Molecular Tracing to Find Source of Protracted Invasive Listeriosis Outbreak, Southern Germany, 2012–2016

Kleta, Sylvia; Hammerl, Jens A.; Dieckmann, Ralf; Malorny, Burkhard; Blettner, Maria; Halbedel, Sven; Prager, Rita; Trost, Eva; Flieger, Antje; Wilking, Hendrik; Vygen-Bonnet, Sabine; Busch, Ulrich; Messelhäußer, Ute; Horlacher, Sabine; Schönberger, Katharina; Lohr, Dorothee; Aichinger, Elisabeth; Luber, Petra; Hensel, Andreas; Dahouk, Sascha Al

doi:10.3201/eid2310.161623

Cited by 40 publications

(32 citation statements)

References 9 publications

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“…ascertainment, and provided evidence for geographical origin and evolutionary context [9,20]. In Listeria, it has improved cluster identification, facilitated retrospective trace-back of unsolved clusters and reduced faulty source attributions [76][77][78][79]. Within a distinct cattle population, we observed high genomic homogeneity within each persistently isolated serotype.…”

Section: Discussionmentioning

confidence: 85%

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada

Wang

Jokinen²,

Laing

et al. 2020

Microbial Genomics

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Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli ; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.

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Section: Discussionmentioning

confidence: 85%

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada

Wang

Jokinen²,

Laing

et al. 2020

Microbial Genomics

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“…2A). A German meat processing company was the source for this outbreak (27), which came to an end after shutdown of the company. The secondlargest complex, complex 2, contained 40 isolates from 2014 to 2017 and included Allelic distances in verified outbreak complexes.…”

Section: Resultsmentioning

confidence: 99%

“…Identification of food vehicles has been difficult in the past, mainly because of the long incubation period of listeriosis of up to 70 days (6,34), and they are known for only 4 of the 38 cgMLST complexes (27,28,35). Food isolates associated with cluster 1 and cluster 2 had been identified by routine screening of food isolates by the German national food safety agency after cgMLST implementation (27,28). This illustrates that comprehensive WGS-based typing of food and human isolates in real time facilitates association of food isolates with human disease clusters in order to stop transmission of L. monocytogenes.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Sequencing of Recent Listeria monocytogenes Isolates from Germany Reveals Population Structure and Disease Clusters

et al. 2018

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causes foodborne outbreaks with high mortality. For improvement of outbreak cluster detection, the German consiliary laboratory for listeriosis implemented whole-genome sequencing (WGS) in 2015. A total of 424 human isolates collected in 2007 to 2017 were subjected to WGS and core-genome multilocus sequence typing (cgMLST). cgMLST grouped the isolates into 38 complexes, reflecting 4 known and 34 unknown disease clusters. Most of these complexes were confirmed by single nucleotide polymorphism (SNP) calling, but some were further differentiated. Interestingly, several cgMLST cluster types were further subtyped by pulsed-field gel electrophoresis, partly due to phage insertions in the accessory genome. Our results highlight the usefulness of cgMLST for routine cluster detection but also show that cgMLST complexes require validation by methods providing higher typing resolution. Twelve cgMLST clusters included recent cases, suggesting activity of the source. Therefore, the cgMLST nomenclature data presented here may support future public health actions.

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“…Hence, they suggested using other techniques including multilocus sequence typing (MLST), multiple-locus variable-number tandem repeat analyses (MLVA), and repetitive element palindromic PCR (rep-PCR), along with PFGE can result in more reliable outcome. In two recent studies, PFGE technique has been combined with MLST (Kleta et al, 2017) and MLVA (Sharapov et al, 2016) to detect Listeria monocytogenes and E. coli O157:H7, respectively.…”

Section: Pulsed-field Gel Electrophoresis (Pfge)mentioning

confidence: 99%

Detection and occurrence of indicator organisms and pathogens

Motlagh

Yang

2019

Water Environment Research

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This review paper focuses on detection and quantification techniques of indicator organisms that can be used for water quality assessment. The environmental pathogens that are critical to understand and better evaluate water quality are also discussed in this paper. Several recent studies using culture-independent methods such as microbial source tracking, pulsed field gel electrophoresis, mitochondrial DNA, and next generation sequencing to assess various environmental samples and water bodies have been reviewed.

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Molecular Tracing to Find Source of Protracted Invasive Listeriosis Outbreak, Southern Germany, 2012–2016

Cited by 40 publications

References 9 publications

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada

Whole-Genome Sequencing of Recent Listeria monocytogenes Isolates from Germany Reveals Population Structure and Disease Clusters

Detection and occurrence of indicator organisms and pathogens

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