Identification Of Pathogenic Microorganisms Research Articles

Incidence of Antibiotic Resistant Escherichia Coli In UTI Suspected Patients-A Single Centered Study

The evaluation of antimicrobial sensitivity patterns has a significant role in prescribing antimicrobial drugs to treat patients suffering from urinary tract infections (UTIs). This study assessed the etiology and antimicrobial susceptibility of the common uropathogens as those were detected in Dhaka, Bangladesh. This study was conducted following the culture and identification of pathogenic microorganisms from patients of all age groups and sexes. A total of 110 urine samples were collected from suspected UTI patients for culture and sensitivity as advised by the physicians. Female patients (76.4%) were dominant over male patients (23.6%) and patients were 0 to 90 years of age. From these samples, 25 Escherichia coli were isolated from culture-positive cases to determine antibiotic sensitivity patterns. Most of these isolates were resistant to Azithromycin (100%), Nalidixic Acid (80%), Cotrimoxazole (54%), Ciprofloxacin (44%) and Cefixime (44%). The present study emphasized the necessity of standard microbiological screening techniques to evaluate the etiological characteristics required to effectively treat UTI patients.
 Stamford Journal of Microbiology, 2023. Vol. 13, Issue 1, p. 21-24

Microbial Characteristics of Lower Respiratory Tract Infections in Patients Referred from Primary Care Hospitals

Objective: This study investigated the microbiological characteristics of severe lower respiratory tract infection patients not respond to initial treatment, and were transferred to a tertiary-level hospital.Material and Methods: This was a multicenter, prospective study conducted across four hospitals: Cho Ray, Pham Ngoc Thach, Gia Dinh People’s Hospital, and Can Tho Central General Hospital. Sputum specimens were collected shortly after admission and subjected to culture and real-time PCR testing.Results: Out of the 252 patients, 170 (67.4%) met the criteria for analysis and identification of pathogenic microorganisms. The most frequently isolated pathogens were Streptococcus pneumoniae (S. pneumonia) and Haemophilus influenzae (H. influenzae), comprising of 27.0% and 13.1%, respectively. Antibiotic susceptibility testing was conducted on 55 patients (32.3%). Among these cases, there were 16 instances of S. pneumoniae, 10 cases of Staphylococcus aureus (S. aureus), 10 cases of Pseudomonas aeruginosa (P. aeruginosa), 14 cases of gram-negative enteric bacteria, 2 cases of H. influenzae, 1 case of Moraxella catarrhalis (M. catarrhalis), 1 case of Enterococcus faecium, and 1 case of M. pneumoniae. The antibiogram results revealed significant findings; including a 70% prevalence of extended-spectrum beta-lactamase and 90% occurrence of Methicillin-Resistant Staphylococcus aureus. The data also indicated high resistance rates; such as 90% resistance to erythromycin, 40-80% to ciprofloxacin, 30-80% to ceftazidime, and 30-40% to imipenem.Conclusion: Pathogens associated with LRTIs referred from primary care hospitals encompass S. pneumonia, H. influenza, and S. aureus. At our facility, piperacillin, imipenem, amikacin, vancomycin, and linezolid emerged as the most effective antibiotics for addressing these LRTIs.

Rapid visualization molecular fluorescence detection of methicillin-resistant Staphylococcus aureus using the multiplex MIRA-qPCR method.

Multidrug-resistant (MDR) bacterial infections constitute a major public health problem worldwide. A rapid method for the detection of methicillin-resistant Staphylococcus aureus (MRSA) is critical for the timely prevention of bacterial infections and the accurate clinical use of drugs. The nuc and mecA genes are potentially indicative of MRSA infection and in this study, a multiplex molecular fluorescence multi-enzyme isothermal rapid amplification visual assay was proposed and established. The method is capable of detecting MRSA at 17min, 40°C amplification, and is well differentiated from common clinical bacteria in specific assays, with 500 colony-forming units (CFU)mL-1 of MRSA detected under optimal conditions. This method has excellent diagnostic capabilities versus classical methods to detect clinical samples and shows potential in the identification of pathogenic microorganisms in a clinical setting.

The credibility of Polish diagnostic microbiological testing in 2021 based on the results of the POLMICRO external laboratory control

<br>Introduction: The paper presents the results of the 28th edition of the Polish National External Quality Assessment Scheme in Microbiology POLMICRO organised by the Centre of Quality Control in Microbiology (CQCM).</br> <br>Aim: The aim of the scheme is the assessment of the credibility of microbiological testing carried out by medical laboratories in Poland.</br> <br>Material and methods: The assessment is based on the analysis of the results obtained by the participants in each round of the POLMICRO, POLMICRO/MIKOLOGIA (MICOLOGY), and POLMICRO/SSE programmes in 2021.</br> <br>Results: Positive results in the full annual cycle were obtained by 95.73% of laboratories participating in the POLMICRO programme and all participants of POLMICRO/MIKOLOGIA (MICOLOGY) and POLMICRO/SSE.</br> <br>Conclusions: Medical diagnostic laboratories participating in the CQCM programmes of external laboratory control demonstrated high competence in such areas of microbiological diagnostics as the identification of pathogenic microorganisms, antimicrobial susceptibility testing, and detection of resistance mechanisms.</br>

Risk factors of in-hospital mortality in patients with pneumocystis pneumonia diagnosed by metagenomics next-generation sequencing.

ObjectivesThe metagenomic next-generation sequencing (mNGS) test is useful for rapid and accurate detection and identification of pathogenic microorganisms. The aim of the present study was to investigate the factors associated with in-hospital mortality in pneumocystis pneumonia (PCP) patients with mNGS-assisted diagnosis.MethodsOur study enrolled 154 patients with mNGS-positive PCP from August 2018 to February 2022 at the First Affiliated Hospital of Zhengzhou University respectively. Patients were divided into the survivor group (n=98) and the death group (n=56) according to whether in-hospital death occurred. Baseline characteristics, patients’ pre-hospital symptoms and patients’ CT imaging performance during hospitalization were carefully compared between the two groups. Risk factors for the occurrence of in-hospital death were sought by selecting indicators that were significantly different between the two groups for modelling and performing multiple logistic regression analysis.ResultsCompared with the in-hospital death patients, the survivors were younger and had higher levels of albumin (ALB) (age: 50.29 ± 14.63 years vs 59.39 ± 12.27 years, p<0.001; ALB: 32.24 ± 5.62 g/L vs 29.34 ± 5.42g/L, p=0.002; respectively), while the levels of lactate dehydrogenase (LDH) and C-reactive protein CRP were lower (LDH: 574.67 ± 421.24 U/L vs 960.80 ± 714.94 U/L, p=0.001; CRP: 54.97 ± 55.92 mg/L vs80.45 ± 73.26 mg/L, p=0.018; respectively). Multiple logistic regression analysis revealed that age, the baseline LDH and CRP levels were all positively associated with high in-hospital mortality [age: OR(95%CI): 1.115 (1.062-1.172), p<0.001; LDH: OR(95%CI): 1.002 (1.001-1.003), p<0.001; CRP: OR(95%CI): 1.008 (1.000-1.017), p=0.045; respectively] while the platelet counts was negatively associated with it [OR(95%CI): 0.986 (0.979-0.992), p<0.001].ConclusionsOld age, high baseline levels of LDH and CRP and low platelet counts were risk factors of the in-hospital mortality in mNGS positive PCP patients.

Application of nucleic acid aptamer-based lateral flow assay in microbe detection

<p indent="0mm">Microbial contamination and infection are global issues in the food and environmental fields that seriously threaten human health. Bacteria and fungi can easily cause food spoilage, resulting in diarrhea and vomiting; viruses can infect humans through different transmission routes, causing severe or even fatal harm. Hence, rapid analysis and identification of pathogenic microorganisms and simultaneous detection of multiple types of microbes have become hot research topics in biochemical analysis and molecular diagnosis. The lateral flow assay (LFA) is a simple, rapid, economical, and efficient detection technology with high sensitivity, simple operation, and environmental friendliness. It can provide instant test results under non-laboratory circumstances, hence becoming an ideal choice for point-of-care testing, which has been applied to rapidly detect various targets. The current conventional principle of the LFA is still based on the specific recognition of the antigen by the antibody. However, as a commonly used target recognition molecule in conventional biochemical and medical detection, the application of antibodies also has certain limitations for rapid and accurate identification of certain targets due to strict control of the production and purification process, as well as susceptibility to the interference of the operating environment, pH, temperature, and other conditions, such as long production cycle, high cost, poor stability, and cross-reactivity. Aptamers are a class of single-stranded DNA (ssDNA) or RNA obtained through the systematic evolution of ligands by exponential enrichment (SELEX), which can usually form a stable secondary structure. Aptamers can be folded into a three-dimensional structure through conformational change and interact with the target through conformation complementarity, π-π stacking between aromatic rings, base stacking, electrostatic interaction, and hydrogen bonding. So far, nearly 300 kinds of aptamers have been discovered. As alternatives, aptamers are easy and facile to modify and label with high sensitivity and specificity. Accordingly, the innovative rapid detection technique can be developed by combining the LFA with an aptamer. This aptamer-based LFA technology can be widely used in qualitative, semi-quantitative, and quantitative detection in food safety, environment, clinical, and other fields. Nowadays, most microbe detection methods are constructed based on this approach. The common strategies of aptamer-based LFAs include the sandwich method, competitive method, and adsorption–desorption method. Diverse ingenious materials such as gold nanoparticles and quantum dots have also been proposed for signal read-out. Different signal capture models, such as colorimetric and fluorescence methods, have been applied for sensitive and accurate detection of a single or multiple target microbe. Furthermore, in view of the unique properties of nucleic acid aptamers, several signal amplification methods can be further involved in the LFA to enhance the sensitivity for target detection. This review introduces the use of aptamers with different structural patterns and labeling types in recent years, as well as a variety of methods to detect microbes, especially for the rapid detection of pathogenic bacteria. Based on the excellent characteristics, the aptamer-based LFA presents more flexibility and selectivity for microbe detection with good applicability, specificity, and sensitivity and can better achieve low-cost, rapid detection. This study is expected to provide a reference for developing nucleic acid aptamer-based LFA technologies, especially for efficient and accurate diagnosis of corona virus disease 2019 (COVID-19), exploiting the novel application scope of LFA technology.

O-143 Characterization of vaginal and endometrial microbiome in patients with chronic endometritis (CE)

Abstract Study question Could vaginal and endometrial microbiome by sequencing 16S rRNA be comparable to classic diagnostic methods or immunohistochemistry CD138 for diagnosis of chronic endometritis? Summary answer A characteristic endometrial and vaginal microbiome is present in patients with chronic endometritis. An abnormal vaginal microbiome correlates with the presence of chronic endometritis. What is known already Chronic endometritis is a disease characterized by persistent inflammation of the endometrial lining. Currently, histopathological evaluation by immunohistochemistry CD138 marker is most common diagnostic method for CE. Microbiome analysis based on subunit 16S rRNA sequencing is a fast tool that can enable the identification of pathogenic microorganisms associated with CE. The main bacteria at vaginal and endometrial level belong to genus Lactobacillus, producers of lactic acid that allows maintaining acidic pH of vagina and acts as barrier against pathogens. Investigations on the effect of an abnormal endometrial and vaginal microbiome could improve assisted reproductive technologies. Study design, size, duration This is a observational pilot study (60 patients and 120 samples). The study population consists of patients attending to our fertility clinic for frozen euploid embryo transfer (FET) from May 2017 to May 2019. Preimplantation Genetic Testing of aneuploidy (PGT-A) was performed at blastocyst stage using Veriseq (Illumina). The inclusion criteria to be meet by patients were: age between 18 and 50 years, own or donated oocytes and use of ICSI. Participants/materials, setting, methods Cohort study with sixty patients undergoing assisted reproductive treatment (TRA) with their own or donated gametes and PGT-A Vaginal and endometrial samples were taken in the cycle prior to embryo transfer. The vaginal and endometrial microbiome was analyzed by mass sequencing of the V3V4 region of 16S rRNA. Bioinformatics analysis was performed using QIIME2 and MicrobiomeAnalyst packages. Alpha, beta diversity and taxonomic characterization were compared with positive and negative CD138 groups for chronic endometritis (CE). Main results and the role of chance Different bacterial communities were detected when vaginal and endometrial samples were analyzed in patients with and without endometritis diagnosed with CD138 immunohistochemistry. In patients with endometritis, a higher alpha diversity index tendency was found in vaginal samples (p = 0.15 for the Shannon index) and significant differences in endometrial samples (p = 0.01 for the Shannon index). In the beta diversity analysis, no significant differences were observed between the groups established as per the diagnosis of endometritis. Vaginal and endometrial samples from women with endometritis showed a microbiome pattern not dominated by Lactobacillus spp. Relative abundance analysis identified the genera Ralstonia and Gardnerella in endometrial sample, and the genera Streptoccoccus and Ureaplasma in vaginal sample of patients diagnosed with CD138 for endometritis. Comparing endometrial and vaginal samples CD138 positive diagnosed for endometritis, alpha diversity (p = 0.06 for the Shannon index and p = 0.08 for the Simpson index) and beta diversity (p &amp;lt; 0.001) showed significant differences. Relative abundance identified the genera Lactobacillus (p = 3.76E-4), Ralstonia (p = 8.19E-4), Delftia (p = 0.004) and Anaerobacillus (p = 0.004) in these sample groups. Limitations, reasons for caution The main limitation of this study is the small sample size. Larger studies including a higher number of samples are needed to confirm the different microbiome pattern observed at the vaginal and endometrial levels in correlation with chronic endometritis. The microbiome pattern has not been analyzed after treatment of CE. Wider implications of the findings Our findings suggest the existence of a characteristic vaginal and endometrial microbiota in patients with chronic endometritis. Different genera and species were identified in patients with and without endometritis depending on whether the sample was endometrial or vaginal. An abnormal vaginal microbiome appears to be strongly correlated with chronic endometritis. Trial registration number Not Applicable

Microbiological Analysis and Identification of Pathogenic Microorganisms on Currency Notes (Congolese Francs) in Kinshasa, Democratic Republic of the Congo

Aims: The incidence of infectious diseases is still a vital concern in developing countries. Recently, hygienists have focused on the risk of transmitted diseases through currency notes. This study aims at the determination of potential pathogenic microorganisms found on the Congolese Francs currency notes circulating in Kinshasa, Democratic Republic of the Congo.&#x0D; Place and Duration of the Study: This study was carried out in Kinshasa city, in the Democratic Republic of the Congo between September 3 and 29, 2019 at the Bacteriology Laboratory of the National Institute for Biomedical Research.&#x0D; Methods: During this study, 36 currency notes of different denominations have been used for microbiological analysis. Currency notes were collected from vendors of the Central market and currency note dealers at Kintambo Magasin market in Kinshasa. The identification of microorganisms (bacteria and fungi) was performed using gram staining and biochemical analyses. Results: The findings reveal the presence of following microorganisms, namely Bacillus spp, Staphylococcus aureus, Staphylococcus spp., Enterobacter spp, Escherichia coli, Serratia spp, Citrobacter spp, Salmonella enteritidis as well as molds on the Congolese currency notes. It should be observed that circulated currency notes in Kinshasa are contaminated by bacteria and fungi. The contamination rate was based on the fact, that money is new, clean or dirty.&#x0D; Conclusion: Congolese currency notes constitute the potential sources of infectious disease transmission if hygienic conditions are not respected. Molecular studies are required in order to determine the antibiotic resistance gene of these microorganisms. As the population does not know how to store these notes properly, their contamination would eventually become a major public health hazard. Therefore, a need of an awareness of the population in order to apply hygienic rules while handling currency notes. This is for the first time that such a study is being carried out in the Democratic Republic of the Congo.

Effective and Rapid Microbial Identification in Pediatric Osteoarticular Infections Using Blood Culture Bottles.

The detection and identification of pathogenic microorganisms are essential for the treatment of osteoarticular infection. However, obtaining a sufficient amount of specimen from pediatric patients is often difficult. Herein, we aimed to demonstrate the effectiveness of the blood culture bottle (BCB) system in pediatric osteoarticular infections. We hypothesized that our BCB culture method is superior to the conventional swab and tissue culture methods in terms of required specimen size, incubation time, and microbial identification rate. We analyzed the prospectively collected data of pediatric patients who underwent surgical treatment for osteoarticular infections between August 2016 and October 2019. Four needles were dipped in the infected fluid or tissue during the surgical procedure as soon as the infected area was exposed and were used to inoculate 2 aerobic pediatric BCBs and 2 anaerobic general BCBs. We also collected 2 conventional swab samples and 2 tissue samples from the identical area. The microbial identification rate and the time required for identification were compared between BCB, swab, and tissue cultures. Forty patients constituted the study group; 13 patients had osteomyelitis, 17 patients had septic arthritis, and 10 patients had both. Of these 40 patients, the microbial identification rate was higher with BCB cultures (27 [68%]) than with swab cultures (18 [45%]; p = 0.004) or tissue cultures (15 [38%]; p < 0.001). Nine samples (9 patients [23%]) were only positive in the BCB culture. Positive microbial growth was not detected with conventional culture methods when microorganisms did not grow on the BCB culture. Compared with swab culture (4.3 ± 1.1 days; p < 0.001) or tissue culture (4.4 ± 1.1 days; p < 0.001), the BCB culture reduced the time required for microbial identification (3.5 ± 0.9 days). In pediatric osteoarticular infections, the BCB culture system improved the microbial identification rate, reduced the time to identification, and permitted a smaller-volume specimen, compared with traditional culture systems. Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.

Identification of Pathogenic Microorganisms in Bronchial Washings and their Antibiotic Sensitivity Profile

This study was carried out to isolate and identify the pulmonary microbial pathogens in bronchial washings. It was intended to make a diagnosis of lower respiratory tract infections in bronchial washings of patients whose sputum specimen failed to expose any aerobic pathogenic microorganism.The study was conducted in Microbiology Laboratory, Allama Iqbal Medical College Lahore. The specimens were taken from patient of tuberculosis, Chest, Medicine, Gynea and ENT wards at Jinnah Hospital Lahore and transported to Microbiology Laboratory, Allama Iqbal Medical College Lahore. All samples were processed for Culture and sensitivity, microbial identification was based on colony morphology, Gram staining, Microscopy, Biochemical and antibiotic susceptibility testing. Out of 126 specimens of bronchial washings 44 (34.92%) specimen revealed no micro-organism on culture media. The remaining 82(65.08%) specimens revealed Pseudomonas aeruginosa 25(30.48%), Acinetobacter,17 (20.73%), Escherichia coli, 07(8.54%), Haemophilus infuenzae 3(3.66%), Proteus mirabiles 2 (2.44%), Klebsiella Pneumonia 3(3.66%); B-haemolytic streptococci 6(7.32%), Streptococcus pneumonia 7(8.54%), Staphylococcus aureus, 6(7.32%); Neisseria meningitidis 3(3.66%); Candida species 3(3.66%). This study suggests that bronchial alveolar washings are superior to sputum specimen in diagnosis of lower respiratory tract infections.

Inflammatory response biomarkers: promising indicators for distinguishing pathogen in severe infection

Severe infection and sepsis are the main causes of mortality in pediatric intensive care units(PICU). Severe infection in critically illness is characterized by acute onset, rapid progression, associated with multiple organs dysfunction, and several pathogens involved.It is critical to distinguish the main pathogen as soon as possible for clinical decision-making.Up to date, precision diagnosis and individualized strategy attract more attention in the field of critical care medicine.The improvements of molecular biology, the combination of multi-omics, and metagenomics sequencing, etc may yield many new insights into precision diagnosis of etiology.Inflammatory response biomarkers are defined as conventional inflammatory factor, acute phase protein(APP), blood RNA biosignature, metabolic molecules, immune cell markers and so on, which are promising indicators for identification of pathogenic microorganisms in severe infection. Key words: Infection; Inflammatory response; Biomarker; Pathogen

Isolation and Distribution of Microorganisms Causing Wound Infections in Diabetic Patients in Kirkuk City, Iraq

Background: Diabetic wound infections are considered one of the main life-threatening diseases among diabetic patients. Foot ulcers are accounting for up to twenty of diabetes-related hospital admission. If leaved untreated, they might result in amputation of feet and legs. The aim of current study was to investigate the isolation and identification of pathogenic microorganisms in wounds of diabetic patients in Kirkuk district, Iraq. Method: Forty diagnosed diabetic patients, (18 males and 22 females)presented with wound infection at Azadi Teaching Hospital, were selected for the study. Swabs of pus and wound exudates were obtained from infected region for bacteriological studies. Then these swabs cultured on blood agar and MacConkey agar for facultative organisms and incubated at 37°C for 24 hours. All cultured isolates were investigated and identified by standard bacteriological and analytical profile index laboratory techniques. Results: Data from current study revealed that single etiology was observed in 24(60%) of isolates. Polymicrobial infections were observed in 4(10%) of patients and 12(30%) isolates were negative. Also, Staphylococcus aureus was the most common cause of infection which comprised 20% of isolates followed by Pseudomonas aeruginosa (15%) isolates. Moreover, it was found that 12 isolates were due to Pseudomonas spp. constituting 30% of isolates followed by Staphylococcus spp. accounting 25%. Conclusion: There is no definite etiology in diabetic wound infections and Pseudomonas spp. were responsible for most of wound infections in diabetic patients.

DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples

We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent.

2211. Impact of Early Fiberoptic Bronchoscopy on Microbiological Diagnostic Rate and Clinical Outcomes of Pneumonia in Acute Leukemia Patients

BackgroundFiberoptic bronchoscopy with BAL (FOB) remains the cornerstone in the diagnosis of pneumonia in immunocompromised patients; however, there is no uniform agreement on the best timing for FOB, and its impact on microbiological diagnostic rate and clinical outcome has not been established.MethodsRetrospective study (October 2017–December 2017, July 2018–January 2019) at MD Anderson Cancer Center. The medical records of adult patients with AML, MDS or ALL who developed pneumonia (CAP, HCAP, HAP excluding VAP) and underwent FOB were reviewed. By definition, patients who underwent FOB within 48 hours after the diagnosis of pneumonia were categorized as early FOB group. We compared demographic, clinical, microbiological data, and outcomes between two groups. Data were analyzed via χ 2, Fisher’s exact and Wilcoxon rank-sum test and logistic regression.ResultsOf 140 patients included, 33 patients (24%) had early FOB and 107 patients (76%) had late FOB. There was no significant difference between two groups in demographic features, radiological findings, ANC and pneumonia severity index. Microbiological diagnostic rate of FOB did not differ between early FOB and late FOB: identification of pathogenic microorganisms (33.3% vs. 36.5%, p = 0.837), bacteria (6.1% vs. 13.1%, P = 0.36), fungi (18.2% vs. 12.2%, P = 0.39) and respiratory virus (12.1% vs. 16.8%, P = 0.6), respectively (Figures 1 and 2). On univariate analysis, the duration of intravenous antibacterial therapy was shorter in early FOB, with a median duration of 8.5 days (IQR 6.5–12) in early FOB and 11 days (IQR 8–18) in late FOB (P = 0.0047) (Figure 3). Multivariable logistic regression analysis showed that late FOB (OR 3.26, 95% CI 1.41 to 7.53, P = 0.0057) and negative bacterial culture on FOB (OR 3.06, 95% CI 1.01 to 9.22, P = 0.048) were significantly associated with longer duration of intravenous antibacterial therapy (≥10 days). There was no significant difference in ICU admission, 30-day and 60-day mortality and re-admission rate.ConclusionEarly FOB was associated with shorter duration of intravenous antibacterial therapy for pneumonia in acute leukemia patients, which has an important impact on both optimization of antimicrobial therapy for patients and improvement of antimicrobial stewardship. Disclosures All authors: No reported disclosures.

Caracterização das infecções relacionadas à assistência à saúde em um hospital de ensino

Justificativa e Objetivos: Caracterizar as principais Infecções Relacionadas à Assistência à Saúde (IRAS) de um hospital público de ensino. Métodos: Estudo epidemiológico, descritivo, retrospectivo, transversal e quantitativo realizado por meio de análise de documentos internos do Serviço de Controle de Infecção Hospitalar (SCIH) referente às infecções de corrente sanguínea, infecções de sítio cirúrgico e pneumonia hospitalar identificadas em pacientes admitidos na instituição entre maio 2017 e maio 2018. Resultados: Foram notificados 846 casos de IRAS no período do estudo. Deste total, foram analisados 582 prontuários, dos quais 298 (51,21%) do sexo masculino e 284 (48,79%) do sexo feminino. Dentre as infecções mais prevalentes, 197 (23,28%) eram do sítio cirúrgico, 183 (21,63%) de pneumonia associada a ventilação mecânica e 164 (19,38%) eram infecção primária de corrente sanguínea. Os microrganismos predominantes encontrados após análise microbiológica foram: Acinetobacter spp. em 33 (21%) infecções, seguido do gênero Pseudomonas spp. em 30 (19,1%) e Enterobacter spp. em 17 (10,8%). As especialidades médicas com maior prevalência de IRAS, foram a neurologia com 218 (25,76%) infecções, clínica geral com 157 (18,55%) e pediatria com 154 (18,20%). Conclusão: As infecções de sitio cirúrgico, pneumonia associada a ventilação mecânica e infecção primária de corrente sanguínea foram prevalentes. O apoio laboratorial foi um grande aliado na identificação do microrganismo patogênico, e os de maior incidência nas IRAS foram Acinetobacter spp., Pseudomonas spp. e Enterobacter spp. com. Na análise por especialidade, a neurologia teve significativa predominância nas infecções relacionadas a assistência.

EDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population.

The early detection and identification of pathogenic microorganisms is essential in order to deploy appropriate mitigation measures. Viruses in the Iridoviridae family, such as those in the Ranavirus genus, can infect amphibian species without resulting in mortality or clinical signs, and they can also infect other hosts than amphibian species. Diagnostic techniques allowing the detection of the pathogen outside the period of host die-off would thus be of particular use. In this study, we tested a method using environmental DNA (eDNA) on a population of common frogs (Rana temporaria) known to be affected by a Ranavirus in the southern Alps in France. In six sampling sessions between June and September (the species’ activity period), we collected tissue samples from dead and live frogs (adults and tadpoles), as well as insects (aquatic and terrestrial), sediment, and water. At the beginning of the breeding season in June, one adult was found dead; at the end of July, a mass mortality of tadpoles was observed. The viral DNA was detected in both adults and tadpoles (dead or alive) and in water samples, but it was not detected in insects or sediment. In live frog specimens, the virus was detected from June to September and in water samples from August to September. Dead tadpoles that tested positive for Ranavirus were observed only on one date (at the end of July). Our results indicate that eDNA can be an effective alternative to tissue/specimen sampling and can detect Ranavirus presence outside die-offs. Another advantage is that the collection of water samples can be performed by most field technicians. This study confirms that the use of eDNA can increase the performance and accuracy of wildlife health status monitoring and thus contribute to more effective surveillance programs.

Application of nanotechnology in biosensors for enhancing pathogen detection.

Rapid detection and identification of pathogenic microorganisms is fundamental to minimizing the spread of infectious disease, and informing clinicians on patient treatment strategies. This need has led to the development of enhanced biosensors that utilize state of the art nanomaterials and nanotechnology, and represent the next generation of diagnostics. A primer on nanoscale biorecognition elements such as, nucleic acids, antibodies, and their synthetic analogs (molecular imprinted polymers), will be presented first. Next the application of various nanotechnologies for biosensor transduction will be discussed, along with the inherent nanoscale phenomenon that leads to their improved performance and capabilities in biosensor systems. A future outlook on characterization and quality assurance, nanotoxicity, and nanomaterial integration into lab-on-a-chip systems will provide the closing thoughts. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > Biosensing.

Volatile fingerprinting of human respiratory viruses from cell culture

Volatile metabolites are currently under investigation as potential biomarkers for the detection and identification of pathogenic microorganisms, including bacteria, fungi, and viruses. Unlike bacteria and fungi, which produce distinct volatile metabolic signatures associated with innate differences in both primary and secondary metabolic processes, viruses are wholly reliant on the metabolic machinery of infected cells for replication and propagation. In the present study, the ability of volatile metabolites to discriminate between respiratory cells infected and uninfected with virus, in vitro, was investigated. Two important respiratory viruses, namely respiratory syncytial virus (RSV) and influenza A virus (IAV), were evaluated. Data were analyzed using three different machine learning algorithms (random forest (RF), linear support vector machines (linear SVM), and partial least squares-discriminant analysis (PLS-DA)), with volatile metabolites identified from a training set used to predict sample classifications in a validation set. The discriminatory performances of RF, linear SVM, and PLS-DA were comparable for the comparison of IAV-infected versus uninfected cells, with area under the receiver operating characteristic curves (AUROCs) between 0.78 and 0.82, while RF and linear SVM demonstrated superior performance in the classification of RSV-infected versus uninfected cells (AUROCs between 0.80 and 0.84) relative to PLS-DA (0.61). A subset of discriminatory features were assigned putative compound identifications, with an overabundance of hydrocarbons observed in both RSV- and IAV-infected cell cultures relative to uninfected controls. This finding is consistent with increased oxidative stress, a process associated with viral infection of respiratory cells.

Microcontact Imprinted Plasmonic Nanosensors: Powerful Tools in the Detection of Salmonella paratyphi.

Identification of pathogenic microorganisms by traditional methods is slow and cumbersome. Therefore, the focus today is on developing new and quicker analytical methods. In this study, a Surface Plasmon Resonance (SPR) sensor with a microcontact imprinted sensor chip was developed for detecting Salmonella paratyphi. For this purpose, the stamps of the target microorganism were prepared and then, microcontact S. paratyphi-imprinted SPR chips were prepared with the functional monomer N-methacryloyl-L-histidine methyl ester (MAH). Characterization studies of the SPR chips were carried out with ellipsometry and scanning electron microscopy (SEM). The real-time Salmonella paratyphi detection was performed within the range of 2.5 × 106–15 × 106 CFU/mL. Selectivity of the prepared sensors was examined by using competing bacterial strains such as Escherichia coli, Staphylococcus aureus and Bacillus subtilis. The imprinting efficiency of the prepared sensor system was determined by evaluating the responses of the SPR chips prepared with both molecularly imprinted polymers (MIPs) and non-imprinted polymers (NIPs). Real sample experiments were performed with apple juice. The recognition of Salmonella paratyphi was achieved using these SPR sensor with a detection limit of 1.4 × 106 CFU/mL. In conclusion, SPR sensor has the potential to serve as an excellent candidate for monitoring Salmonella paratyphi in food supplies or contaminated water and clearly makes it possible to develop rapid and appropriate control strategies.

THE RESULTS OF THE IDENTIFICATION OF BACTERIA ISOLATED FROM THE DIGESTIVE TRACT OF BIRDS MELOPSITTACUS UNDULATUS OF HOME CONTENT

The bacteria of families Enterobacteriaceae, Staphylococcaceae and Streptococcaceae are the main representatives of the micro flora of the digestive canal of budgerigars. The aim of the study is to determine the microbial profile of budgerigars contained in the conditions of Moscow and the Moscow region with the identification of pathogenic microorganisms. The material of the study was presented by clinical mater ial obtained from the 286 specimens of budgerigars. The results of the determination of normal an d pathogenic microflora of the digestive canal of clinically healthy budgerigars birds ( Melopsittacus undulatus ) contained in the conditions of the city of Moscow and the Moscow region are shown in article. The possibility of the bacterial carriage of saprophytic conditio nally pathogenic microorganisms Acinetobacter spp., Alcaligenes spp., Haemophilus spp., Corynebacterium spp., Klebsiella spp., Morganella osloensis, Pasteurella spp., Pseudomonas spp., Stenotrophomonas maltophilia , which may pose a risk of human infection, is revealed.