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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.
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COVID-19 , Técnicas de Diagnóstico Molecular , Técnicas de Amplificação de Ácido Nucleico , SARS-CoV-2 , Saliva , Manejo de Espécimes , Humanos , Saliva/virologia , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , COVID-19/diagnóstico , COVID-19/virologia , COVID-19/urina , Técnicas de Amplificação de Ácido Nucleico/métodos , Manejo de Espécimes/métodos , Técnicas de Diagnóstico Molecular/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , RNA Viral/análise , RNA Viral/urina , RNA Viral/genética , RNA Viral/isolamento & purificação , Teste de Ácido Nucleico para COVID-19/métodos , Sensibilidade e Especificidade , Porto Rico/epidemiologia , Teste para COVID-19/métodosRESUMO
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.
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COVID-19 , Nasofaringe , SARS-CoV-2 , Manejo de Espécimes , Humanos , COVID-19/diagnóstico , Manejo de Espécimes/métodos , Nasofaringe/virologia , Canadá , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/genética , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Peru/epidemiologia , Pandemias , Teste de Ácido Nucleico para COVID-19/métodos , Adulto Jovem , Adolescente , Teste para COVID-19/métodos , IdosoRESUMO
This study was designed to characterize the dynamics of infection of Mycoplasma hyopneumoniae in naïve replacement gilts after introduction to positive systems. Ninety-eight naïve gilts were monitored in three positive commercial farms (A, B, and C). The näive gilts were housed for 21 days in pens adjacently located to older gilt cohorts (named seeders), which have been naturally exposed to the positive farms. The infection dynamics was evaluated by PCR and ELISA, from laryngeal swabs and serum samples, respectively. Samples were collected at 150 (arrival), 165, 180, 210, 240, 270, 300 days of age (doa), and pre-farrowing. Infection occurred rapidly on farms A and B, taking 25.2 and 23.9 days for 95% of gilts to be PCR positive, respectively. There was no influence on the number of seeders at the time of exposure, but their absence (farm C) could explain the extended period it took for gilts to get infected (69.4 days). On average, it took 162.2 days after the first PCR detection for 85% of gilts to stop shedding the bacterium. The serology results were consistent with the herd infection curve. At pre-farrowing, 100% of gilts seroconverted and 36.7% remained PCR positive. A total of 1.33% of piglets were positive at weaning. Fifteen variants were detected among the three farms by MLVA. The acclimation protocol was efficient and easy to perform, and the presence of seeders was likely critical for early acclimation for M. hyopneumoniae.
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Mycoplasma hyopneumoniae , Pneumonia Suína Micoplasmática , Doenças dos Suínos , Suínos , Animais , Feminino , Pneumonia Suína Micoplasmática/epidemiologia , Pneumonia Suína Micoplasmática/microbiologia , Mycoplasma hyopneumoniae/genética , Fazendas , Sus scrofa , Reação em Cadeia da Polimerase/veterináriaRESUMO
The chemical composition of COVID test swabs has not been examined beyond the manufacturer's datasheets. The unprecedented demand for swabs to conduct rapid lateral flow tests and nucleic acid amplification tests led to mass production, including 3D printing platforms. Manufacturing impurities could be present in the swabs and, if so, could pose a risk to human health. We used scanning electron microscopy and energy dispersive X-ray (EDX) spectroscopy to examine the ultrastructure of seven assorted brands of COVID test swabs and to identify and quantify their chemical elements. We detected eight unexpected elements, including transition metals, such as titanium and zirconium, the metalloid silicon, as well as post-transition metals aluminium and gallium, and the non-metal elements sulphur and fluorine. Some of the elements were detected as trace amounts, but for others, the amount was close to reported toxicological thresholds for inhalation routes. Experimental studies have shown that the detrimental effects of unexpected chemical elements include moderate to severe inflammatory states in the exposed epithelium as well as proliferative changes. Given the massive testing still being used in the context of the COVID pandemic, we urge caution in continuing to recommend repeated and frequent testing, particularly of healthy, non-symptomatic, individuals.
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BACKGROUND AND OBJECTIVES: Feline leishmaniasis (FeL) is caused by several species of parasites of the genus Leishmania. The disease can occur with the presence or absence of clinical signs, similar to those observed in other common infectious diseases. In endemic regions for FeL, the infection has been associated with dermatological lesions. Therefore, considering the search for less invasive and more effective diagnostic techniques, we aimed to investigate the presence of Leishmania spp. in domestic cats through Polymerase Chain Reaction (PCR) and high-resolution melting (HRM) analyses of conjunctival, oral, and nasal epithelial cells, and we detected the presence of anti-Leishmania IgG antibodies from serological techniques of the Immunofluorescent Antibody Test (IFAT) and ELISA. METHODS: The PCR and HRM for detection of Leishmania spp. were performed on 36 samples of epithelial cells from the conjunctiva of male and female cats, collected using sterile swabs. The serological tests IFAT and ELISA were also performed. RESULTS: The prevalence of Leishmania donovani infection was 11.1% (4/36) by PCR assay, and those results were confirmed for Leishmania species using the HRM technique. Twenty-four cats (24/36 = 66.7%) were reactive to the IFAT and twenty-two cats were reactive by the ELISA technique (22/36 = 61.1%). INTERPRETATION AND CONCLUSIONS: The use of conjunctival swabs was shown to be a non-invasive, practical, and easy-to-perform technique, and in addition to the genetic sequencing and HRM, it was able to identify the parasitic DNA of L. donovani in cats. This technique can be used for screening diagnosis in future epidemiological surveys of FeL and can be used as a complement to clinical and/or serological tests, as well as associating the clinical history of the animal, for the diagnostic conclusion.
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Throughout the entire coronavirus disease 19 (COVID-19) pandemic, there were disruptions in the supply chain of test materials around the world, primarily in poor- and middle-income countries. The use of 3D prints is an alternative to address swab supply shortages. In this study, the feasibility of the clinical use of 3D-printed swabs for oropharyngeal and nasopharyngeal sampling for the detection of SARS-CoV-2 infection was evaluated. For that purpose, paired samples with the 3D printed and the control swabs were taken from 42 adult patients and 10 pediatric patients, and the results obtained in the detection of SARS-CoV-2 by reverse transcription and quantitative polymerase chain reaction (RT-qPCR) were compared. Additionally, in those cases where the result was positive for SARS-CoV-2, the viral load was calculated by means of a mathematical algorithm proposed by us. For both adults and children, satisfactory results were obtained in the detection of SARS-CoV-2 by RT-qPCR; no significant differences were found in the quantification cycle values between the 3D-printed swab samples and the control samples. Furthermore, we corroborated that the 3D-printed swabs caused less discomfort and pain at the time of sampling. In conclusion, this study shows the feasibility of routinely using 3D-printed swabs for both adults and children. In this way, it is possible to maintain local and cheaper consumption along with fewer distribution difficulties.
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Fecal samples or cloacal swabs are preferred over lethal dissections to study vertebrate gut microbiota for ethical reasons, but it remains unclear which nonlethal methods provide more accurate information about gut microbiota. We compared the bacterial communities of three gastrointestinal tract (GIT) segments, that is, stomach, small intestine (midgut), and rectum (hindgut) with the bacterial communities of the cloaca and feces in the mesquite lizard Sceloporus grammicus. The hindgut had the highest taxonomic and functional alpha diversity, followed by midgut and feces, whereas the stomach and cloaca showed the lowest diversities. The taxonomic assemblages of the GIT segments at the phylum level were strongly correlated with those retrieved from feces and cloacal swabs (rs > 0.84 in all cases). The turnover ratio of Amplicon Sequence Variants (ASVs) between midgut and hindgut and the feces was lower than the ratio between these segments and the cloaca. More than half of the core-ASVs in the midgut (24 of 32) and hindgut (58 of 97) were also found in feces, while less than 5 were found in the cloaca. At the ASVs level, however, the structure of the bacterial communities of the midgut and hindgut were similar to those detected in feces and cloaca. Our findings suggest that fecal samples and cloacal swabs of spiny lizards provide a good approximation of the taxonomic assemblages and beta diversity of midgut and hindgut microbiota, while feces better represent the bacterial communities of the intestinal segments at a single nucleotide variation level than cloacal swabs.
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Microbioma Gastrointestinal , Lagartos , Animais , RNA Ribossômico 16S/genética , Trato Gastrointestinal , Fezes/microbiologia , Bactérias/genéticaRESUMO
Hasta 1983, cuando alcanzaba la increíble tasa de 118 casos por 100.000 habitantes, la fiebre tifoidea era la peor amenaza infecciosa en Santiago, Chile, ciudad que figuraba junto a Ciudad de México, El Cairo y Bombay, como una de las con mayor endemia en el mundo. El Ministerio de Salud respondió formando el Comité de Tifoidea de Chile, con participación de expertos nacionales y del grupo de Myron Levine, de la Universidad de Maryland, que llevó a cabo ingeniosas investigaciones, culpando al río Mapocho, cuyas aguas contaminadas con Salmonella typhi regaban los predios agrícolas vecinos, conformando así un ciclo largo de infección. Las vacunas antitíficas ensayadas (oral Ty21a atenuada y polisacárido capsular Vi inyectable) no mostraron eficacia, los portadores crónicos no se trataron, pero una campaña sanitaria a través de la televisión contribuyó decisivamente a mejorar los hábitos higiénicos de la población, fortalecida por el pánico que causó la llegada del cólera en 1991, y la fiebre tifoidea prácticamente desapareció del escenario.
Until 1983, when reached the incredible frequency of 118 cases for 100.000 habitants, typhoid fever was the worst infectious threat in Santiago, Chile, city that appeared next to Mexico City, Cairo and Bombay, as one of the most endemic in the world. The Ministry of Health responded with the creation of The Chilean Typhoid Committee, with the participation of national experts and Myron Levine's group, which carried out ingenious investigations blaming the Mapocho River, whose waters contaminated with Salmonella typhi irrigated the neighboring farms, thus conforming a long cycle of infection. Typhoid vaccines tested (strain Ty 21a oral and Vi capsular polysaccharide) did not show efficacy, chronic carriers were not treated, but a health campaign on television made a decisive contribution to improving hygiene habits of the population, strengthened by the panic caused by the arrival of cholera in 1991, and typhoid fever practically disappeared from the stage.
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Humanos , História do Século XX , Febre Tifoide/história , Febre Tifoide/prevenção & controle , Salmonella/isolamento & purificação , Microbiologia da Água , Vacinas Tíficas-Paratíficas , Chile , VacinaçãoRESUMO
The objective of this study was to characterize the Mycoplasma hyopneumoniae (M. hyopneumoniae) detection and seroconversion patterns in recently acclimated gilts to be introduced to endemically infected farms using different types of replacement management. Three gilt developing units (GDUs) belonging to sow farms were included in this investigation: two farms managed gilts in continuous flow, and one farm managed gilts all-in/all-out. Two replicates of 35 gilts each were selected per GDU and sampled approximately every 60 days for a total of four or five samplings, per replicate and per GDU. Detection of M. hyopneumoniae was evaluated by PCR, while antibodies were measured using a commercial ELISA assay. Also, M. hyopneumoniae genetic variability was evaluated using Multiple-Locus Variable number tandem repeat Analysis. Detection of M. hyopneumoniae was similar across GDUs. Although a significant proportion of gilts was detected positive for M. hyopneumoniae after acclimation, an average of 30.3 % of gilts was negative at any point during the study. Detection of M. hyopneumoniae antibodies was similar among GDUs regardless of flow type or vaccination protocol. The genetic variability analysis revealed a limited number of M. hyopneumoniae types within each GDU. Results of this study showed a similar pattern of M. hyopneumoniae detection by PCR and seroconversion by ELISA among GDUs, regardless of the type of flow management strategies applied to gilts.
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Mycoplasma hyopneumoniae , Pneumonia Suína Micoplasmática , Doenças dos Suínos , Suínos , Animais , Feminino , Pneumonia Suína Micoplasmática/diagnóstico , Mycoplasma hyopneumoniae/genética , Sus scrofa , Aclimatação , Anticorpos AntibacterianosRESUMO
OBJECTIVES: To describe the most common ocular lesions and demonstrate the frequency of ophthalmic involvement in a group of cats with systemic sporotrichosis. ANIMALS STUDIED: Two hundred seventy-four cats diagnosed with systemic sporotrichosis. The inclusion criteria included previous positive cytopathological examination, histopathological examination, or fungal culture. PROCEDURES: In a prospective case-control study, 274 cats diagnosed with systemic sporotrichosis underwent ophthalmic evaluation and received treatment for systemic sporotrichosis. Of these animals, 63 had ocular abnormalities which were recorded, and conjunctivitis was scored from 0 to 5. Diagnostic techniques utilized included fungal culture, as well as cytopathological (10 eyes; 10 cats), and histopathological examination of the palpebral conjunctiva and eyes (2 eyes). RESULTS: Cytopathological and histopathological examination of the conjunctiva, as well as fungal culture, proved to be important tests for the detection of Sporothrix sp. Five cats without the evidence of ophthalmic abnormalities also had a positive fungal culture. The identified ocular lesions in animals with systemic sporotrichosis included increased serous discharge (79 eyes; 53 cats), blepharoconjunctivitis (33 eyes; 25 cats), conjunctivitis (39 eyes, 20 cats), blepharitis (9 eyes; 8 cats), uveitis (5 eyes; 3 cats), and Florida keratopathy-like lesions (2 eyes; 1 cat). CONCLUSION: Sporotrichosis should be considered a differential diagnosis for conjunctivitis and blepharoconjunctivitis, especially in endemic areas. Fungal culture and cytopathology of ocular discharge and histopathological examinations of the conjunctiva are important for the diagnosis of ophthalmic sporotrichosis, although not all cats underwent laboratory testing in this study. Ocular discharge could be a source of contagion transmission.
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Doenças do Gato , Conjuntivite , Opacidade da Córnea , Esporotricose , Animais , Gatos , Esporotricose/diagnóstico , Esporotricose/veterinária , Estudos de Casos e Controles , Conjuntivite/diagnóstico , Conjuntivite/veterinária , Túnica Conjuntiva , Opacidade da Córnea/veterinária , Doenças do Gato/diagnósticoRESUMO
In this pilot study, we characterize and evaluate 3D-printed swabs for the collection of nasopharyngeal and oropharyngeal secretion samples for the SARS-CoV-2 detection. Swabs are made with the fused deposition modeling technique using the biopolymer polylactic acid (PLA) which is a medical-grade, biodegradable and low-cost material. We evaluated six swabs with mechanical tests in a laboratory and in an Adult Human Simulator performed by healthcare professionals. We proved the adequacy of the PLA swab to be used in the gold standard reverse transcriptase-polymerase chain reaction (qRT-PCR) for viral RNA detection. Then, we did in vitro validation for cell collection using the 3D-printed swabs and RNA extraction for samples from 10 healthy volunteers. The 3D-printed swabs showed good flexibility and maneuverability for sampling and at the same time robustness to pass into the posterior nasopharynx. The PLA did not interfere with the RNA extraction process and qRT-PCR test. When we evaluated the expression of the reference gene (RNase P) used in the SARS-CoV-2 detection, the 3D-printed swabs showed good reproducibility in the threshold cycle values (Ct = 23.5, range 19-26) that is comparable to control swabs (Ct = 24.7, range 20.8-32.6) with p value = 0.47. The 3D-printed swabs demonstrated to be a reliable, and an economical alternative for mass use in the detection of SARS-CoV-2.
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COVID-19 , SARS-CoV-2 , Adulto , Humanos , COVID-19/diagnóstico , Projetos Piloto , Reprodutibilidade dos Testes , Poliésteres , Impressão Tridimensional , RNARESUMO
The aim of this study was to compare the sensitivity of different in vivo and post-mortem samples collected from finishing pigs under field conditions on Mycoplasma hyopneumoniae detection by PCR. Results suggested that tracheobronchial secretions and bronchial swabs conferred the highest sensitivity in vivo and post-mortem, respectively.
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Mycoplasma hyopneumoniae , Pneumonia Suína Micoplasmática , Animais , Mycoplasma hyopneumoniae/genética , Pneumonia Suína Micoplasmática/diagnóstico , Reação em Cadeia da Polimerase/métodos , SuínosRESUMO
Coronavirus disease 2019 (COVID-19) is transmitted person-to-person mainly by close contact or droplets from respiratory tract. However, the actual time of viral shedding is still uncertain as well as the different routes of transmission. We aimed to characterize RNA shedding from nasopharyngeal and rectal samples in prolonged cases of mild COVID-19 in young male soldiers. Seventy patients from three different military locations were monitored after recommending to follow more strict isolation measures to prevent the spread of the virus. Then, nasopharyngeal, rectal, and blood samples were taken. SARS-CoV-2 RNA was detected by RT-PCR and specific antibodies by chemiluminescent immunoassays. The median nucleic acid conversion time (NACT) was 60 days (IQR: 7-85 days). Rectal swabs were taken in 60â% of patients. Seven patients (10â%) were positive in nasopharyngeal and rectal swabs, and five (7.14â%) remained positive in rectal swabs, but negative in nasopharyngeal samples. Four patients (5.71â%) that had been discharged, were positive again after 15 days. No significant difference was found in nucleic acid conversion time between age groups nor clinical classification. Maintaining distancing among different positive patients is essential as a possible re-exposure to the virus could cause a longer nucleic acid conversion time in SARS-COV-2 infections.
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Anticorpos Antivirais/sangue , COVID-19 , Imunoglobulina G/sangue , RNA Viral/análise , COVID-19/diagnóstico , COVID-19/prevenção & controle , Surtos de Doenças , Humanos , Masculino , Militares , SARS-CoV-2 , Eliminação de Partículas ViraisRESUMO
Los trabajadores de la industria están expuestos a distintos tipos de riesgos, incluyendo la exposición laboral a agentes biológicos como virus, bacterias, hongos, parásitos, esporas o toxinas capaces de originar algún tipo de infección, enfermedad o toxicidad. Gran variedad de estos patógenos ha sido identificada sobre distintas superficies dentro de instalaciones de trabajo, persistiendo en algunos casos luego de las jornadas de limpieza habituales, e incluso sobreviviendo por largos períodos de tiempo. Los hallazgos preliminares indican que los procesos de higiene en dos industrias permitieron disminuir de manera estadísticamente significativa la presencia de E. Coli y Sars-Cov-2, en las superficies dentro de las instalaciones. Por el contrario, en una tercera industria se observó que los procesos de higiene y limpieza no lograron reducir eficazmente la presencia de los patógenos La auditoría de higiene en instalaciones de industrias textiles debe incluir la capacidad de hallar e identificar los peligros biológicos que aún estén presentes en superficies, una vez ejecutados los protocolos rutinarios de limpieza y desinfección establecidos por la organización. Para esta labor proponemos la práctica complementaria de tres procedimientos: la determinación microbiológica, mediante torundas o placas de contacto, la determinación visual con luz ultravioleta, para comprobar el grado de eficacia de la limpieza, y la determinación específica, consistente en la detección de ARN de virus SARS-CoV-2 (causante del COVID-19) en muestras ambientales de superficies por el método de PCR en tiempo real(AU)
Industrial workers are exposed to different types of risks, including occupational exposure to biological agents such as viruses, bacteria, fungi, parasites, spores or toxins capable of causing some type of infection, disease or toxicity. A great variety of these pathogens have been identified on different surfaces within work facilities, persisting in some cases after the usual cleaning days, and even surviving for long periods of time. Preliminary findings indicate that hygiene processes in two industries allowed a statistically significant decrease in the presence of E. Coli and Sars-Cov-2, on surfaces within the facilities. On the contrary, in a third industry it was observed that hygiene and cleaning processes failed to effectively reduce the presence of pathogens Hygiene audit in textile industry facilities should include the ability to find and identify biological hazards that are still present on surfaces, once the routine cleaning and disinfection protocols established by the organization have been executed. For this work, we propose the complementary practice of three procedures: microbiological determination, using swabs or contact plates, visual determination with ultraviolet light, to verify the degree of cleaning efficiency, and specific determination, consisting of RNA detection. of SARS-CoV-2 virus (causing COVID-19) in environmental samples of surfaces by the real-time PCR method(AU)
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Humanos , Medidas de Segurança/organização & administração , Riscos Ocupacionais , Escherichia coli , Reação em Cadeia da Polimerase em Tempo Real , SARS-CoV-2 , COVID-19/prevenção & controle , Peru , Indústria Têxtil , Raios Ultravioleta , Desinfecção , Exposição OcupacionalRESUMO
Background: Coronavirus disease 2019 (COVID-19) is a global health problem, which is challenging healthcare worldwide. In this critical review, we discussed the advantages and limitations in the implementation of salivary diagnostic platforms of COVID-19. The diagnostic test of COVID-19 by invasive nasopharyngeal collection is uncomfortable for patients and requires specialized training of healthcare professionals in order to obtain an appropriate collection of samples. Additionally, these professionals are in close contact with infected patients or suspected cases of COVID-19, leading to an increased contamination risk for frontline healthcare workers. Although there is a colossal demand for novel diagnostic platforms with non-invasive and self-collection samples of COVID-19, the implementation of the salivary platforms has not been implemented for extensive scale testing. Up to date, several cross-section and clinical trial studies published in the last 12 months support the potential of detecting SARS-CoV-2 RNA in saliva as a biomarker for COVID-19, providing a self-collection, non-invasive, safe, and comfortable procedure. Therefore, the salivary diagnosis is suitable to protect healthcare professionals and other frontline workers and may encourage patients to get tested due to its advantages over the current invasive methods. The detection of SARS-CoV-2 in saliva was substantial also in patients with a negative nasopharyngeal swab, indicating the presence of false negative results. Furthermore, we expect that salivary diagnostic devices for COVID-19 will continue to be used with austerity without excluding traditional gold standard specimens to detect SARS-CoV-2.
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COVID-19 , RNA Viral , Humanos , SARS-CoV-2 , Saliva , Manejo de EspécimesRESUMO
Coxsackievirus A24 variant (CVA24v), the main causative agent of acute hemorrhagic conjunctivitis (AHC), can be isolated from both the eyes and lower alimentary tract. However, the molecular features of CVA24v in feces is not well-documented. In this study, we compared the VP1 and 3C sequences of CVA24v strains isolated from feces during AHC epidemics in Cuba in 1997, 2003, and 2008-2009 with those obtained from conjunctival swabs during the same epidemic period. The sequence analyses of the 3C and VP1 region of stool isolates from the three epidemics showed a high degree of nucleotide identity (ranging from 97.3-100%) to the corresponding conjunctival isolates. The phylogenetic analysis showed that fecal CVA24v isolates from the 1997 and 2003 Cuban outbreaks formed a clade with CVA24v strains isolated from conjunctival swabs in Cuba and other countries during the same period. There were three amino acid changes (3C region) and one amino acid change (VP1 region) in seven CVA24v strains isolated sequentially over 20 days from fecal samples of one patient, suggesting viral replication in the intestine. Despite these substitutions, the virus from the conjunctival swab and fecal samples were genetically very similar. Therefore, fecal samples should be considered as a reliable alternative sample type for the routine molecular diagnosis and molecular epidemiology of CVA24v, also during outbreaks of AHC.
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Background: Although the nasopharyngeal swab (NPS) is the reference sampling method for the detection of SARS-Cov-2, it is not always possible to collect NPS in some patients. Saliva represents an interesting sampling method because it is less invasive and more convenient in patients with nasal or pharyngeal lesions. Objective: To compare the RT-qPCR test performances of saliva samples with nasal mid-turbinate swab (NMTS) and NPS samples in a cohort of ambulatory patients suspected of having COVID-19. Study Design: For each of the 112 enrolled patients, NPS, NMTS, and saliva samples were collected and tested for SARS-Cov-2 detection using three different target genes (RdRP, N and E genes) by RT-qPCR. Results: Among the positive samples (56/112), saliva samples showed a lower percentage of SARS-Cov-2 detection compared to NPS samples, (85.7 vs. 96.4%), while still a lower percentage was observed for NMTS samples (78.6%). In average, saliva samples showed higher Ct values for all tested target genes, compared to those from NPS and NMTS samples. Conclusions: By using the AllplexTM 2019-nCoV Assay Kit, saliva samples showed lower sensitivity for SARS CoV-2 compared to NPS samples; however, the not detected cases had lower viral burden in NPS samples (CT values >33) representing an interesting alternative sampling method in patients in which it is not possible to take a NPS sample.
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CDC and WHO guidelines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis only recommend synthetic fiber swabs for nasopharyngeal (NP) sampling. We show that cotton-tipped plastic swabs do not inhibit PCR and have equivalent performance to rayon swabs. Cotton-tipped plastic swabs are massively produced worldwide and would prevent swab supply shortages under the current high SARS-CoV-2 testing demands, particularly in developing countries.
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Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/instrumentação , Infecções por Coronavirus/diagnóstico , Equipamentos para Diagnóstico/provisão & distribuição , Equipamentos Descartáveis/provisão & distribuição , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real/instrumentação , Betacoronavirus/genética , COVID-19 , Teste para COVID-19 , Celulose/provisão & distribuição , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/virologia , Fibra de Algodão/provisão & distribuição , Humanos , Nasofaringe , Pandemias , Plásticos/provisão & distribuição , Pneumonia Viral/virologia , RNA Viral/análise , Reação em Cadeia da Polimerase em Tempo Real/métodos , SARS-CoV-2 , Manejo de Espécimes/instrumentação , Manejo de Espécimes/métodosRESUMO
PURPOSE: Intraabdominal abscess (IAA) is a feared complication after laparoscopic appendectomy (LA) for complicated appendicitis. Benefits of obtaining intraoperative culture swabs (ICS) still remain controversial. We aimed to determine whether ICS modify the rate and management of IAA after LA for complicated appendicitis. METHODS: A consecutive series of patients who underwent LA for complicated appendicitis from 2008 to 2018 were included. The cohort was divided into two groups: group 1 (G1), with ICS, and group 2 (G2), without ICS. Demographics, operative variables, pathogen isolation, antibiotic sensitivity, and postoperative outcomes were analyzed. RESULTS: A total of 1639 LA were performed in the study period. Of these, 270 (16.5%) were complicated appendicitis; 90 (33%) belonged to G1 and 180 (67%) to G2. In G1, a higher proportion of patients had generalized peritonitis (G1, 63.3%; G2, 35%; p < 0.01). Seventy-two (80%) patients had positive cultures in G1. The most frequently isolated bacteria were E. coli (66.7%), Bacteroides spp. (34.7%), and Streptococcus spp. (19.4%). In 26 (36%) patients, the initial empiric antibiotic course was modified due to bacterial resistance. The rate of IAA was higher in patients with ICS (G1, 21.1%; G2, 9.4%; p = 0.01). IAA was treated similarly in both groups. A different type of bacteria was isolated in 7 (53.8%) patients with new culture swabs. CONCLUSIONS: Obtaining ICS in LA for complicated appendicitis with further antibiotic adjustment to the initial pathogen did not lower the incidence of postoperative IAA and did not modify the treatment needed for this complication.
Assuntos
Abscesso Abdominal/microbiologia , Apendicectomia/métodos , Apendicite/microbiologia , Apendicite/cirurgia , Técnicas Bacteriológicas/instrumentação , Cuidados Intraoperatórios , Laparoscopia , Complicações Pós-Operatórias/microbiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-IdadeRESUMO
BACKGROUND: Apparently, laryngeal swabs (LS) are more sensitive than nasal swabs (NS) and allow earlier detection of Mycoplasma hyopneumoniae by PCR. However, antecedents about the compared detection of M hyopneumoniae with NS and LS in growing pigs, from naturally infected herds, are lacking in the literature. Thus, this study compared the PCR detection of M hyopneumoniae from NS and LS in pigs of various ages. METHODS: A longitudinal study was performed at two farms where NS and LS were collected from three consecutive groups of 20 pigs at 3, 6, 10, 16 and 22 weeks of age. All samples were analysed by nested PCR for M hyopneumoniae detection. RESULTS: The probability of PCR detection of M hyopneumoniae was higher in LS for pigs of all ages (odds ratio (OR)=1.87; 95 per cent confidence interval (CI) 1.31-2.67) and in 22-week-old pigs (OR=4.87; 95 per cent CI 2.86-8.30). The agreement between both sample types was low to moderate (kappa 0.087-0.508), highlighting that M hyopneumoniae does not appear to colonise the respiratory tract in a generalised and consistent fashion. CONCLUSIONS: The results suggest that LS could be employed at different ages to achieve greater bacterial detection. Considering that LS is a minimally invasive, highly sensitive sample compared with the traditional NS, it could be suggested to employ this sample type for M hyopneumoniae detection in naturally infected pigs.