Draft Genome Sequences of Six Listeria monocytogenes Strains Isolated from Dairy Products from a Processing Plant in Southern Italy

Chiara, Matteo; D’Erchia, Anna Maria; Manzari, Caterina; Minotto, Alice; Montagna, Cosimo; Addante, N.; Santagada, Gianfranco; Latorre, Laura; Pesole, Graziano; Horner, David S.; Parisi, Antonio

doi:10.1128/genomea.00282-14

Cited by 11 publications

(19 citation statements)

References 4 publications

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“…). Thirteen ST121 isolates isolated outside Denmark (Fox et al ., ; Chiara et al ., ; Stessl et al ., ; Lopez‐Alonso et al ., ) were included as this appeared to be the dominant persistent ST type world‐wide. Finally, two reference strains F2365 (Nelson et al ., ) and EGDe (Glaser et al ., ) were included to represent Lineage I and II, respectively.…”

Section: Resultsmentioning

confidence: 98%

“…L. monocytogenes is divided into four Lineages, of which lineage I isolates are often associated with human outbreaks, whereas Lineage II isolates are often associated with food and food processing environments (Valderrama and Cutter, ; Maury et al ., ). Sequence type (ST) 121 (ST121) identified by Multi Locus Sequence Typing (MLST) is a persistent ST, and has been found in fish processing plants (Wulff et al ., ), meat processing plants (Martin et al ., ; Morganti et al ., ) and in many other food processing plants (Hein et al ., ; Chiara et al ., ; Ciolacu et al ., ; Schmitz‐Esser et al ., ). ST121 is the most common ST isolated from food samples; however, it is rarely isolated from infected patients (Althaus et al ., ; Ebner et al ., ; Maury et al ., ).…”

Section: Introductionmentioning

confidence: 98%

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Genome‐wide‐analyses of Listeria monocytogenes from food‐processing plants reveal clonal diversity and date the emergence of persisting sequence types

Knudsen

Nielsen

Marvig

et al. 2017

Environ Microbiol Rep

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Summary Whole genome sequencing is increasing used in epidemiology, e.g. for tracing outbreaks of food‐borne diseases. This requires in‐depth understanding of pathogen emergence, persistence and genomic diversity along the food production chain including in food processing plants. We sequenced the genomes of 80 isolates of Listeria monocytogenes sampled from Danish food processing plants over a time‐period of 20 years, and analysed the sequences together with 10 public available reference genomes to advance our understanding of interplant and intraplant genomic diversity of L. monocytogenes. Except for three persisting sequence types (ST) based on Multi Locus Sequence Typing being ST7, ST8 and ST121, long‐term persistence of clonal groups was limited, and new clones were introduced continuously, potentially from raw materials. No particular gene could be linked to the persistence phenotype. Using time‐based phylogenetic analyses of the persistent STs, we estimate the L. monocytogenes evolutionary rate to be 0.18–0.35 single nucleotide polymorphisms/year, suggesting that the persistent STs emerged approximately 100 years ago, which correlates with the onset of industrialization and globalization of the food market.

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Section: Resultsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 98%

Genome‐wide‐analyses of Listeria monocytogenes from food‐processing plants reveal clonal diversity and date the emergence of persisting sequence types

Knudsen

Nielsen

Marvig

et al. 2017

Environ Microbiol Rep

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“…The isolates linked to the ricotta salata outbreak were typed as VT80 [19, 25], while the two Italian cases were subtyped as ST101, which is grouped in the same Clonal Complex (CC) as ST38 (i.e. CC101).…”

Section: Discussionmentioning

confidence: 99%

Identification of a major Listeria monocytogenes outbreak clone linked to soft cheese in Northern Italy – 2009-2011

et al. 2017

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BackgroundMolecular subtyping and enhanced surveillance in Lombardy region identified a cluster of possibly related listeriosis cases from 2006 to 2010. This cluster grouped 31 isolates that belonged to serotype 1/2a and Sequence Type 38 (ST38) as defined by Multilocus Sequence Typing (MLST).MethodsOur study expanded the previous investigation to include cases from 2011 to 2014 and used Multi-Virulence-Locus Sequence Typing (MVLST) on all ST38 isolates to better understand their epidemiology and possibly identify a common source outbreak.ResultsOut of 306 L. monocytogenes clinical isolates collected, 43 (14.1%) belonged to ST38 with cases occurring in nine out of twelve Lombardy provinces. The ST38 isolates were split by MVLST into two Virulence Types (VTs): VT80 (n = 12) and VT104 (n = 31). VT104 cases were concentrated between 2009 and 2011 in two provinces, Bergamo and Milan. An epidemiologic investigation was performed and in one case, a matching VT104 isolate was retrieved from a soft cheese sample from a patient’s refrigerator.ConclusionsOur findings revealed a major listeriosis outbreak in Northern Italy linked to soft cheese in 2009–2011, which went undetected by local health authorities. Our study shows that integrating subtyping methods with conventional epidemiology can help identify the source of L. monocytogenes outbreak clones.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-017-2441-6) contains supplementary material, which is available to authorized users.

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“…Because we compared only two isolates from each CC, it is unlikely that the results represent differences between the CCs; instead, they illustrate the various magnitudes of genetic difference that can occur among members of a clonal complex within single outbreaks. We next explored in more detail the genetic differences between the two CC101 isolates using publicly available draft genomes of L. monocytogenes strains from the implicated ricotta salata cheese processing facility (25).…”

Section: Resultsmentioning

confidence: 99%

“…The AscI and ApaI patterns were compared in BioNumerics v.6.6.10 using the unweighted pair group method with arithmetic mean; the dendrogram shown to the left of each pair of profiles was produced using the Dice similarity coefficient, with the tolerance and optimization set at 1.5%. types of L. monocytogenes (25): two isolates from CC8 were recovered and sequenced, as were one isolate each from CC121, CC5, CC2, and CC101 (Fig. 1).…”

Section: Fig 2 Asci and Apai Pfge Profiles Of Listeria Monocytogenes mentioning

confidence: 99%

Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing

Bergholz

Bakker

Katz

et al. 2016

Appl Environ Microbiol

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e We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or "epidemic clones" that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation. Listeria monocytogenes is a bacterial pathogen that is almost exclusively transmitted by food. Invasive listeriosis typically presents as sepsis or meningoencephalitis in older adults, those with certain chronic illnesses, and people undergoing immunosuppression. Infections during pregnancy can cause fever and other nonspecific symptoms in the mother with severe outcomes such as fetal loss, premature labor, and neonatal illness and death. Although listeriosis is relatively rare (ϳ1,600 cases occur annually in the United States), approximately 20% of cases are fatal and outbreaks are not uncommon. There are 13 known serotypes of L. monocytogenes, though the majority of human illnesses are caused by serotypes 1/2a, 1/2b, and 4b (1, 2). Molecular subtyping methods have differentiated L. monocytogenes isolates into 4 distinct genetic lineages, with isolates of serotypes 4b and 1/2b typically belonging to lineage I (LI) and isolates of serotype 1/2a typically belonging to lineage II (LII) (3). Strains of lineages III and IV rarely cause listeriosis in humans. Historically, isolates of serotype 4b have caused the greatest proportion of listeriosis outbreaks and the largest number of cases per outbreak (2). In 2011, however, serotypes 1/2a and 1/2b were implic...

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Draft Genome Sequences of Six Listeria monocytogenes Strains Isolated from Dairy Products from a Processing Plant in Southern Italy

Abstract: Here we announce the draft genome sequences of 6 Listeria monocytogenes strains from ricotta cheese produced in a dairy processing plant located in southern Italy and potentially involved in a multistate outbreak of listeriosis in the United States.

Cited by 11 publications

References 4 publications

Genome‐wide‐analyses of Listeria monocytogenes from food‐processing plants reveal clonal diversity and date the emergence of persisting sequence types

Genome‐wide‐analyses of Listeria monocytogenes from food‐processing plants reveal clonal diversity and date the emergence of persisting sequence types

Identification of a major Listeria monocytogenes outbreak clone linked to soft cheese in Northern Italy – 2009-2011

Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing

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