Microbiological Tests Research Articles

Campylobacter: understanding its role as the primary bacterial cause of food-borne illnesses – current state of knowledge

Introduction Campylobacteriosis, caused primarily by Campylobacter jejuni and Campylobacter coli, is a significant public health concern worldwide. Since 2007 it has been the most frequently reported zoonotic disease in humans across the European Union. Campylobacteriosis is also the leading cause of bacterial diarrhea. Aim of the study This review aims to provide a comprehensive overview of the epidemiology, clinical manifestations, transmission dynamics, diagnostic approaches, and prevention strategies associated with Campylobacter infections. Brief description of the state of knowledge The transmission of Campylobacter spp. typically occurs via the fecal-oral route, with contaminated food, especially poultry, and water serving as common sources of infection. Notably, Campylobacter infections exhibit distinct seasonal patterns and demographic trends, with children and young adults being particularly susceptible. Clinical manifestations range from mild gastrointestinal symptoms to more severe complications, such as reactive arthritis, and Guillain-Barré syndrome. Diagnosis usually relies on microbiological testing. Some of these methods require specialized cultivation techniques, with challenges posed by the phenotypic diversity of Campylobacter species. Summary Effective surveillance and prevention strategies are essential for mitigating the burden of campylobacteriosis and its associated sequelae on both individual and population health. Current research focuses on improving preventive measures, underscoring the importance of advancing public health strategies, and further studies into the epidemiology, pathogenesis, and treatment options. These efforts are crucial for effectively addressing Campylobacteriosis and reducing its effects on human health and agriculture.

Allogenic and autologous nondiluted serum eye drops-validation strategy compliant with good manufacturing practice.

Serum eye drops alleviate ocular symptoms of diseases such as sicca syndrome, or chronic graft-versus-host disease. This study was designed for good manufacturing practice validation of our standard manufacturing, storage and transport processes for both autologous and allogenic SEDs. Specifications of quality parameters are lacking and were aimed to be defined. Using sterile collected, coagulated whole blood, serum was separated by centrifugation and filled into single-use eye drop applicator vials. Quality control tests included visual inspection, sterility, leukocyte concentration, pH, vitamin A, TGF-ß and VEGF-A. Samples were collected after manufacture and after 24 h and 6 months of frozen storage (-20°C). Sterility testing was performed after opening the SED applicators at specified intervals. For transport validation, SEDs were packed in insulated transport bags and stored at 20-24°C and 30-32°C for 8 h. Vitamin A, TGF-ß and VEGF-A assays showed no difference in concentration between fresh and 24 h frozen serum. All specifications for pH (aim 7.4) and cellular contamination were met and microbiological contamination tests were negative. Shelf-life was defined as 6 months at -20°C. Once opened, the product must be used within 24 h to avoid bacterial outgrowth. Transporting frozen SEDs from the manufacturer via a local pharmacy to the patient within a maximum of 4 h was demonstrated. The GMP compliance of our production, storage and transport processes for autologous and allogenic SEDs was successfully validated. 100% serum eye drops in single-use applicators can be safely used for up to 24 h after opening.

Computer-aided detection of tuberculosis from chest radiographs in a tuberculosis prevalence survey in South Africa: external validation and modelled impacts of commercially available artificial intelligence software

Computer-aided detection (CAD) can help identify people with active tuberculosis left undetected. However, few studies have compared the performance of commercially available CAD products for screening in high tuberculosis and high HIV settings, and there is poor understanding of threshold selection across products in different populations. We aimed to compare CAD products' performance, with further analyses on subgroup performance and threshold selection. We evaluated 12 CAD products on a case-control sample of participants from a South African tuberculosis prevalence survey. Only those with microbiological test results were eligible. The primary outcome was comparing products' accuracy using the area under the receiver operating characteristic curve (AUC) against microbiological evidence. Threshold analyses were performed based on pre-defined criteria and across all thresholds. We conducted subgroup analyses including age, gender, HIV status, previous tuberculosis history, symptoms presence, and current smoking status. Of the 774 people included, 516 were bacteriologically negative and 258 were bacteriologically positive. Diverse accuracy was noted: Lunit and Nexus had AUCs near 0·9, followed by qXR, JF CXR-2, InferRead, Xvision, and ChestEye (AUCs 0·8-0·9). XrayAME, RADIFY, and TiSepX-TB had AUC under 0·8. Thresholds varied notably across these products and different versions of the same products. Certain products (Lunit, Nexus, JF CXR-2, and qXR) maintained high sensitivity (>90%) across a wide threshold range while reducing the number of individuals requiring confirmatory diagnostic testing. All products generally performed worst in older individuals, people with previous tuberculosis, and people with HIV. Variations in thresholds, sensitivity, and specificity existed across groups and settings. Several previously unevaluated products performed similarly to those evaluated by WHO. Thresholds differed across products and demographic subgroups. The rapid emergence of products and versions necessitates a global strategy to validate new versions and software to support CAD product and threshold selections. Government of Canada.

Formation of cheese pattern when using monospecies cultures

The article presents the results of a study of the influence of monospecies gas-aroma-forming cultures Lactococcus lactis subsp. lactis biovar. diacetylactis (L. diacetylactis) and Leuconostoc subsp. on the peculiarities of pattern formation in cheeses with a low second heating temperature molded from a layer. The studied cultures were used at a dose of 0.6% of the total milk volume as as single starter microflora in the model cheeses (1-M and 2-M) and additional microflora along with the main lactococcal microflora (Lactococcus lactis subsp. lactis; Lactococcus cremoris) in the control cheeses (1-K and 2-K). The model and control cheeses were subjected to microbiological tests (total number of lactic acid microorganisms, number of L. diacetylactis and Leuconostoc subsp.), physicochemical (mass fraction of moisture, pH), biochemical (mass fraction of lactose) and organoleptic studies after pressing and during ripening at the age of 15, 30, 45, 60 days. It has been established that the use of a culture of citrate-fermenting lactococci L. diacetylactis ensures a stable lactic acid fermentation process during the production and ripening of the model and control cheeses, the formation of an elastic consistency and the desired pattern with eyes of a regular round shape. The use of the hetero-fermentative culture Leuconostoc subsp., as single starter microflora, does not guarantee the required level of lactic acid fermentation during cheese production and leads to an increase in the moisture content of the cheese mass after pressing and overacidification of the cheese in the first stages of ripening, which together contributes to the formation of an overly plastic consistency and an overdeveloped pattern in the form of cracks. The use of Leuconostoc subsp. as a gas-aroma-forming component of a traditional starter culture for semi-hard cheeses, also consisting of mesophilic lactococci Lc. lactis subsp. lactis and Lc. cremoris, causes the development of a nest-like pattern, which does not fully ensure the formation of the desired pattern with regular rounded eyes.

The spectrum of infections identified in pregnant women with different types of fetal growth restriction

BACKGROUND: Bacterial, viral and protozoal infections can cause miscarriage, antenatal death, congenital organ abnormalities or other limited consequences depending on the pathogen. The role of infection processes identified during pregnancy on placental pathology and fetal growth restriction. AIM: The aim of this study was to conduct a comparative analysis of infections identified in pregnant women with different types of fetal growth restriction, as well as to assess a potential impact of identified infections on the outcomes of fetal growth restriction in newborns in the same groups. MATERIALS AND METHODS: We performed a retrospective analysis of outcomes for 394 pregnant women with an established diagnosis of fetal growth restriction, who had given birth from 2018 to 2022 in the Perinatal Center of the Arkhangelsk Regional Clinical Hospital. Maternal and neonatal case histories were obtained using a continuous sampling method. Considering the transition to new criteria for establishing the diagnosis of fetal growth restriction in Russia, we formed four study groups, of which only 139 cases met the Delphi criteria of clinical guidelines by Russian Society of Obstetricians and Gynecologists, 2021. In the selected groups, we analyzed the results of microscopic and microbiological tests of various localizations in mothers during antepartum examination, as well as postpartum examination of the placenta and culture tests in newborns in their relation to adverse outcomes. RESULTS: A high prevalence (25–70.4%) of positive bacteriological findings was revealed in all of the study groups. The frequency was highest in the group of pregnant women with fetal growth restriction before 32 weeks (90–92%). Combined infections (two or more localizations) were noted in 59.2% of pregnant women in groups with early fetal growth restriction compared to 23.3% in late fetal growth restriction groups. In all cases, we observed a direct relationship between the severity of fetal growth restriction and the prevalence of infections. The range of infections identified during routine examination of pregnant women is quite limited; Candida spp. (from 40.8% in the control group to 75% in the comparison group), Escherichia coli (from 22.9 to 33.3%, respectively), and Chlamydia trachomatis (from 4.5 to 23.5%, respectively) being identified most commonly. In a morphological study of the placenta, infectious and inflammatory lesions were the most significant and ranged from 100 to 81.4% of cases in groups with early and late fetal growth restriction, respectively, with signs of hematogenous transmission prevailed. When analyzing infectious lesions in fetuses, we have found the presence of three and more localizations of the infectious process in 90 to 45% of cases with a fatal outcome for early and late fetal growth restriction, respectively. In the control groups, similar rates were 40 and 15.8%. When assessing the distribution of various types of infectious process in newborns, Candida spp., Escherichia coli, and Enterococcus faecalis also took the lead in all cases. However, the percentage of the same etiology of maternal and neonatal infections turned out to be very low (from 0 to 31% for individual pathogens), which makes it difficult to apply preventive treatment during pregnancy. CONCLUSIONS: Authors identified indirect but numerous signs of significant involvement of infectious processes in the development of fetal growth restriction, especially its early type, as well as the influence of infections on the outcomes for such newborns. In most cases, infectious processes during pregnancy are subclinical. Current screening of pregnant women is insufficient to identify high-risk groups. Examination of pregnant women for infections carried out by culture tests provide low-component and, most likely, incomplete information.

Microbiological characteristics of the lower airway in adults with bronchiectasis: a prospective cohort study

BackgroundMicrobial infection and colonization are frequently associated with disease progression and poor clinical outcomes in bronchiectasis. Identification of pathogen spectrum is crucial for precision treatment at exacerbation of bronchiectasis.MethodsWe conducted a prospective cohort study in patients with bronchiectasis exacerbation onset and stable state. Bronchoalveolar lavage fluid (BALF) was collected for conventional microbiological tests (CMTs) and metagenomic Next-Generation Sequencing (mNGS). Bronchiectasis patients were monitored for documenting the time to the next exacerbation during longitudinal follow-up.ResultsWe recruited 168 eligible participants in the exacerbation cohorts, and 38 bronchiectasis patients at stable state at longitudinal follow-up. 141 bronchiectasis patients at exacerbation onset had definite or probable pathogens via combining CMTs with mNGS reports. We identified that Pseudomonas aeruginosa, non-tuberculous mycobacteria, Haemophilus influenzae, Nocardia spp, and Staphylococcus aureus were the top 5 pathogens with a higher detection rate in our cohorts via combination of CMTs and mNGS analysis. We also observed strong correlations of Pseudomonas aeruginosa, Haemophilus influenzae, non-tuberculous mycobacteria with disease severity, including the disease duration, Bronchiectasis Severity Index, and lung function. Moreover, the adjusted pathogenic index of potential pathogenic microorganism negatively correlated (r = -0.7280, p < 0.001) with the time to the next exacerbation in bronchiectasis.ConclusionWe have revealed the pathogenic microbial spectrum in lower airways and the negative correlation of PPM colonization with the time to the next exacerbation in bronchiectasis. These results suggested that pathogens contribute to the progression of bronchiectasis.

The Clinical Impact of Different Types of Preoperative Biliary Intervention on Postoperative Biliary Tract Infection of Patients Undergoing Pancreaticoduodenectomy.

Background: For patients with obstructive jaundice and who are indicated for pancreaticoduodenectomy (PD) or biliary intervention, either endoscopic retrograde cholangiopancreatography (ERCP) or percutaneous transhepatic cholangiography and drainage (PTCD) may be indicated preoperatively. However, the possibility of procedure-related postoperative biliary tract infection (BTI) should be a concern. We tried to evaluate the impact of ERCP and PTCD on postoperative BTI. Methods: Patients diagnosed from June 2013 to March 2022 with periampullary lesions and with PD indicated were enrolled in this cohort. Patients without intraoperative bile culture and non-neoplastic lesions were excluded. Clinical information, including demographic and laboratory data, pathologic diagnosis, results of microbiologic tests, and relevant infectious outcomes, was extracted from medical records for analysis. Results: One-hundred-and-sixty-four patients from the cohort (164/689) underwent preoperative biliary intervention, either ERCP (n = 125) or PTCD (n = 39). The positive yield of intraoperative biliary culture was significantly higher in patients who underwent ERCP than in PTCD (90.4% vs. 41.0%, p < 0.001). Although there was no significance, a trend of higher postoperative BTI (13.8% vs. 2.7%) and BTI-related septic shock (5 vs. 0, 4.0% vs. 0%) in the ERCP group was noticed. While the risk factors for postoperative BTI have not been confirmed, a trend suggesting a higher incidence of BTI associated with ERCP procedures was observed, with a borderline p-value (p = 0.05, regarding ERCP biopsy). Conclusions: ERCP in patients undergoing PD increases the positive yield of intraoperative biliary culture. PTCD may be the favorable option if preoperative biliary intervention is indicated.

Development of an all-in-one real-time PCR assay for simultaneous detection of spotted fever group rickettsiae, severe fever with thrombocytopenia syndrome virus and hantaan virus prevalent in central China.

Central China has been reported to be one of the most important endemic areas of zoonotic infection by spotted fever group rickettsiae (SFGR), severe fever with thrombocytopenia syndrome virus (SFTSV) and hantaan virus (HTNV). Due to similar clinical symptoms, it is challenging to make a definite diagnosis rapidly and accurately in the absence of microbiological tests. In the present study, an all-in-one real-time PCR assay was developed for the simultaneous detection of nucleic acids from SFGR, SFTSV and HTNV. Three linear standard curves for determining SFGR-ompA, SFTSV-L and HTNV-L were obtained within the range of 101-106 copies/μL, with the PCR amplification efficiencies ranging from 93.46% to 96.88% and the regression coefficients R2 of >0.99. The detection limit was 1.108 copies/μL for SFGR-ompA, 1.075 copies/μL for SFTSV-L and 1.006 copies/μL for HTNV-L, respectively. Both the within-run and within-laboratory coefficients of variation on the cycle threshold (Ct) values were within the range of 0.53%-2.15%. It was also found there was no statistical difference in the Ct values between single template and multiple templates (PSFGR-ompA = 0.186, PSFTSV-L = 0.612, PHTNV-L = 0.298). The sensitivity, specificity, positive and negative predictive value were all 100% for determining SFGR-ompA and SFTSV-L, 97%, 100%, 100% and 99.6% for HTNV-L, respectively. Therefore, the all-in-one real-time PCR assay appears to be a reliable, sensitive, rapid, high-throughput and low cost-effective method to diagnose the zoonotic infection by SFGR, SFTSV and HTNV.

“Sikil pa'ak”: A proposed food from the Mayan biocultural cuisine for the prevention of metabolic syndrome

Traditional dishes play an important role in the management of diseases linked to metabolic syndrome (MS). In this context, “sikil pa'ak” (SPK), a Mayan cuisine dish made of toasted pumpkin seeds (TPS), tomato sauce with coriander (TSC), and sour orange juice (SOJ), could stand out because of the nutritional and functional properties of its ingredients. This study evaluated the sensory, nutritional, bioactive content, and functional properties of SPK and its ingredients to determine its potential in managing MS. SPK showed a water activity of 1.00 ± 0.04 and color values L* 52.74 ± 0.72, a* 12.59 ± 0.29, b* 30.16 ± 0.67. Microbiological tests confirmed the absence of contaminants. Sensorially, the flavor was the most appreciated attribute, and 29.89% rated it as “I like it very much.” Nutritionally, SPK excelled with high protein, fiber, and lipid contents with values of 24.10, 15.82, and 41.22 g/100g, respectively. The ingredients that contributed most to the content of bioactive compounds in the SPK were TPS in total phenols (TPC: 169.64 μg/mg) and total flavonoids (TFC: 234.93 μg/mg), as well as SOJ in vitamin C (65.49 μg/mg), and TSC in β-carotene (21.12 μg/mg). SPK showed high antioxidant potential (ABTS assay: 53.27%). Although SPK had a moderate effect on lipase inhibition (15.89%) and clot lysis (11.46%), it had high inhibition of α-amylase (55.21%) and plasma recalcification time (507.34 s). The SPK was sensorially appreciated and high in nutrients and bioactive compounds, showing beneficial effects against MS, especially because of TPS and SOJ. This traditional dish could be beneficial for metabolic health.

Rhizobium Inoculant and Seed-Applied Fungicide Effects Improve the Drought Tolerance of Soybean Plants as an Effective Agroecological Solution under Climate Change Conditions.

Rhizobial inoculation in combination with fungicidal seed treatment is an effective solution for improving soybean resistance to modern climate changes due to the maximum implementation of the plant's stress-protective antioxidant properties and their nitrogen-fixing potential, which will contribute to the preservation of the environment. Model ecosystems at different stages of legume-rhizobial symbiosis formation, created by treatment before sowing soybean seeds with a fungicide (fludioxonil, 25 g/L) and inoculation with an active strain of Bradyrhizobium japonicum (titer 109 cells per mL), were subjected to microbiological, biochemical, and physiological testing methods in controlled and field conditions. Seed treatment with fungicide and rhizobia showed different patterns in the dynamics of key antioxidant enzymes in soybean nodules under drought conditions. Superoxide dismutase activity increased by 32.7% under moderate stress, while catalase increased by 90.6% under long-term stress. An increase in the antioxidant enzyme activity induced the regulation of lipoperoxidation processes during drought and after the restoration of irrigation. Regeneration after stress was evident in soybean plants with a combination of fungicide seed treatment and rhizobial inoculant, where enzyme levels and lipoperoxidation processes returned to control plant levels. Applying seed treatment with fungicide and Rhizobium led to the preservation of the symbiotic apparatus functioning in drought conditions. As proof of this, molecular nitrogen fixation by nodules has a higher efficiency of 25.6% compared to soybeans without fungicide treatment. In the field, fungicidal treatment of seeds in a complex with rhizobia inoculant induced prolongation of the symbiotic apparatus functioning in the reproductive period of soybean ontogenesis. This positively affected the nitrogen-fixing activity of soybeans during the pod formation stage by more than 71.7%, as well as increasing soybean yield by 12.7% in the field. The application of Rhizobium inoculant and fungicide to seeds contributed to the development of antioxidant protection of soybean plants during droughts due to the activation of key enzymatic complexes and regulation of lipoperoxidation processes, which have a positive effect on nitrogen fixation and productivity of soybeans. This is a necessary element in soybean agrotechnologies to improve plant adaptation and resilience in the context of modern climate change.

Clinical characteristics and risk factors for mortality in pneumonia-associated acute respiratory distress syndrome patients: a single center retrospective cohort study.

Pathogenic diversity may have contributed to the high mortality of pneumonia-associated acute respiratory distress syndrome (p-ARDS). Metagenomics next-generation sequencing (mNGS) serves as a valuable diagnostic tool for early pathogen identification. However, its clinical utility in p-ARDS remains understudied. There are still limited researches on the etiology, clinical characteristics and risk factors for 28-day mortality in p-ARDS patients. A single center retrospective cohort study of 75 p-ARDS patients was conducted. Patients were categorized into survival and deceased groups based on their 28-day outcomes. A comprehensive clinical evaluation was conducted, including baseline characteristics, laboratory indicators, outcomes and pathogen identification by mNGS and traditional microbiological testing. We then evaluated the diagnostic value of mNGS and identified clinical characteristics and risk factors for 28-day mortality in p-ARDS. The overall ICU mortality was 26.67%, and the 28-day mortality was 57.33%, with 32 cases (42.67%) in the survival group, and 43 cases (57.33%) in the deceased group. Patients in the deceased group were older than those in the survival group (68(59,73) years vs. 59(44,67) years, P=0.04). The average lengths of ICU and hospital stay were 9(5,13) days and 14(7,21) days, respectively. The survival group had longer lengths of ICU and hospital stay (ICU: 11(7,17) days and hospital: 17(9,27) days) compared to the deceased group (ICU: 8(4,11) days and hospital: 12(6,19) days) (P<0.05). Survival patients exhibited lower Acute Physiology and Chronic Health Evaluation (APACHE) II score on the 3rd and 7th days, higher lymphocyte counts, higher CD3+ and CD8+ T cell counts compared to deceased patients (P<0.05). Multivariate logistic regression analysis identified age, APACHE II scores on 3rd and 7th days, CD8+ T cell count and length of ICU as independent risk factors for 28-day mortality in p-ARDS patients. mNGS demonstrated a significantly higher overall pathogen detection rate (70/75, 93.33%) compared to the traditional method (50/75, 66.67%, P=0.022). The average turnaround time (TAT) for mNGS was significantly shorter at 1(1,1) day compared to 4(3,5) days for the traditional method (P<0.001). Metagenome next-generation sequencing can be used as a valuable tool for identifying pathogens in p-ARDS, reducing diagnostic time and improving accuracy. Early application of mNGS alongside traditional methods is recommended for p-ARDS. Furthermore, older age, higher APACHE II scores, lower lymphocyte counts and lymphocyte subset counts were associated with increased mortality in p-ARDS patients, highlighting the importance of timely assessment of immune status and disease severity, especially in elderly.

Diversity of the &amp;lt;i&amp;gt;Ralstonia Solanacearum&amp;lt;/i&amp;gt; Species of Potato Seeds in Mali

Potato brown rot was classified as a quarantine disease because of the complexity of the pathogen &amp;lt;i&amp;gt;Ralstonia solanacearum L&amp;lt;/i&amp;gt;., formerly called &amp;lt;i&amp;gt;Pseudonomas&amp;lt;/i&amp;gt; or &amp;lt;i&amp;gt;Burkholderia solanacearum&amp;lt;/i&amp;gt;. This same bacterium causes the disease bacterial wilt. It is a multifaceted bacterium hence the complex name &amp;lt;i&amp;gt;Ralstonia solanacearum&amp;lt;/i&amp;gt; (CeRs or RASLSSO) or BW (in English). It attacks several plant families, notably nightshades such as potatoes; the tomato; eggplant; chili pepper; tobacco…etc. The potato is the most cultivated plant worldwide. Mali is the second largest producer in West Africa after Nigeria. It imports more than 9,000 to 11,000 tons of seeds each year. Potato cultivation is faced with several biotic and abiotic attacks. Among all these attacks, those caused by bacteria cause the most significant damage. In addition, diseases caused mainly by the &amp;lt;i&amp;gt;Ralstonia solanacearum&amp;lt;/i&amp;gt; complex lack adequate control solutions. Despite everything, today, very few studies are carried out to identify these bacteria in order to prevent their spread in the soil in Mali. This is why the objective of this study is to identify the bacteria responsible for brown rot in potato seeds in Mali. To achieve our objective, a total of 63 samples were taken from nine varieties of imported and locally multiplied potato seeds. The agent responsible for brown rot was isolated on the Triphenyl-Tetrazolium-chloride culture medium, and several microbiological, biochemical and molecular tests were carried out to identify the different isolates selected. As the main results of this study: twenty-seven bacterial isolates, capable of causing brown rot of potato seeds were isolated, the biochemical tests carried out on these isolates showed that they all of race3 and twenty -four isolates were biovar 3; one from biovar 2 and two from biovar 6. The molecular studies carried out using universal primers confirmed the presence of the species &amp;lt;i&amp;gt;Ralstonia solanacearum&amp;lt;/i&amp;gt; with two phylotypes (I and II).

Investigation of an Acute Gastrointestinal Illness Outbreak Linked to Drinking Water in a Higher Educational Institute in East Sikkim, India.

Introduction An acute gastrointestinal illness outbreak was reported in a higher educational institution among students and faculties in East Sikkim, India, from January to February 2023. The investigation was conducted to identify the source of the infection and causative pathogens and prevent the spread of the outbreak. Methods We defined a case as three or more loose stools in 24 hours, abdominal pain, or vomiting with the onset of symptoms between January 16 and February 16, 2023. Active surveillance was conducted by reviewing the affected individuals at the campus and patient registers at the dispensary, where cases were treated. Stool samples, rectal swabs, water samples, and suspected food samples were collected for microbiological testing using conventional culture, multiplex polymerase chain reaction (PCR), and kit-based real-time PCR methods. Results Out of 1,850 residents, 106 (5.7%) were affected by gastrointestinal symptoms like diarrhea, vomiting, etc. The attack rate for females was 23 (1.24%) and for males was 83 (4.49%). The most affected individual median age was 21 years (range: 2-51 years). From the laboratory investigations, most of the cases demonstrated polymicrobial etiologies. Gastroenteritis pathogens like Campylobacter, astrovirus, androtavirusdiarrheagenic Escherichia coli (DEC) (EAEC, EIEC, ETEC, EPEC, and EAEC), Shigella,etc., were detected in the suspected samples. The environmental investigation indicated the presence of rusted and leaky water pipes and sewage pipelines, along with ineffective chlorination of the water plant. Conclusions Based on epidemiological and laboratory investigations, it is conjectured that sewage and fecal contamination of drinking water and poor maintenance of the water distribution system most likely caused the outbreak described in this study. Basic treatment modalities, adequate chlorination, and periodic inspection of the water system were suggested, which controlled the outbreak to a greater extent.

Antioxidant Activities of Ethanolic Extracts Obtained from α-Pinene-Containing Plants and Their Use in Cosmetic Emulsions.

α-Pinene is the bicyclic, unsaturated terpene hydrocarbon present in many plants. Due to its beneficial chemical properties, this compound is of great interest and has found numerous applications as a raw material in many chemical industries as well as in medicine and cosmetics. The aim of this study was to evaluate the antioxidant activities of ethanolic extracts obtained from plants containing α-pinene and to test the properties of cosmetic emulsions prepared with these extracts. The raw plant materials consisted of fresh parts of Pinus sylvestris L., such as cones, needles, and branches, as well as dried unground and ground pinecones; dried and fresh Rosmarinus officinalis leaves; dried Levisticum officinale leaves; and dried Salvia officinalis L. leaves. The plant materials were individually extracted with 40% (v/v), 70% (v/v), and 96% (v/v) ethanol using ultrasound-assisted extraction (UAE) for 15, 30, or 60 min. This method is a green extraction technique, frequently applied to isolate active substances from plants. For the selected plant materials, Soxhlet extraction with 96% (v/v) ethanol was also performed. The qualitative and quantitative analyses of the components in the selected extracts were performed with gas chromatography coupled with mass spectrometry (GC-MS). The antioxidant activities of the extracts were evaluated with the DPPH and ABTS methods. The extracts of three plant materials with the highest antioxidant activities-dried Rosmarinus officinalis leaves, dried Salvia officinalis L. leaves, and dried and ground Pinus sylvestris L. cones-were selected to be incorporated in cosmetic emulsions containing glyceryl monostearate and Olivem 1000 as emulsifiers. The stabilities and antioxidant activities of the emulsions were evaluated. Moreover, the antimicrobial properties of the emulsions using microbiological tests were also determined. The findings suggest that the prepared emulsions are stable cosmetic products with a high antioxidant potential.

Blood RNA signatures outperform CRP triage of tuberculosis lymphadenitis and pericarditis.

Limited data are available on the diagnostic accuracy of blood RNA biomarker signatures for extrapulmonary TB (EPTB). We addressed this question among people investigated for TB lymphadenitis and TB pericarditis, in Cape Town, South Africa. We enrolled 440 consecutive adults referred to a hospital for invasive sampling for presumptive TB lymphadenitis (n=300) or presumptive TB pericarditis (n=140). Samples from the site of disease underwent culture and/or molecular testing for Mycobacterium tuberculosis complex (Mtb). Discrimination of patients with and without TB defined by microbiology or cytology reference standards was evaluated using seven previously reported blood RNA signatures by area under the receiver-operating characteristic curve (AUROC) and sensitivity/specificity at predefined thresholds, benchmarked against blood C-reactive protein (CRP) and the World Health Organization (WHO) target product profile (TPP) for a TB triage test. Decision curve analysis (DCA) was used to evaluate the clinical utility of the best performing blood RNA signature and CRP. Data from 374 patients for whom results were available from at least one microbiological test from the site of disease, and blood CRP and RNA measurements, were included. Using microbiological results as the reference standard in the primary analysis (N=204 with TB), performance was similar across lymphadenitis and pericarditis patients. In the pooled analysis of both cohorts, all RNA signatures had comparable discrimination with AUROC point estimates ranging 0.77-0.82, superior to that of CRP (0.61, 95% confidence interval 0.56-0.67). The best performing signature (Roe3) achieved an AUROC of 0.82 (0.77-0.86). At a predefined threshold of 2 standard deviations (Z2) above the mean of a healthy reference control group, this signature achieved 78% (72-83%) sensitivity and 69% (62-75%) specificity. In this setting, DCA revealed that Roe3 offered greater net benefit than other approaches for services aiming to reduce the number needed to investigate with confirmatory testing to <4 to identify each case of TB. RNA biomarkers show better accuracy and clinical utility than CRP to trigger confirmatory TB testing in patients with TB lymphadenitis and TB pericarditis, but still fall short of the WHO TPP for TB triage tests. South African MRC, EDCTP2, NIH/NIAID, Wellcome Trust, NIHR, Royal College of Physicians London. Evidence before this study: Blood RNA biomarker signatures and CRP measurements have emerged as potential triage tests for TB, but evidence is mostly limited to their performance in pulmonary TB. Microbiological diagnosis of extrapulmonary TB (EPTB) is made challenging by the need for invasive sampling to obtain tissue from the site of disease. This is compounded by lower sensitivity of confirmatory molecular tests for EPTB compared to their performance in pulmonary disease. We performed a systematic review of diagnostic accuracy studies of blood RNA biomarkers or CRP measurements for EPTB, which could mitigate the need for site-of-disease sampling for the diagnosis of TB. We searched PubMed up to 1 st August 2023, using the following criteria: "extrapulmonary [title/abstract] AND tuberculosis [title/abstract] AND biomarker [title/abstract]". Although extrapulmonary TB was included in several studies, none focused specifically on EPTB or included an adequate number of EPTB cases to provide precise estimates of test accuracy. Added value of this study: To the best of our knowledge, we report the first diagnostic accuracy study of blood RNA biomarkers and CRP for TB among people with EPTB syndromes. We examined the performance of seven previously identified blood RNA biomarkers as triage tests for TB lymphadenitis and TB pericarditis compared to a microbiology reference standard among people referred to hospital for invasive sampling in a high TB and HIV prevalence setting. Multiple blood RNA biomarkers showed comparable diagnostic accuracy to that previously reported for pulmonary TB in both EPTB disease cohorts, irrespective of HIV status. All seven blood RNA biomarkers showed superior diagnostic accuracy to CRP for both lymphadenitis and pericarditis, but failed to meet the combined >90% sensitivity and >70% specificity recommended for a blood-based diagnostic triage test by WHO. Nonetheless, in decision curve analysis, an approach of using the best performing blood RNA biomarker to trigger confirmatory microbiological testing showed superior clinical utility in clinical services seeking to reduce the number needed to test (using invasive confirmatory testing) to less than 4 for each EPTB case detected. If acceptable to undertake invasive testing in more than 4 people for each true case detected, then a test-all approach will provide greater net benefit in this TB/HIV hyperendemic setting.Implications of all the available evidence: Blood RNA biomarkers show some potential as diagnostic triage tests for TB lymphadenitis and TB pericarditis, but do not provide the level of accuracy for blood-based triage tests recommended by WHO for community-based tests. CRP has inferior diagnostic accuracy to blood RNA biomarkers and cannot be recommended for diagnostic triage among people with EPTB syndromes referred for invasive sampling.

Utility of Serial Microbial Cell-free DNA Sequencing for Inpatient and Outpatient Pathogen Surveillance Among Allogeneic Hematopoietic Stem Cell Transplant Recipients.

This study characterizes the clinical utility and validity of the Karius test (KT), a plasma microbial cell-free DNA sequencing platform, as an infection surveillance tool among hematopoietic stem cell transplant (HCT) recipients, including monitoring for cytomegalovirus (CMV) and detecting infections relative to standard microbiologic testing (SMT). A prospective, observational cohort study was performed among adult HCT recipients as inpatients and outpatients. Serial KTs were performed starting with 1 sample within 14 days before HCT, then weekly from 7-63 days posttransplant then monthly from 3-12 months post-HCT. Diagnostic performance of KT versus CMV polymerase chain reaction was evaluated with positive percent agreement and negative percent agreement. Infectious events (<12 months post-HCT) were extracted from medical records. For infectious events without positive SMT, 2 clinicians adjudicated KT results to determine if any detections were a probable cause. Difference in time from KT pathogen detection and infection onset was calculated. Of the 70 participants, mean age was 49.9 years. For CMV surveillance, positive percent agreement was 100% and negative percent agreement was 90%. There was strong correlation between CMV DNA and KT molecules per microliter (r 2: 0.84, P < .001). Of the 32 SMT+/KT+ infectious events, KT identified 26 earlier than SMT (median: -12 days) and an additional 5 diagnostically difficult pathogens identified by KT but not SMT. KT detected CMV with high accuracy and correlation with quantitative polymerase chain reaction. Among infectious events, KT demonstrated additive clinical utility by detecting pathogens earlier than SMT and those not detected by SMT.

The microbiological quality of flour products in the UK with respect to Salmonella and Shiga-toxin-producing E. coli (STEC).

To investigate the possible contamination of raw flour and raw flour-based products, such as pancake/batter mixes, with Salmonella, generic E. coli and STEC. Samples included flours available for sale in the UK over a period of four months (January to April 2020). The Bread and Flour regulations, 1998 state the permitted ingredients in flour and bread but it does not specify the regular monitoring of the microbiological quality of flour and flour-based products. Samples of raw flour were collected by local authority sampling officers in accordance with current guidance on microbiological food sampling then transported to the laboratory for examination. Microbiological testing was performed to detect Salmonella spp., generic E. coli and Shiga-toxin-producing Escherichia coli (STEC) characterised for the presence of STEC virulence genes: stx1, stx2 and subtypes, eae, ipah, aggR, lt, sth and stp, using molecular methods (PCR). Of the 882 flours sampled, the incidence of Salmonella was 0.1% (a single positive sample that contained multiple ingredients such as flour, dried egg and dried milk, milled in the UK), and 68 samples (7.7%) contained generic E. coli at a level of >20 CFU/g. Molecular characterisation of flour samples revealed the presence of the Shiga-toxin (stx) gene in 10 samples (5 imported and 5 from the UK) (1.1%), from which STEC was isolated from 7 samples (0.8%). Salmonella and STEC isolates were sequenced to provide further characterisation of genotypes and to compare to sequences of human clinical isolates held in the UKHSA archive. Using our interpretive criteria based on genetic similarity, none of the STEC flour isolates correlated with previously observed human cases, while the singular Salmonella serotype Newport isolate from the mixed ingredient product was similar to a human case in 2019, from the UK, of S. Newport. Although there have been no reported human cases of STEC matching the isolates from these flour samples, some of the same serotypes and stx subtypes detected are known to have caused illness in other contexts. Results indicate that while the incidence was low, there is a potential for the presence of Salmonella and STEC in flour, and a genetic link was demonstrated between a Salmonella isolate from a flour-based product and a human case of salmonellosis.

Evaluating the effectiveness of minimum chlorate technologies employed by manufacturers of skim milk powder from both microbiological quality and chemical residue perspectives

Dairy processors in the Republic of Ireland have adopted chlorine-free chemicals for cleaning and chlorine gas for water disinfection as a means of minimizing chlorate residue in dairy products. For these 'minimum chlorate technologies' to be satisfactory, they must be able to deliver product with acceptable levels of bacteria as well as minimum levels of chlorate and other chlorine based residues. To establish the effectiveness of these technologies, sampling was conducted across the skim milk powder (SMP) manufacturing chain in 3 separate milk processing sites. Across the 3 sites a total of 11 different batches of SMP were sampled in duplicate from the whole milk silo through the manufacturing process to the powder product; yielding a total of 137 samples. Samples were tested for chlorate, perchlorate and trichloromethane alongside a suite of microbiological plate count tests including total bacteria, thermophilic bacteria, thermoduric bacteria and both mesophilic and thermophilic spore-forming bacteria. Chlorate was detected at reportable levels (≥0.01 mg/kg) in 9 of 22 SMP samples analyzed; resulting in a mean chlorate concentration 0.0183 mg/kg. Bacteria were ubiquitous across all samples analyzed with spore-forming bacteria counts ranging from 1.30 to 2.33 log cfu/ g in SMP.

Early Diagnosis of Sepsis: The Role of Biomarkers and Rapid Microbiological Tests.

Sepsis is a medical emergency resulting from a dysregulated response to an infection, causing preventable deaths and a high burden of morbidity. Protocolized and accurate interventions in sepsis are time-critical. Therefore, earlier recognition of cases allows for preventive interventions, early treatment, and improved outcomes. Clinical diagnosis of sepsis by clinical scores cannot be considered an early diagnosis, given that underlying molecular pathophysiological mechanisms have been activated in the preceding hour or days. There is a lack of a widely available tool enhancing preclinical diagnosis of sepsis. Sophisticated technologies for sepsis prediction have several limitations, including high costs. Novel technologies for fast molecular and microbiological diagnosis are focusing on bedside point-of-care combined testing to reach most settings where sepsis represents a challenge.

Clinicopathological discrepancies in the diagnoses of childhood causes of death in the CHAMPS network: An analysis of antemortem diagnostic inaccuracies

IntroductionDetermining aetiology of severe illness can be difficult, especially in settings with limited diagnostic resources, yet critical for providing life-saving care. Our objective was to describe the accuracy of antemortem...