Dataset Information

Genomic Diversity of Listeria monocytogenes Isolated from Clinical and Non-Clinical Samples in Chile.

ABSTRACT: Listeria monocytogenes is the causative agent of listeriosis, which is an uncommon but severe infection associated with high mortality rates in humans especially in high-risk groups. This bacterium survives a variety of stress conditions (e.g., high osmolality, low pH), which allows it to colonize different niches especially niches found in food processing environments. Additionally, a considerable heterogeneity in pathogenic potential has been observed in different strains. In this study, 38 isolates of L. monocytogenes collected in Chile from clinical samples (n = 22) and non-clinical samples (n = 16) were analyzed using whole genome sequencing (WGS) to determine their genomic diversity. A core genome Single Nucleotide Polymorphism (SNP) tree using 55 additional L. monocytogenes accessions classified the Chilean isolates in lineages I (n = 25) and II (n = 13). In silico, Multi-locus sequence typing (MLST) differentiated the isolates into 13 sequence types (ST) in which the most common were ST1 (15 isolates) and ST9 (6 isolates) and represented 55% of the isolates. Genomic elements associated with virulence (i.e., LIPI-1, LIPI-3, inlA, inlB, inlC, inlG, inlH, inlD, inlE, inlK, inlF, and inlJ) and stress survival (i.e., stress survival islet 1 and stress survival islet 2) were unevenly distributed among clinical and non-clinical isolates. In addition, one novel inlA premature stop codon (PMSC) was detected. Comparative analysis of L. monocytogenes circulating in Chile revealed the presence of globally distributed sequence types along with differences among the isolates analyzed at a genomic level specifically associated with virulence and stress survival.

SUBMITTER: Toledo V

PROVIDER: S-EPMC6115834 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Genomic Diversity of <i>Listeria monocytogenes</i> Isolated from Clinical and Non-Clinical Samples in Chile.

Toledo Viviana V den Bakker Henk C HC Hormazábal Juan Carlos JC González-Rocha Gerardo G Bello-Toledo Helia H Toro Magaly M Moreno-Switt Andrea I AI

Genes 20180802 8

<i>Listeria monocytogenes</i> is the causative agent of listeriosis, which is an uncommon but severe infection associated with high mortality rates in humans especially in high-risk groups. This bacterium survives a variety of stress conditions (e.g., high osmolality, low pH), which allows it to colonize different niches especially niches found in food processing environments. Additionally, a considerable heterogeneity in pathogenic potential has been observed in different strains. In this study ...[more]

PMID: 30072604

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Project description:Listeria monocytogenes is a significant foodborne pathogen causing severe systemic infections in humans with high mortality rates. The objectives of this work were to establish a phylogenetic framework of L. monocytogenes from China and to investigate sequence diversity among different serotypes. We selected 17 L. monocytogenes strains recovered from patients and foods in China representing serotypes 1/2a, 1/2b, and 1/2c. Draft genome sequences were determined using Illumina MiSeq technique and associated protocols. Open reading frames were assigned using prokaryotic genome annotation pipeline by NCBI. Twenty-four published genomes were included for comparative genomic and phylogenetic analysis. More than 154,000 single nucleotide polymorphisms (SNPs) were identified from multiple genome alignment and used to reconstruct maximum likelihood phylogenetic tree. The 41 genomes were differentiated into lineages I and II, which consisted of 4 and 11 subgroups, respectively. A clinical strain from China (SHL009) contained significant SNP differences compared to the rest genomes, whereas clinical strain SHL001 shared most recent common ancestor with strain SHL017 from food. Moreover, clinical strains SHL004 and SHL015 clustered together with two strains (08-5578 and 08-5923) recovered from an outbreak in Canada. Partial sequences of a plasmid found in the Canadian strain were also present in SHL004. We investigated the presence of various genes and gene clusters associated with virulence and subgroup-specific genes, including internalins, L. monocytogenes pathogenicity islands (LIPIs), L. monocytogenes genomic islands (LGIs), stress survival islet 1 (SSI-1), and clustered regularly interspaced short palindromic repeats (CRISPR)/cas system. A novel genomic island, denoted as LGI-2 was identified. Comparative sequence analysis revealed differences among the L. monocytogenes strains related to virulence, survival abilities, and attributes against foreign genetic elements. L. monocytogenes from China were genetically diverse. Strains from clinical specimens and food related closely suggesting foodborne transmission of human listeriosis.

Project description:Listeria monocytogenes is an important Gram-positive foodborne pathogen. However, limited information is available on the comprehensive investigation and potential risk of L. monocytogenes in fresh aquatic products, which are popular to consumers in China. This study aimed to determine the occurrence, virulence profiles, and population diversity of L. monocytogenes isolated from aquatic products in China. In total, 846 aquatic product samples were collected between July 2011 and April 2016 from 43 cities in China. Approximately 7.92% (67/846) aquatic product samples were positive for L. monocytogenes, 86.57% positive samples ranged from 0.3 to 10 MPN/g, whereas 5.97% showed over 110 MPN/g by the Most Probable Number method, which included two samples of products intended to be eaten raw. Serogroups I.1 (serotype 1/2a), I.2 (serotype 1/2b), and III (serotype 4c) were the predominant serogroups isolated, whereas serogroup II.1 (serotype 4b) was detected at much lower frequencies. Examination of antibacterial resistance showed that nine antibacterial resistance profiles were exhibited in 72 isolates, a high level susceptibility of 16 tested antibiotics against L. monocytogenes were observed, indicating these common antibacterial agents are still effective for treating L. monocytogenes infection. Multilocus sequence typing revealed that ST299, ST87, and ST8 are predominant in aquatic products, indicating that the rare ST299 (serotype 4c) may have a special ecological niche in aquatic products and associated environments. Except llsX and ptsA, the 72 isolates harbor nine virulence genes (prfA, actA, hly, plcA, plcB, iap, mpl, inlA, and inlB), premature stop codons (PMSCs) in inlA were found in four isolates, three of which belonged to ST9. A novel PMSC was found in 2929-1LM with a nonsense mutation at position 1605 (TGG→TGA). All ST87 isolates harbored the ptsA gene, whereas 8 isolates (11.11%) carried the llsX gene, and mainly belonged to ST1, ST3, ST308, ST323, ST330, and ST619. Taken together, these results first reported potential virulent L. monocytogenes isolates (ST8 and ST87) were predominant in aquatic products which may have implications for public health in China. It is thus necessary to perform continuous surveillance for L. monocytogenes in aquatic products in China.

Project description:Listeria monocytogenes is a pathogen transmitted through food that can cause severe infections in high-risk groups such as pregnant women, elderly, young children and immunocompromised individuals. It is a ubiquitous bacterium that can survive in harsh conditions, such as dry environments, at low temperatures, in brine conditions and at low pH values. It also has the capacity to form biofilms, which makes it particularly successful even in colonizing surfaces within food processing plants. This study analyzed the presence of L. monocytogenes in ready-to-eat food (RTE) such as sausage, cheese, fresh salads, and other types of raw food. 850 samples of refrigerated and packaged food collected in 2008 and 2009 were analyzed. It was found that 25% of these samples were contaminated with L. monocytogenes strains. Serotyping and virulence genes detection by polymerase chain reaction (PCR) identified that strains belonging to serotype 4b, and containing one or more genes encoded by pathogenicity island (LIPI-1), were significantly associated with specific food types. Furthermore, using pulse field gel electrophoresis (PFGE), it was possible to associate isolates from cheese with strains from clinical cases of listeriosis outbreaks that occurred during the same time period within the same geographic regions. In addition, a strong correlation was observed between isolates from frozen seafood and from clinical strains obtained from sporadic cases of listeriosis. In agreement with reports described in other countries, our results shown that Chilean strains of L. monocytogenes from food products include the most virulent serotypes, encoding for the main virulence genes of the LIPI-1, and were clonally related to clinical isolates from sporadic cases and outbreaks of listeriosis. In conclusion, we show that Chilean isolates of L. monocytogenes from RTE and raw food products can cause disease in humans, representing a public health risk that justifies permanent surveillance.

Dataset Information

Genomic Diversity of Listeria monocytogenes Isolated from Clinical and Non-Clinical Samples in Chile.

Publications

Genomic Diversity of <i>Listeria monocytogenes</i> Isolated from Clinical and Non-Clinical Samples in Chile.

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