers targeted a combination of insertion/ deletion mutations and single nucleotide mutations. The PCR amplified products, amplicons, were separated by capillary electrophoresis. Primers were designed to detect changes in size indicative of insertion or deletion mutations including: ORF1A:Del3675_3677, S:Del69_70, S:Del144, S:Del157_158, S:Del242_244, ORF8:Del119_120, and ORF8:ins28269-28273. Allele-specific primers were designed to detect both the wild-type and mutated versions of S:N501Y, S:E484K, and S:L452R.

Residual nasopharyngeal and nasal specimens testing positive for SARS-CoV-2 by RT-PCR or isothermal amplification (IDnow) methods were selected from May 1- June 24, 2021. Variant analysis was performed by multiplex targeted PCR and whole genome sequencing in parallel on the same specimens to determine positive percent agreement.

Results (if a Case Study enter NA)

Variant analysis was performed on 250 specimens detecting each of the major variants of concern Alpha (B.1.1.7, U.K. origin, n= 108), Beta (B.1.351, South Africa origin, n=3), Gamma (P.1, Brazil origin, n=12), Delta (B.1.617.2, Indian origin, n=17), and Iota (B.1.526, New York, n=5). Some specimens with low viral load were detected by only PCR (n=18), only WGS (n=41), or neither (n=20). Overall positive percent agreement was 95% (163/171).

Conclusion

This adjustable method robustly and accurately identifies COVID-19 VOCs utilizing a platform amenable to multiple targets (20-40 targets ranging from 100-500b.p. across four fluorescent channels) using equipment commonly found in routine molecular pathology laboratories. Future directions include adjusting targets to detect new variants.
Molecular Detection of Adenovirus in Tap Water from Coastal Areas Of Karachi Pakistan:The Real-Time PCR Assay
Authors: Kalam A
Published: October 2021

Introduction/Objective

Diarrhea is a major source of morbidity and mortality in low-income and middle-income countries. In underdeveloped countries, diseases caused by viruses identified in environmental samples cause major health problems. Little knowledge about the frequency and pattern of viral contamination of drinking water sources in these resource-poor settings. Adenovirus which causes watery diarrhea, particular has been recognized as important causal pathogen. Adenovirus remains a global threat to public health and an indicator of inequity and lack of social development. Tap water samples from coastal sites in Karachi between 2019 and 2020 over a period of 11 months. The total of 40 tap water sample was examined for infectious Adenovirus by a real time polymerase chain reaction (PCR) amplification.

Methods/Case Report

This Pilot study is conducted on tap water samples from Karachi Pakistan, n=40 are processed. Extraction of nucleic acid from all filtered water samples collected with Sterivex filter units by using Qiagen DNeasy Power Water Sterivex Kit. As per the manufacturer’s instruction. Phocine herpesvirus(PhHV) is added as an external positive control to monitor the efficiency of nucleic acid extraction and amplification. TaqMan Universal PCR Master Mix (Thermo Fisher Scientific) is being used in probe based real time PCR assay,the below 35 Ct value is considered as a positive sample.

Results (if a Case Study enter NA)

Results showed the total of 37.7% of the sources were positive for adenovirus.The level of viral contamination was moderate to high.

Conclusion

The results has been showed that no seasonal pattern for viral contaminations was found after samples obtained during the dry and wet seasons were compared. Further the Real time PCR assay increases the sensitivity and provides the high resolution of pathogen detection.
TERT Immunohistochemistry Expression as a Surrogate of TERT Promoter Mutations in Infiltrating Gliomas
Authors: Moosvi A M , Dono A , Bellman A , Ballester L , Goli P , Esquenazi Y
Published: October 2021

Introduction/Objective

Genomic alterations are critical for the diagnosis of infiltrating gliomas. Mutations in the telomerase reverse transcriptase promoter (TERTp) are sufficient for a diagnosis of glioblastoma in some cases, independent of histologic features. Although DNA sequencing is the preferred method for evaluating TERTp mutations, there are limitations with regards to turn-around-time, accessibility, and cost. In this study, we evaluated the efficacy of using TERT immunohistochemistry (IHC) as a surrogate marker for the identification of TERTp mutations in infiltrating gliomas.

Methods/Case Report

The study cohort consisted of 31 infiltrating gliomas diagnosed following the 2016 WHO classification of CNS tumors by a board-certified neuropathologist. Each case was evaluated by immunohistochemistry (anti-TERT monoclonal antibody) and with a targeted next-generation sequencing (NGS) panel. A systemic literature search was conducted to examine reports of TERT antibody as a surrogate marker of TERTp mutations. TERTp mutation detected by sequencing was considered the gold standard.

Results (if a Case Study enter NA)

TERT immunohistochemistry demonstrated a sensitivity of 61.1% and specificity of 69.2%. Cases were divided into IDH-WT and IDH-mutant infiltrating gliomas. Among the IDH-WT group, 84% contained the TERTp mutation with a sensitivity of 62.5% and specificity of 33.3% for the TERTp IHC. IDH-mutant gliomas showed a 16.2% TERTp mutation rate, and immunohistochemistry had a sensitivity of 50% and 80% specificity. The probability of TERT immunohistochemistry in diagnosing TERTp mutations exhibited a poor likelihood ratio for both the positive and negative test. Literature review included 5 studies with an overall sensitivity and specificity remaining consistently low (<80%), with 2 of these studies evaluating CNS related tumors giving rise to similar diagnostic performance.

Conclusion

TERT IHC has suboptimal sensitivity and specificity for identifying TERTp mutations in IDH-WT and IDH- mutant infiltrating gliomas.