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Results for “pathogen detection”

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PubMed2000

Members of the Arabidopsis HRT/RPP8 family of resistance genes confer resistance to both viral and oomycete pathogens.

Turnip crinkle virus (TCV) inoculation onto TCV-resistant Arabidopsis leads to a hypersensitive response (HR) controlled by the dominant gene HRT. HRT is a member of the class of resistance (R) genes that contain a leucine zipper, a nucleotide binding site, and leucine-rich repeats. The chromosomal position of HRT and its homology to resistance gene RPP8 and two RPP8 homologs indicate that unequal crossing over and gene conversion may have contributed to HRT evolution. RPP8 confers resistance to an oomycete pathogen, Peronospora parasitica. Despite very strong similarities within the HRT/RPP8 family, HRT and RPP8 are specific for the respective pathogens they detect. Hence, the HRT/RPP8 family provides molecular evidence that sequence changes between closely related members of multigene families can generate novel specificities for radically different pathogens. Transgenic plants expressing HRT developed an HR but generally remained susceptible to TCV because of a second gene, RRT, that regulates resistance to TCV. However, several transgenic plants that overexpressed HRT produced micro-HRs or no HR when inoculated with TCV and were resistant to infection. Expression of the TCV coat protein gene in seedlings containing HRT resulted in massive necrosis and death, indicating that the avirulence factor detected by the HRT-encoded protein is the TCV coat protein.

Amino Acid Sequence↗

PubMed2004

Visualisation of zebrafish infection by GFP-labelled Vibrio anguillarum.

Vibrio anguillarum is an invasive pathogen of fish causing a septicaemia called vibriosis. In this work, transparent zebrafish were immersed in water containing green fluorescent protein labelled V. anguillarum. The infection was visualised at the whole fish and single bacterium levels using microscopy. The gastrointestinal tract was the first site where the pathogen was detected. This enteric localisation occurred independently of the flagellum or motility. On the other hand, chemotactic motility was essential for association of the pathogen with the fish surface. In conclusion, the zebrafish infection model provides evidence that the intestine and skin represent sites of infection by V. anguillarum and suggests a host site where chemotaxis may function in virulence.

Animals↗

PubMed2026

Deciphering the etiology of the 2024 outbreak of undiagnosed febrile illness in Panzi, Democratic Republic of the Congo.

In late 2024, an outbreak of over 400 cases of undiagnosed febrile illness, predominantly presenting as fever and cough, was reported in Panzi Health Zone, southwestern Democratic Republic of the Congo. Here we conducted an epidemiological and laboratory investigation to determine the etiology of the outbreak. Clinical data and specimens were prospectively collected from 108 individuals, of whom 59/108 (54.6%) were female. Children aged <5 years were the most affected (47/108, 43.5%); 14/32 (43.7%) were malnourished. Oro/nasopharyngeal swabs from 96/108 individuals were PCR tested; 26 blood samples were sequenced. Plasmodium falciparum was detected in 56/108 (51.8%) individuals. Co-infections were also detected, with influenza A(H1N1)pdm09 virus in 16/56 (28.6%) and severe acute respiratory syndrome coronavirus 2 in 10/56 (17.9%) individuals. No novel pathogens were detected via metagenomics. Our findings suggest that the outbreak was primarily associated with a surge in malaria cases, with concurrent viral respiratory infections. Increasing decentralized laboratory capacity and strengthening broader health systems remain crucial for faster outbreak detection and investigation.

Disease Outbreaks↗

PubMed2001

Phenotypic and genotypic characterization of Cryptosporidium species and isolates.

Recent outbreaks of cryptosporidiosis from contaminated water supplies have led to a need for the detection of Cryptosporidium oocysts from various hosts and contaminating sources. The presence of nonpathogenic species or strains of Cryptosporidium is important for diagnostic purposes as there is a potential for false- positive detection of pathogenic parasites. The present review focuses on phenotypic differences and recent advances in genotypic analyses of the genus Cryptosporidium with an emphasis on detecting various isolates and identifying differences in Cryptosporidium parvum and other species in this genus. The information currently available demonstrates important patterns in DNA sequences of Cryptosporidium, and our understanding of macro- and microevolutionary patterns has increased in recent years. However, current knowledge of Cryptosporidium genetic diversity is far from complete, and the large amount of both phenotypic and genotypic data has led to problems in our understanding of the systematics of this genus.

Animals↗

PubMed1980

Specific proteolysis of human IgA by Streptococcus pneumoniae and Haemophilus influenzae.

Streptococcus pneumoniae and Haemophilus influenzae are among the most common bacterial pathogens responsible for respiratory tract infections in otherwise healthy humans. Thirty-six strains of S. pneumoniae, 62 strains of H. influenzae, six hospital-acquired respiratory pathogens, and a strain of Streptococcus pyogenes were examined for production of IgA protease, a bacterial enzyme whose only known substrate is human IgA1. IgA protease was produced by 100% of the isolates of S. pneumoniae and 98% of the isolates of H. influenzae. The enzyme from both species cleaved human serum and secretory IgA1 proteins, but not human IgA2, IgG, or human serum albumin. None of the hospital-acquired pathogens had detectable IgA protease activity, a finding indicating that the production of this enzyme distinguishes S. pneumoniae and H. influenzae from the opporunistic respiratory pathogens.

Antibodies, Bacterial↗

PubMed2026

Patterns of antimicrobial resistance genes in pathogens across One Health sectors in Ireland: an in silico approach.

As part of a rapid risk assessment, an in silico approach was used to detect antimicrobial resistance (AMR) in pathogenic isolates from humans, animals, and the environment. A total of 11,670 genomic data sets were retrieved from the NCBI Pathogen Detection system for Ireland, which represented 47 pathogenic species, including Salmonella enterica, Escherichia coli/Shigella spp., Staphylococcus aureus, Klebsiella pneumoniae, and Enterococcus faecium. Identifying the most critical pathogenic strains over time is essential, as these organisms significantly contribute to mortality, morbidity, and hospitalization. The analysis identified 799 antimicrobial resistance genes (ARGs), including their allelic diversity, 117 plasmid replicons, and 274 virulence factors. Several critical ARGs, particularly those conferring resistance to beta-lactams, aminoglycosides, quinolones, and colistin, were common across isolates originating from human, animal, and environmental sources, suggesting shared resistance profiles across One Health sectors. Klebsiella pneumoniae, E. coli/Shigella spp., S. enterica, and S. aureus were the dominant hosts of these ARGs and associated mobile genetic elements. Increasing resistance across major antibiotic classes aligned with trends reported across other European countries. This study provides a national-scale in silico comparison of AMR across pathogens and One Health sectors using publicly available genomic data. The findings help reinforce Ireland's AMR surveillance by showing which resistance genes are present and how they spread across critical pathogens in humans, animals, and the environment. These findings highlight the urgent need for improved antibiotic stewardship and integrated One Health surveillance to limit the emergence and spread of AMR.IMPORTANCEAntimicrobial resistance (AMR) is a growing threat to human, animal, and environmental health. This study used publicly available genomic data to identify antimicrobial resistance genes (ARGs) in key bacterial pathogens circulating in Ireland. By analyzing over 11,000 genomes from humans, animals, and the environment, we found that several dangerous resistance genes, including those against last-resort antibiotics, were widespread across different sources. The study highlights which bacteria and resistance genes are most critical and how they may spread between humans, animals, and the environment. These insights provide a national snapshot of AMR, supporting more effective monitoring and prevention strategies. By revealing patterns of resistance and modes of transmission, our findings underscore the importance of coordinated antibiotic stewardship and One Health approaches to slow the emergence and spread of resistant infections, protecting public health and ensuring antibiotics remain effective.

Humans↗

PubMedDate not supplied

Diagnostic PCR: validation and sample preparation are two sides of the same coin.

Increased use of powerful PCR technology for the routine detection of pathogens has focused attention on the need for international validation and preparation of official non-commercial guidelines. Bacteria of epidemiological importance should be the prime focus, although a "validation infrastructure" once established could easily be adapted for PCR-based detection of viruses and parasites. The aim of standardization should be the widespread adoption of diagnostic PCR for routine pathogen testing. European experience provides the impetus for realization of this vision through preparation of quantitative reference DNA material and reagents, production of stringent protocols and tools for thermal cycler performance testing, uncomplicated sample preparation techniques, and extensive ring trials for assessment of the efficacy of selected matrix/pathogen detection protocols.

Humans↗

PubMed1998

Fot 1 insertions in the Fusarium oxysporum f. sp. albedinis genome provide diagnostic PCR targets for detection of the date palm pathogen.

Populations of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease of date palm, are derivatives of a single clonal lineage and exhibit very similar Fot 1 hybridization patterns. In order to develop a sensitive diagnostic tool for F. oxysporum f. sp. albedinis detection, we isolated several DNA clones containing a copy of the transposable element Fot 1 from a genomic library of the date palm pathogen. Regions flanking the insertion sites were sequenced, and these sequences were used to design PCR primers that amplify the DNA regions at several Fot 1 insertion sites. When tested on a large sample of Fusarium isolates, including 286 F. oxysporum f. sp. albedinis isolates, 17 other special forms, nonpathogenic F. oxysporum isolates from palm grove soils, and 8 other Fusarium species, the primer pair TL3-FOA28 allowed amplification of a 400-bp fragment found only in F. oxysporum f. sp. albedinis. Sequence analysis showed that one of the Fot 1 copies was truncated, lacking 182 bp at its 3' terminus. The primer pair BI03-FOA1 amplified a 204-bp fragment which overlapped the Fot 1 truncated copy and its 3' site of insertion in the F. oxysporum f. sp. albedinis genome and identified 95% of the isolates. The primer pairs BIO3-FOA1 and TL3-FOA28 used in PCR assays thus provide a useful diagnostic tool for F. oxysporum f. sp. albedinis isolates.

Cloning, Molecular↗

PubMed1996

The value of cerebrospinal fluid enrichment culture in the diagnosis of acute bacterial meningitis.

The records of cerebrospinal fluid (CSF) examinations for the three-year period ending 30 September 1991 were studied retrospectively. From 3,161 examinations, 66 pathogens were detected, 64 of which were from primary agar plate culture. Enrichment broth culture yielded 219 isolates of which 217 were likely contaminants. Only two pathogens were isolated by enrichment, and in both samples the CSF leucocyte counts were abnormal. The use of enrichment broth culture should be confined to CSF specimens with abnormal leucocyte counts and/or Gram stains.

Acute Disease↗

PubMed2001

'RETCIF': a rapid, sensitive method for detection of viruses, applicable for large numbers of clinical samples.

Rapid detection of viruses in clinical samples is important for continuing appropriate antiviral treatment and discontinuing unnecessary antibacterial treatment, as well as for excluding viral pathogens. Yet detection of viral agents may require numerous susceptible cell lines. Even with the shell vial culture method, it is cumbersome for handling large volumes of specimens. A procedure has been developed, which is time and cost-saving and uses specific cell lines in a 96-well microtitre plate and monoclonal antibodies (RETCIF-rapid enhanced tissue culture immunofluorescence). Each clinical sample was inoculated into 12 different wells with five different cell lines. Enhancement was achieved by sonication, centrifugation and hormonal supplementation to the medium used. Cytomegalovirus (CMV), herpes simplex virus (HSV) and respiratory viruses were detected by monoclonal antibodies on day 2, whilst varicella zoster virus (VZV) and enteroviruses were detected on days 5 and 7, respectively. During July-December 1998, 3298 patient specimens were compared by RETCIF and a modified shell vial method. Either or both methods isolated 779 viruses (24% positivity rate), whilst both methods detected 621. Of the 779 viruses, 87% (679) were isolated by the shell vial method in an average time of 4.9 days. For RETCIF the respective rate was 92.5% (721), in an average time of 3.0 days. The RETCIF method is a time-saving procedure, with higher isolation rates than the shell vial method.

Antibodies, Monoclonal↗

PubMed1998

Diagnosis of infectious endophthalmitis after cataract surgery by polymerase chain reaction.

PURPOSE: To ascertain whether the use of the polymerase chain reaction (PCR) technique leads to more rapid diagnosis of infectious endophthalmitis after cataract surgery. SETTING: University Eye Clinic Regensburg, Germany. METHODS: The aqueous humor and vitreous of 16 eyes with infectious endophthalmitis (10 acute, 6 delayed) were evaluated by microscopy, diagnostic culture, and PCR to detect the infectious agent. RESULTS: Microscopy of the vitreous was positive in 3 eyes and the culture media results were positive in 7 eyes, all with acute endophthalmitis. Significantly fewer positive results were obtained in the aqueous humor. Using PCR, an infectious agent was detected in the aqueous humor of all 16 eyes and in the vitreous of 14. The vitreous sample was negative in 2 eyes with delayed endophthalmitis. CONCLUSIONS: Detection of the infectious agent was more successful using PCR than using conventional microbiological tests, especially in the diagnosis of delayed endophthalmitis where the pathogen was detected in the aqueous humor in all eyes.

Acute Disease↗

PubMed1990

Antibodies to some pathogenic agents in free-living wild species in Tanzania.

A total of 535 sera from eight species of wildlife were collected from different game areas in Tanzania between 1987 and 1989. These sera were tested for antibodies against foot-and-mouth disease, bovine herpes virus types 1 and 2, lumpy skin disease, bovine viral diarrhoea, Akabane, bovine ephemeral fever, bluetongue, enzootic bovine leucosis, African horse sickness and African swine fever viruses and Brucella abortus based on the expected species susceptibility. Sera from buffalo Syncerus caffer, wildebeest Connochaetes taurinus and topi Damaliscus korrigum contained antibodies against the majority of the pathogens tested. Antibodies to fewer pathogens were detected in sera from the other species. No antibodies to lumpy skin disease virus were detected in any of the sera examined. African horse sickness antibodies were detected in sera from Zebra and African swine fever antibodies were detected in wart hog. The occurrence of antibodies to these agents suggests that wild species act as reservoirs of infection for some of these pathogens. However, until the susceptibility of individual species is proven by isolation of the aetiological agents their role must remain speculative.

Animals↗

PubMed2000

The diagnostic value of electron microscopy in human immunodeficiency virus-positive patients with gastrointestinal disease.

BACKGROUND: Our aim was to determine the diagnostic value of electron microscopy in evaluating the etiology of gastrointestinal disease in patients infected with the human immunodeficiency virus (HIV). METHODS: A retrospective review of electron microscopic and light microscopic results of all HIV-positive patients with gastrointestinal and liver diseases was made during a 3-year period from June 1995 to June 1998. RESULTS: A total of 145 HIV-positive patients had their electron microscopy specimens reviewed. Of these, 136 were investigated for diarrhea, and the other 9 for increased liver enzymes. Twenty-seven of the 145 (18.6%) HIV-positive patients had a pathogen identified by electron microscopy, compared with only 13 of 145 (9%) identified by light microscopy (P < 0.005). The sensitivity of light microscopy for detecting opportunistic pathogens was 68%. Twenty-one of the 27 (77.8%) patients diagnosed by electron microscopy had microsporidiosis, and the most commonly diagnosed species was Enterocytozoon bieneusi. Light microscopy failed to identify 12 cases of microsporidiosis and 2 cases of leishmaniasis. CONCLUSIONS: Electron microscopy contributes substantially to the identification of pathogens in HIV-positive patients. Light microscopy failed to identify one of every two pathogens diagnosed by electron microscopy.

Adult↗

PubMed1997

Human herpesvirus-6 infection in liver transplant recipients: documentation of pathogenicity.

BACKGROUND: The new herpesvirus, human herpesvirus-6 (HHV-6), is able to cause clinical illness after transplantation; however, the pathogenic potential and the clinical features of HHV-6 have not been defined in liver transplant recipients. METHODS: We report the first cases of invasive and symptomatic infection due to HHV-6 in liver transplant recipients. RESULTS: HHV-6 infection occurred in four liver transplant recipients at a median of 50 days after transplant (range 17-90 days). Severe cytopenia was observed in all patients; leukopenia (with median leukocyte count of 1400/mm3) was the most commonly effected bone marrow lineage. One of the four patients had interstitial pneumonitis due to HHV-6. No other virus (e.g., cytomegalovirus) or another pathogen was detected in the lungs, blood, or bone marrow in any of the above patients. CONCLUSIONS: Our data suggest that HHV-6 can be a pathogen in liver transplant recipients; idiopathic bone marrow suppression is its predominant clinical sequelae. Recognition of HHV-6 infection is clinically pertinent because HHV-6 is potentially treatable with the currently available antiviral agents.

Adult↗

PubMed2004

Pure shear horizontal SAW biosensor on langasite.

The undetected introduction of pathogens into food or water supplies can produce grave consequences in terms of economic loss and human suffering. Sensitive and selective sensors capable of quickly detecting microbial pathogens are urgently needed to limit the effects of bioterrorist incidents, accidents, or pollution. Shear horizontal surface acoustic wave (SH SAW) devices provide an attractive platform for the design of microbial biosensors that function in liquid media, where Rayleigh-type modes are rapidly attenuated. This paper reports on an exploratory SH SAW delay line designed and fabricated on langasite, La3Ga5SiO14 (LGS), along the novel Euler propagation direction (0 degrees, 22 degrees, 90 degrees). A liquid chamber was fabricated and attached to the top surface, and the device was submitted to liquid and biochemical tests. Moderate (6 dB) additional attenuation of the transmission coefficient, /S21/, was consistently observed when the SH SAW delay line was assembled in the test fixture and submitted to the liquid tests, indicating that LGS is an attractive candidate for liquid sensing. Sensor selectivity can be achieved by integrating the LGS SH SAW delay line with a biochemical recognition layer. A test setup was implemented for the characterization of LGS SH SAW-based biosensors. The delay line response to biomolecule binding was shown by detection of sequential binding of proteins to the SH SAW device delay path. The biotinylated sensor was exposed sequentially to biotin-binding deglycosylated avidin, biotin-modified rabbit IgG, and goat anti-rabbit IgG antibody. As each protein was bound to the sensing surface, marked changes in the delay-line phase were recorded. The reported results demonstrate the capability of these devices to act as biochemical detectors in aqueous solutions, and this work represents the first effort using the novel material LGS in SAW-based biosensor technology.

Acoustics↗

PubMed2005

Effects of cattle feeding regimen and soil management type on the fate of Escherichia coli O157:H7 and salmonella enterica serovar typhimurium in manure, manure-amended soil, and lettuce.

Survival of the green fluorescent protein-transformed human pathogens Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium was studied in a laboratory-simulated lettuce production chain. Dairy cows were fed three different roughage types: high-digestible grass silage plus maize silage (6:4), low-digestible grass silage, and straw. Each was adjusted with supplemental concentrates to high and low crude protein levels. The pathogens were added to manure, which was subsequently mixed (after 56 and 28 days for E. coli O157:H7 and Salmonella serovar Typhimurium, respectively) with two pairs of organically and conventionally managed loamy and sandy soil. After another 14 days, iceberg lettuce seedlings were planted and then checked for pathogens after 21 days of growth. Survival data were fitted to a logistic decline function (exponential for E. coli O157:H7 in soil). Roughage type significantly influenced the rate of decline of E. coli O157:H7 in manure, with the fastest decline in manure from the pure straw diet and the slowest in manure from the diet of grass silage plus maize silage. Roughage type showed no effect on the rate of decline of Salmonella serovar Typhimurium, although decline was significantly faster in the manure derived from straw than in the manure from the diet of grass silage plus maize silage. The pH and fiber content of the manure were significant explanatory factors and were positively correlated with the rate of decline. With E. coli O157:H7 there was a trend of faster decline in organic than in conventional soils. No pathogens were detected in the edible lettuce parts. The results indicate that cattle diet and soil management are important factors with respect to the survival of human pathogens in the environment.

Agriculture↗

PubMed2004

Characterization and molecular methods for detection of a novel spiroplasma pathogenic to Penaeus vannamei.

Traditionally, Spiroplasma spp. have only been isolated from the surfaces of flowers and other plant parts, from the guts and hemolymph of various insects, and from vascular plant fluids (phloem sap) and insects that feed on these fluids. In this article, we report the first pathogenic spiroplasma to be discovered in shrimp and the results of its characterization through histological evaluation, in situ hybridization assays, transmission electron microscopy, 16S rRNA sequence homology, and injection infectivity studies. In addition, molecular methods are described that were developed for the detection of this microorganism, which was determined to be the causative disease agent in Colombian farm-raised Penaeus vannamei suffering from high mortalities. Using standard histological methods and in situ hybridization assays, it was confirmed that P. vannamei was infected with this pathogenic spiroplasma. Histological analysis revealed systemic inflammatory reactions in affected organs/tissues. In an attempt to identify the bacteria, frozen infected P. vannamei samples, from the initial epizootic, were used to sequence the 16S rRNA gene and develop molecular detection methods. The 16S rRNA gene was amplified by PCR and then sequenced. The sequence data were analyzed using the GenBank BLAST search and the results revealed a 98% homology with Spiroplasma citri, a pathogen of citrus trees. The 16S rRNA sequence data were evaluated for development of unique PCR primers to the putative spiroplasma. Using PCR primers developed for the spiralin gene of Spiroplasma spp., a digoxigenin-labeled probe was developed and tested. This probe was species-specific, with no positive reactions or cross-reactivity occurring with other bacterial samples tested in this format.

Animals↗

PubMed2002

Risk evaluation for pathogenic bacteria and viruses in sewage sludge compost.

Composting can be regarded as the most available option for recycling of sewage sludge. However, the existence of pathogenic bacteria and viruses in the compost has been scarcely investigated until now. So there is little information on the infectious risk through agricultural activities or gardening in using the compost. In this study, several kinds of composts were investigated for detection of pathogenic bacteria (Salmonella spp. and Escherichia coli O157) and enteric viruses. It was concluded from the result that these bacteria and viruses could not be detected in 1.0 g-wet of any kinds of composts. Infectious risks through agricultural activities or gardening were evaluated by Monte Carlo simulation in the case that the compost was polluted by Salmonella spp., E. coli O157:117 and Poliovirus 1. Criteria satisfying the acceptable risk (less than 10(-4) per year) for these pathogenic bacteria and virus in the compost were determined from the result of simulations. 1.0 [CFU or PFU/g-wet] was available as the criteria for E. coli O157 and Poliovirus 1 in the compost. On the other hand, the criterion for Salmonella spp. in the compost should be established on a lower concentration than 0.001 CFU/g-wet.

Agriculture↗