Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange

Lüth, Stefanie; Kleta, Sylvia; Dahouk, Sascha Al

doi:10.1016/j.tifs.2018.01.008

Cited by 82 publications

(45 citation statements)

References 53 publications

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“…WGS-based source-attribution studies subsequently confirmed this important role of human-to-human transmission, by demonstrating a clear adaptation of S. Typhimurium ST313, often responsible for invasive disease, to the human host (Okoro et al, 2015). Another example showed variable zoonotic potential among bovine E. coli O157 isolates, with only a minority predicted to be associated with human disease, contrary to preliminary assumptions (Lupolova et al, 2016).…”

Section: Identification Of Transmission Pathwaysmentioning

confidence: 93%

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2019

EFS2

104

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This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and sourceattribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogenhost interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGSbased genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.

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Section: Identification Of Transmission Pathwaysmentioning

confidence: 93%

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2019

EFS2

104

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“…WGS allows an unprecedented subtyping resolution by analysis of the core genome, as well as the accessory genome. Questions related to potential virulence heterogeneity and antimicrobial resistance genes can also be answered, and outbreak investigations have become more precise by correlating epidemiological data with genetic characteristics of the isolates involved (Nielsen et al, 2017;Lüth et al, 2018;Schürch et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Whole‐genome sequencing reveals Listeria monocytogenes diversity and allows identification of long‐term persistent strains in Brazil

Camargo

Moura

Avillan

et al. 2019

Environmental Microbiology

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Summary Advances in whole‐genome sequencing (WGS) technologies have documented genetic diversity and epidemiology of the major foodborne pathogen Listeria monocytogenes (Lm) in Europe and North America, but data concerning South America are scarce. Here, we examined the population structure and genetic diversity of this major foodborne pathogen collected in Brazil. Based on core genome multilocus sequence typing (cgMLST), isolates from lineages I (n = 22; 63%) and II (n = 13; 37%) were distributed into 10 different sublineages (SLs) and represented 31 new cgMLST types (CTs). The most prevalent SLs were SL9 (n = 9; 26%), SL3 (n = 6; 17%) and SL2 and SL218 (n = 5; 14%). Isolates belonging to CTs L2‐SL9‐ST9‐CT4420 and L1‐SL315‐ST520‐CT4429 were collected 3 and 9 years apart, respectively, revealing long‐term persistence of Lm in Brazil. Genetic elements associated with stress survival were present in 60% of isolates (57% SSI‐1 and 3% SSI‐2). Pathogenic islands were present in 100% (LIPI‐1), 43% (LIPI‐3) and 6% (LIPI‐4) of the isolates. Mutations leading to premature stop codons were detected in the prfA and inlA virulence genes. This study is an important contribution to understanding the genomic diversity and epidemiology of Lm in South America. In addition, the results highlight the importance of using WGS to reveal Lm long‐term persistence.

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“…Staphylococcus aureus can rapidly grow in foods, and is known as the most common foodborne microorganism (1). Listeria monocytogenes is another important foodborne bacterium, which can survive in extreme conditions, such as low temperature, high salinity and acidity (2). Bacillus cereus is commonly found in the environment and has the ability to form spores and grow under cold conditions.…”

Section: Introductionmentioning

confidence: 99%

Chemical Composition and Antibacterial and Antioxidant Properties of Essential Oils of Zataria multiflora, Artemisia deracunculus and Mentha piperita

et al. 2019

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Background and objectives: Utilization of essential oils instead of chemical preservatives has received significant attention in recent years. The present study aims to evaluate chemical composition and antibacterial and antioxidant properties of essential oils of Zataria multiflora, Artemisia deracunculus and Mentha piperita. Methods: Chemical profile of the essential oils was analyzed by gas chromatography/mass spectrometry. The microwell dilution and agar disk diffusion methods were used to evaluate the antibacterial properties of the essential oils. Total phenolic content, β-carotene-linoleic acid bleaching test and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays were carried out to determine the antioxidant properties. Results: Menthol (39.18%) and mentone (21.64%) were the main components of the essential oil of M. piperita, while estragol (34.75%) and limonene (15.72%) were the major components of the essential oil of A. dracunculus. The main components of the essential oil of Z. multiflora were carvacrol (36.81%) and thymol (33.04%). The essential oils of M. piperita and Z. multiflora showed greater antimicrobial effects. Moreover, Z. multiflora showed the greatest antioxidant activity among the essential oils. The total phenolic content of Z. multiflora was 228.14±0.45 mg gallic acid equivalent/g. Conclusion: Given their favorable antioxidant and antimicrobial properties, the essential oils of Z. multiflora, A. deracunculus and M. piperita can be used as natural food preservatives.

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Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange

Cited by 82 publications

References 53 publications

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Whole‐genome sequencing reveals Listeria monocytogenes diversity and allows identification of long‐term persistent strains in Brazil

Chemical Composition and Antibacterial and Antioxidant Properties of Essential Oils of Zataria multiflora, Artemisia deracunculus and Mentha piperita

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