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PubMed2004

[Ocular involvement in systemic Loa-Loa filariasis. Case report and review of the literature].

BACKGROUND: Within the last few years there is more and more evidence for nonspecific ocular symptoms caused by "exotic" pathogens. We herewith report another case of such an infection to underline the increasing importance and diagnostic relevance even of rare diseases. PATIENT: A 35-year-old female German patient presented with recurrent left retrobulbar "feeling of pressure" after a 6-month-stay in Central Africa 5 years ago. In addition, she reported on repeated swelling of the skin and joints of her hands and arms. Multiple ophthalmologic and rheumatologic investigations had been carried out without diagnostic results. Her ophthalmologist referred her with the presumed diagnosis of a subconjunctival worm. RESULTS: Slit-lamp biomicroscopy confirmed the original suspicion, and after topical anesthesia a female Loa-Loa worm was easily removed with forceps through a conjunctival incision. The general examination showed symptoms of systemic infection (calabar swelling, eosinophilia). Classification and initiation of treatment with diethylcarbamazine and mebendazole were carried out by the University Institute of Parasitology. CONCLUSION: Loa-Loa is a parasitic infection endemic in the tropical rain forests of Western, Central, and Eastern Africa. It is transmitted by the Chrysops fly. An increasing number of oculosystemic infections in non-African patients with Loa-Loa are being published. Therefore, any patient with an unclassifiable eye affection should also be investigated for those rare pathogens.

Adult↗

PubMedDate not supplied

Isoenzyme analysis of Entamoeba histolytica for evaluation of pathogenicity: detection of zymodeme XIX in South America.

Authors report the results of the isoenzyme analysis of strains of Entamoeba histolytica isolated from international travellers. This recently developed method allows the detection of pathogenic strains by evaluating the electrophoretic mobility of cytoplasmic enzymes and was proved to be more reliable and quickly feasible than previous ones. The experience reported refers to three strains isolated from travellers coming from Ecuador, Brazil and Indonesia, respectively; the zymodeme XIX (in accordance with the Sargeaunt's classification) was identified in all the three cases. This zymodeme has been first detected in 1981 and should currently be considered rare; moreover, it has never been previously reported from the Americas.

Amebiasis↗

PubMed2005

Real-time PCR quantification of bacterial adhesion to Caco-2 cells: competition between bifidobacteria and enteropathogens.

Probiotic bacteria play an important role in protecting the host from intestinal colonization of pathogenic bacteria. We have developed a new analytical approach based on a real-time PCR technique for quantifying Bifidobacterium adhesion to intestinal epithelial cells. Real-time PCR analysis showed that adhesion to enterocyte-like Caco-2 cells represented a variable phenotype in the genus Bifidobacterium, enabling classification of three adhesion behaviors: high adhesiveness (>40 bifidobacterial cells/Caco-2 cell); adhesiveness (5-40 bifidobacterial cells/Caco-2 cell); no adhesiveness (<5 bifidobacterial cells/Caco-2 cell). This molecular methodology was successfully used in competition studies in enteropathogens. All bifidobacterial strains examined evidenced displacement activity towards important enteropathogens (S. typhimurium, Y. enterocolitica and E. coli EPEC). Real-time PCR is a rapid, accurate and sensitive method for detecting and quantifying different bacterial genera and species simultaneously adhering to a epithelial cell monolayer.

Bacterial Adhesion↗

PubMed1996

Three species of Borrelia burgdorferi sensu lato (B. burgdorferi sensu stricto, B afzelii, and B. garinii) identified from cerebrospinal fluid isolates by pulsed-field gel electrophoresis and PCR.

A total of 36 European Borrelia burgdorferi sensu lato cerebrospinal fluid isolates (mainly from southern Germany) were analyzed by pulsed-field gel electrophoresis (PFGE) for large restriction fragment pattern (LRFP) and linear plasmid profiles. Analyzing this large panel of isolates, we detected all three species of B. burgdorferi sensu lato pathogenic for humans in cerebrospinal fluid from patients with Lyme neuroborreliosis by PFGE typing after MluI digestion: 21 B. garinii (58%), 10 B. afzelii (28%), and 4 B. burgdorferi sensu stricto (11%) strains as well as 1 isolate with bands characteristic of both B. afzelii and B. garinii. Species classification by PFGE typing was confirmed by 16S rRNA-specific PCR. Eighteen isolates (11 B. garinii, 6 B. afzelii, and 1 B. burgdorferi sensu stricto isolate) were further characterized by LRFP with four different restriction enzymes (ApaI, KspI, SmaI, and XhoI). All B. afzelii isolates showed identical patterns for each restriction enzyme group. Considerable heterogeneity was demonstrated within the B. garinii group. Subsequent analysis of plasmid profiles revealed only marginal differences for B. afzelii strains but different patterns for B. garinii isolates. In one B. afzelii strain we found a linear plasmid of about 110 kbp not described before. LRFP analysis by PFGE is a suitable tool for the molecular characterization of B. burgdorferi sensu lato strains and allows determination not only of the species but also of the subtypes within B. garinii.

Bacterial Typing Techniques↗

PubMedDate not supplied

[Taxonomy and classification of Rickettsiae].

During the recent 20 years the improvement of the methodological research basis including the molecular and genetic analysis of microorganisms parasites of eukaryotic cells, led to considerable changes in the taxonomy and classification of rickettsiae. This problem was not discussed in the Russian literature. At present the term "rickettsiae" conventionally embraces the group of microorganisms of the class Proteobacteria, nominated as species belonging to the genera Rickettsia, Orientia, Ehrlichia, Coxiella and Bartonella. An original scheme of the modern taxonomy of rickettsiae, pathogenic for man, is presented. The scheme is made with due regard to their phenotypic, clinico-epidemiological and genetic features.

Genotype↗

PubMed1993

[Local and systemic infections with bacteria of group EF-4 in dogs, cats and in a badger: bacteriologic and pathologico-anatomic results].

Bacteria of Group EF-4 were isolated in 7 dogs and in 5 cats from local purulent lesions in areas of natural openings of the head and from bite wounds, from lungs with focal necrotizing pneumonia in 2 additional cats and from internal organs in a badger with septicemia. The organisms grew mostly in pure culture. In conventional biochemical tests, 12 isolates were shown to belong to biovar EF-4a and 3 isolates to EF-4b. Classification as Group EF-4 was confirmed by assimilation tests performed with the commercially available gallery ATB 32 GN. Results of this study indicate that in veterinary medicine, bacteria of Group EF-4 are not only important from an epidemiological point of view, but that they may be more pathogenic for animals than considered hitherto.

Animals↗

PubMed1976

Conidiogenesis in pathogenic hyphomycetes. I. Sporothrix, Exophiala, Geotrichum and Microsporum.

Conidium formation in 5 species of pathogenic hyphomycetous fungi, Sporothrix schenckii, Exophiala salmonis, E. sp., Geotrichum candidum and Microsporum canis were examined using light and scanning electron microscopy. The fungi, grown in pure culture on potato dextrose agar under defined conditions, demonstrated 4 kinds of conidiogenesis. The taxonomic value of the developmental characters in the classification of the Fungi Imperfecti is discussed.

Cell Differentiation↗

PubMed2026

Genomic characterisation of Enterococcus cecorum isolated from broiler chickens in the United Kingdom.

Enterococcus cecorum is an important poultry pathogen associated with lameness and increased mortality, leading to major welfare and economic impacts. Treatment is often challenging because disease is frequently detected late and the organism can localise in bone and joints, limiting antimicrobial efficacy. Presence of antimicrobial resistance (AMR) genes may further complicate treatment. Despite increasing global genomic research, only one recent study has investigated the phylogeny of E. cecorum from conventional UK broiler farms, using limited samples and a restricted time frame. In this study, 283 E. cecorum isolates were analysed, including 158 from the United Kingdom and 125 global non‑UK isolates. UK isolates comprised 123 archived by the Animal and Plant Health Agency (APHA) between 2003 and 2022, predominantly from clinical outbreaks with increased welfare culling and mortality, and 35 isolates from a UK study including clinical and environmental samples. Genome sequencing was used to assess phylogeny, AMR determinants and virulence factors (VFs). Single nucleotide polymorphism phylogenetic analysis identified eight major UK lineages with limited intra‑lineage diversity, indicating that UK isolates were genetically distinct from non‑UK populations. Using a 60‑SNP threshold, APHA isolates formed 18 subclusters, consistent with long‑term persistence and recurrent farm transmission, while multiple subclusters detected on some farms suggested repeated introductions. UK isolates carried fewer AMR genes than non‑UK isolates, with erm(B), lnu(C), tet(M) and tet(L) most prevalent. Screening of VF genes identified nine genes present in all isolates, with the remainder variably distributed. A subset of 60 UK isolates was examined for 13 previously described virulence‑associated genes, with phylogenetic clustering indicating associations between gene presence or absence and clinical status or mortality classification. The capsular polysaccharide gene cpsO was assessed in this subset and most non‑clinical or environmental isolates were cpsO‑negative, although several isolates from high‑mortality outbreaks also lacked this gene. Overall, this study provides insight into the phylogeny, AMR profiles and virulence gene diversity of E. cecorum within the UK broiler sector, supporting targeted surveillance and investigation of pathogenic mechanisms.

Antimicrobial resistance↗

PubMed2026

Temporal Patterns in the Occurrence of Principal Salmonella Serotypes for Raw Meat and Poultry Products in the United States: 1998-2024.

Microbial foodborne pathogens, such as Salmonella, have the characteristic that only some subgroups of these bacteria are highly pathogenic to humans. For the Salmonella species enterica, there are more than 2,600 serotypes. These serotypes can be host-adapted so that for any animal reservoir, such as a particular food animal species, fewer than 10 serotypes make up more than fifty percent of isolates found in the reservoir. The highly concentrated nature of serotypes within a reservoir is a key to the findings of many studies and the cornerstone of some food safety programs. Nevertheless, a key limitation is that the dominant serotypes for a reservoir are likely to change over time. This is problematic because the risk of illness associated with a reservoir can increase dramatically if a more pathogenic serotype replaces one or more less pathogenic serotypes, and vice versa. In the United States, meat and poultry have been sampled continuously by the United States Department of Agriculture Food Safety and Inspection Service (USDA FSIS) for nearly 30 years. For this study, these data are used to describe how the occurrence of the most common serotypes for each sampled commodity has changed over time. Insight into how often and how rapidly the most common serotypes change is important for designing effective mitigation strategies. To aid the development of such a mitigation strategy, we developed a classification system to categorize serotypes based on the direction and magnitude of change in each serotype over time. This information is combined with a ranking system that describes the relative virulence of each serotype using genomic and epidemiological virulence patterns. We then developed a heuristic system to support risk management decisions regarding the potential risks and benefits of applying serotype-specific interventions.

Compositional data↗

PubMed2026

Shared inheritance reveals landscape of somatic and germline cancer risk in TP53.

Pathogenic variants in TP53, the key tumor suppressor gene underlying Li-Fraumeni syndrome (LFS), are among the best-established causes of inherited cancer predisposition. However, large-scale sequencing has revealed that many apparently pathogenic TP53 variants detected in blood are the result of somatic clonal expansions, complicating risk interpretation. Using blood-derived whole-exome data from 469,391 UK Biobank participants, we combined the variant allele fraction (VAF) with haplotype-sharing analysis to distinguish germline and somatic TP53 variants. Germline variants were concentrated at sites linked to partial loss of p53 function and lower disease penetrance, whereas classic LFS alleles appeared to be predominantly somatically acquired. Classic LFS alleles at high VAF conferred markedly increased risk of hematological malignancy but not solid tumors, indicating an important contribution from large TP53-mutant clonal expansions. The prevalence of somatic clonal expansion also correlated with missense variant pathogenicity, suggesting that somatic activity provides an informative in vivo proxy for functional impact. These results provide new insights into TP53-associated cancer risk at the population level, demonstrate that somatic rather than germline risk predominates in middle-aged healthy adults, and provide a scalable framework for variant classification in large-scale population genomics.

Humans↗

PubMed2026

From commensal to pathobiont: The emergence of virulence-enhanced Escherichia coli in China's food-animal systems - insights with future implications.

A fundamental shift in Escherichia coli epidemiology is being driven by convergence of virulence determinants and antimicrobial resistance within linked human-animal-environment systems. In China, the rapid growth of food-animal production, extensive antimicrobial use, and complex food networks are accelerating the emergence and dissemination of virulence-enhanced E. coli pathobionts. This review synthesizes recent epidemiological, genomics, and outbreak data to characterize China's evolving landscape of food-animal-associated E. coli. We highlight a significant shift from classical pathotypes to hybrid lineages that simultaneously carry virulence factors and last-resort antibiotic resistance determinants, including mcr-1, tet(X4), and blaNDM. These traits disseminate rapidly via plasmid-mediated horizontal gene transfer, facilitating rapid adaptation and enabling cross-sectoral One Health transmission. National surveillance, foodborne outbreak investigations, and whole-genome sequencing data show that food-animal reservoirs are active evolutionary niches that drive pathogen diversity and fitness, rather than serving merely as contamination sources. Whole-genome sequencing also pinpoints high-risk clones (e.g., ST394) and plasmid-mediated co-selection of virulence and AMR. The emergence of hybrid pathotypes (e.g., STEC/ETEC) and AMR-virulence co-selection challenges traditional classification and limits the effectiveness of conventional surveillance approaches. The 2017 colistin ban reduced mcr-1, yet ongoing resistance and emerging tet(X4) demand integrated surveillance. Collectively, these findings call for reconceptualizing E. coli as a dynamic genomic entity embedded within a unified ecological network. Addressing this threat requires an integrated One Health strategy including genomic surveillance, agricultural antimicrobial stewardship, and coordinated food-environment-clinical monitoring to prevent high-risk clone emergence and global spread.

Animals↗

PubMed2000

Effect of macrolides as part of initial empiric therapy on medical outcomes for hospitalized patients with community-acquired pneumonia.

OBJECTIVE: The goal of this study was to compare the outcomes of hospitalized patients receiving a nonpseudomonal third-generation cephalosporin with or without a macrolide for the treatment of community-acquired pneumonia (CAP). BACKGROUND: The initial treatment of CAP is usually based on empirically selected antibiotic therapy. The need for coverage of atypical pathogens in hospitalized patients is widely debated, and regional variations may exist. METHODS: All patients admitted to a community hospital or to a university hospital for 1 year who were aged > or =18 years and had a principal discharge diagnosis of pneumonia with no organism specified according to the International Classification of Diseases, Ninth Revision, Clinical Modification were evaluated. Each patient's medical chart was reviewed by a clinical pharmacist at each facility. The following information was collected for each patient using a standardized form: demographic characteristics, coexisting illnesses, length of hospital and intensive care unit stays, antibiotic regimens, length of parenteral and oral therapy, laboratory and radiographic findings (ie, blood urea nitrogen, glucose, hematocrit, sodium, PO2, pH, and pleural effusion), physical examination results, and mortality. Patients treated with a nonpseudomonal third-generation cephalosporin with or without a macrolide were included in this analysis. Categoric variables were compared using the chi-square test or the Fisher exact test, and continuous variables were compared using the Mann-Whitney U test. A P value < 0.05 was considered statistically significant. RESULTS: A total of 213 patients met the entry criteria and were treated with a nonpseudomonal third-generation cephalosporin with (116 patients) or without (97 patients) a macrolide. The mean (+/- SD) age of the patients was 62.2+/-19.6 years; 47% were male. The most common comorbid conditions were chronic obstructive pulmonary disease, diabetes mellitus, congestive heart failure, and cerebrovascular accident (CVA). Of the 116 patients who received a macrolide, the majority (66%) received erythromycin. Other macrolides used were clarithromycin (19%) and oral azithromycin (15%). There were no statistical differences between patients who did and did not receive a macrolide in terms of comorbid illnesses, length of hospital stay (5.2+/-2.8 vs 5.2+/-3.4 days, respectively), length of intravenous antibiotic therapy (4.4+/-2.5 vs 4.1+/-2.3 days, respectively), or mortality (0.9% vs 3.1%, respectively; P = 0.333). The only difference between the groups was in age. Those patients who received a macrolide were significantly younger than those who received only a nonpseudomonal third-generation cephalosporin (57.4+/-19.2 years vs 67.9+/-18.5 years; P < 0.001). However, when age and severity of illness were taken into account, no difference existed between the patients who received a nonpseudomonal third-generation cephalosporin alone or in combination with a macrolide. CONCLUSIONS: We concluded that the addition of a macrolide to a nonpseudomonal third-generation cephalosporin as initial therapy for the treatment of CAP may not be necessary. A randomized, prospective clinical trial comparing a nonpseudomonal third-generation cephalosporin alone and in combination with a macrolide is warranted.

Adult↗

PubMed1999

Differentiation of Serpulina species by NADH oxidase gene (nox) sequence comparisons and nox-based polymerase chain reaction tests.

The NADH oxidase genes (nox) of 18 strains of intestinal spirochaetes were partially sequenced over 1246 bases. Strains examined included 17 representatives from six species of the genus Serpulina, and the type strain 513A(T) of the human intestinal spirochaete Brachyspira aalborgi. Sequences were aligned and used to investigate phylogenetic relationships between the organisms. Nox sequence identities between strains within the genus Serpulina were within the range 86.3-100%, whilst the nox gene of B. aalborgi shared between 78.8-83.0% sequence identity with the nox sequences of the various Serpulina strains. A phenogram produced based on sequence dissimilarities was in good agreement with the current classification of species in the genus Serpulina, although an atypical strongly beta-haemolytic porcine strain (P280/1), previously thought to be S. innocens, appeared distinct from other members of this species. Primer pairs were developed from the nox sequence alignments for use in polymerase chain reaction (PCR) identification of the pathogenic species S. hyodysenteriae (NOX1), S. intermedia (NOX2), and S. pilosicoli (NOX3), and for the combined non-pathogenic species S. innocens and S. murdochii (NOX4). The PCRs were optimised using 80 strains representing all currently described species in the genus Serpulina, as well as the type strain of B. aalborgi. Tests NOX1 and NOX4 specifically amplified DNA from all members of their respective target species, whilst tests NOX2 and NOX3 were less sensitive. NOX2 amplified DNA from all 10 strains of S. intermedia from pigs but from only 4 of 10 strains from chickens, whilst NOX3 amplified DNA from only 18 of 21 S. pilosicoli strains, even at low stringency. Tests NOX1 and NOX4 should prove useful in veterinary diagnostic laboratories, whilst NOX2 and NOX3 require further refinement.

Animals↗

PubMed2005

Hodgkin's lymphoma and tuberculosis coexistence in cervical lymph nodes.

We describe the case of a 47-year-old man admitted to the Department of Hematology because of fever, enlarged cervical and supraclavicular lymph nodes, hepatosplenomegaly and non-specific lung infiltrations. The histopathological examination of the cervical lymph node revealed Hodgkin's lymphoma (HL) NS type I. Clinical evaluation revealed stage IVB according to Ann Arbor classification and the presence of 5 unfavorable prognostic factors according to the International Prognostic Index. Despite BEACOPP chemotherapy (bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone), the enlarged lymph nodes, lung infiltrations and fever persisted. Microbiological and serological tests did not lead to the identification of any viral or bacterial pathogens. Bronchoscopy showed chronic inflammation and post-tuberculosis (TB) scars in bronchi without acid-fast bacilli in bronchoalveolar lavage (BAL) in culture and polymerase chain reaction (PCR) tests. However, the biopsy of the supraclavicular lymph node revealed multiple, caseating and necrotizing granulomatous lesions with scattered Reed-Sternberg (R-S) cells. The auramin staining presented acid-fast bacilli and allowed the diagnosis of productive and caseating TB coexisting with HL. The 4 tuberculostatics regimen and ABVD chemotherapy (adriamycin, bleomycin, vincristine, dacarbazine) resulted in a complete clinical response after 3 months of treatment. In conclusion, the association between HL and TB must be considered, especially in countries where the latter is endemic. The diagnosis may be difficult due to similarities in the clinical course, laboratory tests and imaging procedures.

Antineoplastic Combined Chemotherapy Protocols↗

PubMed1999

Genome organization is not conserved between Bacillus cereus and Bacillus subtilis.

The opportunistic pathogen Bacillus cereus is the genetically stable member of a group of closely related bacteria including the insect pathogen Bacillus thuringiensis and the mammalian pathogen Bacillus anthracis. Physical maps of B. cereus and B. thuringiensis strains show considerable variations in discrete parts of the chromosome, suggesting that certain genome regions are more prone to rearrangements. B. cereus belongs to the same subgroup of Bacillus species as Bacillus subtilis, by both phenotypic and rRNA sequence classification. The analysis of 80 kb of genome sequence sampled from different regions of the B. cereus ATCC 10987 chromosome is reported. Analysis of the sequence and comparison of the localization of the putative genes with that of B. subtilis orthologues show the following: (1) gene organization is not conserved between B. cereus and B. subtilis; (2) several putative genes are more closely related to genes from other bacteria and archaea than to B. subtilis, or may be absent in B. subtilis 168; (3) B. cereus contains a 155 bp repetitive sequence that is not present in B. subtilis. By hybridization, this repeat is present in all B. cereus and B. thuringiensis strains so far investigated.

Bacillus cereus↗

PubMed2004

Epidemiology and clinical presentation of respiratory syncytial virus infection in a Tunisian neonatal unit from 2000 to 2002.

Respiratory syncytial virus (RSV) is an important viral pathogen causing lower respiratory tract infection (LRI) in infants. This study describes the clinical and genetic epidemiology of RSV infection among Tunisian neonates. Nasopharyngeal aspirates collected from 268 newborns with LRI were screened for RSV by immunofluorescence assay. Positive samples were analysed by RT-PCR-hybridisation assay for subgroup classification of RSV genomes. RSV infection was present in 23.1% of neonates, with a predominance in males. Peak incidence occurred in winter. Subgroup classification showed a higher prevalence of group B than group A strains. Nosocomially acquired RSV infection was present in 37% of neonates, 54.3% had an underlying condition predisposing to severe disease and 13% died. The average duration of hospital stay was 10 days and 87% of newborns required supplemental oxygen. As no currently effective treatment is available, preventive measures are a priority in high-risk infants.

Age Distribution↗

PubMed1997

Secondary structure of the 3'-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities.

The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary structure elements, but also regions of high structural flexibility. Flaviviruses, many of which are important human pathogens, have a common genomic organization, but exhibit a significant degree of RNA sequence diversity in the functionally important 3'-NCR. We demonstrate the presence of secondary structures shared by all flaviviruses, as well as structural features that are characteristic for groups of viruses within the genus reflecting the established classification scheme. The significance of most of the predicted structures is corroborated by compensatory mutations. The availability of infectious clones for several flaviviruses will allow the assessment of these structural elements in processes of the viral life cycle, such as replication and assembly.

Algorithms↗

PubMed1996

Trimmatostroma abietis sp. nov. (hyphomycetes) and related species.

Trimmatostroma abietis from the needles of conifers and from stone, mostly in Germany, is described. On the natural substrate it is characterized by stromatic conidiomata. Conidia are mostly two-celled, are arranged in long chains, and originate by intercalary dilatation of fertile hyphae. The wide morphological plasticity of the fungus and its physiological profile are described. Its occurrence as a saprophyte and possibly opportunistic pathogen on plants and as an invader of environments with low water activity, particularly stone surfaces, are discussed. Relationships with other taxa are outlined.

Classification↗