Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination

Rouzeau-Szynalski, Katia; Barretto, Caroline; Fournier, Coralie; Moine, D; Gimonet, Johan; Baert, Leen

doi:10.1016/j.ijfoodmicro.2019.03.007

Cited by 9 publications

(7 citation statements)

References 12 publications

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“…One additional strain, with raw reads in SRA format was obtained from the NCBI SRA dataset (see text footnote 2). The quality of sequencing was checked with FastQC toolkit ( Rouzeau-Szynalski et al, 2019 ). The raw reads of the FJ001 genome were trimmed with trimmomatic software prior to genome assembly.…”

Section: Methodsmentioning

confidence: 99%

Global Genomic Characterization of Salmonella enterica Serovar Telelkebir

Qiu

Nambiar

et al. 2021

Front. Microbiol.

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Non-typhoidal Salmonella (NTS) is a common cause for self-limiting gastroenteritis, representing a public health concern globally. NTS is one of the leading causes of foodborne illnesses in China; however, the invasive infection caused by NTS is largely underappreciated. Here, we reported an NTS invasive infection caused by an infrequently reported serovar Telelkebir (13,23:d:e,n,z15) strain FJ001 in China, which carries antimicrobial-resistant genes [fosA7 and aac(6′)-Iaa] and typhoid-toxin genes (cdtB, pltA, and pltB). By conducting the whole genomic sequencing, we also investigated the relatedness of this strain with an additional 120 global contextual Salmonella enterica serovar Telelkebir (S. Telelkebir) isolates, and assessed the antimicrobial-resistant determinants and key virulence factors using the available genomic dataset. Notably, all 121 (100%) of the S. Telelkebir strains possessed the typhoid toxin genes cdtB, pltA, and pltB, and 58.67% (71/121) of S. Telelkebir harbored antimicrobial-resistant gene fosaA7. The study by core genome multilocus sequence typing (cgMLST) and core single-nucleotide polymorphism (SNP)-based phylogenomic analysis demonstrated that the S. Telelkebir isolates from different sources and locations clustered together. This suggests that regular international travels might increase the likelihood of rapid and extensive transmissions of potentially pathogenic bacteria. For the first time, our study revealed the antimicrobial resistance, virulence patterns, and genetic diversity of the serovar S. Telelkebir isolate in humans and similar isolates over the world. The present study also suggests that genomic investigation can facilitate surveillance and could offer added knowledge of a previously unknown threat with the unique combination of virulent and antimicrobial-resistant determinants.

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Section: Methodsmentioning

confidence: 99%

Global Genomic Characterization of Salmonella enterica Serovar Telelkebir

Qiu

Nambiar

et al. 2021

Front. Microbiol.

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“…Since serotyping remains the first step in Salmonella characterization, several in silico platforms utilizing WGS data to predict the serotypes have been developed (Zhang et al, 2015; Asthon et al, 2016; Yoshida et al, 2016) and evaluated by public health agencies (Yachison et al, 2017). While WGS is increasingly used in routine by public health and regulatory agencies and authorities (e.g., the U.S. Food & Drug Administration (FDA), Public Health England), food industry has only recently started exploring WGS (Rantsiou et al, 2018; Rouzeau-Szynalski et al, 2019). The use of WGS and its application including Salmonella serotyping in routine laboratories are becoming a viable option.…”

Section: Introductionmentioning

confidence: 99%

Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data

Diep¹,

Barretto²,

Portmann³

et al. 2019

Front. Microbiol.

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Salmonella is one of the most common causes of food-borne diseases worldwide. While Salmonella molecular subtyping by Whole Genome Sequencing (WGS) is increasingly used for outbreak and source tracking investigations, serotyping remains as a first-line characterization of Salmonella isolates. The traditional phenotypic method for serotyping is logistically challenging, as it requires the use of more than 150 specific antisera and well trained personnel to interpret the results. Consequently, it is not a routine method for the majority of laboratories. Several rapid molecular methods targeting O and H loci or surrogate genomic markers have been developed as alternative solutions. With the expansion of WGS, in silico Salmonella serotype prediction using WGS data is available. Here, we compared a microarray method using molecular markers, the Check and Trace Salmonella assay (CTS) and a WGS-based serotype prediction tool that targets molecular determinants of serotype (SeqSero) to the traditional phenotypic method using 100 strains representing 45 common and uncommon serotypes. Compared to the traditional method, the CTS assay correctly serotyped 97% of the strains, four strains gave a double serotype prediction. Among the inconclusive data, one strain was not predicted and two strains were incorrectly identified. SeqSero was evaluated with two versions (SeqSero 1 and the alpha test version of SeqSero 2). The correct antigenic formula was predicted by SeqSero 1 for 96 and 95% of strains using raw reads and assembly, respectively. However, 34 and 33% of these predictions included multiple serotypes by raw reads and assembly. With raw reads, one strain was not identified and three strains were discordant with phenotypic serotyping result. With assembly, three strains were not predicted and two strains were incorrectly predicted. While still under development, SeqSero 2 maintained the accuracy of antigenic formula prediction at 98% and reduced multiple serotype prediction rate to 13%. One strain had no prediction and one strain was incorrectly predicted. Our study indicates that the CTS assay is a good alternative for routine laboratories as it is an easy to use method with a short turn-around-time. SeqSero is a reliable replacement for phenotypic serotyping if WGS is routinely implemented.

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“…Research and development (R&D) is an active area where these companies are testing and evaluating the multifaceted use of this technology. Such evaluations are conducted, for example, to compare the accuracy of different sequencing platforms for serotype predictions, to investigate laboratory cross-contaminations 53 , to validate sequence workflows, to understand pathogenic genetic responses to heat stress and source tracking 54 , 55 , and to catalog, characterize and quantify foodborne pathogenic bacteria and the related bacterial communities along the food supply chain 56 .…”

Section: Current Hts Use Challenges and Opportunities In The Food Ind...mentioning

confidence: 99%

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

et al. 2022

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The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.

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Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination

Cited by 9 publications

References 12 publications

Global Genomic Characterization of Salmonella enterica Serovar Telelkebir

Global Genomic Characterization of Salmonella enterica Serovar Telelkebir

Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

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