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PubMed1999

First identification of infectious salmon anaemia virus in North America with haemorrhagic kidney syndrome.

Haemorrhagic kidney syndrome (HKS), a serious disease affecting Atlantic salmon on the east coast of Canada, was determined to be caused by infectious salmon anaemia virus (ISAV) through the isolation of the pathogen on the SHK-1 (salmon head kidney) cell line and confirmation by ISAV-specific immunofluorescent antibody test (IFAT) and reverse transcriptase polymerase chain reaction (RT-PCR). In addition, the defining histopathology of HKS could be reproduced following the injection of material that rendered challenged fish ISAV-positive by cell culture in the absence of any other detectable pathogen. Preliminary nucleotide sequence comparison does not suggest any direct epidemiological connection between the Canadian and Norwegian isolates.

Animals↗

PubMed2026

Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios-a retrospective study from a single center.

BACKGROUND: Plasma cell-free DNA metagenomic next-generation sequencing (mNGS) is a non-invasive comprehensive method for the etiological diagnosis of various infectious diseases. However, research on the early diagnosis and real-world clinical impact of plasma mNGS in patients with suspected infection are still limited. MATERIALS AND METHODS: This study retrospectively included 140 patients with suspected infections who underwent early plasma mNGS and conventional culture testing. Referring to the clinical diagnosis of infectious diseases, the diagnostic performance of plasma mNGS and culture tests was compared, and the application scenarios and clinical effects of plasma mNGS were evaluated. RESULTS: The positive rate of plasma mNGS was significantly higher than that of culture methods (55.71% vs 25.10%, p < 0.001) and blood cultures (55.71% vs 12.86%, p < 0.001). Regarding clinical diagnosis, the sensitivity of plasma mNGS was significantly higher than that of culture (58.27% vs 37.80%, p = 0.002). The combination of mNGS and culture achieved a higher detection sensitivity (69.29%), especially in patients with multi-site co-infections (73.68%) and blood infections (73.17%). Plasma mNGS demonstrated higher sensitivity in patients with procalcitonin (PCT) index > 5 ng/ml or human neutrophil lipocalin (HNL) index > 200 ng/ml. In terms of treatment, a total of 69 patients (54.33%) benefited from plasma mNGS. CONCLUSION: This study highlights the significant improvement in pathogen detection performance by combining conventional culture with plasma mNGS detection, especially in patients with multi-site co-infections and blood infections. Early use of plasma mNGS as an adjunct to culture can better guide clinicians to initiate appropriate anti-infective therapy.

Humans↗

PubMed1985

Pathogenic properties of Campylobacter jejuni: assay and correlation with clinical manifestations.

The pathogenic properties of 20 strains of Campylobacter jejuni isolated from persons with clearly defined clinical manifestations were determined. Cell-free broth filtrates were examined for (i) enterotoxin production by Chinese hamster tissue culture assay and an enzyme-linked immunosorbent assay (ELISA) employing GM1 ganglioside and affinity-purified antiserum to Escherichia coli heat-labile toxin, (ii) cytotoxin production by Vero and HeLa cell tissue culture lines, and (iii) their ability to cause fluid secretion in rat ligated ileal loops. Viable bacteria were examined for invasive properties by an ELISA with the immunoglobulin fraction of antiserum to Formalin-killed bacteria of an invasive strain, and by their effect on fluid secretion and morphology in rat ligated ileal loops. None of the eight isolates obtained from asymptomatic carriers had any detectable pathogenic properties. All six strains isolated from persons with bloody invasive-type diarrhea elaborated a cytotoxin; their viable bacteria had high titers in the ELISA for invasive properties and caused fluid secretion in ligated ileal loops, although consistent morphologic abnormalities and evidence of mucosal invasion, examined by immunofluorescence techniques, were not detected. All six strains isolated from persons with watery secretory-type diarrhea produced an enterotoxin, one elaborated a cytotoxin, and broth filtrates of all strains caused fluid secretion in ligated ileal loops; viable bacteria had low titers in the ELISA for invasive properties and evoked fluid secretion in ligated loops by means of enterotoxin production. These observations show (i) that a correlation exists between the pathogenic properties of the infective C. jejuni strain and gastrointestinal manifestations in the infected host, and (ii) that these pathogenic properties can be identified by in vitro assays, including ELISAs.

Animals↗

PubMed1991

[Clinicopathological study of methicillin-resistant Staphylococcus aureus detected by pulmonary microbial culture in autopsied cases].

Microbial culture of lung specimens from 569 autopsied cases from 1986 to 1989 revealed methicillin-resistant Staphylococcus aureus (MRSA) in 28 cases, which were subsequently analyzed clinicopathologically. The number of MRSA positive cases has markedly increased in recent years (2 cases in 1986, 2 in 1987, 6 in 1988, 18 in 1989). The most frequent underlying disease was neoplasm, which was seen in 17 cases. Of non-neoplastic diseases, liver cirrhosis and diffuse panbronchiolitis were prevalent. Twenty-four cases had received a course of antibiotic therapy. Antibiotics frequently administered were third-generation Cephem and Imipenem/cilastatin sodium (used in 20 cases). Antibiotics o which MRSA was sensitive were administered in only one case (minocycline). Sputum culture was performed in only 10 cases, 5 of which were MRSA positive. MRSA had acquired resistance to fosfomycin and ofloxacin. Histological examination revealed complication by pneumonia in 19 cases. In 7 of these 19 cases, MRSA was the only pathogen detected. Pulmonary MRSA infection detected at autopsy is frequently seen in patients with terminal stage cancer, but it is frequently not diagnosed and is undertreated. This may be a factor responsible for the recent marked increase in the proportion of MRSA in pathogens causing infection within medical institutions.

Cross Infection↗

PubMedDate not supplied

[The isolability of the causative agent of pseudotuberculosis from rodents in Georgia].

Since 1960 the cases of isolating the pseudopathogen agent have been recorded in Georgia at particular regular intervals. The accumulated material mainly involves epizootiological findings, which may provide a definite insight into the prevalence of this disease in Georgia. In 1960-1990, 31 strains were isolated in particular regions and populated areas; these included 17 strains from grey rats, 4 from house mice, 9 from common voles, and 1 from field mice. The particular constancy of isolation of the pseudotuberculosis pathogen from synanthropic rodents indicates that they may really infect humans, contrary to the opinion of G. P. Somov et al. who consider that among the synanthropic rodents there is only a chronic epizootic causing no animal death and that the role of the rodents in the spread of infection among humans is insignificant. However, doubt is cast on the validity of this proposition as the evidence for carriage alone among the rodents is lacking. The special literature contains no information on the dynamics of an epizootic process of pseudotuberculosis among the synanthropic rodents whereas the high pathogen detection rate in the viscera of these animals, recognized by Somov et al., mostly likely confirms the possibility of the course of epizootic manifested by the disease, but not only carriage. There is reason to consider pseudotuberculosis to be a naturally focal disease that is characterized by recurrent epizootics of varying intensity. Therefore, wild and synanthropic rodents may be as a reservoir and a source of infection. The circulation of the pathogen among wild and synanthropic rodents, in terms of their ability to be preserved and breed in the environmental objects, presents a permanent risk of not only sporadic cases, but also pseudotuberculosis outbreaks.

Animals↗

PubMed2026

Seqwin: ultrafast identification of signature sequences in microbial genomes.

MOTIVATION: Polymerase chain reaction (PCR) enables rapid, cost-effective diagnostics but requires prior identification of genomic regions that allow sensitive and specific detection of target microbial groups, herein referred to as microbial signature sequences. We introduce Seqwin, an open-source framework designed to automate microbial genome signature discovery. Tens of thousands of microbial genomes are now available for a single species, limiting the application of existing manual and automated approaches for identifying signatures. Modern approaches that are capable of leveraging all available microbial genomes will ensure sensitive and accurate DNA signature identification and enable robust pathogen detection for clinical, environmental, and public health applications. RESULTS: Seqwin builds weighted pan-genome minimizer graphs and uses a traversal algorithm to identify signature sequences that occur frequently in target genomes but remain rare in non-targets. Unlike earlier tools that depend on strict presence or absence of sequences, Seqwin accommodates natural sequence variation and scales to very large genome collections. When applied to genomes from C. difficile, M. tuberculosis, and S. enterica, Seqwin recovered more high-quality signatures than alternative methods with lower computational burden. Seqwin's analysis of nearly 15 000 S. enterica genomes yielded over 200 candidate signatures in three minutes. Seqwin provides an open-source solution for the long-standing need for scalable microbial signature discovery and diagnostic assay design. AVAILABILITY AND IMPLEMENTATION: Seqwin is available on GitHub (https://github.com/treangenlab/Seqwin) and can be installed via Bioconda (https://bioconda.github.io/recipes/seqwin/README.html). Benchmarking datasets, outputs, and scripts are available on Zenodo (https://doi.org/10.5281/zenodo.19874011).

Software↗

PubMed1989

Chronic colitis after Aeromonas infection.

Three patients with an acute colitis in which the only pathogen detected was either Aeromonas hydrophila or A sobria progressed to a chronic phase after the infection had been eliminated by antibiotic treatment in two and had resolved spontaneously in the third. The final diagnosis in each case was ulcerative colitis. Two of the patients have responded to anti-inflammatory medication but one has required panproctocolectomy. The sequence of symptoms and observations in these cases, as well as in others from the literature involving more familiar pathogens, suggests that bacterial infection may contribute to the development of chronic colitis. This supposition could be tested by extending the follow up of patients with acute infective colitis in a prospective multicentre trial.

Adult↗

PubMedDate not supplied

Physiologic response to a protein, carbohydrate, fat meal in patients with human immunodeficiency virus who underwent small intestinal enteropathy as characterized by a kinetic model of D-xylose absorption.

PURPOSE: Small intestinal human immunodeficiency virus enteropathy is characterized by profound absorptive dysfunction unrelated to histology or pathogens. Frequently an attempt is made to compensate for this intestinal failure by supplementing nutrient intake with nourishing liquid meals. It is not known how the diminished absorptive function in these patients will respond to this intake. With the use of a D-xylose kinetic model of absorption, we determined the absorptive response of patients with small intestinal enteropathy to an isotonic liquid feeding. METHODS: Seven male patients with acquired immunodeficiency syndrome (AIDS), diarrhea, weight loss, and no detectable pathogens (stool studies and duodenal biopsy) were enrolled. After an overnight fast, the patients were studied on three separate days. On day 1, the patients received 15 g oral D-xylose. On day 2, 10 g i.v. D-xylose was given. On day 3, 15 g oral D-xylose was again given along with 250 mL of a liquid polymeric isotonic diet. Serum and urine collections were obtained to calculate the kinetic rate constants and extent of D-xylose absorption. RESULTS: Mean values for the rate constant for absorption of D-xylose, Ka, (0.26/h; N > 0.65) and the rate constant for nonabsorptive loss, K0' (2.47/h; N < 0.353) were very abnormal before the meal. Mean K0 improved (decreased to 0.66), but Ka and bioavailability, F, did not have a statistically significant change after the meal. The improvement in mean K0 with the meal was much more pronounced in the five subjects with high K0 values before the meal (without meal 3.22: with meal 0.67; p < .05). CONCLUSIONS: (1) An isotonic liquid polymeric diet leads to less nonabsorptive loss of D-xylose, but does not affect the extent of D-xylose absorption in this group as a whole. This is probably due to the meal slowing gastric emptying. (2) Improvement in nonabsorptive loss with a meal is most pronounced when there is excessive nonabsorptive loss, K0, without a meal. (3) Improvement in nonabsorptive losses with a meal might predict which patients will benefit from antimotility agents and continued feedings vs those requiring i.v. hyperalimentation.

Administration, Oral↗

PubMed2005

Changes in platelet count after cardiac surgery can effectively predict the development of pathogenic heparin-dependent antibodies.

Cardiopulmonary bypass (CPB) induces the release of platelet factor 4 (PF4) and patients are at risk of heparin-induced thrombocytopenia (HIT). This study was aimed to determine whether an abnormal evolution in platelet count (PC) after CPB is predictive of the development of HIT antibodies. Two abnormal PC patterns were defined: pattern P1, characterized by a decrease in PC following previous correction of thrombocytopenia occurring during CPB, and pattern P2, defined as a persistent low PC in the days following CPB. PC was evaluated for 10 d in 305 consecutive patients before and after CPB. Serotonin release assay (SRA) was carried out between days 8 and 10 to detect pathogenic heparin-dependent antibodies. Moreover, antibodies to heparin-PF4 (H-PF4) complexes were assayed by enzyme-linked immunosorbent assay. PC evolution after CPB was normal in 300 patients although antibodies to H-PF4 were frequently present (53.4%). Changes in PC were abnormal in five patients with pattern P1 (n = 4) or P2 (n = 1). As SRA was positive in four of the five cases, the positive predictive value of abnormal PC pattern for pathogenic HIT antibodies was 80%. Careful follow-up of PC after CPB makes it possible to predict with high specificity (99%) for those patients who develop pathogenic HIT antibodies.

Adolescent↗

PubMed1998

Biochemical and pathogenic properties of Shewanella alga and Shewanella putrefaciens.

We characterized 49 strains of Shewanella spp. from clinical (n = 31) and nonhuman (n = 18) sources. Most Shewanella alga organisms (Gilardi biovar 2; Centers for Disease Control and Prevention [CDC] biotype 2) originated from clinical material (92%), failed to produce acid from carbohydrates other than D-ribose, and were biochemically and enzymatically fairly homogeneous. In contrast, Shewanella putrefaciens organisms (Gilardi biovars 1 and 3; CDC biotype 1) were more often associated with nonhuman sources (70%), were able to utilize a number of sugars (sucrose, L-arabinose, and maltose), and were found to exhibit wider variations in biochemical characteristics; three biotypes within S. putrefaciens were detected. Notable differences between the two species in enzymatic activity, determined with the API-ZYM system (bioMérieux, Hazelwood, Mo.), and cellular fatty acid profiles, determined by the MIDI system (Microbial ID Inc., Newark, Del.), were also detected. Pathogenicity studies of mice indicate that S. alga appears to be the more virulent species, possibly due to the production of a hemolytic substance.

Animals↗

PubMed1993

Transforming growth factor beta 1 (TGF-beta 1) controls expression of major histocompatibility genes in the postnatal mouse: aberrant histocompatibility antigen expression in the pathogenesis of the TGF-beta 1 null mouse phenotype.

The phenotype of the transforming growth factor beta 1 (TGF-beta 1) null mouse has been previously described and is characterized by inflammatory infiltrates in multiple organs leading to a wasting syndrome and death as early as 3 weeks after birth. Since this phenotype occurs in the absence of any detectable pathogen, potential autoimmune disease mechanisms were investigated. We examined major histocompatibility complex (MHC) mRNA expression in tissues of the TGF-beta 1 null mouse and found levels of both the class I and class II MHC mRNA elevated compared to normal or TGF-beta 1 heterozygous littermates. This elevated expression was seen prior to any evidence of inflammatory infiltrates, suggesting a causal relationship between increased MHC expression and activation of immune cell populations. Cell surface expression of MHC molecules was detected by immunohistochemistry and correlated well with mRNA levels. Expression of mRNA for interferon gamma and its receptor was unchanged at the ages when increased MHC expression became apparent. Down-regulation of class I MHC expression by TGF-beta 1 was also demonstrated in vitro in fibroblasts isolated from TGF-beta 1 null mice. These findings suggest that one natural function of TGF-beta 1 is to control expression of both MHC classes. Altered regulation of MHC expression may be a critical step leading to the multifocal inflammation and wasting syndrome seen in the TGF-beta 1 null mouse. These results suggest potential applications for TGF-beta in the management of autoimmune disease, allograft rejection, and other problems associated with altered MHC expression.

Animals↗

PubMed1990

New molecular techniques for microbial epidemiology and the diagnosis of infectious diseases.

A major aim of clinical microbiologists over the last century has been to demonstrate the presence of pathogenic microorganisms in clinical or pathologic samples associated with infectious diseases. With the development of molecular genetics over the last two decades, new technologies have become available that allow more sensitive and specific determinations to be made in shorter periods. Two considerable benefits have accrued: Epidemiologists are now capable of judging clonality among various clinical isolates more powerfully, permitting added accuracy in the evaluation of the epidemic spread of microbes, and clinicians have gained enormous ability to diagnose previously difficult-to-detect pathogens.

Bacteria↗

PubMed1985

Probability of recovering pathogenic Escherichia coli from foods.

The probability of recovering pathogenic Escherichia coli from food by the Bacteriological Analytical Manual method was determined by the effects of several factors: the number of strains per food, the ability of pathogenic strains to survive enrichment, and the frequency of plasmid loss during enrichment. Biochemical patterns indicated the presence of about six E. coli strains per food sample. About half of the strains isolated from humans did not survive enrichment. Among those which grew, plasmid loss, as determined by gel electrophoresis and DNA colony hybridization, ranged from 20 to 95%. The combined effects of failure to survive enrichment and plasmid loss decreased the relative numbers of these strains and reduced the chance of detecting pathogens. To counteract this tendency and obtain a 90 to 95% probability off recovering a given pathogenic strain, 40 to 50 colonies per food sample should be picked during the routine testing of foods.

Anti-Bacterial Agents↗

PubMed1985

Aeromonas-related diarrhea in adults.

We have reviewed the incidence of Aeromonas in patients with enteric disease at our hospital and found it to be the highest of any potential enteric pathogen. Eighty adult patients with diarrhea had Aeromonas isolated from feces, and in 73 Aeromonas was the only potential bacterial or parasitic pathogen detected. The spectrum of illness in patients with Aeromonas-related diarrhea ranged from acute, self-limited diarrhea to a chronic, indolent diarrheal illness. Sixteen percent (13/80) of the patients had evidence of colitis noted during sigmoidoscopy or colonoscopy. Our data (and those from other studies) indicate that Aeromonas is relatively common in the feces of adults with diarrhea; they also indicate the need for prospective, controlled clinical and bacteriological studies to determine whether or not Aeromonas is an important enteric pathogen in adults.

Adult↗

PubMed2005

Molecular assays for targeting human and bovine enteric viruses in coastal waters and their application for library-independent source tracking.

Rapid population growth and urban development along waterways and coastal areas have led to decreasing water quality. To examine the effects of upstream anthropogenic activities on microbiological water quality, methods for source-specific testing are required. In this study, molecular assays targeting human enteroviruses (HEV), bovine enteroviruses (BEV), and human adenoviruses (HAdV) were developed and used to identify major sources of fecal contamination in the lower Altamaha River, Georgia. Two-liter grab samples were collected monthly from five tidally influenced stations between July and December 2002. Samples were analyzed by reverse transcription- and nested-PCR. PCR results were confirmed by dot blot hybridization. Eleven and 17 of the 30 surface water samples tested positive for HAdV and HEV, respectively. Two-thirds of the samples tested positive for either HEV or HAdV, and the viruses occurred simultaneously in 26% of samples. BEV were detected in 11 of 30 surface water samples. Binary logistic regression analysis showed that the presence of both human and bovine enteric viruses was not significantly related to either fecal coliform or total coliform levels. The presence of these viruses was directly related to dissolved oxygen and streamflow but inversely related to water temperature, rainfall in the 30 days preceding sampling, and chlorophyll-a concentrations. The stringent host specificity of enteric viruses makes them good library-independent indicators for identification of water pollution sources. Viral pathogen detection by PCR is a highly sensitive and easy-to-use tool for rapid assessment of water quality and fecal contamination when public health risk characterization is not necessary.

Adenoviruses, Human↗

PubMed2001

Departmental consumption of antibiotic drugs and subsequent resistance: a quantitative link.

OBJECTIVE: To look for a quantitative model linking departmental consumption of antibiotic drugs to the subsequent isolation of resistant hospital-acquired coliform pathogens. MATERIALS AND METHODS: Included in the study were all patients with hospital-acquired bloodstream infections caused by a coliform pathogen, detected in six departments of internal medicine of one university hospital during the period 1991-1996, who had not been hospitalized in the month before the infection (n = 394). Departmental consumption of antibiotics in the year before the infection [expressed as defined daily dosages (DDD)/100 patient days], antibiotic treatment given to the individual patient before the infection, the day of hospital stay on which the infection occurred, and the department and the calendar year were all included in a logistic model to predict the isolation of a resistant pathogen. We looked at five drugs: gentamicin, amikacin, cefuroxime, ceftazidime and ciprofloxacin. RESULTS: Five logistic models were fitted for the resistance to each of the antibiotic drugs. The multivariable-adjusted odds ratios for a pathogen resistant to the specific antibiotic were 1.03 [95% confidence interval (CI) 0.70-1.50] for gentamicin, 1.80 (95% CI 1.00-3.24) for amikacin, 1.12 (95% CI 1.02-1.23) for cefuroxime, 1.45 (95% CI 1.19-1.76) for ceftazidime and 1.06 (95% CI 0.57-1.97) for ciprofloxacin, per 1 DDD/100 patient days. CONCLUSIONS: The departmental consumption of cephalosporin drugs and amikacin in six autonomous departments of medicine in the same hospital was associated with a measurable and statistically significant increase in the probability of infection caused by a resistant pathogen.

Amikacin↗

PubMed1995

The distribution of invA, pagC and spvC genes among Salmonella isolates from animals.

New molecular diagnostic techniques often rely on hybridization or amplification of specific DNA regions to detect pathogenic bacteria. The choice of genes to be used as probes or as the targets of amplification techniques is critical to the success of these procedures. The genes so used might best be those associated with virulent isolates and having a wide distribution among such isolates. In this study three genes, invA, pagC and spvC, thought to be associated with the virulence of salmonellae, were labelled and used to probe the total DNA from 103 Salmonella isolates from animals in an attempt to determine whether these genes might be useful in diagnostic procedures. pagC was detected in 99% of the Salmonella tested, and invA was detected in 94.2% of the isolates. Both pagC and invA were detected with a significantly higher frequency than spvC in isolates from chickens and swine, but no significant difference in detection of these three genes occurred when bovine isolates were examined. Failure to detect any of these genes occurred in only one isolate. Isolates from apparently healthy or from clinically ill chickens and swine could not be distinguished by detecting these three genes. The genes were not detected in the non-Salmonella strains tested. These results suggest that, of these three genes, pagC may be the best choice for use as a probe or polymerase chain reaction target in future detection protocols.

Animals↗

PubMed2003

A review of rotavirus diarrhea in Pakistan: how much do we know?

INTRODUCTION: Rotavirus diarrhea has a worldwide distribution, infecting almost all children by the age of 3-5 years. EPIDEMIOLOGY: A comparable etiological 2-year survey carried out by the W.H.O Diarrheal Disease control (CDD) Program in 1991, in a multicenter study in 5 developing countries including Pakistan revealed that Rotavirus was found to be the most frequently detected pathogen in diarrheal episodes, during the first year of life, with the highest incidence (20%) occurring among 6-11 months old. Two other studies done in Pakistan, in under five children done in Lahore (between 1985 and 1991) and Rawalpindi (between May 1983 and April 1984) showed that Rotavirus was the second most common Diarrhea causing enteric pathogen following E.Coli TRANSMISSION: Rotaviruses are shed in high concentrations 2 days before and as many as 10 days after onset of symptoms in immunocompetent hosts, thus being an important source of viral transmission. CLINICAL COURSE: A multicenter study in 5 developing countries including Pakistan conducted by WHO CDD program revealed that only 1.8 % of cases presented with severe dehydration and these were mostly due to Rotavirus, V. Cholerae and ETEC13. DIAGNOSTIC TESTS: A study conducted in local hospitals in Pakistan during the period of October 1985-April 1986 compared the different diagnostic modalities for the detection of rotavirus in the faeces of children with acute diarrhea. The study all methods detected Rotavirus to varying degrees but ELISA was found to be the most sensitive method with 72.4% stools being positive. PREVENTIVE STRATEGIES: A study was conducted in Lahore (Pakistan) among 72 infants 6 weeks old in 1991 to assess safety and efficacy of RRV vaccine. It was found that of all infants given RRV with OPV, 50% had a two to four-fold rise in neutralization titers against rotavirus. RRV was found to be safe and not associated with adverse reactions in the 6 weeks old infants. CONCLUSION: With regards to Pakistan, there is a great need for defining rotavirus associated disease burden and strain prevalence. We also need to conduct Rotavirus vaccine trials to assess its efficacy and safety in our setting.

Child, Preschool↗