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PubMed2004

[Pathogenicity of fungi isolated from American ginseng seeds and bioassay of fungicides against the pathogenic fungi].

OBJECTIVE: Detect the pathogenicity of fungi isolated from American ginseng seeds and select new fungicides against the pathogenic seed-born fungi. METHOD: inoculate the isolates to American ginseng seedlings to detect the pathogenicity, and seeded the hyphae disk at the center of agar plate containing chemicals to do fungicide bioassay. RESULT: Fusarium sp. isolate 5 and Alternara sp. isolate 13 had pathogenicity to American ginseng seedling. Sportak had the strongest inhibition to the two isolates, Carbendazim had better inhibition and Celest had weak inhibition. CONCLUSION: Sportak and Celest could be used as efficacious candidate chemicals to treat or coat the American ginseng seeds, and substitute Carbendazim, which has been used for many years, to control the diseases occurring in seedling stage of American ginseng.

Alternaria↗

PubMedDate not supplied

Differentiation of pathogenic and non-pathogenic leptospires by means of the polymerase chain reaction.

A polymerase chain reaction was carried out to detect pathogenic leptospires isolated from animals and humans in Argentina. A double set of primers (G1/G2, B64-I/B64-II), described before, were used to amplify by PCR a DNA fragment from serogroups belonging to Leptospira interrogans but did not allow to detect saprophytic strains isolated from soil and water (L. biflexa). This fact represents an advantage since it makes possible the differentiation of pathogenic from non-pathogenic leptospires in cultures. The sensitivity of this assay has been determined, allowing to detect just only 10 leptospires in the reaction tube. Those sets of primers generated either a 285 bp or 360 bp fragment, depending on the pathogenic strain.

Animals↗

PubMed2026

Employing Metagenomics Capture targeted next-generation sequencing for the etiological diagnosis of bloodstream infections.

BACKGROUND: Bloodstream infections (BSIs) represent a significant public health concern. Metagenomic Capture targeted next-generation sequencing technology, as a newly emerging method for pathogen detection, has been applied in the etiological diagnosis of various infectious diseases and demonstrates good diagnostic efficacy. However, there is relatively limited research on the diagnostic value of this technology for the etiological diagnosis of BSIs. METHODS: A comprehensive retrospective analysis was performed on patients suspected of having BSIs who were admitted to the Affiliated Guangdong Second Provincial General Hospital of Jinan University in 2024. These patients underwent both blood culture analysis and Metagenomic Capture targeted next-generation sequencing technology for diagnostic testing, and a detailed comparison of the results was conducted. RESULTS: It was found that the Metagenomic Capture-targeted next-generation sequencing method has a shorter time to result [1.33 (1.18 - 1.69) vs 2.73 (1.89 - 3.84) days, p < 0.001], more pathogenic microbial species detected, higher positive detection rate and higher sensitivity than blood culture. CONCLUSIONS: Metagenomic Capture targeted next-generation sequencing technology is a promising tool for pathogen identification in BSIs, offering substantial methodological advantages in terms of turnaround time, detection breadth, and sensitivity. These diagnostic performance characteristics support its potential utility in clinical microbiology practice.

Humans↗

PubMed2002

Efficacy and tolerability of gatifloxacin in community treatment of acute exacerbations of chronic bronchitis.

BACKGROUND: Recognizing acute exacerbations of chronic bronchitis (AECB) and selecting appropriate antibiotic treatment for patients who would benefit most is a challenge for community-based physicians. OBJECTIVE: The Tequin Clinical Experience Study, an open-label, noncomparative, postmarketing trial, assessed the efficacy and tolerability of gatifloxacin, an 8-methoxy fluoroquinolone, in the treatment of AECB in the community-practice setting. METHODS: Consecutive patients with respiratory tract infections in community-based settings were eligible for participation. Treated patients (N = 2512) included 1107 men (44.1%) and 1405 women (55.9%) aged > or =18 years with a clinical diagnosis of chronic bronchitis. All participants received oral gatifloxacin 400 mg once daily for 7 to 10 days. Clinical response was determined via telephone contact conducted by the investigator or study coordinator using case-report forms or during an office visit after the last dose. The investigator or coordinator collected expectorated or induced sputum specimens that were then smeared on a microscope slide, stored in a tube, and transported to a central reference laboratory for Gram-staining and culture. Of 1388 pretreatment sputum specimens submitted, pathogens were isolated from 424. RESULTS: The most frequently detected pathogens were Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae. All H. influenzae and 99% of S. pneumoniae isolates tested were susceptible to gatifloxacin. Of the 2267 patients with a determinable clinical response, 2084 (91.9% [95% CI, 90.8%-93.0%]) were cured (all acute symptoms improved or returned to baseline level, no new symptoms present, no additional antibiotic required). The 95.8% cure rate in 166 patients with H. influenzae included 100% of those with beta-lactamase-positive strains. Overall, 89.2% of 111 patients with M. catarrhalis were cured; rates were similar regardless of beta-lactamase production. The clinical cure rate in 74 patients with S. pneumoniae was 98.6% and was independent of the degree of penicillin resistance (minimum inhibitory concentration > or =2.0 microg/ mL). All 6 patients infected with S. pneumoniae fully resistant to penicillin were cured. Gatifloxacin was generally well tolerated, and the majority of adverse events were mild to moderate; only 11 drug-related adverse events in 10 patients (0.4%) were serious. Drug-related nausea (3.0%), dizziness (1.5%), diarrhea (1.2%), and vomiting (0.9%) were the most common adverse events. CONCLUSIONS: The high clinical cure rate and favorable tolerability support gatifloxacin as a rational choice for the treatment of AECB in patients such as those in this community-based study.

Adult↗

PubMed2005

Host-pathogen interactions: a proteomic view.

Host-pathogen interactions reflect the balance of host defenses and pathogen virulence mechanisms. Advances in proteomic technologies now afford opportunities to compare protein content between complex biologic systems ranging from cells to animals and clinical samples. Thus, it is now possible to characterize host-pathogen interactions from a global proteomic view. Most reports to date focus on cataloging protein content of pathogens and identifying virulence-associated proteins or proteomic alterations in host response. A more in-depth understanding of host-pathogen interactions has the potential to improve our mechanistic understanding of pathogenicity and virulence, thereby defining novel therapeutic and vaccine targets. In addition, proteomic characterization of the host response can provide pathogen-specific host biomarkers for rapid pathogen detection and characterization, as well as for early and specific detection of infectious diseases. A review of host-pathogen interactions focusing on proteomic analyses of both pathogen and host will be presented. Relevant genomic studies and host model systems will be also be discussed.

Animals↗

PubMed2000

A novel two-color flow cytometric assay for the detection of Cryptosporidium in environmental water samples.

BACKGROUND: Cryptosporidium is an important waterborne pathogen. Detection of Cryptosporidium in concentrated water samples depends on oocyst isolation using immunomagnetic separation (IMS) and/or fluorescence-activated cell sorting (FACS), followed by confirmation using immunofluorescence staining (IFA) and fluorescence microscopy. These methods require highly trained microscopists for oocyst identification and confirmation. Analysis is hampered due to the presence of autofluorescent particles coupled with particles binding nonspecifically with the monoclonal antibodies (mAbs) used for detection. Flow cytometry (FCM) has the potential to be a more specific method for oocyst detection, but such a system would require more than one selection parameter. METHODS: Various mAbs from commercial suppliers were paired with CRY104-PE and evaluated. The mAb combination that best discriminated stained oocyst from detritus was optimized and compared to Cryptosporidium detection utilizing one-color IFA/FACS. RESULTS: A highly specific two-color assay employing the IgG(1) mAb CRY104 was developed. The assay resulted in reductions, up to 20-fold, in the number of non-Cryptosporidium particles detected. The addition of a second selection parameter improved microscopic analysis times and simplified oocyst confirmation by microscopists. CONCLUSIONS: A two-color assay employing competing surface mAbs reduces the number of fluorescent particles sorted, thus improving FCM detection methods for Cryptosporidium.

Animals↗

PubMed1985

Microscopic monitoring of pathogens associated with periodontal diseases. A review.

Microscopic monitoring of the subgingival microbiota to detect pathogens associated with periodontal diseases has been an active area of investigation. Researchers have demonstrated that plaque samples obtained at diseased sites contain more motile bacteria and less coccoid forms than healthy sites. Therapy at diseased locations has resulted in a shift in the microbiota to one that resembles healthy sites. However, the ability to predict disease activity based on morphotype counts still remains unverified. The current literature addressing chairside microscopic assessments as a diagnostic parameter is reviewed and discussed.

Bacteria↗

PubMed2006

Improvement of immunomagnetic separation for Escherichia coli O157:H7 detection by the PickPen magnetic particle separation device.

Conventional immunomagnetic separation (IMS) procedures, which use an external magnetic source to capture magnetic particles against the side of a test tube, are labor-intensive and can have poor sensitivity for the target organism because of high background microflora that is not effectively washed away during the IMS process. This report compares the conventional IMS procedure to a new IMS procedure with an intrasolution magnetic particle transfer device, the PickPen. The IMS target for the majority of these studies is Escherichia coli O157:H7 in various types of samples, including cattle feces, hides, carcasses, and ground beef. Comparison of the two IMS methods showed a significant difference (P < 0.05) in the efficiency of detecting E. coli O157:H7 from cattle carcass surface, cattle hide, and cattle fecal samples. No significant improvement (P > 0.05) in E. coli O157:H7 detection was observed when the PickPen IMS procedure was used to isolate this pathogen from ground beef samples. Use of the PickPen IMS greatly increases the throughput of the IMS procedure and may be more compatible with various emerging technologies for pathogen detection. In addition, the efficacy of sequential IMS for multiple pathogens is reported herein.

Animals↗

PubMed2004

Prevalence of pathogenic Escherichia coli and parasites in infants with diarrhoea in Kumasi, Ghana.

OBJECTIVES: To determine the relative frequencies and prevalence rates of pathogenic Escherichia coli and intestinal parasites in hospitalised infants (0-5 years) in Kumasi. DESIGN: A prospective descriptive study of screening 162 (83 males and 79 females) infants with diarrhoea and 122(64 males and 58 females) non-diarrhoeal infants controls for pathogens (E. coli and intestinal parasites) by standard microbiological methods. SETTING: Komfo Anokye Teaching Hospital and Maternal and Child Hospital, Kumasi, Ghana. RESULTS: From the 162 in the diarrhoeal group 96(59.6%) pathogens, and from the 122 in the control group, eight (6.6%) pathogens were isolated. Enteropathogenic E. coli (EPEC) was the most frequently detected pathogen, accounting for 24(14.8%) of the findings in the diarrhoeal group, five (4.1%) in the non-diarrhoeal control group. Of the 26 EPEC isolates, there were nine serotypes with the three dominant ones being 0125 (6), 0119 (5), and 026 (15). Other agents isolated included Ascaris lumbricoides 18(11.1%) and two (1.6%), Cryptosporidium 13(8.0%) and one (0.8%) for diarrhoeal and non-diarrhoeal infants respectively. The following were detected only in diarrhoeal stools. Giardia lamblia, six (3.7%); Trichomonas hominis, three (1.9%); Trichuris trichiura one (0.6%) and hookworm, one (0.6%). CONCLUSION: From this study, EPEC and Cryptosporidium may be considered as important diarrhoeagenic pathogens and it is hoped that provision of potable water and good sanitation may decrease diarrhoeas in infants caused by these agents.

Case-Control Studies↗

PubMed2003

Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system.

Escherichia coli, Salmonella, Listeria monocytogenes and Campylobacter jejuni are bacterial pathogens commonly implicated in foodborne illnesses. Generally used detection methods (i.e., culture, biochemical testing, ELISA and nucleic acid amplification) can be laborious, time-consuming and require multiple tests to detect all of the pathogens. Our objective was to develop rapid assays to simultaneously detect these four organisms through the presence of antigen or DNA using the Luminex LabMAP system. For nucleic acid detection, organism-specific capture probes corresponding to the 23S ribosomal RNA gene (rrl) were coupled covalently to LabMAP microspheres. Target molecules included synthetic complementary oligonucleotides and genomic DNA isolated from ATCC type strains or other well-characterized strains of each organism. Universal PCR primers were designed to amplify variable regions of bacterial 23S ribosomal DNA, yielding biotinylated amplicons of 86 to 109 bp in length. Varying quantities of targets were hybridized to the combined microsphere sets, labeled with streptavidin-R-phycoerythrin and analyzed on the Luminex(100) system. Results of nucleic acid detection assays, obtained in 30 to 40 min following amplification, correctly and specifically identified each bacterial species with a detection sensitivity of 10(3) to 10(5) genome copies. Capture-sandwich immunoassays were developed with organism-specific antibodies coupled to different microsphere sets. Microspheres were incubated with organism-specific standards and reactivity was assessed with biotinylated detection antibodies and streptavidin-R-phycoerythrin. In the immunoassays, microsphere-associated fluorescence was organism concentration dependent with detectable response at < or = 1000 organisms/ml and with no apparent cross-reactivity. We have demonstrated that the Luminex LabMAP system is a rapid, flexible platform capable of simultaneous, sensitive and specific detection of pathogens. The practical significance of this multiplexing approach would be to provide more timely, economical and comprehensive information than is available with conventional isolation and identification methodologies.

Antigens, Bacterial↗

PubMed2006

Biotechnology offers revolution to fish health management.

Biotechnology has many applications in fish health management. The application of monoclonal antibodies (mAbs) provides a rapid means of pathogen identification; antibodies to immunoglobulins from different fish species can be used to monitor the host response following vaccination; and mAbs also have the potential for screening broodstock for previous exposure to pathogens. Luminex technology exemplifies a novel antibody-based method that can be applied to both pathogen detection and vaccine development. Molecular technologies, such as the polymerase chain reaction (PCR), real time PCR and nucleic acid sequence-based amplification (NASBA), have enabled detection, identification and quantification of extremely low levels of aquatic pathogens, and microarray technologies offer a new dimension to multiplex screening for pathogens and host response. Recombinant DNA technology permits large-scale, low-cost vaccine production, moreover DNA vaccination, proteomics, adjuvant design and oral vaccine delivery will undoubtedly foster the development of effective fish vaccines in the future.

Animals↗

PubMed2004

Universal primer PCR with DGGE for rapid detection of bacterial pathogens.

A universal primer PCR (UPPCR) combined with denaturing gradient gel electrophoresis (DGGE) was evaluated as a method permitting the rapid detection of pathogens. The results show that this method is efficient at amplifying the conserved regions of bacterial 16S rRNA genes with universal primers and can detect causative bacterial pathogens rapidly. Six species of bacteria from fisheries (Pseudomonas fluorescens, Vibrio anguillarum, Aeromonas hydrophila, Vibrio fluvialis, Providencia rettgeri and Aeromonas sobria) were examined. Our results indicate that the approach we undertook can be adopted not only for axenic bacterial populations but also for mixed communities as well. Furthermore, we were able to achieve the rapid detection of multiple bacteria a single in sample. In addition, UPPCR-DGGE was shown to be better than previously reported UPPCR-single-stranded conformation polymorphism (SSCP)-based methods for the rapid detection of bacterial pathogens.

Animals↗

PubMed2003

The use of NASBA for the detection of microbial pathogens in food and environmental samples.

The isothermal amplification method nucleic acid sequence-based amplification (NASBA), which amplifies RNA, has been reported as useful for the detection of microbial pathogens in food and environmental samples. Methods have been published for Campylobacter spp., Listeria monocytogenes and Salmonella enterica ser. Enteritidis in various foods and for Cryptosporidium parvum in water. Both 16S rRNA and various mRNAs have been used as target molecules for detection; the latter may have advantages in allowing specific detection of viable cells. Most of the methods to detect pathogens in foods have employed enrichment in nutrient medium prior to NASBA, as this can ensure sensitivity of detection and encourage the detection of only viable target cells. Although a relatively recent method, NASBA has the potential for adoption as a diagnostic tool for environmental pathogens.

Animals↗

PubMed2005

Autonomous detection of aerosolized biological agents by multiplexed immunoassay with polymerase chain reaction confirmation.

The autonomous pathogen detection system (APDS) is an automated, podium-sized instrument that continuously monitors the air for biological threat agents (bacteria, viruses, and toxins). The system has been developed to warn of a biological attack in critical or high-traffic facilities and at special events. The APDS performs continuous aerosol collection, sample preparation, and detection using multiplexed immunoassay followed by confirmatory PCR using real-time TaqMan assays. We have integrated completely reusable flow-through devices that perform DNA extraction and PCR amplification. The fully integrated system was challenged with aerosolized Bacillus anthracis, Yersinia pestis, Bacillus globigii, and botulinum toxoid. By coupling highly selective antibody- and DNA-based assays, the probability of an APDS reporting a false positive is extremely low.

Aerosols↗

PubMedDate not supplied

[DNA probe for detecting Yersinia pestis and serovariant I of Yersinia pseudotuberculosis by detecting specific DNA repeating sequences].

In order to construct a DNA probe for the plague pathogen detection, we have obtained the recombinant plasmid pRD100 carrying an EcoRI-flanked 140 bp fragment from the genetically silent region of Yersinia pestis species-specific plasmid pYP1. When used as a DNA probe for hybridization of DNA from various strains of 25 bacterial species, this DNA fragment was shown to have the complementary sequences in all investigated Yersinia pestis strains (200), including the plasmid pYP1 lacking ones, and in all the studied Yersinia pseudotuberculosis serotype I strains (80). The search for the probe target in these species has led us to conclusion that it is a specific repeated DNA sequence present in more copies in Yersinia pestis than in Yersinia pseudotuberculosis serotype I. The hybridization of these sequences with the radioactive probe and 24 hours autography makes possible the detection of 1.3 x 10(5) cells of Yersinia pestis and 3 x 10(6) cells of Yersinia pseudotuberculosis serotype I immobilized on the nitrocellulose membranes. Use of the probe for analysis of the nitrocellulose membrane fixed spleen smears from animals that died of experimental plague made possible the detection of Yersinia pestis cells within 48 h.

Base Sequence↗

PubMed2004

[Clinical characteristics of bronchiolitis caused by human metapneumovirus in infants].

OBJECTIVE: The fact that the acute lower respiratory infections (ALRI) are associated with a newly discovered virus, human metapneumovirus (hMPV), has been shown in several studies. The authors conducted this study to understand the etiological and clinical characteristics of bronchiolitis, one of the most common ALRI in infants, caused by hMPV. METHODS: Nasopharyngeal aspirate specimens from 54 out of 126 infants with bronchiolitis admitted to the Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing from November 2002 to February 2003 were examined for hMPV gene fragments by reverse transcription-polymerase chain reaction (RT-PCR). Prior to the detection, the specimens were confirmed as negative for the common respiratory pathogens including RSV, influenza A and B, parainfluenza I, II, III, adenovirus, Mycoplasma pneumoniae by indirect immunofluorescence test, virus isolation and ELISA test. The clinical data of the patients diagnosed etiologically as hMPV infection analyzed included the infants' age, sex, the degree of fever, the severity of wheezing and clinical Lowell score, the findings of chest examination and chest X-ray, the white blood cell count and blood gas analysis, the course of the disease, the major treatments and the outcome of the disease. RESULTS: Twenty-one specimens showed the predicted 213 bp PCR products in agarose gel and the positive rate was 16.7% of all patients (21/126) and 39% of the patients with negative results for common respiratory pathogens detections (21/54). The range of patients' age was 2 - 15 months and the young infants with hMPV bronchiolitis (1 - 6 month of age) accounted for 62% and the male:female ratio was 3.2:1. The patients presented a low-medium grade fever (T < 39 degrees C) accounted for 86%; 81.0% of patients had a white blood cell count lower than 10.0 x 10(9)/L. The radiological findings were patchey opacity in both lungs (68%) and(or) hyperinflation (62%). Assessed by the Lowell score system, 5 out of 21 cases were considered as severe cases. The major clinical findings of hMPV bronchiolitis had no significant difference compared with that of subgroup A hRSV bronchiolitis, and showed longer course of disease than that of subgroup B hRSV bronchiolitis (P < 0.01). CONCLUSIONS: Of the infants with bronchiolitis hospitalized in our hospital from November of 2002 through February of 2003, 16.7% were caused by hMPV infection. These data showed that the major clinical characteristics and the outcome of treatment of hMPV bronchiolitis had no statistically significant difference compared to the cases with either subgroup A or subgroup B hRSV infection.

Bronchiolitis↗

PubMed2003

Autonomous detection of aerosolized Bacillus anthracis and Yersinia pestis.

We have developed and tested a fully autonomous pathogen detection system (APDS) capable of continuously monitoring the environment for airborne biological threat agents. The system is designed to provide early warning to civilians in the event of a terrorist attack. The final APDS will be completely automated, offering aerosol sampling, in-line sample preparation fluidics, multiplexed detection and identification immunoassays, and orthogonal, multiplexed PCR (nucleic acid) amplification and detection. The system performance (current capabilities include aerosol collection, multiplexed immunoassays, sample archiving, data reporting, and alarming) was evaluated in a field test conducted in a Biosafety Level 3 facility, where the system was challenged with, and detected, a series of aerosolized releases containing two live, virulent biological threat agents (Bacillus anthracis and Yersinia pestis). Results presented here represent the first autonomous, simultaneous measurement of these agents.

Aerosols↗

PubMed2025

Whole Genome Sequencing and Genetic Diversity of Respiratory Viruses Detected in Children With Acute Respiratory Infections: A One-Year Cross-Sectional Study in Senegal.

Acute respiratory infections (ARI) are a health priority, especially in countries with limited resources. They are a major cause of morbidity and mortality, especially among children and the elderly. In Senegal, the endemic circulation of respiratory viruses other than influenza has been demonstrated. However, there is a paucity of data exploring the genetic diversity of these viruses based on whole-genome sequencing. In this study, we present data on the genetic diversity of respiratory viruses in children under 15 years old in Senegal, including an overview of the different pathogens detected. Between November 2022 and November 2023, we collected nasopharyngeal swabs from children seen in curative consultations for symptoms of acute respiratory infections. Of the 156 children included, 73.7% tested positive for at least one pathogen. The most frequently detected virus was rhinovirus (50.0%), followed by influenza B (41.6%) and human parainfluenza virus type 3 (7.6%). Combinations of rhinovirus/influenza B, human parainfluenza virus type 2/human parainfluenza virus type 4, and rhinovirus/influenza B/adenovirus were the most frequently identified. A statistically significant association was detected between some of the viruses detected. A high genetic diversity of respiratory viruses circulating in children was revealed. The strains were phylogenetically close to various strains circulating worldwide, suggesting a global circulation of respiratory viruses. Our study provides the first complete genome sequences of human parainfluenza viruses type 2, 3, 4 and human bocavirus from Senegal and thus contributes to the enrichment of international databases on sequences from Senegal and underlines the importance of sequencing in the dynamics of pathogen circulation.

Humans↗