No evidence for a common blood microbiome based on a population study of 9,770 healthy humans

Human blood is conventionally considered sterile but recent studies suggest the presence of a blood microbiome in healthy individuals. Here we characterized the DNA signatures of microbes in the blood of 9,770 healthy individuals using sequencing data from multiple cohorts. After filtering for contaminants, we identified 117 microbial species in blood, some of which had DNA signatures of microbial replication. They were primarily commensals associated with the gut (n = 40), mouth (n = 32) and genitourinary tract (n = 18), and were distinct from pathogens detected in hospital blood cultures. No species were detected in 84% of individuals, while the remainder only had a median of one species. Less than 5% of individuals shared the same species, no co-occurrence patterns between different species were observed and no associations between host phenotypes and microbes were found. Overall, these results do not support the hypothesis of a consistent core microbiome endogenous to human blood. Rather, our findings support the transient and sporadic translocation of commensal microbes from other body sites into the bloodstream

Genomic identification of two Phytobacter diazotrophicus isolates from a neonatal intensive care unit in Singapore

We report the draft genome sequences of two Phytobacter diazotrophicus isolates recovered from a swab specimen from the water faucet located in the Neonatal Intensive Care Unit (ICU), National University Hospital, Singapore. The isolates were misidentified as Cronobacter sakazakii and Klebsiella oxytoca using biochemical methods. Whole-genome sequencing (WGS) was performed to determine their identity

Correction for Hon et al., “Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore”

Author correction for https://doi.org/10.1128/mra.00167-2

CalmBelt: Rapid SARS-CoV-2 Genome Characterization for Outbreak Tracking

10.3389/fmed.2021.790662Frontiers in Medicine879066

Correction for Hon et al., “Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore”

Author correction for https://doi.org/10.1128/mra.00167-2

Relapsing COVID-19 infection as a manifestation of Good syndrome: a case report and literature review

Good syndrome (GS) is a rare acquired immunodeficiency disease characterized by the presence of thymoma with combined B and T cell immunodeficiency in adults. Recurrent bacterial infections, particularly sinopulmonary infections caused by encapsulated bacteria, remain the most common infective presentation of GS; however, relapsing viral infections have also been reported, likely due to impaired T cell-mediated immunity. Relapsing COVID-19 infection, however, has not been previously reported as a manifestation of GS. We present two cases of relapsing COVID-19 infection in patients with GS; in one case, relapsing COVID-19 was the first manifestation of newly diagnosed GS

Development of a modified lymphocyte transformation test for diagnosing drug-induced liver injury associated with an adaptive immune response

Drug-induced liver injury (DILI) is a growing problem. Diagnostic methods to differentiate DILI caused by an adaptive immune response from liver injury of other causes or to identify the responsible drug in patients receiving multiple drugs, herbals and/or dietary supplements (polypharmacy) have not yet been established. The lymphocyte transformation test (LTT) has been proposed as a diagnostic method to determine if a subject with an apparent hypersensitivity reaction has become sensitized to a specific drug. In this test, peripheral blood mononuclear cells (PBMC) collected from a subject are incubated with drug(s) suspected of causing the reaction. Cell proliferation, measured by the incorporation of [3H]-thymidine into new DNA, is considered evidence of a drug-specific immune response. The objectives of the current studies were to: (1) develop and optimize a modified version of the LTT (mLTT) and (2) investigate the feasibility of using the mLTT for diagnosing DILI associated with an adaptive immune response and identifying the responsible drug. PBMC collected from donors with a history of drug hypersensitivity reactions to specific drugs (manifested as skin rash) were used as positive controls for assay optimization. Following optimization, samples collected from 24 subjects enrolled in the U.S. Drug-Induced Liver Injury Network (DILIN) were tested in the mLTT. Using cytokine and granzyme B production as the primary endpoints to demonstrate lymphocyte sensitization to a specific drug, most samples from the DILIN subjects failed to respond. However, robust positive mLTT responses were observed for two of four samples from three DILIN subjects with hepatitis due to isoniazid (INH). We conclude that the mLTT, as performed here on frozen and thawed PBMC, is not a reliable test for diagnosing DILI caused by all drugs, but that it may be useful for confirming the role of the adaptive immune response in DILI ascribed to INH

Relating knowledge, attitude and practice of antibiotic use to extended-spectrum beta-lactamase-producing Enterobacteriaceae carriage: results of a cross-sectional community survey

OBJECTIVES: To study the correlation between knowledge, attitude and practices (KAP) of antibiotic consumption with epidemiology and molecular characteristics of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) carriage, in order to identify modifiable factors and public health interventions to reduce prevalence of multidrug-resistant organism colonisation in the community. DESIGN: Cross-sectional questionnaire of KAP towards antibiotic use and collection of stool samples or rectal swabs. ESBL-PE isolates obtained underwent whole genome sequencing to identify resistance genes. SETTING: A densely populated community in Singapore. PARTICIPANTS: There were 693 healthy community-dwelling questionnaire respondents. Out of which, 305 provided stool samples or rectal swabs. RESULTS: The overall knowledge of antibiotic use was poor (mean score 4.6/10, IQR 3.0-6.0). 80 participants (80/305, 26.2%) carried at least one ESBL-PE isolate. The most common ESBL-PE was Escherichia coli sequence type 131 carrying CTX-M type beta-lactamases (11/71, 15.5%). Living overseas for >1 year (OR 3.3, 95% CI 1.6 to 6.9) but not short-term travel, recent hospitalisation or antibiotic intake was associated with ESBL-PE carriage. Interestingly, higher knowledge scores (OR 2.0, 95% CI 1.03 to 3.9) and having no leftover antibiotics (OR 2.4, 95% CI 1.2 to 4.9) were independent factors associated with ESBL-PE carriage in the multivariate logistic regression model. CONCLUSIONS: While the role of trans-border transmission of antimicrobial resistance is well known, we may have to examine the current recommendation that all antibiotics courses have to be completed. Clinical trials to determine the optimum duration of treatment for common infections are critically important