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PubMed1999

Nongonococcal urethritis--a new paradigm.

Urethritis in men has been categorized historically as gonococcal or nongonococcal (NGU). The major pathogens causing NGU are Chlamydia trachomatis and Ureaplasma urealyticum. Trichomonas vaginalis may be involved occasionally. In up to one-half of cases, an etiologic organism may not be identified. In this review we present recent advances in the diagnosis and management of NGU and discuss how they may be applied in a variety of clinical settings, including specialized STD clinics and primary health care practices. In particular, the development of the noninvasive urine-based nucleic acid amplification tests may warrant rethinking of the traditional classification of urethritis as gonococcal urethritis or NGU. Diagnostic for Chlamydia are strongly recommended because etiologic diagnosis of chlamydial urethritis may have important public health implications, such as the need for partner referral and reporting. A single 1-g dose of azithromycin was found to be therapeutically equivalent to the tetracyclines and may offer the advantage of better compliance.

Chlamydia Infections↗
PubMed2001

Molecular strategy for 'serotyping' of human enteroviruses.

To explore further the phylogenetic relationships between human enteroviruses and to develop new diagnostic approaches, we designed a pair of generic primers in order to study a 1452 bp genomic fragment (relative to the poliovirus Mahoney genome), including the 3' end of the VP1-coding region, the 2A- and 2B-coding regions, and the 5' moiety of the 2C-coding region. Fifty-nine of the 64 prototype strains and 45 field isolates of various origins, involving 21 serotypes and 6 strains untypable by standard immunological techniques, were successfully amplified with these primers. By determining the nucleotide sequence of the genomic fragment encoding the C-terminal third of the VP1 capsid protein we developed a molecular typing method based on RT-PCR and sequencing. If field isolate sequences were compared to human enterovirus VP1 sequences available in databases, nucleotide identity score was, in each case, highest with the homotypic prototype (74.8 to 89.4%). Phylogenetic trees were generated from alignments of partial VP1 sequences with several phylogeny algorithms. In all cases, the new classification of enteroviruses into five identified species was confirmed and strains of the same serotype were always monophyletic. Analysis of the results confirmed that the 3' third of the VP1-coding sequence contains serotype-specific information and can be used as the basis of an effective and rapid molecular typing method. Furthermore, the amplification of such a long genomic fragment, including non-structural regions, is straightforward and could be used to investigate genome variability and to identify recombination breakpoints or specific attributes of pathogenicity.

3' Untranslated Regions↗
PubMed2004

Feline immunodeficiency virus subtypes A, B and C and intersubtype recombinants in Ontario, Canada.

Knowledge of the geographical distribution of feline immunodeficiency virus (FIV) subtypes is important for understanding different disease courses and for vaccine design. Intersubtype recombination may develop in areas where more than one subtype is prevalent and has the potential to create new transmittable variants with novel pathogenic properties. In this study, 40 FIV-positive DNA samples were classified by sequence analysis of the LTR-gag region. Phylogenetic analysis indicated that 32 Canadian FIV isolates clustered with previously identified subtypes A, B and C and that subtype A was most frequent in Ontario. Four strains with inconsistent clade assignment were further analysed by sequencing of the env-LTR regions. Comparisons of phylogenetic trees constructed from the two different regions of the genome and analysis of similarities to reference sequences yielded classification of three samples as A/B and one as A/C intersubtype recombinants. Although the A/B recombinant samples were obtained from unrelated cats in geographically disparate regions, a common breakpoint was consistently identified within gag. In addition, there was no evidence of co-infection with parental strains of subtypes A and B as indicated by PCR-based limiting dilution assays, although these assays allowed for the identification of two different recombinant viruses co-existing in one sample. Both sequences contained the same breakpoint. These findings suggested that a new circulating recombinant FIV may be enzootic in Ontario.

Animals↗
PubMed1993

Purification and characterization of a potent 70-kDa thiol lysyl-proteinase (Lys-gingivain) from Porphyromonas gingivalis that cleaves kininogens and fibrinogen.

We isolated an enzyme from a major periodontal pathogen, Porphyromonas gingivalis (also called Bacteroides gingivalis), that is capable of initially increasing the coagulant activity of high molecular weight kininogen (HK), releasing bradykinin from HK and low molecular weight kininogen (LK), and destroying the light chain (coagulant portion) of HK. This enzyme, a membrane-bound thiol proteinase that preferentially cleaves the P1-Lys position of tripeptide substrates, is also able to rapidly render fibrinogen nonclottable. We will refer to this enzyme as lys-gingivain because of its origin from P. gingivalis, its classification as a thiol proteinase, and its action as a lysyl-amidase. The activity of lys-gingivain is enhanced by beta-mercaptoethanol, and the enzyme has a molecular mass of 68-70 kDa, a pH optimum of 7.4, and is not inactivated by plasma protease inhibitors. The second-order rate constant for the destruction of the coagulant activity of the HK light chain (surface-binding domain) at 23 degrees C is 2.3 x 10(7) M-1 s-1, and, for cleavages that render fibrinogen unclottable, is 2.05 x 10(6) M-1 s-1. These data suggest that lys-gingivain is a very potent proteinase that would be fully functional in anaerobic periodontal crevices and might participate in the pathogenesis of periodontitis. Lys-gingivain appears to be the most potent kininogenase and fibrase to be described to date.

Amino Acid Sequence↗
PubMed1994

Gram-negative bacillary cellulitis in patients with hepatic cirrhosis.

Eight episodes of gram-negative bacillary cellulitis in seven patients with hepatic cirrhosis are reported. The patients comprised five women and two men (mean age 59.6 years). The diagnosis was based on a positive culture of specimens obtained by needle aspiration from cutaneous lesions. All patients had grade C cirrhosis according to Pugh's classification. Cellulitis involved the lower extremities in all cases. Five patients developed bullous lesions, three ulcers, two abscesses and two extensive cutaneous necrosis. A single bacterial species was found in seven cases. Organisms isolated were Klebsiella pneumoniae (3 cases), Escherichia coli (2 cases), Pseudomonas aeruginosa (2 cases), Proteus mirabilis (1 case) and Aeromonas hydrophila (1 case). Bacteremia was documented in six cases. Four patients died, death being related to sepsis in three of them. It is concluded that gram-negative bacilli should be considered as possible pathogens in severe infectious cellulitis in patients with advanced cirrhosis. Microbiological study of cutaneous specimens obtained by needle aspiration may be of high diagnostic value in these cases.

Aged↗
PubMed2025

The British Society for Antimicrobial Chemotherapy Resistance Surveillance Project: methods and limitations.

OBJECTIVES: The BSAC Bacteraemia and Respiratory Resistance Surveillance Programmes provided long-term surveillance of antibiotic resistance in key pathogens of bloodstream and both community- and hospital-acquired respiratory infections in the UK and Ireland. This paper details the methodologies used. Data limitations are discussed. METHODS: Sentinel laboratories across the UK and Ireland contributed up to a fixed annual quota of isolates of defined bacterial groups. For each Programme, a Central Laboratory confirmed bacterial identifications, measured MICs by the BSAC agar dilution method, investigated mechanisms of resistance and determined serotypes of Streptococcus pneumoniae. Identification methods evolved over time, e.g. with adoption of MALDI-TOF. Classification of susceptibility and resistance follows the 2022 (not contemporaneous) EUCAST guidance. RESULTS: Seventy-nine laboratories contributed 30 716 community respiratory isolates from 1999/2000 to 2018/19; 65 laboratories contributed 13 508 hospital respiratory isolates from 2008/09 to 2018/19; 81 laboratories contributed 56 064 bacteraemia isolates from 2001 to 2019. Although large and teaching hospitals were over-represented, the resistance rates for bacteraemia organisms collected in England mirror more extensive (but less standardized or detailed) national data gathered from laboratories by the UK Health Security Agency and its predecessor organizations, which provided a bespoke data extract. CONCLUSIONS: These surveillance Programmes have provided comprehensive and reliable information on antibiotic susceptibility in the UK and Ireland over two decades. Detailed results, showing resistance trends and mechanisms of antibiotic resistance, are presented in five papers in this Supplement.

Antimicrobial Stewardship↗
PubMed2006

The bacterial species definition in the genomic era.

The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.

Bacteria↗
PubMedDate not supplied

[Microsporidiasis in AIDS patients with chronic diarrhea. Expieriences at the National Institute of Nutrition "Salvador Zubrirán"].

BACKGROUND: Microsporidium sp. has been considered as a rare cause of diarrhea in AIDS patients. However, the improvement of some histochemical stains in the analysis of small bowel biopsies has shown an increase in its prevalence. In Mexico there are no series reporting intestinal microsporidiasis. DESIGN: Small bowel biopsies of 98 patients with AIDS and chronic diarrhea stained with HE and Giemsa were reviewed (January 1987-December 1994). The clinical, demographic and laboratory information was obtained from the clinical charts. RESULTS: In 50 patients an opportunistic microorganism was identified in the small bowel biopsy (51%). Microsporidium sp. was identified in 30 patients (31%). The clinical charts were reviewed in all but six cases. Of the 24 patients with microsporidiasis as the cause of diarrhea, 17 were male and seven female with a median age, of 33 years, old. Homosexuality was the main risk factor in males (11/17), and blood transfusion in females (4/7). A low socioeconomical classification was found in 75% cases. The initial manifestation of AIDS was diarrhea in 16/24 (67%), CD4 count cell below 200 mm3 was identified in 13/24 patients and more than 200 mm3 in 2/24. The stool examination and the original histologic interpretations were negative for Microsporidium sp. Lymphoplasmocytic inflammatory infiltrate with eosinophils in the lamina propia and atrophy was frequently seen. A pale red and gray color was observed in spore and merogonial phases of Microsporidium stained with Giemsa. CONCLUSION: Microsporidium sp. was present as the only pathogen in 31% of the small bowel biopsies reviewed by light microscopy. Diarrhea due to Microsporidium sp. is frequently seen in advanced stages of AIDS with CD4 count cell below 200 mm3 Giemsa stain in the evaluation of small biopsies is a cheap and useful method to, identify Microsporidium sp.

AIDS-Related Opportunistic Infections↗
PubMed1994

From bedside to bench and back. The diagnosis and biology of bullous diseases.

The history of dermatology is replete with examples where astute physicians have made key observations that have led to the recognition of distinct diseases and syndromes. While clinicians may be either lumpers or splitters, their unifying theme has been that of identifying common elements among patients to assist in their diagnosis, classification, and treatment. Light microscopy, electron microscopy, immunopathologic techniques, and molecular biology have provided dermatologists additional data to assist in their analysis of incompletely understood and poorly classified skin diseases. Application of these techniques over the past 40 years to patients with bullous diseases has led to the development of many new concepts including the following: (1) patients with bullous diseases have autoantibodies that target disease-specific antigens that represent important structural components of normal human skin; (2) autoantibodies from patients with certain bullous diseases are pathogenic in experimental animal models; and (3) some of the same structural proteins targeted by autoantibodies in patients with acquired autoimmune bullous diseases are mutated in patients with inherited bullous diseases. An overview of these concepts is the subject of this brief review.

Animals↗
PubMed1992

Universal occurrence of glomerular abnormalities in patients receiving liver transplants.

We conducted a prospective study of renal histology and function in 18 consecutive nonalcoholic patients who underwent orthotopic liver transplantation (OLT). Despite well-preserved renal function, all patients had abnormal renal biopsies. Four patterns of glomerular injury were identified: minor glomerular abnormalities (eight patients), hepatic glomerulosclerosis (seven), membranoproliferative glomerulonephritis (one), and IgA nephropathy (one). In one patient there was insufficient tissue to allow classification. There was a trend toward lower plasma bilirubin and higher plasma albumin in patients with minor glomerular abnormalities than in the group of patients with more severe forms of glomerular injury (29 v 82 mumol/L, 35.5 v 30 g/L; P = 0.1, 0.1 greater than P greater than 0.05, respectively). Glomerular changes persisted in the three patients who died within 7 weeks post-OLT. IgM immunofluorescence was present in all biopsies and IgA in 11. IgM-containing circulating immune complexes occurred in five patients, suggesting a pathogenic role for IgM immune complex deposition. The significance of cirrhosis-associated glomerular abnormalities is not yet known. They may contribute to the hepatorenal syndrome and the renal dysfunction that occurs in up to 94% of patients post-OLT.

Adolescent↗
PubMed2025

Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings.

MOTIVATION: Rare diseases collectively affect 5% of the population. However, fewer than 50% of rare disease patients receive a molecular diagnosis after whole genome sequencing. Supervised machine learning is a valuable approach for the pathogenicity scoring of human genetic variants. However, existing methods are often trained on curated but limited central repositories, resulting in poor accuracy when tested on external cohorts. Yet, large collections of variants generated at hospitals and research institutions remain inaccessible to machine-learning purposes because of privacy and legal constraints. Federated learning (FL) algorithms have been recently developed enabling institutions to collaboratively train models without sharing their local datasets. RESULTS: Here, we present a proof-of-concept study evaluating the effectiveness of FL for the clinical classification of genetic variants. A comprehensive array of diverse FL strategies was assessed for coding and non-coding Single Nucleotide Variants as well as Copy Number Variants. Our results showed that federated models generally achieved comparable or superior performance to traditional centralized learning. In addition, federated models reached a robust generalization to independent sets with smaller data fractions as compared to their centralized model counterparts. Our findings support the adoption of FL to establish secure multi-institutional collaborations in human variant interpretation. AVAILABILITY AND IMPLEMENTATION: All source code required to reproduce the results presented in this article, implemented in Python, is available under the GNU General Public License v3 at https://github.com/RausellLab/FedLearnVar.

Humans↗
PubMed1985

Adherence of coagulase-negative staphylococci to plastic tissue culture plates: a quantitative model for the adherence of staphylococci to medical devices.

The adherence of coagulase-negative staphylococci to smooth surfaces was assayed by measuring the optical densities of stained bacterial films adherent to the floors of plastic tissue culture plates. The optical densities correlated with the weight of the adherent bacterial film (r = 0.906; P less than 0.01). The measurements also agreed with visual assessments of bacterial adherence to culture tubes, microtiter plates, and tissue culture plates. Selected clinical strains were passed through a mouse model for foreign body infections and a rat model for catheter-induced endocarditis. The adherence measurements of animal passed strains remained the same as those of the laboratory-maintained parent strain. Spectrophotometric classification of coagulase-negative staphylococci into nonadherent and adherent categories according to these measurements had a sensitivity, specificity, and accuracy of 90.6, 80.8, and 88.4%, respectively. We examined a previously described collection of 127 strains of coagulase-negative staphylococci isolated from an outbreak of intravascular catheter-associated sepsis; strains associated with sepsis were more adherent than blood culture contaminants and cutaneous strains (P less than 0.001). We also examined a collection of 84 strains isolated from pediatric patients with cerebrospinal fluid (CSF) shunts; once again, pathogenic strains were more adherent than were CSF contaminants (P less than 0.01). Finally, we measured the adherence of seven endocarditis strains. As opposed to strains associated with intravascular catheters and CSF shunts, endocarditis strains were less adherent than were saprophytic strains of coagulase-negative staphylococci. The optical densities of bacterial films adherent to plastic tissue culture plates serve as a quantitative model for the study of the adherence of coagulase-negative staphylococci to medical devices, a process which may be important in the pathogenesis of foreign body infections.

Animals↗
PubMed2004

Segmentally variable genes: a new perspective on adaptation.

Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host-pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein-protein, protein-nucleic acid, or protein-small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment.

Acclimatization↗
PubMed1975

Motility-indole-lysine-sulfide medium.

A medium designed for the detection of motility, indole, lysine decarboxylase and deaminase reactions, and H2S production was devised and evaluated. Results, using 157 strains of enteric pathogens, were in agreement with reference methods. When 300 isolates from fecal cultures were screened using this medium, Shigella was easily differentiated from Escherichia and more of the Proteus species, especially P. morganii, could be eliminated from further study.

Agar↗
PubMedDate not supplied

[Neuropathic pain syndromes: from their diagnosis to the return to work. Proposal of a model for rapid evaluation and therapy based on their pathogenic mechanisms].

The therapeutic approach to neuropathic pain differs significantly among physicians. This is in large part because of the relative paucity of randomized clinical trials and the scarcity of comparative studies with different drugs. Clinical studies on the efficacy of a drug or a technique are generally referred to the pathologic diagnosis and not to the pain mechanism. We have learned from animal models the different pain mechanisms which may be involved in the peripheral nerves and the spinal cord. Unfortunately, one mechanism could be responsible for many different symptoms, while the same symptom can be caused by different mechanisms. The authors propose a simple model to evaluate the patients in order to define the mechanisms involved an to select the treatment strategy. The diagnostic model allows classification of the patient into four groups according to pain mechanism (spinal neurons sensitization due to deafferentation, ectopic discharges in peripheral nociceptive C fibers, spinal neurons sensitization due to ectopic discharges in peripheral nociceptive C fibers, spinal neurons sensitization due to nociceptors sensitization). The authors propose also a second step in which a fifth mechanism, adrenosensitivity, is evaluated. Treatment options may target any of the mechanisms discussed. Drugs and analgesic techniques can be classified according to their action on pain mechanisms. The authors identify in the literature some drugs and techniques which can be tested in each defined groups. A complementary and multidisciplinary rehabilitative approach of chronic pain patients is recommended.

Adrenergic alpha-Agonists↗
PubMed2004

Taxonomic and phylogenetic status of non-tuberculous mycobacteria in a Caribbean setting.

This report describes detailed taxonomic and phylogenetic analysis of 15 non-tuberculous mycobacteria (NTMs) isolated from human pathological specimens in a Caribbean setting (12 slow-growers and three rapid-growers) that were not identified by cultural and biochemical tests and drug-susceptibility results. These isolates were further studied using PCR restriction fragment length polymorphism analysis (PRA) of a 441bp hsp65 fragment, as well as the sequencing of 16S rDNA and hsp65 DNA, and HPLC of the mycolic acids. Our results showed that taxonomic position of well-defined NTMs was resolved by PRA and sequencing of hsp65, nonetheless, it was not suitable to investigate rarely observed or new strains that required 16S rDNA sequencing and HPLC for a definite response. Unrooted neighbor-joining phylogenetic trees were drawn based upon the 16S rDNA and hsp65 sequences of the 15 NTMs compared with those from described species (73 for 16S rDNA and 45 for hsp65). For most of the NTMs not showing an exactly matching sequence with either hsp65 or 16S rDNA in the GenBank, the phylogenetic tree was able to provide with useful indications about their relatedness to known species. In such a case, a concording HPLC pattern with the sequence data and the place of the strain within the tree could lead to a potential identification. We also identified three identical isolates that define a new mycobacterial species within the group of M. simiae-related mycobacteria. The isolation and characterization of mycobacteria from new settings may lead to identify potential pathogens that may propogate in future because of increased human migration, travels, and climatic and ecological changes of the modern world.

Adolescent↗
PubMed2005

Development of posttransplant antidonor HLA antibodies is associated with acute humoral rejection and early graft dysfunction.

BACKGROUND: The goal of this study was to determine whether the production of posttransplant antibodies directed against donor HLA mismatches (donor specific antibody; DSA) is associated with renal allograft rejection and early graft dysfunction. METHODS: Forty-nine adult renal allograft recipients with increased risk of rejection were enrolled during the period of October 2001 through May 2003 and were prospectively monitored for the development of anti-HLA antibodies. RESULTS: Of 49 patients, eight (16.3 %) patients were diagnosed with acute humoral rejection (AHR) and 11/49 (22.4%) patients were diagnosed with acute cellular rejection (ACR). A strong association between pretransplant HLA sensitization and AHR was found (P=0.005). Of the eight patients diagnosed with AHR, the majority developed DSA before or concomitant with episodes of rejection (P<0.001). Only 3 of 41 patients (7.3%) without AHR developed DSA. The pathogenic role of alloantibodies was further substantiated by analyzing their association with graft function as measured by serum creatinine levels. The average serum creatinine after the third month posttransplantation in DSA producers was 2.24+/-1.01 mg/dL, while in non-DSA patients the average serum creatinine was 1.41+/-0.37 mg/dL (P<0.01). CONCLUSION: This study reveals a strong association between the production of DSA, AHR, and early graft dysfunction. Our findings indicate that prospective monitoring for anti-HLA antibodies following transplantation is a useful test for the diagnosis and classification of AHR for identifying patients at risk of early graft dysfunction.

Acute Disease↗
PubMed2001

Risk factors for human disease emergence.

A comprehensive literature review identifies 1415 species of infectious organism known to be pathogenic to humans, including 217 viruses and prions, 538 bacteria and rickettsia, 307 fungi, 66 protozoa and 287 helminths. Out of these, 868 (61%) are zoonotic, that is, they can be transmitted between humans and animals, and 175 pathogenic species are associated with diseases considered to be 'emerging'. We test the hypothesis that zoonotic pathogens are more likely to be associated with emerging diseases than non-emerging ones. Out of the emerging pathogens, 132 (75%) are zoonotic, and overall, zoonotic pathogens are twice as likely to be associated with emerging diseases than non-zoonotic pathogens. However, the result varies among taxa, with protozoa and viruses particularly likely to emerge, and helminths particularly unlikely to do so, irrespective of their zoonotic status. No association between transmission route and emergence was found. This study represents the first quantitative analysis identifying risk factors for human disease emergence.

Animals↗