ON‐rep‐seq as a rapid and cost‐effective alternative to whole‐genome sequencing for species‐level identification and strain‐level discrimination of <i>Listeria monocytogenes</i> contamination in a salmon processing plant

Thomassen, Gunn Merethe Bjørge; Krych, Łukasz; Knøchel, Susanne; Mehli, Lisbeth

doi:10.1002/mbo3.1246

Cited by 5 publications

(5 citation statements)

References 71 publications

(102 reference statements)

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“…The results of other authors suggest that the dominant STs in food are ST155 and ST121 among L. monocytogenes of food origin [ 23 , 24 , 25 ]. It seems that such isolates may have a molecular background that allows them to survive in food and food production areas [ 26 , 27 ]. There are few reports characterizing L. monocytogenes in fish and in the fish-processing environment.…”

Section: Discussionmentioning

confidence: 99%

A Comprehensive Virulence and Resistance Characteristics of Listeria monocytogenes Isolated from Fish and the Fish Industry Environment

Zakrzewski

Kurpas

Zadernowska

et al. 2023

IJMS

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Listeria monocytogenes is an important pathogen, often associated with fish, that can adapt and survive in products and food processing plants, where it can persist for many years. It is a species characterized by diverse genotypic and phenotypic characteristics. Therefore, in this study, a total of 17 L. monocytogenes strains from fish and fish-processing environments in Poland were characterized for their relatedness, virulence profiles, and resistance genes. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IIa and IIb; sequence types (ST) were ST6 and ST121; and clonal complexes (CC) were CC6 and CC121. Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with the publicly available genomes of L. monocytogenes strains recovered in Europe from humans with listeriosis. Despite differential genotypic subtypes, most strains had similar antimicrobial resistance profiles; however, some of genes were located on mobile genetic elements that could be transferred to commensal or pathogenic bacteria. The results of this study showed that molecular clones of tested strains were characteristic for L. monocytogenes isolated from similar sources. Nevertheless, it is worth emphasizing that they could present a major public health risk due to their close relation with strains isolated from human listeriosis.

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Section: Discussionmentioning

confidence: 99%

A Comprehensive Virulence and Resistance Characteristics of Listeria monocytogenes Isolated from Fish and the Fish Industry Environment

Zakrzewski

Kurpas

Zadernowska

et al. 2023

IJMS

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“…There was a significant correlation between the groups of designed rep-PCR and VNTR, showing Cramer's V coefficient = 0.814. Subsequently, in 2019, a method was reported to conduct species-level identification and strain-level differentiation in real-time through a combination of nanopore sequencing and rep-PCR using Oxford Nanopore Technologies (Krych et al, 2019;Thomassen et al, 2021Thomassen et al, , 2022. Newly developed commercial DNA chips are also used to analyze the rep-PCR patterns (Bernasconi et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Third, since the method in this study distinguish the strains by reading PCR band patterns, this result may vary depending on conditions such as electrophoresis. Therefore, further study needs to be combined with advanced techniques (e.g., nanopore sequencing) (Krych et al, 2019;Thomassen et al, 2021Thomassen et al, , 2022 that can reduce differences between experimental conditions using M. intracellulare isolated from clinically diagnosed patients with relapse and NTM control isolated from patients with pulmonary disease.…”

Section: Discussionmentioning

confidence: 99%

A novel repeat sequence-based PCR (rep-PCR) using specific repeat sequences of Mycobacterium intracellulare as a DNA fingerprinting

Shin

Kim

et al. 2023

Front. Microbiol.

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Repetitive sequence-based PCR (rep-PCR) is a potential epidemiological technique that can provide high-throughput genotype fingerprints of heterogeneous Mycobacterium strains rapidly. Previously published rep-PCR primers, which are based on nucleotide sequences of Gram-negative bacteria may have low specificity for mycobacteria. Moreover, it was difficult to ensure the continuity of the study after the commercial rep-PCR kit was discontinued. Here, we designed a novel rep-PCR for Mycobacterium intracellulare, a major cause of nontuberculous mycobacterial pulmonary disease with frequent recurrence. We screened the 7,645 repeat sequences for 200 fragments from the genome of M. intracellulare ATCC 13950 in silico, finally generating five primers with more than 90% identity for a total of 226 loci in the genome. The five primers could make different band patterns depending on the genome of three different M. intracellulare strains using an in silico test. The novel rep-PCR with the five primers was conducted using 34 bacterial samples of 7 species containing 25 M. intracellulare clinical isolates, compared with previous published rep-PCRs. This shows distinguished patterns depending on species and blotting assay for 6 species implied the sequence specificity of the five primers. The Designed rep-PCR had a 95–98% of similarity value in the reproducibility test and showed 7 groups of fingerprints in M. intracellulare strains. Designed rep-PCR had a correlation value of 0.814 with VNTR, reference epidemiological method. This study provides a promising genotype fingerprinting method for tracing the recurrence of heterogeneous M. intracellulare.

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“…The isolate of Listeria monocytogenes used in the multi-species biofilm experiment was detected in the same salmon-processing plant during routine controls. This isolate was selected for the experiment as it was found to be of sequence type (ST) 8 [ 38 ]. This sequence type has been known to persist in food-processing environments and has been associated with food-borne outbreaks of listeriosis from salmon products [ 39 , 40 ].…”

Section: Methodsmentioning

confidence: 99%

High Disinfectant Tolerance in Pseudomonas spp. Biofilm Aids the Survival of Listeria monocytogenes

Thomassen,

Reiche,

Hjørungnes

et al. 2023

Microorganisms

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Pseudomonas spp. are the most commonly found bacteria in food-processing environments due to properties such as a high growth rate at low temperatures, a high tolerance of antimicrobial agents, and biofilm formation. In this study, a set of Pseudomonas isolates originating from cleaned and disinfected surfaces in a salmon processing facility were screened for biofilm formation at 12 °C. A high variation in biofilm formation between the isolates was observed. Selected isolates, in both planktonic and biofilm states, were tested for resistance/tolerance to a commonly used disinfectant (peracetic acid-based) and antibiotic florfenicol. Most isolates showed a much higher tolerance in the biofilm state than in the planktonic state. In a multi-species biofilm experiment with five Pseudomonas strains with and without a Listeria monocytogenes strain, the Pseudomonas biofilm appeared to aid the survival of L. monocytogenes cells after disinfection, underscoring the importance of controlling the bacterial load in food-processing environments.

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ON‐rep‐seq as a rapid and cost‐effective alternative to whole‐genome sequencing for species‐level identification and strain‐level discrimination of Listeria monocytogenes contamination in a salmon processing plant

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 5 publications

References 71 publications

A Comprehensive Virulence and Resistance Characteristics of Listeria monocytogenes Isolated from Fish and the Fish Industry Environment

A Comprehensive Virulence and Resistance Characteristics of Listeria monocytogenes Isolated from Fish and the Fish Industry Environment

A novel repeat sequence-based PCR (rep-PCR) using specific repeat sequences of Mycobacterium intracellulare as a DNA fingerprinting

High Disinfectant Tolerance in Pseudomonas spp. Biofilm Aids the Survival of Listeria monocytogenes

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