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PubMed1996

Preoperative bacterial colonization and its influence on postoperative wound infections in plastic surgery.

During two separate periods a total of 654 patients were included in a clinical study relating preoperative bacterial colonization to occurrence of postoperative wound infection in plastic surgery. During the second period one half of the patients were randomized to receive prophylactic azithromycin. Bacteriological samples were collected from the nasal vestibulum during both periods, and additionally from the surgical field during the second period. All patients had preoperative chlorhexidine bathing. The bacteriological findings were categorized as either normal flora or potentially pathogenic bacteria, and as either having no growth. Surgical wounds were divided into four contamination classes. Postoperative follow-up was 30 days, and assessment of wound infection was based on a graded scale. We did not find any statistically significant relation between preoperative bacterial colonization and postoperative wound infection, regardless of place of sample collection, method of bacterial classification, class of contamination or use of prophylactic azithromycin.

Adolescent↗

PubMed2006

System-wide genomic and biochemical comparisons of sialic acid biology among primates and rodents: Evidence for two modes of rapid evolution.

Numerous vertebrate genes are involved in the biology of the oligosaccharide chains attached to glycoconjugates. These genes fall into diverse groups within the conventional Gene Ontology classification. However, they should be evaluated together from functional and evolutionary perspectives in a "biochemical systems" approach, considering each monosaccharide unit's biosynthesis, activation, transport, modification, transfer, recycling, degradation, and recognition. Sialic acid (Sia) residues are monosaccharides at the outer end of glycans on the cell-surface and secreted molecules of vertebrates, mediating recognition by intrinsic or extrinsic (pathogen) receptors. The availability of multiple genome sequences allows a system-wide comparison among primates and rodents of all genes directly involved in Sia biology. Taking this approach, we present further evidence for accelerated evolution in Sia-binding domains of CD33-related Sia-recognizing Ig-like lectins. Other gene classes are more conserved, including those encoding the sialyltransferases that attach Sia residues to glycans. Despite this conservation, tissue sialylation patterns are shown to differ widely among these species, presumably because of rapid evolution of sialyltransferase expression patterns. Analyses of N- and O-glycans of erythrocyte and plasma glycopeptides from these and other mammalian taxa confirmed this phenomenon. Sia modifications on these glycopeptides also appear to be undergoing rapid evolution. This rapid evolution of the sialome presumably results from the ongoing need of organisms to evade microbial pathogens that use Sia residues as receptors. The rapid evolution of Sia-binding domains of the inhibitory CD33-related Sia-recognizing Ig-like lectins is likely to be a secondary consequence, as these inhibitory receptors presumably need to keep up with recognition of the rapidly evolving "self"-sialome.

Amino Acid Sequence↗

PubMed2001

Survival of fecal coliforms in dry-composting toilets.

The dry-composting toilet, which uses neither water nor sewage infrastructure, is a practical solution in areas with inadequate sewage disposal and where water is limited. These systems are becoming increasingly popular and are promoted to sanitize human excreta and to recycle them into fertilizer for nonedible plants, yet there are few data on the safety of this technology. This study analyzed fecal coliform reduction in approximately 90 prefabricated, dry-composting toilets (Sistema Integral de Reciclamiento de Desechos Orgánicos [SIRDOs]) that were installed on the U.S.-Mexico border in Ciudad Juárez, Chihuahua, Mexico. The purpose of this study was to determine fecal coliform reduction over time and the most probable method of this reduction. Biosolid waste samples were collected and analyzed at approximately 3 and 6 months and were classified based on U.S. Environmental Protection Agency standards. Results showed that class A compost (high grade) was present in only 35.8% of SIRDOs after 6 months. The primary mechanism for fecal coliform reduction was found to be desiccation rather than biodegradation. There was a significant correlation (P = 0.008) between classification rating and percent moisture categories of the biosolid samples: drier samples had a greater proportion of class A samples. Solar exposure was critical for maximal class A biosolid end products (P = 0.001). This study only addressed fecal coliforms as an indicator organism, and further research is necessary to determine the safety of composting toilets with respect to other pathogenic microorganisms, some of which are more resistant to desiccation.

Bacteriological Techniques↗

PubMed2026

Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis.

BACKGROUND: Metagenomic sequencing can potentially transform clinical microbiology by enabling rapid pathogen identification and antimicrobial resistance (AMR) prediction in critically ill patients with bloodstream infections. However, the clinical use of metagenomic sequencing has been constrained by its speed, accuracy, and technical feasibility. Our aim was to develop and evaluate a direct-from-positive blood culture workflow using Oxford Nanopore sequencing that overcomes these limitations and delivers rapid, accurate results. METHODS: In this metagenomic pipeline analysis, 211 positive (130 aerobic and 81 anaerobic) and 62 negative (30 aerobic and 32 anaerobic) randomly selected blood cultures were processed from Oxford University Hospitals for comparing species identification, AMR detection, and time-to-result against standard culture-based diagnostics performed by the hospital's routine microbiology laboratory. Species prediction was performed using Kraken2 with a comprehensive standard database, applying heuristic and random forest classification models. Additionally, we benchmarked AMR classification tools and databases, including ResFinder, CARD, and NCBI AMRFinderPlus. FINDINGS: Across all samples, our method achieved 97% sensitivity and 94% specificity for species identification compared with that of routine culture and matrix-assisted laser desorption ionisation time-of-flight-based diagnostics; both sensitivity and specificity increased to 100% after adjudication of plausible additional infections. We detected 19 additional infections (13 polymicrobial, five previously unidentifiable, and one in a culture-negative sample) and delivered species identification results within 3 h 20 min (IQR 3 h 7 min-3 h 27 min), approximately 10 h earlier than routine diagnostic methods. For the ten most common clinically relevant pathogens, our method yielded AMR results 20 h earlier than current antimicrobial susceptibility testing, with an overall sensitivity of 88% and specificity of 93%. Performance varied by species. For Staphylococcus aureus, the AMR prediction sensitivity was 100% and specificity was 99%, and for Escherichia coli, the prediction sensitivity was 91% and specificity was 94%. INTERPRETATION: These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to close diagnostic gaps, reduce empirical antibiotic use, and enable rapid targeted treatment. Nonetheless, improvements in AMR prediction for some species and drugs, along with further multisite validation, are required before clinical implementation. FUNDING: National Institute for Health Research (NIHR) Oxford Biomedical Research Centre.

Humans↗

PubMed1995

Primary central nervous system lymphomas--new pathological developments.

Primary central nervous system lymphomas (PCNSL) show increased incidence both in immunocompromised high-risk groups and in the general population. They are extranodal diffuse non-Hodgkin's lymphomas with a morphology similar to systemic lymphomas, but differ in their biological and molecular behaviour. The majority are large B-cell variants of high-grade malignancy; low-grade subtypes and T-cell lymphomas are rare; up to 50% remain unclassified according to the New Working Formulation and updated Kiel classification. Monoclonality of immunoglobulin receptor gene rearrangement can be diagnostically useful. The pathogenesis of PCNSL is obscure. Epstein-Barr virus (EBV) genome/proteins expression in two-thirds of HIV-related PCNSL but only in 15% of those in immunocompetent patients suggest different EBV latency stages in both types; human herpesvirus type 6 does not appear to play a pathogenic role. Comparison of expression patterns of integrin chains and adhesion molecules are very similar for PCNSL and nodal lymphomas suggesting that they are not selective mediators of lymphoma cell homing to the brain. In HIV-negative PCNSL they appear not to be influenced by EBV. Studies of protooncogenes (bcl-1 and bcl-2 genes) revealed no rearrangement in PCNSL, suggesting that they are not involved in the pathogenesis of PCNSL that probably do not differ cytogenetically from nodal B-cell lymphomas. Since most of the currently known molecular parameters are probably not the primary pathogenic events, the molecular genetics and pathogenesis of PCNSL are still to be elucidated.

Cell Adhesion Molecules↗

PubMed2004

Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster.

Aspergillus fumigatus is the most ubiquitous opportunistic filamentous fungal pathogen of human. As an initial step toward sequencing the entire genome of A. fumigatus, which is estimated to be approximately 30 Mb in size, we have sequenced a 922 kb region, contained within 16 overlapping bacterial artificial chromosome (BAC) clones. Fifty-four percent of the DNA is predicted to be coding with 341 putative protein coding genes. Functional classification of the proteins showed the presence of a higher proportion of enzymes and membrane transporters when compared to those of Saccharomyces cerevisiae. In addition to the nitrate assimilation gene cluster, the quinate utilisation gene cluster is also present on this 922 kb genomic sequence. We observed large scale synteny between A. fumigatus and Aspergillus nidulans by comparing this sequence to the A. nidulans genetic map of linkage group VIII.

Aspergillus fumigatus↗

PubMed2001

[Characterization and distribution of Citrobacter species in a university hospital].

OBJECTIVE: [corrected] a) To identify Citrobacter strains following the conventional biochemical reaction of Brenner and col; b) to evaluate the sensitivity and specificity of the O'Hara's method compared with Brenner's method, and c) to determine the rate and distribution of the strains in the clinical isolates. MATERIAL AND METHODS: One hundred and twenty two clinical isolates, characterized as Citrobacter spp. were collected between May of 1994 and August of 1997. Clinical isolates included inpatients and outpatients from Hospital de Clínicas. Strains were identified following the methods of Brenner and O'Hara. RESULTS: Methods of Brenner identified 111 of 122 strains: C. freundii 59 of 111; C. koseri 18 of 111; C. werkmanii 15 of 111; C. braakii 9 of 111; C. youngae 6 of 111 and C. amalonaticus 4 of 111. O'Hara's methods identified 104 of 111 strains (94%). C. freundii was recovered most frequently from urine and feces (p Fisher < 0.026 and 0.039 respectively), while C. koseri was isolated from urine principally (p Fisher < 0.0372). CONCLUSIONS: The genus Citrobacter is an important opportunistic pathogen that can be identified in clinical microbiology laboratories using O'Hara's method.

Bacteremia↗

PubMed2005

Mycobacterium avium complex pulmonary disease in immunocompetent patients.

Mycobacterium avium complex is becoming increasingly recognized as one of the most common mycobacterial pathogens in humans. It is rapidly becoming a significant cause of pulmonary disease even in those with an intact immunity. In 1997, the American Thoracic Society published recommendations for the diagnosis and treatment of nontuberculous mycobacteria. On the basis of the authors' clinical experience of the myriad presentations of pulmonary Mycobacterium avium complex disease in an immunocompetent host, a clinical classification is proposed. The current data are summarized, and a practical approach to management of the various pulmonary forms of the disease is provided.

Alveolitis, Extrinsic Allergic↗

PubMed2006

Kinetic characterization of the monofunctional glycosyltransferase from Staphylococcus aureus.

The glycosyltransferase (GT) module of class A penicillin-binding proteins (PBPs) and monofunctional GTs (MGTs) belong to the GT51 family in the sequence-based classification of GTs. They both possess five conserved motifs and use lipid II precursor (undecaprenyl-pyrophosphate-N-acetylglucosaminyl-N-acetylmuramoyl- pentapeptide) to synthesize the glycan chain of the bacterial wall peptidoglycan. MGTs appear to be dispensable for growth of some bacteria in vitro. However, new evidence shows that they may be essential for the infection process and development of pathogenic bacteria in their hosts. Only a small number of class A PBPs have been characterized so far, and no kinetic data are available on MGTs. In this study, we present the principal enzymatic properties of the Staphylococcus aureus MGT. The enzyme catalyzes glycan chain polymerization with an efficiency of approximately 5,800 M(-1) s(-1) and has a pH optimum of 7.5, and its activity requires metal ions with a maximum observed in the presence of Mn2+. The properties of S. aureus MGT are distinct from those of S. aureus PBP2 and Escherichia coli MGT, but they are similar to those of E. coli PBP1b. We examined the role of the conserved Glu100 of S. aureus MGT (equivalent to the proposed catalytic Glu233 of E. coli PBP1b) by site-directed mutagenesis. The Glu100Gln mutation results in a drastic loss of GT activity. This shows that Glu100 is also critical for catalysis in S. aureus MGT and confirms that the conserved glutamate of the first motif EDXXFXX(H/N)X(G/A) is likely the key catalytic residue in the GT51 active site.

Enzyme Activation↗

PubMed1981

Classification and actual antigenic composition of Salmonellae.

The synthesis by Enterobacteriaceae grown on artificial media of proteins, with a diversity of specificities previously found with the help of antiprotein sera, is confirmed with antibacterial sera prepared with species belonging to different serogroups. An earlier recognition of the existence of these materials was hindered by the devised schemes of classification and the claims relating 'O' factors to the bacterial polysaccharides. The synthesis, on artificial media, of mixtures of heterologous proteins by all the analysed species is no proof that their behaviour in vivo is identical; notwithstanding their high amounts in the mixtures, few of the heterologous proteins are involved in cross-protection of a host against its natural pathogen.

Animals↗

PubMed1994

Are there special considerations relevant to trials of biologic agents?

Although biologic agents have been developed to effect change in observed or hypothesized pathogenic pathways, discrepancies between biological and clinical effects are well recognized. In trials of these agents, biological and clinical effects need to be evaluated. While the biological effects require assessment to test the proposed primary effect and significant influences, clinical evaluation should use the same set of assessment procedures as pharmacological agents. The disease controlling antirheumatic therapy (DC-ART) classification with its requirement for longterm efficacy poses problems for the biological agents, which, in general, have demonstrated short term benefit. They may be best accommodated in a new "remission induction" category or, alternatively, as part of longterm combination therapy either with pharmaceuticals or with other biologicals to fulfill DC-ART requirements.

Antirheumatic Agents↗

PubMedDate not supplied

[Reactualization of the concept of unitary psychosis introduced by Joseph Guislain].

This paper reminds the concept of a unitary nosological and pathogenic process that may be traced back to Joseph Guislain (1797-1860). The "phrénalgie initiale" was regarded as the initial stage of psychic illness by Guislain (Leçons orales, Ghent, 1852). That vision inspired the work of Wilhelm Griesinger (1817-1869) who further elaborated the concept of "Einheitspsychose" (Psychose unique--Unitary psychosis). That concept partially inspired Emil Kräpelin (1856-1926). Current classification systems like ICD-10 and DSM-III-R attempt to synthesize different views and the concept of unitary psychosis is actualized in the contemporary transnosography.

Belgium↗

PubMed2000

Genetic classification of "Rickettsia heilongjiangii" and "Rickettsia hulinii," two Chinese spotted fever group rickettsiae.

To determine the phylogenetic position of two new rickettsial strains isolated from ticks in China, 16S ribosomal DNA, gltA, and ompA (apart from the tandem repeat units) genes were amplified by PCR and sequenced. The phylogenetic relationships between these strains and other rickettsiae were inferred from the comparison of sequences of the three genes by the parsimony, neighbor-joining, and maximum-likelihood methods. The results demonstrated that the 054 strain, a rickettsia pathogenic in humans, and the HL-93 strain were related and clustered together with Rickettsia japonica. Significant statistical bootstrap values (100 and 92%) supported the nodes in this cluster. Based on previous genotypic and antigenic data and the phylogenetic analysis presented here, the 054 and HL-93 strains should be considered as new species, and we formally propose that they be named "Rickettsia heilongjiangii" and "Rickettsia hulinii," respectively.

Animals↗

PubMed1983

Septic arthritis caused by Kingella kingae.

Kingella kingae is a slow-growing, fastidious gram-negative coccobacillus that is a normal inhabitant of the oropharynx of man, but it has rarely been implicated as a human pathogen. Two cases of septic arthritis caused by this organism are reported along with a review of seven previously reported cases of infections caused by this organism. Bone and joint infections predominate. Gram's-stained smears of pus from bone or joint fluid aspirate have been negative for organisms, and a delay of growth in cultures with initial difficulty in classification of the isolate is characteristic. Kingella kingae organisms have been uniformly sensitive to the penicillins and all other commonly used antibiotics that were tested. Response to treatment was good in all nine patients found to have infections caused by this organism.

Anti-Bacterial Agents↗

PubMed2025

Opportunistic screening for broad range of medically relevant secondary findings: Laboratory benefits and burdens.

PURPOSE: Exome and genome sequencing enable opportunistic screening for secondary findings (SFs). We report on exome analysis for a broad range of medically relevant SFs in the setting of the Incidental Genomics randomized clinical trial (NCT03597165). METHODS: Participants had exome sequencing and were randomized to receive only primary cancer findings (control) or cancer findings and a choice of SFs (intervention). RESULTS: Across 279 participants, there were 4441 unique variants in SF genes: 5.0% (221) were reportable pathogenic/likely pathogenic variants, and 81.4% (3615) were nonreportable variants of uncertain significance (VUS). Intervention arm participants had on average 2.6 (SD 1.66, range 0-9) pathogenic/likely pathogenic variants and 29.5 VUS (SD 13.2, range 2-74). SFs for monogenic disease risk were reported in 35.3% (49/139) of participants (American College of Medical Genetics and Genomics non-cancer subset in 1.4%) and carrier status in 89.3% (117/131). In the intervention arm, variant filtration was 7.7 times longer per case (95% CI 5.3 to 11.3, P < .0001), variant classification was 13.3 times longer (95% CI 10.6 to 16.5, P < .0001), and report preparation was 3.3 times longer (95% CI 2.6 to 4.1, P < .0001). CONCLUSION: Although the yield of reportable SFs was high, this was accompanied by many nonreportable VUS and increased efforts for exome analysis.

Humans↗

PubMed2026

Complicated urinary tract infections: evolving definitions, clinical burden, and treatment landscape amid antimicrobial resistance.

INTRODUCTION: Complicated urinary tract infection (cUTI) is a common and heterogeneous infection associated with substantial morbidity, high healthcare utilization, and increasing antimicrobial resistance. Evolving definitions, increasing device use, and changing patient populations have altered its epidemiology and management. Marked variability in diagnostic criteria, clinical trial endpoints within and outside registrational settings, and treatment strategies complicates clinical decision-making and interpretation of therapeutic advances. AREAS COVERED: This review examines contemporary cUTI epidemiology, classification frameworks, and drivers of disease burden. It evaluates resistance trends and their therapeutic implications, alongside stewardship-based management strategies, including empiric antibiotic selection, intravenous-to-oral transition, treatment duration, and source control. Challenges in catheter-associated infection, recurrence, and regulatory endpoint design are discussed, together with the emerging role of novel agents targeting resistant Gram-negative pathogens. EXPERT OPINION: Rising multidrug resistance and limited oral options are reshaping cUTI management, necessitating individualized, stewardship-aligned therapy guided by illness severity and local epidemiology. Current regulatory endpoints inadequately reflect patient-centered outcomes, particularly in the context of asymptomatic bacteriuria. Expanding availability of effective oral agents may enable earlier discharge and outpatient care. Integration of rapid diagnostics and risk stratification will be essential to optimize therapy, limit resistance, and improve outcomes.

Humans↗

PubMed2004

Ancient coevolution of baculoviruses and their insect hosts.

If the relationships between baculoviruses and their insect hosts are subject to coevolution, this should lead to long-term evolutionary effects such as the specialization of these pathogens for their hosts. To test this hypothesis, a phylogeny of the Baculoviridae, including 39 viruses from hosts of the orders Lepidoptera, Diptera, and Hymenoptera, was reconstructed based on sequences from the genes lef-8 and ac22. The tree showed a clear division of the baculoviruses according to the order of their hosts. This division highlighted the need to reconsider the classification of the baculoviruses to include one or possibly two new genera. Furthermore, the specialization of distinct virus lineages to particular insect orders suggests ancient coevolutionary interactions between baculoviruses and their hosts.

Animals↗

PubMed2003

Beta-lactamases: a survey of protein diversity.

Bacterial resistance to beta-lactam antibiotics and beta-lactamase inhibitors is an ever increasing problem that threatens the clinical utility of drugs that form the cornerstone of the antibiotic armamentarium. Especially among Gram-negative pathogens, elaboration of structurally and mechanistically novel beta-lactamase enzymes is the most important means by which resistance occurs. An appreciation of the tremendous diversity of these drug-modifying enzymes will assist in understanding why so few generally effective inhibitory agents exist for these unique drug targets. This review will give a general background on the reaction mechanisms and classification schemes of the more than 340 beta-lactamase enzymes described to date. A discussion will follow highlighting the emerging Class A SHV and TEM-derived extended-spectrum (ESBLs), and inhibitor-resistant enzymes, non-TEM, non-SHV Class A ESBLs, and carbapenemases, Class B metallo-beta-lactamases and some of their novel inhibitors, plasmid and chromosomally encoded Class C enzymes, and finally, the OXA-type oxacillinases, ESBLs, and carbapenemases of Class D. The clinical importance of multiple resistance mechanisms in conjunction with the production of beta-lactamase enzymes is emphasized.

Enzyme Inhibitors↗