Urinary bladder metastasis from breast cancer: a rare cause of hematuria

Breast cancer is the most common cancer in women globally as well as in Kenya. The most common sites of metastases reported include the bones, liver and lung. Metastasis to the urinary bladder is relatively uncommon with only a few case reports in literature. It can therefore be easily overlooked as a cause of hematuria in these patients. We describe a rare case of a patient with breast cancer who presented with urinary bladder metastasis as a late complication of her illness

Informing healthcare operations with integrated pathology, clinical, and epidemiology data: Lessons from a single institution in Kenya during COVID-19 waves

Pathology, clinical care teams, and public health experts often operate in silos. We hypothesized that large data sets from laboratories when integrated with other healthcare data can provide evidence that can be used to optimize planning for healthcare needs, often driven by health-seeking or delivery behavior. From the hospital information system, we extracted raw data from tests performed from 2019 to 2021, prescription drug usage, and admission patterns from pharmacy and nursing departments during the COVID-19 pandemic in Kenya (March 2020 to December 2021). Proportions and rates were calculated. Regression models were created, and a t-test for differences between means was applied for monthly or yearly clustered data compared to pre-COVID-19 data. Tests for malaria parasite, Mycobacterium tuberculosis, rifampicin resistance, blood group, blood count, and histology showed a statistically significant decrease in 2020, followed by a partial recovery in 2021. This pattern was attributed to restrictions implemented to control the spread of COVID-19. On the contrary, D-dimer, fibrinogen, CRP, and HbA1c showed a statistically significant increase (p-value \u3c0.001). This pattern was attributed to increased utilization related to the clinical management of COVID-19. Prescription drug utilization revealed a non-linear relationship to the COVID-19 positivity rate. The results from this study reveal the expected scenario in the event of similar outbreaks. They also reveal the need for increased efforts at diabetes and cancer screening, follow-up of HIV, and tuberculosis patients. To realize a broader healthcare impact, pathology departments in Africa should invest in integrated data analytics, for non-communicable diseases as well

A rare case of breast carcinoma metastasis into a meningioma in a 64-year-old female patient

This report discusses the occurrence of tumor-to-tumor metastasis—an atypical phenomenon in oncology where a secondary malignancy develops within an existing primary tumor. The case of a 64-year-old woman is presented, who, with a history of stage II invasive ductal carcinoma of the breast treated with mastectomy and chemoradiotherapy, developed neurological symptoms indicative of a secondary brain tumor. MRI and subsequent histopathological analysis post-craniotomy confirmed a meningioma with a metastatic breast carcinoma, demonstrating the clinical importance of considering tumor-to-tumor metastasis in similar patient histories

Pattern and trends of Helicobacter pylori genotypes in gastric cancer: A Kenyan 8-year study

Background: Notable geographic and temporal variations in the prevalence and genotypes of Helicobacter pylori, in relation to gastric pathologies, have been observed; however, their significance and trends in African populations is scarcely described. The aim of this study, was to investigate the association of H. pylori and its respective CagA and vacuolating cytotoxin A (VacA) genotypes with gastric adenocarcinoma, and to describe the trends of H. pylori genotypes over an 8-year period (2012–2019). Materials and methods: A total of 286 samples of gastric cancer cases and benign controls (one-to-one matching), from three main cities in Kenya, between 2012 and 2019 were included. Histologic evaluation, and CagA and VacA genotyping using PCR, was performed. Distribution of H. pylori genotypes was presented in proportions. To determine association, a univariate analysis was conducted using a Wilcoxon rank sum test for continuous variables, and a Chi-squared test or Fisher’s exact test for categorical data. Results: The VacA s1m1 genotype was associated with gastric adenocarcinoma, {odds ratio (OR) = 2.68 [confidence interval (CI) of 95%: 0.83–8.65]; p = 0.108}, whilst VacA s2m2 was associated with a reduced probability of gastric adenocarcinoma [OR = 0.23 (CI 95%: 0.07–0.78); p = 0.031]. No association between cytotoxin associated gene A (CagA) and gastric adenocarcinoma was observed. Conclusion: Over the study period, an increase in all genotypes of H. pylori was seen, and although no predominant genotype was noted, there was significant year-to-year variation, with VacA s1 and VacA s2 showing the greatest variation. VacA s1m1 and VacA s2m2 were associated with increased, and reduced risk of gastric cancer, respectively. Intestinal metaplasia and atrophic gastritis did not appear to be significant in this population

High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses

Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden

Clinical validation of a multiplex PCR-based detection assay using saliva or nasopharyngeal samples for SARS-Cov-2, influenza A and B

The COVID-19 pandemic has resulted in significant diversion of human and material resources to COVID-19 diagnostics, to the extent that influenza viruses and co-infection in COVID-19 patients remains undocumented and pose serious public-health consequences. We optimized and validated a highly sensitive RT-PCR based multiplex-assay for the detection of SARS-CoV-2, influenza A and B viruses in a single-test. This study evaluated clinical specimens (n = 1411), 1019 saliva and 392 nasopharyngeal swab (NPS), tested using two-assays: FDA-EUA approved SARS-CoV-2 assay that targets N and ORF1ab gene, and the PKamp-RT-PCR based assay that targets SARS-CoV-2, influenza viruses A and B. Of the 1019 saliva samples, 17.0% (174/1019) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [91.9% (160/174) vs. 87.9% (153/174)], respectively. Of the 392 NPS samples, 10.4% (41/392) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [97.5% (40/41) vs. 92.1% (39/41)], respectively. This study presents clinical validation of a multiplex-PCR assay for testing SARS-CoV-2, influenza A and B viruses, using NPS and saliva samples, and demonstrates the feasibility of implementing the assay without disrupting the existing laboratory workflow

Clinical Validation of a Sensitive Test for Saliva Collected in Healthcare and Community Settings with Pooling Utility for Severe Acute Respiratory Syndrome Coronavirus 2 Mass Surveillance

The clinical performance of saliva compared with nasopharyngeal swabs (NPSs) has shown conflicting results in healthcare and community settings. In the present study, a total of 429 matched NPS and saliva sample pairs, collected in either healthcare or community setting, were evaluated. Phase-1 (protocol U) tested 240 matched NPS and saliva sample pairs; phase 2 (SalivaAll protocol) tested 189 matched NPS and saliva sample pairs, with an additional sample homogenization step before RNA extraction. A total of 85 saliva samples were evaluated with both protocols. In phase-1, 28.3% (68/240) samples tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from saliva, NPS, or both. The detection rate from saliva was lower compared with that from NPS samples (50.0% versus 89.7%). In phase-2, 50.2% (95/189) samples tested positive for SARS-CoV-2 from saliva, NPS, or both. The detection rate from saliva was higher compared with that from NPS samples (97.8% versus 78.9%). Of the 85 saliva samples evaluated with both protocols, the detection rate was 100% for samples tested with SalivaAll, and 36.7% with protocol U. The limit of detection with SalivaAll protocol was 20 to 60 copies/mL. The pooled testing approach demonstrated a 95% positive and 100% negative percentage agreement. This protocol for saliva samples results in higher sensitivity compared with NPS samples and breaks the barrier to using pooled saliva for SARS-CoV-2 testing

Identification and characterization of a plastid-localized Arabidopsis glyoxylate reductase isoform: comparison with a cytosolic isoform and implications for cellular redox homeostasis and aldehyde detoxification

Enzymes that reduce the aldehyde chemical grouping (i.e. H-C=O) to its corresponding alcohol could be crucial in maintaining plant health. Recently, recombinant expression of a cytosolic enzyme from Arabidopsis thaliana (L.) Heynh (designated as glyoxylate reductase 1 or AtGR1) revealed that it effectively catalyses the in vitro reduction of both glyoxylate and succinic semialdehyde (SSA). In this paper, web-based bioinformatics tools revealed a second putative GR cDNA (GenBank Accession No. AAP42747; designated herein as AtGR2) that is 57% identical on an amino acid basis to GR1. Sequence encoding a putative targeting signal (N-terminal 43 amino acids) was deleted from the full-length GR2 cDNA and the resulting truncated gene was co-expressed with the molecular chaperones GroES/EL in Escherichia coli, enabling production and purification of soluble recombinant protein. Kinetic analysis revealed that recombinant GR2 catalysed the conversion of glyoxylate to glycolate (Km glyoxylate=34 μM), and SSA to γ-hydroxybutyrate (Km SSA=8.96 mM) via an essentially irreversible, NADPH-based mechanism. GR2 had a 350-fold higher preference for glyoxylate than SSA, based on the performance constants (kcat/Km). Fluorescence microscopic analysis of tobacco (Nicotiana tabacum L.) suspension cells transiently transformed with GR1 linked to the green fluorescent protein (GFP) revealed that GR1 was localized to the cytosol, whereas GR2-GFP was localized to plastids via targeting information contained within its N-terminal 45 amino acids. The identification and characterization of distinct plastidial and cytosolic glyoxylate reductase isoforms is discussed with respect to aldehyde detoxification and the plant stress response

Proposal of RT-PCReBased Mass Population Screening for Severe Acute Respiratory Syndrome Coronavirus 2 (Coronavirus Disease 2019)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing has lagged in many countries because of test kit shortages and analytical process bottlenecks. This study investigated the feasibility and accuracy of a sample pooling approach for wide-scale population screening for coronavirus disease 2019. A total of 940 nasopharyngeal swab samples (934 negative and 6 positive) previously tested for SARS-CoV-2 were deidentified and assigned random numbers for analysis, and 94 pools of 10 samples each were generated. Automated RNA extraction, followed by RT-PCR, was performed in a 96-well plate. Positive pools were identified, and the individual samples were reanalyzed. Of the 94 pools/wells, four were positive [Ct values: N (22.7 to 28.3), ORF1ab (23.3 to 27.2), and internal control (34.4 to 35.4)]. The 40 samples comprising the four pools were identified and reanalyzed individually; six samples were positive, with Ct values of N gene, ORF1ab, and internal control comparable to their respective wells. Additional experiments were performed on samples with high Ct values, and overall results showed 91.6% positive and 100% negative agreement compared with individual testing approach. Thus, 940 samples were tested in 148 reactions compared with 940 reactions in routine screening. The sample pooling strategy may help catch up with testing needs and minimal turnaround times and facilitate enormous savings on laboratory supplies, extraction, and PCR kits currently in short supply

Comparison of Xpert Mtb/Rif with Histology for the Detection of Mycobacterium Tuberculosis in Formalin Fixed Paraffin Embedded Tissues at Aga Khan University Hospital, Nairobi

Background: Diagnosis of extrapulmonary tuberculosis (EPTB) continues to be a challenge due to the complexity of the causative organism and the wide array of pathologic features seen in this infection. A number of studies have shown polymerase chain reaction (PCR) for EPTB to be a feasible, sensitive and specific test for diagnosis of tuberculosis (TB) of which, the World Health Organisation (WHO) has given recommendations. As pertains EPTB, Xpert MTB/RIF may be used in place of conventional tests such as microscopy, histopathology and culture in lymph nodes and other tissues from patients suspected to have EPTB. It has been demonstrated that Xpert MTB/RIF can be used for fresh or frozen tissues specimens with good results. However, the use of formalin fixed paraffin embedded (FFPE) tissues, a widely available and rich source of clinical material, on the Xpert platform is yet to be described. Objectives: The aim of this study was to demonstrate the potential utility of Xpert MTB/RIF in the detection of Mycobacterium tuberculosis from FFPE tissues with histological features suggestive of tuberculosis. We compared Xpert MTB/RIF to histology for the detection of Mycobacterium tuberculosis from FFPE tissues. In those cases with a positive Xpert result, we determined the prevalence of rifampicin resistance in EPTB. Methods: Eighty randomly selected archived FFPE tissues exhibiting histological features suggestive of TB (necrotizing granulomatous inflammation, non-necrotizing granulomatous inflammation, chronic inflammation, necrotizing inflammation and suppurative inflammation) from January 1, though December 31, 2014 were retrieved. All the cases were subjected to microscopic evaluation of Haematoxylin and Eosin (H&E) stained and Ziehl-Neelsen (ZN) slides. With prior deparaffinization and lysis, all cases were also subjected to the Xpert MTB/RIF assay. Only 79 cases were included in the final analysis. This was after exclusion of one case due to an error in the Xpert MTB/RIF assay. The outcome measures were proportions of positively identified cases by each test. The data were analysed using chi - square test. Results: Xpert MTB/RIF assay detected 32.9% more cases than microscopy (53.2% versus 20.3%) which was statistically significant, (p= 0.002). None of the cases tested positive for rifampicin resistance. Seven cases however, had an indeterminate rifampicin resistance result. Conclusion: With prior deparaffinization and lysis, FFPE tissues can also be subjected to the Xpert MTB/RIF assay. A validation study to determine the clinical utility of this assay for FFPE tissues is recommended