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Enterovirus D68 (EV-D68) infections are associated with severe respiratory disease and acute flaccid myelitis (AFM). The European Non-Polio Enterovirus Network (ENPEN) aimed to investigate the epidemiological and genetic characteristics of EV-D68 and its clinical impact during the fall-winter season of 2021/22. From 19 European countries, 58 institutes reported 10,481 (6.8%) EV-positive samples of which 1,004 (9.6%) were identified as EV-D68 (852 respiratory samples). Clinical data was reported for 969 cases. 78.9% of infections were reported in children (0-5 years); 37.9% of cases were hospitalised. Acute respiratory distress was commonly noted (93.1%) followed by fever (49.4%). Neurological problems were observed in 6.4% of cases with six reported with AFM. Phylodynamic/Nextstrain and phylogenetic analyses based on 694 sequences showed the emergence of two novel B3-derived lineages, with no regional clustering. In conclusion, we describe a large-scale EV-D68 European upsurge with severe clinical impact and the emergence of B3-derived lineages., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Objectives: To assess the performances of three commonly used antigen rapid diagnostic tests used as self-tests in asymptomatic individuals in the Omicron period., Methods: We performed a cross-sectional diagnostic test accuracy study in the Omicron period in three public health service COVID-19 test sites in the Netherlands, including 3600 asymptomatic individuals aged ≥ 16 years presenting for SARS-CoV-2 testing for any reason except confirmatory testing after a positive self-test. Participants were sampled for RT-PCR (reference test) and received one self-test (either Acon Flowflex [Flowflex], MP Biomedicals (MPBio), or Siemens-Healthineers CLINITEST [CLINITEST]) to perform unsupervised at home. Diagnostic accuracies of each self-test were calculated., Results: Overall sensitivities were 27.5% (95% CI, 21.3-34.3%) for Flowflex, 20.9% (13.9-29.4%) for MPBio, and 25.6% (19.1-33.1%) for CLINITEST. After applying a viral load cut-off (≥5.2 log10 SARS-CoV-2 E-gene copies/mL), sensitivities increased to 48.3% (37.6-59.2%), 37.8% (22.5-55.2%), and 40.0% (29.5-51.2%), respectively. Specificities were >99% for all tests in most analyses., Discussion: The sensitivities of three commonly used SARS-CoV-2 antigen rapid diagnostic tests when used as self-tests in asymptomatic individuals in the Omicron period were very low. Antigen rapid diagnostic test self-testing in asymptomatic individuals may only detect a minority of infections at that point in time. Repeated self-testing in case of a negative self-test is advocated to improve the diagnostic yield, and individuals should be advised to re-test when symptoms develop., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: Enterovirus-D68 (EV-D68) predominantly causes respiratory disease. However, EV-D68 infections also have been associated with central nervous system (CNS) complications, most specifically acute flaccid myelitis (AFM). Diagnosing EV-D68-associated CNS disease is challenging since viral RNA is rarely detected in cerebrospinal fluid (CSF)., Objective: In order to determine an EV antibody index (AI), we evaluated the value of a commercially available quantitative ELISA to detect EV-specific antibodies in paired CSF and blood., Study Design: Nine paired CSF and blood samples were obtained from patients with EV-D68-associated AFM or from patients with a confirmed EV-associated CNS disease. EV-specific antibodies were detected using a quantitative ELISA. A Reiber diagram analysis was performed, by which the AI was calculated. Subsequently, EV ELISA results were compared with an EV-D68 virus neutralization test., Results: ELISA detected EV-specific antibodies in 1 out of the 3 patients with EV-D68-associated AFM and in 3 out of the 6 patients with confirmed EV-associated CNS disease. In these patients, the AI was indicative for intrathecal antibody production against enterovirus. Assay comparison showed that EV-D68 neutralizing antibody detection increased the sensitivity of EV-D68 antibody detection., Conclusions: A quantitative EV IgG ELISA in combination with Reiber diagram analysis and AI-calculation can be used as a diagnostic tool for EV-associated CNS disease, including EV-D68. An EV-D68 specific ELISA will improve the sensitivity of the tool. With the growing awareness that the detection of non-polio enteroviruses needs to be improved, diagnostic laboratories should consider implementation of EV serology., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: The relation between viral load and disease severity in childhood acute respiratory tract infections (ARI) is not fully understood., Objectives: To assess the clinical relevance of the relation between viral load, determined by cycle threshold (CT) value of real-time reverse transcription-polymerase chain reaction assays and disease severity in children with single- and multiple viral ARI., Study Design: 582 children with ARI were prospectively followed and tested for 15 viruses. Correlations were calculated between CT values and clinical parameters., Results: In single viral ARI, statistically significant correlations were found between viral loads of Respiratory Syncytial Virus (RSV) and hospitalization and between viral loads of Human Coronavirus (HCoV) and a disease severity score. In multiple-viral ARI, statistically significant correlations between viral load and clinical parameters were found. In RSV-Rhinovirus (RV) multiple infections, a low viral load of RV was correlated with a high length of hospital stay and a high duration of extra oxygen use. The mean CT value for RV, HCoV and Parainfluenza virus was significantly lower in single- versus multiple infections., Conclusion: Although correlations between CT values and clinical parameters in patients with single and multiple viral infection were found, the clinical importance of these findings is limited because individual differences in host-, viral and laboratory factors complicate the interpretation of statistically significant findings. In multiple infections, viral load cannot be used to differentiate between disease causing virus and innocent bystanders., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) is important to identify patients colonized with this pathogen and implement infection control precautions. We aimed to improve the combined use of the mecA gene polymerase chain reaction (PCR) and the SA442 PCR to detect MRSA in clinical screening samples. In a true MRSA the mecA copy number will be equal to the SA442 copy number, whereas in samples with a methicillin-sensitive Staphylococcus aureus (MSSA) combined with a methicillin-resistant coagulase-negative Staphylococcus (MRCNS) the copy numbers will usually differ. Here we introduce a PCR system, relative quantification PCR (RQ-PCR), which takes this difference into account. RQ-PCR identifies true MRSA in clinical samples with a specificity that is comparable to the SCCmec-based PCRs., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Objective: Real-time polymerase chain reaction (RT-PCR) testing is a quick sensitive method for detecting respiratory pathogens. We evaluated the diagnostic yield of RT-PCR assays and measured the effect of rapid reporting on patient care., Methods: In a controlled clinical trial, nasal wash specimens were obtained from patients <12 years of age with suspected acute respiratory infections. In addition to the standard hospital protocol, RT-PCR assays for 17 pathogens were performed. The RT-PCR results were communicated to the clinicians within 12 to 36 hours in the intervention group and after 4 weeks in the control group., Results: A total of 583 patients were included (mean age: 8.1 months [range: 0-107.5 months]): 298 in the intervention group and 285 in the control group. Eighty-two percent of nasal wash specimens tested positive for ≥1 pathogen. Respiratory syncytial virus was the most frequently encountered (55%) pathogen. There were no significant differences between the groups with respect to hospital admissions (intervention group: 223 admissions; control group: 211 admissions; P = .825), length of hospital stay (mean ± SD: 3.68 ± 2.68 days [intervention group] and 3.96 ± 2.67 days [control group]; P = .178), or duration of antibiotic use (mean ± SD: 6.52 ± 2.15 days [intervention group] and 6.97 ± 2.86 days [control group]; P = .490), when antibiotic treatment had been initiated., Conclusions: RT-PCR testing has a high yield of viral diagnoses, but rapid communication does not lead to decreases in hospital admissions, shorter hospital stays, or less antibiotic use for children with acute respiratory infections.

* Sexual reproduction does not occur in bacteria. The point of departure in bacterial reproduction is always that one individual divides itself into two identical descendants. * In the bacterial world, however, there is certainly exchange of hereditary characteristics (DNA). This type of exchange is called horizontal gene transfer. * There are 3 basic ways for the exchange of DNA between bacteria: conjugation, transduction and natural transformation. Each of these has its specific impact on the species. * During conjugation, a piece of DNA is copied in one bacterium and transferred to another via a temporary connection, a conjugative pilus. In this way, for example, a particular gene that codes for resistance against antibiotics can be transmitted. * In transduction, the transfer of DNA takes place with the aid of bacteriophages. The gene that codes for the toxin produced by Vibrio cholerae is spread by transduction. * In transformation, DNA that is located outside the cell is fragmented and imported into the cell, after which, via recombination, the DNA replaces a piece of original DNA in the chromosome of the host. Transformation is responsible for, among other things, antigen variation in the pneumococcal capsule. Antigen variation helps the pneumococci to resist the immune response leading to the forming of antibodies and adequate opsonisation.

In several bacterial species that show natural transformation, dprA has been described as a competence gene. The DprA protein has been suggested to be involved in the protection of incoming DNA. However, members of the dprA gene family (also called smf) can be detected in virtually all bacterial species, which suggests that their gene products have a more general function. We examined the function of the DprA/Smf homologue of Escherichia coli. Escherichia coli dprA/smf is able to partially restore transformation in a Haemophilus influenzae dprA mutant, which shows that dprA/smf genes from competent and noncompetent species are interchangeable with respect to their involvement in natural transformation. From this, we conclude that natural transformation is probably an additional function of these genes. Subsequently, the dprA/smf gene was deleted in various recombination mutants of E. coli, and the resultant phenotype was tested. All the resultant E. coli dprA/smf mutants did not differ from their parent strains with respect to transformation, Hfr-conjugation, recombination and DNA repair. Therefore, a role of DprA/Smf in DNA recombination could not be established and the basic function of dprA/smf remains unclear.

A 58-year-old man presented with hoarseness and a sore throat for the previous 3 months, which were caused by a laryngeal infection with the fungus Histoplasma capsulatum. He had been infected during a stay in Indonesia. Both his hoarseness as well as the Histoplasma antigen titres in serum responded to therapy with itraconazol. H. capsulatum is found in tropical and subtropical areas worldwide, but infections are most commonly reported from the south of the United States of America. If not asymptomatic, the disease most often presents with pulmonary symptoms. A histoplasmosis presenting as a laryngeal infection is relatively uncommon and can be mistaken for papillomatosis or carcinoma. The diagnosis can be made by microscopy and culture of the fungus; an antigen test is available in the United States.

Genetic analysis of two Helicobacter pylori strains isolated from a single gastric biopsy showed evidence of extensive horizontal gene transfer. Several large recombinations were identified in the rdxA gene, which is involved in metronidazole resistance.

Like other bacterial species with a high frequency of inter-strain recombination, the human gastric pathogen Helicobacter pylori is competent for natural transformation. Recent data, however, indicate that its DNA-uptake system differs significantly from that in other species that contain DNA-uptake systems related to type IV pili. Instead, in H. pylori it has been suggested that the five proteins that form the transmembrane channel of the transformation system are closely related to subunits of type IV secretion systems.

This study examined whether the simultaneous presence of metronidazole-susceptible and -resistant Helicobacter pylori colonies in a single biopsy specimen is caused by a multiple strain infection with a susceptible and a resistant strain or by two subpopulations within a single strain. Single colonies obtained from seven biopsy specimens known to harbour both susceptible and resistant Helicobacter pylori were fingerprinted by restricted fragment length polymorphism typing of the ureC gene and by the random amplified polymorphic DNA procedure. Metronidazole susceptibility was determined by the E test. The results indicated that the occurrence of metronidazole-resistant and metronidazole-susceptible bacteria within a single biopsy does not imply the presence of a multiple strain infection with one resistant and one sensitive strain.

Helicobacter pylori is naturally competent for transformation, but the DNA uptake system of this bacterium is only partially characterized, and nothing is known about the regulation of competence in H. pylori. To identify other components involved in transformation or competence regulation in this species, we screened a mutant library for competence-deficient mutants. This resulted in the identification of a novel, Helicobacter-specific competence gene (comH) whose function is essential for transformation of H. pylori with chromosomal DNA fragments as well as with plasmids. Complementation of comH mutants in trans completely restored competence. Unlike other transformation genes of H. pylori, comH does not belong to a known family of orthologous genes. Moreover, no significant homologs of comH were identified in currently available databases of bacterial genome sequences. The comH gene codes for a protein with an N-terminal leader sequence and is present in both highly competent and less-efficient transforming H. pylori strains. A comH homolog was found in Helicobacter acinonychis but not in Helicobacter felis and Helicobacter mustelae.

Genetic recombination in Helicobacter pylori is believed to be involved in host adaptation of this gastric pathogen and uptake of DNA by natural transformation can result in changes in virulence factors as well as antigenic variation. To elucidate the mechanisms involved in natural transformation we tested two genes with homology to known competence genes (dprA and traG) for their role in this process. Insertion mutants in these genes were constructed in two different H. pylori strains and their competence by natural transformation was compared to the wild-type. Mutation of the traG homolog did not reduce competence. Mutation of the dprA gene, however, severely impaired natural transformation both with plasmid and chromosomal DNA. Our data indicate that dprA and comB3 are essential parts of a common pathway for chromosomal and plasmid transformation.