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Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Munk, Patrick ; Brinch, Christian ; Møller, Frederik Duus ; [et al.]

Springer Science and Business Media LLC ; 2023

In: Nature Communications Vol. 14, No. 1 ( 2023-01-12)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2023-01-12)

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-023-35890-w

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2023

detail.hit.zdb_id: 2553671-0

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Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Munk, Patrick ; Brinch, Christian ; Møller, Frederik Duus ; [et al.]

Springer Science and Business Media LLC ; 2022

In: Nature Communications Vol. 13, No. 1 ( 2022-12-01)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-12-01)

Abstract: Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-022-34312-7

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2022

detail.hit.zdb_id: 2553671-0

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Danish Integrated Antimicrobial Resistance Monitoring and Research Program

Hammerum, Anette M. ; Heuer, Ole E. ; Emborg, Hanne-Dorthe ; [et al.]

Centers for Disease Control and Prevention (CDC) ; 2007

In: Emerging Infectious Diseases Vol. 13, No. 11 ( 2007-11), p. 1633-1639

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In: Emerging Infectious Diseases, Centers for Disease Control and Prevention (CDC), Vol. 13, No. 11 ( 2007-11), p. 1633-1639

Type of Medium: Online Resource

ISSN: 1080-6040 , 1080-6059

URL: Article

DOI: 10.3201/eid1311.070421

Language: English

Publisher: Centers for Disease Control and Prevention (CDC)

Publication Date: 2007

detail.hit.zdb_id: 2004375-2

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Antimicrobial susceptibility of Haemophilus parasuis and Histophilus somni from pigs and cattle in Denmark

Aarestrup, Frank M ; Seyfarth, Anne Mette ; Angen, Øystein

Elsevier BV ; 2004

In: Veterinary Microbiology Vol. 101, No. 2 ( 2004-6), p. 143-146

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In: Veterinary Microbiology, Elsevier BV, Vol. 101, No. 2 ( 2004-6), p. 143-146

Type of Medium: Online Resource

ISSN: 0378-1135

URL: Article

DOI: 10.1016/j.vetmic.2004.02.012

Language: English

Publisher: Elsevier BV

Publication Date: 2004

detail.hit.zdb_id: 1498996-7

SSG: 22

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Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm

Quero, Grazia Marina ; Piredda, Roberta ; Basili, Marco ; [et al.]

Springer Science and Business Media LLC ; 2023

In: Microbial Ecology Vol. 86, No. 2 ( 2023-08), p. 1319-1330

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In: Microbial Ecology, Springer Science and Business Media LLC, Vol. 86, No. 2 ( 2023-08), p. 1319-1330

Abstract: Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host’s tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.

Type of Medium: Online Resource

ISSN: 0095-3628 , 1432-184X

URL: Article

DOI: 10.1007/s00248-022-02120-7

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2023

detail.hit.zdb_id: 1462065-0

detail.hit.zdb_id: 188257-0

SSG: 12

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Effect of Abolishment of the Use of Antimicrobial Agents for Growth Promotion on Occurrence of Antimicrobial Resistance in Fecal Enterococci from Food Animals in Denmark

Aarestrup, Frank Møller ; Seyfarth, Anne Mette ; Emborg, Hanne-Dorthe ; [et al.]

American Society for Microbiology ; 2001

In: Antimicrobial Agents and Chemotherapy Vol. 45, No. 7 ( 2001-07), p. 2054-2059

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In: Antimicrobial Agents and Chemotherapy, American Society for Microbiology, Vol. 45, No. 7 ( 2001-07), p. 2054-2059

Abstract: From 1995 to 2000, a total of 673 Enterococcus faecium and 1,088 Enterococcus faecalis isolates from pigs together with 856 E. faecium isolates from broilers were isolated and tested for susceptibility to four classes of antimicrobial agents used for growth promotion as part of the Danish program of monitoring for antimicrobial resistance. The four antimicrobials were avilamycin, erythromycin, vancomycin, and virginiamycin. Major changes in the use of antimicrobial agents for growth promotion have occurred during the last 6 years in Denmark. The government banned the use of avoparcin in 1995 and of virginiamycin in 1998. Furthermore, the producers have voluntarily stopped all use beginning in 1999. The avoparcin ban in 1995 was followed by a decrease in the occurrence of glycopeptide-resistant E. faecium (GRE) in broilers, from 72.7% in 1995 to 5.8% in 2000. The occurrence of glycopeptide resistance among isolates from pigs remained constant at around 20% from 1995 to 1997. It was shown that, in GRE from pigs, the genes encoding macrolide and glycopeptide resistance were genetically linked and that, following the decrease in the use of tylosin during 1998 and 1999, the occurrence of GRE in pigs decreased to 6.0% in 2000. From 1995 to 1997 the occurrence of erythromycin resistance among E. faecium and E. faecalis isolates from pigs was almost 90%. Use of tylosin decreased considerably during 1998 and 1999, and this decrease was followed by decreases in the occurrence of resistance to 46.7 and 28.1% among E. faecium and E. faecalis isolates from pigs, respectively. Erythromycin resistance among E. faecium isolates from broilers reached a maximum of 76.3% in 1997 but decreased to 12.7% in 2000 concomitantly with more limited use of virginiamycin. Use of virginiamycin increased from 1995 to 1997 and was followed by an increased occurrence of virginiamycin resistance among E. faecium isolates in broilers, from 27.3% in 1995 to 66.2% in 1997. In January 1998 the use of virginiamycin was banned in Denmark, and the occurrence of virginiamycin resistance decreased to 33.9% in 2000. Use of avilamycin increased from 1995 to 1996 and was followed by an increase in avilamycin resistance among E. faecium isolates from broilers, from 63.6% in 1995 to 77.4% in 1996. Since 1996 avilamycin usage has decreased, followed by a decrease in resistance to 4.8% in 2000. Our observations show that it is possible to reduce the occurrence of antimicrobial resistance in a national population of food animals when the selective pressure is removed. Cases in which resistance to vancomycin was linked to resistance to erythromycin were exceptions. In such cases resistance did not decrease until the use of both avoparcin and tylosin was limited.

Type of Medium: Online Resource

ISSN: 0066-4804 , 1098-6596

URL: Article

DOI: 10.1128/AAC.45.7.2054-2059.2001

RVK:

XA 24552

Language: English

Publisher: American Society for Microbiology

Publication Date: 2001

detail.hit.zdb_id: 1496156-8

SSG: 12

SSG: 15,3

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IncI1 ST3 and IncI1 ST7 plasmids from CTX-M-1-producing Escherichia coli obtained from patients with bloodstream infections are closely related to plasmids from E. coli of animal origin

Valcek, Adam ; Roer, Louise ; Overballe-Petersen, Søren ; [et al.]

Oxford University Press (OUP) ; 2019

In: Journal of Antimicrobial Chemotherapy Vol. 74, No. 8 ( 2019-08-01), p. 2171-2175

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In: Journal of Antimicrobial Chemotherapy, Oxford University Press (OUP), Vol. 74, No. 8 ( 2019-08-01), p. 2171-2175

Abstract: Fully sequenced IncI1 plasmids obtained from CTX-M-1-producing Escherichia coli of human and animal origin were compared. Methods Twelve E. coli isolates sharing identical ESBL genes and plasmid multilocus STs sequenced on Illumina and MinION platforms were obtained from the Danish antimicrobial resistance surveillance programme, DANMAP. After de novo assembly, the sequences of plasmids harbouring blaCTX-M-1 were manually curated and ORFs annotated. Within-group comparisons were performed separately for the IncI1 ST3 plasmid type and the IncI1 ST7 plasmid type. The IncI1 ST3 plasmid group was obtained from 10 E. coli isolates (2 from patients with bloodstream infections, 6 from food and 2 from animals). The IncI1 ST7 plasmids originated from E. coli isolates obtained from a patient with bloodstream infection and from a pig. Sequences of IncI1 ST3 and IncI1 ST7 plasmids harbouring blaCTX-M-1 with determined origin were retrieved from GenBank and used for comparison within the respective group. Results The 10 IncI1 ST3 blaCTX-M-1 plasmids were highly similar in structure and organization with only minor plasmid rearrangements and differences in the variable region. The IncI1 ST7 blaCTX-M-1 plasmids also showed high similarity in structure and organization. The high level of similarity was also observed when including plasmids from E. coli of animal origin from Australia, Switzerland, the Netherlands and France. Conclusions This study shows broad spread of a very successful CTX-M-1-producing IncI1 type plasmid among E. coli of both human and animal origin.

Type of Medium: Online Resource

ISSN: 0305-7453 , 1460-2091

URL: Article

DOI: 10.1093/jac/dkz199

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2019

detail.hit.zdb_id: 1467478-6

SSG: 15,3

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ST131 fimH 22 Escherichia coli isolate with a bla CMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin

Roer, Louise ; Overballe-Petersen, Søren ; Hansen, Frank ; [et al.]

Oxford University Press (OUP) ; 2019

In: Journal of Antimicrobial Chemotherapy Vol. 74, No. 3 ( 2019-03-01), p. 557-560

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In: Journal of Antimicrobial Chemotherapy, Oxford University Press (OUP), Vol. 74, No. 3 ( 2019-03-01), p. 557-560

Type of Medium: Online Resource

ISSN: 0305-7453 , 1460-2091

URL: Article

DOI: 10.1093/jac/dky484

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2019

detail.hit.zdb_id: 1467478-6

SSG: 15,3

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Results of Use of WHO Global Salm-Surv External Quality Assurance System for Antimicrobial Susceptibility Testing of Salmonella Isolates from 2000 to 2007

Hendriksen, Rene S. ; Seyfarth, Anne Mette ; Jensen, Arne B. ; [et al.]

American Society for Microbiology ; 2009

In: Journal of Clinical Microbiology Vol. 47, No. 1 ( 2009-01), p. 79-85

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In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 47, No. 1 ( 2009-01), p. 79-85

Abstract: An international External Quality Assurance System (EQAS) for antimicrobial susceptibility testing of Salmonella was initiated in 2000 by the World Health Organization (WHO) Global Salm-Surv in order to enhance the capacities of national reference laboratories to obtain reliable data for surveillance purposes worldwide. Seven EQAS iterations have been conducted from 2000 to 2007. In each iteration, participating laboratories submitted susceptibility results from 10 to 15 antimicrobial agents for eight Salmonella isolates and an Escherichia coli reference strain (ATCC 25922). A total of 287 laboratories in 102 countries participated in at least one EQAS iteration. A large number of laboratories reported results for the E. coli ATCC 25922 reference strain which were outside the quality control ranges. Critical deviations for susceptibility testing of the Salmonella isolates varied from 4% in 2000 to 3% in 2007. Consistent difficulties were observed in susceptibility testing of amoxicillin-clavulanic acid, cefotaxime, ceftazidime, streptomycin, sulfonamides, and tetracycline. Regional variations in performance were observed, with laboratories in central Asia, Africa, and the Middle East not performing as well as those in other regions. Results from the WHO Global Salm-Surv EQAS show that most laboratories worldwide are capable of correctly performing antimicrobial susceptibility testing of Salmonella isolates, but they also indicate that further improvement for some laboratories is needed. In particular, further training and dissemination of information on quality control, appropriate interpretive criteria (breakpoints), and harmonization of the methodology worldwide through WHO Global Salm-Surv and other programs will contribute to the generation of comparable and reliable antimicrobial susceptibility data (D. M. A. Lo Fo Wong, R. S. Hendriksen, D. J. Mevius, K. T. Veldman, and F. M. Aarestrup, Vet. Microbiol. 115:128-139, 2006).

Type of Medium: Online Resource

ISSN: 0095-1137 , 1098-660X

URL: Article

DOI: 10.1128/JCM.00894-08

RVK:

XA 10000

Language: English

Publisher: American Society for Microbiology

Publication Date: 2009

detail.hit.zdb_id: 1498353-9

SSG: 12

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Antimicrobial resistant E. coli and enterococci in pangasius fillets and prawns in Danish retail imported from Asia.

Ellis-Iversen, Johanne ; Seyfarth, Anne Mette ; Korsgaard, Helle ; [et al.]

Elsevier BV ; 2020

In: Food Control Vol. 114 ( 2020-08), p. 106958-

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In: Food Control, Elsevier BV, Vol. 114 ( 2020-08), p. 106958-

Type of Medium: Online Resource

ISSN: 0956-7135

URL: Article

DOI: 10.1016/j.foodcont.2019.106958

Language: English

Publisher: Elsevier BV

Publication Date: 2020

detail.hit.zdb_id: 2020604-5

SSG: 21

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