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Borowiak M, Kreitlow A, Malorny B, Lämmler C, Prenger-Berninghoff E, Plötz M, Abdulmawjood A. Arcanobacterium canis strain DSM 25104 isolated from an English bulldog suffering from otitis externa: complete genome sequence. Microbiol Resour Announc 2024; 13:e0062423. [PMID: 38099684 DOI: 10.1128/mra.00624-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/21/2023] [Indexed: 01/18/2024] Open
Abstract
Many species of the genus Arcanobacterium are known as opportunistic pathogens and have been isolated in association with infectious diseases in humans and animals. Here, we present the complete genome sequence of another opportunistic pathogenic representative, namely Arcanobacterium canis, isolated from the otitis externa of an English bulldog.
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Affiliation(s)
- Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR) , Berlin, Germany
| | - Antonia Kreitlow
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover , Hannover, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR) , Berlin, Germany
| | - Christoph Lämmler
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen , Gießen, Germany
| | - Ellen Prenger-Berninghoff
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen , Gießen, Germany
| | - Madeleine Plötz
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover , Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover , Hannover, Germany
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2
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Bartsch LJ, Borowiak M, Deneke C, Gruetzke J, Hammerl JA, Malorny B, Szabo I, Alter T, Nguyen KK, Fischer J. Genetic characterization of a multidrug-resistant Salmonella enterica serovar Agona isolated from a dietary supplement in Germany. Front Microbiol 2023; 14:1284929. [PMID: 38033583 PMCID: PMC10686068 DOI: 10.3389/fmicb.2023.1284929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Agona has a history of causing food-borne outbreaks and any emergence of multidrug-resistant (MDR) isolates in novel food products is of concern. Particularly, in food products frequently consumed without sufficient heating prior to consumption. Here, we report about the MDR isolate, 18-SA00377, which had been isolated from a dietary supplement in Germany in 2018 and submitted to the German National Reference Laboratory for Salmonella. WGS-based comparative genetic analyses were conducted to find a potential reservoir of the isolate itself or mobile genetic elements associated with MDR. As a phylogenetic analysis did not yield any closely related S. Agona isolates, either globally or from Germany, a detailed analysis of the largest plasmid (295,499 bp) was performed as it is the main carrier of resistances. A combined approach of long-read and short-read sequencing enabled the assembly of the isolate's chromosome and its four plasmids. Their characterization revealed the presence of 23 different antibiotic resistance genes (ARGs), conferring resistance to 12 different antibiotic drug classes, as well as genes conferring resistance to six different heavy metals. The largest plasmid, pSE18-SA00377-1, belongs to the IncHI2 plasmid family and carries 16 ARGs, that are organized as two distinct clusters, with each ARG associated with putative composite transposons. Through a two-pronged approach, highly similar plasmids to pSE18-SA00377-1 were identified in the NCBI database and a search for Salmonella isolates with a highly similar ARG resistance profile was conducted. Mapping and structural comparisons between pSE18-SA00377-1 and these plasmids and Salmonella isolates showed that both the plasmid backbone and identical or similar ARG clusters can be found not only in Salmonella isolates, originating mostly from a wide variety of livestock, but also in a diverse range of bacterial genera of varying geographical origins and isolation sources. Thus, it can be speculated that the host range of pSE18-SA00377-1 is not restricted to Salmonella and its spread already occurred in different bacterial populations. Overall, this hints at a complex history for pSE18-SA00377-1 and highlights the importance of surveilling multidrug-resistant S. enterica isolates, especially in novel food items that are not yet heavily regulated.
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Affiliation(s)
- Lee Julia Bartsch
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Maria Borowiak
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Josephine Gruetzke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens-Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Jaudou S, Deneke C, Tran ML, Salzinger C, Vorimore F, Goehler A, Schuh E, Malorny B, Fach P, Grützke J, Delannoy S. Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-Producing Escherichia coli in Presence of Commensal E. coli. Microorganisms 2023; 11:2043. [PMID: 37630603 PMCID: PMC10458860 DOI: 10.3390/microorganisms11082043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The characterization of Shiga toxin-producing Escherichia coli (STEC) is necessary to assess their pathogenic potential, but isolation of the strain from complex matrices such as milk remains challenging. In previous work, we have shown the potential of long-read metagenomics to characterize eae-positive STEC from artificially contaminated raw milk without isolating the strain. The presence of multiple E. coli strains in the sample was shown to potentially hinder the correct characterization of the STEC strain. Here, we aimed at determining the STEC:commensal ratio that would prevent the characterization of the STEC. We artificially contaminated pasteurized milk with different ratios of an eae-positive STEC and a commensal E. coli and applied the method previously developed. Results showed that the STEC strain growth was better than the commensal E. coli after enrichment in acriflavine-supplemented BPW. The STEC was successfully characterized in all samples with at least 10 times more STEC post-enrichment compared to the commensal E. coli. However, the presence of equivalent proportions of STEC and commensal E. coli prevented the full characterization of the STEC strain. This study confirms the potential of long-read metagenomics for STEC characterization in an isolation-free manner while refining its limit regarding the presence of background E. coli strains.
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Affiliation(s)
- Sandra Jaudou
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Carlus Deneke
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Mai-Lan Tran
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Carina Salzinger
- National Reference Laboratory for Escherichia coli Including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - André Goehler
- National Reference Laboratory for Escherichia coli Including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Elisabeth Schuh
- National Reference Laboratory for Escherichia coli Including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Burkhard Malorny
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Patrick Fach
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Josephine Grützke
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Sabine Delannoy
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
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Burkhardt W, Salzinger C, Fischer J, Malorny B, Fischer M, Szabo I. The nematode worm Caenorhabditis elegans as an animal experiment replacement for assessing the virulence of different Salmonella enterica strains. Front Microbiol 2023; 14:1188679. [PMID: 37362934 PMCID: PMC10285400 DOI: 10.3389/fmicb.2023.1188679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
Caenorhabditis (C.) elegans has become a popular toxicological and biological test organism in the last two decades. Furthermore, the role of C. elegans as an alternative for replacing or reducing animal experiments is continuously discussed and investigated. In the current study, we investigated whether C. elegans survival assays can help in determining differences in the virulence of Salmonella enterica strains and to what extent C. elegans assays could replace animal experiments for this purpose. We focused on three currently discussed examples where we compared the longevity of C. elegans when fed (i) with S. enterica serovar Enteritidis vaccination or wild-type strains, (ii) with lipopolysaccharide (LPS) deficient rough or LPS forming smooth S. enterica serovar Enteritidis, and (iii) with an S. enterica subsp. diarizonae strain in the presence or absence of the typical pSASd plasmid encoding a bundle of putative virulence factors. We found that the C. elegans survival assay could indicate differences in the longevity of C. elegans when fed with the compared strain pairs to a certain extent. Putatively higher virulent S. enterica strains reduced the lifespan of C. elegans to a greater extent than putatively less virulent strains. The C. elegans survival assay is an effective and relatively easy method for classifying the virulence of different bacterial isolates in vivo, but it has some limitations. The assay cannot replace animal experiments designed to determine differences in the virulence of Salmonella enterica strains. Instead, we recommend using the described method for pre-screening bacterial strains of interest to select the most promising candidates for further animal experiments. The C. elegans assay possesses the potential to reduce the number of animal experiments. Further development of the C. elegans assay in conjunction with omics technologies, such as transcriptomics, could refine results relating to the estimation of the virulent potential of test organisms.
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Mencía-Ares O, Borowiak M, Argüello H, Cobo-Díaz JF, Malorny B, Álvarez-Ordóñez A, Carvajal A, Deneke C. Genomic Insights into the Mobilome and Resistome of Sentinel Microorganisms Originating from Farms of Two Different Swine Production Systems. Microbiol Spectr 2022; 10:e0289622. [PMID: 36377950 PMCID: PMC9769681 DOI: 10.1128/spectrum.02896-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a threat to public health due to long-term antimicrobial use (AMU), which promotes the bacterial acquisition of antimicrobial resistance determinants (ARDs). Within food-producing animals, organic and extensive Iberian swine production is based on sustainable and eco-friendly management systems, providing an excellent opportunity to evaluate how sustained differences in AMU impact the development and spread of AMR. Here, through a whole-genome sequencing approach, we provide an in-depth characterization of the resistome and mobilome and their interaction in 466 sentinel bacteria, namely, Escherichia coli, Enterococcus spp., Campylobacter coli, and Staphylococcus spp., recovered from 37 intensive and organic-extensive pig farms. Both ARDs and mobile genetic elements (MGEs) were primarily taxon-associated, with higher similarities among bacteria which were closely phylogenetically related. E. coli exhibited the most diverse resistome and mobilome, with 85.4% mobilizable ARDs, 50.3% of which were plasmid-associated. Staphylococcus spp. exhibited a broad repertoire of ARDs and MGEs, with 52.3% of its resistome being mobilizable. Although Enterococcus spp. carried the highest number of ARDs per isolate and its plasmidome was similar in size to that of E. coli, 43.7% of its resistome was mobilizable. A narrow spectrum of ARDs constituted the C. coli resistome, with point mutations as its main AMR driver. A constrained AMU, as observed in organic-extensive herds, determined a reduction in the quantitative composition of the resistome and the complexity of the resistome-mobilome interaction. These results demonstrate taxon-associated AMR-MGE interactions and evidence that responsible AMU can contribute to reducing AMR pressure in the food chain. IMPORTANCE This study provides the first integral genomic characterization of the resistome and mobilome of sentinel microorganisms for antimicrobial resistance (AMR) surveillance from two different swine production systems. Relevant differences were observed among taxa in the resistomes and mobilomes they harbored, revealing their distinctive risk in AMR dissemination and spread. Thus, Escherichia coli and, to a lesser extent, Staphylococcus spp. constituted the main reservoirs of mobilizable antimicrobial resistance genes, which were predominantly plasmid-associated; in contrast to Campylobacter coli, whose resistome was mainly determined by point mutations. The reduced complexity of mobilome-resistome interaction in Enterococcus spp. suggested its limited role in AMR dissemination from swine farms. The significant differences in antimicrobial use among the studied farms allowed us to assess the suitability of whole-genome sequencing as a rapid and efficient technique for the assessment of mid- to long-term on-farm interventions for the reduction of antimicrobial use and the evaluation of AMR status.
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Affiliation(s)
- Oscar Mencía-Ares
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Héctor Argüello
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - José Francisco Cobo-Díaz
- Department of Food Hygiene and Technology, Veterinary Faculty, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Veterinary Faculty, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Ana Carvajal
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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6
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Jaudou S, Deneke C, Tran ML, Schuh E, Goehler A, Vorimore F, Malorny B, Fach P, Grützke J, Delannoy S. A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics. Microb Genom 2022; 8:mgen000911. [PMID: 36748417 PMCID: PMC9836091 DOI: 10.1099/mgen.0.000911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are a cause of severe human illness and are frequently associated with haemolytic uraemic syndrome (HUS) in children. It remains difficult to identify virulence factors for STEC that absolutely predict the potential to cause human disease. In addition to the Shiga-toxin (stx genes), many additional factors have been reported, such as intimin (eae gene), which is clearly an aggravating factor for developing HUS. Current STEC detection methods classically rely on real-time PCR (qPCR) to detect the presence of the key virulence markers (stx and eae). Although qPCR gives an insight into the presence of these virulence markers, it is not appropriate for confirming their presence in the same strain. Therefore, isolation steps are necessary to confirm STEC viability and characterize STEC genomes. While STEC isolation is laborious and time-consuming, metagenomics has the potential to accelerate the STEC characterization process in an isolation-free manner. Recently, short-read sequencing metagenomics have been applied for this purpose, but assembly quality and contiguity suffer from the high proportion of mobile genetic elements occurring in STEC strains. To circumvent this problem, we used long-read sequencing metagenomics for identifying eae-positive STEC strains using raw cow's milk as a causative matrix for STEC food-borne outbreaks. By comparing enrichment conditions, optimizing library preparation for MinION sequencing and generating an easy-to-use STEC characterization pipeline, the direct identification of an eae-positive STEC strain was successful after enrichment of artificially contaminated raw cow's milk samples at a contamination level as low as 5 c.f.u. ml-1. Our newly developed method combines optimized enrichment conditions of STEC in raw milk in combination with a complete STEC analysis pipeline from long-read sequencing metagenomics data. This study shows the potential of the innovative methodology for characterizing STEC strains from complex matrices. Further developments will nonetheless be necessary for this method to be applied in STEC surveillance.
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Affiliation(s)
- Sandra Jaudou
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany,*Correspondence: Sandra Jaudou,
| | - Carlus Deneke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mai-Lan Tran
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Elisabeth Schuh
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - André Goehler
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Burkhard Malorny
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Patrick Fach
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Josephine Grützke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sabine Delannoy
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,*Correspondence: Sabine Delannoy,
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Alssahen M, Kreitlow A, Sammra O, Lämmler C, Borowiak M, Malorny B, Siebert U, Wohlsein P, Prenger-Berninghoff E, Plötz M, Abdulmawjood A. Arcanobacterium buesumense sp. nov., isolated from an anal swab of a male harbour seal (Phoca vitulina). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A polyphasic taxonomic study was performed on an unidentified previously described
Arcanobacterium
-like Gram-positive strain 2701T isolated from an anal swab of a dead male harbour seal. Comparative 16S rRNA sequencing showed that the bacterium belonged to the genus
Arcanobacterium
in the family
Arcanobacteriaceae
. The genome sequence of the strain was obtained by Borowiak et al. []. The genome had a G+C content of 49 mol% and a total length of 1.94 Mb. The presence of the major menaquinone MK-9(H4) supported the affiliation of the isolate with the genus
Arcanobacterium
. The polar lipid profile consisted of diphosphatidylglycerol and an unidentified phospholipid as major components and two unidentified lipids, a further unidentified phospholipid, two unidentified phosphoglycolipids as well as phosphatidylglycerol. The major fatty acids were C16 : 0, C18 : 1 and C18 : 0. Biochemical and phylogenetic analyses clearly distinguished the isolate from other members of the genus
Arcanobacterium
and closely related other species. Based on these results, it is proposed that the unknown
Arcanobacterium
sp. strain 2701T should be classified as representing a novel species with the name Arcanobacterium buesumense sp. nov. The type strain is 2701T (=DSM 112952T=LMG 32446T).
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Affiliation(s)
- Mazen Alssahen
- Institute for Infectious Diseases of Animals, Justus Liebig University Gießen, Frankfurter Straße 85-91, D-35392 Gießen, Germany
| | - Antonia Kreitlow
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Osama Sammra
- Institute for Infectious Diseases of Animals, Justus Liebig University Gießen, Frankfurter Straße 85-91, D-35392 Gießen, Germany
| | - Christoph Lämmler
- Institute for Infectious Diseases of Animals, Justus Liebig University Gießen, Frankfurter Straße 85-91, D-35392 Gießen, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Max-Dohrn Str. 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Max-Dohrn Str. 8-10, 10589 Berlin, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Hannover, Germany
| | - Peter Wohlsein
- Institute of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Ellen Prenger-Berninghoff
- Institute for Infectious Diseases of Animals, Justus Liebig University Gießen, Frankfurter Straße 85-91, D-35392 Gießen, Germany
| | - Madeleine Plötz
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
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Juraschek K, Malekzadah J, Malorny B, Käsbohrer A, Schwarz S, Meemken D, Hammerl JA. Characterization of qnrB-carrying plasmids from ESBL- and non-ESBL-producing Escherichia coli. BMC Genomics 2022; 23:365. [PMID: 35549890 PMCID: PMC9101827 DOI: 10.1186/s12864-022-08564-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Escherichia coli carrying clinically important antimicrobial resistances [i.e., against extended-spectrum-beta-lactamases (ESBL)] are of high concern for human health and are increasingly detected worldwide. Worryingly, they are often identified as multidrug-resistant (MDR) isolates, frequently including resistances against quinolones/fluoroquinolones. RESULTS Here, the occurrence and genetic basis of the fluoroquinolone resistance enhancing determinant qnrB in ESBL-/non-ESBL-producing E. coli was investigated. Overall, 33 qnrB-carrying isolates out of the annual German antimicrobial resistance (AMR) monitoring on commensal E. coli (incl. ESBL-/AmpC-producing E. coli) recovered from food and livestock between 2013 and 2018 were analysed in detail. Whole-genome sequencing, bioinformatics analyses and transferability evaluation was conducted to characterise the prevailing qnrB-associated plasmids. Furthermore, predominant qnrB-carrying plasmid-types were subjected to in silico genome reconstruction analysis. In general, the qnrB-carrying E. coli were found to be highly heterogenic in their multilocus sequence types (STs) and their phenotypic resistance profiles. Most of them appeared to be MDR and exhibited resistances against up to ten antimicrobials of different classes. With respect to qnrB-carrying plasmids, we found qnrB19 located on small Col440I plasmids to be most widespread among ESBL-producing E. coli from German livestock and food. This Col440I plasmid-type was found to be highly conserved by exhibiting qnrB19, a pspF operon and different genes of unassigned function. Furthermore, we detected plasmids of the incompatibility groups IncN and IncH as carriers of qnrB. All qnrB-carrying plasmids also exhibited virulence factors and various insertion sequences (IS). The majority of the qnrB-carrying plasmids were determined to be self-transmissible, indicating their possible contribution to the spread of resistances against (fluoro)quinolones and other antimicrobials. CONCLUSION In this study, a diversity of different plasmid types carrying qnrB alone or in combination with other resistance determinants (i.e., beta-lactamase genes) were found. The spread of these plasmids, especially those carrying antimicrobial resistance genes against highest priority critically important antimicrobial agents, is highly unfavourable and can pose a threat for public health. Therefore, the dissemination pathways and evolution of these plasmids need to be further monitored.
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Affiliation(s)
- Katharina Juraschek
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589, Berlin, Germany.
| | - Janina Malekzadah
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589, Berlin, Germany
| | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589, Berlin, Germany
| | - Annemarie Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589, Berlin, Germany
- Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
| | - Diana Meemken
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
- Institute of Food Safety and Food Hygiene, Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Jens Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589, Berlin, Germany.
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Neubert K, Zuchantke E, Leidenfrost RM, Wünschiers R, Grützke J, Malorny B, Brendebach H, Al Dahouk S, Homeier T, Hotzel H, Reinert K, Tomaso H, Busch A. Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures. BMC Genomics 2021; 22:822. [PMID: 34773979 PMCID: PMC8590783 DOI: 10.1186/s12864-021-08115-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/12/2021] [Indexed: 02/08/2023] Open
Abstract
Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods. Results We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a “long-read first” approach. Conclusions Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08115-x.
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Affiliation(s)
- Kerstin Neubert
- Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany.,German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Eric Zuchantke
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Robert Maximilian Leidenfrost
- Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17a, 09648, Mittweida, Germany
| | - Röbbe Wünschiers
- Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17a, 09648, Mittweida, Germany
| | - Josephine Grützke
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Holger Brendebach
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Sascha Al Dahouk
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Timo Homeier
- Friedrich-Loeffler-Institut, Institute of Epidemiology, Südufer, 10 17493, Greifswald, Insel Riems, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Knut Reinert
- Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Anne Busch
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany. .,Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Jena, Germany.
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10
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Uelze L, Bloch A, Borowiak M, Grobbel M, Deneke C, Fischer M, Malorny B, Pietsch M, Simon S, Szabó I, Tausch SH, Fischer J. What WGS Reveals about Salmonella enterica subsp. enterica in Wildlife in Germany. Microorganisms 2021; 9:1911. [PMID: 34576806 PMCID: PMC8471515 DOI: 10.3390/microorganisms9091911] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/26/2021] [Accepted: 09/06/2021] [Indexed: 11/28/2022] Open
Abstract
The aim of this study was to gain an overview of the genetic diversity of Salmonella found in wildlife in Germany. We were particularly interested in exploring whether wildlife acts as a reservoir of certain serovars/subtypes or antimicrobial resistance (AMR) genes. Moreover, we wanted to explore the potential of Salmonella in spreading from wildlife to livestock and humans. To answer these questions, we sequenced 260 Salmonella enterica subsp. enterica isolates sampled between 2002 and 2020 from wildlife across Germany, using short-read whole genome sequencing. We found, consistent with previous findings, that some Salmonella sequence types are associated with certain animal species, such as S. Choleraesuis ST145 with wild boar and S. Enteritidis ST183 with hedgehogs. Antibiotic resistance was detected in 14.2% of all isolates, with resistance against important WATCH group antibiotics present in a small number of isolates. We further found that wildlife isolates do not form separate phylogenetic clusters distant to isolates from domestic animals and foodstuff, thus indicating frequent transmission events between these reservoirs. Overall, our study shows that Salmonella in German wildlife are diverse, with a low AMR burden and close links to Salmonella populations of farm and food-production environments.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Angelina Bloch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Mirjam Grobbel
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Matthias Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Michael Pietsch
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstr. 37, 38855 Wernigerode, Germany; (M.P.); (S.S.)
| | - Sandra Simon
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstr. 37, 38855 Wernigerode, Germany; (M.P.); (S.S.)
| | - István Szabó
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (L.U.); (A.B.); (M.B.); (M.G.); (C.D.); (M.F.); (B.M.); (I.S.); (S.H.T.)
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11
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Uelze L, Borowiak M, Deneke C, Fischer J, Flieger A, Simon S, Szabó I, Tausch SH, Malorny B. Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432. Microb Genom 2021; 7. [PMID: 34338625 PMCID: PMC8549363 DOI: 10.1099/mgen.0.000604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike most Salmonella enterica subsp. diarizonae, which are predominantly associated with cold-blooded animals such as reptiles, the serovar IIIb 61:k:1,5,(7) (termed SASd) is regarded as host-adapted to sheep. The bacterium is rarely associated with disease in humans but, nevertheless, SASd isolates are sporadically obtained from human clinical samples. It is unclear whether these transmissions are directly linked to sheep or whether transmissions may, for example, occur through other domestic animals also carrying SASd. For this reason, we utilized whole-genome sequencing to investigate a set of 119 diverse SASd isolates, including sheep-associated and human-associated isolates, as well as isolates obtained from other matrices. We discovered that serovar IIIb 61:k:1,5,(7) is composed of two distinct lineages defined by their sequence types ST432 and ST439. These two lineages are distinguished by a number of genetic features, as well as their prevalence and reservoir. ST432 appears to be the more prevalent sequence type, with the majority of isolates investigated in this study belonging to ST432. In contrast, only a small number of isolates were attributed to ST439. While ST432 isolates were of sheep, human or other origin, all ST439 isolates with source information available, were obtained from human clinical samples. Regarding their genetic features, lineage ST432 shows increased pseudogenization, harbours a virB/D4 plasmid that encodes a type IV secretion system (T4SS) and does not possess the iro gene cluster, which encodes a salmochelin siderophore for iron acquisition. These characteristics likely contribute to the ability of ST432 to persistently colonize the intestines of sheep. Furthermore, we found isolates of the lineage ST432 to be highly clonal, with little variation over the sampling period of almost 20 years. We conclude from the genomic comparisons that SASd underlies a microevolutionary process and that it is specifically lineage ST432 that should be considered as host-adapted to sheep.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Antje Flieger
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - Sandra Simon
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - István Szabó
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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12
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Kreitlow A, Becker A, Schotte U, Malorny B, Plötz M, Abdulmawjood A. Establishment and validation of a loop-mediated isothermal amplification (LAMP) assay targeting the ttrRSBCA locus for rapid detection of Salmonella spp. in food. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Pauly N, Hammerl JA, Schwarz S, Grobbel M, Meemken D, Malorny B, Tenhagen BA, Käsbohrer A, Irrgang A. Co-occurrence of the blaVIM-1 and blaSHV-12 genes on an IncHI2 plasmid of an Escherichia coli isolate recovered from German livestock. J Antimicrob Chemother 2021; 76:531-533. [PMID: 33175149 PMCID: PMC7816165 DOI: 10.1093/jac/dkaa436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- N Pauly
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - J A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - S Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - M Grobbel
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - D Meemken
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
| | - B Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - B-A Tenhagen
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - A Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Vienna, Austria
| | - A Irrgang
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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14
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Deneke C, Uelze L, Brendebach H, Tausch SH, Malorny B. Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST. Front Microbiol 2021; 12:649517. [PMID: 34220740 PMCID: PMC8244591 DOI: 10.3389/fmicb.2021.649517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/25/2021] [Indexed: 02/05/2023] Open
Abstract
Whole-genome sequencing (WGS)-based outbreak investigation has proven to be a valuable method for the surveillance of bacterial pathogens. Its utility has been successfully demonstrated using both gene-by-gene (cgMLST or wgMLST) and single-nucleotide polymorphism (SNP)-based approaches. Among the obstacles of implementing a WGS-based routine surveillance is the need for an exchange of large volumes of sequencing data, as well as a widespread reluctance to share sequence and metadata in public repositories, together with a lacking standardization of suitable bioinformatic tools and workflows. To address these issues, we present chewieSnake, an intuitive and simple-to-use cgMLST workflow. ChewieSnake builds on the allele calling software chewBBACA and extends it by the concept of allele hashing. The resulting hashed allele profiles can be readily compared between laboratories without the need of a central allele nomenclature. The workflow fully automates the computation of the allele distance matrix, cluster membership, and phylogeny and summarizes all important findings in an interactive HTML report. Furthermore, chewieSnake can join allele profiles generated at different laboratories and identify shared clusters, including a stable and intercommunicable cluster nomenclature, thus facilitating a joint outbreak investigation. We demonstrate the feasibility of the proposed approach with a thorough method comparison using publically available sequencing data for Salmonella enterica. However, chewieSnake is readily applicable to all bacterial taxa, provided that a suitable cgMLST scheme is available. The workflow is freely available as an open-source tool and can be easily installed via conda or docker.
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Affiliation(s)
- Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Laura Uelze
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Holger Brendebach
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Simon H Tausch
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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15
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Grützke J, Gwida M, Deneke C, Brendebach H, Projahn M, Schattschneider A, Hofreuter D, El-Ashker M, Malorny B, Al Dahouk S. Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen. Microb Genom 2021; 7. [PMID: 33945456 PMCID: PMC8209726 DOI: 10.1099/mgen.0.000552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Metagenomics is a valuable diagnostic tool for enhancing microbial food safety because (i) it enables the untargeted detection of pathogens, (ii) it is fast since primary isolation of micro-organisms is not required, and (iii) it has high discriminatory power allowing for a detailed molecular characterization of pathogens. For shotgun metagenomics, total nucleic acids (NAs) are isolated from complex samples such as foodstuff. Along with microbial NAs, high amounts of matrix NAs are extracted that might outcompete microbial NAs during next-generation sequencing and compromise sensitivity for the detection of low abundance micro-organisms. Sensitive laboratory methods are indispensable for detecting highly pathogenic foodborne bacteria like Brucella spp., because a low infectious dose is sufficient to cause human disease through the consumption of contaminated dairy or meat products. In our study, we applied shotgun metagenomic sequencing for the identification and characterization of Brucella spp. in artificially and naturally contaminated raw milk from various ruminant species. With the depletion of eukaryotic cells prior to DNA extraction, Brucella was detectable at 10 bacterial cells ml−1, while at the same time microbiological culture and isolation of the fastidious bacteria commonly failed. Moreover, we were able to retrieve the genotype of a Brucella isolate from a metagenomic dataset, indicating the potential of metagenomics for outbreak investigations using SNPs and core-genome multilocus sequence typing (cgMLST). To improve diagnostic applications, we developed a new bioinformatics approach for strain prediction based on SNPs to identify the correct species and define a certain strain with only low numbers of genus-specific reads per sample. This pipeline turned out to be more sensitive and specific than Mash Screen. In raw milk samples, we simultaneously detected numerous other zoonotic pathogens, antimicrobial resistance genes and virulence factors. Our study showed that metagenomics is a highly sensitive tool for biological risk assessment of foodstuffs, particularly when pathogen isolation is hazardous or challenging.
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Affiliation(s)
- Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mayada Gwida
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Holger Brendebach
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Michaela Projahn
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Dirk Hofreuter
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Maged El-Ashker
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Department of Internal Medicine III, RWTH Aachen University Hospital, Aachen, Germany
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16
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Deneke C, Brendebach H, Uelze L, Borowiak M, Malorny B, Tausch SH. Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS. Genes (Basel) 2021; 12:644. [PMID: 33926025 PMCID: PMC8145556 DOI: 10.3390/genes12050644] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/13/2023] Open
Abstract
Sequencing of whole microbial genomes has become a standard procedure for cluster detection, source tracking, outbreak investigation and surveillance of many microorganisms. An increasing number of laboratories are currently in a transition phase from classical methods towards next generation sequencing, generating unprecedented amounts of data. Since the precision of downstream analyses depends significantly on the quality of raw data generated on the sequencing instrument, a comprehensive, meaningful primary quality control is indispensable. Here, we present AQUAMIS, a Snakemake workflow for an extensive quality control and assembly of raw Illumina sequencing data, allowing laboratories to automatize the initial analysis of their microbial whole-genome sequencing data. AQUAMIS performs all steps of primary sequence analysis, consisting of read trimming, read quality control (QC), taxonomic classification, de-novo assembly, reference identification, assembly QC and contamination detection, both on the read and assembly level. The results are visualized in an interactive HTML report including species-specific QC thresholds, allowing non-bioinformaticians to assess the quality of sequencing experiments at a glance. All results are also available as a standard-compliant JSON file, facilitating easy downstream analyses and data exchange. We have applied AQUAMIS to analyze ~13,000 microbial isolates as well as ~1000 in-silico contaminated datasets, proving the workflow's ability to perform in high throughput routine sequencing environments and reliably predict contaminations. We found that intergenus and intragenus contaminations can be detected most accurately using a combination of different QC metrics available within AQUAMIS.
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Affiliation(s)
| | | | | | | | | | - Simon H. Tausch
- Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (C.D.); (H.B.); (L.U.); (M.B.); (B.M.)
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17
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Juraschek K, Borowiak M, Tausch SH, Malorny B, Käsbohrer A, Otani S, Schwarz S, Meemken D, Deneke C, Hammerl JA. Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli. Microorganisms 2021; 9:microorganisms9030598. [PMID: 33799479 PMCID: PMC8000739 DOI: 10.3390/microorganisms9030598] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/01/2023] Open
Abstract
Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing to whole-genome sequence (WGS)-based detection of resistance determinants for a better understanding of the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, transposons). However, the use of WGS data in monitoring purposes requires suitable techniques, standardized parameters and approved guidelines for reliable AMR gene detection and prediction of their association with mobile genetic elements (plasmids). In this study, different sequencing and assembly strategies were tested for their suitability in AMR monitoring in Escherichia coli in the routines of the German National Reference Laboratory for Antimicrobial Resistances. To assess the outcomes of the different approaches, results from in silico predictions were compared with conventional phenotypic- and genotypic-typing data. With the focus on (fluoro)quinolone-resistant E.coli, five qnrS-positive isolates with multiple extrachromosomal elements were subjected to WGS with NextSeq (Illumina), PacBio (Pacific BioSciences) and ONT (Oxford Nanopore) for in depth characterization of the qnrS1-carrying plasmids. Raw reads from short- and long-read sequencing were assembled individually by Unicycler or Flye or a combination of both (hybrid assembly). The generated contigs were subjected to bioinformatics analysis. Based on the generated data, assembly of long-read sequences are error prone and can yield in a loss of small plasmid genomes. In contrast, short-read sequencing was shown to be insufficient for the prediction of a linkage of AMR genes (e.g., qnrS1) to specific plasmid sequences. Furthermore, short-read sequencing failed to detect certain duplications and was unsuitable for genome finishing. Overall, the hybrid assembly led to the most comprehensive typing results, especially in predicting associations of AMR genes and mobile genetic elements. Thus, the use of different sequencing technologies and hybrid assemblies currently represents the best approach for reliable AMR typing and risk assessment.
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Affiliation(s)
- Katharina Juraschek
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Correspondence: (K.J.); (J.A.H.)
| | - Maria Borowiak
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Simon H. Tausch
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Burkhard Malorny
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Annemarie Käsbohrer
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Saria Otani
- DTU Food, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs Lyngby, Denmark;
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Diana Meemken
- Institute of Food Safety and Food Hygiene, Working Group Meat Hygiene, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Carlus Deneke
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Jens Andre Hammerl
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Correspondence: (K.J.); (J.A.H.)
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Uelze L, Becker N, Borowiak M, Busch U, Dangel A, Deneke C, Fischer J, Flieger A, Hepner S, Huber I, Methner U, Linde J, Pietsch M, Simon S, Sing A, Tausch SH, Szabo I, Malorny B. Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany. Front Microbiol 2021; 12:626941. [PMID: 33643254 PMCID: PMC7902525 DOI: 10.3389/fmicb.2021.626941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/21/2021] [Indexed: 02/03/2023] Open
Abstract
Despite extensive monitoring programs and preventative measures, Salmonella spp. continue to cause tens of thousands human infections per year, as well as many regional and international food-borne outbreaks, that are of great importance for public health and cause significant socio-economic costs. In Germany, salmonellosis is the second most common cause of bacterial diarrhea in humans and is associated with high hospitalization rates. Whole-genome sequencing (WGS) combined with data analysis is a high throughput technology with an unprecedented discriminatory power, which is particularly well suited for targeted pathogen monitoring, rapid cluster detection and assignment of possible infection sources. However, an effective implementation of WGS methods for large-scale microbial pathogen detection and surveillance has been hampered by the lack of standardized methods, uniform quality criteria and strategies for data sharing, all of which are essential for a successful interpretation of sequencing data from different sources. To overcome these challenges, the national GenoSalmSurv project aims to establish a working model for an integrated genome-based surveillance system of Salmonella spp. in Germany, based on a decentralized data analysis. Backbone of the model is the harmonization of laboratory procedures and sequencing protocols, the implementation of open-source bioinformatics tools for data analysis at each institution and the establishment of routine practices for cross-sectoral data sharing for a uniform result interpretation. With this model, we present a working solution for cross-sector interpretation of sequencing data from different sources (such as human, veterinarian, food, feed and environmental) and outline how a decentralized data analysis can contribute to a uniform cluster detection and facilitate outbreak investigations.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Natalie Becker
- Department of Food, Feed and Commodities, Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Antje Flieger
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Hepner
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Michael Pietsch
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sandra Simon
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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19
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Kreitlow A, Becker A, Schotte U, Malorny B, Plötz M, Abdulmawjood A. Evaluation of different target genes for the detection of Salmonella sp. by loop-mediated isothermal amplification. Lett Appl Microbiol 2020; 72:420-426. [PMID: 33030743 DOI: 10.1111/lam.13409] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022]
Abstract
The loop-mediated isothermal amplification (LAMP) technique was used to investigate six salmonella-specific sequences for their suitability to serve as targets for the pathogen identification. Sequences selected for designing LAMP primers were genes invA, bcfD, phoP, siiA, gene62181533 and a region within the ttrRSBCA locus. Primers including single nucleotide polymorphisms were configured as degenerate primers. Specificity of the designed primer sets was determined by means of 46 salmonella and 32 other food- and waterborne bacterial reference species and strains. Primers targeting the ttrRSBCA locus showed 100 % inclusivity of target and exclusivity of other test species and strains. Other primer sets revealed deficiencies, especially regarding Salmonella enterica subsp. II-IV and Salmonella bongori. Additionally, primers targeting the siiA gene failed to detect S. enterica subsp. enterica serotypes Newport and Stanley, whereas bcfD primers did not amplify DNA of S. enterica subsp. enterica serotype Schleissheim. TtrRSBCA primers, providing short detection times and constant melting temperatures of amplification products, achieved best overall performance.
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Affiliation(s)
- A Kreitlow
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - A Becker
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - U Schotte
- Department A - Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kronshagen, Germany
| | - B Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - M Plötz
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - A Abdulmawjood
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
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20
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Uelze L, Borowiak M, Bönn M, Brinks E, Deneke C, Hankeln T, Kleta S, Murr L, Stingl K, Szabo K, Tausch SH, Wöhlke A, Malorny B. German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing. Front Microbiol 2020; 11:573972. [PMID: 33013811 PMCID: PMC7516015 DOI: 10.3389/fmicb.2020.573972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/14/2020] [Indexed: 12/05/2022] Open
Abstract
We compared the consistency, accuracy and reproducibility of next-generation short read sequencing between ten laboratories involved in food safety (research institutes, state laboratories, universities and companies) from Germany and Austria. Participants were asked to sequence six DNA samples of three bacterial species (Campylobacter jejuni, Listeria monocytogenes and Salmonella enterica) in duplicate, according to their routine in-house sequencing protocol. Four different types of Illumina sequencing platforms (MiSeq, NextSeq, iSeq, NovaSeq) and one Ion Torrent sequencing instrument (S5) were involved in the study. Sequence quality parameters were determined for all data sets and centrally compared between laboratories. SNP and cgMLST calling were performed to assess the reproducibility of sequence data collected for individual samples. Overall, we found Illumina short read data to be more accurate (higher base calling accuracy, fewer miss-assemblies) and consistent (little variability between independent sequencing runs within a laboratory) than Ion Torrent sequence data, with little variation between the different Illumina instruments. Two laboratories with Illumina instruments submitted sequence data with lower quality, probably due to the use of a library preparation kit, which shows difficulty in sequencing low GC genome regions. Differences in data quality were more evident after assembling short reads into genome assemblies, with Ion Torrent assemblies featuring a great number of allele differences to Illumina assemblies. Clonality of samples was confirmed through SNP calling, which proved to be a more suitable method for an integrated data analysis of Illumina and Ion Torrent data sets in this study.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Markus Bönn
- Landesamt für Verbraucherschutz Sachsen-Anhalt (LAV), Halle (Saale), Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut (MRI), Kiel, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, AG Molecular Genetics and Genome Analysis, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Sylvia Kleta
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Larissa Murr
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - Kerstin Stingl
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Kathrin Szabo
- Department 5, Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Anne Wöhlke
- Food and Veterinary Institute, Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Braunschweig, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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21
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Uelze L, Borowiak M, Deneke C, Szabó I, Fischer J, Tausch SH, Malorny B. Reply to Li et al., "GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently Affect Salmonella Serotype Prediction Using SeqSero2". Appl Environ Microbiol 2020; 86:e01260-20. [PMID: 32680857 PMCID: PMC7480391 DOI: 10.1128/aem.01260-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Laura Uelze
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Carlus Deneke
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - István Szabó
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Jennie Fischer
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Simon H Tausch
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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22
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Sammra O, Foster G, Hassan AA, Alssahen M, Lämmler C, Glaeser SP, Kämpfer P, Busse HJ, Borowiak M, Malorny B, Ritchie CM, Prenger-Berninghoff E, Abdulmawjood A. Arcanobacterium bovis sp. nov., isolated from the milk of a cow with mastitis. Int J Syst Evol Microbiol 2020; 70:4105-4110. [PMID: 32589570 DOI: 10.1099/ijsem.0.004230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic study was performed on an unidentified Arcanobacterium-like Gram-stain-positive bacterium designated strain C605018/01/1T isolated from a milk sample collected from the udder of a cow at post mortem. Comparative 16S rRNA gene sequencing showed that the bacterium belonged to the genus Arcanobacterium and was most closely related to the type strain of Arcanobacterium pluranimalium (99.76 %); sequence similarities to all other Arcanobacterium species were below 97 %. The wet-lab DNA-DNA hybridization values among strain C605018/01/1T and A. pluranimalium DSM 13483ᵀ were low, 16.9 % (reciprocal, 49.8 %). Pertaining to the whole genome sequence with a total length of 2.02 Mb and 1654 protein counts, the novel strain C605018/01/01T displayed a G+C content of 51.6 % mol%. The presence of the major menaquinone MK-9(H4) supported the affiliation of this strain to the genus Arcanobacterium. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol-mannoside and unidentified glycolipid and aminophospholipids. Based on these results it is proposed that strain C605018/01/1T should be classified as representing a novel species, Arcanbacterium bovis sp. nov. The type strain C605018/01/1T (CCUG 45425T=DSM 107286T=BCCM/LMG 30783T).
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Affiliation(s)
- Osama Sammra
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Geoffrey Foster
- SRUC Veterinary Services, An Lochran,10 Inverness Campus,Inverness IV2 5NA, UK
| | - Abdulwahed Ahmed Hassan
- Department of Veterinary Public Health (DVPH), College of Veterinary Medicine, Mosul University, Mosul, Iraq
| | - Mazen Alssahen
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Christoph Lämmler
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), D-10609 Berlin, Department for Biological Safety, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), D-10609 Berlin, Department for Biological Safety, Berlin, Germany
| | | | - Ellen Prenger-Berninghoff
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
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23
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Munck N, Leekitcharoenphon P, Litrup E, Kaas R, Meinen A, Guillier L, Tang Y, Malorny B, Palma F, Borowiak M, Gourmelon M, Simon S, Banerji S, Petrovska L, Dallman TJ, Hald T. Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods. Sci Data 2020; 7:75. [PMID: 32127544 PMCID: PMC7054362 DOI: 10.1038/s41597-020-0417-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/03/2020] [Indexed: 11/22/2022] Open
Abstract
Zoonotic Salmonella causes millions of human salmonellosis infections worldwide each year. Information about the source of the bacteria guides risk managers on control and preventive strategies. Source attribution is the effort to quantify the number of sporadic human cases of a specific illness to specific sources and animal reservoirs. Source attribution methods for Salmonella have so far been based on traditional wet-lab typing methods. With the change to whole genome sequencing there is a need to develop new methods for source attribution based on sequencing data. Four European datasets collected in Denmark (DK), Germany (DE), the United Kingdom (UK) and France (FR) are presented in this descriptor. The datasets contain sequenced samples of Salmonella Typhimurium and its monophasic variants isolated from human, food, animal and the environment. The objective of the datasets was either to attribute the human salmonellosis cases to animal reservoirs or to investigate contamination of the environment by attributing the environmental isolates to different animal reservoirs.
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Affiliation(s)
- Nanna Munck
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Eva Litrup
- Foodborne Infections, Department of Bacteria, Parasites and Fungi, Statens Serum Institute, Copenhagen, Denmark
| | - Rolf Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anika Meinen
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Laurent Guillier
- Université Paris Est, ANSES, Laboratory for Food Safety, F-94701, Maisons-Alfort, France
| | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Federica Palma
- Université Paris Est, ANSES, Laboratory for Food Safety, F-94701, Maisons-Alfort, France
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Michèle Gourmelon
- Ifremer, Environment and Microbiology Laboratory, RBE, SGMM, Plouzané, France
| | - Sandra Simon
- National Reference Center for Salmonella and other bacterial enteric pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sangeeta Banerji
- National Reference Center for Salmonella and other bacterial enteric pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | | | - Tine Hald
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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24
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Golz JC, Epping L, Knüver MT, Borowiak M, Hartkopf F, Deneke C, Malorny B, Semmler T, Stingl K. Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential. Sci Rep 2020; 10:3686. [PMID: 32111893 PMCID: PMC7048796 DOI: 10.1038/s41598-020-60320-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/05/2020] [Indexed: 11/09/2022] Open
Abstract
Campylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter.
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Affiliation(s)
- Julia C Golz
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Lennard Epping
- Robert Koch Institute, Microbial Genomics, Berlin, Germany
| | - Marie-Theres Knüver
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment, Department of Biological Safety, Study Centre for Genome Sequencing and Analysis, Berlin, Germany
| | - Felix Hartkopf
- Robert Koch Institute, Microbial Genomics, Berlin, Germany
| | - Carlus Deneke
- German Federal Institute for Risk Assessment, Department of Biological Safety, Study Centre for Genome Sequencing and Analysis, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment, Department of Biological Safety, Study Centre for Genome Sequencing and Analysis, Berlin, Germany
| | | | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany.
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25
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Alssahen M, Hassan AA, Sammra O, Lämmler C, Saarnisto MR, Borowiak M, Malorny B, Rau J, Prenger-Berninghoff E, Plötz M, Abdulmawjood A. Epidemiological analysis of Arcanobacterium phocae isolated from cases of mink dermatitis of a single farm. Vet Microbiol 2020; 243:108618. [PMID: 32273004 DOI: 10.1016/j.vetmic.2020.108618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 11/17/2022]
Abstract
The present study was designed to identify nine Arcanobacterium phocae strains isolated from cases of mink dermatitis of a single farm in Finland and characterize the strains for epidemiological relationships. All nine strains and previously described A. phocae used for comparative purposes were identified and further characterized phenotypically, by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), by Fourier Transform Infrared Spectroscopy (FT-IR) and genotypically by detection of phocaelysin encoding gene phl with a previously developed loop-mediated isothermal amplification (LAMP) assay and by sequencing 16S rRNA gene and gene phl, the elongation factor tu encoding gene tuf and the β subunit of bacterial RNA polymerase encoding gene rpoB. Genetic relatedness among isolates was determined using whole-genome single nucleotide polymorphism (wgSNP) analysis. The wgSNP results, partly the MALDI-TOF MS and FT-IR analyses and sequencing of the genes, revealed that the nine A. phocae strains recovered from a single farm showed close sequence similarities among each other and differed from previously investigated A. phocae strains isolated from other farms and animals in Finland and from the A. phocae type strain. This indicated a close epidemiological relationship of the A. phocae strains isolated from a single farm and that the nine A. phocae strains of the present study might have developed from a common ancestor.
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Affiliation(s)
- Mazen Alssahen
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Frankfurter Straße 85-91, 35392 Gießen, Germany
| | - Abdulwahed Ahmed Hassan
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Frankfurter Straße 85-91, 35392 Gießen, Germany
| | - Osama Sammra
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Frankfurter Straße 85-91, 35392 Gießen, Germany
| | - Christoph Lämmler
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Frankfurter Straße 85-91, 35392 Gießen, Germany.
| | - Mirja Raunio Saarnisto
- The Research and Laboratory Services Department, Veterinary Bacteriology and Pathology Research Unit, Finnish Food Safety Authority Evira, Keskuskatu 23, 60100 Seinäjoki, Finland
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Max-Dohrn Str. 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Max-Dohrn Str. 8-10, 10589 Berlin, Germany
| | - Jörg Rau
- Chemisches und Veterinäruntersuchungsamt Stuttgart (CVUAS), Schaflandstraße 3/2, 70736 Fellbach, Germany
| | - Ellen Prenger-Berninghoff
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Frankfurter Straße 85-91, 35392 Gießen, Germany
| | - Madelein Plötz
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
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26
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Borowiak M, Baumann B, Fischer J, Thomas K, Deneke C, Hammerl JA, Szabo I, Malorny B. Development of a Novel mcr-6 to mcr-9 Multiplex PCR and Assessment of mcr-1 to mcr-9 Occurrence in Colistin-Resistant Salmonella enterica Isolates From Environment, Feed, Animals and Food (2011-2018) in Germany. Front Microbiol 2020; 11:80. [PMID: 32117115 PMCID: PMC7011100 DOI: 10.3389/fmicb.2020.00080] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/15/2020] [Indexed: 11/15/2022] Open
Abstract
The polymyxin antibiotic colistin has been used in decades for treatment and prevention of infectious diseases in livestock. Nowadays, it is even considered as last-line treatment option for severe human infections caused by multidrug- and carbapenem-resistant Gram-negative bacteria. Therefore, the discovery of plasmid-mediated mobile colistin resistance (mcr) genes raised major public health concern. The aim of our study was to analyze colistin-resistant Salmonella enterica strains from animals, food, feed and the environment collected at the National Reference Laboratory for Salmonella in Germany on the presence of mcr-1 to mcr-9 genes. Altogether 407 colistin-resistant (MIC >2 mg/L) Salmonella isolates received between 2011 and 2018 were selected and screened by PCR using a published mcr-1 to mcr-5 as well as a newly developed mcr-6 to mcr-9 multiplex PCR protocol. 254 of 407 (62.4%) isolates harbored either mcr-1 (n = 175), mcr-4 (n = 53), mcr-5 (n = 18) or mcr-1 and mcr-9 (n = 8). The number of mcr-positive isolates ranged from 19 (2017) to 64 (2012) per year. WGS revealed that none of our isolates harbored the mcr-9.1 gene. Instead, two novel mcr-9 variants were observed, which both were affected by frameshift mutations and are probably non-functional. The mcr-harboring isolates were mainly derived from animals (77.2%) or food (20.1%) and could be assigned to ten different Salmonella serovars. Many of the isolates were multidrug-resistant. Co-occurrence of mcr-1 and AmpC or ESBL genes was observed in eight isolates. Our findings suggest that mcr genes are widely spread among colistin-resistant Salmonella isolates from livestock and food in Germany. Potential transfer of mcr-harboring isolates along the food chain has to be considered critically.
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Affiliation(s)
| | | | | | | | | | | | | | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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Uelze L, Grützke J, Borowiak M, Hammerl JA, Juraschek K, Deneke C, Tausch SH, Malorny B. Typing methods based on whole genome sequencing data. One Health Outlook 2020; 2:3. [PMID: 33829127 PMCID: PMC7993478 DOI: 10.1186/s42522-020-0010-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/08/2020] [Indexed: 05/12/2023]
Abstract
Whole genome sequencing (WGS) of foodborne pathogens has become an effective method for investigating the information contained in the genome sequence of bacterial pathogens. In addition, its highly discriminative power enables the comparison of genetic relatedness between bacteria even on a sub-species level. For this reason, WGS is being implemented worldwide and across sectors (human, veterinary, food, and environment) for the investigation of disease outbreaks, source attribution, and improved risk characterization models. In order to extract relevant information from the large quantity and complex data produced by WGS, a host of bioinformatics tools has been developed, allowing users to analyze and interpret sequencing data, starting from simple gene-searches to complex phylogenetic studies. Depending on the research question, the complexity of the dataset and their bioinformatics skill set, users can choose between a great variety of tools for the analysis of WGS data. In this review, we describe the relevant approaches for phylogenomic studies for outbreak studies and give an overview of selected tools for the characterization of foodborne pathogens based on WGS data. Despite the efforts of the last years, harmonization and standardization of typing tools are still urgently needed to allow for an easy comparison of data between laboratories, moving towards a one health worldwide surveillance system for foodborne pathogens.
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Affiliation(s)
- Laura Uelze
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Josephine Grützke
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Katharina Juraschek
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Simon H. Tausch
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
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Szabo K, Malorny B, Stoyke M. Correction to: Etablierung der § 64 LFGB Arbeitsgruppen „NGS – Bakteriencharakterisierung“ und „NGS – Speziesidentifizierung“. J Verbrauch Lebensm 2019. [DOI: 10.1007/s00003-019-01262-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The article Etablierung
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Malorny B, Ribeiro Duarte AS, Torpdahl M, da Silva Felício MT, Guerra B, Rossi M, Herman L. Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms. EFSA J 2019; 17:e05898. [PMID: 32626197 PMCID: PMC7008917 DOI: 10.2903/j.efsa.2019.5898] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.
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Malorny B, Cook N, D'Agostino M, De Medici D, Croci L, Abdulmawjood A, Fach P, Karpiskova R, Aymerich T, Kwaitek K, Kuchta T, Hoorfar J. Multicenter Validation of PCR-Based Method for Detection of Salmonella in Chicken and Pig Samples. J AOAC Int 2019. [DOI: 10.1093/jaoac/87.4.861] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
As part of a standardization project, an interlaboratory trial including 15 laboratories from 13 European countries was conducted to evaluate the performance of a noproprietary polymerase chain reaction (PCR)-based method for the detection of Salmonella on artificially contaminated chicken rinse and pig swab samples. The 3 levels were 1–10, 10–100, and 100–1000 colony-forming units (CFU)/100 mL. Sample preparations, including inoculation and pre-enrichment in buffered peptone water (BPW), were performed centrally in a German laboratory; the pre-PCR sample preparation (by a resin-based method) and PCR assay (gel electrophoresis detection) were performed by the receiving laboratories. Aliquots of BPW enrichment cultures were sent to the participants, who analyzed them using a thermal lysis procedure followed by a validated Salmonella-specific PCR assay. The results were reported as negative or positive. Outlier results caused, for example, by gross departures from the experimental protocol, were omitted from the analysis. For both the chicken rinse and the pig swab samples, the diagnostic sensitivity was 100%, with 100% accordance (repeatability) and concordance (reproducibility). The diagnostic specificity was 80.1% (with 85.7% accordance and 67.5% concordance) for chicken rinse, and 91.7% (with 100% accordance and 83.3% concordance) for pig swab. Thus, the interlaboratory variation due to personnel, reagents, thermal cyclers, etc., did not affect the performance of the method, which will be proposed as part of a developing international PCR standard.
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Affiliation(s)
- Burkhard Malorny
- Federal Institute for Risk Assessment, National Salmonella Reference Laboratory, Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Nigel Cook
- DEFRA Central Science Laboratory, Sand Hutton, Y0411LZ York, United Kingdom
| | - Martin D'Agostino
- DEFRA Central Science Laboratory, Sand Hutton, Y0411LZ York, United Kingdom
| | - Dario De Medici
- Istituto Superiore di Sanità, Viale Regina Elena No. 299, 00161 Rome, Italy
| | - Luciana Croci
- Istituto Superiore di Sanità, Viale Regina Elena No. 299, 00161 Rome, Italy
| | - Amir Abdulmawjood
- Institute of Veterinary Food Science, Justus-Liebig University Giessen, Frankfurter Str. 92, D-35392 Giessen, Germany
| | - Patrick Fach
- Agence Française de Sécurité Sanitaire des Aliments, 1 à 5 rue de Belfort, 94700 Maisons Alfort, France
| | - Renata Karpiskova
- National Institute of Public Health, Centre for Food Chain Hygiene, Palackeho 1-3, 61242 Brno, Czech Republic
| | - Teresa Aymerich
- Institute for Food and Agricultural Research and Technology, Granja Camps I Armet S/N, 17121 Monells, Spain
| | - Krysztof Kwaitek
- National Veterinary Research Institute, Partyzanow 57, 24-100 Pulawy, Poland
| | - Tomas Kuchta
- Food Research Institute, Priemyselna 4, SK-82475 Bratislava, Slovakia
| | - Jeffrey Hoorfar
- Danish Institute for Food and Veterinary Research, 27 Bülowsvej, DK-1790 Copenhagen V, Denmark
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Abdulmawjood A, Bülte M, Roth S, Schönenbrücher H, Cook N, D’Agostino M, Malorny B, Jordan K, Pelkonen S, Hoorfar J. Toward an International Standard for PCR-Based Detection of Foodborne Escherichia coli O157: Validation of the PCR-Based Method in a Multicenter Interlaboratory Trial. J AOAC Int 2019. [DOI: 10.1093/jaoac/87.4.856] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The performance of a polymerase chain reaction (PCR) method for detection of Escherichia coli O157, previously validated on DNA extracted from pure cultures, was evaluated on spiked cattle swabs through an interlaboratory trial, including 12 participating laboratories from 11 European countries. Twelve cattle swab samples, spiked at 4 levels (0, 1–10, 10–100, and 100–1000 colony-forming units, in triplicate) with E. coli O157 were prepared centrally in the originating laboratory; the receiving laboratories performed pre-PCR treatment followed by PCR. The results were reported as positive when the correct amplicons were present after gel electrophoresis. The statistical analysis, performed on 10 sets of reported results, determined the diagnostic sensitivity to be 92.2%. The diagnostic specificity was 100%. The accordance (repeatability) was 90.0%, calculated from all positive inoculation levels. The concordance (reproducibility) was 85.0%, calculated from all positive inoculation levels. The concordance odds ratio (degree of interlaboratory variation calculated from all positive inoculation levels) was 1.58, indicating the robustness of the PCR method. Thus, the interlaboratory variation due to personnel, reagents, minor temperature or pH fluctuations and, not least, thermal cyclers, did not affect the performance of the method, which is currently being considered as part of an international PCR standard.
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Affiliation(s)
- Amir Abdulmawjood
- Institute of Veterinary Food Science, Frankfurter str.92, 35392 Giessen, Germany
| | - Michael Bülte
- Institute of Veterinary Food Science, Frankfurter str.92, 35392 Giessen, Germany
| | - Stefanie Roth
- Institute of Veterinary Food Science, Frankfurter str.92, 35392 Giessen, Germany
| | - Hahn Schönenbrücher
- Institute of Veterinary Food Science, Frankfurter str.92, 35392 Giessen, Germany
| | - Nigel Cook
- DEFRA Central Science Laboratory, Sand Hutton, YO41 1LZ York, United Kingdom
| | - Martin D’Agostino
- DEFRA Central Science Laboratory, Sand Hutton, YO41 1LZ York, United Kingdom
| | - Burkhard Malorny
- Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Kieran Jordan
- Dairy Product Research Center, Moorepark, Fermoy, County Cork, Ireland
| | - Sinikka Pelkonen
- National Veterinary and Food Research Institute, Neulaniementie 4, Kuopio, Finland
| | - Jeffrey Hoorfar
- Danish Food and Veterinary Research Institute, 27 Bülowsvej, DK-1790 Copenhagen V, Denmark
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Uelze L, Borowiak M, Deneke C, Jacobs C, Szabó I, Tausch SH, Malorny B. First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep. Gut Pathog 2019; 11:48. [PMID: 31636715 PMCID: PMC6791114 DOI: 10.1186/s13099-019-0330-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s). Results We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation. Conclusions With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.
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Affiliation(s)
- Laura Uelze
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Cécile Jacobs
- Landeslabor Schleswig-Holstein, Max-Eyth-Straße 5, 24537 Neumünster, Germany
| | - István Szabó
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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Meinen A, Simon S, Banerji S, Szabo I, Malorny B, Borowiak M, Hadziabdic S, Becker N, Luber P, Lohr D, Harms C, Plenge-Bönig A, Mellou K, Mandilara G, Mossong J, Ragimbeau C, Weicherding P, Hau P, Dědičová D, Šafaříková L, Nair S, Dallman TJ, Larkin L, McCormick J, De Pinna E, Severi E, Kotila S, Niskanen T, Rizzi V, Deserio D, Flieger A, Stark K. Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017. Euro Surveill 2019; 24:1800543. [PMID: 31507266 PMCID: PMC6737830 DOI: 10.2807/1560-7917.es.2019.24.36.1800543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/29/2019] [Indexed: 11/20/2022] Open
Abstract
In spring 2016, Greece reported an outbreak caused by a previously undescribed Salmonella enterica subsp. enterica serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presumptive vehicle. Subsequently, Germany, Czech Republic, Luxembourg and the United Kingdom (UK) reported infections with this novel serotype via EPIS-FWD. Concerned countries in collaboration with the European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA) adopted a common outbreak case definition. An outbreak case was defined as a laboratory-confirmed notification of the novel Salmonella serotype. Between March 2016 and April 2017, 47 outbreak cases were notified (Greece: n = 22; Germany: n = 13; Czech Republic: n = 5; Luxembourg: n = 4; UK: n = 3). Whole genome sequencing revealed the very close genetic relatedness of isolates from all affected countries. Interviews focusing on sesame product consumption, suspicious food item testing and trace-back analysis following Salmonella spp. detection in food products identified a company in Greece where sesame seeds from different countries were processed. Through European collaboration, it was possible to identify and recall sesame spread as one contaminated food item serving as vehicle of infection and trace it back to its origin.
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Affiliation(s)
- Anika Meinen
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
- These authors contributed equally
| | - Sandra Simon
- These authors contributed equally
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Sangeeta Banerji
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Istvan Szabo
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Sead Hadziabdic
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Natalie Becker
- Federal Office of Consumer Protection and Food Safety, Crisis Unit Office, Foodborne Outbreaks, Prevention, Berlin, Germany
| | - Petra Luber
- Federal Office of Consumer Protection and Food Safety, Crisis Unit Office, Foodborne Outbreaks, Prevention, Berlin, Germany
| | - Dorothee Lohr
- Baden-Wuerttemberg State Health Office, Stuttgart, Germany
| | - Carolin Harms
- Institute for Hygiene and Environment Hamburg, Department of Microbiology, Hamburg, Germany
| | - Anita Plenge-Bönig
- Institute for Hygiene and Environment Hamburg, Infectious Disease Surveillance Unit, Hamburg, Germany
| | - Kassiani Mellou
- Hellenic National Public Health Organization, Athens, Greece
| | - Georgia Mandilara
- National School of Public Health, National Reference Centre for Salmonella, Athens, Greece
| | - Joël Mossong
- Laboratoire National de Santé, Département de Microbiologie, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Département de Microbiologie, Dudelange, Luxembourg
| | | | - Patrick Hau
- Direction de la Santé, Luxembourg, Luxembourg
| | - Daniela Dědičová
- Státní zdravotní ústav (National Institute of Public Health), Prague, Czech Republic
| | - Lucie Šafaříková
- Státní zdravotní ústav (National Institute of Public Health), Prague, Czech Republic
| | | | | | | | | | | | - Ettore Severi
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | - Saara Kotila
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | - Taina Niskanen
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | | | | | - Antje Flieger
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Klaus Stark
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
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Grützke J, Malorny B, Hammerl JA, Busch A, Tausch SH, Tomaso H, Deneke C. Fishing in the Soup - Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing. Front Microbiol 2019; 10:1805. [PMID: 31447815 PMCID: PMC6691356 DOI: 10.3389/fmicb.2019.01805] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/22/2019] [Indexed: 01/22/2023] Open
Abstract
In food safety the detection of food contaminations with pathogenic microorganisms is a race against time and often outpaced by error-prone epidemiological approaches. For evidence-based outbreak investigations fast and reliable techniques and procedures are required to identify the source of infection. Metagenomics has the potential to become a powerful tool in the field of modern food safety, since it allows the detection, identification and characterization of a broad range of pathogens in a single experiment without pre-cultivation within a couple of days. Nevertheless, sample handling, sequencing and data analysis are challenging and can introduce errors and biases into the analysis. In order to evaluate the potential of metagenomics in food safety, we generated a mock community containing DNA of foodborne bacteria. Herewith, we compare the aptitude of the two prevalent approaches - 16S rDNA amplicon sequencing and whole genome shotgun sequencing - for the detection of foodborne bacteria using different parameters during sample preparation, sequencing and data analysis. 16S rDNA sequencing did not only result in high deviations from the expected sample composition on genus and species level, but more importantly lacked the detection of several pathogenic species. While shotgun sequencing is more suitable for species detection, abundance estimation, genome assembly and species characterization, the performance can vary depending on the library preparation kit, which was confirmed for a naturally Francisella tularensis contaminated game meat sample. The application of the Nextera XT DNA Library Preparation Kit for shotgun sequencing did not only result in lower reference genome recovery and coverage, but also in distortions of the mock community composition. For data analysis, we propose a publicly available workflow for pathogen detection and characterization and demonstrate its benefits on the usability of metagenomic sequencing in food safety by analyzing an authentic metagenomic sample.
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Affiliation(s)
- Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens Andre Hammerl
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anne Busch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Hammerl JA, Borowiak M, Schmoger S, Shamoun D, Grobbel M, Malorny B, Tenhagen BA, Käsbohrer A. mcr-5 and a novel mcr-5.2 variant in Escherichia coli isolates from food and food-producing animals, Germany, 2010 to 2017. J Antimicrob Chemother 2019; 73:1433-1435. [PMID: 29444245 DOI: 10.1093/jac/dky020] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jens A Hammerl
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Silvia Schmoger
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Dina Shamoun
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Mirjam Grobbel
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Bernd-Alois Tenhagen
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Annemarie Käsbohrer
- German Federal Institute for Risk Assessment, Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany.,Institute for Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
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Roschanski N, Hadziabdic S, Borowiak M, Malorny B, Tenhagen BA, Projahn M, Kaesbohrer A, Guenther S, Szabo I, Roesler U, Fischer J. Detection of VIM-1-Producing Enterobacter cloacae and Salmonella enterica Serovars Infantis and Goldcoast at a Breeding Pig Farm in Germany in 2017 and Their Molecular Relationship to Former VIM-1-Producing S. Infantis Isolates in German Livestock Production. mSphere 2019; 4:e00089-19. [PMID: 31189558 PMCID: PMC6563352 DOI: 10.1128/msphere.00089-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/23/2019] [Indexed: 01/30/2023] Open
Abstract
In 2011, VIM-1-producing Salmonella enterica serovar Infantis and Escherichia coli were isolated for the first time in four German livestock farms. In 2015/2016, highly related isolates were identified in German pig production. This raised the issue of potential reservoirs for these isolates, the relation of their mobile genetic elements, and potential links between the different affected farms/facilities. In a piglet-producing farm suspicious for being linked to some blaVIM-1 findings in Germany, fecal and environmental samples were examined for the presence of carbapenemase-producing Enterobacteriaceae and Salmonella spp. Newly discovered isolates were subjected to Illumina whole-genome sequencing (WGS) and S1 pulsed-field gel electrophoresis (PFGE) hybridization experiments. WGS data of these isolates were compared with those for the previously isolated VIM-1-producing Salmonella Infantis isolates from pigs and poultry. Among 103 samples, one Salmonella Goldcoast isolate, one Salmonella Infantis isolate, and one Enterobacter cloacae isolate carrying the blaVIM-1 gene were detected. Comparative WGS analysis revealed that the blaVIM-1 gene was part of a particular Tn21-like transposable element in all isolates. It was located on IncHI2 (ST1) plasmids of ∼290 to 300 kb with a backbone highly similar (98 to 100%) to that of reference pSE15-SA01028. SNP analysis revealed a close relationship of all VIM-1-positive S Infantis isolates described since 2011. The findings of this study demonstrate that the occurrence of the blaVIM-1 gene in German livestock is restricted neither to a certain bacterial species nor to a certain Salmonella serovar but is linked to a particular Tn21-like transposable element located on transferable pSE15-SA01028-like IncHI2 (ST1) plasmids, being present in all of the investigated isolates from 2011 to 2017.IMPORTANCE Carbapenems are considered one of few remaining treatment options against multidrug-resistant Gram-negative pathogens in human clinical settings. The occurrence of carbapenemase-producing Enterobacteriaceae in livestock and food is a major public health concern. Particularly the occurrence of VIM-1-producing Salmonella Infantis in livestock farms is worrisome, as this zoonotic pathogen is one of the main causes for human salmonellosis in Europe. Investigations on the epidemiology of those carbapenemase-producing isolates and associated mobile genetic elements through an in-depth molecular characterization are indispensable to understand the transmission of carbapenemase-producing Enterobacteriaceae along the food chain and between different populations to develop strategies to prevent their further spread.
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Affiliation(s)
- Nicole Roschanski
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Sead Hadziabdic
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Michaela Projahn
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Annemarie Kaesbohrer
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
- Institute of Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Sebastian Guenther
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Istvan Szabo
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
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Rebelo AR, Bortolaia V, Kjeldgaard JS, Pedersen SK, Leekitcharoenphon P, Hansen IM, Guerra B, Malorny B, Borowiak M, Hammerl JA, Battisti A, Franco A, Alba P, Perrin-Guyomard A, Granier SA, De Frutos Escobar C, Malhotra-Kumar S, Villa L, Carattoli A, Hendriksen RS. Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes. ACTA ACUST UNITED AC 2019; 23. [PMID: 29439754 PMCID: PMC5824125 DOI: 10.2807/1560-7917.es.2018.23.6.17-00672] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background and aimPlasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.3, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing.
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Affiliation(s)
- Ana Rita Rebelo
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Jette S Kjeldgaard
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Susanne K Pedersen
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Inge M Hansen
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | | | | | - Maria Borowiak
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Antonio Battisti
- National Reference Laboratory for antimicrobial resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | - Alessia Franco
- National Reference Laboratory for antimicrobial resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | - Patricia Alba
- National Reference Laboratory for antimicrobial resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | | | - Sophie A Granier
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | | | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
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Borowiak M, Szabo I, Baumann B, Junker E, Hammerl JA, Kaesbohrer A, Malorny B, Fischer J. VIM-1-producing Salmonella Infantis isolated from swine and minced pork meat in Germany. J Antimicrob Chemother 2018; 72:2131-2133. [PMID: 28369508 DOI: 10.1093/jac/dkx101] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Istvan Szabo
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Beatrice Baumann
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Ernst Junker
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Jens A Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Annemarie Kaesbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Jennie Fischer
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
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39
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Borowiak M, Fischer J, Hammerl JA, Hendriksen RS, Szabo I, Malorny B. Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B. J Antimicrob Chemother 2018; 72:3317-3324. [PMID: 28962028 DOI: 10.1093/jac/dkx327] [Citation(s) in RCA: 357] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/04/2017] [Indexed: 01/17/2023] Open
Abstract
Objectives Plasmid-mediated mobilized colistin resistance is currently known to be caused by phosphoethanolamine transferases termed MCR-1, MCR-2, MCR-3 and MCR-4. However, this study focuses on the dissection of a novel resistance mechanism in mcr-1-, mcr-2- and mcr-3-negative d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B (Salmonella Paratyphi B dTa+) isolates with colistin MIC values >2 mg/L. Methods A selected isolate from the strain collection of the German National Reference Laboratory for Salmonella was investigated by WGS and bioinformatical analysis to identify novel phosphoethanolamine transferase genes involved in colistin resistance. Subsequently PCR screening, S1-PFGE and DNA-DNA hybridization were performed to analyse the prevalence and location of the identified mcr-5 gene. Cloning and transformation experiments in Escherichia coli DH5α and Salmonella Paratyphi B dTa+ control strains were carried out and the activity of MCR-5 was determined in vitro by MIC testing. Results In this study, we identified a novel phosphoethanolamine transferase in 14 mcr-1-, mcr-2- and mcr-3-negative Salmonella Paratyphi B dTa+ isolates with colistin MIC values >2 mg/L that were received during 2011-13. The respective gene, further termed as mcr-5 (1644 bp), is part of a 7337 bp transposon of the Tn3 family and usually located on related multi-copy ColE-type plasmids. Interestingly, in one isolate an additional subclone with a chromosomal location of the mcr-5 transposon was observed. Conclusions Our findings suggest that the transfer of colistin-resistance-mediating phosphoethanolamine transferase genes from bacterial chromosomes to mobile genetic elements has occurred in multiple independent events raising concern regarding their variety, prevalence and impact on public health.
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Affiliation(s)
- Maria Borowiak
- German Federal Institute for Risk Assessment, BfR, Department for Biological Safety, Berlin, Germany
| | - Jennie Fischer
- German Federal Institute for Risk Assessment, BfR, Department for Biological Safety, Berlin, Germany
| | - Jens A Hammerl
- German Federal Institute for Risk Assessment, BfR, Department for Biological Safety, Berlin, Germany
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kgs Lyngby, Denmark
| | - Istvan Szabo
- German Federal Institute for Risk Assessment, BfR, Department for Biological Safety, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment, BfR, Department for Biological Safety, Berlin, Germany
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40
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Hadziabdic S, Borowiak M, Bloch A, Malorny B, Szabo I, Guerra B, Kaesbohrer A, Fischer J. Complete Genome Sequence of an Avian Native NDM-1-Producing Salmonella enterica subsp. enterica Serovar Corvallis Strain. Genome Announc 2018; 6:e00593-18. [PMID: 29954902 PMCID: PMC6025930 DOI: 10.1128/genomea.00593-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/20/2022]
Abstract
Carbapenems are an important class of β-lactams and one of the last options for treating severe human infections. We present here the complete genome sequence of avian native carbapenemase-producing Salmonella enterica subsp. enterica serovar Corvallis strain 12-01738, harboring a blaNDM-1-carrying IncA/C2 plasmid, isolated in 2012 from a wild bird (Milvus migrans) in Germany.
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Affiliation(s)
- Sead Hadziabdic
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Angelina Bloch
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Istvan Szabo
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Annemarie Kaesbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Jennie Fischer
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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41
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Kleta S, Hammerl JA, Dieckmann R, Malorny B, Borowiak M, Halbedel S, Prager R, Trost E, Flieger A, Wilking H, Vygen-Bonnet S, Busch U, Messelhäußer U, Horlacher S, Schönberger K, Lohr D, Aichinger E, Luber P, Hensel A, Al Dahouk S. Molecular Tracing to Find Source of Protracted Invasive Listeriosis Outbreak, Southern Germany, 2012-2016. Emerg Infect Dis 2018; 23:1680-1683. [PMID: 28930013 PMCID: PMC5621528 DOI: 10.3201/eid2310.161623] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We investigated 543 Listeria monocytogenes isolates from food having a temporal and spatial distribution compatible with that of the invasive listeriosis outbreak occurring 2012–2016 in southern Germany. Using forensic microbiology, we identified several products from 1 manufacturer contaminated with the outbreak genotype. Continuous molecular surveillance of food isolates could prevent such outbreaks.
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42
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Leekitcharoenphon P, Garcia‐Graells C, Botteldoorn N, Dierick K, Kempf I, Olkkola S, Rossi M, Nykäsenoja S, Malorny B, Stingl K, Battisti A, Franco A, Mossong J, Veldman K, Mevius D, Wasyl D, Wieczorek K, Osek J, Clemente L, Lacatus A, Nicorescu I, García MA, Escobar CDF, Ferrer MD, Ugarte‐Ruiz M, Anjum MF, Teale C, Ågren J, Hendriksen RS, Aarestrup FM. Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP). ACTA ACUST UNITED AC 2018. [DOI: 10.2903/sp.efsa.2018.en-1398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pimlapas Leekitcharoenphon
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
| | | | - Nadine Botteldoorn
- Institut Scientifique Santé Publique (WIV‐ISP) Faculty of Veterinary University of Zaragoza
| | - Katelijne Dierick
- Institut Scientifique Santé Publique (WIV‐ISP) Faculty of Veterinary University of Zaragoza
| | | | - Satu Olkkola
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | - Mirko Rossi
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | - Suvi Nykäsenoja
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | | | - Kerstin Stingl
- NRL for the Analysis and Testing of Zoonoses (Salmonella)
| | - Antonio Battisti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana Italy
| | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana Italy
| | | | - Kees Veldman
- Central Veterinary Institute (CVI) part of Wageningen UR The Netherlands
| | - Dik Mevius
- Central Veterinary Institute (CVI) part of Wageningen UR The Netherlands
| | | | | | - Jacek Osek
- National Veterinary Research Institute Poland
| | - Lurdes Clemente
- INIAV ‐ National Institute for Agrarian and Veterinary Research Microbiology and Mycology Laboratory Portugal
| | - Angela Lacatus
- Institute for Hygiene and Veterinary Public Health Romania
| | | | | | | | | | - María Ugarte‐Ruiz
- VISAVET Health Surveillance Centre Universidad Complutense Madrid Spain
| | | | | | | | - Rene S. Hendriksen
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
| | - Frank M. Aarestrup
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
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Hadziabdic S, Fischer J, Malorny B, Borowiak M, Guerra B, Kaesbohrer A, Gonzalez-Zorn B, Szabo I. In Vivo Transfer and Microevolution of Avian Native IncA/C 2blaNDM-1-Carrying Plasmid pRH-1238 during a Broiler Chicken Infection Study. Antimicrob Agents Chemother 2018; 62:e02128-17. [PMID: 29437622 PMCID: PMC5913973 DOI: 10.1128/aac.02128-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/29/2018] [Indexed: 12/13/2022] Open
Abstract
The emergence and spread of carbapenemase-producing Enterobacteriaceae (CPE) in wildlife and livestock animals pose an important safety concern for public health. With our in vivo broiler chicken infection study, we investigated the transfer and experimental microevolution of the blaNDM-1-carrying IncA/C2 plasmid (pRH-1238) introduced by avian native Salmonella enterica subsp. enterica serovar Corvallis without inducing antibiotic selection pressure. We evaluated the dependency of the time point of inoculation on donor (S Corvallis [12-SA01738]) and plasmid-free Salmonella recipient [d-tartrate-fermenting (d-Ta+) S Paratyphi B (13-SA01617), referred to here as S Paratyphi B (d-Ta+)] excretion by quantifying their excretion dynamics. Using plasmid profiling by S1 nuclease-restricted pulsed-field gel electrophoresis, we gained insight into the variability of the native plasmid content among S Corvallis reisolates as well as plasmid acquisition in S Paratyphi B (d-Ta+) and the enterobacterial gut microflora. Whole-genome sequencing enabled us to gain an in-depth insight into the microevolution of plasmid pRH-1238 in S Corvallis and enterobacterial recipient isolates. Our study revealed that the fecal excretion of avian native carbapenemase-producing S Corvallis is significantly higher than that of S Paratyphi (d-Ta+) and is not hampered by S Paratyphi (d-Ta+). Acquisition of pRH-1238 in other Enterobacteriaceae and several events of plasmid pRH-1238 transfer to different Escherichia coli sequence types and Klebsiella pneumoniae demonstrated an interspecies broad host range. Regardless of the microevolutionary structural deletions in pRH-1238, the single carbapenem resistance marker blaNDM-1 was maintained on pRH-1238 throughout the trial. Furthermore, we showed the importance of the gut E. coli population as a vector of pRH-1238. In a potential scenario of the introduction of NDM-1-producing S Corvallis into a broiler flock, the pRH-1238 plasmid could persist and spread to a broad host range even in the absence of antibiotic pressure.
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Affiliation(s)
- Sead Hadziabdic
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Jennie Fischer
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Beatriz Guerra
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Annemarie Kaesbohrer
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Bruno Gonzalez-Zorn
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Istvan Szabo
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
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Szabo I, Grafe M, Kemper N, Junker E, Malorny B. Genetic basis for loss of immuno-reactive O-chain in Salmonella enterica serovar Enteritidis veterinary isolates. Vet Microbiol 2017; 204:165-173. [PMID: 28532797 DOI: 10.1016/j.vetmic.2017.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 11/25/2022]
Abstract
Fifty-two rough Salmonella enterica serovar Enteritidis (S. Enteritidis) isolates from broilers and the environment were characterized for their serological and genotypic properties. Under routine diagnostic serotyping methods such isolates lack the immuno-reactivity of the O-chain of the lipopolysaccharide (LPS), and are referred to as non-typeable. Using a modified slide agglutination method, the isolates could be differentiated into three different serological variants. Twenty-six isolates (50%) were defined as semi-rough, nineteen isolates (37%) as deep-rough, four isolates (8%) as rough and three isolates could not be assigned. Genetically, all semi-rough isolates lacked the wzyB gene encoding the O-antigen polymerase. Two isolates carried a frameshift mutation in wzyB. In 15 of 23 cases deep-rough or rough isolates had a single point mutation, a single - or double-nucleotide insert or deletion in the wbaP gene. The mutational changes lead to expression of truncated (premature) protein, resulting in the loss of the immuno-reactive O-chain. Both rough and smooth S. Enteritidis isolates showed identical or highly similar XbaI-PFGE profiles. Our results indicate that the loss of a functional LPS in S. Enteritidis isolates is caused by a variety of different mutation events within the wzyB (semi-rough) or the wbaP (deep-rough) gene and is not a result of a vertical spread of a specific S. Enteritidis subtype. The defect of the LPS may be a common evolutionary mechanism through which host defence can be escaped.
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Affiliation(s)
- Istvan Szabo
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany.
| | - Marianne Grafe
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany; University of Potsdam, Am Neuen Palais 10, D-14469 Potsdam, Germany
| | - Nicole Kemper
- University of Veterinary Medicine Hannover, Foundation, Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Ernst Junker
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany
| | - Burkhard Malorny
- Federal Institute for Risk Assessment, Department for Biological Safety, National Reference Laboratory for Salmonella, Max-Dohrn-Str 8-10, D-10589 Berlin, Germany
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45
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García P, Malorny B, Rodicio MR, Stephan R, Hächler H, Guerra B, Lucarelli C. Horizontal Acquisition of a Multidrug-Resistance Module (R-type ASSuT) Is Responsible for the Monophasic Phenotype in a Widespread Clone of Salmonella Serovar 4,[5],12:i:. Front Microbiol 2016; 7:680. [PMID: 27242707 PMCID: PMC4861720 DOI: 10.3389/fmicb.2016.00680] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/26/2016] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium incapable of expressing the second-phase flagellar antigen (fljAB operon), and it is recognized to be one of the most prevalent serovars causing human infections. A clonal lineage characterized by phage type DT193, PulseNet PFGE profile STYMXB.0131 and multidrug resistance to ampicillin, streptomycin, sulphonamides and tetracycline (R-type ASSuT) is commonly circulating in Europe. In this study we determined the deletions affecting the fljAB operon and the resistance region responsible for the R-type ASSuT in a strain of Salmonella enterica serovar 4,5,12:i:- DT193/STYMXB.0131, through an approach based on PCRs and Southern blot hybridization of genomic DNA. Using a set of nine specific PCRs, the prevalence of the resistance region was assessed in a collection of 144 S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains isolated from Germany, Switzerland and Italy. A 28 kb-region is embedded between the loci STM2759 and iroB, replacing the DNA located in between, including the fljAB operon. It encompasses the genes bla TEM-1, strA-strB, sul2 and tet(B) responsible for the R-type ASSuT together with genes involved in plasmid replication and orfs of unknown function characteristically located on IncH1 plasmids. Its location and internal structure is fairly conserved in S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains regardless of the isolation source or country. Hence, in the S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 clonal lineage widespread in Germany, Switzerland and Italy, a resistance region derived from IncH1 plasmids has replaced the chromosomal region encoding the second flagellar phase and is an example of the stabilization of new plasmid-derived genetic material due to integration into the bacterial chromosome.
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Affiliation(s)
- Patricia García
- Department of Functional Biology, Area of Microbiology, University of OviedoOviedo, Spain
| | - Burkhard Malorny
- Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
| | - M. Rosario Rodicio
- Department of Functional Biology, Area of Microbiology, University of OviedoOviedo, Spain
| | - Roger Stephan
- Vetsuisse Faculty, National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of ZurichZürich, Switzerland
| | - Herbert Hächler
- Vetsuisse Faculty, National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of ZurichZürich, Switzerland
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
| | - Claudia Lucarelli
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di SanitàRome, Italy
- European Public Health Microbiology Training Programme, European Centre for Disease Prevention and ControlStockholm, Sweden
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Maurischat S, Szabo I, Baumann B, Malorny B. Rapid real-time PCR methods to distinguish Salmonella Enteritidis wildtype field isolates from vaccine strains Salmovac SE/Gallivac SE and AviPro SALMONELLA VAC E. J Microbiol Methods 2015; 112:92-8. [DOI: 10.1016/j.mimet.2015.03.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 03/16/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
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Maurischat S, Rossow M, Ellerbroek L, Pichner R, Malorny B. [Salmonella spp. prevalence and contamination risk factors in broiler and broiler meat of Gallus gallus in Germany and the European Union]. Berl Munch Tierarztl Wochenschr 2015; 128:3-13. [PMID: 25876278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In order to reduce the prevalence of the Salmonella enterica serovars Typhimurium and Enteritidis as a main causative agent of human salmonellosis originating from poultry flocks and products, the EU regulations 2160/2003 and 2073/2005 and the German Hühner-Salmonellen-Verordnung were established ten years ago. A literature review shows that this aim could be reached to a large extend in many areas of the food production chain, e.g. in breeding and husbandry facilities in most EU member states including Germany. Nevertheless some exceptions exist, and there are other S. enterica serovars which have a human pathogenic potential comparable to S. Typhimurium and S. Enteritidis. Furthermore recent publications show, that especially processes in transport and slaughter of poultry can prevent successful husbandry sanitation measures. Especially in these areas a reasonable potential for hygiene improvements still exists. Based on the prevalence data obtained between 1996 and 2011 this review summarizes recent knowledge concerning possible risks of Salmonella cross contamination and suggests potential starting points for their mitigation.
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Toboldt A, Tietze E, Helmuth R, Junker E, Fruth A, Malorny B. Molecular epidemiology of Salmonella enterica serovar Kottbus isolated in Germany from humans, food and animals. Vet Microbiol 2014; 170:97-108. [PMID: 24559660 DOI: 10.1016/j.vetmic.2014.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/15/2014] [Accepted: 01/23/2014] [Indexed: 11/18/2022]
Abstract
Salmonella enterica serovar Kottbus has been continuously isolated from poultry and poultry meat, especially from turkey. We investigated by comparative molecular typing 95 S. Kottbus isolates obtained in Germany between 2000 and 2011 from poultry/poultry meat, pig/pork, cattle, reptiles, the environment as well as from human cases to identify potential infection sources for humans, especially the role of poultry and poultry products as vehicle in transmission of S. Kottbus isolates to humans. Multilocus sequence typing analysis detected three main genetic lineages. Most human isolates belonged to lineage 1 represented by sequence types ST212 and ST808. Part of the isolates isolated from cattle and pork were also linked to this lineage. Nevertheless, human isolates and especially isolates from poultry/poultry meat, and with less extend from other livestock, grouped in lineage 2 represented by ST582. Four additional isolates from reptiles and humans belonging to ST1669 represented the third lineage. The three lineages were also reflected by pulsed-field gel electrophoresis typing data and DNA microarray analysis of 102 pathogenicity genes. Antimicrobial resistance especially to nalidixic acid and ciprofloxacin was predominantly observed in isolates assigned to lineage 2, which contains predominantly resistant isolates compared to lineage 1 and 3. Sequencing of the quinolone resistance-determining region of gyrA revealed a point mutation in codon 83 or 87 responsible for nalidixic acid resistance and MIC values for ciprofloxacin between 0.125 and 0.25mg/l. Overall, this study showed that in Germany a specific S. Kottbus lineage (ST582), which is well-established in poultry, can be transmitted to humans by poultry meat and, consequently, poses a risk for human health.
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Affiliation(s)
- Anne Toboldt
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany; Free University Berlin, Department of Biology, Chemistry and Pharmacy, Takustr. 3, 14195 Berlin, Germany
| | - Erhard Tietze
- Robert Koch Institute, Wernigerode Branch, Division Enteropathogenic Bacteria and Legionella, National Reference Centre for Salmonellae and other Bacterial Enteric Pathogens, Burgstr. 37, 38855 Wernigerode, Germany
| | - Reiner Helmuth
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany
| | - Ernst Junker
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany
| | - Angelika Fruth
- Robert Koch Institute, Wernigerode Branch, Division Enteropathogenic Bacteria and Legionella, National Reference Centre for Salmonellae and other Bacterial Enteric Pathogens, Burgstr. 37, 38855 Wernigerode, Germany
| | - Burkhard Malorny
- Federal Institute for Risk Assessment, National Reference Laboratory for Salmonella, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
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Bayer C, Bernard H, Prager R, Rabsch W, Hiller P, Malorny B, Pfefferkorn B, Frank C, de Jong A, Friesema I, Stark K, Rosner BM. An outbreak of Salmonella Newport associated with mung bean sprouts in Germany and the Netherlands, October to November 2011. Euro Surveill 2014; 19. [DOI: 10.2807/1560-7917.es2014.19.1.20665] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- C Bayer
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
- Postgraduate Training for Applied Epidemiology (PAE, German Field Epidemiology Training Programme), Robert Koch Institute, Berlin, Germany
| | - H Bernard
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
| | - R Prager
- Robert Koch Institute, Division of Bacterial Infections and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - W Rabsch
- Robert Koch Institute, Division of Bacterial Infections and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - P Hiller
- Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - B Malorny
- Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - B Pfefferkorn
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - C Frank
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
| | - A de Jong
- Dutch Food and Consumer Product Safety Authority (NVWA), Utrecht, the Netherlands
| | - I Friesema
- The National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, the Netherlands
| | - K Stark
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
| | - B M Rosner
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
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Gallati C, Stephan R, Hächler H, Malorny B, Schroeter A, Nüesch-Inderbinen M. Characterization of Salmonella enterica subsp. enterica serovar 4,[5],12:i:- clones isolated from human and other sources in Switzerland between 2007 and 2011. Foodborne Pathog Dis 2013; 10:549-54. [PMID: 23614800 DOI: 10.1089/fpd.2012.1407] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar 4,[5],12:i:- is a monophasic variant of Salmonella Typhimurium. In this study, a total of 651 human and 107 food and environmental isolates of serovar 4,[5],12:i:- recovered from 2007 through 2011 in Switzerland were characterized by antibiotic resistance profiles and pulsed-field gel electrophoresis (PFGE). In addition, a selection of isolates belonging to the most frequent PFGE patterns was further subjected to multilocus variable-number tandem-repeat analysis (MLVA) and phage typing. Over the years 2007-2011, the reports of salmonellosis caused by Salmonella enterica serovar 4,[5],12:i:- significantly increased. A high prevalence of multidrug-resistant isolates, mainly showing an ampicillin-streptomycin-sulfonamide-tetracycline resistance pattern (ASSuT), was observed. In addition, four extended spectrum beta lactamase (ESBL) (CTX-M-55)-producing isolates were found. XbaI PFGE analysis of all isolates revealed over 150 different pulsotypes, and generally showed a considerable diversity within the monophasic isolates. Nevertheless, among these we identified seven dominant profiles, which encompassed 66% of all isolates tested. The PFGE type STYMXB.0131 dominated among human as well as food isolates. Multilocus variable-number tandem-repeat analysis profile 3-12-10-0-0211, which, in many cases, coincided with PFGE type STYMXB.0131 and phage type DT193 were the most prevalent types found for the isolates further characterized by these typing methods. Our data provide strong evidence for a spread of two specific Salmonella serovar 4,[5],12:i:- clones (PFGE pattern STYMXB.0131, resistance type ASSuT) and (PFGE pattern STYMXB.0131, resistance type SSuT). In contrast to the human isolates, the pork/poultry isolates expressed predominantly the SSuT resistance type.
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Affiliation(s)
- Christine Gallati
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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