Laboratory Identification Research Articles

Investigation of Biochemical and Inflammatory Markers in COVID-19 Patients Hospitalized in the Intensive Care Unit: An Observational Study in Northern Iran

Background: Since the first documentation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there has been a notable emphasis on it in a brief period, especially as the mortality rate and confirmed cases steadily rise. The rapid and accurate laboratory identification of an ongoing COVID-19 infection is essential for efficient pandemic control. For diagnostic purposes, various testing methods have been developed to detect the severity of COVID-19. These diagnostic methods play a crucial role in identifying and managing the spread of the virus within communities worldwide. Methods: This cross-sectional observational study was conducted from February to June 2020, spanning four months. Patient clinical records and laboratory biomarkers data were collected. Results: In this study, 263 patients were involved, with an average age of 59.38 ± 15.26 years, and 51.3% of them (135 patients) were male. The typical hospital stay was 9.25 ± 6.9 days. The patients were divided into three groups: Those who survived (49.4%), those receiving treatment (4.9%), and those who did not survive (45.6%), with all treated patients surviving. An important connection was observed between serum lactate dehydrogenase (LDH), creatine phosphokinase (CPK), urea, leukocytosis, lymphopenia, high polymorphonuclear neutrophil (PMN) counts, and poor patient outcomes (P-value < 0.05). Elevated aspartate transaminase (AST) levels also showed a close relationship with adverse outcomes (P-value = 0.05). Furthermore, most patients with hyponatremia, high fasting blood glucose, and elevated serum creatinine levels did not survive, despite lacking statistical significance. Conclusions: Serum biomarkers serve as prognostic indicators for the severity of COVID-19 patients. Leveraging these markers aids in promptly diagnosing patients at high mortality risk and facilitates more effective treatments in the disease's initial phases. These biomarkers can help healthcare providers identify patients at higher risk of complications and guide the implementation of targeted interventions to improve patient outcomes.

Diffuse interstellar bands as dust indicators: The contribution from 3D maps

Three-dimensional (3D) distributions of the 862 nm diffuse interstellar band (DIB) carrier have been computed based on Gaia parallaxes and DIB catalogues, in parallel with 3D maps of dust extinction density. Three-dimensional maps provide local diagnostics and information on the distribution of structures in addition to line-of-sight (LOS) integrated quantities, and allow us to focus on poorly studied low-extinction areas. They make cross-matching with other catalogues possible through estimates of the DIB and extinction along any given path. We re-examined the relationships between the density of DIB carriers and the absorption and emission properties of spatially co-located dust. Along with laboratory identifications of carriers, these properties may shed light on the formation and evolution of this organic matter. They may also help to model dust emission and absorption properties in a more detailed way. We used the 3D maps of 862 nm DIBs and of dust extinction, as well as available DIB equivalent width (EW) catalogues and published measurements of parameters characterizing the dust extinction law and the dust emission. We studied the relationships between the extinction-normalized 862 nm DIB EW and the extinction level, the total-to-selective extinction ratio $R_V$, and the dust far-IR emission spectral index beta . We re-visited the link between several DIBs and the UV absorption bump at 220 nm. The ratio of the 862 nm DIB carrier density to the optical extinction density (DIB$_ norm $) is increasing in low-density clouds, confirming with local values the trend seen in the LOS data. In both cases, the coefficients of a fitted power law fall within the range of those measured towards SDSS high-latitude targets for 20 different bands, ranking this DIB among those with a high increase, above that of the broad 4430 DIB. This is consistent with the recent measurement of a larger scale height above the Plane for the 862 nm DIB compared to that of the 4430 DIB. Using map-integrated 862 nm DIB EWs and extinctions along the paths to APOGEE targets with published proxies $R'_V$ for the total-to-selective extinction ratio, we found that, despite a large scatter, DIB$_ norm $ is positively correlated with $R'_V$ for those stars with low to moderate extinctions ($A_V$= 0.2 to 2--3 mag). Independently, using stars from the 862 nm DIB catalogue located outside the disk and for the same regime of extinction, DIB$_ norm $ is found to be globally anti-correlated with the Planck opacity spectral index beta . This is consistent with the observed anti-correlation between beta and $R'_ V $. In the light of a recent result on the variability of the carbon/silicate ratio in dust grains as a source of this anti-correlation, it suggests that DIB$_ norm $ increases with the fraction of carbonaceous to silicate grains in the co-located dust, in agreement with the carbonaceous nature of DIB carriers and recent evidences for a spatial correlation between DIB$_ norm $ and the fluxes of carbon-rich ejecta of asymptotic giant branch (AGB) stars. At higher extinction both trends disappear, and there is evidence for a trend reversal. Regarding the link between the height of the 220 nm UV absorption bump and extinction-normalized EWs of DIBs, we found that two factors explain the absence of previous clear results: the correlation disappears when we move from sigma -type to zeta -type DIBs and/or from single-cloud LOSs to paths crossing multiple clouds distant from each other; zeta -type bands can be used to predict low and high values of the bump height, provided one adds a correcting factor linked to the ambient radiation field (e.g. the 5780/5797 DIB ratio). We show examples of simple models of the bump height based on the 5780 band, the 5850 band and the 5780/5797 DIB ratio. We also found an anti-correlation between DIB$_ norm $ and the width of the bump, which similarly disappears from sigma -type to zeta -type DIBs. This suggests that a fraction of the bump is generated outside the dense molecular clouds. There are complex relationships between DIBs and dust; however, massive measurements of DIBs and extinction and the derived 3D maps may provide some constraints on the density, the nature, and the contribution to extinction and emission of the co-located dust. This requires large stellar spectroscopic surveys and space-based measurements of UV extinction.

A-161 Diagnosis of Lupus Anticoagulant Cases using Deep Neural Networks

Abstract Background Laboratory identification of lupus anticoagulant (LAC) is critical for diagnosing antiphospholipid antibody syndrome, a common cause of unprovoked thromboembolic events and pregnancy morbidity. Commonly used clot-based assays for LAC include the dilute Russell’s viper venom time (DRVVT) and activated partial thromboplastin time (APTT), but these are susceptible to anticoagulant interferences. Despite standardization efforts, LAC interpretation remains challenging due to pre- and post-analytical complexity and limited expertise. This study explored the use of deep neural networks (DNN) to facilitate LAC diagnosis. Methods Retrospective data for LAC profiling with 13 features performed at Mayo Clinic between 2021 and 2022 was collected. The profiles of 7,202 patients were randomly divided into training (n=4608), validation (n=1153), and test cohorts (n=1441). Diagnostic outputs including LAC positivity (determined by DRVVT or APTT) and the presence of warfarin (WAR) and heparin (HEP), were confirmed by expert assessment. Three DNN architectures were developed and evaluated (Figure 1): (1) four single output DNN models with a domain knowledge driven selection of input features, (2) four single output DNN models using the same 13 inputs across all models, and (3) a multi-output DNN model. Model performance was evaluated using the F1 score and the index of balanced accuracy (IBA) for each output label. Results Architecture 1 achieved high diagnostic accuracy with IBA values of 0.989-1.000 for all four outputs and F1 scores of 0.945-0.991. Architecture 2 exhibited F1 scores of 0.902-0.973 and IBA values of 0.935-0.992. Architecture 3 achieved F1 scores of 0.933-0.967 and IBA values of 0.941-0.983. Conclusions All three architectures accurately classify LAC and common anticoagulation effects. The comparable performance of architectures 1 and 2 suggests that manual feature extraction is unnecessary. Given its relative simplicity and versatility, architecture 3 is the preferred choice for implementation in a clinical laboratory to standardize LAC diagnosis.

Development of a One-Step Multiplex qPCR Assay for Detection of Methicillin and Vancomycin Drug Resistance Genes in Antibiotic-Resistant Bacteria.

The most common antibiotic-resistant bacteria in Korea are methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Pathogen identification in clinical laboratories can be divided into traditional phenotype- and genotype-based methods, both of which are complementary to each other. The genotype-based method using multiplex real-time polymerase chain reaction (PCR) is a rapid and accurate technique that analyzes material at the genetic level by targeting genes simultaneously. Accordingly, we aimed to develop a rapid method for studying the genetic characteristics of antibiotic-resistant bacteria and to provide an experimental guide for the efficient antibiotic resistance gene analysis of mecA detection for MRSA and vanA or vanB detection for VRE using a one-step multiplex qPCR assay at an early stage of infection. As a result, the sensitivity and specificity of the mecA gene for clinical S. aureus isolates, including MRSA and methicillin-susceptible S. aureus, were 97.44% (95% CI, 86.82-99.87%) and 96.15% (95% CI, 87.02-99.32%), respectively. The receiver operating characteristic area under the curve for the diagnosis of MRSA was 0.9798 (*** p < 0.0001). Therefore, the molecular diagnostic method using this newly developed one-step multiplex qPCR assay can provide accurate and rapid results for the treatment of patients with MRSA and VRE infections.

Genomics Insights into Mycolicibacterium Hassiacum Causing Infection in a Cat with Pyogranulomatous Dermatitis and Panniculitis.

Mycolicibacterium hassiacum (homotypic synonym: Mycobacterium hassiacum) represents an ungrouped thermotolerant rapidly growing mycobacteria (RGM) species occasionally associated with infections and disease in humans. In this report, we describe a case of pyogranulomatous dermatitis and panniculitis due to M. hassiacum in an immunocompetent adult cat. To the best of our knowledge, this represents the first report of M. hassiacum infection in animals. We also report the results of the in-depth genome characterization of the isolate using a combined short- and long-read whole-genome sequencing (WGS) approach. We observed the lack of acquired-resistance genes and no evidence of mutations in housekeeping genes associated with resistance to rifampicin and isoniazid. We detected some virulence factors in our isolate, such as some associated with the interaction of mycobacteria with host cells, and the presence of multiple copies of heavy metal resistance genes (arsB, arsR, and arsL/cadL). In conclusion, M. hassiacum should be included among the RGM species associated with feline subcutaneous atypical mycobacteriosis (SAM). A reliable and fast RGM laboratory identification and characterization is important not only for an accurate etiological diagnosis but also for a correct approach to SAM treatment options.

Theoretical investigation of interstellar 3-pyrroline: formation and, rotational and vibrational spectroscopy

ABSTRACT The recent detection of CN-functionalized aromatics partly addresses the long-standing mystery of the apparent absence of five- and six-membered rings in interstellar environments. Nitrogen (N)-heterocycles, which are crucial as the fundamental structures of nucleobases, have been a focus of these aromatic searches due to their biological significance. Although N-heterocycles have not been conclusively detected in astrophysical environments, their presence in chondrites and meteorites signifies their interstellar and circumstellar connection. Precise spectral data identify the unique signatures of molecules, confirming their presence in space. In this light, this work reports an extensive computational investigation on interstellar 3-pyrroline, a five-membered ring N-heterocycle. This includes an alternative formation route in cold interstellar environments and highly accurate rotational and vibrational spectroscopy. The results indicate that 3-pyrroline can form on dust grain surfaces from vinyl cyanide, as its formation from pyrrole through double hydrogenation may lead to the formation of pyrrole itself via an H2-abstraction process. 3-Pyrroline’s rotational transition at 52.3 GHz offers a potential tool for its detection in cold interstellar regions. Additionally, the strongest infrared (IR) features of 3-pyrroline at 16.09 and $\sim$3.50 $\mu$m are observable with JWST. The provided data are crucial for laboratory identification and future interstellar observations of 3-pyrroline at both radio and IR wavelengths.

Risk Predictors of Severity in Egyptian Patients with Covid-19 Infection

Abstract Background In modern human history, infectious diseases have posed a threat to public health several times, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a global public health crisis. Objective Identification of demographic, laboratory and radiological predictors of progression of COVID-19 infection in Egyptian patients. A special concern is focused on the poor prognostic factors associated with mortality, this will help to classify and monitor COVID-19 patients to deliver best medical care in order to decrease mortality and morbidity in Egyptian patients. Patients and Methods A single-center, retrospective cohort study. This study was conducted in Almaza Fever Hospital after obtaining approval from the Research Ethical Committee. Results The current study conducted on (325) known positive COVID-19 patients divided into 2 groups: Group I (204) patients and Group II (121) patients. It was found that an increase in age among Group II (mean age was 66.22 ± 12.18) in comparison to Group I (mean age was 47.78 ± 14.73) with a statistically significant difference (p-value &amp;lt;0.001). There was no statistically significant difference (p-value 0.432) between Sex and severe disease patients. Among Group II (121) out of the total study population 103 (85%) of these were found to have co-morbidities (highly significant, p value &amp;lt; 0.001. Moreover, there was a higher prevalence of co-morbidities among non survivors however this didn’t reach the level of statistical significance (p-value 0.174). The current study showed that there was an increase in hematological parameters (TLC, Neutrophils), biochemical parameters (Urea, Creatinine, AST, D-Dimer, Ferritin, CRP, LDH, IL-6) and a decrease in Lymphocytes within Group II in comparison with Group I with statistically Significant difference (p-value &amp;lt; 0.001), also there was a trend toward higher levels of ALT in group II, however this didn’t reach the level of statistical significance (p-value 0.068). Statistically significant difference (p-value &amp;lt; 0.001) was found between disease severity and CT findings as from a total of (121) severe disease patients 105(86.8%) had CORADS (4-5). Conclusion The current study shows old age, elevated biochemical parameters (creatinine, urea, AST, D-dimer, IL-6, CRP, ferritin and LDH), hematological parameters (TLC) and extensive lung affection could be considered predictors of severity and mortality among Covid-19 patients. Also lymphopenia and associated co-morbidities are considered predictors of severity.

Characterization and preparation of food-derived peptides on improving osteoporosis: A review

Osteoporosis is a systemic bone disease characterized by reduced bone mass and deterioration of the microstructure of bone tissue, leading to an increased risk of fragility fractures and affecting human health worldwide. Food-derived peptides are widely used in functional foods due to their low toxicity, ease of digestion and absorption, and potential to improve osteoporosis. This review summarized and discussed methods of diagnosing osteoporosis, treatment approaches, specific peptides as alternatives to conventional drugs, and the laboratory preparation and identification methods of peptides. It was found that peptides interacting with RGD (arginine-glycine-aspartic acid)-binding active sites in integrin could alleviate osteoporosis, analyzed the interaction sites between these osteogenic peptides and integrin, and further discussed their effects on improving osteoporosis. These may provide new insights for rapid screening of osteogenic peptides, and provide a theoretical basis for their application in bone materials and functional foods.

Potential Environmental Reservoirs of Candida auris: A Systematic Review.

Candida auris, a multidrug-resistant yeast, poses significant challenges in healthcare settings worldwide. Understanding its environmental reservoirs is crucial for effective control strategies. This systematic review aimed to review the literature regarding the natural and environmental reservoirs of C. auris. Following the PRISMA guidelines, published studies until October 2023 were searched in three databases: PubMed, Web of Science, and Scopus. Information regarding the origin, sampling procedure, methods for laboratory identification, and antifungal susceptibility was collected and analyzed. Thirty-three studies published between 2016 and 2023 in 15 countries were included and analyzed. C. auris was detected in various environments, including wastewater treatment plants, hospital patient care surfaces, and natural environments such as salt marshes, sand, seawater, estuaries, apples, and dogs. Detection methods varied, with molecular techniques often used alongside culture. Susceptibility profiles revealed resistance patterns. Phylogenetic studies highlight the potential of environmental strains to influence clinical infections. Despite methodological heterogeneity, this review provides valuable information for future research and highlights the need for standardized sampling and detection protocols to mitigate C. auris transmission.

Diagnostic accuracy of automation and non-automation techniques for identifying Burkholderia pseudomallei: A systematic review and meta-analysis

BackgroundBurkholderia pseudomallei, a Gram-negative pathogen, causes melioidosis. Although various clinical laboratory identification methods exist, culture-based techniques lack comprehensive evaluation. Thus, this systematic review and meta-analysis aimed to assess the diagnostic accuracy of culture-based automation and non-automation methods. MethodsData were collected via PubMed/MEDLINE, EMBASE, and Scopus using specific search strategies. Selected studies underwent bias assessment using QUADAS-2. Sensitivity and specificity were computed, generating pooled estimates. Heterogeneity was assessed using I2 statistics. ResultsThe review encompassed 20 studies with 2988 B. pseudomallei samples and 753 non-B. pseudomallei samples. Automation-based methods, particularly with updating databases, exhibited high pooled sensitivity (82.79%; 95% CI 64.44–95.85%) and specificity (99.94%; 95% CI 98.93–100.00%). Subgroup analysis highlighted superior sensitivity for updating-database automation (96.42%, 95% CI 90.01–99.87%) compared to non-updating (3.31%, 95% CI 0.00–10.28%), while specificity remained high at 99.94% (95% CI 98.93–100%). Non-automation methods displayed varying sensitivity and specificity. In-house latex agglutination demonstrated the highest sensitivity (100%; 95% CI 98.49–100%), followed by commercial latex agglutination (99.24%; 95% CI 96.64–100%). However, API 20E had the lowest sensitivity (19.42%; 95% CI 12.94–28.10%). Overall, non-automation tools showed sensitivity of 88.34% (95% CI 77.30–96.25%) and specificity of 90.76% (95% CI 78.45–98.57%). ConclusionThe study underscores automation's crucial role in accurately identifying B. pseudomallei, supporting evidence-based melioidosis management decisions. Automation technologies, especially those with updating databases, provide reliable and efficient identification.

Rapid identification of lactic acid bacteria at species/subspecies level via ensemble learning of Ramanomes.

Rapid and accurate identification of lactic acid bacteria (LAB) species would greatly improve the screening rate for functional LAB. Although many conventional and molecular methods have proven efficient and reliable, LAB identification using these methods has generally been slow and tedious. Single-cell Raman spectroscopy (SCRS) provides the phenotypic profile of a single cell and can be performed by Raman spectroscopy (which directly detects vibrations of chemical bonds through inelastic scattering by a laser light) using an individual live cell. Recently, owing to its affordability, non-invasiveness, and label-free features, the Ramanome has emerged as a potential technique for fast bacterial detection. Here, we established a reference Ramanome database consisting of SCRS data from 1,650 cells from nine LAB species/subspecies and conducted further analysis using machine learning approaches, which have high efficiency and accuracy. We chose the ensemble meta-classifier (EMC), which is suitable for solving multi-classification problems, to perform in-depth mining and analysis of the Ramanome data. To optimize the accuracy and efficiency of the machine learning algorithm, we compared nine classifiers: LDA, SVM, RF, XGBoost, KNN, PLS-DA, CNN, LSTM, and EMC. EMC achieved the highest average prediction accuracy of 97.3% for recognizing LAB at the species/subspecies level. In summary, Ramanomes, with the integration of EMC, have promising potential for fast LAB species/subspecies identification in laboratories and may thus be further developed and sharpened for the direct identification and prediction of LAB species from fermented food.

Causes of dangerous fungal diseases of potatoes in the western region of Ukraine due to climate change

Goal. To determine the species composition of pathogens of potato fungal diseases in the western region of the forest-steppe zone under climatic changes.&#x0D; Methods. Research was conducted during 2021—2022 on the basis of the Ukrainian Plant Quarantine Research Station of the Institute of Plant Protection using laboratory (identification of pathogens) and field (examination of potato plantations and analysis of tuber material) methods.&#x0D; Results. According to the research results, the most common fungal diseases on vegetative plants during the studied period were: anthracnose (Colletotrichum coccodes (Wallr.) S. Hughes), Alternaria solani (Ellis &amp; G. Martin) L.R. Jones &amp; Grout, Alternaria alternata (Fr.) Keissl.), fusarium wilt (Fusarium oxysporum Sсhl.) and late blight (Phytophthora infestans (Mont.) de Bary). As a result of phytopathological analysis of tubers, it was established that the greatest danger during potato storage is caused by pathogens of the genera Fusarium, Phoma, Colletotrichum, Phytophthora, causing fusarium, fomosis, anthracnose, phytophthora and mixed types of rot. the causative agents of fusarium were identified — Fusarium oxysporum Sсhl., F. sambucinum Fuck., F. solani Vart.; phomoza — Rhoma exigua Desm. var. exigua rhizoctonia — Rhizoctonia solani (J. G. Kühn) [teleomorph Thanatephorus cucumeris (A. B. Frank) Donk]; Alternaria solani (Ellis &amp; G. Martin) L.R. Jones &amp; Grout; Alternaria alternata (Fr.) Keissl.; anthracnose — Colletotrichum coccodes (Wallr.) S. Hughes, late blight — Phytophthora infestans (Mont.) de Bary); the share of fusarium was 42.1%, the causative agent of anthracnose — 27.5%.&#x0D; Conclusions. Fungal diseases (anthracnose, fusarium wilt) of potatoes, which at the end of the twentieth century were considered to be of limited distribution, have become widespread, which requires their further study in order to optimize crop protection.

Comparative evaluation of the detection rate, workflow and associated costs of a multiplex PCR panel versus conventional methods in diagnosis of infectious gastroenteritis.

Introduction. Infectious gastroenteritis is a common reason for consulting a physician. Although most cases of gastrointestinal illness are self-limiting, the identification of the etiologic pathogen by stool specimen analysis is important in cases of more severe illness and for epidemiological reasons.Due to the broad range of causative pathogens, the conventional examination of a stool specimen is labour-intensive and usually requires different diagnostic methods. Multiplex PCR tests [e.g. BioFire Gastrointestinal (GI) Panel] allow the rapid detecting of up to 22 pathogens in one test.Hypothesis. Using a multiplex PCR panel to test stool specimens for infectious gastroenteritis pathogens can improve the detection rate, reduce the time-to-result and hands-on time and lower the costs of a microbiology laboratory.Aim. This study was aimed at evaluating the detection rate, the workflow and associated costs of stool specimen management using the BioFire GI Panel versus conventional methods.Methodology. Stool specimens were evaluated prospectively during the routine operation. Pathogen detection rate, hands-on time, time-to-result and material and personnel costs were determined for the BioFire GI Panel and conventional methods-the latter based on physician request and excluding viral testing.Results. Analysing 333 specimens collected between 2019 and 2020, the detection rate of enteropathogens was significantly higher with a positivity rate of 39.9 % using the multiplex PCR panel compared with 15.0 % using the conventional methods. The BioFire GI Panel presented results in a median time of 2.2 h compared with 77.5 h for culture and 22.1 h for antigen testing, noting that no tests were performed at weekends except for toxinogenic Clostridioides difficile. Based on list prices, the BioFire GI Panel was nine times more expensive compared with conventional methods, whereas hands-on-time was significantly lower using the BioFire GI Panel.Conclusion. Multiplex PCR panels are valuable tools for laboratory identification of infectious agents causing diarrhoea. The higher costs of such a multiplex PCR panel might be outweighed by the higher detection rate, ease of handling, rapid results and most likely improved patient management. However, these panels do not provide information on antimicrobial susceptibility testing. Therefore, if this is necessary for targeted therapy or if outbreak monitoring and control is required, specimens must still be cultured.

Non-tuberculous mycobacteria hybridisation profiles in the GenoType MTBDRplus assay: experience from a diagnostic routine of a high-throughput laboratory.

Introduction. Disease caused by non-tuberculous mycobacteria (NTM) is an emergent problem. Because NTM pulmonary disease and tuberculosis (TB) have similar clinical presentations, many cases of NTM may be misdiagnosed as TB before laboratory identification of the NTM species.Hypothesis/Gap Statement. Clinical laboratories should always perform differentiation between Mycobacterium tuberculosis complex (MTBC) and NTM to guide patients' correct treatment.Aim. To describe the characteristics and to identify mycobacterial isolates presumptively classified as MTBC by macroscopic characteristics in culture media that tested negative in GenoType MTBDRplus.Methodology. All cultures from February 2019 to December 2021 showing MTBC macroscopic characteristics were processed by GenoType MTBDRplus. MTBC-negative cultures underwent species identification by immunochromatography, line probe assays and PRA-hsp65. Patients' data were obtained from Brazilian surveillance systems.Results. Only 479 (3.1%) of 15 696 isolates presumptively identified as MTBC were not confirmed by GenoType MTBDRplus and were then subjected to identification. A total of 344 isolates were shown to be NTM, of which 309 (64.5%) and 35 (7.3%) were identified to the species and genus levels, respectively. Of the 204 NTM isolates with MTBC characteristics, the most frequent species were M. fortuitum (n=52, 25.5%), M. abscessus complex (MABC; n=27, 13.2%) and M. avium complex (MAC; n=26, 12.7%). Regarding the GenoType MTBDRplus results from NTM isolates, there were diverse hybridisation profiles with rpoB gene's different wild-type (WT) probes. Seventy-six (16.1%) of the 473 patients were classified as having NTM disease, the most frequent being MAC (n=15, 19.7%), MABC (n=13, 17.1%), M. kansasii (n=10, 13.2%) and M. fortuitum (n=6, 7.9%).Conclusion. Because the signs and symptoms of pulmonary TB are similar to those of pulmonary mycobacteriosis and treatment regimens for TB and NTM are different, identifying the disease-causing species is paramount to indicate the correct management. Thus, in the laboratory routine, when an isolate presumptively classified as MTBC is MTBC-negative, it is still essential to perform subsequent identification.

Laboratory Diagnostics Accuracy for COVID-19 versus Post-COVID-19 Syndrome in Lung Disease Patients with Multimorbidity.

The laboratory tests and identification of risk factors such as comorbidities are essential in the management, treatment and prognosis of patients with chronic respiratory diseases. Performing rigorous monitoring among patients with post-COVID-19 syndrome and early identification of risk factors associated with poor prognosis are crucial in improving patient outcomes. In the present study, 182 patients diagnosed with COVID-19 and PCI during 2020-2022 were included. A clinical and epidemiological evaluation was performed for each patient. Laboratory tests at admission included complete blood count, Erythrocyte Sedimentation Rate (ESR) and biochemical tests. Receiver operating curve (ROC) and area under the curve (AUC) were calculated to compare the diagnostic performance of each parameter. Regarding comorbidities, arterial hypertension, diabetes mellitus and obesity were the most frequent ones. In the case of chronic lung diseases, asthma and Chronic Obstructive Pulmonary Disease (COPD) were the most frequent. Pleurisy was found especially in patients with PCI Variations in serum LDH values were observed, especially in severe forms of COVID-19 in 2020, with a mean value of 481.44 U/L, compared to patients with PCI, whose mean values (122 U/L) were within the biological range of reference. High neutrophil/lymphocyte ratio (NLR) values quantified in this study were especially associated with moderate and severe forms of COVID-19 and also PCI. The Spearman correlation coefficient was determined to measure the correlations between the clinical parameters of all investigated subjects. A value of p < 0.05 was considered statistically significant. The statistical results indicated that serum lactate dehydrogenase (LDH), glucose and C-reactive protein (CRP) are sensitive markers with a diagnostic role in COVID-19, and lymphocyte (Ly) count, CRP, ESR and glucose were evidenced to be target markers in PCI. LDH values were observed to be statistically significant (p < 0.005) in patients with COVID-19 and obesity evaluated in 2021, while Ly count was statistically significant (p = 0.05) in patients with PCI and arterial hypertension. Regarding comorbidities, it has been observed that obesity, arterial hypertension and cardiovascular diseases represent risk factors in COVID-19/PCI, associated especially with the severe forms of the disease.

Factor XIII deficiency, a rare coagulopathy: case reports

Introduction: Hereditary Factor XIII (FXIII) deficiency is a rare autosomal recessive hemostatic disorder with an estimated incidence of one case per two million individuals and a higher prevalence in descendants of consanguineous relationships. Possible clinical manifestations include intracranial hemorrhage, umbilical cord bleeding at birth, hematoma, spontaneous abortions, and menometrorrhagia. Objective: To highlight the peculiarities of this hemostatic disorder, as well as the recommended management. Case Report: The authors describe two cases of FXIII deficiency with different hemorrhagic manifestations. Case 1 presented extensive spontaneous hematoma in the right thigh, while Case 2 had umbilical cord bleeding at birth and intracranial hemorrhage, requiring hemotherapy support. Both patients had normal results in screening laboratory tests for coagulation disorders. Coagulation factor serum levels and diagnostic assessments identified mild Factor XIII deficiency in Case 1 and severe deficiency in Case 2. The patient in Case 1 is under regular control and follow-up, while the patient in Case 2 is on a monthly prophylactic regimen with FXIII infusion. Conclusion: The diagnosis of FXIII deficiency in patients with significant bleeding should be considered if screening coagulation tests are normal. The Scientific and Standardization Committee of the International Society on Thrombosis and Haemostasis has established an algorithm for laboratory diagnosis and identification of different forms of FXIII deficiency. Quantitative determination of FXIII activity, antigenic assays, and molecular studies are necessary.

ТРУДНОСТИ ВЕРИФИКАЦИИ ПРИЧИН ГЕМОРРАГИЧЕСКОГО СИНДРОМА В ПРАКТИКЕ ВРАЧА-НЕОНАТОЛОГА

Problems related to the study of the coagulation status of patients during the neonatal period are well known to neonatologists. Hemorrhagic disorders in the period of the newborn can be caused by deficiency of vitamin K-dependent factors, intrauterine infection, hereditary coagulopathy, primary and secondary disorders of platelet hemostasis and a number of other reasons. Clinical manifestations of hemorrhagic syndrome in a newborn child are non-specific, allowing to suspect the type of blood flow, however, conducting selective hemostatic therapy is possible only after laboratory identification of the disease. Among congenital coagulopathies, hemophilia A is the most frequently encountered, while clinical manifestations of the disease occur during the neonatal period only in the case of the presence of a severe form of the disease. Meanwhile, in the practice of pediatricians and neonatologists, vascular tumors are encountered quite rarely, including Kazabach-Merritt syndrome – a potentially life-threatening condition in which hemangioendotheliomas grow rapidly and reach gigantic sizes, combined with severe thrombocytopenia and coagulopathy. In this article, two clinical cases of severe hemophilia A in newborn boys with basic factor VIII activity of less than 1% are presented, as well as a case of infantile hemangioendothelioma of the liver in a newborn baby. In the article, the directions of the laboratory search for disorders of primary and secondary hemostasis were analyzed, which allowed the diagnosis to be clarified and the appropriate hemostatic therapy to be selected.

Virulence Gene Properties and Phylogenetic Relationship of Salmonella Serotypes Isolated from Different Sources in North of Iran

Background: Salmonella species can cause various infections in humans and animals. The presence of certain genes determines the virulence of a Salmonella serotype. Objectives: The current research endeavor was undertaken to assess the virulence characteristics and genotypic traits of Salmonella serotypes extracted from various sources within the geographical boundaries of Iran. Methods: Salmonella isolates, previously retrieved and preserved in the veterinary microbiology laboratory, underwent serotyping and polymerase chain reaction (PCR) identification of nine virulence-associated genes. Genotyping was carried out using random amplified polymorphic DNA-PCR (RAPD-PCR). Results: All Salmonella isolates showed the presence of invA, sdiA, hilA, and iroB virulence genes. There were a total of 17 different virulence gene patterns among Salmonella serotypes. The presence of fliC and sefA genes and their related patterns were significant among S. typhimurium and S. enteritidis serotypes, respectively (P &lt; 0.05). In the RAPD-PCR fingerprinting, 11 distinct clusters were obtained, and 16 isolates (26.66%) were classified as untypeable strains. There was a significant association between RAPD genotypes and Salmonella serotypes (P &lt; 0.05), while the association between these RAPD patterns and the source of the isolates was not significant (P &gt; 0.05). Conclusions: According to the results, Salmonella serotypes from non-human sources carry significant virulence determinants and show similar genotypic patterns with human isolates. These findings provide valuable insights into the virulence properties and genetic diversity of Salmonella serotypes in Iran, which could inform the development of effective control and prevention strategies for salmonellosis in the region.

The effect of changing diagnostic method from culture to PCR on the number of episodes of human campylobacteriosis in Denmark: a retrospective study (2015-2022).

This study is important because it shows the potential epidemiological silence associated with the use of culture as the primary diagnostic method for the laboratory identification of human campylobacteriosis. Also, we show how polymerase chain reaction methods are associated with a systematic increase in the number of human campylobacteriosis episodes as reported by routine disease surveillance. These findings are operationally relevant and have public health implications because they tell how crucial it is to consider changes in diagnostic methods, e.g., in the epidemiological analysis of historical data and in the interpretation of future data in light of the past. We also believe that this study highlights how the synergy between microbiology and epidemiology is essential for disease surveillance.

Environmental characterization and cartographic modeling of wild plant habitats at the northern coastal zone of Egypt

Assessing natural vegetation through conventional methods faces considerable constraints, such as limited geographical scope, reduced precision, a lack of historical data, high expenses and time demands. The study aims to use environmental and spectral data to identify and map natural vegetation and plant species along the Mediterranean coast of Egypt. This involves employing spatial analyses and cartographic modeling techniques, marking an initial effort in this endeavor. To fulfill this aim, a total number of 70 wild plant habitats were surveyed and sampled for further laboratory identification of plant species. Multispectral and thermal bands of Landsat imagery were processed to generate land cover map, as well as calculate Normalized Difference Vegetation Index (NDVI) and Land Surface Temperature (LST) to be integrated with the naturally grown plants in a cartographic model to predict the wild plant habitats. Coastal wild plant habitats were sparsely located and associated with a vegetation density ranging from 0.096 to 0.280 with an average of 0.167. Besides, the LST of these habitats fluctuated from 30.559 to 38.652 with an average of 34.361°C. Although the wild plant habitats at the Northern coastal region of Egypt are similar in environmental and climatic conditions, there are variability in NDVI and LST of each single habitat (pure or mixed). On the other hand, the lowest LST were associated with Erodium laciniatum/Rumex pictus and Erodium laciniatum habitats reporting 30.559 and 30.741°C, respectively. However, Lotus halophilus mixed with Ifloga spicata habitats reported the highest LST (38.652°C). The high vegetation density is mainly characterized by low LST which indicates the mixed wild plant habitats. The developed cartographic model showed a narrow strip along the Mediterranean region as highly suitable habitats for wild plant growth. The model can be used to map pure and mixed habitats of various wild plants with an accuracy exceeding 90%. The model was applied for mapping Arthrocnemum macrostachyum showing that the middle coastal region is most suitable for its growth. It’s recommended to integrate remotely sensed data with spatial analyses for the environmental analyses of natural plants. Present findings support researchers and scientists interested in environmental, botanic, and medical studies.