51
|
Paduro C, Montero DA, Chamorro N, Carreño LJ, Vidal M, Vidal R. Ten years of molecular epidemiology surveillance of Listeria monocytogenes in Chile 2008–2017. Food Microbiol 2020; 85:103280. [DOI: 10.1016/j.fm.2019.103280] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 01/30/2023]
|
52
|
Atti Le giornate della ricerca scientificae delle esperienze professionali dei giovani: Società Italiana di Igiene, Medicina Preventiva e Sanità Pubblica (SItI) Roma 20-21 dicembre 2019. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2020; 60:E1-E85. [PMID: 32258536 PMCID: PMC7105054 DOI: 10.15167/2421-4248/jpmh2019.60.4s3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
53
|
Antunes P, Novais C, Peixe L. Food-to-Humans Bacterial Transmission. Microbiol Spectr 2020; 8:10.1128/microbiolspec.mtbp-0019-2016. [PMID: 31950894 PMCID: PMC10810214 DOI: 10.1128/microbiolspec.mtbp-0019-2016] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 12/17/2022] Open
Abstract
Microorganisms vehiculated by food might benefit health, cause minimal change within the equilibrium of the host microbial community or be associated with foodborne diseases. In this chapter we will focus on human pathogenic bacteria for which food is conclusively demonstrated as their transmission mode to human. We will describe the impact of foodborne diseases in public health, the reservoirs of foodborne pathogens (the environment, human and animals), the main bacterial pathogens and food vehicles causing human diseases, and the drivers for the transmission of foodborne diseases related to the food-chain, host or bacteria features. The implication of food-chain (foodborne pathogens and commensals) in the transmission of resistance to antibiotics relevant to the treatment of human infections is also evidenced. The multiplicity and interplay of drivers related to intensification, diversification and globalization of food production, consumer health status, preferences, lifestyles or behaviors, and bacteria adaptation to different challenges (stress tolerance and antimicrobial resistance) from farm to human, make the prevention of bacteria-food-human transmission a modern and continuous challenge. A global One Health approach is mandatory to better understand and minimize the transmission pathways of human pathogens, including multidrug-resistant pathogens and commensals, through food-chain.
Collapse
Affiliation(s)
- Patrícia Antunes
- Faculdade de Ciências da Nutrição e Alimentação, Universidade do Porto, Porto, Portugal
| | - Carla Novais
- Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| |
Collapse
|
54
|
Taylor AJ, Stasiewicz MJ. Persistent and sporadic Listeria monocytogenes strains do not differ when growing at 37 °C, in planktonic state, under different food associated stresses or energy sources. BMC Microbiol 2019; 19:257. [PMID: 31744459 PMCID: PMC6862832 DOI: 10.1186/s12866-019-1631-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
Background The foodborne pathogen Listeria monocytogenes causes the potentially lethal disease listeriosis. Within food-associated environments, L. monocytogenes can persist for long periods and increase the risk of contamination by continued presence in processing facilities or other food-associated environments. Most research on phenotyping of persistent L. monocytogenes’ has explored biofilm formation and sanitizer resistance, with less data examining persistent L. monocytogenes’ phenotypic responses to extrinsic factors, such as variations in osmotic pressure, pH, and energy source availability. It was hypothesized that isolates of persistent strains are able to grow, and grow faster, under a broader range of intrinsic and extrinsic factors compared to closely related isolates of sporadic strains. Results To test this hypothesis, 95 isolates (representing 74 isolates of 20 persistent strains and 21 isolates of sporadic strains) from a series of previous studies in retail delis, were grown at 37 °C, in (i) stress conditions: salt (0, 5, and 10% NaCl), pH (5.2, 7.2, and 9.2), and sanitizer (benzalkonium chloride, 0, 2, and 5 μg/mL) and (ii) energy sources: 25 mM glucose, cellobiose, glycogen, fructose, lactose, and sucrose; the original goal was to follow up with low temperature experiments for treatments where significant differences were observed. Growth rate and the ability to grow of 95 isolates were determined using high-throughput, OD600, growth curves. All stress conditions reduced growth rates in isolates compared to control (p < 0.05). In addition, growth varied by the tested energy sources. In chemically defined, minimal media there was a trend toward more isolates showing growth in all replicates using cellobiose (p = 0.052) compared to the control (glucose) and fewer isolates able to grow in glycogen (p = 0.02), lactose (p = 2.2 × 10− 16), and sucrose (p = 2.2 × 10− 16). Still, at least one isolate was able to consistently grow in every replicate for each energy source. Conclusions The central hypothesis was rejected, as there was not a significant difference in growth rate or ability to grow for retail deli isolates of persistent strains compared to sporadic strains for any treatments at 37 °C. Therefore, these data suggest that persistence is likely not determined by a phenotype unique to persistent strains grown at 37 °C and exposed to extrinsic stresses or variation in energy sources.
Collapse
Affiliation(s)
- Alexander J Taylor
- Department of Food Science and Human Nutrition, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| |
Collapse
|
55
|
Tamburro M, Sammarco ML, Fanelli I, Ripabelli G. Characterization of Listeria monocytogenes serovar 1/2a, 1/2b, 1/2c and 4b by high resolution melting analysis for epidemiological investigations. Int J Food Microbiol 2019; 310:108289. [DOI: 10.1016/j.ijfoodmicro.2019.108289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/24/2019] [Accepted: 08/04/2019] [Indexed: 02/07/2023]
|
56
|
Papić B, Golob M, Kušar D, Pate M, Zdovc I. Source tracking on a dairy farm reveals a high occurrence of subclinical mastitis due to hypervirulent Listeria monocytogenes clonal complexes. J Appl Microbiol 2019; 127:1349-1361. [PMID: 31432571 DOI: 10.1111/jam.14418] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Abstract
AIMS An extensive source investigation was conducted on a dairy farm with neurolisteriosis and subclinical mastitis cases to identify infection source and potential transmission routes of Listeria monocytogenes. METHODS AND RESULTS A total of 36 L. monocytogenes isolates were obtained from animal clinical cases (neurolisteriosis and udder infection) and the farm environment (silage, faeces, water). Isolates were typed using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). Their virulence potential was assessed using the gentamicin protection assay and WGS-based identification of virulence genes. PFGE and WGS revealed a high genetic diversity of L. monocytogenes. An epidemiological link was confirmed for isolates from (i) several subclinical mastitis cases, (ii) silage and subclinical mastitis cases and (iii) different water sources. The neurolisteriosis isolate belonged to clonal complex (CC) 1, but infection source was not identified. A high occurrence (9/47 cows; 19·1%) of subclinical mastitis was observed with isolates belonging to CC2, CC4 and CC11. CONCLUSIONS The dairy farm environment was contaminated with diverse L. monocytogenes strains, including genotypes associated with human disease. Several isolates harboured genetic determinants associated with increased infectious potential in humans. SIGNIFICANCE AND IMPACT OF THE STUDY Results suggest that subclinical listerial mastitis should not be neglected as a potential source of milk contamination. The presence of hypervirulent CCs in subclinical mastitis cases calls for the implementation of improved mastitis detection.
Collapse
Affiliation(s)
- B Papić
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - M Golob
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - D Kušar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - M Pate
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - I Zdovc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
57
|
Gelbíčová T, Florianová M, Tomáštíková Z, Pospíšilová L, Koláčková I, Karpíšková R. Prediction of Persistence of Listeria monocytogenes ST451 in a Rabbit Meat Processing Plant in the Czech Republic. J Food Prot 2019; 82:1350-1356. [PMID: 31313961 DOI: 10.4315/0362-028x.jfp-19-030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This study was focused on characterization of the genetic diversity of Listeria monocytogenes isolated from packed fresh rabbit meat obtained from one producer via retail outlets. The partial aim was to compare the characteristics of a suspect persistent strain with strains from human cases. The occurrence of L. monocytogenes in vacuum-packed rabbit meat was monitored during 2013 to 2016. All strains were characterized by serotyping, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Selected strains, which represented each year, were analyzed using the whole genome sequencing method. L. monocytogenes was detected in 21 (38%) of 56 originally packed rabbit meat samples from one food producer during the whole monitored period. All strains showed the identical serotype (1/2a), AscI/ApaI pulsotype (735/2), and sequence type (ST451). The clonal similarity of strains from rabbit meat was also confirmed on the basis of core genome MLST (on 1,701 loci). This fact suggests the occurrence of a suspect persistent strain in the meat processing plant. Results of core genome MLST enabled us to unambiguously exclude rabbit meat as a source of listeriosis in humans caused by the indistinguishable AscI/ApaI pulsotype and sequence type, although all strains carried all genes important for the virulence of L. monocytogenes. No specific genes that may be associated with its persistence in the food processing environment were detected among the tested strains of ST451.
Collapse
Affiliation(s)
- Tereza Gelbíčová
- Department of Bacteriology, Veterinary Research Institute, Brno, 621 00, Czech Republic
| | - Martina Florianová
- Department of Bacteriology, Veterinary Research Institute, Brno, 621 00, Czech Republic
| | - Zuzana Tomáštíková
- Department of Bacteriology, Veterinary Research Institute, Brno, 621 00, Czech Republic
| | - Lucie Pospíšilová
- Department of Bacteriology, Veterinary Research Institute, Brno, 621 00, Czech Republic
| | - Ivana Koláčková
- Department of Bacteriology, Veterinary Research Institute, Brno, 621 00, Czech Republic
| | - Renáta Karpíšková
- Department of Bacteriology, Veterinary Research Institute, Brno, 621 00, Czech Republic
| |
Collapse
|
58
|
Acar S, Bulut E, Stasiewicz MJ, Soyer Y. Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates. Int J Food Microbiol 2019; 307:108275. [PMID: 31408739 DOI: 10.1016/j.ijfoodmicro.2019.108275] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/02/2023]
Abstract
Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolates were found to have a multi-drug resistance profile (kanamycin, streptomycin, nalidixic acid, tetracycline, sulfonamide, and sometimes to ampicillin) and high prevalence (91%) in Turkish poultry in our previous studies. To investigate the mechanism behind multi-drug antimicrobial resistance (AMR) and high prevalence in Turkish poultry, 23 of the isolates were sequenced for comparative genomic analyses including: SNP-based comparison to S. Infantis from other countries, comparison of antimicrobial resistance genes (AMGs) with AMR phenotypes, and plasmid identification and annotation. Whole-genome SNP-based phylogenetic analysis found that all 23 Turkish S. Infantis isolates formed a distinct, well-supported clade, separate from 243 comparison S. Infantis genomes in GenomeTrakr identified as from the US and EU; the isolates most closely related to the cluster of these Turkish isolates were from Israel and Egypt. AMGs identified by bioinformatic analysis, without differentiating chromosomal or plasmid located genes, implied AMR phenotypes with 94% similarity overall to wet lab data, which was performed by phenotypic and conventional PCR methods. Most of the S. Infantis (21/23) isolates had identifiable plasmids, with 76% (16/21) larger than 100 kb and 48% (10/21) larger than 200 kb. A plasmid larger than 200 kb, with the incompatibility type of IncX1, similar to United States S. Infantis plasmid N55391 (99% query coverage and 99% identity overall), which itself is similar to Italian and Hungarian S. Infantis plasmids. Turkish S. Infantis plasmids had different beta-lactam resistance genes (blaTEM-70, blaTEM-148 and blaTEM-198) than the gene blaCTX-M-65 found in S. Infantis plasmids from other countries. This is the first observation of these three genes in S. Infantis isolates. The plasmids larger than 200 kb had two distinct regions of interest: Site 1 and Site 2. Site 1 (around 130 kb) had virulence- and bacteriocin- associated genes such as bacteriocin secretion system and type II toxin-antitoxin system genes (vagC, ccdA, ccdB, mchE, cvaB) and an aminoglycoside resistance gene (str). Site 2 (around 75-110 kb) had the antimicrobial resistance genes (aadA, sulI, tetA, tetR) and mercury (mer) resistance gene on tranposons Tn552 and Tn501. Presence of these AMR and virulence genes suggests they may have a role in the emergence of S. Infantis in poultry and support treating this serotype as a an important human health hazard.
Collapse
Affiliation(s)
- Sinem Acar
- Department of Food Engineering, Middle East Technical University, Ankara 06810, Turkey
| | - Ece Bulut
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yeşim Soyer
- Department of Food Engineering, Middle East Technical University, Ankara 06810, Turkey.
| |
Collapse
|
59
|
Brown E, Dessai U, McGarry S, Gerner-Smidt P. Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States. Foodborne Pathog Dis 2019; 16:441-450. [PMID: 31194586 PMCID: PMC6653787 DOI: 10.1089/fpd.2019.2662] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Whole-genome sequencing (WGS) is increasingly used by food regulatory and public health agencies in the United States to facilitate the detection, investigation, and control of foodborne bacterial outbreaks, and food regulatory and other activities in support of food safety. WGS has added a level of precision to the surveillance leading to faster and more efficient decision making in the preparedness and response to foodborne infections. In this review, we report the history of WGS technology at the Centers for Disease Control & Prevention (CDC), the Food and Drug Administration (FDA), and the United States Department of Agriculture's Food Safety and Inspection Service (USDA/FSIS) as it applies to food safety. The basic principle of the method, the analysis, and interpretation of the data are explained as is its major strengths and limitations. We also describe the benefits and possibilities of the WGS technology to the food industry throughout the farm-to-fork continuum and the prospects of metagenomic sequencing applied directly to the sample specimen with or without pre-enrichment culture.
Collapse
Affiliation(s)
- Eric Brown
- 1 Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland
| | - Uday Dessai
- 2 Office of Public Health Science, Food Safety and Inspection Service, United States Department of Agriculture, Washington, District of Columbia
| | - Sherri McGarry
- 3 Enteric Diseases Laboratory Branch, Centers for Disease Control & Prevention, Atlanta, Georgia
| | - Peter Gerner-Smidt
- 3 Enteric Diseases Laboratory Branch, Centers for Disease Control & Prevention, Atlanta, Georgia
| |
Collapse
|
60
|
Gilbert GL, Degeling C, Johnson J. Communicable Disease Surveillance Ethics in the Age of Big Data and New Technology. Asian Bioeth Rev 2019; 11:173-187. [PMID: 32218872 PMCID: PMC7091643 DOI: 10.1007/s41649-019-00087-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/07/2019] [Accepted: 05/01/2019] [Indexed: 11/29/2022] Open
Abstract
Surveillance is essential for communicable disease prevention and control. Traditional notification of demographic and clinical information, about individuals with selected (notifiable) infectious diseases, allows appropriate public health action and is protected by public health and privacy legislation, but is slow and insensitive. Big data-based electronic surveillance, by commercial bodies and government agencies (for profit or population control), which draws on a plethora of internet- and mobile device-based sources, has been widely accepted, if not universally welcomed. Similar anonymous digital sources also contain syndromic information, which can be analysed, using customised algorithms, to rapidly predict infectious disease outbreaks, but the data are nonspecific and predictions sometimes misleading. However, public health authorities could use these online sources, in combination with de-identified personal health data, to provide more accurate and earlier warning of infectious disease events-including exotic or emerging infections-even before the cause is confirmed, and allow more timely public health intervention. Achieving optimal benefits would require access to selected data from personal electronic health and laboratory (including pathogen genomic) records and the potential to (confidentially) re-identify individuals found to be involved in outbreaks, to ensure appropriate care and infection control. Despite existing widespread digital surveillance and major potential community benefits of extending its use to communicable disease control, there is considerable public disquiet about allowing public health authorities access to personal health data. Informed public discussion, greater transparency and an ethical framework will be essential to build public trust in the use of new technology for communicable disease control.
Collapse
Affiliation(s)
- Gwendolyn L. Gilbert
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
- Sydney Health Ethics, Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Chris Degeling
- Research for Social Change, Faculty of Social Sciences, University of Wollongong, Wollongong, Australia
| | - Jane Johnson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
- Sydney Health Ethics, Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| |
Collapse
|
61
|
Yoshimura D, Kajitani R, Gotoh Y, Katahira K, Okuno M, Ogura Y, Hayashi T, Itoh T. Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP. Microb Genom 2019; 5. [PMID: 31099741 PMCID: PMC6562250 DOI: 10.1099/mgen.0.000261] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacteria are highly diverse, even within a species; thus, there have been many studies which classify a single species into multiple types and analyze the genetic differences between them. Recently, the use of whole-genome sequencing (WGS) has been popular for these analyses, and the identification of single-nucleotide polymorphisms (SNPs) between isolates is the most basic analysis performed following WGS. The performance of SNP-calling methods therefore has a significant effect on the accuracy of downstream analyses, such as phylogenetic tree inference. In particular, when closely related isolates are analyzed, e.g. in outbreak investigations, some SNP callers tend to detect a high number of false-positive SNPs compared with the limited number of true SNPs among isolates. However, the performances of various SNP callers in such a situation have not been validated sufficiently. Here, we show the results of realistic benchmarks of commonly used SNP callers, revealing that some of them exhibit markedly low accuracy when target isolates are closely related. As an alternative, we developed a novel pipeline BactSNP, which utilizes both assembly and mapping information and is capable of highly accurate and sensitive SNP calling in a single step. BactSNP is also able to call SNPs among isolates when the reference genome is a draft one or even when the user does not input the reference genome. BactSNP is available at https://github.com/IEkAdN/BactSNP.
Collapse
Affiliation(s)
- Dai Yoshimura
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Rei Kajitani
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yasuhiro Gotoh
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuyuki Katahira
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Miki Okuno
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yoshitoshi Ogura
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- 2Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takehiko Itoh
- 1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| |
Collapse
|
62
|
Jagadeesan B, Baert L, Wiedmann M, Orsi RH. Comparative Analysis of Tools and Approaches for Source Tracking Listeria monocytogenes in a Food Facility Using Whole-Genome Sequence Data. Front Microbiol 2019; 10:947. [PMID: 31143162 PMCID: PMC6521219 DOI: 10.3389/fmicb.2019.00947] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/15/2019] [Indexed: 12/04/2022] Open
Abstract
As WGS is increasingly used by food industry to characterize pathogen isolates, users are challenged by the variety of analysis approaches available, ranging from methods that require extensive bioinformatics expertise to commercial software packages. This study aimed to assess the impact of analysis pipelines (i.e., different hqSNP pipelines, a cg/wgMLST pipeline) and the reference genome selection on analysis results (i.e., hqSNP and allelic differences as well as tree topologies) and conclusion drawn. For these comparisons, whole genome sequences were obtained for 40 Listeria monocytogenes isolates collected over 18 years from a cold-smoked salmon facility and 2 other isolates obtained from different facilities as part of academic research activities; WGS data were analyzed with three hqSNP pipelines and two MLST pipelines. After initial clustering using a k-mer based approach, hqSNP pipelines were run using two types of reference genomes: (i) closely related closed genomes (“closed references”) and (ii) high-quality de novo assemblies of the dataset isolates (“draft references”). All hqSNP pipelines identified similar hqSNP difference ranges among isolates in a given cluster; use of different reference genomes showed minimal impacts on hqSNP differences identified between isolate pairs. Allelic differences obtained by wgMLST showed similar ranges as hqSNP differences among isolates in a given cluster; cgMLST consistently showed fewer differences than wgMLST. However, phylogenetic trees and dendrograms, obtained based on hqSNP and cg/wgMLST data, did show some incongruences, typically linked to clades supported by low bootstrap values in the trees. When a hqSNP cutoff was used to classify isolates as “related” or “unrelated,” use of different pipelines yielded a considerable number of discordances; this finding supports that cut-off values are valuable to provide a starting point for an investigation, but supporting and epidemiological evidence should be used to interpret WGS data. Overall, our data suggest that cgMLST-based data analyses provide for appropriate subtype differentiation and can be used without the need for preliminary data analyses (e.g., k-mer based clustering) or external closed reference genomes, simplifying data analyses needs. hqSNP or wgMLST analyses can be performed on the isolate clusters identified by cgMLST to increase the precision on determining the genomic similarity between isolates.
Collapse
Affiliation(s)
- Balamurugan Jagadeesan
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland
| | - Leen Baert
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
63
|
Rothrock MJ, Micciche AC, Bodie AR, Ricke SC. Listeria Occurrence and Potential Control Strategies in Alternative and Conventional Poultry Processing and Retail. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00033] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
64
|
Listeria monocytogenes isolates from ready to eat plant produce are diverse and have virulence potential. Int J Food Microbiol 2019; 299:23-32. [PMID: 30939364 DOI: 10.1016/j.ijfoodmicro.2019.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 11/24/2022]
Abstract
Listeria monocytogenes is sporadically detected on a range of ready to eat fresh produce lines, such as spinach and rocket, and is a threat to public health. However, little is known about the diversity of L. monocytogenes present on fresh produce and their potential pathogenicity. In this work, fifteen Listeria monocytogenes isolates from the UK fresh produce supply chain were characterised using whole genome sequencing (WGS). Additionally, isolates were characterised based on their ability to form biofilm. Whole genome sequencing data was used to determine the sequence type of isolates based on multi-locus sequence typing (MLST), construct a core single nucleotide polymorphism (SNP) phylogeny and determine the presence of virulence and resistance associated genes. MLST revealed 9 distinct sequence types (STs) spanning 2 lineages (I & II) with one isolate belonging to the ST6 subtype, strains from which have been recently implicated in two large, food-associated L. monocytogenes outbreaks in South Africa and across Europe. Although most of the 15 isolates were different, comparison of core genome SNPs showed 4 pairs of 'indistinguishable' strains (<5 SNPs difference). Virulence profiling revealed that some isolates completely lacked the Listeria pathogenicity island-3 (LIPI-3) amongst other virulence factors. Investigation of the inlA gene showed that no strains in this study contained a premature stop codon (PMSC), an indicator of attenuated virulence. Assessment of biofilm production showed that isolates found in the fresh produce supply chain differ in their ability to form biofilm. This trait is considered important for L. monocytogenes to persist in environments associated with food production and processing. Overall the work indicates that a genetically diverse range of L. monocytogenes strains is present in the UK fresh produce supply chain and the virulence profiles found suggests that at least some of the strains are capable of causing human illness. Interestingly, the presence of some genetically indistinguishable isolates within the 15 isolates examined suggests that cross-contamination in the fresh produce environment does occur. These findings have useful implications in terms of food safety and for informing microbial surveillance programmes in the UK fresh produce supply chain.
Collapse
|
65
|
Reimer A, Weedmark K, Petkau A, Peterson CL, Walker M, Knox N, Kent H, Mabon P, Berry C, Tyler S, Tschetter L, Jerome M, Allen V, Hoang L, Bekal S, Clark C, Nadon C, Van Domselaar G, Pagotto F, Graham M, Farber J, Gilmour M. Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria. Microb Genom 2019; 5. [PMID: 30648944 PMCID: PMC6412057 DOI: 10.1099/mgen.0.000237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian Listeria outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence.
Collapse
Affiliation(s)
- Aleisha Reimer
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Kelly Weedmark
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Aaron Petkau
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Matthew Walker
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Natalie Knox
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Heather Kent
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Philip Mabon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Chrystal Berry
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Shaun Tyler
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Morganne Jerome
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Vanessa Allen
- 3Public Health Ontario, Toronto, ON, M5G 1M1, Canada
| | - Linda Hoang
- 4British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Sadjia Bekal
- 5Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, H9X 3R5, Canada
| | - Clifford Clark
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Celine Nadon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Franco Pagotto
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Morag Graham
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Jeff Farber
- 6University of Guelph, Guelph, ON, N1G 2W, Canada
| | - Matthew Gilmour
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| |
Collapse
|
66
|
Taylor AJ, Stasiewicz MJ. CRISPR-Based Subtyping Using Whole Genome Sequence Data Does Not Improve Differentiation of Persistent and Sporadic Listeria monocytogenes Strains. J Food Sci 2019; 84:319-326. [PMID: 30620778 DOI: 10.1111/1750-3841.14426] [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] [Received: 09/11/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Abstract
The foodborne pathogen Listeria monocytogenes can persist in food-associated environments for long periods. To identify persistent strains, the subtyping method pulsed-field gel electrophoresis (PFGE) is being replaced by whole genome sequence (WGS)-based subtyping. It was hypothesized that analyzing specific mobile genetic elements, CRISPR (Clustered Regularly Interspaced Short Palindromic Short Repeat) spacer arrays, extracted from WGS data, could differentiate persistent and sporadic isolates within WGS-based clades. To test this hypothesis, 175 L. monocytogenes isolates, previously recovered from retail delis, were analyzed for CRISPR spacers using CRISPRFinder. These isolates represent 23 phylogenetic clades defined by WGS-based single nucleotide polymorphisms and closely related sporadic isolates. In 174/175 (99.4%) of isolates, at least one array with one spacer was identified. Numbers of spacers in a single array ranged from 1 to 28 spacers. Isolates were grouped into 13 spacer patterns (SPs) based on observed variability in the presence or absence of whole spacers. SP variation was consistent with WGS-based clades forming patterns of (i) one SP to one clade, (ii) one SP across many clades, (iii) many SPs within one clade, and (iv) many SPs across many clades. Unfortunately, SPs did not appear to differentiate persistent from sporadic isolates within any WGS-based clade. Overall, these data show that (i) CRISPR arrays are common in WGS data for these food-associated L. monocytogenes and (ii) CRISPR subtyping cannot improve the identification of persistent or sporadic isolates from retail delis. PRACTICAL APPLICATION: CRISPR spacer arrays are present in L. monocytogenes isolates and CRISPR spacer patterns are consistent with previous subtyping methods. These mobile genetic artifacts cannot improve the differentiation between persistent and sporadic L. monocytogenes isolates, used in this study. While CRISPR-based subtyping has been useful for other pathogens, it is not useful in understanding persistence in L. monocytogenes. Thus, the food safety community might be able to use CRISPRs in other areas, but CRISPRs do not seem likely to improve the differentiation of persistence in L. monocytogenes isolates from retail delis.
Collapse
Affiliation(s)
- Alexander J Taylor
- Dept. of Food Science and Human Nutrition, Coll. of Agricultural, Consumer, and Environmental Sciences, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew J Stasiewicz
- Dept. of Food Science and Human Nutrition, Coll. of Agricultural, Consumer, and Environmental Sciences, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
67
|
Bardsley CA, Boyer RR, Rideout SL, Strawn LK. Survival of Listeria monocytogenes on the surface of basil, cilantro, dill, and parsley plants. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.07.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
68
|
Cherifi T, Carrillo C, Lambert D, Miniaï I, Quessy S, Larivière-Gauthier G, Blais B, Fravalo P. Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes. BMC Microbiol 2018; 18:220. [PMID: 30572836 PMCID: PMC6302515 DOI: 10.1186/s12866-018-1363-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/02/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The aim of this study was to characterize the genomes of 30 Listeria monocytogenes isolates collected at a pig slaughterhouse to determine the molecular basis for their persistence. RESULTS Comparison of the 30 L. monocytogenes genomes showed that successive isolates (i.e., persistent types) recovered from thew sampling site could be linked on the basis of single nucleotide variants confined to prophage regions. In addition, our study revealed the presence among these strains of the bcrABC cassette which is known to produce efflux pump-mediated benzalkonium chloride resistance, and which may account for the persistence of these isolates in the slaughterhouse environment. The presence of the bcrABC cassette was confirmed by WGS and PCR and the resistance phenotype was determined by measuring minimum inhibitory concentrations. Furthermore, the BC-resistant strains were found to produce lower amounts of biofilm in the presence of sublethal concentrations of BC. CONCLUSIONS High resolution SNP-based typing and determination of the bcrABC cassette may provide a means of distinguishing between resident and sporadic L. monocytogenes isolates, and this in turn will support better management of this pathogen in the food industry.
Collapse
Affiliation(s)
- Tamazight Cherifi
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Catherine Carrillo
- Food Microbiology Research Team, Canadian Food Inspection Agency, Ottawa, ON Canada
| | - Dominic Lambert
- Food Microbiology Research Team, Canadian Food Inspection Agency, Ottawa, ON Canada
| | - Ilhem Miniaï
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Sylvain Quessy
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Guillaume Larivière-Gauthier
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| | - Burton Blais
- Food Microbiology Research Team, Canadian Food Inspection Agency, Ottawa, ON Canada
| | - Philippe Fravalo
- Chaire de Recherche en Salubrité des Viandes, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Centre de Recherche sur les Maladies Infectieuses Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
- Groupe de Recherche et D’enseignement En Salubrité Des Aliments, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC Canada
| |
Collapse
|
69
|
Wang YU, Pettengill JB, Pightling A, Timme R, Allard M, Strain E, Rand H. Genetic Diversity of Salmonella and Listeria Isolates from Food Facilities. J Food Prot 2018; 81:2082-2089. [PMID: 30485763 DOI: 10.4315/0362-028x.jfp-18-093] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Food production-related facilities (farms, packing houses, etc.) are monitored for foodborne pathogens, and data from these facilities can provide a rich source of information about the population structure and genetic diversity of Salmonella and Listeria. This information is of both academic interest for understanding the evolutionary forces acting on these organisms and of practical interest to those responsible for controlling pathogens in facilities and to those analyzing data from facilities in the context of public health decision making. We have collected information about all positive isolates from facility inspections performed by the U.S. Food and Drug Administration for which whole genome sequencing data are available. The within- and between-facilities observed genetic diversity of isolates was computed and related to the common origin of isolates (as the common collected facility). This relationship provides quantification for assessing the relationship between isolates based on their genetic similarity quantified by single-nucleotide polymorphisms (SNPs). Our results show that if the genetic distance ( D) between two isolates is low, then more likely than not they are from the same facility or have some overlap in their supply chain. For example, if the genetic distance is no more than 20 SNPs, the probability ( P) that two isolates come from the same facility = 0.66 for Salmonella and 0.70 for Listeria. However, if two isolates come from different facilities, their genetic distance is likely large (for Salmonella, P( D > 20 SNPs) = 0.99982; for Listeria, P( D > 20 SNPs) = 0.99949); even if two isolates come from the same facility, their genetic distance is also very likely large (for Salmonella, P( D > 20 SNPs) = 0.794; for Listeria, P( D > 20 SNPs) = 0.692). These results provide insight into what SNP thresholds might be appropriate when determining whether two isolates are from the same facility and thus would be of interest to those investigating foodborne outbreaks and conducting traceback investigations.
Collapse
Affiliation(s)
- Y U Wang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, USA
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, USA
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, USA
| | - Ruth Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, USA
| | - Errol Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, USA
| | - Hugh Rand
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, USA
| |
Collapse
|
70
|
Cook PW, Nightingale KK. Use of omics methods for the advancement of food quality and food safety. Anim Front 2018; 8:33-41. [PMID: 32002228 DOI: 10.1093/af/vfy024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Peter W Cook
- Center for Food Safety, University of Georgia, Griffin, GA.,Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | | |
Collapse
|
71
|
Rivera D, Toledo V, Reyes-Jara A, Navarrete P, Tamplin M, Kimura B, Wiedmann M, Silva P, Moreno Switt AI. Approaches to empower the implementation of new tools to detect and prevent foodborne pathogens in food processing. Food Microbiol 2018; 75:126-132. [DOI: 10.1016/j.fm.2017.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/13/2017] [Indexed: 11/15/2022]
|
72
|
Van Walle I, Björkman JT, Cormican M, Dallman T, Mossong J, Moura A, Pietzka A, Ruppitsch W, Takkinen J. Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015. Euro Surveill 2018; 23:1700798. [PMID: 30131096 PMCID: PMC6205253 DOI: 10.2807/1560-7917.es.2018.23.33.1700798] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background and aimThe trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEA-wide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/EEA countries from 2010-15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58‒68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.
Collapse
Affiliation(s)
- Ivo Van Walle
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | | | | | - Joël Mossong
- Laboratoire national de santé, Dudelange, Luxembourg
| | - Alexandra Moura
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Biology of Infection Unit, Inserm U1117, Paris, France
| | - Ariane Pietzka
- Österreichische Agentur für Gesundheit und Ernährungssicherheit, Graz/Vienna, Austria
| | - Werner Ruppitsch
- Österreichische Agentur für Gesundheit und Ernährungssicherheit, Graz/Vienna, Austria
| | - Johanna Takkinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| |
Collapse
|
73
|
Smith A, Moorhouse E, Monaghan J, Taylor C, Singleton I. Sources and survival of Listeria monocytogenes on fresh, leafy produce. J Appl Microbiol 2018; 125:930-942. [PMID: 30039586 DOI: 10.1111/jam.14025] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/31/2018] [Accepted: 06/18/2018] [Indexed: 12/26/2022]
Abstract
Listeria monocytogenes is an intracellular human pathogen which enters the body through contaminated food stuffs and is known to contaminate fresh leafy produce such as spinach, lettuce and rocket. Routinely, fresh leafy produce is grown and processed on a large scale before reaching the consumer through various products such as sandwiches and prepared salads. From farm to fork, the fresh leafy produce supply chain (FLPSC) is complex and contains a diverse range of environments where L. monocytogenes is sporadically detected during routine sampling of produce and processing areas. This review describes sources of the bacteria in the FLPSC and outlines the physiological and molecular mechanisms behind its survival in the different environments associated with growing and processing fresh produce. Finally, current methods of source tracking the bacteria in the context of the food supply chain are discussed with emphasis on how these methods can provide additional, valuable information on the risk that L. monocytogenes isolates pose to the consumer.
Collapse
Affiliation(s)
- A Smith
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | | | - J Monaghan
- Crop and Environment Sciences, Harper Adams University, Newport, UK
| | - C Taylor
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - I Singleton
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| |
Collapse
|
74
|
Pightling AW, Pettengill JB, Luo Y, Baugher JD, Rand H, Strain E. Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations. Front Microbiol 2018; 9:1482. [PMID: 30042741 PMCID: PMC6048267 DOI: 10.3389/fmicb.2018.01482] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 12/05/2022] Open
Abstract
Whole-genome sequence (WGS) analysis has revolutionized the food safety industry by enabling high-resolution typing of foodborne bacteria. Higher resolving power allows investigators to identify origins of contamination during illness outbreaks and regulatory activities quickly and accurately. Government agencies and industry stakeholders worldwide are now analyzing WGS data routinely. Although researchers have published many studies that assess the efficacy of WGS data analysis for source attribution, guidance for interpreting WGS analyses is lacking. Here, we provide the framework for interpreting WGS analyses used by the Food and Drug Administration's Center for Food Safety and Applied Nutrition (CFSAN). We based this framework on the experiences of CFSAN investigators, collaborations and interactions with government and industry partners, and evaluation of the published literature. A fundamental question for investigators is whether two or more bacteria arose from the same source of contamination. Analysts often count the numbers of nucleotide differences [single-nucleotide polymorphisms (SNPs)] between two or more genome sequences to measure genetic distances. However, using SNP thresholds alone to assess whether bacteria originated from the same source can be misleading. Bacteria that are isolated from food, environmental, or clinical samples are representatives of bacterial populations. These populations are subject to evolutionary forces that can change genome sequences. Therefore, interpreting WGS analyses of foodborne bacteria requires a more sophisticated approach. Here, we present a framework for interpreting WGS analyses that combines SNP counts with phylogenetic tree topologies and bootstrap support. We also clarify the roles of WGS, epidemiological, traceback, and other evidence in forming the conclusions of investigations. Finally, we present examples that illustrate the application of this framework to real-world situations.
Collapse
Affiliation(s)
- Arthur W. Pightling
- Biostatistics and Bioinformatics, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | | | | | | | | | | |
Collapse
|
75
|
Zoellner C, Ceres K, Ghezzi-Kopel K, Wiedmann M, Ivanek R. Design Elements of Listeria Environmental Monitoring Programs in Food Processing Facilities: A Scoping Review of Research and Guidance Materials. Compr Rev Food Sci Food Saf 2018; 17:1156-1171. [PMID: 33350161 DOI: 10.1111/1541-4337.12366] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/04/2018] [Accepted: 05/11/2018] [Indexed: 01/08/2023]
Abstract
Occurrence of Listeria monocytogenes (Lm), the causative agent of listeriosis, in food processing facilities presents considerable challenges to food producers and food safety authorities. Design of an effective, risk-based environmental monitoring (EM) program is essential for finding and eliminating Lm from the processing environment to prevent product contamination. A scoping review was conducted to collate and synthesize available research and guidance materials on Listeria EM in food processing facilities. An exhaustive search was performed to identify all available research, industry and regulatory documents, and search results were screened for relevance based on eligibility criteria. After screening, 198 references were subjected to an in-depth review and categorized according to objectives for conducting Listeria sampling in food processing facilities and food sector. Mapping of the literature revealed research and guidance gaps by food sector, as fresh produce was the focus in only 10 references, compared to 72 on meat, 52 on fish and seafood, and 50 on dairy. Review of reported practices and guidance highlighted key design elements of EM, including the number, location, timing and frequency of sampling, as well as methods of detection and confirmation, and record-keeping. While utilization of molecular subtyping methods is a trend that will continue to advance understanding of Listeria contamination risks, improved study design and reporting standards by researchers will be essential to assist the food industry optimize their EM design and decision-making. The comprehensive collection of documents identified and synthesized in this review aids continued efforts to minimize the risk of Lm contaminated foods.
Collapse
Affiliation(s)
- Claire Zoellner
- Dept. of Population Medicine and Diagnostic Sciences, Cornell Univ., Ithaca, N.Y. 14850, U.S.A
| | - Kristina Ceres
- Dept. of Population Medicine and Diagnostic Sciences, Cornell Univ., Ithaca, N.Y. 14850, U.S.A
| | - Kate Ghezzi-Kopel
- Albert R. Mann Library, Univ. Library, 237 Mann Dr, Ithaca, N.Y. 14853, U.S.A
| | - Martin Wiedmann
- Dept. of Food Science, Cornell Univ., Ithaca, N.Y. 14853, U.S.A
| | - Renata Ivanek
- Dept. of Population Medicine and Diagnostic Sciences, Cornell Univ., Ithaca, N.Y. 14850, U.S.A
| |
Collapse
|
76
|
Prevalence and persistence of Listeria monocytogenes in premises and products of small food business operators in Northern Ireland. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
77
|
Fegan N, Jenson I. The role of meat in foodborne disease: Is there a coming revolution in risk assessment and management? Meat Sci 2018; 144:22-29. [PMID: 29716760 DOI: 10.1016/j.meatsci.2018.04.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022]
Abstract
Meat has featured prominently as a source of foodborne disease and a public health concern. For about the past 20 years the risk management paradigm has dominated international thinking about food safety. Control through the supply chain is supported by risk management concepts, as the public health risk at the point of consumption becomes the accepted outcome based measure. Foodborne pathogens can be detected at several points in the supply chain and determining the source of where these pathogens arise and how they behave throughout meat production and processing are important parts of risk based approaches. Recent improvements in molecular and genetic based technologies and data analysis for investigating source attribution and pathogen behaviour have enabled greater insights into how foodborne outbreaks occur and where controls can be implemented. These new approaches will improve our understanding of the role of meat in foodborne disease and are expected to have a significant impact on our understanding in the coming years.
Collapse
Affiliation(s)
- Narelle Fegan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, 671 Sneydes Rd, Werribee, VIC 3030, Australia.
| | - Ian Jenson
- Meat and Livestock Australia, Level 1, 40 Mount Street, North Sydney, NSW 2060, Australia
| |
Collapse
|
78
|
Pasquali F, Palma F, Guillier L, Lucchi A, De Cesare A, Manfreda G. Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology. Front Microbiol 2018; 9:596. [PMID: 29662481 PMCID: PMC5890179 DOI: 10.3389/fmicb.2018.00596] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 03/15/2018] [Indexed: 01/15/2023] Open
Abstract
Listeria monocytogenes is a foodborne pathogen adapted to survive and persist in multiple environments. Following two previous studies on prevalence and virulence of L. monocytogenes ST121 and ST14 repeatedly collected in a the same rabbit-meat processing plant, the research questions of the present study were to: (1) assess persistence of L. monocytogenes isolates from the rabbit-plant; (2) select genes associated to physiological adaptation to the food-processing environment; (3) compare presence/absence/truncation of these genes in newly sequenced and publicly available ST121 and ST14 genomes. A total of 273 draft genomes including ST121 and ST14 newly sequenced and publicly available draft genomes were analyzed. Whole-genome Single Nucleotide Polymorfism (wgSNP) analysis was performed separately on the assemblies of ST121 and ST14 draft genomes. SNPs alignments were used to infer phylogeny. A dataset of L. monocytogenes ecophysiology genes was built based on a comprehensive literature review. The 94 selected genes were screened on the assemblies of all ST121 and ST14 draft genomes. Significant gene enrichments were evaluated by statistical analyses. A persistent ST14 clone, including 23 out of 27 newly sequenced genomes, was circulating in the rabbit-meat plant along with two not persistent clones. A significant enrichment was observed in ST121 genomes concerning stress survival islet 2 (SSI-2) (alkaline and oxidative stress), qacH gene (resistance to benzalkonium chloride), cadA1C gene cassette (resistance to 70 mg/l of cadmium chloride) and a truncated version of actA gene (biofilm formation). Conversely, ST14 draft genomes were enriched with a full-length version of actA gene along with the Listeria Genomic Island 2 (LGI 2) including the ars operon (arsenic resistance) and the cadA4C gene cassette (resistance to 35 mg/l of cadmium chloride). Phenotypic tests confirmed ST121 as a weak biofilm producer in comparison to ST14. In conclusion, ST121 carried the qacH gene and was phenotypically resistant to quaternary ammonium compounds. This property might contribute to the high prevalence of ST121 in food processing plants. ST14 showed greater ability to form biofilms, which might contribute to the occasional colonization and persistence on harborage sites where sanitizing procedures are difficult to display.
Collapse
Affiliation(s)
- Frédérique Pasquali
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Federica Palma
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Laurent Guillier
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Maisons-Alfort, France
| | - Alex Lucchi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Alessandra De Cesare
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Gerardo Manfreda
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| |
Collapse
|
79
|
Heir E, Møretrø T, Simensen A, Langsrud S. Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments. Int J Food Microbiol 2018; 275:46-55. [PMID: 29631210 DOI: 10.1016/j.ijfoodmicro.2018.03.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 02/05/2023]
Abstract
Interactions and competition between resident bacteria in food processing environments could affect their ability to survive, grow and persist in microhabitats and niches in the food industry. In this study, the competitive ability of L. monocytogenes strains grown together in separate culture mixes with other L. monocytogenes (L. mono mix), L. innocua (Listeria mix), Gram-negative bacteria (Gram- mix) and with a multigenera mix (Listeria + Gram- mix) was investigated in biofilms on stainless steel and in suspensions at 12 °C. The mixed cultures included resident bacteria from processing surfaces in meat and salmon industry represented by L. monocytogenes (n = 6), L. innocua (n = 5) and Gram-negative bacteria (n = 6; Acinetobacter sp., Pseudomonas fragi, Pseudomonas fluorescens, Serratia liquefaciens, Stenotrophomonas maltophilia). Despite hampered in growth in mixed cultures, L. monocytogenes established in biofilms with counts at day nine between 7.3 and 9.0 log per coupon with the lowest counts in the Listeria + G- mix that was dominated by Pseudomonas. Specific L. innocua inhibited growth of L. monocytogenes strains differently; inhibition that was further enhanced by the background Gram-negative microbiota. In these multispecies and multibacteria cultures, the growth competitive effects lead to the dominance of a strong competitor L. monocytogenes strain that was only slightly inhibited by L. innocua and showed strong competitive abilities in mixed cultures with resident Gram-negative bacteria. The results indicates complex patterns of bacterial interactions and L. monocytogenes inhibition in the multibacteria cultures that only partially depend on cell contact and likely involve various antagonistic and bacterial tolerance mechanisms. The study indicates large variations among L. monocytogenes in their competitiveness under multibacterial culture conditions that should be considered in further studies towards understanding of L. monocytogenes persistence in food processing facilities.
Collapse
Affiliation(s)
- Even Heir
- Nofima, The Norwegian Institute of Food, Fishery and Aquaculture Research, N-1430 Aas, Norway.
| | - Trond Møretrø
- Nofima, The Norwegian Institute of Food, Fishery and Aquaculture Research, N-1430 Aas, Norway
| | - Andreas Simensen
- Nofima, The Norwegian Institute of Food, Fishery and Aquaculture Research, N-1430 Aas, Norway
| | - Solveig Langsrud
- Nofima, The Norwegian Institute of Food, Fishery and Aquaculture Research, N-1430 Aas, Norway
| |
Collapse
|
80
|
|
81
|
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]
|
82
|
Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Fernández Escámez PS, Girones R, Herman L, Koutsoumanis K, Nørrung B, Robertson L, Ru G, Sanaa M, Simmons M, Skandamis P, Snary E, Speybroeck N, Ter Kuile B, Threlfall J, Wahlström H, Takkinen J, Wagner M, Arcella D, Da Silva Felicio MT, Georgiadis M, Messens W, Lindqvist R. Listeria monocytogenes contamination of ready-to-eat foods and the risk for human health in the EU. EFSA J 2018; 16:e05134. [PMID: 32760461 PMCID: PMC7391409 DOI: 10.2903/j.efsa.2018.5134] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Food safety criteria for Listeria monocytogenes in ready-to-eat (RTE) foods have been applied from 2006 onwards (Commission Regulation (EC) 2073/2005). Still, human invasive listeriosis was reported to increase over the period 2009-2013 in the European Union and European Economic Area (EU/EEA). Time series analysis for the 2008-2015 period in the EU/EEA indicated an increasing trend of the monthly notified incidence rate of confirmed human invasive listeriosis of the over 75 age groups and female age group between 25 and 44 years old (probably related to pregnancies). A conceptual model was used to identify factors in the food chain as potential drivers for L. monocytogenes contamination of RTE foods and listeriosis. Factors were related to the host (i. population size of the elderly and/or susceptible people; ii. underlying condition rate), the food (iii. L. monocytogenes prevalence in RTE food at retail; iv. L. monocytogenes concentration in RTE food at retail; v. storage conditions after retail; vi. consumption), the national surveillance systems (vii. improved surveillance), and/or the bacterium (viii. virulence). Factors considered likely to be responsible for the increasing trend in cases are the increased population size of the elderly and susceptible population except for the 25-44 female age group. For the increased incidence rates and cases, the likely factor is the increased proportion of susceptible persons in the age groups over 45 years old for both genders. Quantitative modelling suggests that more than 90% of invasive listeriosis is caused by ingestion of RTE food containing > 2,000 colony forming units (CFU)/g, and that one-third of cases are due to growth in the consumer phase. Awareness should be increased among stakeholders, especially in relation to susceptible risk groups. Innovative methodologies including whole genome sequencing (WGS) for strain identification and monitoring of trends are recommended.
Collapse
|
83
|
Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. ACTA ACUST UNITED AC 2017; 22:30544. [PMID: 28662764 PMCID: PMC5479977 DOI: 10.2807/1560-7917.es.2017.22.23.30544] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/11/2017] [Indexed: 11/21/2022]
Abstract
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.
Collapse
Affiliation(s)
- Celine Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Canada.,These authors contributed equally to this work
| | - Ivo Van Walle
- These authors contributed equally to this work.,European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Josefina Campos
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | - Isabel Chinen
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | | | - Brent Gilpin
- Institute of Environmental Science and Research Limited; Christchurch, New Zealand
| | | | - Kai Man Kam
- Chinese University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | - Enrique Perez
- Pan American Health Organization/World Health Organization, Washington, DC, United States
| | - Eija Trees
- Centers for Disease Control and Prevention, United States
| | - Kristy Kubota
- Association of Public Health Laboratories, United States
| | - Johanna Takkinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | | | -
- The members of the FWD-NEXT Expert Panel are listed at the end of the article
| |
Collapse
|
84
|
Rantsiou K, Kathariou S, Winkler A, Skandamis P, Saint-Cyr MJ, Rouzeau-Szynalski K, Amézquita A. Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment. Int J Food Microbiol 2017; 287:3-9. [PMID: 29246458 DOI: 10.1016/j.ijfoodmicro.2017.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/16/2017] [Accepted: 11/12/2017] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other -omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.
Collapse
Affiliation(s)
- Kalliopi Rantsiou
- Department of Agriculture, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy.
| | - Sophia Kathariou
- North Carolina State University, Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, USA
| | - Annet Winkler
- Mondelez International, Kraft Foods R&D, Unterbiberger St. 15, D-81737 Munich, Germany
| | - Panos Skandamis
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Technology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | | | - Alejandro Amézquita
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| |
Collapse
|
85
|
Hammons SR, Etter AJ, Wang J, Wu T, Ford T, Howard MT, Oliver HF. Evaluation of Third-Party Deep Cleaning as a Listeria monocytogenes Control Strategy in Retail Delis. J Food Prot 2017; 80:1913-1923. [PMID: 29053422 DOI: 10.4315/0362-028x.jfp-17-113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 06/27/2017] [Indexed: 11/11/2022]
Abstract
The objective of this study was to develop and assess the efficacy of an aggressive deep cleaning sanitation standard operating procedure (DC-SSOP) in nine retail delicatessens to reduce persistent Listeria monocytogenes environmental contamination. The DC-SSOP was developed from combined daily SSOPs recommended by the Food Marketing Institute and input from experts in Listeria control from food manufacturing and sanitation. The DC-SSOP was executed by a trained professional cleaning service during a single 12-h shutdown period. A modified protocol from the U.S. Food and Drug Administration Bacteriological Analytical Manual was used to detect L. monocytogenes in samples from 28 food and nonfood contact surfaces that were collected immediately before and after each cleaning and in samples collected monthly for 3 months. The DC-SSOP significantly reduced L. monocytogenes prevalence overall during the 3-month follow-up period and produced variable results for persistent L. monocytogenes isolates. Six delis with historically low to moderate L. monocytogenes prevalence had no significant changes in the number of samples positive for L. monocytogenes after deep cleaning. Deep cleaning in very high prevalence delis (20 to 30% prevalence) reduced L. monocytogenes by 25.6% (Padj < 0.0001, n = 294) overall during the follow-up period. Among delis with extremely high prevalence (>30%), positive samples from nonfood contact surfaces were reduced by 19.6% (Padj = 0.0002, n = 294) during the follow-up period. The inability of deep cleaning to completely eliminate persistent L. monocytogenes was likely due to the diverse infrastructures in each deli, which may require more individualized intervention strategies.
Collapse
Affiliation(s)
- Susan R Hammons
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.]), Purdue University, West Lafayette, Indiana 47907
| | - Andrea J Etter
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.]), Purdue University, West Lafayette, Indiana 47907.,Purdue Interdisciplinary Life Sciences Program, Purdue University, West Lafayette, Indiana 47907
| | - Jingjin Wang
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.]), Purdue University, West Lafayette, Indiana 47907
| | - Tongyu Wu
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.]), Purdue University, West Lafayette, Indiana 47907
| | - Thomas Ford
- Ecolab, Inc., Greensboro, North Carolina 27409, USA
| | | | - Haley F Oliver
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.]), Purdue University, West Lafayette, Indiana 47907
| |
Collapse
|
86
|
Etter AJ, Hammons SR, Roof S, Simmons C, Wu T, Cook PW, Katubig A, Stasiewicz MJ, Wright E, Warchocki S, Hollingworth J, Thesmar HS, Ibrahim SA, Wiedmann M, Oliver HF. Enhanced Sanitation Standard Operating Procedures Have Limited Impact on Listeria monocytogenes Prevalence in Retail Delis. J Food Prot 2017; 80:1903-1912. [PMID: 29053419 DOI: 10.4315/0362-028x.jfp-17-112] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/16/2017] [Indexed: 11/11/2022]
Abstract
In a recent longitudinal surveillance study in 30 U.S. retail delicatessens, 9.7% of environmental surfaces were positive for Listeria monocytogenes, and we found substantial evidence of persistence. In this study, we aimed to reduce the prevalence and persistence of L. monocytogenes in the retail deli environment by developing and implementing practical and feasible intervention strategies (i.e., sanitation standard operating procedures; SSOPs). These SSOPs were standardized across the 30 delis enrolled in this study. SSOP implementation was verified by systems inherent to each retailer. Each deli also was equipped with ATP monitoring systems to verify effective sanitation. We evaluated intervention strategy efficacy by testing 28 food and nonfood contact surfaces for L. monocytogenes for 6 months in all 30 retail delis. The efficacy of the intervention on the delis compared with preintervention prevalence level was not statistically significant; we found that L. monocytogenes could persist despite implementation of enhanced SSOPs. Systematic and accurate use of ATP monitoring systems varied widely among delis. The findings indicate that intervention strategies in the form of enhanced daily SSOPs were not sufficient to eliminate L. monocytogenes from highly prevalent and persistently contaminated delis and that more aggressive strategies (e.g., deep cleaning or capital investment in redesign or equipment) may be necessary to fully mitigate persistent contamination.
Collapse
Affiliation(s)
- Andrea J Etter
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.]).,Purdue Interdisciplinary Life Sciences Program, Purdue University, West Lafayette, Indiana 47907
| | - Susan R Hammons
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.])
| | - Sherry Roof
- Department of Food Science, Cornell University, Ithaca, New York 14853 (ORCID: http://orcid.org/0000-0003-2712-0793 [M.J.S.])
| | - Courtenay Simmons
- Department of Food Science, Cornell University, Ithaca, New York 14853 (ORCID: http://orcid.org/0000-0003-2712-0793 [M.J.S.])
| | - Tongyu Wu
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.])
| | - Peter W Cook
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.])
| | - Alex Katubig
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Matthew J Stasiewicz
- Department of Food Science, Cornell University, Ithaca, New York 14853 (ORCID: http://orcid.org/0000-0003-2712-0793 [M.J.S.]).,Department of Food Science & Human Nutrition, University of Illinois Urbana-Champaign, Urbana, Illinois 61801
| | - Emily Wright
- Department of Food Science, Cornell University, Ithaca, New York 14853 (ORCID: http://orcid.org/0000-0003-2712-0793 [M.J.S.])
| | - Steven Warchocki
- Department of Food Science, Cornell University, Ithaca, New York 14853 (ORCID: http://orcid.org/0000-0003-2712-0793 [M.J.S.])
| | | | | | - Salam A Ibrahim
- Food Microbiology and Biotechnology Laboratory, Department of Family and Consumer Science, North Carolina A & T State University, Greensboro, North Carolina 27411-1064, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York 14853 (ORCID: http://orcid.org/0000-0003-2712-0793 [M.J.S.])
| | - Haley F Oliver
- Department of Food Science (ORCID: http://orcid.org/0000-0001-6756-8790 [T.W.])
| |
Collapse
|
87
|
Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J. High Throughput Sequencing for Detection of Foodborne Pathogens. Front Microbiol 2017; 8:2029. [PMID: 29104564 PMCID: PMC5655695 DOI: 10.3389/fmicb.2017.02029] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/04/2017] [Indexed: 12/23/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.
Collapse
Affiliation(s)
- Camilla Sekse
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Arne Holst-Jensen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Gro S. Johannessen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bjørn Spilsberg
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, Norway
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
88
|
Palma F, Pasquali F, Lucchi A, De Cesare A, Manfreda G. Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant. Ital J Food Saf 2017; 6:6879. [PMID: 29071246 PMCID: PMC5641673 DOI: 10.4081/ijfs.2017.6879] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/26/2017] [Accepted: 07/28/2017] [Indexed: 12/31/2022] Open
Abstract
Listeria monocytogenes is a food-borne pathogen able to survive and grow in different environments including food processing plants where it can persist for month or years. In the present study the discriminatory power of Whole Genome Sequencing (WGS)-based analysis (cgMLST) was compared to that of molecular typing methods on 34 L. monocytogenes isolates collected over one year in the same rabbit meat processing plant and belonging to three genotypes (ST14, ST121, ST224). Each genotype included isolates indistinguishable by standard molecular typing methods. The virulence potential of all isolates was assessed by Multi Virulence-Locus Sequence Typing (MVLST) and the investigation of a representative database of virulence determinant genes. The whole genome of each isolate was sequenced on a MiSeq platform. The cgMLST, MVLST, and in silico identification of virulence genes were performed using publicly available tools. Draft genomes included a number of contigs ranging from 13 to 28 and N50 ranging from 456298 to 580604. The coverage ranged from 41 to 187X. The cgMLST showed a significantly superior discriminatory power only in comparison to ribotyping, nevertheless it allows the detection of two singletons belonging to ST14 that were not observed by other molecular methods. All ST14 isolates belonged to VT107, which 7-loci concatenated sequence differs for only 4 nucleotides to VT1 (Epidemic clone III). Analysis of virulence genes showed the presence of a fulllength inlA version in all ST14 isolates and of a mutated version including a premature stop codon (PMSC) associated to attenuated virulence in all ST121 isolates.
Collapse
Affiliation(s)
- Federica Palma
- Department of Food and Agricultural Sciences, Alma Mater Studiorum- University of Bologna, Bologna, Italy
| | - Frédérique Pasquali
- Department of Food and Agricultural Sciences, Alma Mater Studiorum- University of Bologna, Bologna, Italy
| | - Alex Lucchi
- Department of Food and Agricultural Sciences, Alma Mater Studiorum- University of Bologna, Bologna, Italy
| | - Alessandra De Cesare
- Department of Food and Agricultural Sciences, Alma Mater Studiorum- University of Bologna, Bologna, Italy
| | - Gerardo Manfreda
- Department of Food and Agricultural Sciences, Alma Mater Studiorum- University of Bologna, Bologna, Italy
| |
Collapse
|
89
|
Fagerlund A, Møretrø T, Heir E, Briandet R, Langsrud S. Cleaning and Disinfection of Biofilms Composed of Listeria monocytogenes and Background Microbiota from Meat Processing Surfaces. Appl Environ Microbiol 2017; 83:e01046-17. [PMID: 28667108 PMCID: PMC5561291 DOI: 10.1128/aem.01046-17] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/23/2017] [Indexed: 11/20/2022] Open
Abstract
Surfaces of food processing premises are exposed to regular cleaning and disinfection (C&D) regimes, using biocides that are highly effective against bacteria growing as planktonic cells. However, bacteria growing in surface-associated communities (biofilms) are typically more tolerant toward C&D than their individual free-cell counterparts, and survival of pathogens such as Listeria monocytogenes may be affected by interspecies interactions within biofilms. In this study, Pseudomonas and Acinetobacter were the most frequently isolated genera surviving on conveyor belts subjected to C&D in meat processing plants. In the laboratory, Pseudomonas, Acinetobacter, and L. monocytogenes dominated the community, both in suspensions and in biofilms formed on conveyor belts, when cultures were inoculated with eleven-genus cocktails of representative bacterial strains from the identified background flora. When biofilms were exposed to daily C&D cycles mimicking treatments used in food industry, the levels of Acinetobacter and Pseudomonas mandelii diminished, and biofilms were instead dominated by Pseudomonas putida (65 to 76%), Pseudomonas fluorescens (11 to 15%) and L. monocytogenes (3 to 11%). The dominance of certain species after daily C&D correlated with high planktonic growth rates at 12°C and tolerance to C&D. In single-species biofilms, L. monocytogenes developed higher tolerance to C&D over time, for both the peracetic acid and quaternary ammonium disinfectants, indicating that a broad-spectrum mechanism was involved. Survival after C&D appeared to be a common property of L. monocytogenes strains, as persistent and sporadic subtypes showed equal survival rates in complex biofilms. Biofilms established preferentially in surface irregularities of conveyor belts, potentially constituting harborage sites for persistent contamination.IMPORTANCE In the food industry, efficient production hygiene is a key measure to avoid the accumulation of spoilage bacteria and eliminate pathogens. However, the persistence of bacteria is an enduring problem in food processing environments. This study demonstrated that environmental bacteria can survive foam cleaning and disinfection (C&D) at concentrations used in the industrial environment. The phenomenon was replicated in laboratory experiments. Important characteristics of persisting bacteria were a high growth rate at low temperature, a tolerance to the cleaning agent, and the ability to form biofilms. This study also supports other recent research suggesting that strain-to-strain variation cannot explain why certain subtypes of Listeria monocytogenes persist in food processing environments while others are found only sporadically. The present investigation highlights the failure of regular C&D and a need for research on improved agents that efficiently detach the biofilm matrix.
Collapse
Affiliation(s)
- Annette Fagerlund
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Trond Møretrø
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Even Heir
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Solveig Langsrud
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| |
Collapse
|
90
|
Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept. Int J Food Microbiol 2017; 257:157-164. [DOI: 10.1016/j.ijfoodmicro.2017.06.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 11/20/2022]
|
91
|
Knudsen GM, Nielsen JB, Marvig RL, Ng Y, Worning P, Westh H, Gram L. Genome-wide-analyses of Listeria monocytogenes from food-processing plants reveal clonal diversity and date the emergence of persisting sequence types. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:428-440. [PMID: 28574206 DOI: 10.1111/1758-2229.12552] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 05/27/2017] [Indexed: 06/07/2023]
Abstract
Whole genome sequencing is increasing used in epidemiology, e.g. for tracing outbreaks of food-borne diseases. This requires in-depth understanding of pathogen emergence, persistence and genomic diversity along the food production chain including in food processing plants. We sequenced the genomes of 80 isolates of Listeria monocytogenes sampled from Danish food processing plants over a time-period of 20 years, and analysed the sequences together with 10 public available reference genomes to advance our understanding of interplant and intraplant genomic diversity of L. monocytogenes. Except for three persisting sequence types (ST) based on Multi Locus Sequence Typing being ST7, ST8 and ST121, long-term persistence of clonal groups was limited, and new clones were introduced continuously, potentially from raw materials. No particular gene could be linked to the persistence phenotype. Using time-based phylogenetic analyses of the persistent STs, we estimate the L. monocytogenes evolutionary rate to be 0.18-0.35 single nucleotide polymorphisms/year, suggesting that the persistent STs emerged approximately 100 years ago, which correlates with the onset of industrialization and globalization of the food market.
Collapse
Affiliation(s)
- Gitte M Knudsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jesper Boye Nielsen
- Department of Clinical Microbiology, Hvidovre Hospital, MRSA KnowledgeCenter, Hvidovre, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Yin Ng
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peder Worning
- Department of Clinical Microbiology, Hvidovre Hospital, MRSA KnowledgeCenter, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, MRSA KnowledgeCenter, Hvidovre, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
92
|
Dahl V, Sundqvist L, Hedenström I, Löfdahl M, Alm E, Ringberg H, Lindblad M, Wallensten A, Thisted Lambertz S, Jernberg C. A nationwide outbreak of listeriosis associated with cold-cuts, Sweden 2013-2014. Infect Ecol Epidemiol 2017. [PMID: 28649304 PMCID: PMC5475333 DOI: 10.1080/20008686.2017.1324232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In January 2014, the Public Health Agency of Sweden noticed an increase in listeriosis cases. Isolates from 10 cases had identical pulsed field gel electrophoresis (PFGE) profiles, suggesting a common source. We investigated the outbreak to identify the source and stop transmission. We looked for cases in 2013–2014 and also compared cases notified after February 2014 to randomly selected controls. We surveyed food items consumed two weeks prior to symptom onset. Listeria monocytogenes isolates found by food producers were PFGE-typed. Patient and food isolates with the outbreak PFGE profile were whole-genome sequenced and 51 cases with identical PFGE profile were identified; 12/20 cases and 108/186 controls responded to the survey. All cases were exposed to cold-cuts, compared with 72% of controls (p = 0.034). Five isolates of L. monocytogenes with the outbreak PFGE profile were found in cold-cuts from a food producer which stopped production in February 2014, but cases appeared until October 2014. Whole-genome sequencing showed that cold-cut and patient isolates differed by eight single nucleotide polymorphisms. Three patient isolates differed more and were probably not part of the outbreak. Epidemiological and microbiological results indicated cold-cuts as a possible source of the outbreak.
Collapse
Affiliation(s)
- Viktor Dahl
- Department of Monitoring and Evaluation, The Public Health Agency of Sweden, Stockholm, Sweden.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Lena Sundqvist
- Department of Monitoring and Evaluation, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Ingela Hedenström
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Margareta Löfdahl
- Department of Monitoring and Evaluation, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Erik Alm
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Håkan Ringberg
- Regional Office of Communicable Disease Control and Prevention, Region Skåne, Malmö, Sweden
| | - Mats Lindblad
- Food Control Department, The National Food Agency, Uppsala, Sweden
| | - Anders Wallensten
- Department of Monitoring and Evaluation, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Susanne Thisted Lambertz
- Science Department, The National Food Agency, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Cecilia Jernberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| |
Collapse
|
93
|
Nowak J, Cruz CD, Tempelaars M, Abee T, van Vliet AHM, Fletcher GC, Hedderley D, Palmer J, Flint S. Persistent Listeria monocytogenes strains isolated from mussel production facilities form more biofilm but are not linked to specific genetic markers. Int J Food Microbiol 2017; 256:45-53. [PMID: 28599174 DOI: 10.1016/j.ijfoodmicro.2017.05.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/29/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
Abstract
Contamination of mussels with the human pathogen Listeria monocytogenes occurs during processing in the factory, possibly from bacteria persisting in the factory's indoor and outdoor areas. In this study, a selection of persistent (n=8) and sporadic (n=8) L. monocytogenes isolates associated with mussel-processing premises in New Zealand were investigated for their phenotypic and genomic characteristics. To identify traits that favour or contribute to bacterial persistence, biofilm formation, heat resistance, motility and recovery from dry surfaces were compared between persistent and sporadic isolates. All isolates exhibited low biofilm formation at 20°C, however, at 30°C persistent isolates showed significantly higher biofilm formation after 48h using cell enumeration and near significant difference using the crystal violet assay. All 16 isolates were motile at 20°C and 30°C and motility was fractionally higher for sporadic isolates, but no significant difference was observed. We found persistent isolates tend to exhibit greater recovery after incubation on dry surfaces compared to sporadic isolates. Two of the three most heat-resistant isolates were persistent, while four of five isolates lacking heat resistance were sporadic isolates. Comparison of genome sequences of persistent and sporadic isolates showed that there was no overall clustering of persistent or sporadic isolates, and that differences in prophages and plasmids were not associated with persistence. Our results suggest a link between persistence and biofilm formation, which is most likely multifactorial, combining subtle phenotypic and genotypic differences between isolates.
Collapse
Affiliation(s)
- Jessika Nowak
- The New Zealand Institute for Plant & Food Research Limited, Mt Albert, Auckland, New Zealand; Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand.
| | - Cristina D Cruz
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Centre for Drug Research, University of Helsinki, Helsinki, Finland
| | - Marcel Tempelaars
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Graham C Fletcher
- The New Zealand Institute for Plant & Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Duncan Hedderley
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North, New Zealand
| | - Jon Palmer
- Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand
| | - Steve Flint
- Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand
| |
Collapse
|
94
|
Genetic Stability and Evolution of the sigB Allele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference. Appl Environ Microbiol 2017; 83:AEM.00306-17. [PMID: 28389543 DOI: 10.1128/aem.00306-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/03/2017] [Indexed: 11/20/2022] Open
Abstract
Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion of sigB, which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverse Listeria isolates. In this study, evolutionary approaches were used to assess the validity of sigB allelic typing for Listeria For a data set of 4,280 isolates, sigB allelic typing showed a Simpson's index of diversity of 0.96. Analyses of 164 sigB allelic types (ATs) found among the 6 Listeriasensu stricto species, representing these 4,280 isolates, indicate that neither frequent homologous recombination nor positive selection significantly contributed to the evolution of sigB, confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; Listeria welshimeri displayed the lowest sigB diversity and was the only species in which sigB evolved in a clocklike manner, implying a unique natural history. Among the four L. monocytogenes lineages, sigB evolution followed a molecular clock only in lineage IV. Moreover, sigB displayed a significant negative Tajima D value in lineage II, suggesting a recent population bottleneck followed by lineage expansion. The absence of positive selection along with the violation of the molecular clock suggested a nearly neutral mechanism of Listeriasensu strictosigB evolution. While comparison with a whole-genome sequence-based phylogeny revealed that the sigB phylogeny did not correctly reflect the ancestry of L. monocytogenes lineage IV, the availability of a large sigB AT database allowed accurate species classification.IMPORTANCEsigB allelic typing has been widely used for species delineation and subtyping of Listeria However, an informative evaluation of this method from an evolutionary perspective was missing. Our data indicate that the genetic stability of sigB is affected by neither frequent homologous recombination nor positive selection, which supports that sigB allelic typing provides reliable subtyping and classification of Listeria sensu stricto strains. However, multigene data are required for accurate phylogeny reconstruction of Listeria This study thus contributes to a better understanding of the evolution of sigB and confirms the robustness of the sigB subtyping system for Listeria.
Collapse
|
95
|
A 3-year multi-food study of the presence and persistence of Listeria monocytogenes in 54 small food businesses in Ireland. Int J Food Microbiol 2017; 249:18-26. [DOI: 10.1016/j.ijfoodmicro.2017.02.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 01/24/2017] [Accepted: 02/20/2017] [Indexed: 12/31/2022]
|
96
|
Ibarra-Sánchez L, Van Tassell M, Miller M. Invited review: Hispanic-style cheeses and their association with Listeria monocytogenes. J Dairy Sci 2017; 100:2421-2432. [DOI: 10.3168/jds.2016-12116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/14/2016] [Indexed: 11/19/2022]
|
97
|
Nielsen EM, Björkman JT, Kiil K, Grant K, Dallman T, Painset A, Amar C, Roussel S, Guillier L, Félix B, Rotariu O, Perez‐Reche F, Forbes K, Strachan N. Closing gaps for performing a risk assessment on Listeria monocytogenes in ready‐to‐eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis. ACTA ACUST UNITED AC 2017. [DOI: 10.2903/sp.efsa.2017.en-1151] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
98
|
Singleton Sequence Type 382, an Emerging Clonal Group of Listeria monocytogenes Associated with Three Multistate Outbreaks Linked to Contaminated Stone Fruit, Caramel Apples, and Leafy Green Salad. J Clin Microbiol 2017; 55:931-941. [PMID: 28053218 PMCID: PMC5328462 DOI: 10.1128/jcm.02140-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/28/2016] [Indexed: 12/11/2022] Open
Abstract
Three multistate outbreaks between 2014 and 2016, involving case patients in and outside the United States, were linked to stone fruit, caramel apples, and packaged leafy green salad contaminated with Listeria monocytogenes singleton sequence type 382 (ST382), a serotype IVb-v1 clone with limited genomic divergence. Isolates from these outbreaks and other ST382 isolates not associated with these outbreaks were analyzed by whole-genome sequencing (WGS) analysis. The primary differences among ST382 strains were single nucleotide polymorphisms (SNPs). WGS analysis differentiated ST382 from a clonal complex 1 outbreak strain co-contaminating the caramel apples. WGS clustered food, environmental, and clinical isolates within each outbreak, and also differentiated among the three outbreak strains and epidemiologically unrelated ST382 isolates, which were indistinguishable by pulsed-field gel electrophoresis. ST382 appeared to be an emerging clone that began to diverge from its ancestor approximately 32 years before 2016. We estimated that there was 1.29 nucleotide substitution per genome (2.94 Mbp) per year for this clone.
Collapse
|
99
|
Collins C, Didelot X. Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes. Methods Mol Biol 2017; 1535:109-137. [PMID: 27914076 DOI: 10.1007/978-1-4939-6673-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.
Collapse
Affiliation(s)
- Caitlin Collins
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| |
Collapse
|
100
|
Overney A, Jacques-André-Coquin J, Ng P, Carpentier B, Guillier L, Firmesse O. Impact of environmental factors on the culturability and viability of Listeria monocytogenes under conditions encountered in food processing plants. Int J Food Microbiol 2016; 244:74-81. [PMID: 28073080 DOI: 10.1016/j.ijfoodmicro.2016.12.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/01/2023]
Abstract
The ability of Listeria monocytogenes to adhere to and persist on surfaces for months or even years may be responsible for its transmission from contaminated surfaces to food products. Hence the necessity to find effective means to prevent the establishment of L. monocytogenes in food processing environments. The aim of this study was to assess, through a fractional experimental design, the environmental factors that could affect the survival of L. monocytogenes cells on surfaces to thereby prevent the persistence of this pathogen in conditions mimicking those encountered in food processing plants: culture with smoked salmon juice or meat exudate, use of two materials with different hygiene status, biofilm of L. monocytogenes in pure-culture or dual-culture with a Pseudomonas fluorescens strain, application of a drying step after cleaning and disinfection (C&D) and comparison of two strains of L. monocytogenes. Bacterial survival was assessed by culture, qPCR to quantify total cells, and propidium monoazide coupled with qPCR to quantify viable cells and highlight viable but non-culturable (VBNC) cells. Our results showed that failure to apply C&D causes cell persistence on surfaces. Moreover, the sanitation procedure leads only to a loss of culturability and appearance of VBNC populations. However, an additional daily drying step after C&D optimises the effectiveness of these procedures to reduce culturable populations. Our results reinforce the importance to use molecular tools to monitor viable pathogens in food processing plants to avoid underestimating the amounts of cells using only methods based on cell culture.
Collapse
Affiliation(s)
- Anaïs Overney
- Université Paris-Est, Anses, Laboratory for Food Safety, 94701 Maisons-Alfort, France
| | | | - Patricia Ng
- Université Paris-Est, Anses, Laboratory for Food Safety, 94701 Maisons-Alfort, France
| | - Brigitte Carpentier
- Université Paris-Est, Anses, Laboratory for Food Safety, 94701 Maisons-Alfort, France
| | - Laurent Guillier
- Université Paris-Est, Anses, Laboratory for Food Safety, 94701 Maisons-Alfort, France
| | - Olivier Firmesse
- Université Paris-Est, Anses, Laboratory for Food Safety, 94701 Maisons-Alfort, France.
| |
Collapse
|