1,721,078 research outputs found
Social structure and Escherichia coli sharing in a group-living wild primate, Verreaux’s sifaka
No full textBACKGROUND: Epidemiological models often use information on host social contacts to predict the potential impact of infectious diseases on host populations and the efficiency of control measures. It can be difficult, however, to determine whether social contacts are actually meaningful predictors of transmission. We investigated the role of host social structure in the transmission of Escherichia coli in a wild population of primates, Verreaux’s sifakas (Propithecus verreauxi). Using multilocus sequence typing (MLST), we compared genetic similarities between E. coli isolates from different individuals and groups to infer transmission pathways. RESULTS: Correlation of social and transmission networks revealed that membership to the same group significantly predicted sharing of E. coli MLST sequence types (ST). Intergroup encounter rate and a measure of space-use sharing provided equally potent explanations for type sharing between social groups when closely related STs were taken into account, whereas animal age, sex and dispersal history had no influence. No antibiotic resistance was found, suggesting low rates of E. coli spillover from humans into this arboreal species. CONCLUSIONS: We show that patterns of E. coli transmission reflect the social structure of this group-living lemur species. We discuss our results in the light of the species’ ecology and propose scent-marking, a type of social contact not considered in previous epidemiological studies, as a likely route of transmission between groups. However, further studies are needed to explicitly test this hypothesis and to further elucidate the relative roles of direct contact and environmental transmission in pathogen transfer
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Evolution of Enterohemorrhagic Escherichia coli O26 Based on Single-Nucleotide Polymorphisms
No full textEnterohemorrhagic Escherichia coli (EHEC) O26:H11/H- is the predominant non-O157 EHEC serotype among patients with diarrhea, bloody diarrhea, and hemolytic uremic syndrome (HUS) worldwide. To elucidate their phylogeny and association between their phylogenetic background and clinical outcome of the infection, we investigated 120 EHEC O26:H11/H- strains isolated between 1965 and 2012 from asymptomatic carriers and patients with diarrhea or HUS. Whole-genome shotgun sequencing (WGS) was applied to ten representative EHEC O26 isolates to determine single nucleotide polymorphism (SNP) localizations within a predefined set of core genes. A multiplex SNP assay, comprising a randomly distributed subset of 48 SNPs, was established to detect SNPs in 110 additional EHEC O26 strains. Within approximately 1 Mb of core genes, WGS resulted in 476 high-quality bi-allelic SNP localizations. Forty-eight of these were subsequently investigated in 110 EHEC O26 and four different SNP clonal complexes (SNP-CC) were identified. SNP-CC2 was significantly associated with the development of HUS. Within the subsequently established evolutionary model of EHEC O26, we dated the emergence of human EHEC O26 to approximately 19,700 years ago and demonstrated a recent evolution within humans into the 4 SNP-CCs over the past 1,650 years. WGS and subsequent SNP typing enabled us to gain new insights into the evolution of EHEC O26 suggesting a common theme in this EHEC group with analogies to EHEC O157. In addition, the SNP-CC analysis may help to assess a risk in infected individuals for the progression to HUS and to implement more specific infection control measures
In vitro activity of antibiotic monotherapy and combination therapy with bacteriophages against Staphylococcus aureus LVAD-driveline infections.
Full text linkLeft-ventricular assist devices (LVADs) are increasingly used as a bridge to heart transplantation and destination therapy. These devices, especially the driveline, are susceptible to difficult-to-treat infections, associated with high morbidity and mortality rates. Staphylococcus aureus (S. aureus) is a major causative pathogen of LVAD infections. Antibiotic resistance and biofilm formation can complicate the treatment of these infections. A novel in vitro assay was developed to study the antibiotic susceptibility of S. aureus biofilm grown on LVAD drivelines. Besides antibiotic monotherapy, the effect of various antibiotics combined with rifampicin was studied. Additionally, we explored the efficacy of four individual phages and phage-antibiotic combinations as potential treatment strategies. Our data showed a decrease of susceptibility of the S. aureus biofilms to antibiotic monotherapy compared to planktonic S. aureus. With only rifampicin and erythromycin monotherapy resulting in full bacterial clearance. Combining antibiotics with rifampicin showed similar antimicrobial efficacy against S. aureus biofilms as rifampicin monotherapy. While both individual phages and a phage cocktail were effective against planktonic bacteria, phage efficacy was limited against S. aureus in biofilm. Combining phages with antibiotics did not clearly improve treatment efficacy, compared to antibiotic monotherapy. Contrarily, it even increased bacterial growth when phage administration preceded antibiotic treatment. Here, both antibiotic- and phage monotherapy showed reduced efficacy on LVAD-driveline biofilms. Additionally, phages did not show an additive value to antibiotic treatment of LVAD driveline infections. Further studies are needed to elucidate optimal treatment strategies for LVAD-driveline infections.IMPORTANCECurrent treatment strategies for S. aureus LVAD-driveline infections are based on in vitro antibiotic susceptibility of planktonic bacteria. However, LVAD infections are most often biofilm-related, which decreases antibiotic susceptibility significantly, resulting in discrepancies between in vitro antibiotic susceptibility and in vivo treatment success. Here, we have developed a novel in vitro assay to determine antibiotic susceptibility of S. aureus biofilm, grown in conditions relevant to LVAD-driveline infections. Next to antibiotic susceptibility, the susceptibility of this biofilm to bacteriophage mono- and combination treatment with antibiotics was evaluated as an alternative treatment strategy. In the future, this assay can be used to provide a better insight in in vivo antibiotic- and bacteriophage susceptibility of LVAD-driveline biofilms. Thereby improving in vivo treatment strategies for LVAD-driveline infections
Direct whole genome sequencing of sputum accurately identifies drug resistant Mycobacterium tuberculosis faster than MGIT culture sequencing
Full text linkThe current methods available to diagnose antimicrobial resistant Mycobacterium tuberculosis infections require positive culture or only test a limited number of resistance-associated mutations. Rapid, accurate identification of antimicrobial resistance enables prompt initiation of effective treatment. Here, we determine the utility of whole-genome sequencing (WGS) M. tuberculosis directly from routinely obtained diagnostic sputum samples to provide a comprehensive resistance profile compared to Mycobacterial Growth Indicator Tube (MGIT) WGS. We sequenced M. tuberculosis from 43 sputum samples by targeted DNA enrichment using the Agilent SureSelectXT kit, and 43 MGIT positive samples from each participant. Thirty two (74%) sputum samples and 43 (100%) MGIT samples generated whole genomes. Time to antimicrobial resistance profile and concordance was compared with Xpert MTB/RIF and phenotypic resistance testing from culture of the same samples. Antibiotic susceptibility could be predicted from WGS of sputum within 5 days of sample receipt and up to 24 days earlier than WGS from MGIT culture and up to 31 days earlier than phenotypic testing. Direct sputum results could be reduced to 3 days with faster hybridisation and if only regions encoding drug resistance are sequenced. We show that direct sputum sequencing has the potential to provide comprehensive resistance detection significantly faster than MGIT whole genome sequencing or phenotypic testing of resistance from culture in a clinical setting. This improved turnaround time enables prompt, appropriate treatment with associated patient and health service benefit. Improvements in sample preparation are necessary to ensure comparable sensitivity and complete resistance profile predictions in all cases
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Genomic investigation reveals contaminated detergent as the source of an Extended-Spectrum-β-Lactamase-producing Klebsiella michiganensis outbreak in a neonatal unit
No full textBackground: Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which sources of transmission can be challenging to elucidate. We describe the use of whole genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Methods: Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read (Illumina) and long-read (MinION, Oxford Nanopore Technologies) sequencing was used to confirm species taxonomy, define antimicrobial resistance genes and determine phylogenetic relationships using single nucleotide polymorphism (SNP) profiling. Results: A total of 21 organisms (10 patient-derived and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from multiple detergent dispensing bottles were either identical or closely related by SNP comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk-expressing equipment. No new cases were identified once the detergent bottles were removed. Conclusions: Environmental reservoirs may be an important source in outbreaks of multi-drug resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses
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