Percentage Of Positive Samples Research Articles

EDNA monitoring detects new outbreak wave of corallivorous seastar (Acanthaster cf. solaris) at Lizard Island, Great Barrier Reef

Crown-of-thorns seastar (CoTS, Acanthaster cf. solaris) outbreaks remain a significant cause of coral loss on the Great Barrier Reef (GBR) and across the West-Pacific Ocean. Previous outbreaks on the GBR have only been discovered once fully established, which constrains opportunities for effective control. Early detection of outbreaks would provide an important opportunity for early intervention and increase understanding of outbreak cause(s). Here, we assess the utility of environmental DNA (eDNA) monitoring to detect the initiation of a population outbreak at Lizard Island over five years (2019–2023), compared with density estimates obtained using Scooter-Assisted Large Area Diver-based (SALAD) surveys. At each of the five eDNA sampling sites, 30 replicate samples were collected annually and analysed with CoTS-specific primer sets and digital droplet PCR. Both methods detected distinct increases in CoTS densities from 2020/21 onwards, indicating the start of a new population outbreak. A large part of the observed variation in eDNA (expressed as the percentage of positive samples) was explained by changes in recorded CoTS density, confirming that eDNA data provide a quantitative estimate for adult CoTS abundance. SALAD surveys and eDNA are new and complementary monitoring methods that facilitate early detection of CoTS outbreaks, which will enable more effective management intervention.

Mycotoxin patulin contamination in various fruits and estimating its dietary impact on the consumers: From orchard to table

The present research examined patulin's presence across the whole supply chain of selected fruits. A comprehensive analysis was conducted on 442 samples of fruits (oranges, apples, apricots, lemons, and guava) to determine the presence of patulin contamination. This analysis used Liquid Chromatography (HPLC) with a UV detector. The findings indicate that 17, 23, and 28 % of selected fruit samples tested positive for patulin levels in farm, transportation, and market samples. However, the sample collected during the transportation step showed that 56 % (percentage of positive samples) of fruits have patulin levels greater than 50 μg/kg, and 41 % (percentage of positive samples) have greater levels than 50 μg/kg in market samples. The findings of the one-way analysis of variance indicated that no statistically significant variation existed between the amounts of patulin across the various stages of the food supply chain system (p > 0.05). Nevertheless, the analysis of the correlation study, namely Kendall's tau_b and Spearman's rho, denote a robust association between the levels of patulin and the food supply system. The apple samples exhibited the most significant average dietary intake of patulin, with an average value of 0.11 μg/kg bw/day. The maximum mean hazard quotient (HQ) of 0.28 was also recorded. The prevalence and incidence of patulin in specific fruits were found to be relatively high, and it was observed that market samples had elevated levels of patulin in the selected fruits.

Wastewater surveillance of enteric viruses in eastern Argentina: High rates of detection and first report of NoV GI.5 and GII.20

Individuals infected with enteric viruses excrete them in their feces for an extended period, whether symptomatic or asymptomatic. This characteristic, combined with the capability of these viruses to persist in the environment, forms the core of our research. The objective of our study was to investigate the presence of viruses associated with diarrhea and hepatitis: Hepatitis A virus (HAV), Hepatitis E virus (HEV), Norovirus GI (NoV GI), Norovirus GII (NoV GII), and Rotavirus (RV) by RT-real time PCR, in untreated wastewater samples (n=100) collected in the period July 2020 to August 2021 from two low-income neighborhoods in the district of La Plata, Buenos Aires, Argentina. Globally, the percentage of positive samples was 25 % for HEV, 27 % for RV, 14 % for NoV GII, 1 % for NoV GI, and no detectable samples were found for HAV. HEV, RV, and NoV GII were detected in most of the studied months, with the highest detection rates of RV and NoV GII during the winter season. Regarding RV positive samples, the gene encoding the VP8* protein of three samples was sequenced and phylogenetic analysis revealed that the detected strains belonged to genotypes P[8] and P[3]. Additionally, four NoV strains were also genetically characterized by amplifying a fragment corresponding to the ORF-1/ORF-2 junction region. The identified strains were NoV GI.5, NoV GII.4, NoV GII.17 and NoV GII.20. Our results provide relevant information and serve as scientific evidence of the importance of considering wastewater analysis as a feasible strategy to determine the circulation of enteric viruses in the population, with the further benefit of predicting emerging strains. Moreover, this study represents the first report of the circulation of NoV GII.20 and GI.5 genotypes in our country.

TRENDS OF SYPHILIS AMONG BLOOD DONORS AT A TERTIARY CARE CENTER IN WESTERN RAJASTHAN: AN OBSERVATIONAL STUDY WITH SPECIAL REFERENCE TO THE IMPACT OF COVID-19

Objective: This observational study aimed to determine the prevalence and trends of syphilis among blood donors at a tertiary care center in Western Rajasthan and assess the impact of the COVID-19 pandemic on testing and diagnosis rates. Methods: The study included 208,264 blood donors who donated blood at the blood center from 2017 to 2022. The blood samples were tested for all mandatory transfusion-transmitted infections (TTIs), including syphilis. Data were analyzed using descriptive statistics. Results: The overall seropositivity of TTIs was 1.97%, with a moderate prevalence of syphilis among blood donors. The percentage of syphilis-positive samples varied each year, with the highest percentage in 2020 (1.02%) and the lowest in 2019 (0.68%). The study found decreasing trends of syphilis prevalence among blood donors over the years. However, the percentage of positive samples in 2020 was higher than in the other years, potentially due to the impact of the COVID-19 pandemic. Conclusion: The study provides valuable insights into the prevalence and trends of syphilis among blood donors in Western Rajasthan and the impact of the COVID-19 pandemic on testing and diagnosis rates. The findings may inform strategies for maintaining access to sexual and reproductive health services during times of crisis, as well as for the prevention and control of syphilis in the region.

Occurrence and distribution of Salmonella serovars associated with human infection isolated from irrigation waters and food-producing animals in southern Italy: eleven-year monitoring (2011-2021).

Salmonella is one of the main zoonotic agents causing foodborne diseases in Europe. The main reservoirs of the infection are represented by domestic and wild animals, and the infection occurs by direct contact or following the consumption of contaminated food or water. The study aimed to evaluate the presence of Salmonella spp. in food-producing animals and irrigation waters in southern Italy and the serovar distribution. From 2011 to 2021, a total of 473 samples from 6 different animal species (bovine, buffalo, goat, ovine, swine, poultry, and wild boars) and 313 irrigation water samples were collected and analyzed. The overall percentage of positive samples was 56.87% in organs, 50.85% in feces, and 20.45% in irrigation waters. By animal species, the most frequently detected serovar was Salmonella Typhimurium in bovine (17.39%), in buffalo (13.10%) and swine (28.21%), and S. Kentucky (24.78%) in poultry. The subspecies diarizonaeIIIb was frequently detected in goats (40.00%) and ovine (83.33%), while salamaeII (14.12%) and diarizonaeIIIb (11.76%) were frequently isolated in wild boars. In the irrigation water samples, the most frequently detected serovar was S. Napoli (25%). Results revealed that, although in Europe, control strategies aimed at preventing the spread of Salmonella have been implemented, the prevalence of this pathogen in food-producing animals and irrigation waters is high. Considering the risk to public health associated with the contamination of products or foods, more stringent control interventions are needed at primary production and along the food chain.

First molecular detection of shiga toxin-producing Escherichia coli in dogs from serbia: a potential threat to human health?

Shiga toxin‑producing Escherichia coli (STEC) are considered one of the most significant E. coli pathotypes transmitted by food, causing life‑threatening conditions in children and elderly people. The aim of this study was to investigate the presence and determine the prevalence of STEC in dogs in Serbia by conventional PCR method, targeting three major virulence genes (stx1, stx2, and eae). The overall percentage of positive samples was 12.87% (13/101), with the stx2 gene, the more potent of the two toxins, found in all the positive samples. The finding of eae gene in combination with stx genes (8/13) within the same genetic pool implies the potential presence of enterohemorrhagic E. coli or the potential emergence of these strains, considering an efficient mechanism of horizontal transfer of three major virulence genes. Our results also highlight dogs' lifestyle as a risk factor for STEC colonisation. These E. coli strains, according to our results, are more likely to be found in dogs living outdoors than those kept in house. Due to significant prevalence of STEC in dogs determined in this research and due to close contact between dogs and humans, dogs could be considered a source of human infections.

Investigating the Spread of Antimicrobial Drug-Resistant Microorganisms in Dairy Sheep Farms: A Follow-Up Study

Recently, we investigated the spread of antimicrobial drug-resistant (AMR) microorganisms in five dairy sheep farms in Greece to identify indicators for improved field surveillance. The high percentage of samples of feeds and milk positive to Escherichia coli and Staphylococci, including AMR isolates, recorded in this previous study generated the interest to further investigate the parameters likely to affect positivity of these certain indicators in the same farms. For this reason, 76 samples were collected, comprising milk collected from the raw milk tank (n = 5), swabs from milking shells (n = 48), feeds (n = 6), and home-grown feeds (n = 17). Samples were processed for the detection of the pathogens mentioned above and the assessment of AMR using conventional microbiology and the polymerase chain reaction. The overall percentage of positive samples was 71.1%. The percentage of isolates that were characterised as AMR of those detected was 27.8% (30% Staphylococci, 21.4% E. coli). The results indicate that AMR testing in milking shell swabs is advisable for improving AMR stewardship and should be regarded as complimentary to testing samples from the raw milk tank, because these may not depict the microbial burden of milking shells. Furthermore, the spread and antimicrobial resistance of tested bacteria in feeds are characterised by considerable variability and should therefore be assessed longitudinally.

Rapid, accurate, and novel diagnostic technique for respiratory pathogens: Clinical application of loop-mediated isothermal amplification assay in older patients with pneumonia, a multicenter prospective observational study.

Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method using only one type of enzyme that can amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. Chips for Complicated Infection Detection (CCID) is based on LAMP. This study translate CCID into clinical application and evaluate its diagnostic value for pneumonia. Eighty one older patients with pneumonia were prospectively enrolled from January 1 to July 23, 2021, and 57 sputum/airway secretion and 35 bronchoalveolar lavage fluid samples were collected and analyzed by CCID and conventional microbiological tests (CMTs). Samples were collected, transported, monitored, and managed by a multidisciplinary team using a sample management information system. CCID turnaround time was 50 min, and the detection limit was 500 copies/reaction. The percentage of positive samples was significantly higher using CCID than CMTs, especially for Klebsiella pneumoniae (odds ratio [OR], 9.0; 95% confidence interval [CI], 1.1-70.5; p < 0.05), Enterococcus faecalis (OR, ∞; p < 0.01), Stenotrophomonas maltophilia (OR, ∞; p < 0.01), fungi (OR, 26.0; 95% CI, 3.6-190.0; p < 0.01), and viruses (CCID only; p < 0.01). In addition, the percentage of positive results was significantly higher using CCID than CMTs in patients who used antibiotics for more than 3 days (91.9% vs. 64.9%; p < 0.01). Analyzing clinical impact, 55 cases (59.8%) benefited from CCID. CCID allows the rapid and accurate detection of pneumonia in older patients. Moreover, this technique is less affected by previous antibiotic treatment and can improve patient care.

A global dataset for prevalence of Salmonella Gallinarum between 1945 and 2021

Pullorum disease and fowl typhoid are among the most significant poultry diseases worldwide. However, the global burden of these diseases remains unknown. Most importantly, the parameters contributing to the prevalence of Salmonella Gallinarum variants are not well documented. Therefore, in this study, we present a systematic review and meta-analysis of the global prevalence of Salmonella Gallinarum during 1945–2021. In total, 201 studies were identified for qualitative analysis (>900 million samples). The meta-analysis was subjected to over 183 screened studies. The global prevalence of S. Gallinarum (percentage of positive samples in total samples) was 8.54% (95% CI: 8.43–8.65) and showed a V-shaped recovery over time. Pullorum disease is most common in Asia, particularly in eastern China. Further investigations on chicken origin samples revealed significant differences in S. Gallinarum prevalence by gender, breed, raising mode, economic use, and growth stage, indicating a critical role of vertical transmission. Together, this study offered an updated, evidence-based dataset and knowledge regarding S. Gallinarum epidemics, which might significantly impact decision-making policy with targeted interventions.

Development of Nonstructural Protein-Based Indirect ELISA to Identify Elephant Endotheliotropic Herpesvirus (EEHV) Infection in Asian Elephants (Elephas maximus).

Simple SummaryElephant endotheliotropic herpesvirus hemorrhagic disease (EEHV-HD) is one of the most important viral infectious diseases in young Asian elephants (Elephas maximus). To date, adult elephants that have been infected with EEHV have displayed mostly mild clinical signs, while they are believed to serve as EEHV shedders to other elephants. Hence, the diagnostic tools employed for monitoring EEHV-active infection are important. In this study, partial EEHV-DNA polymerase (DNApol) nonstructural proteins (NSPs) were used to detect anti-EEHV antibodies through the use of an in-house indirect enzyme-linked immunosorbent assay (ELISA), in comparison to the results of a PCR test. The developed EEHV-DNApol ELISAs demonstrated values of 77.9% sensitivity and 87.7% specificity, respectively. The results demonstrated that the sera obtained from elephants that exhibited no clinical signs of EEHV infection, and who were negative according to PCR tests of the blood, reported values of 14% seropositivity for EEHV-DNApol. Our results indicate that these asymptomatic, active EEHV-infected elephants could likely serve as the source of EEHV shedding in the herd. The developed EEHV-DNApol NSPs-based ELISA test employed in the present study may be of use for routine monitoring and identification of EEHV shedders in elephant herds, and could be an alternative diagnostic tool for EEHV detection in Asian elephants.Disease caused by elephant endotheliotropic herpesvirus (EEHV) infection is the most highly fatal hemorrhagic disease in Asian elephant calves worldwide. To date, adult elephants that have been infected with EEHV have predominantly displayed mild clinical signs, while they are believed to serve as EEHV shedders to other elephants. Hence, the diagnostic tools employed for monitoring EEHV-active infection are considered vitally important. In this study, partial EEHV-DNA polymerase (DNApol) nonstructural proteins (NSPs) were used to detect anti-EEHV antibodies through the use of an in-house indirect enzyme-linked immunosorbent assay (ELISA). The results were then compared to those obtained from a PCR test. In this study, a total of 175 serum samples were collected from Asian elephants living in elephant camps located in Chiang Mai and Lampang Provinces, Thailand. The elephants were aged between 2 and 80 years old. The overall percentages of positive samples by the PCR and EEHV-DNApol ELISA tests were 4% (21/175) and 12% (21/175), respectively. The ELISAs demonstrated values of 77.9% (95% posterior probability interval (PPI) = 52.5–95%) sensitivity and 87.7% (PPI = 82.5–91.9%) specificity, respectively. Accordingly, the sera obtained from the elephants exhibiting no clinical signs of EEHV infection, and those who were negative according to PCR tests, revealed a value of 14% seropositivity for EEHV-DNApol. Our results indicate that these asymptomatic, active EEHV-infected elephants could likely serve as a source of EEHV shedding within elephant herds. Consequently, the developed EEHV-DNApol NSPs-based ELISA test employed in the present study may be of use for routine monitoring and identification of EEHV shedders in elephant herds, and could be an alternative diagnostic tool for EEHV detection in Asian elephants.

Impacts of a post-transport/pre-processing rest period on the growth performance, anthelmintic efficacy, and serum metabolite changes in cattle entering a feed yard.

A total of 80 crossbred, high-risk heifers (initially 250 ± 4.2 kg BW), were transported from an Oklahoma City, Oklahoma sale barn to the Kansas State University Beef Cattle Research Center. Cattle were unloaded and randomly placed into one of four receiving pens and provided ad libitum hay and water. Each pen was randomly assigned to one of the four rest times before processing: (1) immediately upon arrival (0); (2) after a 6-h rest period (6); (3) after a 24-h rest period (24); and (4) after a 48-h rest period (48). After all cattle were processed, heifers were allotted into individual pens with ad libitum access to a receiving ration and water. Heifers were weighed individually on d 0, 7, 14, 21, 28, and 35 to calculate average daily gain (ADG). Feed added and refusals were measured daily to determine dry matter intake (DMI). A fecal egg count reduction test and analysis of blood serum metabolites were also conducted. All data were analyzed using the GLIMMIX procedure of SAS (v. 9.4, Cary, NC) with individual animal as the experimental unit. Processing time did not impact (P > 0.05) heifer BW or ADG. From d 0 to 35, DMI decreased linearly (P = 0.027) as rest time increased. The number of days for heifers to reach a DMI of 2.5% BW was linearly increased (P = 0.023) as rest time increased. There was no evidence of differences (P ≥ 0.703) among rest times for feed efficiency. While morbidity did not differ between treatments (P > 0.10), mortality increased linearly (P = 0.026) as the time of rest increased. A significant processing time × day interaction (P < 0.0001) was observed for the prevalence of fecal parasites, where the percentage of positive samples was significantly lower 14-d after anthelmintic treatment, regardless of the processing time. Serum IBR titer for heifers processed at either 0 or 6-h upon arrival was significantly higher (P < 0.01) on d 35 compared to d 0. Heifers processed after a 48-h rest period had significantly higher glucose values (P < 0.01) on d 0 compared to heifers processed at 0, 6, or 24-h. In summary, rest time prior to processing did not impact receiving calf growth performance. A 6-h rest period upon arrival appeared to be most beneficial to DMI. Anthelmintic treatment at processing reduced the parasitic load in heifers processed at all times. Vaccine titer did not increase after initial processing in heifers processed 24- or 48-h after arrival, indicating the seroconversion of IBR antibodies during the longer rest period.

Seroprevalence of COVID-19 in Riyadh city during the early increase of COVID-19 infections in Saudi Arabia, June 2020

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged in December 2019 and caused a global pandemic of the Coronavirus Disease 2019 (COVID-19). More than 170 million cases have been reported worldwide with mortality rate of 1–3%. The detection of SARS-CoV-2 by molecular testing is limited to acute infections, therefore serological studies provide a better estimation of the virus spread in a population. This study aims to evaluate the seroprevalence of SARS-CoV-2 in the major city of Riyadh, Saudi Arabia during the sharp increase of the pandemic, in June 2020. Serum samples from non-COVID patients (n = 432), patients visiting hospitals for other complications and confirmed negative for COVID-19, and healthy blood donors (n = 350) were collected and evaluated using an in-house enzyme-linked immunosorbent assay (ELISA). The overall percentage of positive samples was 7.80% in the combined two populations (n = 782). The seroprevalence was lower in the blood donors (6%) than non-COVID-19 patients (9.25%), p = 0.0004. This seroprevalence rate is higher than the documented cases, indicating asymptomatic or mild unreported COVID-19 infections in these two populations. This warrants further national sero-surveys and highlights the importance of real-time serological surveillance during pandemics.

SARS-CoV-2 RNA Recovery from Air Sampled on Quartz Fiber Filters: A Matter of Sample Preservation?

The airborne route of transmission of SARS-CoV-2 was confirmed by the World Health Organization in April 2021. There is an urge to establish standardized protocols for assessing the concentration of SARS-CoV-2 RNA in air samples to support risk assessment, especially in indoor environments. Debates on the airborne transmission route of SARS-CoV-2 have been complicated because, among the studies testing the presence of the virus in the air, the percentage of positive samples has often been very low. In the present study, we report preliminary results on a study for the evaluation of parameters that can influence SARS-CoV-2 RNA recovery from quartz fiber filters spotted either by standard single-stranded SARS-CoV-2 RNA or by inactivated SARS-CoV-2 virions. The analytes were spiked on filters and underwent an active or passive sampling; then, they were preserved at −80 °C for different numbers of days (0 to 54) before extraction and analysis. We found a mean recovery of 2.43%, except for the sample not preserved (0 days) that showed a recovery of 13.51%. We found a relationship between the number of days and the recovery percentage. The results presented show a possible issue that relates to the quartz matrix and SARS-CoV-2 RNA recovery. The results are in accordance with the already published studies that described similar methods for SARS-CoV-2 RNA field sampling and that reported non-detectable concentrations of RNA. These outcomes could be false negatives due to sample preservation conditions. Thus, until further investigation, we suggest, as possible alternatives, to keep the filters: (i) in a sealed container for preservation at 4 °C; and (ii) in a viral transport medium for preservation at a temperature below 0 °C.

Environmental detection of Mycoplasma hyopneumoniae in breed-to-wean farms

There is a need to develop cost-effective and non-invasive approaches to sample large populations to evaluate the disease status of breeding herds. In this study we assessed the detection of the M. hyopneumoniae genetic material in environmental surfaces and air of farrowing rooms, and skin (udder, snout and vagina) of lactating sows at weaning, in farms having different M. hyopneumoniae infection status (negative, positive sub-clinically infected and positive clinically affected). Mycoplasma hyopneumoniae was detected in air, air deposition particles, dam and stall surfaces of the positive clinically affected herd. Mycoplasma hyopneumoniae could only be detected in dam and stall surfaces in sub-clinically infected herds. Mycoplasma hyopneumoniae was not detected in all samples collected in the negative herd. The cycle threshold of the positive PCR samples were not statistically different between sample types or farms. However, a significant difference (p < 0.05) was observed in the percentage of positive samples between the positive clinically affected farm and the rest. Likewise, M. hyopneumoniae was detected in the environment and surfaces at weaning in positive breeding herds. Further testing and validation is recommended for environmental and surface samples before they can be employed as part of the M. hyopneumoniae diagnostic process. In addition, results from this study highlight potential sources of M. hyopneumoniae infection for piglets in breeding herds, especially during an outbreak.

SARS-CoV-2 detection in bioaerosols using a liquid impinger collector and ddPCR.

The airborne route is the dominant form of COVID‐19 transmission, and therefore, the development of methodologies to quantify SARS‐CoV‐2 in bioaerosols is needed. We aimed to identify SARS‐CoV‐2 in bioaerosols by using a highly efficient sampler for the collection of 1–3 µm particles, followed by a highly sensitive detection method. 65 bioaerosol samples were collected in hospital rooms in the presence of a COVID‐19 patient using a liquid impinger sampler. The SARS‐CoV‐2 genome was detected by ddPCR using different primer/probe sets. 44.6% of the samples resulted positive for SARS‐CoV‐2 following this protocol. By increasing the sampled air volume from 339 to 650 L, the percentage of positive samples went from 41% to 50%. We detected five times less positives with a commercial one‐step RT‐PCR assay. However, the selection of primer/probe sets might be one of the most determining factor for bioaerosol SARS‐CoV‐2 detection since with the ORF1ab set more than 40% of the samples were positive, compared to <10% with other sets. In conclusion, the use of a liquid impinger collector and ddPCR is an adequate strategy to detect SARS‐CoV‐2 in bioaerosols. However, there are still some methodological aspects that must be adjusted to optimize and standardize a definitive protocol.

Detection of Epstein-Barr virus in gastric adenocarcinoma: qPCR and FISH comparison

EBV-associated gastric cancer accounts for about 10% of all gastric carcinomas worldwide. We aimed to verify the prevalence of EBV in gastric adenocarcinoma samples using FISH and qPCR and comparing the results obtained by both techniques. Gastric cancer samples from 191 cases were analyzed. The FISH assay was performed to detect small EBV RNAs (EBER1) and qPCR was performed to detect the EBV-EBNA-1 gene region. Cohen’s kappa index and the chi-square test were used to compare the methodologies and investigate correlations with the clinical-pathological data of the gastric adenocarcinoma patients. Most of the patients were men, and the average age was 60 years. The intestinal subtype cancer presented more aggressive stages with 90% of patients having a reactive FISH for EBV (EBV+), although the virus infection frequency in epithelial gastric tissue was only 1%. No positive association with clinicopathological features and EBV+ was found by FISH. Using qPCR analysis, the percentage of positive samples was lower (52.4%), and a positive association was found in samples from older patients (> 60 years). Interestingly, 71 qPCR-negative cases were detected by FISH in the presence of non-epithelial cells and in 10 qPCR-positive cases with no evidence of EBV according to FISH. The concordance between the two techniques was low, with only 57.6%. FISH is more informative for associating the gastric carcinoma with EBV positivity in tumor/epithelial cells; however, qPCR can provide relevant information regarding the progression and characteristics of neoplasia.

Diagnostic value of detection of pathogens in bronchoalveolar lavage fluid by metagenomics next-generation sequencing in organ transplant patients with pulmonary infection

To evaluate the diagnostic value of metagenomics next-generation sequencing (mNGS) in detecting pathogens in bronchoalveolar lavage fluid (BALF) for pulmonary infection in solid organ transplant patients in intensive care unit (ICU). A retrospective study was conducted, the BALF samples from 46 patients with post organ transplant pneumonia/suspected pneumonia admitted to the Department of Critical Care Medicine of the First Affiliated Hospital of University of Science and Technology of China from August 2018 to August 2021 were collected, all tested by simultaneous mNGS and conventional comprehensive microbial test (CMT), and the results of CMT were used as the reference standard to compare the differences in the diagnostic value of mNGS and CMT for pulmonary infections in solid organ transplant patients, and to analyze the diagnostic value of mNGS for mixed infections. (1) Pneumonia pathogens: a total of 31 pathogens were detected in 35 patients, including bacteria (16 species), fungi (9 species) and viruses (6 species). Among them, 25 pathogens were detected by mNGS and CMT, and only 19 pathogens were detected by mNGS. Among the microorganisms isolated by mNGS method, the detection rates of Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae were higher [51.4% (18/35), 42.9% (15/35), 31.4% (11/35), respectively]; Candida albicans, Aspergillus and Pneumocystis carinii were the most commonly detected fungi [31.4% (11/35), 22.9% (8/35), 22.9% (8/35), respectively]; 20 patients were positive for the virus, and the most commonly detected viruses were cytomegalovirus, herpesvirus and EB virus [28.6% (10/35), 20.0% (7/35), 17.1% (6/35), respectively]. In addition, one case of Brucella was detected by mNGS. (2) Diagnostic efficiency: as far as bacterial detection is concerned, 20 cases of negative results were obtained by CMT detection of 35 samples included in the study, and a total of 10 cases of positive results were obtained by mNGS detection of negative samples; the percentage of mNGS positive samples was significantly higher than that of CMT positive samples [odds ratio (OR) = 5.5, 95% confidence interval (95%CI) = 1.2-24.8, P = 0.02]. When compared with CMT, the sensitivity and specificity of mNGS were 93.3% and 50.0%, and the positive predictive value (PPV) and negative predictive value (NPV) were 58.3%, 91.1%. As far as fungal detection was concerned, there was no significant difference in the percentage of positive samples between the two methods (OR = 1.5, 95%CI = 0.5-4.2, P = 0.60); the sensitivity and specificity of mNGS were 72.2% and 64.7%, and the PPV and NPV were 68.4%, 68.8%; CMT test of the 35 included samples produced 17 negative results, and mNGS test of the negative samples produced 6 positive results. A total of 20 patients tested positive for the virus by mNGS. In addition, 23 patients (65.7%) were diagnosed with pulmonary mixed infection. The use of mNGS to detect pathogens in BALF can improve the sensitivity and specificity of bacterial identification of pulmonary infection in critically ill organ transplant patients, and mNGS has obvious advantages in detecting virus and identifying mixed infections.

A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic.

The outbreak of coronavirus infectious disease-2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the world. Several studies have shown that detecting SARS-CoV-2 in untreated wastewater can be a useful tool to identify new outbreaks, establish outbreak trends, and assess the prevalence of infections. On 06 May 2021, over a year into the pandemic, we conducted a scoping review aiming to summarize research data on SARS-CoV-2 in sewage. Papers dealing with raw sewage collected at wastewater treatment plants, sewer networks, septic tanks, and sludge treatment facilities were included in this review. We also reviewed studies on sewage collected in community settings such as private or municipal hospitals, healthcare facilities, nursing homes, dormitories, campuses, airports, aircraft, and cruise ships. The literature search was conducted using the electronic databases PubMed, EMBASE, and Web Science Core Collection. This comprehensive research yielded 1090 results, 66 of which met the inclusion criteria and are discussed in this review. Studies from 26 countries worldwide have investigated the occurrence of SARS-CoV-2 in sewage of different origin. The percentage of positive samples in sewage ranged from 11.6 to 100%, with viral concentrations ranging from ˂LOD to 4.6 × 108 genome copies/L. This review outlines the evidence currently available on wastewater surveillance: (i) as an early warning system capable of predicting COVID-19 outbreaks days or weeks before clinical cases; (ii) as a tool capable of establishing trends in current outbreaks; (iii) estimating the prevalence of infections; and (iv) studying SARS-CoV-2 genetic diversity. In conclusion, as a cost-effective, rapid, and reliable source of information on the spread of SARS-CoV-2 and its variants in the population, wastewater surveillance can enhance genomic and epidemiological surveillance with independent and complementary data to inform public health decision-making during the ongoing pandemic.Graphic Supplementary InformationThe online version contains supplementary material available at 10.1007/s12560-021-09498-6.

PARÁSITOS EN REPTILES DEL CENTRO DE CONSERVACIÓN Y REHABILITACIÓN DE ANIMALES DE VIDA SILVESTRE DE UNA UNIVERSIDAD PÚBLICA-BRASIL

The medical clinic for reptiles has grown in recent years, whether by attending free-living animals in rehabilitation centers or by acquiring them as pets. The knowledge of the parasitic fauna of the Reptilia Class is important for the identification of pathogenic agents and effective therapy. Fecal samples were collected from 35 animals of the Orders Crocodylia (N=3), Squamata (N=3) and Testudines (N=29) attended from 2013 to 2018 at the Center for Conservation and Rehabilitation of Wild Animals (PRESERVAS) of the Universidade Federal do Rio Grande do Sul (UFRGS). Fecal samples were processed by the methods of Willis, Lutz and Sheather at the Laboratory of Helminthology at UFRGS. The percentage of positive samples was 17.14% (6/35): three Trachemys dorbogni (Dumeril & Bibron 1835) presenting Serpinema spp., Physaloptera spp. and Strongyloidea, respectively; two Caiman latirostris (Daudin, 1802) with Strongyloides spp. and Augusticaecum spp., respectively, and Iguana iguana (Linnaeus, 1758) with Eimeria spp. This study expands the list of parasites in reptiles from the state of Rio Grande do Sul.

SIGNIFICANCE OF SEROLOGICAL MONITORING FOR POULTRY ORNITOBACTERIOSIS THERAPY

One of the main problems of poultry diseases is respiratory diseases. Among them a special place is occupied by ornithobacteriosis (ORT). Losses from ORT consist of: direct losses as a result of the disease - death of chickens, increased culling due to lameness, low live weight gain (up to 40%), reduction of carcass categories, reduction of egg production by 6-20%; indirect losses associated with the immune-suppressive effect of ornithobacteria, which increase the risk of other infections and prevent the formation of post-vaccination immunity. The diagnosis is established on the basis of epizootological data, clinical signs, pathological and anatomical changes, bacteriological and serological tests, positive bioassay. In most cases, infections caused by ornithobacteria are not diagnosed in time, the pathogen is difficult to isolate due to complications of other pathogens, or because experts are currently insufficiently aware of the ability of ORT to cause disease. ORT can be isolated by bacteriological method only at an early stage of the disease. The most relevant method of diagnosis is PCR. The advantage of the method is not only the isolation of DNA of individual cells of the pathogen in the sample, but also the ability to detect all serotypes. In addition, PCR is a successful diagnosis in the detection of ORT nucleic acid not only in tissue samples, but also in feces, eggs, dust, which is important for timely diagnosis. Enzyme-linked immunosorbent assay (ELISA) is used to control the presence of ornithobacteriosis in bird. The presence of antibodies to this pathogen in poultry of many species indicates its wide circulation.&#x0D; Thus, when conducting serological monitoring of blood serum from different age groups of broilers aged 1-44 days, the percentage of positive samples ranged from 40 to 100, which indicates the circulation of the field strain of the pathogen ornithobacteriosis. The percentage of positive serum from broilers to ORT was: from 1 to 5 days - from 88 to 50, from 6 to 10 days serum were negative, while at 17, 21 days and from 32 days to the end of cultivation (44 days) – 100 %. The percentage of positive batches at the end of fattening ranged from 42-53 days in the range from 75 to 100%, indicating the circulation of the field strain of the ornithobacteriosis pathogen antibiotic therapy against this disease.