Highest Number Of Positive Samples Research Articles

First Molecular Detection of SARS-CoV-2 in Sewage and Wastewater in Ghana.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is shed in the stool of infected individuals and can be detected in sewage and wastewater contaminated with infected stool. This study is aimed at detecting the virus and its potential survival in sewage and wastewater in Ghana. The cross-sectional study included samples from 16 validated environmental surveillance sites in 7 regions of Ghana. A total of 354 samples composed of wastewater (280) and sewage (74) were collected from November 2020 to November 2022. Overall, 17% of the samples were positive for SARS-CoV-2 by real-time PCR, with 6% in sewage and 11% in wastewater. The highest number of positive samples was collected from the Greater Accra Region (7.3%) with the least recorded in the Bono East Region (0.6%). Further characterization of the positive samples using the next-generation sequencing (NGS) approach yielded two variants: Alpha (B.1.1.7) and Delta (AY.36). Attempts to isolate SARS-CoV-2 in the Vero cell line were not successful probably due to the low viral load concentrations (Ct values > 35) or prolonged exposure to high temperatures rendering the virus noninfectious. Our findings suggest that SARS-CoV-2 RNA in sewage and wastewater may not be infectious, but the prevalence shows that the virus persists in the communities within Ghana.

Isolation and identification of <i>Brucella abortus</i> and <i>B. melitensis</i> in ruminants with a history of abortion: the first report from Eritrea

Brucella species have never been isolated or documented in Eritrea. The present study was initiated to isolate and identify Brucella species that infect livestock in Eritrea. A total of 316 blood sera, 137 milk, 71 vaginal swabs, a placental cotyledon, and a fetal stomach content were sampled from 208 goat, 102 sheep, and 6 cattle. Series testing protocol starting with Rose Bengal plate test, followed by c-ELISA, culturing, and then multiplex AMOS-PCR was followed. The purpose-sampling strategy was applied, and animals with a history of abortion in the last three weeks were sampled to increase the probability of capturing Brucella species. Isolation was conducted on Burcella media agar, and Brucella broth was added with Brucella selective supplement containing 2,500IU polymyxin B, 12,500IU bacitracin, 50.0 mg cycloheximide, 2.5mg nalidixic acid, 50,000 IU nystatin, and 10.0 mg vancomycin. Accordingly, 41 animals were positive for a series of serological tests. The overall Brucella seropositive detection proportion was 13.0%, and goats constituted the majority 78% (n=32). The highest number of positive samples were from the Maekel region. Six Brucella organisms were successfully isolated from two milk samples, two vaginal swabs, one placental cotyledon, and one fetal stomach content obtained from seropositive animals. Among the  Brucella isolates, five were B. melitensis, while the remaining one was B. abortus as per the multiplex AMOS- PCR assay. The present  study documented the first B. abortus and B. melitensis isolates in Eritrea. Milk, vaginal discharges, placental cotyledon, and aborted  fetus were identified as sources of Brucella for livestock and livestock keepers. Besides, the findings highlight a reasonable proportion of  the reproductive disorders in cattle and small ruminants could be due to brucellosis. This calls for public sector intervention to control the  diseases in animals and to enhance community awareness of good practices such as drinking boiled milk and avoiding contact with  infected tissues and body discharges to prevent potential public health risks from zoonosis. 

Use of immuno-flow cytometry and real-time PCR disclose the epidemiological behaviour of Erwinia amylovora populations during the winter in Portuguese pear orchards

AbstractThe persistence and progression of Erwinia amylovora in naturally infected orchards is still not fully understood and the majority of studies have been carried out under controlled or artificial infections. A major hurdle stems from the inability to characterize the viability of the bacterium in its natural state. Most standard tests, including real-time qPCR, fail to differentiate live from dead cells, while culture dependent methods lack sensitivity. Even in orchards with recurring infections, the detection of E. amylovora is erratic. Immuno-flow cytometry (IFCM) is considered a high throughput tool in clinics and food industry but has been rarely used as diagnostic test for plant pathogens. Two pear orchards with fire blight history, located in the central part of Portugal, were selected for epidemiological monitoring between February and June, from 2019 to 2022. A total of 440 samples were tested using EPPO standard diagnostic protocols. To address the epidemiological behaviour of E. amylovora, we devised an IFCM test using specific monoclonal antibodies and viability dyes, validated in a subset of 149 samples, testing positive in routine diagnostic tests. Our IFCM test was able to differentiate live and dead E. amylovora in naturally infected samples with concentrations as low as 3.54 × 104 cell·mL−1, confirming positive results for 91% these samples, while 19.4% were considered positive by isolation, 38% using conventional PCR and 95% for real-time qPCR. Temporal analysis showed the highest number of positive samples regardless of the method employed in April, May and June, while viability values measured with IFCM were the highest in April, coinciding with the exit of dormancy and early flowering of pear trees. Integrative analysis of E. amylovora viability and population dynamics over the growing season allowed identification of distinct outbreak risks associated with these Portuguese pear orchards.

B-158 Application of Statistical Analysis as a Tool to Monitor the Variation of SARS-CoV-2 and Other Respiratory Viruses

Abstract Background After the emergence of SARS-CoV-2 and its worldwide spread, only a few studies have correlated its co-circulation with other respiratory viral pathogens (RVP). The current report aims to identify the pattern of SARS-CoV-2 positivity in individuals co-infected with influenza A (FluA), influenza B (FluB), or respiratory syncytial virus (RSV) in São Paulo, Brazil. Methods Study Population and Characteristics: This study was a retrospective analysis from a clinical laboratory database in São Paulo, Brazil from January 15 to March 10, 2022. Test results for respiratory viral co-infections were recorded for individuals with SARS-CoV-2, FluA, FluB, or RSV. Nasopharyngeal swab samples were evaluated for the molecular diagnosis of respiratory virus infections using a real-time multiplex-PCR panel to search for specific genes for the detection of SARS-CoV-2, FluA, FluB, and RSV. Only samples positive for one or more pathogens (including SARS-CoV-2) were included in the study. We further stratified the specimens by SARS-CoV-2 positivity, comparing those that also tested positive for an RVP in each group. Statistical Analysis: Kruskal-Wallis analysis of variance followed by Dunn’s multiple comparison tests was used. Results with P < 0.05 were considered statistically significant. Georeferencing analysis of SARS-CoV-2 mono-infection or co-infection with another respiratory virus was performed using an online available software application. Results A total of 28 932 samples were positive for at least one RVP, meeting the study criteria. Among those, a total of 93.13% were from individuals diagnosed with SARS-CoV-2 only, 2.99% positive for SARS-CoV-2 and FluA, and 0.99% positive for SARS-CoV-2 and RSV. There was no significant difference observed between genders nor individuals with mono-infection or co-infection. The analysis of age group showed a significant variation in positive cases between SARS-CoV-2 vs SARS-CoV-2 and FluA in the 0 to 10-year-old population (P = 0.017) and between SARS-CoV-2 vs SARS-CoV-2 and RSV in the 0 to 5-year-old population (P = 0.018). The highest number of positive samples for both SARS-CoV-2 and RSV was detected in the southern region of São Paulo (55.7%), compared to the north and east regions (44.3%). Conclusion Differences in diagnostic patterns of COVID-19 compared to other respiratory viral infections RVP co-infections are important for a better understanding of clinical outcomes, improved patient management, and better public health planning.

Legionella spp. Monitoring in the Water Supply Systems of Accommodation Facilities in Sardinia, Italy: A Two-Year Retrospective Analysis.

Travel-associated Legionnaires' disease is a significant public health concern worldwide. A high number of cases are reported every year among travellers who stay at guest houses, hotels, and spas. Indeed, hot water systems, showers, and air-conditioning systems can be contaminated by Legionella, which grows at 25-42 °C. Studies have shown that in Sardinia, especially during the summer months, the water circulation in the hotels' pipes is exposed to extremely high temperatures. As a result, this study was conducted to assess the colonization of hotel water systems by Legionella in Sardinia, concerning a recent EU directive 2020/2184 for drinking water with a limit of 1000 CFU /L. Methods. A total of 112 accommodation facilities were analyzed, of which 61.3% were found to be colonized with Legionella, and out of a total of 807 samples, 32.5% were positive for Legionella presence. The results showed a higher number of positive samples in the summer season. This was also associated with the higher concentration presence of >1000 CFU/L in the samples. Consequently, this study confirms that local hotel operators should improve their water safety and prevention plans, especially in spring and summer.

Analyzing the Frequency of Premalignant Lesions and Oral Malignancy in Indian Subjects Attending Outpatient Department From the Low Socioeconomic Group.

Oral cancer is a rapidly growing disease among Indian subjects mainly in the low socioeconomic group. Socially and economically marginalized subjects are at high risk for oral cancer because of smoke and smokeless tobacco consumption. To evaluate the prevalence of precancerous lesions and oral cancerand evaluate tobacco as a causative factor in Indian subjects visiting the outpatient department of the institute. Around 658 subjects were analyzed forfrequency of premalignant lesions and oral malignancy in Indian subjects from the low socioeconomic group. Patientsvisited for pain, burning, or ulceration in the oral cavity were clinically assessed for any tissue growths, leathery alterations, ulcerative changes,and white or red lesions in the oral cavity. Results:The overall prevalence of smokeless and smoking tobacco was 78.8% (n=518) and 65.2% (n=429) respectively in the present study. Around 39.8% (n=262) of samples were stained positive for precancerous and cancerous lesions of the oral cavity. The highest number of positive samples were from buccal mucosa with 36.2% (n=238) subjects and 6.1% (n=40) for labial mucosa. Oral cancer is highly prevalent in Indian subjects owing to high tobacco consumption rates and habits warranting the cessation center a priority. Also, early detection and screening are vital to attaining better outcomes. More tobacco cessation centers areneededto stop the habit and early diagnosis will prevent dysplastic changes.

Evaluating the virulence factors of Salmonella typhi isolated from children suffering from severe diarrhea using molecular genetic techniques

Abstract. Jaber AS. 2023. Evaluating the virulence factors of Salmonella typhi isolated from children suffering from severe diarrhea using molecular genetic techniques. Biodiversitas 24: 3543-3549. Salmonella enterica subsp. serotype Typhi is the bacteria that causes typhoid fever. Although its prevalence has significantly decreased in affluent nations, it continues to be a leading cause of illness and mortality in emerging nations. Because of changes in ecology, eating habits, and agricultural and food production techniques, Salmonella infections have increased in frequency in industrialized countries. This study aimed to use qualitative RT-PCR (based on the ttr gene) and conventional PCR to measure the frequency of Salmonella typhi in Iraqi children with chronic diarrhea (based on PagN and TolC genes). This study included 100 stool samples collected from children suffering from continuous diarrhea. Those samples were inoculated on CHROM-agar and incubated 37°C for 18-24 hours, then Salmonella was identified using a Vitek 2 compact system. DNA has been extracted, and qRT-PCR has been done to detect Salmonella sp. by the amplification of the ttr gene. Then PCR also done to amplify TolC and PagN genes. The amplified products then sequenced to reveal mutations within the amplified regions. The results of PagN gene showed 41 samples were positive, and 40 samples were positive for TolC. Results of qRT-PCR according to the ttr gene amplification showed 38 samples positive. The blood group O+ showed a higher number of positive samples (13), and males showed higher positive samples than females (23 and 15, respectively). Sequencing revealed various number of mutations within the amplified regions of both PagN and TolC in the samples which isolated from children with the longest period of illness.

Canine circovirus genomic characterization in dogs with and without diarrheal syndrome in Medellín, Colombia.

Canine circovirus (CanineCV) is an emerging agent described for the first time in 2011, it infects domestic and wild canids, mainly associated with gastrointestinal signs; however, it has also been reported in samples obtained from animals without clinical signs, so its pathogenesis and epidemiology are still poorly understood. In Colombia, the CanineCV was first reported in 2020 from CPV-2 positive dogs. In the present work, CanineCV was detected in 30% of fecal samples obtained from dogs with or without diarrhea, in the city of Medellín, Colombia. No coinfection with CPV-2 was found. The highest number of positive samples was found in the subgroup of animals with diarrhea. Phylogenetic and evolutionary analyses confirmed the separation of the CanineCV genomes into five different clades with a European origin of the Colombian viruses and at least two different introductions of the CanineCV into the country. Our results highlight the importance of the CanineCV in Colombian dog populations and the need for continue surveillance of emerging pathogens in canine populations.

Phenotypic Characterization of Virulence Factors in Multidrug-Resistant Salmonella typhi Serovars Isolated from Clinical Specimens in Bauchi Metropolis

Background: Typhoid fever is one of the most common infectious diseases in developing countries including Nigeria. Globally, typhoid fever is an important cause of morbidity and mortality in many regions of the world. People most at risk for serious complications due to Salmonella infections include older adults, pregnant women, infants, children, and people who have compromised immune systems.
 Design and Duration: The study involves the collection of blood and stool specimens across all ages and gender between ages 0-70 years who present with fever and diarrhoea among other symptoms of typhoid in selected hospitals within Bauchi from January 2019 to August 2020.
 Aim: The aim of this research is to phenotypically characterize virulence factors in Multidrug-Resistant Salmonella typhi serovars isolated from clinical specimens in selected hospitals within Bauchi.
 Materials and Methods: A total of 518 blood and stool specimens were collected from selected health facilities within Bauchi metropolis to determine the presence of Salmonellae pathogens. Phenotypic identification of Salmonella typhi was performed using standard microbiological procedures, virulence factors were investigated and the Kirby Bauer Disk Diffusion method was used for the determination of the antimicrobial susceptibility and Multidrug Resistant pattern of the isolates.
 Results and Discussion: Highest number of specimens collected was among patients with fever. Age groups 31-40 and 0-10 had the highest frequencies of occurrence respectively while age group 61-70 had the least. There was no significant difference between the age group and the number of isolates as p>0. 05. Highest frequency of S. typhi was found within the Female gender while Males recorded the lowest. The stool had the highest number of positive samples 31(21.6%) and blood had the least 17(4. 5%). Flagella was present in 18(37.5%) of 48 virulence isolates and was the most prevalent. Haemolysin was the least prevalent 4(8.3%) in all the isolates in our study. In the present study, 37(77.0%) of S. typhi isolates were resistant to 2 or more antimicrobial agents (Multidrug resistance). The highest resistance was observed in Oxacillin 46(95.8%). The isolates were sensitive to Ciprofloxacin 31(64.5%), Colistin Sulphate 29(60.4%), and Ceftriaxone 28(58.3%). All isolates 48(100%) were Multidrug-resistant and sensitive to Ciprofloxacin, Colistin Sulphate, Ceftriaxone, and Amikacin.
 Conclusion: This study established that Salmonella typhi was more prevalent in the middle age group, female out-patient with most cases of fever, diarrhoea, and sometimes both. Most of the Salmonella typhi recovered from this study were more from stool than blood. Of all of the isolates in this study 48(9.2%) produced two or more virulent factors, with flagella as the commonest across all the MDR isolates; which is indicative of a significant relationship between virulence factors and multidrug resistance. The emergence of multidrug-resistant strains of Salmonella has added to the urgent need for the development of more effective control measures.

Dithiotreitol pre-treatment of synovial fluid samples improves microbiological counts in peri-prosthetic joint infection

PurposeSynovial fluid cultures of periprosthetic joint infections (PJI) may be limited by bacteria living in the fluids as biofilm-aggregates. The antibiofilm pre-treatment of synovial fluids with dithiotreitol (DTT) could improve bacterial counts and microbiological early stage diagnosis in patients with suspected PJI.MethodsSynovial fluids collected from 57 subjects, affected by painful total hip or knee replacement, were divided into two aliquots, one pre-treated with DTT and one with normal saline. All samples were plated for microbial counts. Sensitivity of cultural examination and bacterial counts of pre-treated and control samples were then calculated and statistically compared.ResultsDithiothreitol pre-treatment led to a higher number of positive samples, compared to controls (27 vs 19), leading to a statistically significant increase in the sensitivity of the microbiological count examination from 54.3 to 77.1% and in colony-forming units count from 1884 ± 2.129 CFU/mL with saline pre-treatment to 20.442 ± 19.270 with DTT pre-treatment (P = 0.02).ConclusionsTo our knowledge, this is the first report showing the ability of a chemical antibiofilm pre-treatment to increase the sensitivity of microbiological examination in the synovial fluid of patients with peri-prosthetic joint infection. If confirmed by larger studies, this finding may have a significant impact on routine microbiological procedures applied to synovial fluids and brings further support to the key role of bacteria living in biofilm-formed aggregates in joint infections.

Ready-to-eat foods as a possible source of Helicobacter pylori

Ready-to-eat (RTE) foods can be risky for consumers as they are not usually cooked or heated before consumption. We set out to assess RTE foods available in the Czech market network as a possible source of Helicobacter pylori. Attention was paid to RTE foods containing at least one ingredient of animal origin. A total of 50 food samples were chosen and divided into 3 categories. The “composite foods” category (n = 29) included sandwiches (n = 5), baguettes (n = 11), tortillas (n = 6), buns (n = 2), toast bread (n = 1), croissant (n = 1), bagels (n = 2), and pretzel (n = 1). The “salads” category included commercially produced mixed salads (n = 13). The “other” category (n = 8) included smoked salmon (n = 2), smoked mackerel (n = 2), smoked herring (n = 1), marinated salmon (n = 1), surimi (n = 1) and carpaccio (n = 1). The samples were analysed using nested-PCR. The glmM gene of H. pylori was detected in 50% (n = 25) of all samples. The “composite foods” category had the highest number of positive samples 58.6% (n = 21), followed by “other” with 50% (n = 4), and “salads” with 30.8% (n = 4). The results of our study showed that consumers eating RTE foods may be exposed to a risk of infection with H. pylori.

Comparison of Different Copromicroscopic Techniques in the Diagnosis of Intestinal and Respiratory Parasites of Naturally Infected Dogs and Cats.

Simple SummaryAppropriate fecal examinations are very important for diagnosing parasitic diseases in dogs and cats. In this study, four different conventional copromicroscopic techniques (flotation, McMaster, Mini-FLOTAC, and Baermann) were evaluated for their performance in detecting intestinal and extra-intestinal parasitic elements in canine and feline feces. Stool samples from 100 dogs and 105 cats, respectively, were tested with the above techniques. Flotation and Mini-FLOTAC gave the best results in detecting intestinal and respiratory parasitoses by Toxocara spp., Toxascaris leonina, Ancylostomatidae, Cystoisospora spp., Trichuris vulpis and Capillaria spp., whereas the Baermann test was the best method for the detection of infections caused by metastrongyloids. These data provide useful information for veterinary clinicians on the most appropriate techniques to use during diagnostic paths in clinical settings.Several copromicroscopic techniques, including tools belonging to the FLOTAC group, are available for the qualitative and/or quantitative diagnosis of canine and feline parasitoses. The present study was carried out to compare the diagnostic performance of different copromicroscopic methods for detecting common intestinal and extra-intestinal parasites of dogs and cats. Fecal samples of 100 dogs and 105 cats were randomly selected from different regions of Italy. All samples were subjected to conventional flotation, McMaster, Mini-FLOTAC, and Baermann. Fifty-six dogs and twenty-five cats were found positive to at least one technique, and, among them, flotation (55% and 20.9% of the dogs and cats, respectively) and Mini-FLOTAC (52% and 20.9% of the dogs and cats, respectively) detected the highest number of positive samples. Larvae of the feline metastrongyloids Aelurostrongylus abstrusus and Troglostrongylus brevior were identified only using the Baermann test in two (1.9%) and one (0.9%) cat respectively. No larvae were found with the Baermann examination of dog feces or any of the other methods. The present results show that the Mini-FLOTAC represents a possible alternative to conventional flotation in clinical settings for the detection of intestinal and respiratory parasites e.g., Toxocara spp., Toxascaris leonina, Ancylostomatidae, Cystoisospora spp., Trichuris vulpis and Capillaria spp., although Baermann’s test remains the most recommended technique for the diagnosis of infections caused by metastrongyloid lungworms.

Seroprevalence and predisposing factors of rabies antibodies in unvaccinated dogs in Sierra Leone.

This study determines the seroprevalence and associated factors of rabies in unvaccinated dogs in Sierra Leone. Rabies control is poorly coordinated in Sierra Leone which was ranked as the third hungriest country in the world. Due to limited access to rabies vaccines, the need for comprehensive serological data on dogs for control of the disease is expedient. A random multistage technique considering high, medium and low incident areas of rabies cases in dog-populated communities was adopted. Samples were collected from dogs with owners which were at least 1-year old. Samples were analysed using a commercial ELISA in accordance to manufacturer's instructions. 25.2% of the total 270 samples tested positive for the presence of rabies antibodies. Kenema district had the highest number of positive samples, followed by the Bombali district and Moyamba district the least. Predisposing factors, including sex, the status of castration, the type of settlement, district and the availability of fences at locations where dogs are kept, had significant effects (p<0.05) on the exposure of dogs to rabies. The 25.2% antibody seroprevalence obtained is very low. Concerted effort should be made to enhance rabies vaccination through an awareness campaign and provision of vaccine to dog owners. Good waste disposal and management practices to reduce open garbage disposal in communities will go a long way to limit the stray-dog population and minimize rabies outbreaks especially in third-world countries where rabies vaccines are not accessible.

Presence and Virulence Characteristics of Shiga Toxin Escherichia coli and Non-Shiga Toxin-Producing Escherichia coli O157 in Products from Animal Protein Supply Chain Enterprises in South Africa.

Consumption of food that is contaminated with Shiga toxin–producing Escherichia coli (STEC) has been linked to serious foodborne disease outbreaks. Our aim was to provide a descriptive study on the presence and virulence factors of STEC and non-STEC O157 isolates recovered from 2017 diverse meat and meat product samples from all provinces of South Africa (n = 1758) and imported meat from South Africa's major ports of entry (n = 259). A cross-sectional study was undertaken to analyze raw intact meat, raw processed (nonintact) meat, and ready-to-eat (RTE) meat from cattle, game, sheep, pork, and poultry. Isolation was performed using International Organization for Standardization-based microbiological techniques, while detection and characterization were performed using real-time PCR (RT-PCR) and conventional PCR targeting the stx1, stx2, eae, and ehxA genes. A total of 28 of 1758 (1.59%; confidence interval [CI] 1.1–2) samples from the domestic market tested positive (n = 10 Escherichia coli O157:H7; n = 14 Escherichia coli O157: non-H7; and n = 4 non-O157 STEC), while 4/259 (1.54%; CI 0.4–4) samples from ports of entry tested positive for Escherichia coli O157:H7 based on RT-PCR. On average, diverse samples from domestic meat and meat products from cattle showed the highest number of positive samples (22/1758; 1.3%; CI 0.8–2). RT-PCR detected more positive samples (n = 32) compared with culture (n = 17). Sixteen different virulence factor combinations were observed. Our findings demonstrate a relatively low presence of diverse STEC strains along the meat value chain. To our knowledge, this is the first extensive report in South Africa to analyze STEC and non-STEC O157 from local and imported samples from many animal species. This is important as it reveals virulence factors in STEC strains circulating in meat and meat products in South Africa, which contribute to the risk of infection.

Residuos de antimicrobianos encontrados en aves de corral comercializadas en tiendas minoristas de la zona Metropolitana de Guadalajara, Jalisco

The increased demand to produce large quantities of meat and animal products for human consumption has promoted the indiscriminate use of antimicrobials. The increased use of these substances in the production of poultry, has negative consequences on Public Health due to the fact that the accumulation of antimicrobial residues in the organs and tissues of poultry might reach the consumer. The presence of antimicrobial residues can cause problems of hypersensitivity in humans, or the emergence of antimicrobial resistant pathogens. The purpose of this work was to assess the presence of antimicrobial residues in kidney and muscle tissue of poultry, commercialized in four municipalities of the Metropolitan Area of Guadalajara, Jalisco. The results show that kidney samples had a higher number of positive results compared to muscle tissue. Inhibitors of the folate pathway (sulfamethazine) were the antimicrobials with the highest number of positive results in kidney samples. In contrast, in muscle tissue, β-Lactam (penicillin) were the antimicrobials with the highest number of positive samples. Regarding the analysis of the results by municipalities, it was observed that one of them showed a greater number of positive samples for all the classes of antimicrobials evaluated. This work shows the presence of antimicrobial residues in kidney and muscle tissues of poultry, commercialized in retail sites. Therefore, it is necessary to increase efforts to monitor and control the use of antimicrobial in poultry farms.

Sampling Methods and Risk Stratification Regarding Environmental Contamination by SARS-CoV-2.

Transmission of COVID-19 through close contact and droplets is well established, but the influence of aerosol and surface contamination remains to be determined. Literature is scarce and inconsistent about the viable virus particles free-distance from infected patients, as well as about different swabbing methods for surface contamination evaluation. The aim of this study was to evaluate the most sensitive method for the assessment of surface contamination, classify the likelihood of environmental contamination in risk zones and compare the environmental contamination between oxygenation and ventilatory support. Swabs from potentially contaminated surfaces in a COVID-19 ward, with patients treated with different types of oxygen and ventilatory support, were collected. Three types of swabs were compared in order to evaluate the most sensitive collection method. For risk zone categorization, areas were divided according to the distance from the patient. Of the 63 swabs collected, 17 (27%) tested positive for the presence of SARS-CoV-2. The highest positivity rate was observed with the sterile premoistened swab with saline (n = 8; 38%), but without statistically significant differences. The highest number of positive samples were collected from the high-risk zones, specifically those located one meter from the patient (n = 13; 48%), with statistically significant differences. Only the rooms of patients supported with non-invasive ventilation or high-flow nasal cannula had evidence of bedroom contamination, with 45% and 27% of swab positivity, with statistically significant differences. Our findings favour the premoistened swab without transport medium for surface contamination assessment, even though without statistical differences. A statistically significant trend supporting the division in risk zones, according to the distance from the patient, was also identified. The higher positivity rate from the non-invasive ventilation and high-flow nasal cannula bedrooms suggests a significant association between ventilatory strategies and surface contamination, probably due to higher particle dispersion. Our findings support the use of the sterile premoistened swab without preservation medium, the classification of risk areas considering the distance from the patient, and the variability of RNA dispersion between oxygenation and ventilatory support.

Unraveling the Contact Network Patterns between Commercial Turkey Operation in North Carolina and the Distribution of Salmonella Species.

Salmonellosis originating from poultry poses a significant threat to human health. Surveillance within production is thus needed to minimize risk. The objectives of this work were to investigate the distribution of Salmonella spp. from a commercial turkey operation and describe the animal movement patterns to investigate the association between contact network structure and Salmonella infection status. Four years of routine growout farm samples along with data on facility location, time since barns were built, production style, and bird movement data were utilized. From all of the surveillance samples collected, Salmonella serotyping was performed on positive samples and results showed that the most represented groups were C1 (28.67%), B (24.37%) and C2 (17.13%). The serovar Infantis (26.44%) was the most highly represented, followed by Senftenberg (12.76%) and Albany (10.93%). Results illustrated the seasonality of Salmonella presence with a higher number of positive samples being collected in the second half of each calendar year. We also demonstrated that Salmonella was more likely to occur in samples from older farms compared to farms built more recently. The contact network connectivity was low, although a few highly connected farms were identified. Results of the contact network showed that the farms which tested positive for Salmonella were not clustered within the network, suggesting that even though Salmonella dissemination occurs via transferring infected birds, for this study case it is unlikely the most important route of transmission. In conclusion, this study identified seasonality of Salmonella with significantly more cases in the second half of each year and also uncovered the role of between-farm movement of birds as not a major mode of Salmonella transmission.

Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan.

BackgroundPakistan has been experiencing intervals of sporadic cases and localized outbreaks in the last two decades. No proper study has been carried out in order to find out the environmental burden of toxigenic V. cholerae as well as how temporal and environmental factors associated in driving cholera across the country.MethodsWe tested waste water samples from designated national environment surveillance sites in Pakistan with RT-PCR assay. Multistage sampling technique were utilized for samples collection and for effective sample processing Bag-Mediated Filtration system, were employed. Results were analysed by district and month wise to understand the geographic distribution and identify the seasonal pattern of V. cholera detection in Pakistan.ResultsBetween May 2019, and February 2020, we obtained and screened 160 samples in 12 districts across Pakistan. Out of 16 sentinel environmental surveillance sites, 15 sites showed positive results against cholera toxigenic gene with mostly lower CT value (mean, 34±2) and have significant difference (p < 0.05). The highest number of positive samples were collected from Sindh in month of November, then in June it is circulating in different districts of Pakistan including four Provinces respectively.ConclusionV. cholera detection do not follow a clear seasonal pattern. However, the poor sanitation problems or temperature and rainfall may potentially influence the frequency and duration of cholera across the country. Occurrence of toxigenic V. cholerae in the environment samples showed that cholera is endemic, which is an alarming for a potential future cholera outbreaks in the country.

Gut microbiota and urinary tract infections in children

Aim. To evaluate the role of intestinal dysbiosis in the development of urinary tract infections in children admitted to a multidisciplinary hospital.Materials and Methods. We performed a bacteriological analysis of 2,694 urine samples collected from ≤ 3-years-old children who have been admitted to a multidisciplinary hospital (Kemerovo, Russian Federation). Urine specimens were inoculated by the 4-sector technique. Concurrently, we quantified the intestinal microbiota and its antimicrobial resistance in 100 children with urinary tract infections.Results. Titers of pathogenic microbes significantly differed in patients from distinct units (p = 0.02). The highest number of positive samples was detected in the neonatal pathology and neonatal intensive care units (43.8% each) as well as urology unit (37.9%). The most frequent pathogens belonged to Enterobacteriaceae family, in particular Escherichia coli, Klebsiella spp., Enterobacter spp., and Proteus spp. All studied children (100/100) suffered from intestinal dysbiosis. Titers of Bifidobacterium spp. and Lactobacillus spp. were reduced to 6 (5.0; 8.0) and 5 (4.0; 6.0) lg CFU/g, respectively. In 89.2% children, Escherichia coli lac+ levels were elevated to 9-10 lg CFU/g. Of note, 18.9% children had high Escherichia coli lac- titers [8 (6.0; 9.0) lg] and 24.3% had high Escherichia coli hly+ titers [5 (4.5; 6.0) lg] in the intestine. We have also found a high frequency (44.6%) and density [8.1 (7.0; 8.5) lg] of Klebsiella spp., in the intestinal mucosa of such patients. Notably, Enterobacter spp. and Proteus spp. were abundant [7 (5.0; 8.0) CFU/g] in the intestinal microbiota of 10.8% children. The prevalence of resistance strains in the studied setting reached 63%.Conclusions. More than 75% children with urinary tract infections suffer from intestinal dysbiosis. The microbiome of these patients was predominantly composed of Enterobacteriaceae and was characterized by high titers of Escherichia coli lac+, Klebsiella spp., Enterobacte spp., and Proteus spp. Similar profile of antimicrobial resistance in urinary and intestinal isolates of enterobacteria suggests intestinal microbiome as the main source of pathogens causing urinary tract infections in children. 

Determination of Urinary Mycotoxin Biomarkers Using a Sensitive Online Solid Phase Extraction-UHPLC-MS/MS Method.

In the course of assessing the human exposure to mycotoxins, biomarker-based approaches have proven to be important tools. Low concentration levels, complex matrix compositions, structurally diverse analytes, and the large size of sample cohorts are the main challenges of analytical procedures. For that reason, an online solid phase extraction-ultra high-performance liquid chromatography-tandem mass spectrometry (online SPE-UHPLC-MS/MS) method was developed, allowing for the sensitive, robust, and rapid analysis of 11 relevant mycotoxins and mycotoxin metabolites in human urine. The included spectrum of analytes comprises aflatoxin M1 (AFM1), altenuene (ALT), alternariol monomethyl ether (AME), alternariol (AOH), citrinin (CIT) and its metabolite dihydrocitrinone (DH-CIT), fumonisin B1 (FB1), ochratoxin A (OTA), and zearalenone (ZEN) as well as α- and β-zearalenol (α- and β-ZEL). Reliable quantitation was achieved by means of stable isotope dilution, except for ALT, AME and AOH using matrix calibrations. The evaluation of method performance displayed low limits of detection in the range of pg/mL urine, satisfactory apparent recovery rates as well as high accuracy and precision during intra- and interday repeatability. Within the analysis of Zimbabwean urine samples (n = 50), the applicability of the newly developed method was shown. In addition to FB1 being quantifiable in all analyzed samples, six other mycotoxin biomarkers were detected. Compared to the occurrence rates obtained after analyzing the same sample set using an established dilute and shoot (DaS) approach, a considerably higher number of positive samples was observed when applying the online SPE method. Owing to the increased sensitivity, less need of sample handling, and low time effort, the herein presented online SPE approach provides a valuable contribution to human biomonitoring of mycotoxin exposure.