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A snapshot of diversity: Intraclonal variation of Escherichia coli clones as commensals and pathogens

Stegger, Marc ; Leihof, Rikke Fleron ; Baig, Sharmin ; [et al.]

Elsevier BV ; 2020

In: International Journal of Medical Microbiology Vol. 310, No. 3 ( 2020-04), p. 151401-

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In: International Journal of Medical Microbiology, Elsevier BV, Vol. 310, No. 3 ( 2020-04), p. 151401-

Type of Medium: Online Resource

ISSN: 1438-4221

URL: Article

DOI: 10.1016/j.ijmm.2020.151401

RVK:

XA 49980

Language: English

Publisher: Elsevier BV

Publication Date: 2020

detail.hit.zdb_id: 2020515-6

SSG: 12

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Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome

Aziz, Maliha ; Palmer, Amber ; Iversen, Søren ; [et al.]

Springer Science and Business Media LLC ; 2023

In: Scientific Reports Vol. 13, No. 1 ( 2023-04-14)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2023-04-14)

Abstract: Dolosigranulum pigrum —a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting mur J, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 10 4 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-023-32709-y

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2023

detail.hit.zdb_id: 2615211-3

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Complete genome of a methicillin-resistant Staphylococcus vitulinus from Danish ground beef meat carrying a mecA2 resistance gene and a novel ccr allotype

Looman, Esmée Lauren ; van Tienen, Paula ; Ng, Duncan Y.K. ; [et al.]

Elsevier BV ; 2020

In: Journal of Global Antimicrobial Resistance Vol. 23 ( 2020-12), p. 221-223

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In: Journal of Global Antimicrobial Resistance, Elsevier BV, Vol. 23 ( 2020-12), p. 221-223

Type of Medium: Online Resource

ISSN: 2213-7165

URL: Article

DOI: 10.1016/j.jgar.2020.09.013

Language: English

Publisher: Elsevier BV

Publication Date: 2020

detail.hit.zdb_id: 2710046-7

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First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023

Rasmussen, Morten ; Møller, Frederik Trier ; Gunalan, Vithiagaran ; [et al.]

European Centre for Disease Control and Prevention (ECDC) ; 2023

In: Eurosurveillance Vol. 28, No. 36 ( 2023-09-07)

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In: Eurosurveillance, European Centre for Disease Control and Prevention (ECDC), Vol. 28, No. 36 ( 2023-09-07)

Abstract: We describe 10 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant BA.2.86 detected in Denmark, including molecular characteristics and results from wastewater surveillance that indicate that the variant is circulating in the country at a low level. This new variant with many spike gene mutations was classified as a variant under monitoring by the World Health Organization on 17 August 2023. Further global monitoring of COVID-19, BA.2.86 and other SARS-CoV-2 variants is highly warranted.

Type of Medium: Online Resource

ISSN: 1560-7917

URL: Article

DOI: 10.2807/1560-7917.ES.2023.28.36.2300460

Language: English

Publisher: European Centre for Disease Control and Prevention (ECDC)

Publication Date: 2023

detail.hit.zdb_id: 2059112-3

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The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection

Rendboe, Amalie Katrine ; Johannesen, Thor Bech ; Ingham, Anna Cäcilia ; [et al.]

Springer Science and Business Media LLC ; 2020

In: BMC Microbiology Vol. 20, No. 1 ( 2020-12)

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In: BMC Microbiology, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2020-12)

Abstract: Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients’ quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities. Results Based on an assessment of 〉 800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico , and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis . The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of 〈 10 copies/μL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of S. epidermidis . Conclusions The Epidome method is designed for use on primary samples to obtain important information on S. epidermidis abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.

Type of Medium: Online Resource

ISSN: 1471-2180

URL: Article

DOI: 10.1186/s12866-020-02041-w

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2041505-9

SSG: 12

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Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations

Both, Anna ; Huang, Jiabin ; Qi, Minyue ; [et al.]

Public Library of Science (PLoS) ; 2021

In: PLOS Pathogens Vol. 17, No. 2 ( 2021-2-5), p. e1009304-

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In: PLOS Pathogens, Public Library of Science (PLoS), Vol. 17, No. 2 ( 2021-2-5), p. e1009304-

Abstract: S . epidermidis is a substantial component of the human skin microbiota, but also one of the major causes of nosocomial infection in the context of implanted medical devices. We here aimed to advance the understanding of S . epidermidis genotypes and phenotypes conducive to infection establishment. Furthermore, we investigate the adaptation of individual clonal lines to the infection lifestyle based on the detailed analysis of individual S . epidermidis populations of 23 patients suffering from prosthetic joint infection. Analysis of invasive and colonizing S . epidermidis provided evidence that invasive S . epidermidis are characterized by infection-supporting phenotypes (e.g. increased biofilm formation, growth in nutrient poor media and antibiotic resistance), as well as specific genetic traits. The discriminating gene loci were almost exclusively assigned to the mobilome. Here, in addition to IS 256 and SCC mec , chromosomally integrated phages was identified for the first time. These phenotypic and genotypic features were more likely present in isolates belonging to sequence type (ST) 2. By comparing seven patient-matched nasal and invasive S . epidermidis isolates belonging to identical genetic lineages, infection-associated phenotypic and genotypic changes were documented. Besides increased biofilm production, the invasive isolates were characterized by better growth in nutrient-poor media and reduced hemolysis. By examining several colonies grown in parallel from each infection, evidence for genetic within-host population heterogeneity was obtained. Importantly, subpopulations carrying IS insertions in agrC , mutations in the acetate kinase (AckA) and deletions in the SCC mec element emerged in several infections. In summary, these results shed light on the multifactorial processes of infection adaptation and demonstrate how S . epidermidis is able to flexibly repurpose and edit factors important for colonization to facilitate survival in hostile infection environments.

Type of Medium: Online Resource

ISSN: 1553-7374

URL: Article

DOI: 10.1371/journal.ppat.1009304

DOI: 10.1371/journal.ppat.1009304.g001

DOI: 10.1371/journal.ppat.1009304.g002

DOI: 10.1371/journal.ppat.1009304.g003

DOI: 10.1371/journal.ppat.1009304.g004

DOI: 10.1371/journal.ppat.1009304.g005

DOI: 10.1371/journal.ppat.1009304.g006

DOI: 10.1371/journal.ppat.1009304.g007

DOI: 10.1371/journal.ppat.1009304.g008

DOI: 10.1371/journal.ppat.1009304.g009

DOI: 10.1371/journal.ppat.1009304.g010

DOI: 10.1371/journal.ppat.1009304.g011

DOI: 10.1371/journal.ppat.1009304.g012

DOI: 10.1371/journal.ppat.1009304.g013

DOI: 10.1371/journal.ppat.1009304.g014

DOI: 10.1371/journal.ppat.1009304.t001

DOI: 10.1371/journal.ppat.1009304.s001

DOI: 10.1371/journal.ppat.1009304.s002

DOI: 10.1371/journal.ppat.1009304.s003

DOI: 10.1371/journal.ppat.1009304.s004

DOI: 10.1371/journal.ppat.1009304.s005

DOI: 10.1371/journal.ppat.1009304.s006

DOI: 10.1371/journal.ppat.1009304.s007

DOI: 10.1371/journal.ppat.1009304.s008

DOI: 10.1371/journal.ppat.1009304.s009

DOI: 10.1371/journal.ppat.1009304.s010

DOI: 10.1371/journal.ppat.1009304.s011

DOI: 10.1371/journal.ppat.1009304.s012

DOI: 10.1371/journal.ppat.1009304.s013

DOI: 10.1371/journal.ppat.1009304.s014

DOI: 10.1371/journal.ppat.1009304.s015

DOI: 10.1371/journal.ppat.1009304.s016

DOI: 10.1371/journal.ppat.1009304.s017

DOI: 10.1371/journal.ppat.1009304.s018

DOI: 10.1371/journal.ppat.1009304.s019

DOI: 10.1371/journal.ppat.1009304.s020

DOI: 10.1371/journal.ppat.1009304.s021

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2021

detail.hit.zdb_id: 2205412-1

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Table_1.DOCX

Peng, Pai ; Baldry, Mara ; Gless, Bengt H. ; [et al.]

Frontiers Media SA ; 2019

In: Frontiers in Microbiology Vol. 10 ( 2019-9-27)

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In: Frontiers in Microbiology, Frontiers Media SA, Vol. 10 ( 2019-9-27)

Type of Medium: Online Resource

ISSN: 1664-302X

URL: Article

DOI: 10.3389/fmicb.2019.02212

DOI: 10.3389/fmicb.2019.02212.s001

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2019

detail.hit.zdb_id: 2587354-4

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Increase in invasive group A streptococcal infections and emergence of novel, rapidly expanding sub-lineage of the virulent Streptococcus pyogenes M1 clone, Denmark, 2023

Johannesen, Thor Bech ; Munkstrup, Charlotte ; Edslev, Sofie Marie ; [et al.]

European Centre for Disease Control and Prevention (ECDC) ; 2023

In: Eurosurveillance Vol. 28, No. 26 ( 2023-06-29)

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In: Eurosurveillance, European Centre for Disease Control and Prevention (ECDC), Vol. 28, No. 26 ( 2023-06-29)

Abstract: A highly virulent sub-lineage of the Streptococcus pyogenes M1 clone has been rapidly expanding throughout Denmark since late 2022 and now accounts for 30% of the new invasive group A streptococcal infections. We aimed to investigate whether a shift in variant composition can account for the high incidence rates observed over winter 2022/23, or if these are better explained by the impact of COVID-19-related restrictions on population immunity and carriage of group A Streptococcus .

Type of Medium: Online Resource

ISSN: 1560-7917

URL: Article

DOI: 10.2807/1560-7917.ES.2023.28.26.2300291

Language: English

Publisher: European Centre for Disease Control and Prevention (ECDC)

Publication Date: 2023

detail.hit.zdb_id: 2059112-3

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Novel SCC mec type XIII (9A) identified in an ST152 methicillin-resistant Staphylococcus aureus

Baig, Sharmin ; Johannesen, Thor Bech ; Overballe-Petersen, Søren ; [et al.]

Elsevier BV ; 2018

In: Infection, Genetics and Evolution Vol. 61 ( 2018-07), p. 74-76

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In: Infection, Genetics and Evolution, Elsevier BV, Vol. 61 ( 2018-07), p. 74-76

Type of Medium: Online Resource

ISSN: 1567-1348

URL: Article

DOI: 10.1016/j.meegid.2018.03.013

Language: English

Publisher: Elsevier BV

Publication Date: 2018

detail.hit.zdb_id: 2057622-5

SSG: 12

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Data_Sheet_1.zip

Sørensen, Patricia E. ; Baig, Sharmin ; Stegger, Marc ; [et al.]

Frontiers Media SA ; 2021

In: Frontiers in Microbiology Vol. 12 ( 2021-12-13)

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In: Frontiers in Microbiology, Frontiers Media SA, Vol. 12 ( 2021-12-13)

Abstract: Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli , it may be associated with loss of fitness, which could be exploited in phage therapy.

Type of Medium: Online Resource

ISSN: 1664-302X

URL: Article

DOI: 10.3389/fmicb.2021.782757

DOI: 10.3389/fmicb.2021.782757.s001

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2021

detail.hit.zdb_id: 2587354-4

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