The CGE Tool Box

Larsen, Mette Voldby; Joensen, Katrine Grimstrup; Zankari, Ea; Ahrenfeldt, Johanne; Lukjancenko, Oksana; Kaas, Rolf Sommer; Roer, Louise; Leekitcharoenphon, Pimlapas; Saputra, Dhany; Cosentino, Salvatore; Thomsen, Martin Christen Frølund; Cisneros, Jose Luis Bellod; Jurtz, Vanessa Isabell; Rasmussen, Simon; Petersen, Thomas Nordahl; Hasman, Henrik; Sicheritz-Pontén, Thomas; Aarestrup, Frank Møller; Lund, Ole

doi:10.1007/978-3-319-43751-4_5

Cited by 7 publications

(4 citation statements)

References 50 publications

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“…It is therefore not known if the detected bovine isolates displayed the same resistance phenotype, it might be that not all detected genes are expressed. Previous studies (Zankari et al, 2012; Larsen et al, 2017) have shown that there is a high correspondence between the resistance geno- and phenotype and thus, we did not find it necessary to carry out phenotyping of the LA-MRSA CC398 isolates analyzed in present study.…”

Section: Discussionmentioning

confidence: 91%

LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production

et al. 2019

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The possible spillover from pigs into other production animals incites concern for unresolved reservoirs of human exposure. The present investigation was therefore initiated, to elucidate if Danish veal and dairy farms constitute a reservoir of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) CC398 and to potentially identify the source of introduction. We collected nasal swab samples from 17 Danish veal farms, 2 slaughterhouses, and received bulk tank milk samples from 286 dairy farms. All samples were analyzed by culturing and screening on MRSA selective plates and presumed MRSA was verified by MALDI-TOF and PCR. MRSA isolates were subjected to spa typing and whole-genome sequencing. LA-MRSA was found on two veal farms in one and three calves, respectively, with subsequent follow-up samples found negative. Eight of 286 dairy farms (2.8%) were found LA-MRSA positive and follow-up samples, from five farms showed intermittent detection of LA-MRSA. The spa types, t034 and t011, were the most common while a single isolate from a dairy farm belonged to spa type t843 associated to mecC-MRSA CC130 and is the first report of mecC-MRSA in the Danish dairy production. A phylogenetic analysis showed that some of the isolates grouped within or close to the dominant Danish pig clusters, suggesting spillover into cattle farms. Other isolates clustered outside the dominant pig clusters suggesting that other routes of introduction cannot be excluded. Results of the investigation indicated a contamination of veal farms while some dairy farms seemed to be a permanent reservoir. Thus, Danish cattle represent a low prevalence reservoir of LA-MRSA CC398, which at present, is not of major human health concern.

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Section: Discussionmentioning

confidence: 91%

LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production

et al. 2019

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“…To further genotype Salmonella isolates, the whole genome of strains was uploaded to the PubMLST database (https://pubmlst.org/ (accessed on 8 October 2021)) for multilocus sequence typing (MLST) and cgMLST analysis [27]. Salmonella housekeeping gene sequences were downloaded from PubMLST, including aroC, dnaN, hemD, hisD, purE, sucA, and thrA.…”

Section: Molecular Typing and Phylogenetic Treementioning

confidence: 99%

“…The whole genomes of all S. Thompson isolates were uploaded to the databases ResFinder 4.1 of the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/ ResFinder/ (accessed on 2 October 2021)) [27] and the Virulence Factor Database (VFBD; http://www.mgc.ac.cn/VFs/ (accessed on 2 October 2021)) for predictions of resistance and virulence genes [29].…”

Section: Resistance Genes and Virulence Factorsmentioning

confidence: 99%

Resistance and Pathogenicity of Salmonella Thompson Isolated from Incubation End of a Poultry Farm

Zhang

Liu

Chen

et al. 2022

Veterinary Sciences

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Salmonella Thompson, an important foodborne pathogen, is rarely found to be pathogenic to poultry. Accidentally, S. Thompson was found to be pathogenic to embryos of white feather broiler at a poultry farm in China. Therefore, this study aimed to explore antimicrobial resistance and pathogenicity of clinical S. Thompson isolated from dead poultry embryos. The phylogenetic tree based on 16S rRNA and seven housekeeping genes showed that the 14 clinical S. Thompson were closely related. The core-genome multilocus sequence typing of 14 clinical S. Thompson based on whole-genome sequencing was cgST-12774, consistent with the only two strains of S. Thompson from humans in China as reported in the NCBI database. The antimicrobial resistance gene analysis demonstrated that all strains carried aac(6′)-Iaa and the polymyxin resistance gene mcr-9. Antimicrobial sensitivity tests for 18 antibiotics showed that S. Thompson isolates displayed resistance against streptomycin (100%), ampicillin (35.7%), and doxycycline (14.3%), but sensitivity to polymyxin B, proving that the mcr-9 gene had not appeared resistance phenotype. Virulence genes Salmonella pathogenicity island (SPI) SPI1-5, type I fimbriae gene (fimA), flagellar assembly genes (bcfC, flhD, fliA, fliC, fljB, flgK, and lpfC), and other virulence genes (iroN, pagC, and cigR) were found in each S. Thompson isolate. Additionally, the bacterial inoculation experiment with 1-day-old chicks revealed that clinical S. Thompson was highly pathogenic to newborn chicks after yolk sac inoculation. This study highlighted that the S. Thompson isolated from poultry embryos and the S. Thompson causing human foodborne diarrhea in some parts of China belong to the same cgMLST typology (cgST-12774) and showed the pathogenicity of this clinical S. Thompson to chicks.

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“…These include timely inference of bacterial subtyping and antimicrobial resistance (AMR) profiling, traditionally determined by time-consuming laboratory procedures. Today, these technologies are employed in different combinations by individual researchers and clinical bioinformaticians around the world [7].…”

Section: Introductionmentioning

confidence: 99%

Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities

et al. 2023

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The global surveillance and outbreak investigation of antimicrobial resistance (AMR) is amidst a paradigm shift from traditional biology to bioinformatics. This is due to developments in whole-genome-sequencing (WGS) technologies, bioinformatics tools, and reduced costs. The increased use of WGS is accompanied by challenges such as standardization, quality control (QC), and data sharing. Thus, there is global need for inter-laboratory WGS proficiency test (PT) schemes to evaluate laboratories' capacity to produce reliable genomic data. Here, we present the results of the first iteration of the Genomic PT (GPT) organized by the Global Capacity Building Group at the Technical University of Denmark in 2020. Participating laboratories sequenced two isolates and corresponding DNA of Salmonella enterica , Escherichia coli and Campylobacter coli , using WGS methodologies routinely employed at their laboratories. The participants' ability to obtain consistently good-quality WGS data was assessed based on several QC WGS metrics. A total of 21 laboratories from 21 European countries submitted WGS and meta-data. Most delivered high-quality sequence data with only two laboratories identified as overall underperforming. The QC metrics, N50 and number of contigs, were identified as good indicators for high-sequencing quality. We propose QC thresholds for N50 greater than 20 000 and 25 000 for Campylobacter coli and Escherichia coli, respectively, and number of contigs >200 bp greater than 225, 265 and 100 for Salmonella enterica , Escherichia coli and Campylobacter coli , respectively. The GPT2020 results confirm the importance of systematic QC procedures, ensuring the submission of reliable WGS data for surveillance and outbreak investigation to meet the requirements of the paradigm shift in methodology.

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The CGE Tool Box

Cited by 7 publications

References 50 publications

LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production

LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production

Resistance and Pathogenicity of Salmonella Thompson Isolated from Incubation End of a Poultry Farm

Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities

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