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Results for “pathogen detection”

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PubMed1991

Etiology of acute diarrhoea among children in developing countries: a multicentre study in five countries.

A 2-year etiological survey of acute diarrhoea in children aged 0-35 months who were attending treatment facilities was carried out using a standardized protocol in five hospitals in China, India, Mexico, Myanmar, and Pakistan. A total of 3640 cases of diarrhoea and 3279 age- and sex-matched controls were studied; about 60% of the patients were aged less than 1 year and 60% were male. An enteric pathogen was detected in 68% of the cases and in 30% of the controls. In all the study centres, the pathogens most strongly associated with disease were rotavirus (16% of cases, 2% of controls), Shigella spp. (11% of cases, 1% of controls) and enterotoxigenic Escherichia coli (16% of cases, 5% of controls). Rotavirus was commonest among 6-11-month-olds, accounting for 20% of all cases in this age group; 71% of all rotavirus episodes occurred during the first year of life. Shigella spp. were commonest among those aged 12-23 months and 24-35 months, accounting for 22% and 27% of the cases, respectively. The proportion of cases that yielded no pathogen was inversely related to age, being highest (41%) among infants below 6 months of age and lowest (19%) among those aged 24-35 months. These results suggest that microbe-specific intervention strategies for the control of childhood diarrhoeal diseases in developing countries should focus on rotavirus, Shigella spp. and enterotoxigenic E. coli.

Child, Preschool↗

PubMed1993

Prospective study of nosocomial enteric infections in a pediatric hospital, Calcutta.

Hospital acquired enteric infections were investigated by studying 3138 children under 5 years of age who were admitted without diarrhea in nine medical words of a pediatric hospital, Calcutta during the period between March and September 1987. Three hundred and twenty (10.2%) children developed nosocomial diarrhea during their hospital stay. Fecal samples from 178 nosocomial diarrhea, 345 hospitalized diarrhea cases, 178 hospital controls and 200 outpatient controls were collected for detection of established enteropathogens. There were no statistically significant differences in the detection of most of the enteropathogens from fecal samples of nosocomial diarrhea, hospitalized diarrhea and hospital controls. Enteric pathogens were detected at a higher frequency (statistically significant) from fecal samples of nosocomial diarrhea cases as compared to outpatient controls. This study highlights the importance of most of the enteropathogens like Shigella, Salmonella, rotavirus, enteropathogenic E. coli as the cause of hospital cross infection. This study reinforces the importance of developing preventive measures in order to reduce the frequency of illness.

Case-Control Studies↗

PubMedDate not supplied

Time course of radiometric detection of positive blood cultures in childhood.

We have determined the time course of radiometric detection of microbial growth in 2348 positive blood culture specimens obtained at Wyler Children's Hospital during a 5-year interval. Overall 72 and 88% of isolates were detected within 48 and 72 hours after sampling, respectively. For pathogenic organisms aerobic detection was generally more rapid and more inclusive than anaerobic detection. At 48 hours of incubation the detection of six potential pathogens (Salmonella sp., Haemophilus influenzae, Group D streptococci, Neisseria meningitidis, coagulase-negative staphylococci, Candida sp.) was significantly delayed compared with detection of other pathogenic organisms recovered from blood. At 72 hours of incubation the detection rates remained less than 95% for H. influenzae, Staphylococcus aureus, Klebsiella sp., coagulase-negative staphylococci, Group D streptococci and Candida sp. These data should assist clinical decisions regarding duration of antibiotic therapy for the presumptive diagnosis of bacteremia in children.

Anti-Bacterial Agents↗

PubMed1997

Multiplex PCR for avian pathogenic mycoplasmas.

Mycoplasma infections are of great concern in avian medicine, because they cause economic losses in commercial poultry production. A multiplex polymerase chain reaction (PCR) was optimized to simultaneously detect four pathogenic species of avian mycoplasmas. Four sets of oligonucleotide primers specific for Mycoplasma gallisepticum (MG), M. synoviae (MS), M. meleagridis (MM) and M. iowae (MI) were used in the test. By using agarose gel electrophoreses for detection of the PCR-amplified DNA products, the sensitivity of detection was between 1 pg for MG, 1 pg for MS, 100 fg for MM and 100 pg for MI after 35 cycles of PCR. Similar sensitivity of these primers was achieved with broth cultures of these four organisms.

Animals↗

PubMed2002

Microbial source tracking: state of the science.

Although water quality of the Nation's lakes, rivers and streams has been monitored for many decades and especially since the passage of the Clean Water Act in 1972, many still do not meet the Act's goal of "fishable and swimmable". While waterways can be impaired in numerous ways, the protection from pathogenic microbe contamination is most important for waters used for human recreation, drinking water and aquaculture. Typically, monitoring methods used for detecting potential pathogenic microorganisms in environmental waters are based upon cultivation and enumeration of fecal indicator bacteria (i.e. fecal coliforms, E. coli, and fecal enterococci). Currently, there is increasing interest in the potential for molecular fingerprinting methods to be used not only for detection but also for identification of fecal contamination sources. Molecular methods have been applied to study the microbial ecology of environmental systems for years and are now being applied to help improve our waters by identifying problem sources and determining the effect of implemented remedial solutions. Management and remediation of water pollution would be more cost-effective if the correct sources could be identified. This review provides an outline of the main methods that either have been used or have been suggested for use in microbial source tracking and some of the limitations associated with those methods.

Electrophoresis, Gel, Pulsed-Field↗

PubMed2003

A conductometric biosensor for biosecurity.

The paper describes the development of a conductometric biosensor for detecting foodborne pathogens. The biosensor consists of two components: an immunosensor that is based on electrochemical sandwich immunoassay, and a reader for signal measurement. The architecture of the immunosensor utilizes a lateral flow system that allows the liquid sample to move from one pad to another. The biosensor provides a specific, sensitive, low volume, and near real-time detection mechanism. Results are presented to highlight the performance of the biosensor for enterohemorrhagic Escherichia coli O157:H7 and Salmonella spp., which are of concern to biosecurity. The lower limit of detection is approximately 7.9 x 10(1) colony forming units per milliliter within a 10-min process. The ability to change the specificity of the antibodies will enable the biosensor to be used as a detection device for other types of foodborne pathogens.

Biosensing Techniques↗

PubMed1988

Isolation of a phytoalexin-detoxification gene from the plant pathogenic fungus Nectria haematococca by detecting its expression in Aspergillus nidulans.

Detoxification of the pea phytoalexin pisatin via demethylation, mediated by a cytochrome P-450 monooxygenase, is thought to be important for pathogenicity of the fungus Nectria haematococca on pea. To isolate a fungal gene encoding pisatin demethylating activity (pda), we transformed Aspergillus nidulans with a genomic library of N. haematococca DNA constructed in a cosmid which carried the A. nidulans trpC gene. Transformants were selected for Trp+ and then screened for pda. One transformant among 1250 tested was Pda+ and was less sensitive to pisatin in culture than Pda- A. nidulans. The cosmid containing the gene (PDA) conferring this activity was recovered by phage lambda packaging of transformant genomic DNA. When A. nidulans was transformed with the cloned cosmid, 98% of the Trp+ transformants were Pda+. RNA blots probed with a 3.35 kb subclone carrying PDA indicated that the gene is expressed constitutively in A. nidulans but is inducible by pisatin in N. haematococca.

Ascomycota↗

PubMed2005

Sequence analysis of the Escherichia coli O15 antigen gene cluster and development of a PCR assay for rapid detection of intestinal and extraintestinal pathogenic E. coli O15 strains.

A collection of 33 Escherichia coli serogroup O15 strains was studied with regard to O:H serotypes and virulence markers and for detection of the O-antigen-specific genes wzx and wzy. The strains were from nine different countries, originated from healthy or diseased humans and animals and from food, and were isolated between 1941 and 2003. On the basis of virulence markers and clinical data the strains could be split into different pathogroups, such as uropathogenic E. coli, enteropathogenic E. coli, Shiga toxin-producing E. coli, and enteroaggregative E. coli. H serotyping and genotyping of the flagellin (fliC) gene revealed 11 different H types and a close association between certain H types, virulence markers, and pathogroups was found. Nucleotide sequence analysis of the O-antigen gene cluster revealed putative genes for biosynthesis of O15 antigen. PCR assays were developed for sensitive and specific detection of the O15-antigen-specific genes wzx and wzy. The high pathotype diversity found in the collection of 33 O15 strains contrasted with the high level of similarity found in the genes specific to the O15 antigen. This might indicate that the O15 determinant has been spread by horizontal gene transfer to a number of genetically unrelated strains of E. coli.

Escherichia coli↗

PubMed2005

Detection of DNA of 'Candidatus Mycoplasma haemominutum' and Spiroplasma sp. in unfed ticks collected from vegetation in Japan.

DNA fragments of 'Candidatus Mycoplasma haemominutum', a feline heamobartonella pathogen, were detected from unfed Ixodes ovatus collected from vegetation in Hokkaido, Fukushima and Yamaguchi Prefectures, and unfed Haemaphysalis flava in Yamaguchi Prefecture. This finding suggests that ixodid tick is a possible vector of 'C. Mycoplasma haemominutum'. Spiroplasma DNA was also detected from unfed I. ovatus in Hokkaido, Fukushima and Yamaguchi Prefectures. The analysis of nucleotides sequence suggested that this Spiroplasma was distinct from registered species.

Animals↗

PubMed2002

Detection of EspB using reversed passive latex agglutination: application to determination of enteropathogenic Escherichia coli.

We developed a new practical method to identify enteropathogenic Escherichia coli (EPEC) by detecting the pathogenic factor, EspB. E. coli were cultured in Dulbecco's Modification of Eagle's Medium (DMEM), and EspB was detected in the culture supernatant by reversed passive latex agglutination (RPLA). All 63 E. coli strains harboring the eaeA gene encoding intimin were positive for RPLA, and all 25 strains without the eaeA gene were negative. Among these 63 eaeA-positive strains, 38 Shiga toxin-producing E. coli (STEC) produced Shiga toxin (Stx) under the same culture conditions (DMEM). Subtypes of EspB alpha, beta and gamma were antigenically cross-reactive to each other as determined by RPLA and Western blotting. A kit for Stx detection (RPLA) is commercially available and therefore this RPLA for detection of EspB could be a practical method to define EPEC in both clinical laboratories and the field.

Antibodies, Bacterial↗

PubMed2006

Diarrhea in American infants and young children in the community setting: incidence, clinical presentation and microbiology.

OBJECTIVE: The characteristics and microbiology of the full spectrum of pediatric diarrhea occurring in the U.S. community setting are not well-understood. METHODS: Six-month prospective cohort study of 604 healthy 6- to 36-month-old children recruited by the Slone Center Office-based Research Network. RESULTS: The incidence of parent-defined diarrhea was 2.2 episodes per person-year. The median duration of diarrhea was 2 days with a median of 6 stools per episode. Outpatient visits and hospitalization were prompted by 9.7 and 0.3% of episodes, respectively. The most common microorganisms identified in healthy baseline stools were atypical enteropathogenic Escherichia coli (12.2%), enteroaggregative Escherichia coli (3.7%), Clostridium difficile (3.5%) and Clostridium perfringens (2.9%), and each of these was no more common in diarrhea stools. In contrast, all of the viruses analyzed were more prevalent in diarrhea specimens than in baseline specimens: enteric adenovirus (5.7% diarrhea versus 1.4% baseline), rotavirus (5.2% versus 1.4%), astrovirus (3.5% versus 1.4%), Sapporo-like virus (3.0% versus 0.8%) and norovirus (1.9% versus 0.8%). A likely pathogen was detected in 20.6% of diarrhea specimens. Vomiting and > or =16 stools in an episode were predictive of isolating a pathogen from the stool, each with a relative risk of approximately 2. CONCLUSIONS: Healthy young children in this study experienced more than 2 cases of diarrhea per person-year, but most were brief and do not require medical attention. Although most diarrhea-associated pathogens were viruses, no likely pathogen was found in almost 80% of cases; possible etiologies for these cases include currently unknown gastrointestinal infections, nongastrointestinal illnesses and dietary/environmental factors.

Adenoviruses, Human↗

PubMed1991

Immunoglobulin E in the feces of children and adolescents from some tropical and subtropical countries.

Eighteen of 27 individuals, aged from 6 months to 19 years (mean 5 years, 7 months), from countries in the tropics or the subtropics had either intestinal parasitic infestations or intestinal enteropathogenic bacterial infections or both. Fourteen of those with intestinal pathogens had detectable concentrations of IgE in their fecal extracts, ranging from less than 0.5 to 420 IU/ml extract (mean 33 IU/ml). This rate of occurrence was significantly higher than the number of IgE-positive fecal extracts in a group of 54 healthy nonallergic Norwegian children (p less than 0.001), but did not differ from that of a group of 40 allergic children (p greater than 0.20). The individuals with intestinal helminthic infection had the highest fecal IgE concentrations. Of the 9 individuals who did not have any demonstrable intestinal pathogen, low concentrations of IgE could be detected in feces from only 2, which did not differ from the rate in the healthy Norwegian controls. The concentrations of IgE in the feces of the subjects from tropical/subtropical regions correlated linearly with the corresponding serum concentrations of IgE (r = 0.69; p less than 0.001). The results indicate that the combined load of intestinal pathogens, including helminths, protozoa, and enteropathogenic bacteria, may stimulate IgE production in the gut.

Adolescent↗

PubMed2004

The use of differential display to isolate viral genomic sequence for rapid development of PCR-based detection methods. A test case using Taura syndrome virus.

The purpose of this study was to explore the efficacy of using differential display (DD) to isolate viral genomic sequence using tissues from infected organisms so that a PCR procedure to detect the pathogen may be developed rapidly. The model virus used was the Taura syndrome virus (TSV), a ssRNA virus that cause high rates of mortality at shrimp farms. Two random primers in combination with four anchored primers were used to isolate five cDNAs, ranging in size from 241 to 822 bp, that were differentially expressed in TSV-infected shrimp (Litopenaeus vannamei). PCR experiments revealed that four of the five encoded shrimp genes while the fifth was likely to be a TSV gene. Evidence that the putative TSV sequence is part of the TSV genome was obtained by the 97% sequence identity it shared with the published TSV genome. PCR primers were designed successfully using the differential display sequence to develop a RT-PCR-based method to detect TSV. Because differential display does not require physical isolation of the virus and only a small amount of infected sample is needed, the technique may be useful as a method to isolate nucleic acid sequences from emerging pathogens so that PCR primers for their detection may be developed rapidly.

Animals↗

PubMed2005

Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses.

Invasive fungal infections have emerged as a major cause of morbidity and mortality in immunocompromised patients. Conventional identification of pathogenic fungi in clinical microbiology laboratories is time-consuming and, therefore, often imperfect for the early initiation of an adequate antifungal therapy. We developed a diagnostic microarray for the rapid and simultaneous identification of the 12 most common pathogenic Candida and Aspergillus species. Oligonucleotide probes were designed by exploiting the sequence variations of the internal transcribed spacer (ITS) regions of the rRNA gene cassette to identify Candida albicans, Candida dubliniensis, Candida krusei, Candida glabrata, Candida tropicalis, Candida parapsilosis, Candida guilliermondii, Candida lusitaniae, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, and Aspergillus terreus. By using universal fungal primers (ITS 1 and ITS 4) directed toward conserved regions of the 18S and 28S rRNA genes, respectively, the fungal ITS target regions could be simultaneously amplified and fluorescently labeled. To establish the system, 12 pre-characterized fungal strains were analyzed; and the method was validated by using 21 clinical isolates as blinded samples. As the microarray was able to detect and clearly identify the fungal pathogens within 4 h after DNA extraction, this system offers an interesting potential for clinical microbiology laboratories.

Aspergillosis↗

PubMed1996

Detection and identification of human pathogenic Leishmania and Trypanosoma species by hybridization of PCR-amplified mini-exon repeats.

A single pair of PCR primers within a conserved region of the mini-exon repeat was used to amplify the repeats from 10 species of pathogenic Leishmania belonging to four major clinical groups and also from three species of Trypanosoma. Oligonucleotide hybridization probes for the detection and identification of the PCR-amplified repeats were constructed from alignments of mini-exon intron and intergenic sequences. The probes generated from mini-exon intergenic regions of the L. (V.) braziliensis, L. (L.) donovani, and L. (L.) mexicana species hybridized specifically to their cognate groups without discriminating between the species within the groups. The probes for L. (L.) major and L. (L.) aethiopica were species-specific, while the L. (L.) tropica probe also hybridized with the L. (L.) aethiopica mini-exon repeat. The mini-exon intron-derived probes for T. cruzi, T. rangeli, and T. brucei were species-specific. This method involving the detection of specific PCR-amplified products produced using a single primer set represents a novel sensitive and specific assay for multiple trypanosomatid species and groups.

Animals↗

PubMed2000

Prevalence of sexually transmitted infections among clients of female commercial sex workers in Thailand.

BACKGROUND: Clients of commercial sex workers are considered at high risk for the acquisition and transmission of sexually transmitted diseases (STDs). Identification and treatment of infections in this group could help to reduce the transmission of STDs. GOAL: To ascertain the prevalence of sexually transmitted organisms in male clients of female sex workers in Thailand by analysis of seminal fluid collected after intercourse. STUDY DESIGN: Used condoms were collected from 291 male clients attending a brothel in Hat Yai, Thailand during a 7-day period. Nucleic acid was extracted from seminal fluid and tested by polymerase chain reaction for the presence of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, herpes simplex virus (HSV) and HIV sequences. RESULTS: Overall, 17 (6%), 47 (16%), and 2 (1%) of specimens were positive for C trachomatis, N gonorrhoeae and T vaginalis respectively. HSV sequences were found in 24 (8%) of the specimens: 14 specimens (5%) with HSV type 1, and 11 specimens (4%) with HSV type 2. HIV RNA was detected in two samples (1%). Overall, 75 specimens (26%) were positive for one or more infections, and more than one pathogen was detected in 16 specimens (5%). CONCLUSION: This study reports a high rate of STDs among clients of female sex workers in Thailand. Consequently, this population is a significant risk for transmitting STDs to commercial sex workers and to other noncommercial partners. Strategies that target this population of men are needed to reduce STD and HIV transmission.

DNA Primers↗

PubMed2004

Viral etiology of acute respiratory tract infections in children presenting to hospital: role of polymerase chain reaction and demonstration of multiple infections.

BACKGROUND: Viral lower respiratory tract infections are a leading cause of hospitalization for young children. METHODS: We used polymerase chain reaction (PCR) and conventional methods of cell culture and antigen detection to establish the viral etiology of acute respiratory tract infections in 75 hospitalized children. RESULTS: One or more viral pathogens were detected in 65 (87%) children, with respiratory syncytial virus being the most commonly identified virus (36 children). Other viruses identified included influenza virus types A and B, parainfluenzavirus type 3, adenovirus, enterovirus, rhinovirus, coronavirus and human metapneumovirus. PCR increased the diagnostic yield significantly compared with antigen detection and culture, with 39 (21%) diagnoses identified by this method. Multiple infections were identified in 20 (27%) children. CONCLUSIONS: PCR-based methodologies offer increased sensitivity for the detection of most respiratory viruses in young children. The inclusion of PCR into diagnostic testing strategies is needed to broaden our understanding of the natural ecology of respiratory viruses and the significance of multiple infections.

Acute Disease↗

PubMed2002

Rapid detection and enumeration of Naegleria fowleri in surface waters by solid-phase cytometry.

A new method for the rapid and accurate detection of pathogenic Naegleria fowleri amoebae in surface environmental water was developed. The method is based on an immunofluorescent assay combined with detection by solid-phase cytometry. In this study we developed and compared two protocols using different reporter systems conjugated to antibodies. The monoclonal antibody Ac5D12 was conjugated with biotin and horseradish peroxidase, and the presence of cells was revealed with streptavidin conjugated to both R-phycoerythrin and cyanine Cy5 (RPE-Cy5) and tyramide-fluorescein isothiocyanate, respectively. The RPE-Cy5 protocol was the most efficient protocol and allowed the detection of both trophozoite and cyst forms in water. The direct counts obtained by this new method were not significantly different from those obtained by the traditional culture approach, and results were provided within 3 h. The sensitivity of the quantitative method is 200 cells per liter. The limit is due only to the filtration capacity of the membrane used.

Animals↗