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Lachmann R, Halbedel S, Lüth S, Holzer A, Adler M, Pietzka A, Al Dahouk S, Stark K, Flieger A, Kleta S, Wilking H. Invasive listeriosis outbreaks and salmon products: a genomic, epidemiological study. Emerg Microbes Infect 2022; 11:1308-1315. [PMID: 35380514 PMCID: PMC9132468 DOI: 10.1080/22221751.2022.2063075] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Invasive listeriosis, caused by Listeria (L.) monocytogenes, is a severe foodborne infection, especially for immunocompromised individuals. The aim of our investigation was the identification and analysis of listeriosis outbreaks in Germany with smoked and graved salmon products as the most likely source of infection using whole-genome sequencing (WGS) and patient interviews. In a national surveillance programme, WGS was used for subtyping and core genome multi locus sequence typing (cgMLST) for cluster detection of L. monocytogenes isolates from listeriosis cases as well as food and environmental samples in Germany. Patient interviews were conducted to complement the molecular typing. We identified 22 independent listeriosis outbreaks occurring between 2010 and 2021 that were most likely associated with the consumption of smoked and graved salmon products. In Germany, 228 cases were identified, of 50 deaths (22%) reported 17 were confirmed to have died from listeriosis. Many of these 22 outbreaks were cross-border outbreaks with further cases in other countries. This report shows that smoked and graved salmon products contaminated with L. monocytogenes pose a serious risk for listeriosis infection in Germany. Interdisciplinary efforts including WGS and epidemiological investigations were essential to identifying the source of infection. Uncooked salmon products are high-risk foods frequently contaminated with L. monocytogenes. In order to minimize the risk of infection for consumers, food producers need to improve hygiene measures and reduce the entry of pathogens into food processing. Furthermore, susceptible individuals should be better informed of the risk of acquiring listeriosis from consuming smoked and graved salmon products.
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Affiliation(s)
- Raskit Lachmann
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Stefanie Lüth
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Alexandra Holzer
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Marlen Adler
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Graz, Austria
| | - Sascha Al Dahouk
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Klaus Stark
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Sylvia Kleta
- German Federal Institute for Risk Assessment, National Reference Laboratory for Listeria Monocytogenes, Berlin, Germany
| | - Hendrik Wilking
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
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2
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Vidovic S, Paturi G, Gupta S, Fletcher GC. Lifestyle of Listeria monocytogenes and food safety: Emerging listericidal technologies in the food industry. Crit Rev Food Sci Nutr 2022; 64:1817-1835. [PMID: 36062812 DOI: 10.1080/10408398.2022.2119205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Listeria monocytogenes, a causative agent of listeriosis, is a major foodborne pathogen. Among pathogens, L. monocytogenes stands out for its unique ecological and physiological characteristics. This distinct lifestyle of L. monocytogenes has a significant impact on food safety and public health, mainly through the ability of this pathogen to multiply at refrigeration temperature and to persist in the food processing environment. Due to a combination of these characteristics and emerging trends in consumer preference for ready-to-eat and minimally processed food, there is a need to develop effective and sustainable approaches to control contamination of food products with L. monocytogenes. Implementation of an efficient and reliable control strategy for L. monocytogenes must first address the problem of cross-contamination. Besides the preventive control strategies, cross-contamination may be addressed with the introduction of emerging post packaging non-thermal or thermal hurdles that can ensure delivery of a listericidal step in a packed product without interfering with the organoleptic characteristics of a food product. This review aims to present the most relevant findings underlying the distinct lifestyle of L. monocytogenes and its impact on food safety. We also discuss emerging food decontamination technologies that can be used to better control L. monocytogenes.
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Affiliation(s)
- Sinisa Vidovic
- Food Safety Preservation Team, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Gunaranjan Paturi
- Food Safety Preservation Team, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Sravani Gupta
- Food Safety Preservation Team, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Graham C Fletcher
- Food Safety Preservation Team, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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3
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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4
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Gulumbe BH, Bazata AY, Bagwai MA. Campylobacter Species, Microbiological Source Tracking and Risk Assessment of Bacterial pathogens. BORNEO JOURNAL OF PHARMACY 2022. [DOI: 10.33084/bjop.v5i2.3363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Campylobacter species continue to remain critical pathogens of public health interest. They are responsible for approximately 500 million cases of gastroenteritis per year worldwide. Infection occurs through the consumption of contaminated food and water. Microbial risk assessment and source tracking are crucial epidemiological strategies to monitor the outbreak of campylobacteriosis effectively. Various methods have been proposed for microbial source tracking and risk assessment, most of which rely on conventional microbiological techniques such as detecting fecal indicator organisms and other novel microbial source tracking methods, including library-dependent microbial source tracking and library-independent source tracking approaches. However, both the traditional and novel methods have their setbacks. For example, while the conventional techniques are associated with a poor correlation between indicator organism and pathogen presence, on the other hand, it is impractical to interpret qPCR-generated markers to establish the exact human health risks even though it can give information regarding the potential source and relative human risk. Therefore, this article provides up-to-date information on campylobacteriosis, various approaches for source attribution, and risk assessment of bacterial pathogens, including next-generation sequencing approaches such as shotgun metagenomics, which effectively answer the questions of potential pathogens are there and in what quantities.
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5
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Marzlan AA, Hussin ASM, Bourke P, Chaple S, Barroug S, Muhialdin BJ. Combination of Green Extraction Techniques and Essential Oils to Develop Active Packaging for Improving the Quality and Shelf Life for Chicken Meat. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.2013499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Anis Asyila Marzlan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Anis Shobirin Meor Hussin
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, Seri Kembangan, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Paula Bourke
- School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
- School of Biological Science, Institute for Global Food Security, Queens University Belfast, Belfast, Northern Ireland
| | - Sonal Chaple
- School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Soukaina Barroug
- School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
| | - Belal J Muhialdin
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, Minnesota, USA
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Genome Typing and Epidemiology of Human Listeriosis in New Zealand, 1999 to 2018. J Clin Microbiol 2021; 59:e0084921. [PMID: 34406797 DOI: 10.1128/jcm.00849-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study describes the epidemiology of listeriosis in New Zealand between 1999 and 2018 as well as the retrospective whole-genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population, and non-pregnancy-associated cases were more prevalent than pregnancy-associated cases (averages of 19 and 5 cases per annum, respectively). WGS data was assessed using multilocus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST, respectively) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%), and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Among the 49 cgMLST types containing two or more isolates, 18 cgMLST types were found with 2 to 4 isolates each (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0 to 2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP analysis also produced results comparable to those from wgMLST. The low genetic diversity within these clusters suggests a potential common source, but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis together with thorough exposure information from cases could potentially identify future outbreaks more rapidly, including those that may have been undetected for some time over different geographical regions.
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7
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Wilking H, Lachmann R, Holzer A, Halbedel S, Flieger A, Stark K. Ongoing High Incidence and Case-Fatality Rates for Invasive Listeriosis, Germany, 2010-2019. Emerg Infect Dis 2021; 27:2485-2488. [PMID: 34424172 PMCID: PMC8386774 DOI: 10.3201/eid2709.210068] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We used 10 years of surveillance data to describe listeriosis frequency in Germany. Altogether, 5,576 cases were reported, 91% not pregnancy associated; case counts increased over time. Case-fatality rate was 13% in non–pregnancy-associated cases, most in adults ≥65 years of age. Detecting, investigating, and ending outbreaks might have the greatest effect on incidence
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8
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Identification of the source of a Listeria monocytogenes outbreak by investigational tracing. J Verbrauch Lebensm 2021. [DOI: 10.1007/s00003-021-01336-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractThe number of identified listeriosis outbreaks has increased since the sequence typing of Listeria monocytogenes isolates was established in Germany. Due to the nature of the disease, listeriosis outbreaks are difficult to solve. We present investigational tracing as a simple and rapid method to conduct outbreak investigations. The method was applied in 2019 to stop a prolonged listeriosis outbreak in Germany. The starting point for the investigational tracing was nine health care facilities (HCF). Single cases developed listeriosis while they were staying at the nine facilities. Data were collected from companies that delivered foods to HCF and from ready-to-eat (RTE) foods that were consumed there. Following a step-wise approach, data analysis identified similarities in the food supply of the HCF. Food data were heterogeneous and needed to be standardised. Own brands and changing article numbers were challenging aspects during the identification of manufacturers. The analysis of the delivering companies revealed no similarities. Detailed information about the consumed risk foods for Listeria contamination became available for six HCF. All facilities served a wide variety of cold cut meat products to their in-patients. Investigational tracing revealed that only meat products from one out of 29 food business operators had been consumed in all six HCF. Further activities of the authorities enabled the identification of the outbreak strain on food products and in the processing environment of this company. A product recall and the measures taken stopped the listeriosis outbreak. Thus, investigational tracing can be crucial for the clarification of listeriosis outbreaks.
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Halbedel S, Wilking H, Holzer A, Kleta S, Fischer MA, Lüth S, Pietzka A, Huhulescu S, Lachmann R, Krings A, Ruppitsch W, Leclercq A, Kamphausen R, Meincke M, Wagner-Wiening C, Contzen M, Kraemer IB, Al Dahouk S, Allerberger F, Stark K, Flieger A. Large Nationwide Outbreak of Invasive Listeriosis Associated with Blood Sausage, Germany, 2018-2019. Emerg Infect Dis 2021; 26:1456-1464. [PMID: 32568037 PMCID: PMC7323541 DOI: 10.3201/eid2607.200225] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive listeriosis is a severe foodborne infection in humans and is difficult to control. Listeriosis incidence is increasing worldwide, but some countries have implemented molecular surveillance programs to improve recognition and management of listeriosis outbreaks. In Germany, routine whole-genome sequencing, core genome multilocus sequence typing, and single nucleotide polymorphism calling are used for subtyping of Listeria monocytogenes isolates from listeriosis cases and suspected foods. During 2018–2019, an unusually large cluster of L. monocytogenes isolates was identified, including 134 highly clonal, benzalkonium-resistant sequence type 6 isolates collected from 112 notified listeriosis cases. The outbreak was one of the largest reported in Europe during the past 25 years. Epidemiologic investigations identified blood sausage contaminated with L. monocytogenes highly related to clinical isolates; withdrawal of the product from the market ended the outbreak. We describe how epidemiologic investigations and complementary molecular typing of food isolates helped identify the outbreak vehicle.
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Doghri I, Cherifi T, Goetz C, Malouin F, Jacques M, Fravalo P. Counteracting Bacterial Motility: A Promising Strategy to Narrow Listeria monocytogenes Biofilm in Food Processing Industry. Front Microbiol 2021; 12:673484. [PMID: 34149663 PMCID: PMC8206544 DOI: 10.3389/fmicb.2021.673484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/04/2021] [Indexed: 12/21/2022] Open
Abstract
Listeria monocytogenes (L. monocytogenes) is often associated with processed food as it can form biofilms that represent a source of contamination at all stages of the manufacturing chain. The control and prevention of biofilms in food-processing plants are of utmost importance. This study explores the efficacy of prospect molecules for counteracting bacterial mechanisms leading to biofilm formation. The compounds included the phytomolecule tomatidine, zinc chloride (ZnCl2), ethylenediaminetetraacetic acid (EDTA), and a more complexed mixture of bacterial compounds from coagulase-negative staphylococci (CNS exoproducts). Significant inhibition of L. monocytogenes biofilm formation was evidenced using a microfluidic system and confocal microscopic analyses (p < 0.001). Active molecules were effective at an early stage of biofilm development (≥50% of inhibition) but failed to disperse mature biofilms of L. monocytogenes. According to our findings, prevention of surface attachment was associated with a disruption of bacterial motility. Indeed, agar cell motility assays demonstrated the effectiveness of these molecules. Overall, results highlighted the critical role of motility in biofilm formation and allow to consider flagellum-mediated motility as a promising molecular target in control strategies against L. monocytogenes in food processing environments.
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Affiliation(s)
- Ibtissem Doghri
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.,Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Montreal, QC, Cananda
| | - Tamazight Cherifi
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.,Chaire de Recherche en Salubrité des Viandes (CRSV), Montreal, QC, Cananda
| | - Coralie Goetz
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.,Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Montreal, QC, Cananda
| | - François Malouin
- Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Montreal, QC, Cananda.,Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mario Jacques
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.,Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Montreal, QC, Cananda
| | - Philippe Fravalo
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.,Chaire de Recherche en Salubrité des Viandes (CRSV), Montreal, QC, Cananda
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Complete Genome Sequences of Three Clinical Listeria monocytogenes Sequence Type 8 Strains from Recent German Listeriosis Outbreaks. Microbiol Resour Announc 2021; 10:10/18/e00303-21. [PMID: 33958403 PMCID: PMC8103873 DOI: 10.1128/mra.00303-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We report here the closed genome sequences of three clinical Listeria monocytogenes strains of multilocus sequence typing (MLST) sequence type 8 (ST8). These strains are representatives of three separate listeriosis outbreak clusters (Alpha1, Pi4, and Sigma1) that affected Germany between 2012 and 2020.
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12
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Fischer MA, Wamp S, Fruth A, Allerberger F, Flieger A, Halbedel S. Population structure-guided profiling of antibiotic resistance patterns in clinical Listeria monocytogenes isolates from Germany identifies pbpB3 alleles associated with low levels of cephalosporin resistance. Emerg Microbes Infect 2021; 9:1804-1813. [PMID: 32691687 PMCID: PMC7473133 DOI: 10.1080/22221751.2020.1799722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Numbers of listeriosis illnesses have been increasing in Germany and the European Union during the last decade. In addition, reports on the occurrence of antibiotic resistance in Listeria monocytogenes in clinical and environmental isolates are accumulating. The susceptibility towards 14 antibiotics was tested in a selection of clinical L. monocytogenes isolates to get a more precise picture of the development and manifestation of antibiotic resistance in the L. monocytogenes population. Based on the population structure determined by core genome multi locus sequence typing (cgMLST) 544 out of 1220 sequenced strains collected in Germany between 2009 and 2019 were selected to cover the phylogenetic diversity observed in the clinical L. monocytogenes population. All isolates tested were susceptible towards ampicillin, penicillin and co-trimoxazole – the most relevant antibiotics in the treatment of listeriosis. Resistance to daptomycin and ciprofloxacin was observed in 493 (91%) and in 71 (13%) of 544 isolates, respectively. While all tested strains showed resistance towards ceftriaxone, their resistance levels varied widely between 4 mg/L and >128 mg/L. An allelic variation of the penicillin binding protein gene pbpB3 was identified as the cause of this difference in ceftriaxone resistance levels. This study is the first population structure-guided analysis of antimicrobial resistance in recent clinical isolates and confirms the importance of penicillin binding protein B3 (PBP B3) for the high level of intrinsic cephalosporin resistance of L. monocytogenes on a population-wide scale.
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Affiliation(s)
- Martin A Fischer
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Wamp
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Angelika Fruth
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | | | - Antje Flieger
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany.,German Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany.,German Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
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13
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Bedi JS, Vijay D, Dhaka P, Singh Gill JP, Barbuddhe SB. Emergency preparedness for public health threats, surveillance, modelling & forecasting. Indian J Med Res 2021; 153:287-298. [PMID: 33906991 PMCID: PMC8204835 DOI: 10.4103/ijmr.ijmr_653_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 11/04/2022] Open
Abstract
In the interconnected world, safeguarding global health security is vital for maintaining public health and economic upliftment of any nation. Emergency preparedness is considered as the key to control the emerging public health challenges at both national as well as international levels. Further, the predictive information systems based on routine surveillance, disease modelling and forecasting play a pivotal role in both policy building and community participation to detect, prevent and respond to potential health threats. Therefore, reliable and timely forecasts of these untoward events could mobilize swift and effective public health responses and mitigation efforts. The present review focuses on the various aspects of emergency preparedness with special emphasis on public health surveillance, epidemiological modelling and capacity building approaches. Global coordination and capacity building, funding and commitment at the national and international levels, under the One Health framework, are crucial in combating global public health threats in a holistic manner.
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Affiliation(s)
- Jasbir Singh Bedi
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Deepthi Vijay
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Pankaj Dhaka
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Jatinder Paul Singh Gill
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sukhadeo B. Barbuddhe
- Department of Meat Safety, ICAR-National Research Centre on Meat, Chengicherla, Hyderabad, Telangana, India
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14
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Lüth S, Halbedel S, Rosner B, Wilking H, Holzer A, Roedel A, Dieckmann R, Vincze S, Prager R, Flieger A, Al Dahouk S, Kleta S. Backtracking and forward checking of human listeriosis clusters identified a multiclonal outbreak linked to Listeria monocytogenes in meat products of a single producer. Emerg Microbes Infect 2021; 9:1600-1608. [PMID: 32657219 PMCID: PMC7473094 DOI: 10.1080/22221751.2020.1784044] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Due to its high case fatality rate, foodborne listeriosis is considered a major public health concern worldwide. We describe one of the largest listeriosis outbreaks in Germany with 83 cases of invasive listeriosis between 2013 and 2018. As part of the outbreak investigation, we identified a highly diverse Listeria monocytogenes population at a single producer of ready-to-eat meat products. Strikingly, the extensive sampling after identification of a first match between a cluster of clinical isolates and a food isolate allowed for a linkage between this producer and a second, previously unmatched cluster of clinical isolates. Bacterial persistence in the processing plant and indications of cross-contamination events explained long-term contamination of food that led to the protracted outbreak. Based on screening for virulence factors, a pathogenic phenotype could not be ruled out for other strains circulating in the plant, suggesting that the outbreak could have been even larger. As most isolates were sensitive to common biocides used in the plant, hard to clean niches in the production line may have played a major role in the consolidation of the contamination. Our study demonstrates how important it is to search for the origin of infection when cases of illness have occurred (backtracking), but also clearly highlights that it is equally important to check whether a contamination at food or production level has caused disease (forward checking). Only through this two-sided control strategy, foodborne disease outbreaks such as listeriosis can be minimized, which could be a real improvement for public health.
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Affiliation(s)
- Stefanie Lüth
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Sven Halbedel
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
| | - Bettina Rosner
- Department of Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Hendrik Wilking
- Department of Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Alexandra Holzer
- Department of Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Alice Roedel
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ralf Dieckmann
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Szilvia Vincze
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Rita Prager
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, Germany
| | - Antje Flieger
- Department of Infectious Diseases, Robert Koch-Institute, Wernigerode, 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
| | - Sylvia Kleta
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Lüth S, Deneke C, Kleta S, Al Dahouk S. Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes. Microb Genom 2021; 7:mgen000491. [PMID: 33275089 PMCID: PMC8115905 DOI: 10.1099/mgen.0.000491] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/21/2020] [Indexed: 12/26/2022] Open
Abstract
Where classical epidemiology has proven to be inadequate for surveillance and control of foodborne pathogens, molecular epidemiology, using genomic typing methods, can add value. However, the analysis of whole genome sequencing (WGS) data varies widely and is not yet fully harmonised. We used genomic data on 494 Listeria monocytogenes isolates from ready-to-eat food products and food processing environments deposited in the strain collection of the German National Reference Laboratory to compare various procedures for WGS data analysis and to evaluate compatibility of results. Two different core genome multilocus sequence typing (cgMLST) schemes, different reference genomes in single nucleotide polymorphism (SNP) analysis and commercial as well as open-source software were compared. Correlation of allele distances from the different cgMLST approaches was high, ranging from 0.97 to 1, and unified thresholds yielded higher clustering concordance than scheme-specific thresholds. The number of detected SNP differences could be increased up to a factor of 3.9 using a specific reference genome compared with a general one. Additionally, specific reference genomes improved comparability of SNP analysis results obtained using different software tools. The use of a closed or a draft specific reference genome did not make a difference. The harmonisation of WGS data analysis will finally guarantee seamless data exchange, but, in the meantime, knowledge on threshold values that lead to comparable clustering of isolates by different methods may improve communication between laboratories. We therefore established a translation code between commonly applied cgMLST and SNP methods based on optimised clustering concordances. This code can work as a first filter to identify WGS-based typing matches resulting from different methods, which opens up a new perspective for data exchange and thereby accelerates time-critical analyses, such as in outbreak investigations.
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Affiliation(s)
- Stefanie Lüth
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Berlin, Germany
| | - Carlus Deneke
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - Sylvia Kleta
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - Sascha Al Dahouk
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
- RWTH Aachen University Hospital, Department of Internal Medicine, Aachen, Germany
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Lachmann R, Halbedel S, Adler M, Becker N, Allerberger F, Holzer A, Boone I, Falkenhorst G, Kleta S, Al Dahouk S, Stark K, Luber P, Flieger A, Wilking H. Nationwide outbreak of invasive listeriosis associated with consumption of meat products in health care facilities, Germany, 2014-2019. Clin Microbiol Infect 2020; 27:1035.e1-1035.e5. [PMID: 32979571 DOI: 10.1016/j.cmi.2020.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/27/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Invasive listeriosis is a severe foodborne infection caused by Listeria(L.)monocytogenes. The aim of this investigation was to verify and describe a molecular cluster of listeriosis patients and identify factors leading to this outbreak. METHODS Whole genome sequencing and core genome multilocus sequence typing were used for subtyping L. monocytogenes isolates from listeriosis cases and food samples in Germany. Patient interviews and investigational tracing of foodstuffs offered in health-care facilities (HCF), where some of the cases occurred, were conducted. RESULTS We identified a German-wide listeriosis outbreak with 39 genetically related cases occurring between 2014 and 2019. Three patients died as a result of listeriosis. After identification of HCF in different regions of Germany for at least 13 cases as places of exposure, investigational tracing of food supplies in six prioritized HCF revealed meat products from one company (X) as a commonality. Subsequently the outbreak strain was analysed in six isolates from ready-to-eat meat products and one isolate from the production environment of company X. No further Sigma1 cases were detected after recall of the meat products from the market and closure of company X (as of August 2020). CONCLUSIONS Interdisciplinary efforts including whole genome sequencing, epidemiological investigations in patients and investigational tracing of foods were essential to identify the source of infections, and thereby prevent further illnesses and deaths. This outbreak underlines the vulnerability of hospitalized patients for foodborne diseases, such as listeriosis. Food producers and HCF should minimize the risk of microbiological hazards when producing, selecting and preparing food for patients.
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Affiliation(s)
- Raskit Lachmann
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany.
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Marlen Adler
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - Natalie Becker
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | | | - Alexandra Holzer
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Idesbald Boone
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Gerhard Falkenhorst
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Sylvia Kleta
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Klaus Stark
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Petra Luber
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Hendrik Wilking
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
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17
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Yan S, Li M, Luque-Sastre L, Wang W, Hu Y, Peng Z, Dong Y, Gan X, Nguyen S, Anes J, Bai Y, Xu J, Fanning S, Li F. Susceptibility (re)-testing of a large collection of Listeria monocytogenes from foods in China from 2012 to 2015 and WGS characterization of resistant isolates. J Antimicrob Chemother 2020; 74:1786-1794. [PMID: 30989181 DOI: 10.1093/jac/dkz126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/04/2019] [Accepted: 03/05/2019] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES Our aim was to determine the antimicrobial susceptibilities of 2862 Listeria monocytogenes cultured from various foods in China and to use WGS to characterize the antimicrobial resistance and virulence genotypes of those expressing a resistance phenotype. METHODS The susceptibilities of 2862 L. monocytogenes were determined by broth microdilution. Twenty-eight L. monocytogenes were found to be resistant to one to four antibiotics. All 28 resistant isolates were subsequently sequenced using short-read high accuracy protocols. The corresponding genomes were assembled and further analysis was carried out using appropriate bioinformatics pipelines. RESULTS All 28 resistant L. monocytogenes were classified into five STs (ST3, ST8, ST9, ST155 and ST515). Both ST9 and ST155 were dominant and their genotypes correlated with their resistance phenotypes. All ST9 isolates were MDR and could be phylogenetically classified into two clusters. One was relatively close to clinical origins and one to food. Downstream analysis of the genetic contexts in which these resistance genotypes were found suggested that these may have been acquired from other bacteria by horizontal transfer or insertion into the chromosome. All isolates harboured Listeria pathogenicity island (LIPI)-1 and LIPI-2, and only two harboured LIPI-3. CONCLUSIONS This study reported on the antimicrobial susceptibilities of 2862 foodborne L. monocytogenes along with the genomic characterization of 28 resistant isolates, 11 of which expressed an MDR phenotype. These data showed that this bacterium can acquire resistance by horizontal gene transfer in and between species. This study may necessitate a re-evaluation of risk to public health, associated with this bacterial species.
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Affiliation(s)
- Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Laura Luque-Sastre
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Scott Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - João Anes
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Yao Bai
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
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18
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada. Microb Genom 2020; 6. [PMID: 32496181 PMCID: PMC7371104 DOI: 10.1099/mgen.0.000376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | | | - Chad R Laing
- National Centre for Animal Disease, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
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19
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Chen Y, Chen Y, Pouillot R, Dennis S, Xian Z, Luchansky JB, Porto-Fett ACS, Lindsay JA, Hammack TS, Allard M, Van Doren JM, Brown EW. Genetic diversity and profiles of genes associated with virulence and stress resistance among isolates from the 2010-2013 interagency Listeria monocytogenes market basket survey. PLoS One 2020; 15:e0231393. [PMID: 32352974 PMCID: PMC7192433 DOI: 10.1371/journal.pone.0231393] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022] Open
Abstract
Whole genome sequencing (WGS) was performed on 201 Listeria monocytogenes isolates recovered from 102 of 27,389 refrigerated ready-to-eat (RTE) food samples purchased at retail in U.S. FoodNet sites as part of the 2010-2013 interagency L. monocytogenes Market Basket Survey (Lm MBS). Core genome multi-locus sequence typing (cgMLST) and in-silico analyses were conducted, and these data were analyzed with metadata for isolates from five food groups: produce, seafood, dairy, meat, and combination foods. Six of 201 isolates, from 3 samples, were subsequently confirmed as L. welshimeri. Three samples contained one isolate per sample; mmong the 96 samples that contained two isolates per sample, 3 samples each contained two different strains and 93 samples each contained duplicate isolates. After 93 duplicate isolates were removed, the remaining 102 isolates were delineated into 29 clonal complexes (CCs) or singletons based on their sequence type. The five most prevalent CCs were CC155, CC1, CC5, CC87, and CC321. The Shannon's diversity index for clones per food group ranged from 1.49 for dairy to 2.32 for produce isolates, which were not significantly different in pairwise comparisons. The most common molecular serogroup as determined by in-silico analysis was IIa (45.6%), followed by IIb (27.2%), IVb (20.4%), and IIc (4.9%). The proportions of isolates within lineages I, II, and III were 48.0%, 50.0% and 2.0%, respectively. Full-length inlA was present in 89.3% of isolates. Listeria pathogenicity island 3 (LIPI-3) and LIPI-4 were found in 51% and 30.6% of lineage I isolates, respectively. Stress survival islet 1 (SSI-1) was present in 34.7% of lineage I isolates, 80.4% of lineage II isolates and the 2 lineage III isolates; SSI-2 was present only in the CC121 isolate. Plasmids were found in 48% of isolates, including 24.5% of lineage I isolates and 72.5% of lineage II isolates. Among the plasmid-carrying isolates, 100% contained at least one cadmium resistance cassette and 89.8% contained bcrABC, involved in quaternary ammonium compound tolerance. Multiple clusters of isolates from different food samples were identified by cgMLST which, along with available metadata, could aid in the investigation of possible cross-contamination and persistence events.
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Affiliation(s)
- Yi Chen
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Yuhuan Chen
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Régis Pouillot
- Consultant, Buenos Aires, Argentina, United States of America
| | - Sherri Dennis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Zhihan Xian
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - John B. Luchansky
- USDA Agricultural Research Service, Wyndmoor, Pennsylvania, United States of America
| | - Anna C. S. Porto-Fett
- USDA Agricultural Research Service, Wyndmoor, Pennsylvania, United States of America
| | - James A. Lindsay
- USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Thomas S. Hammack
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Jane M. Van Doren
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
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20
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Prevalence and characteristics of pks gene cluster harbouring Klebsiella pneumoniae from bloodstream infection in China. Epidemiol Infect 2020; 148:e69. [PMID: 32160933 PMCID: PMC7118716 DOI: 10.1017/s0950268820000655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bloodstream infection (BSI), caused by Klebsiella pneumoniae, is associated with high morbidity and mortality, where the pks gene cluster plays a major role in their occurrence and prevalence. Information on the prevalence and characteristics of this gene cluster in K. pneumoniae is currently limited in mainland China. We therefore undertook a multicentre longitudinal study which revealed the prevalence, overall, community-onset and hospital-acquired BSI to be 20.5%, 28.3% and 13.0%, respectively. Compared to pks-negative, pks-positive isolates were significantly more susceptible to antimicrobial agents with a low incidence (5.1%) of multidrug-resistance and with infrequent extended-spectrum beta-lactamase (ESBL) production. Among pks-positive isolates, ST23 (78/117) and ST65 (20/117) were the dominant sequence types, and the majority harboured virulence genes. Community-onset BSI patients infected with pks-positive isolates had a higher proportion of liver abscesses and a lower proportion of biliary obstructions (P < 0.05). The pks-positive isolates were mostly sporadic in the phylogenetic tree, with a 65.8 and 47.0 average allele difference between Clade 1 and Clade 2, respectively. We concluded that although pks-positive K. pneumoniae were generally susceptible to antimicrobials, the high prevalence of such isolates in community cases and the genotoxicity, merits further investigation.
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21
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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] [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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22
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Roedel A, Dieckmann R, Brendebach H, Hammerl JA, Kleta S, Noll M, Al Dahouk S, Vincze S. Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics. Appl Environ Microbiol 2019; 85:e01253-19. [PMID: 31375490 PMCID: PMC6805086 DOI: 10.1128/aem.01253-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/24/2019] [Indexed: 01/02/2023] Open
Abstract
Contamination of food during processing is recognized as a main transmission route of Listeria monocytogenes To prevent microbial contamination, biocides are widely applied as disinfectants in food processing plants. However, there are concerns about the development of antimicrobial resistance in foodborne pathogens due to widespread biocide usage. In our study, 93 L. monocytogenes isolates from German food production facilities were (i) tested for biocide and antibiotic susceptibility using broth microdilution assays, (ii) analyzed for links between reduced biocide susceptibility and antibiotic resistance, and (iii) characterized by whole-genome sequencing, including the detection of genes coding for biocide tolerance, antibiotic resistance, and other virulence factors. Fifteen L. monocytogenes isolates were tolerant to benzalkonium chloride (BAC), and genes conferring BAC tolerance were found in 13 of them. Antibiotic resistance was not associated with biocide tolerance. BAC-tolerant isolates were assigned to 6 multilocus sequence type (MLST) clonal complexes, and most of them harbored internalin A pseudogenes with premature stop codons or deletions (n = 9). Our study demonstrated a high genetic diversity among the investigated isolates including genotypes that are frequently involved in human infections. Although in vitro adaptation studies to biocides have raised concerns about increasing cross-resistance to antibiotics, our results do not provide evidence for this phenomenon in field isolates.IMPORTANCE Foodborne pathogens such as L. monocytogenes can persist in food production environments for a long time, causing perennial outbreaks. Hence, bacterial pathogens are able to survive cleaning and disinfection procedures. Accordingly, they may be repeatedly exposed to sublethal concentrations of disinfectants, which might result in bacterial adaptation to these biocides. Furthermore, antibiotic coresistance and cross-resistance are known to evolve under biocide selection pressure in vitro Hence, antimicrobial tolerance seems to play a crucial role in the resilience and persistence of foodborne pathogens in the food chain and might reduce therapeutic options in infectious diseases.
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Affiliation(s)
- A Roedel
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - R Dieckmann
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - H Brendebach
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - J A Hammerl
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - S Kleta
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - M Noll
- University of Applied Sciences and Arts, Institute for Bioanalysis, Coburg, Germany
| | - S Al Dahouk
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - S Vincze
- German Federal Institute for Risk Assessment, Berlin, Germany
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23
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Motlagh AM, Yang Z. Detection and occurrence of indicator organisms and pathogens. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2019; 91:1402-1408. [PMID: 31505073 PMCID: PMC7169830 DOI: 10.1002/wer.1238] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
This review paper focuses on detection and quantification techniques of indicator organisms that can be used for water quality assessment. The environmental pathogens that are critical to understand and better evaluate water quality are also discussed in this paper. Several recent studies using culture-independent methods such as microbial source tracking, pulsed field gel electrophoresis, mitochondrial DNA, and next generation sequencing to assess various environmental samples and water bodies have been reviewed. PRACTITIONER POINTS: Various waterborne pathogens and cases of outbreak occurances due to presence of pathogens are studied in this review paper. Recent studies for detecting major indicator organisms to evaluate the presence of pathogens in water bodies are reviewed. Culture-independent techniques as robust tools to detect and quantify waterborne pathogens are discussed in this review paper.
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Affiliation(s)
- Amir M. Motlagh
- Department of Civil EngineeringCalifornia State UniversitySacramentoCalifornia
| | - Zhengjian Yang
- Department of Civil EngineeringCalifornia State UniversitySacramentoCalifornia
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24
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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] [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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25
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Kukleci E, Smulders FJM, Hamidi A, Bauer S, Paulsen P. Prevalence of Foodborne Pathogenic Bacteria, Microbial Levels of Hygiene Indicator Bacteria, and Concentrations of Biogenic Amines in Ready-to-Eat Meat Products at Retail in the Republic of Kosovo. J Food Prot 2019; 82:1135-1140. [PMID: 31225975 DOI: 10.4315/0362-028x.jfp-19-060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIGHLIGHTS RTE meat products from the Republic of Kosovo were tested for contamination. L. monocytogenes was more prevalent in dried or fermented than in cooked-cured meats. E. coli and Enterobacteriaceae were more prevalent in nonpackaged dried or fermented meats. Concentrations of biogenic amines were higher in dried or fermented than in cooked-cured meats.
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Affiliation(s)
- Egzon Kukleci
- 1 Faculty of Agriculture and Veterinary Medicine, University of Prishtina, Bulevardi "Bill Clinton" N.N., 10000 Prishtina, Republic of Kosovo.,2 Institute of Meat Hygiene, Meat Technology and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, A 1210 Vienna, Austria
| | - Frans J M Smulders
- 2 Institute of Meat Hygiene, Meat Technology and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, A 1210 Vienna, Austria
| | - Afrim Hamidi
- 1 Faculty of Agriculture and Veterinary Medicine, University of Prishtina, Bulevardi "Bill Clinton" N.N., 10000 Prishtina, Republic of Kosovo
| | - Susanne Bauer
- 2 Institute of Meat Hygiene, Meat Technology and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, A 1210 Vienna, Austria
| | - Peter Paulsen
- 2 Institute of Meat Hygiene, Meat Technology and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, A 1210 Vienna, Austria
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26
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Su X, Cao G, Zhang J, Pan H, Zhang D, Kuang D, Yang X, Xu X, Shi X, Meng J. Characterization of internalin genes in Listeria monocytogenes from food and humans, and their association with the invasion of Caco-2 cells. Gut Pathog 2019; 11:30. [PMID: 31198443 PMCID: PMC6558679 DOI: 10.1186/s13099-019-0307-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023] Open
Abstract
Background Internalins are surface proteins that are utilized by Listeria monocytogenes to facilitate its invasion into human intestinal epithelial cells. The expression of a full-length InlA is one of essential virulence factors for L. monocytogenes to cross the intestinal barrier in order to invade epithelial cells. Results In this study, the gene sequences of inlA in 120 L. monocytogenes isolates from food (n = 107) and humans (n = 13) were analyzed. Premature stop codon (PMSC) mutations in inlA were identified in 51 isolates (50 from food and 1 from human). Six mutation types of PMSCs were identified. Among the 51 isolates with PMSCs in inlA, there were 44 serogroup 1/2c, 3c isolates from food, of which seven belonged to serogroups 1/2a, 3a. A total of 153,382 SNPs in 2247 core genes from 42 genomes were identified and used to construct a phylogenetic tree. Serotype 1/2c isolates with inlA PMSC mutations were grouped together. Cell culture studies on 21 isolates showed that the invasion to Caco-2 cells was significantly reduced among isolates with inlA PMSC mutations compared to those without PMSC mutations (P < 0.01). The PMSC mutations in inlA correlated with the inability of the L. monocytogenes isolates to invade Caco-2 cells (Pearson’s coefficient 0.927, P < 0.01). Conclusion Overall, the study has revealed the reduced ability of L. monocytogenes to invade human intestinal epithelial cells in vitro was linked to the presence of PMSC mutations in inlA. Isolates with PMSC mutations shared the same genomic characteristics indicating the genetic basis on the potential virulence of L. monocytogenes invasion. Electronic supplementary material The online version of this article (10.1186/s13099-019-0307-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xudong Su
- 1Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Guojie Cao
- 2Department of Nutrition & Food Science, University of Maryland, College Park, MD 20742 USA
| | - Jianmin Zhang
- 1Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Haijian Pan
- 1Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Daofeng Zhang
- 1Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Dai Kuang
- 1Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xiaowei Yang
- 1Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xuebin Xu
- 3Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336 China
| | - Xianming Shi
- 1Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianghong Meng
- 2Department of Nutrition & Food Science, University of Maryland, College Park, MD 20742 USA
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Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L, Chapman J, Grant K. The use of next generation sequencing for improving food safety: Translation into practice. Food Microbiol 2019; 79:96-115. [PMID: 30621881 PMCID: PMC6492263 DOI: 10.1016/j.fm.2018.11.005] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 01/06/2023]
Abstract
Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.
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Affiliation(s)
- Balamurugan Jagadeesan
- Nestlé Research, Nestec Ltd, Route du Jorat 57, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland.
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, MS-CO-3, 1600 Clifton Road, 30329-4027, Atlanta, USA
| | - Marc W Allard
- US Food and Drug Administration, 5001 Campus Drive, College Park, MD, 02740, USA
| | - Sébastien Leuillet
- Institut Mérieux, Mérieux NutriSciences, 3 route de la Chatterie, 44800, Saint Herblain, France
| | - Anett Winkler
- Cargill Deutschland GmbH, Cerestarstr. 2, 47809, Krefeld, Germany
| | - Yinghua Xiao
- Arla Innovation Center, Agro Food Park 19, 8200, Aarhus, Denmark
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France
| | - Jos Van Der Vossen
- The Netherlands Organisation for Applied Scientific Research, TNO, Utrechtseweg 48, 3704 HE, Zeist, NL, the Netherlands
| | - Silin Tang
- Mars Global Food Safety Center, Yanqi Economic Development Zone, 101407, Beijing, China
| | - Mitsuru Katase
- Fuji Oil Co., Ltd., Sumiyoshi-cho 1, Izumisano Osaka, 598-8540, Japan
| | - Peter McClure
- Mondelēz International, Linden 3, Bournville Lane, B30 2LU, Birmingham, United Kingdom
| | - Bon Kimura
- Tokyo University of Marine Science & Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Lay Ching Chai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - John Chapman
- Unilever Research & Development, Postbus, 114, 3130 AC, Vlaardingen, the Netherlands
| | - Kathie Grant
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, United Kingdom.
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28
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Zhang X, Niu Y, Liu Y, Lu Z, Wang D, Cui X, Chen Q, Ma X. Isolation and Characterization of Clinical Listeria monocytogenes in Beijing, China, 2014-2016. Front Microbiol 2019; 10:981. [PMID: 31139159 PMCID: PMC6517826 DOI: 10.3389/fmicb.2019.00981] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/18/2019] [Indexed: 12/15/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen with a significant impact on public health worldwide. A great number of outbreaks caused by L. monocytogenes has been reported, especially in the United States, and European countries. However, listeriosis has not yet been included in notifiable disease in China, and thus information on this infection has been scarce among the Chinese population. In this study, we described a 3-year surveillance of listeriosis in Beijing, China. Fifty-six L. monocytogenes strains isolated from 49 clinical infectious cases (27 pregnancy-associated infections and 22 non-pregnancy-associated infections) were analyzed by serotyping, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and antimicrobial susceptibility testing between 2014 and 2016 in Beijing. The predominant serogroups were 1/2a,3a and 1/2b,3b,7 which accounted for 92% of the overall isolates. Four strains were serogroup 4b,4d,4e, isolated from patients with pregnancy-associated infections. Based on PFGE, these isolates were divided into 32 pulsotypes (PTs) and 3 clusters associated with serogroups. Ten PTs were represented by more than one isolate with PT09 containing the most number of isolates. MLST differentiated the isolates into 18 STs, without new ST designated. The three most common STs were ST8 (18.4%), ST5 (16.3%), and ST87 (12.2%), accounting for 46.9% of the isolates. STs prevalent in other parts of the world were also present in China such as ST1, ST2, ST5, ST8, and ST9 which caused maternal fetal infections or outbreaks. However, the STs and serogroup distribution of clinical L. monocytogenes in Beijing, China was different from those in other countries. Strains of ST1 and ST2 were isolated from patients with pregnancy-associated infection, whereas none of ST155 isolates caused pregnancy-associated cases. Surveillance of molecular characterization will provide important information for prevention of listeriosis. This study also enhances our understanding of genetic diversity of clinical L. monocytogenes in China.
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Affiliation(s)
- Xiaoai Zhang
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
| | - Yanlin Niu
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
| | - Yuzhu Liu
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
| | - Zheng Lu
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
| | - Di Wang
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
| | - Xia Cui
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
| | - Qian Chen
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
| | - Xiaochen Ma
- Beijing Center for Disease Prevention and Control, Institute for Nutrition and Food Hygiene, Beijing, China
- Research Centre for Preventive Medicine of Beijing, Beijing, China
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29
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Halbedel S, Prager R, Banerji S, Kleta S, Trost E, Nishanth G, Alles G, Hölzel C, Schlesiger F, Pietzka A, Schlüter D, Flieger A. A Listeria monocytogenes ST2 clone lacking chitinase ChiB from an outbreak of non-invasive gastroenteritis. Emerg Microbes Infect 2019; 8:17-28. [PMID: 30866756 PMCID: PMC6455121 DOI: 10.1080/22221751.2018.1558960] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/27/2022]
Abstract
An outbreak with a remarkable Listeria monocytogenes clone causing 163 cases of non-invasive listeriosis occurred in Germany in 2015. Core genome multi locus sequence typing grouped non-invasive outbreak isolates and isolates obtained from related food samples into a single cluster, but clearly separated genetically close isolates obtained from invasive listeriosis cases. A comparative genomic approach identified a premature stop codon in the chiB gene, encoding one of the two L. monocytogenes chitinases, which clustered with disease outcome. Correction of this premature stop codon in one representative gastroenteritis outbreak isolate restored chitinase production, but effects in infection experiments were not found. While the exact role of chitinases in virulence of L. monocytogenes is still not fully understood, our results now clearly show that ChiB-derived activity is not required to establish L. monocytogenes gastroenteritis in humans. This limits a possible role of ChiB in human listeriosis to later steps of the infection.
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Affiliation(s)
- Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Rita Prager
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Sangeeta Banerji
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Sylvia Kleta
- German Federal Institute for Risk AssessmentBerlin, Germany
| | - Eva Trost
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Gopala Nishanth
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Georg Alles
- Paderborn District, Health Office, Paderborn, Germany
| | - Christina Hölzel
- Faculty of Agricultural and Nutritional Sciences, CAU Kiel, Kiel, Germany
- Milk Hygiene, Faculty of Veterinary Medicine, LMU Munich, Oberschleißheim, Germany
| | - Friederike Schlesiger
- Chemical and Veterinary Analytical Institute Ostwestfalen-Lippe (CVUA-OWL), Detmold, Germany
| | - Ariane Pietzka
- German-Austrian Binational Consiliary Laboratory for Listeria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Dirk Schlüter
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- Organ-specific Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
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30
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Tracing of Listeria monocytogenes Contamination Routes in Fermented Sausage Production Chain by Pulsed-Field Gel Electrophoresis Typing. Foods 2018; 7:foods7120198. [PMID: 30518118 PMCID: PMC6306841 DOI: 10.3390/foods7120198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/19/2018] [Accepted: 12/03/2018] [Indexed: 01/03/2023] Open
Abstract
In this study, the presence of Listeria monocytogenes was assessed along the production process of fermented sausages in a small-scale facility. Following the isolation of the pathogen from the final product (ISO 11290-1), retrospective sampling was performed during the production of a new batch of sausages, including raw materials, casings, additives, sausage mixtures, sausages during fermentation, and environmental samples. L. monocytogenes was recovered from the following sampling points: the defrosting room and the cuttering, mixing, stuffing, and fermentation phases. Ten strains were isolated, molecularly confirmed as L. monocytogenes by means of a molecular detection system, and subjected to pulsed-field gel electrophoresis (PFGE) typing. On the basis of an unweighted pair group method with arithmetic mean (UPGMA) dendrogram from Ascl pulsotypes, the strains were indistinguishable (no band difference). The same pulsotypes of strains present in both batches of sausages, as well as in environmental samples, indicated the persistence of L. monocytogenes in the sausage production unit.
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31
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Ezeoke I, Galac MR, Lin Y, Liem AT, Roth PA, Kilianski A, Gibbons HS, Bloch D, Kornblum J, Del Rosso P, Janies DA, Weiss D. Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks. PLoS One 2018; 13:e0202615. [PMID: 30485280 PMCID: PMC6261407 DOI: 10.1371/journal.pone.0202615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/05/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND While overall rates of meningococcal disease have been declining in the United States for the past several decades, New York City (NYC) has experienced two serogroup C meningococcal disease outbreaks in 2005-2006 and in 2010-2013. The outbreaks were centered within drug use and sexual networks, were difficult to control, and required vaccine campaigns. METHODS Whole Genome Sequencing (WGS) was used to analyze preserved meningococcal isolates collected before and during the two outbreaks. We integrated and analyzed epidemiologic, geographic, and genomic data to better understand transmission networks among patients. Betweenness centrality was used as a metric to understand the most important geographic nodes in the transmission networks. Comparative genomics was used to identify genes associated with the outbreaks. RESULTS Neisseria meningitidis serogroup C (ST11/ET-37) was responsible for both outbreaks with each outbreak having distinct phylogenetic clusters. WGS did identify some misclassifications of isolates that were more distant from the outbreak strains, as well as those that should have been included based on high genomic similarity. Genomes for the second outbreak were more similar than the first and no polymorphism was found to either be unique or specific to either outbreak lineage. Betweenness centrality as applied to transmission networks based on phylogenetic analysis demonstrated that the outbreaks were transmitted within focal communities in NYC with few transmission events to other locations. CONCLUSIONS Neisseria meningitidis is an ever changing pathogen and comparative genomic analyses can help elucidate how it spreads geographically to facilitate targeted interventions to interrupt transmission.
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Affiliation(s)
- Ifeoma Ezeoke
- Bureau of Communicable Disease, Department of Health and Mental Hygiene, New York, NY, United States of America
| | - Madeline R. Galac
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, United States of America
| | - Ying Lin
- Bureau of Public Health Laboratory, Department of Health and Mental Hygiene, New York, NY, United States of America
| | - Alvin T. Liem
- Department of Microbiology, US Army Edgewood Chemical and Biological Center, Aberdeen Proving Ground, MD, United States of America
- DCS Corporation, Alexandria, VA, United States of America
| | - Pierce A. Roth
- Department of Microbiology, US Army Edgewood Chemical and Biological Center, Aberdeen Proving Ground, MD, United States of America
- DCS Corporation, Alexandria, VA, United States of America
| | - Andrew Kilianski
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, United States of America
| | - Henry S. Gibbons
- Department of Microbiology, US Army Edgewood Chemical and Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Danielle Bloch
- Bureau of Communicable Disease, Department of Health and Mental Hygiene, New York, NY, United States of America
| | - John Kornblum
- Bureau of Public Health Laboratory, Department of Health and Mental Hygiene, New York, NY, United States of America
| | - Paula Del Rosso
- Bureau of Communicable Disease, Department of Health and Mental Hygiene, New York, NY, United States of America
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, United States of America
| | - Don Weiss
- Bureau of Communicable Disease, Department of Health and Mental Hygiene, New York, NY, United States of America
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32
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Overexpressing ovotransferrin and avian β-defensin-3 improves antimicrobial capacity of chickens and poultry products. Transgenic Res 2018; 28:51-76. [PMID: 30374651 DOI: 10.1007/s11248-018-0101-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/22/2018] [Indexed: 02/08/2023]
Abstract
Zoonotic and foodborne diseases pose a significant burden, decreasing both human and animal health. Modifying chickens to overexpress antimicrobials has the potential to decrease bacterial growth on poultry products and boost chicken innate immunity. Chickens overexpressing either ovotransferrin or avian β-defensin-3 (AvβD3) were generated using Tol-2 transposons. Transgene expression at the RNA and protein level was seen in egg white, breast muscle, and serum. There were significant differences in the immune cell populations in the blood, bursa, and spleen associated with transgene expression including an increased proportion of CD8+ cells in the blood of ovotransferrin and AvβD3 transgenic birds. Expression of the antimicrobials inhibited the in vitro growth of human and chicken bacterial pathogens and spoilage bacteria. For example, transgene expression significantly reduced growth of aerobic and coliform bacteria in breast muscle and decreased the growth of Salmonella enterica in egg white. Overall these results indicate that overexpression of antimicrobials in the chicken can impact the immune system and increase the antimicrobial capacity of poultry products.
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33
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Lopez-Valladares G, Danielsson-Tham ML, Tham W. Implicated Food Products for Listeriosis and Changes in Serovars of Listeria monocytogenes Affecting Humans in Recent Decades. Foodborne Pathog Dis 2018; 15:387-397. [PMID: 29958028 DOI: 10.1089/fpd.2017.2419] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Listeriosis is a foodborne disease with a high fatality rate, and infection is mostly transmitted through ready-to-eat (RTE) foods contaminated with Listeria monocytogenes, such as gravad/smoked fish, soft cheeses, and sliced processed delicatessen (deli) meat. Food products/dishes stored in vacuum or in modified atmospheres and with extended refrigerator shelf lives provide an opportunity for L. monocytogenes to multiply to large numbers toward the end of the shelf life. Elderly, pregnant women, neonates, and immunocompromised individuals are particularly susceptible to L. monocytogenes. Listeriosis in humans manifests primarily as septicemia, meningitis, encephalitis, gastrointestinal infection, and abortion. In the mid 1990s and early 2000s a shift from L. monocytogenes serovar 4b to serovar 1/2a causing human listeriosis occurred, and serovar 1/2a is becoming more frequently linked to outbreaks of listeriosis, particularly in Europe and Northern America. Consumer lifestyle has changed, and less time is available for food preparation. Modern lifestyle has markedly changed eating habits worldwide, with a consequent increased demand for RTE foods; therefore, more RTE and take away foods are consumed. There is a concern that many Listeria outbreaks are reported from hospitals. Therefore, it is vitally important that foods (especially cooked and chilled) delivered to hospitals and residential homes for senior citizens and elderly people are reheated to at least 72°C: cold food, such as turkey deli meat and cold-smoked and gravad salmon should be free from L. monocytogenes. Several countries have zero tolerance for RTE foods that support the growth of Listeria.
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Affiliation(s)
- Gloria Lopez-Valladares
- School of Hospitality, Culinary Arts and Meal Science, Örebro University , Grythyttan, Sweden
| | | | - Wilhelm Tham
- School of Hospitality, Culinary Arts and Meal Science, Örebro University , Grythyttan, Sweden
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34
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Schjørring S, Gillesberg Lassen S, Jensen T, Moura A, Kjeldgaard JS, Müller L, Thielke S, Leclercq A, Maury MM, Tourdjman M, Donguy MP, Lecuit M, Ethelberg S, Nielsen EM. Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017. ACTA ACUST UNITED AC 2018; 22. [PMID: 29258647 PMCID: PMC5743096 DOI: 10.2807/1560-7917.es.2017.22.50.17-00762] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human isolate from 2016 within the same cgMLST cluster as the Danish isolates (L2-SL8-ST8-CT771). The salmon product came from a third European Union country. WGS can rapidly link human cases and food isolates across Europe.
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Affiliation(s)
- Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Gillesberg Lassen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tenna Jensen
- The Danish Veterinary and Food Administration, Copenhagen, Denmark
| | - Alexandra Moura
- Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Jette S Kjeldgaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Luise Müller
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Stine Thielke
- The Danish Veterinary and Food Administration, Copenhagen, Denmark
| | - Alexandre Leclercq
- Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Mylene M Maury
- Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Mathieu Tourdjman
- Santé Publique France, the French Public Health Agency, Saint-Maurice, France
| | | | - Marc Lecuit
- Paris Descartes University, Sorbonne Paris Cité, Division of Infectious Diseases, Necker-Enfants Malades University Hospital, Institut Imagine, F-75743 Paris, France
.,Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Eva M Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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Whole-Genome Sequencing of Recent Listeria monocytogenes Isolates from Germany Reveals Population Structure and Disease Clusters. J Clin Microbiol 2018; 56:JCM.00119-18. [PMID: 29643197 DOI: 10.1128/jcm.00119-18] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/24/2018] [Indexed: 12/29/2022] Open
Abstract
Listeria monocytogenes causes foodborne outbreaks with high mortality. For improvement of outbreak cluster detection, the German consiliary laboratory for listeriosis implemented whole-genome sequencing (WGS) in 2015. A total of 424 human L. monocytogenes isolates collected in 2007 to 2017 were subjected to WGS and core-genome multilocus sequence typing (cgMLST). cgMLST grouped the isolates into 38 complexes, reflecting 4 known and 34 unknown disease clusters. Most of these complexes were confirmed by single nucleotide polymorphism (SNP) calling, but some were further differentiated. Interestingly, several cgMLST cluster types were further subtyped by pulsed-field gel electrophoresis, partly due to phage insertions in the accessory genome. Our results highlight the usefulness of cgMLST for routine cluster detection but also show that cgMLST complexes require validation by methods providing higher typing resolution. Twelve cgMLST clusters included recent cases, suggesting activity of the source. Therefore, the cgMLST nomenclature data presented here may support future public health actions.
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Jordan K, McAuliffe O. Listeria monocytogenes in Foods. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 86:181-213. [PMID: 30077222 DOI: 10.1016/bs.afnr.2018.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Listeria monocytogenes causes listeriosis, a rare foodborne disease with a mortality rate of 20%-30%. The elderly and immunocompromised are particularly susceptible to listeriosis. L. monocytogenes is ubiquitous in nature and can contaminate food-processing environments, posing a threat to the food chain. This is particularly important for ready-to-eat foods as there is no heat treatment or other antimicrobial step between production and consumption. Thus, occurrence and control of L. monocytogenes are important for industry and public health. Advances in whole-genome sequence technology are facilitating the investigation of disease outbreaks, linking sporadic cases to outbreaks, and linking outbreaks internationally. Novel control methods, such as bacteriophage and bacteriocins, can contribute to a reduction in the occurrence of L. monocytogenes in the food-processing environment, thereby reducing the risk of food contamination and contributing to a reduction in public health issues.
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Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.01.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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