bluuebunny/crossref_metadata_2025_split huggingface dataset:
False Negative Rate (2%) of Lynch Syndrome Screening Utilizing A Two-Antibody (PMS2/MSH6) Immunohistochemistry Panel: Failure To Detect a Subset of MSH2-Deficient Endometrial Carcinomas
Authors: Wood R , Murray S , Offman S , Carter M 
Published: October 2020

Abstract

Introduction/Objective
Lynch syndrome (LS) is an inherited condition caused by defective DNA mismatch repair (MMR), leading to a higher incidence of cancers of multiple sites. Screening for LS is now recommended for new diagnoses of endometrial cancer (EC) using either two- (PMS2, MSH6) or four-antibody (2/4Ab) (PMS2, MSH6, MSH2, MLH1) immunohistochemical (IHC) panels. The 2Ab panel assumes consistent loss of expression of the minor dimer component, PMS2 or MSH6, when the major component, MLH1 or MSH2, respectively, is lost due to mutation. Recent studies have indicated that 2Ab testing may lead to underdiagnosis of MSH2-deficient tumors in cases where MSH6 staining is weak or focal, potentially leading to underdiagnosis of LS.

Methods
We conducted a retrospective study using archived slides for 293 cases of EC (identified via LIS search from 2016-2019) that were screened using the 2Ab panel (expanded to 4Ab when PMS2 or MSH6 were negative). MSH6 expression was reviewed; if weak, focal (less than 10% staining), or both, MSH2 IHC was performed. When a previously undetected loss of MSH2 expression was found, the attending clinician was informed such that referral to medical genetics could be arranged.

Results
Results Overall, 68 (23.2%) tumors were MMR deficient, with 54 (18.4%) showing MLH1/PMS2 loss, 7 (2.4%) with MSH2/MSH6 loss, 2 (0.7%) with isolated PMS2 loss, 4 (1.4%) with isolated MSH6 loss, and 6 (2.0%) with isolated MSH2 loss (i.e. intact but weak/focal MSH6, seen in biopsy and hysterectomy specimens). Interestingly, 1 tumor (1.5%) demonstrated loss of MSH6, MLH1 and PMS2. Two tumors (0.7%) with isolated MSH2 loss were previously unrecognized as MMR-deficient and hence at high risk for LS. Both cases were evaluated by PCR for microsatellite instability (MSI) and confirmed to have high-degree MSI.

Conclusion
This study identifies the frequency of mismatch repair deficient endometrial cancers in Atlantic Canada, highlights a potential pitfall of using two-stain IHC screening for Lynch syndrome, and supports emerging recommendations for universal Lynch syndrome screening in EC.
Human BK Polyomavirus Nephropathy (BKVN) In Non- Kidney-Transplant Patients
Authors: Chen Wongworawat Y , Zuppan C 
Published: October 2020

Abstract

Introduction/Objective
Human BK polyomavirus nephropathy (BKVN) occurs in up to 10% of renal transplant recipients, and can result in graft loss. Transplant biopsy is the gold standard to diagnose BKVN, and SV40 immunohistochemical (IHC) staining is helpful in confirming the diagnosis. BKVN is uncommon outside the setting of renal transplantation. To understand more about its occurrence in other contexts, we reviewed our renal biopsies files for cases of BKVN.

Methods
Our renal biopsy files for the past 20 years were reviewed for all cases with a diagnosis of BKVN or polyoma virus infection, and the clinical characteristics of the affected patients noted.

Results
Evidence of BKVN was found in 44 renal biopsies, of which 39 (86%) were renal transplant patients. Of the remaining five patients (14%), two had undergone heart transplantation, one lung transplantation, one was undergoing chemotherapy for acute lymphoblastic leukemia, and one patient had active HIV infection. All patients had elevated serum creatinine, and four out of five patients had documented BK viremia. Four of the five biopsies showed typical tubular injury with viral nuclear cytopathic changes (inclusions). In the lung transplant patient, the biopsy showed advanced chronic tubulointerstitial injury without distinct viral inclusions, but SV40 staining confirmed the presence of BK virus antigen.

Conclusion
The BKVN is distinctly uncommon outside the context of kidney transplantation. In our series, 14% of patients with BKVN were not kidney transplant recipients, but all were immune compromised in some fashion. The pathologic features of BKVN appear similar, regardless of whether the host is a renal transplant recipient or not.
Although uncommon, it is important to consider the possibility of BKVN in non-renal transplant patients with persistent or progressive renal dysfunction.
Scopes and Challenges In Educating The Clinical And Nursing Staffs Regarding The COVID -19 Specimen Collection And Processing For Testing In The Municipal Public Health System Based Ambulatory Care Health Clinics In New York City
Authors: Huq Ronny F M 
Published: October 2020

Abstract

Introduction/Objective
With the emergence of Novel COVID-19 infection in the New York City, at the initial phase a very limited information and guidelines were available from the federal and state health authorities and only state lab could provide the COVID -19 testing. Sparsity of the authentic information and up surging of the misinformation in the social media and rapidly evolving different reference testing laboratories were creating confusions and challenges among our clinic providers and nursing staffs. With periodic incorporation of updates on standardized protocol and guidelines, we formulated a plan and delivered that in a coordinated manner in educating the clinical and nursing staffs regarding the COVID -19 specimen collection and processing for testing to overcome that.

Methods
We gathered all the communications for COVID -19 from the federal, state and city health authorities and our corporate management about the testing methods, collection and processing requirements and specimen pickups. We verified and customized that information, prepared and circulated them in detailed PowerPoint presentation and then updated that periodically with any addition or changes in the testing reference labs and/or their specimen requirements.

Results
With periodic, standardized and updated guidelines and detailed verified information and instructions for sample processing, a uniform and much coordinated specimen collection and processing could be achieved and all of our five-borough spanning multisite municipal ambulatory clinics could collect and process the COVID-19 specimens properly.

Conclusion
Centralized, Planned and concerted education planning and timely delivering that to the clinical and nursing staffs could tremendously help in answering many relevant queries and curtailing confusion and properly collecting and handling the specimens in emerging infection like COVID-19 in a large city municipal ambulatory care health system.
Genotyping of the Galactosemia GALT 591 A&gt;G Mutation by Pyrosequencing
Authors: Bamford J B , Ramirez J M , Prewit W A , Robinson W J , Bennett K M 
Published: October 2020

Abstract

Introduction/Objective
This project aimed to design a pyrosequencing assay capable of genetically analyzing the presence of GALT 591 A&gt;G mutation for the diagnosis of galactosemia. Galactosemia is an autosomal recessive disorder that affects enzyme activity of galactose-1-phosphate uridylytransferase (GALT). This enzyme is responsible for proper processing of galactose to glucose; if not broken down the accumulation of galactose in the body results in developmental delays, clouding of the eyes, speech difficulties, and intellectual disabilities. Pyrosequencing offers a valuable platform in assessing whether patients are wild type unaffected (A:A), heterozygous carrier (A:G), or homozygous affected (G:G) at the alleles within the GALT 591 locus by measuring percentage of the wild type A allele and the mutant G allele.

Methods
PCR primers were designed for the mutation locus, and PCR amplification was optimized for the target 77 bp product, with verification by gel electrophoresis. The pyrosequencing assay was designed and validated on the Qiagen PyroMark Q24 instrument. Control samples included commercially purchased DNA from the Coriell Cell Repository.

Results
One hundred and thirty-three reactions were utilized to establish the following assay validation parameters: accuracy (100% for G:G, 95% for A:G and A:A), precision (determined by mean and standard deviation with a standard deviation of 0.6 for G:G, 4.55 for A:G and 4.85 for A:A), and limit of detection (10 ng DNA pre-PCR and 2 µL of PCR product loaded). Twenty-six blinded samples were utilized to test assay clinical performance, as compared against a high resolution melt curve assay.

Conclusion
It was determined that detection of GALT 591 A&gt;G via pyrosequencing is highly sensitive and specific with a clinical sensitivity of 100% and a clinical specificity of 95.83%. It was concluded that this assay could be applied in a clinical environment for GALT 591 A&gt;G genotyping to aid in galactosemia diagnosis.
Rat-Bite Fever: Updated Recommendations For Culture And Isolation Of Streptobacillus Moniliformis Using An Automated Continuous Blood Culture Instrument In A Clinical Setting
Authors: Szewc A M , Bell M E , Kelly A J , McQuiston J R 
Published: October 2020

Abstract

Introduction/Objective
Rat-bite fever and Haverhill fever are difficult to diagnose in a clinical setting due mostly to clinicians and laboratory professionals being unable to culture the causative agent-Streptobacillus moniliformis. SPS in blood culture bottles has historically been implicated as the complicating factor.

Methods
Utilizing the BDFX40 automated continuous blood culture bottle system and novel quantitative PCR data, we present how blood volume is critical in order to consistently detect, isolate and grow the organism in the presence of SPS using modern laboratory instrumentation in a clinical setting.

Results
We demonstrate here that 10ml of blood was determined to provide optimal results for detection and growth of S. moniliformis in 0.05% SPS. For all isolates tested, 100% (n=56) were detected or alerted as positive by the instrument, with the longest time required for detection being 102 hours (n=1) and the fastest time to detection being recorded at 13.4 hours. (n=1) with an average time of 26.5 hours (n=56).

Conclusion
During the course of this study, we determined that blood inoculum volume played a significant role in organism growth and detection. We found that in 100% of the isolates tested (and all the variations of testing within), SPS (up to a concentration of 0.05% w/v) in blood culture media appeared to be counteracted, allowing for the growth detection and culturing of S. moniliformis using an automated continuous blood culture system when 10ml of blood was used as an inoculum. This is the first study to report and suggest that a specific blood volume is critical when utilizing a closed commercial blood culture system to detect S. moniliformis, this research is the largest study of Streptobacillus moniliformis isolates to date.
Incidence Of Enteropathogenic Escherichia Coli Among Infants At Eleyele Comprehensive Health Centre, Ile-Ife
Authors: Faseyi K T 
Published: October 2020

Abstract

Introduction/Objective
This work was carried out to find the incidence of enteropathogenic Escherichia Coli in children below five years of age who complained of having diarrhea at Eleyele Comprehensive Health Centre, Obafemi Awolowo University Teaching Hospital Complex, Ile-Ife.

Methods
All specimen were cultured as routinely done in Bacteriology Laboratory in Obafemi Awolowo University Teaching Hospital for stool samples. Colonies of lactose fermenters were processed after overnight incubation at 37°c. Non lactose fermenter colonies were discarded. Out of 200 colonies isolates on MacConkey Agar, there were 150 lactose fermenters and these were all processed. Biochemical examination on sugars, for the production of acid and gas, indole production, motility, citrate utilization, voges-prokauer and Methyl red tests.

Results
Out of 150 strains, only 80 strains obeyed IMVic ++ -- reactions. These were serotyped to know the enteropathogenic strains. From the result obtained, 23 strains reacted positively with polyvalent antisera (Polyvalent 2, 3, 4 antisera) out of which 13 strains gave a positive reaction with corresponding monovalent antisera. 5 strains from polyvalent 2 antisera, 5 strains from polyvalent 3 antisera, and 3 strains from polyvalent 4 antisera. In close study of this work, total percentage of female with Diarrhea cases were 44.5% total percentage of male with diarrhea cases were 55.5%. Out of these 80, Escherichia coli were isolated, from these 13 enteropathogenic Escherichia coli strains were isolated (16.25%). Patient with age group below 2 years gave 9 strains 69.2%, 2-3 years gave 2 strains (15.4%), 3-4 years gave 1 strain (7.7%) and 4-5 years gave 1 strain (7.7%). Also close examination of result revealed that male children had the greater percentage of Enteropathogenic infection with 8 strains out of the 13 strains serotyped (61.5%) and female children with 5 strains (38.5%).

Conclusion
Escherichia coli remain an important cause of infant diarrhea. Although epidemics of infant diarrhea caused by enteropathogenic Escherichia coli have almost disappeared from the developed countries, it is still very common in developing countries. The relative importance of enteropathogenic Escherichia coli as a cause of infant diarrhea need to be reassessed and new diagnostic techniques will also help to simplify this task.
Cerebral Phaeohyphomycosis Due to Cladophialophora Bantiana in a Kidney Transplant Patient
Authors: Yu K , Devi P , Pulinthanathu R 
Published: October 2020

Abstract
Casestudy: Phaeohyphomycosis is a group of infections caused by pigmented, black, dematiaceous fungi and is responsible for cutaneous, superficial and deep mycoses, disseminated infection and brain abscesses. The primary agents involved include Alternaria spp., Exophiala spp. and Cladophialophora spp. Cerebral phaeohyphomycosis is particularly devastating with mortality rates as high as 70-80%. These fungi are becoming increasingly important opportunistic pathogens in solid organ transplant recipients (SOTR). We report a case of cerebral phaeohyphomycosis in a 65-year-old male with living donor kidney transplant for four years and has been maintained on immunosuppressive therapy with tacrolimus and prednisone. The patient presented with aphasia, frontal headache, loss of peripheral vision of right eye, and mental status change for three months due to several left- sided parieto-occipital brain abscesses. Left occipital abscess resection and parietal partial lobectomy were performed to reduce intracranial hypertension and to remove abscesses. Histopathological evaluation revealed brain abscess with pigmented fungal organisms with elongated, branched and septate. The pus aspirated during surgical excision of brain lesions grew black mold, identified as Cladophialophora bantiana. The patient’s neurological neurological condition had imporved after several weeks of combination antifungal therapy with posaconazole, liposomal amphotericin, and flucytosine. The lesions were initially suspected to be of tuberculous etiology, which was ruled out by histopathological examination. Such diagnostic dilemmas are common in the infection caused by Cladophialophora, which can cause treatment delay and death. Early diagnosis is therefore mandatory for the rapid treatment and survival of patients. As the number of SOTR increases, so does the incidence of fungal infections in that population. Surgery, along with antifungal therapy and a reduction in immunosuppression, are the cornerstones of treatment.
Incidental Prostate Infections: Developing the Prostate Microbiome
Authors: Daniel D , Zuretti A 
Published: October 2020

Abstract

Introduction/Objective
About 1 in 9 men will be diagnosed with prostate cancer in their lifetime. The traditional method of diagnosis is via a 12 core, trans-rectal biopsy. While this has been an appropriate method of investigation, a rectal approach to the prostate core made it difficult to differentiate prostatic bacterial infection from fecal contamination. Utilizing a sterile trans-perineal approach for biopsy, we were able to establish a true microbiome of the prostate, without contamination.

Methods
This is a prospective, IRB approved study. Men who were required to have prostate biopsies were offered a trans-perineal or trans rectal method of biopsy. Those who opted for trans-perineal biopsy with a negative urine culture met the inclusion criteria. Urine culture was performed prior to scheduling for the procedure. At time of biopsy, sterile cultures were taken from the rectum and one randomly selected prostate core. Cultures were grown for 5 days, and the results were recorded.

Results
Of the 93 patients who met inclusion criteria, eight men contained various bacteria within the sterilely accessed prostate core. Of the eight prostate cores which grew positive cultures, five of those patients had an isolated prostatic infection, without rectal or urinary co-infection. The most common infections included E. coli (n=2) and Klebsiella species (n=3).

Conclusion
New techniques in the performance of prostate biopsy provides the microbiology laboratory unique opportunities for investigation. This is the beginning of the study of the prostate microbiome, and future correlation with prostate cancer and isolated prostate infection are areas of future inquiry.
Comparative Evaluation of RT-LAMP and RT-PCR for Detection of HIV-1 in the Sudan
Authors: Yassin M E 
Published: October 2020

Abstract

Introduction/Objective
Rapid, simple, cost effective, nucleic acid based test for detecting HIV-1 in areas with limited resources is badly needed. Loop-mediated isothermal amplification (LAMP) is a technique that allows the amplification of nucleic acids DNA and RNA with high specificity, sensitivity and rapidity under isothermal conditions. This study was conducted to evaluate RT-LAMP method for HIV-1 detection in comparison with RT-PCR.

Methods
In the present study, ninety EDTA blood samples were studied; seventy samples were collected from HIV-1 infected patients and 20 samples from HIV-1 negative participants. All samples subjected to RT-LAMP and RT-PCR assay targeting HIV-1 p24 gene. Additionally nine positive samples were subjected to viral load measurement using COBAS® TaqMan® HIV-1 Test, version 2.0 (v2.0), and five samples were subjected to direct DNA sequencing of p24 gene phylogenetic analysis.

Results
Of the 70 HIV-1 positive samples, 68 (97.1%) and 61 (87.1%) positive samples were detected using RT-LAMP and RT-PCR respectively. Whereas, all the 20 HIV-1 negative samples were confirmed negative by RT- LAMP, 2 (10%) were positive by RT-PCR. Furthermore, the limit of detection (LOD) for both RT-LAMP and RT-PCR assays was determined to be 130 and 325 copies/ml respectively. The viral loads for the nine samples ranged between 1.92E+4 C/ml – 1.04C6/ml. The sequencing of five samples showed similarity of the Sudanese isolates with the neighboring countries Uganda, Saudi Arabia and also Senegal and even more closely sub-grouped with the Tanzanian counterpart.

Conclusion
RT-LAMP was successfully performed under minimal laboratory conditions demonstrating it as a very useful for use in fields setting and limited resources region.
Prevalence of TEM and SHV Genes in Diarrheaogenic Escherichia Coli Resistant to Beta Lactam Antibiotics in Egyptian Infants
Authors: Soliman Y M , Elsafty A 
Published: October 2020

Abstract

Introduction/Objective
Diarrhea is considered as the fifth leading cause of mortality in children worldwide. It kills 1 of 9 children according to CDC and causes morbidity in 1.7 billion pediatric cases every year. The most pathogenic strain of diarrheaogenic Escherichia coli (DEC) in Egypt is entero-hemorrhagic Escherichia coli (9.38%), while the most prevalent is entero-toxigenic Escherichia coli (15.63%). The aim of this study is to measure the percentage of TEM and SHV genes in diarrheagenic Escherichia coli (DEC) that are resistant to beta lactam antibiotics among infants. Indicating the essence of different antibiotics prescription for treatment in such cases.

Methods
Inclusion criteria included age between 2 months and 12 months. Stool samples from 196 cases of acute diarrhea were collected from inpatient and outpatient pediatric clinic in pediatric department at Zagazig University hospitals in Egypt. In 56 samples, diarrheaogenic Escherichia coli strains were confirmed by multiplex PCR after being biochemically identified. Culture and susceptibility tests were conducted. Resistant DEC strains were tested for the presence of TEM and SHV genes using universal primers for conventional PCR.

Results
By using culture and susceptibility test, 91.1% (51 cases) of isolated DEC strains were found to be resistant to amoxicillin-clavulanic acid. 78.6% (44 cases) resistant to ampicillin-sulbactam. 28.6% (16 cases) resistant to cefotaxime. 28.6% (16 cases) resistant to ceftazidime. 28.6% (16 cases) resistant to cefuroxime. 26.8% (15 cases) resistant to cefoxitin. 26.8% (15 cases) resistant to ceftriaxone. 14.3% (8 cases) resistant to cefepime. 10.7% (6 cases) resistant to aztreonam. 3.5% (2 cases) resistant to imipenem. By using conventional PCR, TEM gene was positive in 28.6% (16 cases) and SHV gene in 7.1% of (4 cases).

Conclusion
TEM gene was detected in 28.6% (16 out of 56 true positive DEC cases) and SHV gene in 7.1% (4 out of 56 true positive DEC cases). Around 28.6% of diarrheaogenic Escherichia coli or about 8% of infantile diarrhea (16 out of 196 total cases) were found to be resistant to different beta lactam antibiotics due to presence of TEM and SHV genes. This reflects the usefulness of other type antibiotics for treatment in such percentage.