Laboratory validation of the automated diagnosis of intestinal parasites via fecal sample processing for the recovery of intestinal parasites through the dissolved air flotation technique.

BACKGROUND: Techniques for diagnosing intestinal parasites need technological advancements in the preanalytical (collection/processing) and analytical (detection) stages. The dissolved air flotation (DAF) technique effectively recovers parasites from processed feces for routine diagnosis. Artificial intelligence (AI) is a practical and affordable alternative to modernize the analysis stage of microscopy images and generates high efficiency in the parasitological examination of feces. METHODS: The objective of this study was to standardize a laboratory protocol for stool processing using the DAF technique in conjunction with an automated diagnosis of intestinal parasites (DAPI) system. A total of 400 samples were obtained to perform the tests with the use of DAF to verify the recovery of the parasites as a function of the chemical reagent (polymer and surfactant), the volume of the flotation tube, and standardization of smear assembly on a microscopy slide, with automated analysis by DAPI. The DAF protocol that obtained the most satisfactory results in terms of parasite recovery (P < 0.05) and slide positivity was compared with the Three Fecal Test (TF-Test) protocol with manual (microscopists) and automated (DAPI) evaluation. We compared the sensitivity with the modified TF-Test technical protocol and the diagnostic agreement with the gold standard (Kappa) result. RESULTS: There was no significant difference in the parasite recovery between the 10 ml and 50 ml tubes (P > 0.05). The surfactants showed a range of parasite recoveries between 41.9% and 91.2% in the float supernatant. We obtained a maximum positivity of 73% of the assembled slides when we applied DAF processing with 7% CTAB surfactant and 57% positivity with the modified TF-Test technique. Regarding diagnostic performance, the TF-Test-modified and DAF techniques used in fecal processing for subsequent computerized analysis by AI presented sensitivities of 86% and 94%, with kappa agreements of 0.62 and 0.80 (substantial), respectively. CONCLUSIONS: The DAF protocol defined in this study and the DAPI system are innovative processes for parasite recovery and fecal debris elimination that are favorable for effectively detecting pathogenic structures in laboratory diagnosis.

Academic accountability to local communities and society through Programme Science: a case study from the HPV self-sampling programme HOPE in Peru.

INTRODUCTION: Health challenges in the 21st century underscore the need for adaptable and innovative approaches in public health. Academic institutions can and should contribute much more effectively to generate and translate scientific knowledge that will result in better programmes to improve societal health. Academic accountability to local communities and society requires universities to actively engage with local communities, understanding the context, their needs, and leveraging their knowledge and local experience. The Programme Science initiative provides a framework to optimize the scale, quality and impact of public health programmes, by integrating diverse approaches during the iterative cycle of research and practice within the strategic planning, programme implementation and programme management and evaluation. We illustrate how the Programme Science framework could be a useful tool for academic institutions to accomplish accountability to local communities and society through the experience of Project HOPE in Peru. DISCUSSION: Project HOPE applied the Programme Science framework to introduce HPV self-sampling into a women's health programme in Peru. Collaboration with local authorities and community members was pivotal in all phases of the project, ensuring interventions aligned with community needs and addressing social determinants of health. The HOPE Ladies-community women trained and empowered to promote and provide the HPV kits-crafted the messages used through the study and developed strategies to reach individuals and provided support to women's journey through health centres. By engaging communities in co-creating knowledge and addressing health inequities, academic institutions can generate contextually relevant and socially just scientific knowledge. The active participation of community women in Project HOPE was instrumental in improving service utilization and addressing barriers to self-sampling. CONCLUSIONS: The Programme Science approach offers a pathway for academic institutions to enhance their accountability to communities and society at large. By embedding researchers within public health programmes and prioritizing community engagement, academic institutions can ensure that research findings directly inform policy improvements and programmatic decisions. However, achieving this requires a realignment of research agendas and recognition of the value of community engagement. Establishing Programme Science networks involving academia, government and funding entities can further reinforce academic accountability and enhance the impact of public health programmes.

Evaluation of nasal swab and nasal wipe for detection of Influenza A in swine using Bayesian latent class analysis.

Influenza A virus (IAV) is an important pathogen in Brazilian swine herds, and monitoring the viral circulation is essential to control and reduce the transmission. Surveillance programs for IAV are often based on individual piglets level sampling, making the evaluation of the available diagnostic tools crucial to assessing IAV circulation in herds. Thus, two sample collection methodologies were compared in pig herds in southern Brazil to detect IAV by RT-qPCR: nasal swab (NS) and nasal wipe (NW). A Bayesian latent class model (BLCM) was set for two tests and two populations. The NW and NS used are more specific (higher than 95 % for both) than sensitive. The sensitivity for NW was lower than the NS, 84.14 % (70 % - 95 %; posterior probability interval (PPI): 95 %) and 87.15 % (73 % - 97 %; PPI: 95 %), respectively, and the specificity was 95 % (90 % - 99 %; PPI: 95 %) and 99 % (96 % - 100 %; PPI: 95 %), respectively. Although the wipe sample collection loses both sensitivity and specificity compared with nasal swab, differences in test performance were very limited and PPIs largely overlapped. Therefore NW can also be considered a valuable tool. The decision about the use of both techniques should be based on the trade-off between their performance limitations and feasibility in routine monitoring.

HPV Self-Sampling in the Workplace: A Qualitative Study of Benefits, Barriers, and Opportunities for Improvement Perceived by Health Professionals and Managers.

AIM: To inform the implementation of Human Papillomavirus Self-Sampling (HPV-SS) in the workplace, we assessed the perspectives of healthcare professionals and managers on the benefits, barriers, and opportunities for improvement of a pilot program. METHODS: A qualitative descriptive study based on in-depth telephone interviews was conducted between June and August 2023. Data were analyzed through inductive thematic analysis. Fifteen health professionals from different companies and fifteen managers from the Mexican Institute of Social Security (IMSS) were interviewed. RESULTS: Participants identified several benefits of the HPV-SS, including ease of use, privacy, convenience, affordability, reduced workplace absences, and promotion of a prevention culture. However, there were also individual and organizational barriers to program implementation. The former consisted of women's concerns about collecting a reliable sample or injuring themselves, lack of confidence in the HPV test, fear of positive results, and discomfort caused by the brush used to collect the sample. Organizational barriers included failure to follow up on positive test results, lack of knowledge of program indicators, perceived negative impact on the established Pap smear cervical cancer screening indicator, and the lack of government regulations supporting HPV testing. To improve the program, participants suggested disseminating information through mass media campaigns and social networks, providing companies with additional support from IMSS preventive staff, extending the work hours of IMSS Family Medicine clinics, and training IMSS health staff on the follow-up of women with HPV test results. CONCLUSIONS: The study findings suggest potential areas for improvement in HPV-SS programs.

Evaluation of self-collected nasal, urine, and saliva samples for molecular detection of SARS-CoV-2 using an EUA approved RT-PCR assay and a laboratory developed LAMP SARS-CoV-2 test.

As the SARS-CoV-2 virus spread throughout the world, millions of positive cases of COVID-19 were registered and, even though there are millions of people already vaccinated against SARS-CoV-2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS-CoV-2 molecular testing availability, we evaluated the diagnostic accuracy of self-collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT-PCR) COVID-19 kit to detect SARS-CoV-2. We also created a colorimetric loop-mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS-CoV-2, as another strategy to increase the availability of molecular testing in community-based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS-CoV-2 on the 7500 Fast Dx RT-PCR using the TaqPath RT-PCR COVID-19 molecular test. Data was interpreted by the COVID-19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene-Biomarks' SARS-CoV-2 Rapid Colorimetric LAMP LDT and the TaqPath RT-PCR COVID-19 test. Our results suggest that self-collected saliva is superior to nasal and urine samples for COVID-19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT-PCR tests for the detection of SARS-CoV-2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics.

Electron Microscopy of Cryptococcus neoformans: Processing Challenges to Avoid Artifacts.

This chapter describes methodological details for preparing specimens of Cryptococcus neoformans (although it can be applied to any species of the genus) and their subsequent analysis by scanning and transmission electron microscopy. Adaptations to conventional protocols for better preservation of the sample, as well as to avoid artifacts, are presented. The protocols may be used to examine both the surface ultrastructure and the interior of this pathogenic fungus in detail.

Original article: novelty of Canadian manufacture nasopharyngeal swabs for collection of samples being tested for SARS-CoV-2 in a pandemic setting.

Objectives: The COVID-19 pandemic caused a global shortage of nasopharyngeal (NP) swabs, required for RT-PCR testing. Canadian manufacturers were contacted to share NP swab innovations. The primary objective was to determine whether novel NP test swabs were comparable to commercially available swabs regarding user characteristics, ability to collect a specimen, and diagnostic performance using RT-PCR testing. Methods: Participants were randomized by swab (test/control) and nostril (left/right). A calculated positive percent agreement ≥90% was considered successful. Mean Ct values of viral genes and housekeeping gene (RNase P) were considered similar if a Ct difference ≤ 2 between control and test group was obtained. There also was a qualitative assessment of swabs usability. Results: 647 participants were enrolled from Huaycan Hospital in Lima, Peru, distributed over 8 NP swabs brands. Seven brands agreed to share their results. There were no statistically significant differences between the test swabs of these 7 brands and control swabs. Conclusion: All the seven brands are comparable to the commercially available flocked swabs used for SARS-CoV-2 regarding test results agreement, ability to collect a specimen, and user characteristics.

Use of FTA card for the detection of two RNA (CSFV and SV-A) and two DNA viruses (ASFVand SuHV-1) of importance in veterinary medicine.

The FTA card has emerged as a promising alternative for nucleic acid extraction. The FTA card is a filter paper impregnated with chemicals that preserve and stabilize the genetic material present in the sample, allowing for its storage and transport at room temperature. The aim of this study was to test the card for the detection of RNA and DNA nucleic acids. Two RNA viruses (Senecavirus A and classical swine fever virus) and two DNA viruses (African swine fever virus and suid alphaherpesvirus 1) were tested, and in all cases, there was a decrease in sensitivity. The methods exhibited good repeatability and demonstrated a rapid and practical use for sample transport and nucleic acid extraction.

Diagnostic performance, stability, and acceptability of self-collected saliva without additives for SARS-CoV-2 molecular diagnosis.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19), leading to a global pandemic. The molecular diagnosis of this virus is mostly performed by collecting upper respiratory samples, which has many disadvantages, including patient discomfort and the need for trained healthcare professionals. Although saliva has emerged as a more comfortable sample, the use of additives to preserve viral RNA is expensive and, in some cases, difficult for self-collection. METHOD: This study evaluated the diagnostic performance by RT-PCR and stability of self-collected saliva using wide-mouth specimen collection cups without stabilization and/or inactivation buffers for SARS-CoV-2 detection, compared to nasopharyngeal samples and saliva collected with additives. Additionally, the study assessed the acceptability of this sample collection method among participants and healthcare personnel. RESULTS: The study included 1281 volunteers with a 24.6% positive infection rate. Saliva demonstrated comparable diagnostic performance to nasopharyngeal samples, with a sensitivity of 87.6% and specificity of 99.6%, for a total percent agreement of 96.4%. The study also showed that viral RNA in saliva remained stable for at least 72 h at different temperatures. Notably, saliva samples without additives exhibited a lower RdRp Ct compared to samples with additives, suggesting that the absence of stabilization and/or inactivation buffers does not significantly affect its performance. The study highlighted the acceptability of saliva among patients and healthcare personnel due to its noninvasive nature and ease of collection. CONCLUSIONS: This research supports the implementation of self-collected saliva as a comfortable and user-friendly alternative sample for SARS-CoV-2 diagnosis.

Sampling is decisive to determination of Leishmania (Viannia) species.

BACKGROUND: Accuracy of molecular tools for the identification of parasites that cause human cutaneous leishmaniasis (CL) could largely depend on the sampling method. Non-invasive or less-invasive sampling methods such as filter paper imprints and cotton swabs are preferred over punch biopsies and lancet scrapings for detection methods of Leishmania based on polymerase chain reaction (PCR) because they are painless, simple, and inexpensive, and of benefit to military and civilian patients to ensure timely treatment. However, different types of samples can generate false negatives and there is a clear need to demonstrate which sample is more proper for molecular assays. METHODOLOGY: Here, we compared the sensitivity of molecular identification of different Leishmania (Viannia) species from Peru, using three types of sampling: punch biopsy, filter paper imprint and lancet scraping. Different composite reference standards and latent class models allowed to evaluate the accuracy of the molecular tools. Additionally, a quantitative PCR assessed variations in the results and parasite load in each type of sample. PRINCIPAL FINDINGS: Different composite reference standards and latent class models determined higher sensitivity when lancet scrapings were used for sampling in the identification and determination of Leishmania (Viannia) species through PCR-based assays. This was consistent for genus identification through kinetoplastid DNA-PCR and for the determination of species using FRET probes-based Nested Real-Time PCR. Lack of species identification in some samples correlated with the low intensity of the PCR electrophoretic band, which reflects the low parasite load in samples. CONCLUSIONS: The type of clinical sample can directly influence the detection and identification of Leishmania (Viannia) species. Here, we demonstrated that lancet scraping samples consistently allowed the identification of more leishmaniasis cases compared to filter paper imprints or biopsies. This procedure is inexpensive, painless, and easy to implement at the point of care and avoids the need for anesthesia, surgery, and hospitalization and therefore could be used in resource limited settings for both military and civilian populations.

Prevalencia de Staphylococcus aureusy su sensibilidad antibiótica en aislamientos en infecciones de piel y partes blandas en pacientes ambulatorios / Staphylococcus aureus prevalence and antimicrobial susceptibility in isolates from skin and soft tissue infections in outpatients

ntroducción: Las infecciones de piel y partes blandas (IPPB) constituyen la tercera causa de consulta en nuestro centro. S.aureus es el agente etiológico más frecuente en este tipo de infecciones y la meticilino resistencia es clínicamente el mecanismo de resistencia más importante. El objetivo de este trabajo fue analizar la prevalencia de los distintos agentes etiológicos en IPPB en pacientes ambulatorios, así como también estudiar su sensibilidad a los antibióticos y resistencias acompañantes más frecuentes. Materiales y métodos: Estudio descriptivo y retrospectivo que incluyó todas las muestras provenientes de IPPB de pacientes ambulatorios desde octubre de 2017 a abril de 2022. Resultados: Se obtuvieron 180 cultivos positivos de muestras provenientes de IPPB durante el periodo estudiado, 12 fueron infecciones polimicrobianas. En total se obtuvieron 307 aislamientos: el microorganismo aislado con mayor frecuencia fue S.aureus (111; 36,2%). Se hallaron 71 SAMR (64%) y 40 SAMS (36%). De los SAMR, 67 (95%) fueron comunitarios (SAMRC) por criterios microbiológicos, y 4 SAMR hospitalarios (5%). De las cepas SAMRC, 44 (66%) no presentaron resistencias acompañantes, 15 (22% ) fueron resistentes a eritromicina, 12 (18%) a gentamicina y 7 (10%) a clindamicina. Conclusiones: El microorganismo más frecuentemente aislado en IPPB en pacientes ambulatorios fue el S.aureus y 67 aislamientos fueron categorizados como SAMRC por lo cual es necesario considerar al SAMRC como un patógeno frecuente. Debido a la baja resistencia hallada para CLI y TMS ambos podrían ser de elección en el tratamiento empírico en las IPPB en pacientes ambulatorios

Background:S. aureus is the main cause of skin and soft tissues infections (SSTIs) in immunocompetent patients. This type of infection is the third cause of medical consultation in our center. Our objective was to evaluate the prevalence of S. aureus, as well as its sensitivity to antimicrobials, isolated from skin and soft tissue samples from outpatients at an interzonal general acute care hospital located in Buenos Aires, Argentina.Methods: Descriptive and retrospective study that included all outpatient SSTIs samples from October 2017 to April 2022.Results: We obtained 215 positive cultures of samples from SSTIs during the study period. Of a total of 276 isolates: the most frequently isolated microorganism wasS. aureus (111; 40.22%). The prevalence of S. aureuswas 51.63%. We found 71 MRSA (63.96%). Of the SAMR strains, 60.56% did not present accompanying resistance, and only 8 isolates (11.27%) showed resistance to clindamycin. All SAMRs remained sensitive to minocycline and trimethoprim-sulfamethoxazole.Conclusions: The most frequently isolated microorganism in SSTIs was S. aureus and 71 isolates were categorized as SAMR, therefore it is necessary to consider SAMR as a frequent pathogen. Due to the low resistance found for CLI and TMS, they should be considered for empirical treatment in SSTIs in outpatients

Modified Procedure for Simple and Rapid Collection of Zebrafish Fluid Samples for Biochemical Analyses.

This study addresses the challenge of collecting blood samples from zebrafish for biochemical analysis. Traditional methods are cumbersome due to low blood flow and rapid coagulation. Based on a previously published technique, we simplified the process by applying an anticoagulant solution directly to the incision site. The modified protocol involves immersing the fish in an ice bath, making a cross-sectional incision, and immediately applying anticoagulant solution. Centrifugation of the specimens provides a streamlined and efficient approach to zebrafish fluid sample collection, compatible with classic biochemical marker analyses.

Self-sampling for HPV testing in cervical cancer screening: A scoping review.

Cervical cancer is the third most common gynecological cancer worldwide. Its origin is linked to intraepithelial lesions caused by high-risk Human Papillomavirus (HPV) types, detected in 99.7% of cases. Early screening is essential to prevent cancer development from these lesions. Molecular methods are more specific and offer the possibility of being performed through a self-collected sample by the patient, thus contributing to increasing screening coverage for this pathology. This study aim was to map the medical-scientific literature on existing protocols for self-sampling for HPV testing in cervical cancer screening. A search strategy was developed using the following keywords and their synonyms: "self-sampling," "professional sampling," and "HPV", on the databases: MEDLINE, Cochrane Library, Virtual Health Library - BVS, Scopus, National Institute for Health Research NHS EED, Web of Science, and EMBASE. The search strategy was formulated to identify relevant studies and describe their main characteristics, such as patient acceptance of self-sampling, cost differences between the tests used, and the accuracy of self-sampling compared to the gold standard test. A total of 876 studies were found, and 33 of those studies were included in this review. Out of these, 10 studies were domized clinical trials involving 46,751 patients, and 23 observational studies included 142,795 patients. Regarding acceptance, most studies reported a preference for self-sampling. Sensitivity analyses from various studies also showed that the low cost of self-sampling kits generally increased cost-effectiveness. The study concluded that using HPV testing on self-collected samples is a viable strategy for monitoring women with HPV.

Evaluation of blastocyst re-expansion, quality in relation to storage temperature, and sexing using blastocoel fluid after manual perforation with a hand-held needle involving in vivo produced equine embryos.

The present study was designed to evaluate equine blastocyst re-expansion rate, quality, and sex following perforation of the blastocoel, collection of blastocoel fluid (BF), and PCR amplification of free DNA. Experiment 1 tested the feasibility of the BF sample collection with a hand-held, small-gauged needle (26g) and subsequent PCR amplification of the TSP-Y gene for males and AMEL-Y gene for males and AMEL-X gene for females. Experiment 2 tested the application of the technique. Equine embryos were collected via uterine flushes 8d after ovulation. Thereafter, embryos (n = 19) were initially assessed and transferred to a 50 µL droplet of holding medium in which the blastocoel was manually perforated as in Experiment 1. Within 1 min of detecting a diameter decrease or collapse, the entire volume of each droplet of medium was collected and stored at -20 °C until PCR. In Experiment 1, amplification of the TSP-Y gene was positive for males at 60% (9/15) and negative for females at 40% (6/15). In Experiment 2, a total of 42 embryos were randomly assigned to a collapsed embryo (CE) or intact embryo (IE) groups and stored at room temperature (RT, 25 °C) or cold temperature (CT, 5 °C) for 24h as follows: 1) CERT, n = 11; 2) CECT n = 11; 3) IERT, n = 10; and 4) IECT, n = 10. After 24h, embryo diameter and quality were reassessed. For all collapsed embryos (n = 19), blastocoel fluid was subjected to double PCR amplification of the TSPY gene with blood from adult male and female horses as controls. Positive gene amplification indicated 57.9% (11/19) of embryos were male and negative amplification indicated 31.6% (6/19) of embryos were female. Relative to the least diameter (0%) after perforation of collapsed embryos or fullest diameter (100%) of intact embryos at T0, percentage change in diameter and quality Grade 1 or 2 embryos after 24h of storage for all groups were, respectively: 31.2% and 54% for CERT group, 28.2% and 0% for CECT group, 25.9% and 100% for IERT group, 4.3% and 80% for IECT group, respectively. Thus, needle-induced leakage and collapse of the blastocoel at T0 resulted in a high rate of blastocyst re-expansion (69%) with many embryos (54%) achieving good quality at T24 with potential for transfer as either male or female embryos. For both collapsed and intact embryos, it was observed that storage for 24h at room temperature (25 °C) was associated with improved embryo growth and morphological quality compared to storage at cold temperature (5 °C).

Isolation of potential zoonotic Mycobacterium spp. from diseased freshwater angelfish (Pterophyllum scalare) from an aquarium / Isolamento de Mycobacterium spp. potencialmente zoonótica de peixes anjo de água doce (Pterophyllum scalare) doentes de um aquário

Nontuberculous mycobacteria infection is one of the most common chronic bacterial diseases in ornamental aquarium fish and appears to be directly related to stressful husbandry practices. Furthermore, it also represents zoonotic potential. Here we present the isolation and characterization of non-tuberculous mycobacteria from diseased freshwater angelfish (Pterophyllum scalare) in São Paulo, Brazil. Nine discarded breeding females with signs of disease were evaluated. The fish exhibited lethargy, loss of appetite, cachexia, skin ulcers, and exophthalmia. At necropsy, four fishes presented macroscopic granulomas in the spleen. Mycobacterium chelonae, M. fortuitum, M. gordonae, M. intracellulare and M. peregrinum were isolated and identified by hsp65 PCR restriction analysis. Histopathological analysis revealed microscopic lesions compatible with mycobacteriosis, and Mycobacterium bacillus were observed by Ziehl-Neelsen stain. Notably, all Mycobacterium species identified in this study have already been reported in human patients; therefore, diseased animals may be a source of infection for people who handle fish and aquariums.

A infecção por micobactérias não tuberculosas é uma das doenças bacterianas crônicas mais comuns em peixes ornamentais de aquário e parece estar diretamente relacionada a práticas de manejo estressantes. Além disso, também representa potencial zoonótico. Aqui, apresentamos o isolamento e a caracterização de micobactérias não tuberculosas de peixes-anjo de água doce doentes (Pterophyllum scalare) em São Paulo, Brasil. Foram avaliadas nove fêmeas reprodutoras descartadas com sinais de doença. Os peixes exibiam letargia, perda de apetite, caquexia, úlceras cutâneas e exoftalmia. Na necropsia, quatro peixes apresentaram granulomas macroscópicos no baço. Mycobacterium chelonae, M. fortuitum, M. gordonae, M. intracellulare e M. peregrinum foram isolados e identificados por análise de restrição por PCR de hsp65. A análise histopatológica revelou lesões microscópicas compatíveis com micobacteriose, e o bacilo de Mycobacterium foi observado pela coloração de Ziehl-Neelsen. Notavelmente, todas as espécies de Mycobacterium identificadas neste estudo já foram relatadas em pacientes humanos; portanto, animais doentes podem ser uma fonte de infecção para pessoas que manipulam peixes e aquários.

Influenza A, like Omicron SARS-CoV-2, Is Similarly Detected in Saliva or Nasopharyngeal Samples via RT-qPCR.

After the Coronavirus pandemic, the importance of virus surveillance was highlighted, reinforcing the constant necessity of discussing and updating the methods for collection and diagnoses, including for other respiratory viruses. Although the nasopharyngeal swab is the gold-standard sample for detecting and genotyping SARS-CoV-2 and Influenza viruses, its collection is uncomfortable and requires specialized teams, which can be costly. During the pandemic, non-invasive saliva samples proved to be a suitable alternative for SARS-CoV-2 diagnosis, but for Influenza virus the use of this sample source is not recognized yet. In addition, most SARS-CoV-2 comparisons were conducted before the Omicron variant emerged. Here, we aimed to compare Influenza A and Omicron RT-qPCR analysis of nasopharyngeal swabs and saliva self-collection in paired samples from 663 individuals. We found that both nasopharyngeal swab and saliva collection are efficient for the diagnosis of Omicron (including sub-lineages) and for Influenza A, with high sensitivity and accuracy (>90%). The kappa index is 0.938 for Influenza A and 0.905 for SARS-CoV-2. These results showed excellent agreement between the two samples reinforcing saliva samples as a reliable source for detecting Omicron and highlighting saliva as a valid sample source for Influenza detection, considering this cheaper and more comfortable alternative.

Sensitivity of PCR in conjunctival swab samples for the diagnosis of canine visceral leishmaniasis: a systematic review and meta-analysis.

To compare the sensitivity of conjunctival swab (CS) and conventional samples (blood, spleen, liver, lymphoid and cutaneous tissue) in the diagnosis of canine visceral leishmaniasis (CVL) by polymerase chain reaction (PCR), a systematic review and meta-analysis was carried out using PubMed, Science Direct, Scopus, Web of Science, VHL/BVS (Virtual Health Library), CAPES, and Scielo databases. Articles published from 2002 to 2022 were considered and the review was updated in Jul 2023. From the total of 371 identified studies, 8 met all the eligibility criteria and were included in this review. Data from 658 CVL-positive dogs and 2541 PCR results were considered. Using a random effect model, data on the sensitivity of the test was compared between intervention (CS samples) and comparison (all the other samples) groups. Overall, the use of CS in the PCR diagnosis of CVL produced 12% higher sensitivity (p=0.013) in the test than all the other samples in combination. The animals' clinical condition did not influence (p>0.142) this overall result. However, when CS was individually compared to each of the conventional samples, the consistent result was observed (p=0.012) only in the CS versus bone marrow comparison. Given their rapid acquisition, minimal invasiveness, and lower cost relative to conventional samples, CS samples present a promising alternative for the molecular diagnosis of CVL.

Sample Preparation in Microbial Metabolomics: Advances and Challenges.

Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.

Coordination chemistry applied to anti-doping analysis: Cobalt quantification as its diethyldithiocarbamate complex by liquid chromatography coupled to high resolution tandem mass spectrometry.

Cobalt was included on the World Anti-Doping Agency Prohibited List in 2015 due to its effect on stimulus of erythropoiesis via stabilization of hypoxia-inducible factor. Although it has proven benefits for performance enhancement, the unavailability of inductively coupled plasma-mass spectrometry on routine of the accredited laboratories is a factor that reduces its applicability in anti-doping analysis. Therefore, an analytical method for quantification of urinary cobalt as its diethyldithiocarbamate complex by liquid chromatography coupled with high-resolution tandem mass spectrometry was developed and validated. Palladium was proposed as internal standard and rhodium as a complexation control. A microwave-assisted acid digestion of the urine samples was essential, not only to eliminate the matrix effect but mainly to avoid the non-specific bond of cobalt to endogenous molecules. A linear method was obtained over the studied range from a negative urine control to a spiked concentration of 25 ng/mL, with an estimated limit of quantification of 2.5 ng/mL, and an adequate combined standard uncertainty of 11.4%. Considering that all reagents are commercially available, the proposed strategy is feasible to be included on routine sample preparation. Monitoring urinary cobalt concentrations globally opens the perspective to support the anti-doping system to define a suitable threshold value and to understand its potential misuse by athletes seeking for performance improvement.