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      Asymptomatic Bacteriuria (ABU) in Elderly: Prevalence, Virulence, Phylogeny, Antibiotic Resistance and Complement C3 in Urine

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          Abstract

          Background: The incidence of asymptomatic bacteriuria (ABU) increases with age and is most common for persons 80 years of age and above and in elderly living in nursing homes. The distinction between ABU and urinary tract infection (UTI) is often difficult, especially in individuals, who are unable to communicate their symptoms, and there is a lack of objective methods to distinguish between the two entities. This can lead to overuse of antibiotics, which results in the selection and dissemination of antibiotic resistant isolates. Materials and methods: From voided midstream urine samples of 211 participants ≥60 years old from nursing homes, an activity center and a general practitioners clinic, we collected 19 ABU, 16 UTI and 22 control urine samples and compared them with respect to levels of complement component C3 in urine as determined by an ELISA assay relative to creatinine levels in the same urine samples, as measured by a creatinine assay. Further, we studied all Escherichia coli isolates for selected virulence genes by multiplex PCR, and by whole-genome sequencing (WGS) for genotypes and phylogenetic clustering. Antibiotic susceptibility was determined by microtiter broth dilution. Results: We identified a prevalence of ABU of 18.9% in nursing home residents, whereas ABU was only found in 4% of elderly living in the community ( p < 0.001). E. coli from ABU patients were significantly more antibiotic resistant than E. coli from UTIs ( p = 0.01). Prevalence of classical virulence genes, detected by multiplex PCR, was similar in E. coli isolates from ABU and UTI patients. Whole-genome sequencing of the E. coli isolates showed no specific clustering of ABU isolates compared to UTI isolates. Three isolates from three different individuals from one of the nursing homes showed signs of transmission. We demonstrated a significantly increased level of C3/creatinine ratio in ABU and UTI samples compared to healthy controls; however, there was no significant difference between the ABU and UTI group with respect to C3 level, or virulence factor genes. Conclusion: ABU was significantly more prevalent in the elderly residing in nursing homes than in the elderly living at home. Antibiotic resistance was more prevalent in E. coli from nursing homes than in UTI isolates, but there was no difference in prevalence of virulence associated genes between the two groups and no phylogenetic clustering, as determined by WGS relative to the two types of E. coli bacteriuria. The similar complement C3 response in ABU and UTI patients may indicate that ABU should be reconsidered as an infection albeit without symptoms.

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          Prokka: rapid prokaryotic genome annotation.

          T Seemann (2014)
          The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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            Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

            We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of approximately 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.
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              The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

              Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0524-x) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Role: Academic Editor
                Role: Academic Editor
                Journal
                Microorganisms
                Microorganisms
                microorganisms
                Microorganisms
                MDPI
                2076-2607
                14 February 2021
                February 2021
                : 9
                : 2
                : 390
                Affiliations
                [1 ]Department of Microbiology and Infection Control, Statens Serum Institut, 2200 Copenhagen, Denmark; rikke@ 123456leihof.dk
                [2 ]Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark; karen.leth.nielsen.01@ 123456regionh.dk
                Author notes
                [* ]Correspondence: niels.frimodt-moeller@ 123456regionh.dk ; Tel.: +45-612-247-147
                Article
                microorganisms-09-00390
                10.3390/microorganisms9020390
                7918685
                33672892
                8d6b9f08-5331-45e9-81c4-2afe97e41c83
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 16 December 2020
                : 05 February 2021
                Categories
                Article

                asymptomatic bacteriuria,urinary tract infection,escherichia coli,virulence,phenotype,complement c3,whole-genome sequencing

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