1
|
Centorotola G, Ziba MW, Cornacchia A, Chiaverini A, Torresi M, Guidi F, Cammà C, Bowa B, Mtonga S, Magambwa P, D’Alterio N, Scacchia M, Pomilio F, Muuka G. Listeria monocytogenes in ready to eat meat products from Zambia: phenotypical and genomic characterization of isolates. Front Microbiol 2023; 14:1228726. [PMID: 37711697 PMCID: PMC10498467 DOI: 10.3389/fmicb.2023.1228726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
The contamination of ready to eat foods (RTE) products due to Listeria monocytogenes could compromise the products safety becoming a great risk for the consumers. The high presence of L. monocytogenes in RTE products has been described worldwide, but few data are available about these products from African countries. The aims of this study were to report the presence of L. monocytogenes in Zambian RTE products, providing genomic characterization and data on similarity with African circulating strains using whole genome sequencing (WGS). A total of 304 RTE products, produced by different Zambian manufacturers, were purchased at retail, from major supermarkets located in Lusaka, Zambia, comprising 130 dairy and 174 meat products. L. monocytogenes was detected only in 18 (10.3%) RTE meat products of the 174 samples tested. The MLST analysis grouped the 18 L. monocytogenes isolates in 7 clonal complexes (CCs): CC1 (n = 5), CC2 (n = 4), CC9 (n = 4), CC5 (n = 2), CC121 (n = 1), CC155 (n = 1), and CC3 (n = 1). According to the cgMLST results, several clusters were detected, in particular belonging to hyper-virulent clones CC1 and CC2. Regarding the virulence factors, a complete L. monocytogenes Pathogenicity Island 3 (LIPI-3) was present both in the CC1 and CC3, in addition to LIPI-1. Several resistance genes and mobile genetic elements were detected, including Stress Islands, the bcrABC cassette and Tn6188_qac transposon, plasmids and intact prophages. Despite being a first preliminary work with a limited number of samples and isolates, this study helped to increase existing knowledge on contaminated RTE products in Zambia, confirming the presence of hyper-virulent L. monocytogenes CCs, which could play an important role in human diseases, posing a public health concern for consumers.
Collapse
Affiliation(s)
- Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Maureen Wakwamba Ziba
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Marina Torresi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Benson Bowa
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Samson Mtonga
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Phelly Magambwa
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Massimo Scacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Geoffrey Muuka
- Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| |
Collapse
|
2
|
Wiktorczyk-Kapischke N, Skowron K, Wałecka-Zacharska E. Genomic and pathogenicity islands of Listeria monocytogenes-overview of selected aspects. Front Mol Biosci 2023; 10:1161486. [PMID: 37388250 PMCID: PMC10300472 DOI: 10.3389/fmolb.2023.1161486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Listeria monocytogenes causes listeriosis, a disease characterized by a high mortality rate (up to 30%). Since the pathogen is highly tolerant to changing conditions (high and low temperature, wide pH range, low availability of nutrients), it is widespread in the environment, e.g., water, soil, or food. L. monocytogenes possess a number of genes that determine its high virulence potential, i.e., genes involved in the intracellular cycle (e.g., prfA, hly, plcA, plcB, inlA, inlB), response to stress conditions (e.g., sigB, gadA, caspD, clpB, lmo1138), biofilm formation (e.g., agr, luxS), or resistance to disinfectants (e.g., emrELm, bcrABC, mdrL). Some genes are organized into genomic and pathogenicity islands. The islands LIPI-1 and LIPI-3 contain genes related to the infectious life cycle and survival in the food processing environment, while LGI-1 and LGI-2 potentially ensure survival and durability in the production environment. Researchers constantly have been searching for new genes determining the virulence of L. monocytogenes. Understanding the virulence potential of L. monocytogenes is an important element of public health protection, as highly pathogenic strains may be associated with outbreaks and the severity of listeriosis. This review summarizes the selected aspects of L. monocytogenes genomic and pathogenicity islands, and the importance of whole genome sequencing for epidemiological purposes.
Collapse
Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| |
Collapse
|
3
|
Wiktorczyk-Kapischke N, Skowron K, Wałecka-Zacharska E, Grudlewska-Buda K, Wnuk K, Buszko K, Gospodarek-Komkowska E. Assessment of the influence of selected stress factors on the growth and survival of Listeria monocytogenes. BMC Microbiol 2023; 23:27. [PMID: 36690941 PMCID: PMC9872351 DOI: 10.1186/s12866-023-02766-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 01/10/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Listeria monocytogenes are Gram-positive rods, which are the etiological factor of listeriosis. L. monocytogenes quickly adapts to changing environmental conditions. Since the main source of rods is food, its elimination from the production line is a priority. The study aimed to evaluate the influence of selected stress factors on the growth and survival of L. monocytogenes strains isolated from food products and clinical material. RESULTS We distinguished fifty genetically different strains of L. monocytogenes (PFGE method). Sixty-two percent of the tested strains represented 1/2a-3a serogroup. Sixty percent of the rods possessed ten examined virulence genes (fbpA, plcA, hlyA, plcB, inlB, actA, iap, inlA, mpl, prfA). Listeria Pathogenicity Island 1 (LIPI-1) was demonstrated among 38 (76.0%) strains. Majority (92.0%) of strains (46) were sensitive to all examined antibiotics. The most effective concentration of bacteriophage (inhibiting the growth of 22 strains; 44.0%) was 5 × 108 PFU. In turn, the concentration of 8% of NaCl was enough to inhibit the growth of 31 strains (62.0%). The clinical strain tolerated the broadest pH range (3 to 10). Five strains survived the 60-min exposure to 70˚C, whereas all were alive at each time stage of the cold stress experiment. During the stress of cyclic freezing-defrosting, an increase in the number of bacteria was shown after the first cycle, and a decrease was only observed after cycle 3. The least sensitive to low nutrients content were strains isolated from frozen food. The high BHI concentration promoted the growth of all groups. CONCLUSIONS Data on survival in stress conditions can form the basis for one of the hypotheses explaining the formation of persistent strains. Such studies are also helpful for planning appropriate hygiene strategies within the food industry.
Collapse
Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland.
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Kacper Wnuk
- Department of Theoretical Foundations of Biomedical Sciences and Medical Computer Science, Ludwik Rydygier Collegium Medium in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Katarzyna Buszko
- Department of Theoretical Foundations of Biomedical Sciences and Medical Computer Science, Ludwik Rydygier Collegium Medium in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| |
Collapse
|
4
|
XIAN ZHIHAN, YOO JIYOON, PATEL CHADNI, YANG HELEN, DENG XIANGYU, HAMMACK THOMAS, CHEN YI. Comparison between qPCR, VIDAS immunoassays and agar streaking for the detection of Listeria monocytogenes from food and environmental surfaces containing and not containing Listeria innocua. J Food Prot 2022; 86:100013. [PMID: 37018852 DOI: 10.1016/j.jfp.2022.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/12/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022]
Abstract
Comparisons among a qPCR assay, VIDAS® assays and a conventional agar streaking method following the same enrichment for the detection of Listeria monocytogenes were performed under two challenging conditions. In the first comparison, L. innocua and L. monocytogenes were coinoculated into sausages at ratios (L. innocua-to-L. monocytogenes) of 10, 100, 1000, and 10 000. qPCR provided the most sensitive detection at all ratios after both 24-h and 48-h enrichments. A modified VIDAS® LMO2 assay (i.e., replacement of the kit-specified enrichment scheme with the enrichment scheme used in this study) and agar streaking yielded equivalent results when the ratio was 10 and 100; agar streaking was more sensitive when the ratio was 1000; neither method could detect L. monocytogenes at the ratio of 10 000. Enrichment duration of 48 h was needed for modified VIDAS® to detect L. monocytogenes when the ratio was 1000. Agar streaking after 24-h enrichment isolated L. monocytogenes better than after 48-h enrichment when the ratio was 100 and 1000. In the second comparison, we followed the validation guidelines of AOAC International and inoculated L. monocytogenes, without any L. innocua, onto lettuce and stainless-steel surfaces at low levels. The numbers of positive samples detected by qPCR, VIDAS® LIS assay, modified VIDAS® LMO2 assay, and agar streaking after 48-h enrichment were not statistically different. Our data showed that qPCR was the most sensitive method, while agar streaking and VIDAS® performed reasonably well. Streaking after 24-h enrichment was needed when background flora could overgrow L. monocytogenes during prolonged enrichment, and this is critical for confirming rapid screening assays. Appropriate selection of enrichment duration and rapid assays will enhance the testing of L. monocytogenes in food and environmental samples.
Collapse
|
5
|
Yan L, Pei X, Miao J, Li Y, Yang S, Peng Z, Yang X, Mei L, Yang Q, Ren H, Yang D, Shi H. Surveillance and examination of microbial contamination in ice cream in China. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
This study investigated the microbial contamination of ice cream in China. A total of 2,887 ice cream samples were collected from different regions of China. Contamination by the aerobic plate count (APC), coliforms, and three foodborne pathogens, such as Listeria monocytogenes, Staphylococcus aureus, and Salmonella spp., was detected in the samples. L. monocytogenes isolates were further analyzed for antibiotic susceptibility and multi-locus sequence typing (MLST). The results showed that APC was more than 10 5 CFU/g in 6.10% (176/2887) and coliform was more than 10 2 CFU/g in 15.69% (453/2887) of all samples. The positive rates of S. aureus, L. monocytogenes, and Salmonella spp. were 0.66%, 0.62%, and 0.10%, respectively. Of these, S. aureus contamination was more than 10 2 CFU/g in two samples, and L. monocytogenes in the positive sample was in the range of 0.3–240 MPN/g, with a median of 4.3 MPN/g. The hygienic status of the packaged samples was much better than that of the bulk samples (P < 0.05). Catered samples were more frequently and heavily contaminated than samples from retail and wholesale outlets (P < 0.05). No significant differences were observed in samples bought from urban and rural areas (P >0.05). For 18 L. monocytogenes strains isolated from ice cream, the resistance rate of nine antibiotics was 5.56% (1/18). By MLST, the L. monocytogenes strains were classified into 9 sequence types (STs), of which ST8 was most common (6 isolates). These above results indicate that a potential health risk to the public may be caused by ice cream, particularly susceptible populations.
Collapse
Affiliation(s)
- Lin Yan
- Hebei Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University , Shijiazhuang, China
- China National Center for Food Safety Risk Assessment (CFSA), Chaoyang District , Beijing, China
| | - Xiaoyan Pei
- China National Center for Food Safety Risk Assessment (CFSA), Chaoyang District , Beijing, China
| | - Junjie Miao
- Hebei Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University , Shijiazhuang, China
| | - Ying Li
- China National Center for Food Safety Risk Assessment (CFSA), Chaoyang District , Beijing, China
| | - Shuran Yang
- China National Center for Food Safety Risk Assessment (CFSA), Chaoyang District , Beijing, China
| | - Zixin Peng
- China National Center for Food Safety Risk Assessment (CFSA), Chaoyang District , Beijing, China
| | - Xiaorong Yang
- Sichuan Provincial Center for Disease Control and Prevention , Chengdu, China
| | - Lingling Mei
- Zhejiang Provincial Center for Disease Control and Prevention , Hangzhou, China
| | - Qingwen Yang
- Yunnan Provincial Center for Disease Control and Prevention , Kunming, China
| | - Huan Ren
- Hebei Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University , Shijiazhuang, China
| | - Dajin Yang
- China National Center for Food Safety Risk Assessment (CFSA), Chaoyang District , Beijing, China
| | - Hongmei Shi
- Hebei Key Laboratory of Environment and Human Health, School of Public Health, Hebei Medical University , Shijiazhuang, China
| |
Collapse
|
6
|
Guidi F, Lorenzetti C, Centorotola G, Torresi M, Cammà C, Chiaverini A, Pomilio F, Blasi G. Atypical Serogroup IVb-v1 of Listeria monocytogenes Assigned to New ST2801, Widely Spread and Persistent in the Environment of a Pork-Meat Producing Plant of Central Italy. Front Microbiol 2022; 13:930895. [PMID: 35832815 PMCID: PMC9271897 DOI: 10.3389/fmicb.2022.930895] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we characterized 84 Listeria monocytogenes (Lm) strains having an atypical IVb-v1 profile and isolated in a meat producing plant of Central Italy. They were assigned to the new MLST type ST2801 (CC218). The new ST was widespread in the food-producing environment where it was able to persist for over a year even after cleaning and sanitation. Cluster analysis identified three main clusters genetically close to each other (0-22 allelic differences and 0-28 SNPs) from two different cgMLST types, suggesting a common source. The coexistence of closely related clusters over time could be the result of a different evolution path starting from a common ancestor first introduced in the plant and/or the consequence of the repetitive reintroduction of closely related clones probably by raw materials. All the strains presented several determinants for heavy metals resistance, stress response, biofilm production, and multidrug efflux pumps with no significant differences among the clusters. A total of 53 strains carried pLI100 and the j1776 plasmids, while in one strain, the pLM33 was found in addition to pLI100. Only the strains carrying plasmids presented cadA and cadC for cadmium resistance and the mco gene encoding a multicopper oxidase and gerN for an additional Na+/H+-K+ antiporter. All the strains presented a virulence profile including a full-length inlA gene and the additional LIPI-3. The isolation of a new ST with a large pattern of stress-adaptation genes and able to persist is an important contribution to deepening the current knowledge on the uncommon IVb-v1 and in general on the genomic diversity of Lm.
Collapse
Affiliation(s)
- Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati,” Perugia, Italy
| | - Cinzia Lorenzetti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati,” Perugia, Italy
| | - Gabriella Centorotola
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Marina Torresi
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Cesare Cammà
- Centro di Referenza Nazionale per Sequenze Genomiche di Microrganismi Patogeni, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Alexandra Chiaverini
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Francesco Pomilio
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Giuliana Blasi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati,” Perugia, Italy
| |
Collapse
|
7
|
Peng X, Ed-Dra A, Yue M. Whole genome sequencing for the risk assessment of probiotic lactic acid bacteria. Crit Rev Food Sci Nutr 2022; 63:11244-11262. [PMID: 35694810 DOI: 10.1080/10408398.2022.2087174] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Probiotic bacteria exhibit beneficial effects on human and/or animal health, and have been widely used in foods and fermented products for decades. Most probiotics consist of lactic acid bacteria (LAB), which are used in the production of various food products but have also been shown to have the ability to prevent certain diseases. With the expansion of applications for probiotic LAB, there is an increasing concern with regard to safety, as cases with adverse effects, i.e., severe infections, transfer of antimicrobial resistance genes, etc., can occur. Currently, in vitro assays remain the primary way to assess the properties of LAB. However, such methodologies are not meeting the needs of strain risk assessment on a high-throughput scale, in the context of the evolving concept of food safety. Analyzing the complete genetic information, including potential virulence genes and other determinants with a negative impact on health, allows for assessing the safe use of the product, for which whole-genome sequencing (WGS) of individual LAB strains can be employed. Genomic data can also be used to understand subtle differences in the strain level important for beneficial effects, or protect patents. Here, we propose that WGS-based bioinformatics analyses are an ideal and cost-effective approach for the initial in silico microbial risk evaluation, while the technique may also increase our understanding of LAB strains for food safety and probiotic property evaluation.
Collapse
Affiliation(s)
- Xianqi Peng
- Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | | | - Min Yue
- Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
| |
Collapse
|
8
|
Russini V, Spaziante M, Varcasia BM, Diaconu EL, Paolillo P, Picone S, Brunetti G, Mattia D, De Carolis A, Vairo F, Bossù T, Bilei S, De Marchis ML. A Whole Genome Sequencing-Based Epidemiological Investigation of a Pregnancy-Related Invasive Listeriosis Case in Central Italy. Pathogens 2022; 11:667. [PMID: 35745521 PMCID: PMC9228178 DOI: 10.3390/pathogens11060667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Listeriosis is currently the fifth most common foodborne disease in Europe. Most cases are sporadic; however, outbreaks have also been reported. Compared to other foodborne infections, listeriosis has a modest incidence but can cause life-threatening complications, especially in elderly or immunocompromised people and pregnant women. In the latter case, the pathology can be the cause of premature birth or spontaneous abortion, especially if the fetus is affected during the first months of gestation. The causative agent of listeriosis, Listeria monocytogenes, is characterized by the innate ability to survive in the environment and in food, even in adverse conditions and for long periods. Ready-to-eat food represents the category most at risk for contracting listeriosis. This study presents the result of an investigation carried out on a case of maternal-fetal transmission of listeriosis which occurred in 2020 in central Italy and which was linked, with a retrospective approach, to other cases residing in the same city of the pregnant woman. Thanks to the use of next-generation sequencing methodologies, it was possible to identify an outbreak of infection, linked to the consumption of ready-to-eat sliced products sold in a supermarket in the investigated city.
Collapse
Affiliation(s)
- Valeria Russini
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Martina Spaziante
- Regional Service Surveillance and Control for Infectious Diseases (SERESMI), National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (M.S.); (F.V.)
| | - Bianca Maria Varcasia
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Elena Lavinia Diaconu
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy;
| | - Piermichele Paolillo
- UO Neonatologia, Patologia Neonatale e Terapia Intensiva Neonatale (TIN), Policlinico Casilino General Hospital, 00169 Rome, Italy; (P.P.); (S.P.)
| | - Simonetta Picone
- UO Neonatologia, Patologia Neonatale e Terapia Intensiva Neonatale (TIN), Policlinico Casilino General Hospital, 00169 Rome, Italy; (P.P.); (S.P.)
| | - Grazia Brunetti
- Pathology-Microbiology Laboratory, Policlinico Casilino General Hospital, 00169 Rome, Italy;
| | - Daniela Mattia
- Dipartimento di Prevenzione, Servizio Veterinario Area B—Igiene Alimenti di Origine Animale (SIOA), ASL Roma 6, 00072 Rome, Italy;
| | - Angela De Carolis
- Dipartimento di Prevenzione, Servizio di Igiene degli Alimenti e della Nutrizione (SIAN), ASL Roma 6, 00044 Rome, Italy;
| | - Francesco Vairo
- Regional Service Surveillance and Control for Infectious Diseases (SERESMI), National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (M.S.); (F.V.)
| | - Teresa Bossù
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Stefano Bilei
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| | - Maria Laura De Marchis
- Food Microbiology Unit, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (V.R.); (B.M.V.); (T.B.); (S.B.)
| |
Collapse
|
9
|
Chen Y, Simonetti T, Peter K, Jin Q, Brown E, LaBorde LF, Macarisin D. Genetic Diversity of Listeria monocytogenes Isolated From Three Commercial Tree Fruit Packinghouses and Evidence of Persistent and Transient Contamination. Front Microbiol 2022; 12:756688. [PMID: 35082763 PMCID: PMC8784831 DOI: 10.3389/fmicb.2021.756688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Whole genome analysis was performed on 501 isolates obtained from a previous survey which recovered 139 positive environmental sponge samples (i.e., up to 4 isolates per sample) from a total of 719 samples collected at 40 standardized sites in 3 commercial apple packinghouse facilities (i.e., P1, P2, and P3) over 3 successive seasons in a single production year. After excluding duplicated isolates, the data from 156 isolates revealed the clonal diversity of L. monocytogenes and allowed the detection of transient contamination, persistent contamination, and cross-area transmission events. Facility P2 with the poorest sanitary conditions had the least diversity (Shannon's index of 0.38). P2 contained a Clonal Complex (CC) 554, serogroup IVb-v1 strain that persisted throughout the year and spread across the entire facility, a singleton Sequence Type (ST) 1003, lineage III strain that persisted through two seasons and spread across two areas of the facility, and 3 other clones from transient contaminations. P1 and P3, facilities with better sanitary conditions, had much higher diversity (i.e., 15 clones with a Shannon's index of 2.49 and 10 clones with a Shannon's index of 2.10, respectively) that were the result of transient contamination. Facilities P1 and P3 had the highest incidence (43.1%) of lineage III isolates, followed by lineage I (31.3%) and lineage II (25.5%) isolates. Only 1 isolate in the three facilities contained a premature stop codon in virulence gene inlA. Fourteen samples yielded 2-3 clones per sample, demonstrating the importance of choosing appropriate methodologies and selecting a sufficient number of isolates per sample for studying L. monocytogenes diversity. Only 1 isolate, belonging to CC5 and from facility P3, contained a known plasmid, and this was also the only isolate containing benzalkonium chloride tolerance genes. The persistent CC554 strain did not exhibit stronger sanitizer resistance than other isolates and did not contain any confirmed molecular determinants of L. monocytogenes stress resistance that were differentially present in other isolates, such as genes involved in sanitizer tolerance, heavy metal resistance, biofilm-forming, stress survival islet 1 (SSI-1), stress survival islet 2 (SSI-2) or Listeria genomic island (LGI2).
Collapse
Affiliation(s)
- Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
| | - Tobin Simonetti
- Department of Food Science, Pennsylvania State University, University Park, PA, United States
| | - Kari Peter
- Fruit Research and Extension Center, Pennsylvania State University, University Park, PA, United States
| | - Qing Jin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
| | - Eric Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
| | - Luke F LaBorde
- Department of Food Science, Pennsylvania State University, University Park, PA, United States
| | - Dumitru Macarisin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), College Park, MD, United States
| |
Collapse
|
10
|
Antimicrobial Susceptibility Profile and Whole-Genome Analysis of a Strong Biofilm-Forming Bacillus Sp. B87 Strain Isolated from Food. Microorganisms 2022; 10:microorganisms10020252. [PMID: 35208707 PMCID: PMC8876208 DOI: 10.3390/microorganisms10020252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Members of the Bacillus cereus group are considered to be foodborne pathogens commonly associated with diarrheal and emetic gastrointestinal syndromes. Biofilm formation is a major virulence determinant of various pathogenic bacteria, including the B. cereus strains, since it can protect the bacteria against antimicrobial agents and the host immune response. Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. Based on the analysis of the phylogenetic relationship, the isolate was phylogenetically mapped close to Bacillus pacificus. Antimicrobial susceptibility testing revealed that the isolate was resistant to tetracycline and β-lactam antimicrobial agents, which corresponded with the genotypic characterization using the whole-genome analysis. The genome of Bacillus sp. B87 carried the three-component non-hemolytic enterotoxin (NHE), which is a type of enterotoxin that causes diarrheal symptoms. In addition, the genome also contained several genes that participate in biofilm formation, including the pelDEADAFG operon. These findings expand our understanding of antimicrobial resistance and virulence in Bacillus species based on the link between genotypic and phenotypic characterization.
Collapse
|
11
|
Guidi F, Chiaverini A, Repetto A, Lorenzetti C, Centorotola G, Bazzucchi V, Palombo B, Gattuso A, Pomilio F, Blasi G. Hyper-Virulent Listeria monocytogenes Strains Associated With Respiratory Infections in Central Italy. Front Cell Infect Microbiol 2021; 11:765540. [PMID: 34746033 PMCID: PMC8564288 DOI: 10.3389/fcimb.2021.765540] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes (Lm) is a foodborne pathogen causing listeriosis. Invasive forms of the disease mainly manifest as septicaemia, meningitis and maternal-neonatal infections. Lm-associated respiratory infections are very rare and little known. We reported two Lm respiratory infection cases occurred in Central Italy during the summer of 2020, in the midst of the SARS-CoV2 pandemic. In addition to collect the epidemiological and clinical characteristics of the patients, we used Whole Genome Sequencing to study the genomes of the Lm isolates investigating their virulence and antimicrobial profiles and the presence of genetic mobile elements. Both the strains belonged to hypervirulent MLST clonal complexes (CC). In addition to the Listeria Pathogenicity Island 1 (LIPI-1), the CC1 strain also carried LIPI-3 and the CC4 both LIPI-3 and LIPI-4. Genetic determinants for antimicrobial and disinfectants resistance were found. The CC1 genome presented prophage sequences but they did not interrupt the comK gene, involved in the phagosomal escape of Lm. None of the strains carried plasmids. Lm is an important, although rare, opportunistic pathogen for respiratory tract and lung infections. To avoid dangerous diagnostic delays of these severe clinical forms, it is important to sensitize hospital laboratories to this rare manifestation of listeriosis considering Lm in the differential diagnosis of respiratory infections.
Collapse
Affiliation(s)
- Fabrizia Guidi
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Perugia, Italy
| | - Alexandra Chiaverini
- Laboratorio Nazionale di Riferimento per Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Antonella Repetto
- Struttura complessa di Microbiologia, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Cinzia Lorenzetti
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Perugia, Italy
| | - Gabriella Centorotola
- Laboratorio Nazionale di Riferimento per Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Viviana Bazzucchi
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Perugia, Italy
| | - Barbara Palombo
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Perugia, Italy
| | - Antonietta Gattuso
- Dipartimento di Sicurezza Alimentare, Nutrizione e Sanità Pubblica Veterinaria, Istituto Superiore di Sanità, Rome, Italy
| | - Francesco Pomilio
- Laboratorio Nazionale di Riferimento per Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Giuliana Blasi
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, Perugia, Italy
| |
Collapse
|
12
|
Genome Typing and Epidemiology of Human Listeriosis in New Zealand, 1999 to 2018. J Clin Microbiol 2021; 59:e0084921. [PMID: 34406797 DOI: 10.1128/jcm.00849-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study describes the epidemiology of listeriosis in New Zealand between 1999 and 2018 as well as the retrospective whole-genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population, and non-pregnancy-associated cases were more prevalent than pregnancy-associated cases (averages of 19 and 5 cases per annum, respectively). WGS data was assessed using multilocus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST, respectively) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%), and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Among the 49 cgMLST types containing two or more isolates, 18 cgMLST types were found with 2 to 4 isolates each (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0 to 2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP analysis also produced results comparable to those from wgMLST. The low genetic diversity within these clusters suggests a potential common source, but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis together with thorough exposure information from cases could potentially identify future outbreaks more rapidly, including those that may have been undetected for some time over different geographical regions.
Collapse
|
13
|
Genomic Analysis of Prophages Recovered from Listeria monocytogenes Lysogens Found in Seafood and Seafood-Related Environment. Microorganisms 2021; 9:microorganisms9071354. [PMID: 34206706 PMCID: PMC8303350 DOI: 10.3390/microorganisms9071354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 11/23/2022] Open
Abstract
A prophage is a phage-related sequence that is integrated into a bacterial chromosome. Prophages play an important role in bacterial evolution, survival, and persistence. To understand the impact of Listeria prophages on their host genome organizations, this work sequenced two L. monocytogenes strains (134LM and 036LM), previously identified as lysogens by mitomycin C induction. Draft genomes were generated with assembly sizes of 2,953,877 bp and 3,000,399 bp. One intact prophage (39,532 bp) was inserted into the comK gene of the 134LM genome. Two intact prophages (48,684 bp and 39,488 bp) were inserted in tRNA-Lys and elongation-factor genes of the 036LM genome. The findings confirmed the presence of three corresponding induced phages previously obtained by mitomycin C induction. Comparative genomic analysis of three prophages obtained in the newly sequenced lysogens with 61 prophages found in L. monocytogenes genomes, available in public databases, identified six major clusters using whole genome-based phylogenetic analysis. The results of the comparative genomic analysis of the prophage sequences provides knowledge about the diversity of Listeria prophages and their distribution among Listeria genomes in diverse environments, including different sources or geographical regions. In addition, the prophage sequences and their insertion sites contribute to the genomic diversity of L. monocytogenes genomes. These data of prophage sequences, prophage insertion sites, and prophage sequence comparisons, together with ANIb confirmation, could be useful for L. monocytogenes classification by prophages. One potential development could be refinement of prophage typing tools for monitoring or surveillance of L. monocytogenes contamination and transmission.
Collapse
|
14
|
Commichaux S, Javkar K, Ramachandran P, Nagarajan N, Bertrand D, Chen Y, Reed E, Gonzalez-Escalona N, Strain E, Rand H, Pop M, Ottesen A. Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads. BMC Genomics 2021; 22:389. [PMID: 34039264 PMCID: PMC8157722 DOI: 10.1186/s12864-021-07702-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. RESULTS We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. CONCLUSION The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.
Collapse
Affiliation(s)
- Seth Commichaux
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
- Biological Science Graduate Program, University of Maryland, College Park, MD, USA.
| | - Kiran Javkar
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, USA
| | - Padmini Ramachandran
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 13862, Singapore
| | - Denis Bertrand
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, 13862, Singapore
| | - Yi Chen
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Elizabeth Reed
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | | | - Errol Strain
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, USA
| | - Hugh Rand
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Andrea Ottesen
- Center for Veterinary Medicine, Food and Drug Administration, Laurel, MD, USA
| |
Collapse
|
15
|
Stewart DS, Rana YS, Deng K, Vijayakumar G, Yin L, Salazar JK, Tortorello ML. Effect of Time, Temperature, and Transport Media on the Recovery of Listeria monocytogenes from Environmental Swabs. J Food Prot 2021; 84:811-819. [PMID: 33290508 DOI: 10.4315/jfp-20-334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/06/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT Environmental monitoring for Listeria monocytogenes in food processing environments is key for ensuring the safety of ready-to-eat foods. For sampling, swabs are often hydrated with a wetting or transport medium that may contain neutralizers and other ingredients. After swabbing the environment, the swabs may then be transported or shipped cold to an off-site laboratory for testing, ideally within 48 h. Extended shipping times may subject the pathogen to increased temperatures in the presence of the wetting medium, organics, and other chemicals from the processing facility that could confound detection. This study evaluated growth and detection of L. monocytogenes on stainless steel exposed to either buffer or sodium hypochlorite before drying. Swabs were rehydrated with Butterfield's phosphate buffer, neutralizing buffer, Letheen broth, or Dey-Engley neutralizing broth before swabbing. Swabs were stored in the presence of no added food, cheese whey, or ice cream under both optimal (4°C) and suboptimal (15°C) temperatures for up to 72 h. Overall, there was no growth of L. monocytogenes at 4°C through 72 h of storage, although enrichment from these swabs was dependent on the presence and type of food matrix. Pathogen growth during storage at 15°C was more variable and depended on both the food matrix and transport media used, with Dey-Engley and Letheen broths allowing for the highest population increases. Overall, more enrichments resulting in L. monocytogenes detections were observed when using Letheen broth and neutralizing buffer than Dey-Engley broth, which resulted in fewer detections at 15°C. Logistic regression and Cochran-Mantel-Haenszel analyses determined that storage temperature, transport media, and food matrix all significantly affected detection of L. monocytogenes, whereas storage time did not have a clear effect on recovery from swabs. HIGHLIGHTS
Collapse
Affiliation(s)
- Diana S Stewart
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, 6502 South Archer Road, Bedford Park, Illinois 60501.,(ORCID: https://orcid.org/0000-0002-3792-1845 [D.S.S.])
| | - Yadwinder Singh Rana
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, Illinois 60501
| | - Kaiping Deng
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, Illinois 60501
| | - Geethaanjali Vijayakumar
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, Illinois 60501
| | - Lanlan Yin
- Bioinformatics and Biostatistics Staff, U.S. Food and Drug Administration, College Park, Maryland 20742, USA
| | - Joelle K Salazar
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, 6502 South Archer Road, Bedford Park, Illinois 60501
| | - Mary Lou Tortorello
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, 6502 South Archer Road, Bedford Park, Illinois 60501
| |
Collapse
|
16
|
Lüth S, Deneke C, Kleta S, Al Dahouk S. Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes. Microb Genom 2021; 7:mgen000491. [PMID: 33275089 PMCID: PMC8115905 DOI: 10.1099/mgen.0.000491] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/21/2020] [Indexed: 12/26/2022] Open
Abstract
Where classical epidemiology has proven to be inadequate for surveillance and control of foodborne pathogens, molecular epidemiology, using genomic typing methods, can add value. However, the analysis of whole genome sequencing (WGS) data varies widely and is not yet fully harmonised. We used genomic data on 494 Listeria monocytogenes isolates from ready-to-eat food products and food processing environments deposited in the strain collection of the German National Reference Laboratory to compare various procedures for WGS data analysis and to evaluate compatibility of results. Two different core genome multilocus sequence typing (cgMLST) schemes, different reference genomes in single nucleotide polymorphism (SNP) analysis and commercial as well as open-source software were compared. Correlation of allele distances from the different cgMLST approaches was high, ranging from 0.97 to 1, and unified thresholds yielded higher clustering concordance than scheme-specific thresholds. The number of detected SNP differences could be increased up to a factor of 3.9 using a specific reference genome compared with a general one. Additionally, specific reference genomes improved comparability of SNP analysis results obtained using different software tools. The use of a closed or a draft specific reference genome did not make a difference. The harmonisation of WGS data analysis will finally guarantee seamless data exchange, but, in the meantime, knowledge on threshold values that lead to comparable clustering of isolates by different methods may improve communication between laboratories. We therefore established a translation code between commonly applied cgMLST and SNP methods based on optimised clustering concordances. This code can work as a first filter to identify WGS-based typing matches resulting from different methods, which opens up a new perspective for data exchange and thereby accelerates time-critical analyses, such as in outbreak investigations.
Collapse
Affiliation(s)
- Stefanie Lüth
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Berlin, Germany
| | - Carlus Deneke
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - Sylvia Kleta
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - Sascha Al Dahouk
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
- RWTH Aachen University Hospital, Department of Internal Medicine, Aachen, Germany
| |
Collapse
|
17
|
In-Depth Longitudinal Study of Listeria monocytogenes ST9 Isolates from the Meat Processing Industry: Resolving Diversity and Transmission Patterns Using Whole-Genome Sequencing. Appl Environ Microbiol 2020; 86:AEM.00579-20. [PMID: 32414794 PMCID: PMC7357480 DOI: 10.1128/aem.00579-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
Listeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment, and certain types can be established in food factories. The sequence type ST9 dominates in meat processing environments, and this work was undertaken to obtain data needed for the tracking of this subtype. By using whole-genome sequencing (WGS), we revealed the presence of cross-contamination routes between meat factories as well as within a single factory, including the spread from different reservoirs within the same room. It was also possible to estimate the time frame of persistence in the factory, as well as when and how new clones had entered. The present work contributes valuable information about the diversity of ST9 and exemplifies the potential power of WGS in food safety management, allowing the determination of relationships between strains both in an international context and locally between and within factories. Listeria monocytogenes is a pathogen mostly associated with the consumption of ready-to-eat foods and can cause severe disease and death. It can be introduced into food chains from raw materials, but often the contamination source is the food production environment, where certain clones can persist for years. In the meat chain, ST9 is one of the most commonly encountered L. monocytogenes sequence types, and for effective source tracking, the divergence and spread of ST9 must be understood. In this study, whole-genome sequencing (WGS) was used to characterize and track 252 L. monocytogenes ST9 isolates collected from four Norwegian meat processing plants between 2009 and 2017. The isolates formed distinct clusters relative to genomes found in public databases, and all but three isolates clustered into two major clonal populations. Different contamination patterns were revealed, e.g., evidence of contamination of two factories with a clone that diverged from its ancestor in the late 1990s through a common source of raw materials; breach of hygienic barriers within a factory, leading to repeated detection of two clones in the high-risk zone during a 4- to 6-year period; entry through the purchase and installation of second-hand equipment harboring a previously established clonal population; and spreading and diversification of two clones from two reservoirs within the same production room over a 9-year period. The present work provides data on the diversity of ST9, which is crucial for epidemiological investigations and highlights how WGS can be used for source tracking within food processing factories. IMPORTANCEListeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment, and certain types can be established in food factories. The sequence type ST9 dominates in meat processing environments, and this work was undertaken to obtain data needed for the tracking of this subtype. By using whole-genome sequencing (WGS), we revealed the presence of cross-contamination routes between meat factories as well as within a single factory, including the spread from different reservoirs within the same room. It was also possible to estimate the time frame of persistence in the factory, as well as when and how new clones had entered. The present work contributes valuable information about the diversity of ST9 and exemplifies the potential power of WGS in food safety management, allowing the determination of relationships between strains both in an international context and locally between and within factories.
Collapse
|
18
|
Yang H, Hoffmann M, Allard MW, Brown EW, Chen Y. Microevolution and Gain or Loss of Mobile Genetic Elements of Outbreak-Related Listeria monocytogenes in Food Processing Environments Identified by Whole Genome Sequencing Analysis. Front Microbiol 2020; 11:866. [PMID: 32547499 PMCID: PMC7272582 DOI: 10.3389/fmicb.2020.00866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/14/2020] [Indexed: 01/03/2023] Open
Abstract
Whole genome sequencing (WGS) analyses have been instrumental in traceback investigations of Listeria monocytogenes (Lm). To demonstrate how long-read sequencing analysis can capture and describe relationships among isolates from clinical, food, and environmental sources, we analyzed 366 long-read- and shotgun-sequenced isolates from 16 Lm outbreak strains associated with cantaloupe, leafy green, stone fruit, caramel apple, mung bean sprout, multiple cheese products, multiple ice cream products, and their production environments. The analyses demonstrated that outbreak strains could be distributed in different areas and zones of food production environments through persistent or repeated contamination. Multi-strain and multi-clone contamination were common. Further, WGS could differentiate among isolates collected at different time points or from different production lines in the same facility, revealing microevolution events in processing environments. Our comparison between complete and shotgun genomes showed that isolates of the same outbreak strain diversified mostly by gain/loss of plasmids and chromosome-borne prophages that constitute 2 to 5% of the chromosome. In contrast, other genes missing in the shotgun genomes were randomly scattered, constituting ~0.5% of the chromosome. Among different outbreak strains of the same CC, most gene-scale differences were due to gain/loss of mobile genetic elements, such as plasmids, chromosome-borne prophages, a Tn916 like transposon, and Listeria Genomic Island 2. The nucleotide variations in the same prophage and the same plasmid shared among isolates of the same outbreak strain were limited, which enabled different WGS tools to unambiguously cluster isolates of the same outbreak strain. In some outbreak strains, correlation between prophage gain/loss and single nucleotide polymorphism (SNP) accumulations in the genome backbone were observed.
Collapse
Affiliation(s)
- Helen Yang
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Marc W Allard
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| |
Collapse
|
19
|
Chen Y, Chen M, Wang J, Wu Q, Cheng J, Zhang J, Sun Q, Xue L, Zeng H, Lei T, Pang R, Ye Q, Wu S, Zhang S, Wu H, Li W, Kou X. Heterogeneity, Characteristics, and Public Health Implications of Listeria monocytogenes in Ready-to-Eat Foods and Pasteurized Milk in China. Front Microbiol 2020; 11:642. [PMID: 32351479 PMCID: PMC7174501 DOI: 10.3389/fmicb.2020.00642] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
Listeria monocytogenes is a foodborne pathogen with a high mortality rate in humans. This study aimed to identify the pathogenic potential of L. monocytogenes isolated from ready-to-eat (RTE) foods and pasteurized milk in China on the basis of its phenotypic and genotypic characteristics. Approximately 7.7% (44/570) samples tested positive for L. monocytogenes among 10.8% (39/360) RTE and 2.4% (5/210) pasteurized milk samples, of which 77.3% (34/44) had < 10 MPN/g, 18.2% (8/44) had 10-110 MPN/g, and 4.5% (2/44) had > 110 MPN/g. A total of 48 strains (43 from RTE foods and five from milk samples) of L. monocytogenes were isolated from 44 positive samples. PCR-serogroup analysis revealed that the most prevalent serogroup was II.2 (1/2b-3b-7), accounting for 52.1% (25/48) of the total, followed by serogroup I.1 (1/2a-3a) accounting for 33.3% (16/48), serogroup I.2 (1/2c-3c) accounting for 12.5% (6/48), and serogroup II.1 (4b-4d-4e) accounting for 2.1%. All isolates were grouped into 11 sequence types (STs) belonging to 10 clonal complexes (CCs) and one singleton (ST619) via multi-locus sequence typing. The most prevalent ST was ST87 (29.2%), followed by ST8 (22.9%), and ST9 (12.5%). Virulence genes determination showed that all isolates harbored eight virulence genes belonging to Listeria pathogenicity islands 1 (LIPI-1) (prfA, actA, hly, mpl, plcA, plcB, and iap) and inlB. Approximately 85.4% isolates carried full-length inlA, whereas seven isolates had premature stop codons in inlA, six of which belonged to ST9 and one to ST5. Furthermore, LLS (encoded by llsX gene, representing LIPI-3) displays bactericidal activity and modifies the host microbiota during infection. LIPI-4 enhances neural and placental tropisms of L. monocytogenes. Results showed that six (12.5%) isolates harbored the llsX gene, and they belonged to ST1/CC1, ST3/CC3, and ST619. Approximately 31.3% (15/48) isolates (belonging to ST87/CC87 and ST619) harbored ptsA (representing LIPI-4), indicating the potential risk of this pathogen. Antimicrobial susceptibility tests revealed that > 95% isolates were susceptible to 16 antimicrobials; however, 60.4 and 22.9% isolates were intermediately resistant to streptomycin and ciprofloxacin, respectively. The results show that several isolates harbor LIPI-3 and LIPI-4 genes, which may be a possible transmission route for Listeria infections in consumers.
Collapse
Affiliation(s)
- Yuetao Chen
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Moutong Chen
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qingping Wu
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Jianheng Cheng
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Qifan Sun
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Liang Xue
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Haiyan Zeng
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Tao Lei
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Rui Pang
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Qinghua Ye
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Shi Wu
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Shuhong Zhang
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Haoming Wu
- Guangdong Institute of Microbiology, Guangdong Academic of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Wenzhi Li
- Infinitus (China) Company, Ltd., Guangzhou, China
| | - Xiuying Kou
- Infinitus (China) Company, Ltd., Guangzhou, China
| |
Collapse
|
20
|
Evolution of Listeria monocytogenes in a Food Processing Plant Involves Limited Single-Nucleotide Substitutions but Considerable Diversification by Gain and Loss of Prophages. Appl Environ Microbiol 2020; 86:AEM.02493-19. [PMID: 31900305 PMCID: PMC7054086 DOI: 10.1128/aem.02493-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022] Open
Abstract
Knowledge about the genetic evolution of L. monocytogenes in food processing facilities over multiple years is generally lacking. This information is critical to interpret WGS findings involving food or food-associated isolates. This study suggests that L. monocytogenes that persists in processing facilities may evolve with a low single-nucleotide mutation rate mostly driven by negative (i.e., purifying) selection but with rapid diversification of prophages. Hence, isolation of L. monocytogenes with few single-nucleotide polymorphism (SNP) differences in different locations (e.g., supplier plants and receiving plants) is possible, highlighting the importance of epidemiological and detailed isolate metadata for interpreting WGS data in traceback investigation. Our study also shows how advanced WGS data analyses can be used to support root cause analysis efforts and may, for example, pinpoint the time when a persistence event started (which then potentially could be linked to facility changes, introduction of new equipment, etc.). Whole-genome sequencing (WGS) is becoming the standard method for subtyping Listeria monocytogenes. Interpretation of WGS data for isolates from foods and associated environments is, however, challenging due to a lack of detailed data on Listeria evolution in processing facilities. Here, we used previously collected WGS data for 40 L. monocytogenes isolates obtained from a cold-smoked salmon processing facility between 1998 and 2015 to probe the L. monocytogenes molecular evolution in this facility, combined with phenotypic assessment of selected isolates. Isolates represented three clusters (1, 2, and 3); cluster 3 isolates (n = 32) were obtained over 18 years. The average mutation rate for cluster 3 was estimated as 1.15 × 10−7 changes per nucleotide per year (∼0.35 changes per genome per year); the most recent common ancestors (MRCAs) of subclusters 3a and 3b were estimated to have occurred around 1958 and 1974, respectively, within the age of the facility, suggesting long-term persistence in this facility. Extensive prophage diversity was observed within subclusters 3a and 3b, which have one shared and six unique prophage profiles for each subcluster (with 16 prophage profiles found among all 40 isolates). The plasmid-borne sanitizer tolerance operon bcrABC was found in all cluster 2 and 3 isolates, while the transposon-borne sanitizer tolerance gene qacH was found in one cluster 1 isolate; presence of these genes was correlated with the ability to survive increased concentrations of sanitizers. Selected isolates showed significant variation in the ability to attach to surfaces, with persistent isolates attaching better than transient isolates at 21°C. IMPORTANCE Knowledge about the genetic evolution of L. monocytogenes in food processing facilities over multiple years is generally lacking. This information is critical to interpret WGS findings involving food or food-associated isolates. This study suggests that L. monocytogenes that persists in processing facilities may evolve with a low single-nucleotide mutation rate mostly driven by negative (i.e., purifying) selection but with rapid diversification of prophages. Hence, isolation of L. monocytogenes with few single-nucleotide polymorphism (SNP) differences in different locations (e.g., supplier plants and receiving plants) is possible, highlighting the importance of epidemiological and detailed isolate metadata for interpreting WGS data in traceback investigation. Our study also shows how advanced WGS data analyses can be used to support root cause analysis efforts and may, for example, pinpoint the time when a persistence event started (which then potentially could be linked to facility changes, introduction of new equipment, etc.).
Collapse
|
21
|
Ottesen A, Ramachandran P, Chen Y, Brown E, Reed E, Strain E. Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream. BMC Infect Dis 2020; 20:83. [PMID: 31996135 PMCID: PMC6990534 DOI: 10.1186/s12879-019-4747-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 12/28/2019] [Indexed: 11/13/2022] Open
Abstract
Background The more quickly bacterial pathogens responsible for foodborne illness outbreaks can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the vehicle and source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, “quasimetagenomic” approach ie; direct sequencing of microbiological enrichments (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, 5 days earlier than response that focuses on culture and sequencing of an individual isolate. This expedited approach could save lives, prevent illnesses and potentially minimize unnecessary destruction of food. Methods Naturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 h of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes. Results Quasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture). Conclusions The speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and potentially with continued optimization of the entire chain of response, contribute to minimized food waste.
Collapse
Affiliation(s)
- Andrea Ottesen
- Center for Food Safety and Applied Nutrition (CFSAN), FDA 5001 Campus Drive, College Park, MD, 20740, USA.
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition (CFSAN), FDA 5001 Campus Drive, College Park, MD, 20740, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition (CFSAN), FDA 5001 Campus Drive, College Park, MD, 20740, USA
| | - Eric Brown
- Center for Food Safety and Applied Nutrition (CFSAN), FDA 5001 Campus Drive, College Park, MD, 20740, USA
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition (CFSAN), FDA 5001 Campus Drive, College Park, MD, 20740, USA
| | - Errol Strain
- Center for Veterinary Medicine (CVM), FDA 8301 Muirkirk Rd, Laurel, MD, 20708, USA
| |
Collapse
|
22
|
Zhang Y, Liao YT, Salvador A, Sun X, Wu VCH. Prediction, Diversity, and Genomic Analysis of Temperate Phages Induced From Shiga Toxin-Producing Escherichia coli Strains. Front Microbiol 2020; 10:3093. [PMID: 32038541 PMCID: PMC6986202 DOI: 10.3389/fmicb.2019.03093] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a notorious foodborne pathogen containing stx genes located in the sequence region of Shiga toxin (Stx) prophages. Stx prophages, as one of the mobile elements, are involved in the transfer of virulence genes to other strains. However, little is known about the diversity of prophages among STEC strains. The objectives of this study were to predict various prophages from different STEC genomes and to evaluate the effect of different stress factors on Stx prophage induction. Forty bacterial whole-genome sequences of STEC strains obtained from National Center for Biotechnology Information (NCBI) were used for the prophage prediction using PHASTER webserver. Eight of the STEC strains from different serotypes were subsequently selected to quantify the induction of Stx prophages by various treatments, including antibiotics, temperature, irradiation, and antimicrobial agents. After induction, Stx1-converting phage Lys8385Vzw and Stx2-converting phage Lys12581Vzw were isolated and further confirmed for the presence of stx genes using conventional PCR. Phage morphology was observed by transmission electron microscopy. The prediction results showed an average of 8–22 prophages, with one or more encoding stx, were predicted from each STEC genome obtained in this study. Additionally, the phylogenetic analysis revealed high genetic diversity of Stx prophages among the 40 STEC genomes. However, the sequences of Stx prophages in the genomes of STEC O45, O111, and O121 strains, in general, shared higher genetic homology than those in other serotypes. Interestingly, most STEC strains with two or more stx genes carried at least one each of Stx1 and Stx2 prophages. The induction results indicated EDTA and UV were the most effective inducers of Stx1 and Stx2 prophages of the 8 selected STECs, respectively. Additionally, both Stx-converting phages could infect non-pathogenic E. coli (WG5, DH5α, and MG1655) and form new lysogens. The findings of this study confirm that Stx prophages can be induced by environmental stress, such as exposure to solar radiation, and lysogenize other commensal E. coli strains.
Collapse
Affiliation(s)
- Yujie Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Yen-Te Liao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Alexandra Salvador
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Xiaohong Sun
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Vivian C H Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| |
Collapse
|
23
|
Survival of outbreak, food, and environmental strains of Listeria monocytogenes on whole apples as affected by cultivar and wax coating. Sci Rep 2019; 9:12170. [PMID: 31434982 PMCID: PMC6704171 DOI: 10.1038/s41598-019-48597-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/08/2019] [Indexed: 11/20/2022] Open
Abstract
The 2014–2015 U.S. nationwide outbreak of listeriosis linked to apples used in commercially produced, prepackaged caramel apples was the first implication of whole apples in outbreaks of foodborne illnesses. Two case patients of this outbreak didn’t consume caramel apples but did eat whole apples, suggesting that contaminated whole apple may serve as a vehicle for foodborne listeriosis. The current study evaluated the effect of conventional fruit coating with wax and that of apple cultivar on the survival of outbreak-associated and non-outbreak Listeria monocytogenes strains on Red Delicious, Granny Smith and Fuji apples during 160 days under simulated commercial storage. L. monocytogenes survived in calyxes and stem ends of apples of all 3 cultivars through the duration of the experiment. After 2 months of storage, significantly (p < 0.05) larger L. monocytogenes populations were recovered from apples coated with wax than those un-waxed, regardless of the cultivar. No differences in survival amongst L. monocytogenes strains (serotypes 1/2a and 4b) from clinical, food, and environmental sources were observed. The observation that coating with wax facilitates prolonged survival of L. monocytogenes on whole apples is novel and reveals gaps in understanding of microbiological risks associated with postharvest practices of tree fruit production.
Collapse
|
24
|
Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM, Van Oyen H, Robert A. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.
Collapse
Affiliation(s)
- Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| | - Tine Descamps
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nele A. M. Boon
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| |
Collapse
|
25
|
Wang J, Liu S, Liu B, Niu X, Deng X. Luteolin Inhibits Listeriolysin O Translation by Directly Targeting the Coding Region of the hly mRNA. Front Microbiol 2019; 10:1496. [PMID: 31312194 PMCID: PMC6614183 DOI: 10.3389/fmicb.2019.01496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/14/2019] [Indexed: 11/16/2022] Open
Abstract
Listeriolysin O (LLO) is necessary for bacterial escape from the phagosome into the cytoplasm, which suggests that targeting LLO may be an alternative strategy to combat Listeria monocytogenes-mediated infection. Here, luteolin, a natural compound without anti-bacterial activity, as indentified as effective inhibitor of LLO by translationally inhibiting the production of LLO. Additionally, luteolin-treated L. monocytogenes displayed reductions in cytoplasmic growth, cytotoxicity and phagosome escape within macrophages. Molecular modeling and mutational analysis revealed a direct interaction between luteolin and the 5′ coding region (A818, U819, G820, and U830 located in nt 814–849) of the mRNA of hly, the gene encoding LLO, which interfered with its translation. Together, our data demonstrate that luteolin may be used as a novel therapeutic and lead compound for treating L. monocytogenes infection.
Collapse
Affiliation(s)
- Jianfeng Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Shui Liu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Bowen Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaodi Niu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| |
Collapse
|
26
|
Gerner-Smidt P, Besser J, Concepción-Acevedo J, Folster JP, Huffman J, Joseph LA, Kucerova Z, Nichols MC, Schwensohn CA, Tolar B. Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases. Front Public Health 2019; 7:172. [PMID: 31316960 PMCID: PMC6610495 DOI: 10.3389/fpubh.2019.00172] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/10/2019] [Indexed: 11/13/2022] Open
Abstract
Infections caused by pathogens commonly acquired from consumption of food are not always transmitted by that route. They may also be transmitted through contact to animals, other humans or the environment. Additionally, many outbreaks are associated with food contaminated from these non-food sources. For this reason, such presumed foodborne outbreaks are best investigated through a One Health approach working across human, animal and environmental sectors and disciplines. Outbreak strains or clones that have propagated and continue to evolve in non-human sources and environments often show more sequence variation than observed in typical monoclonal point-source outbreaks. This represents a challenge when using whole genome sequencing (WGS), the new gold standard for molecular surveillance of foodborne pathogens, for outbreak detection and investigation. In this review, using recent examples from outbreaks investigated in the United States (US) some aspects of One Health approaches that have been used successfully to solve such outbreaks are presented. These include using different combinations of flexible WGS based case definition, efficient epidemiological follow-up, traceback, surveillance, and testing of potential food and environmental sources and animal hosts.
Collapse
Affiliation(s)
- Peter Gerner-Smidt
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - John Besser
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jeniffer Concepción-Acevedo
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jason P Folster
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jasmine Huffman
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lavin A Joseph
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Zuzana Kucerova
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Megin C Nichols
- The Outbreak Response and Prevention Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Colin A Schwensohn
- The Outbreak Response and Prevention Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Beth Tolar
- The Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| |
Collapse
|
27
|
Relevance of Food Microbiology Issues to Current Trends (2008-2018) in Food Production and Imported Foods. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
28
|
Smith AM, Tau NP, Smouse SL, Allam M, Ismail A, Ramalwa NR, Disenyeng B, Ngomane M, Thomas J. Outbreak of Listeria monocytogenes in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates. Foodborne Pathog Dis 2019; 16:524-530. [PMID: 31062992 PMCID: PMC6653791 DOI: 10.1089/fpd.2018.2586] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of Listeria monocytogenes isolates associated with this outbreak. Bacteria were identified using the VITEK-2 COMPACT 15 microbial identification system. WGS was performed using Illumina MiSeq technology. WGS data were analyzed using CLC Genomics Workbench Software and free-to-use on-line analysis tools/pipelines. Multilocus sequence typing (MLST) showed that 91% of clinical isolates were sequence type 6 (ST6), determining that the outbreak was largely associated with L. monocytogenes ST6. Epidemiological and laboratory findings led to investigation of a large ready-to-eat processed meat production facility in South Africa, named Enterprise Foods. L. monocytogenes ST6 was found in environmental sampling swabs of the production facility and in ready-to-eat processed meat products (including polony, a product similar to bologna sausage) manufactured at the facility. ST6 isolates, sourced at the Enterprise Foods production facility and from Enterprise food products, were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates; these nonclinical ST6 isolates showed <10 SNP differences when compared to clinical ST6 isolates. Core-genome MLST showed that clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggestive of a high probability of epidemiological relatedness. WGS data interpreted together with epidemiological data concluded that the source of the listeriosis outbreak was ready-to-eat processed meat products manufactured by Enterprise Foods. Listeriosis has now been added to the South African list of mandatory notifiable medical conditions. Surveillance systems have been strengthened to facilitate prevention and early detection of listeriosis outbreaks.
Collapse
Affiliation(s)
- Anthony M Smith
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nomsa P Tau
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon L Smouse
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ntsieni R Ramalwa
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mimmy Ngomane
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
29
|
Whole genome sequencing uses for foodborne contamination and compliance: Discovery of an emerging contamination event in an ice cream facility using whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2019; 73:214-220. [PMID: 31039448 DOI: 10.1016/j.meegid.2019.04.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 11/21/2022]
Abstract
We review how FDA surveillance identifies several ways that whole genome sequencing (WGS) improves actionable outcomes for public health and compliance in a case involving Listeria monocytogenes contamination in an ice cream facility. In late August 2017 FDA conducted environmental sampling inside an ice cream facility. These isolates were sequenced and deposited into the GenomeTrakr databases. In September 2018 the Centers for Disease Control and Prevention contacted the Florida Department of Health after finding that the pathogen analyses of three clinical cases of listeriosis (two in 2013, one in 2018) were highly related to the aforementioned L. monocytogenes isolates collected from the ice cream facility. in 2017. FDA returned to the ice cream facility in late September 2018 and conducted further environmental sampling and again recovered L. monocytogenes from environmental subsamples that were genetically related to the clinical cases. A voluntary recall was issued to include all ice cream manufactured from August 2017 to October 2018. Subsequently, FDA suspended this food facility's registration. WGS results for L. monocytogenes found in the facility and from clinical samples clustered together by 0-31 single nucleotide polymorphisms (SNPs). The FDA worked together with the Centers for Disease Control and Prevention, as well as the Florida Department of Health, and the Florida Department of Agriculture and Consumer Services to recall all ice cream products produced by this facility. Our data suggests that when available isolates from food facility inspections are subject to whole genome sequencing and the subsequent sequence data point to linkages between these strains and recent clinical isolates (i.e., <20 nucleotide differences), compliance officials should take regulatory actions early to prevent further potential illness. The utility of WGS for applications related to enforcement of FDA compliance programs in the context of foodborne pathogens is reviewed.
Collapse
|
30
|
Carroll LM, Wiedmann M, Mukherjee M, Nicholas DC, Mingle LA, Dumas NB, Cole JA, Kovac J. Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges. Front Microbiol 2019; 10:144. [PMID: 30809204 PMCID: PMC6379260 DOI: 10.3389/fmicb.2019.00144] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/21/2019] [Indexed: 12/21/2022] Open
Abstract
The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize B. cereus group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the B. cereus group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 B. cereus group isolates were obtained from human cases (n = 7) and food samples (n = 26). Emetic (n = 30) and diarrheal (n = 3) isolates were most closely related to B. paranthracis (group III) and B. cereus sensu stricto (group IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely related and formed a well-supported clade distinct from publicly available emetic group III genomes with an identical sequence type (ST 26). The 30 emetic group III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly available emetic group III ST 26 B. cereus group genomes by a mean of 301.7-528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain B. cereus ATCC 14579. We hypothesize that the outbreak was a single source outbreak caused by emetic group III B. cereus belonging to the B. paranthracis species, although food samples were not tested for presence of the emetic toxin cereulide. In addition to showcasing how WGS can be used to characterize B. cereus group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by B. cereus group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.
Collapse
Affiliation(s)
- Laura M. Carroll
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Manjari Mukherjee
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - David C. Nicholas
- New York State Department of Health, Corning Tower, Empire State Plaza, Albany, NY, United States
| | - Lisa A. Mingle
- New York State Department of Health, Wadsworth Center, Albany, NY, United States
| | - Nellie B. Dumas
- New York State Department of Health, Wadsworth Center, Albany, NY, United States
| | - Jocelyn A. Cole
- New York State Department of Health, Wadsworth Center, Albany, NY, United States
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
31
|
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
|
32
|
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
|
33
|
Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
Collapse
Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| |
Collapse
|
34
|
Portmann AC, Fournier C, Gimonet J, Ngom-Bru C, Barretto C, Baert L. A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica. Front Microbiol 2018; 9:446. [PMID: 29593690 PMCID: PMC5861296 DOI: 10.3389/fmicb.2018.00446] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/26/2018] [Indexed: 11/13/2022] Open
Abstract
Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations. Despite its increased use, no standards or guidelines are available today for the use of WGS in outbreak and/or trace-back investigations. Here we present a validation of our complete (end-to-end) WGS workflow for Listeria monocytogenes and Salmonella enterica including: subculture of isolates, DNA extraction, sequencing and bioinformatics analysis. This end-to-end WGS workflow was evaluated according to the following performance criteria: stability, repeatability, reproducibility, discriminatory power, and epidemiological concordance. The current study showed that few single nucleotide polymorphism (SNPs) were observed for L. monocytogenes and S. enterica when comparing genome sequences from five independent colonies from the first subculture and five independent colonies after the tenth subculture. Consequently, the stability of the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite the few genomic variations that can occur during subculturing steps. Repeatability and reproducibility were also demonstrated. The WGS workflow was shown to have a high discriminatory power and has the ability to show genetic relatedness. Additionally, the WGS workflow was able to reproduce published outbreak investigation results, illustrating its capability of showing epidemiological concordance. The current study proposes a validation approach comprising all steps of a WGS workflow and demonstrates that the workflow can be applied to L. monocytogenes or S. enterica.
Collapse
Affiliation(s)
| | - Coralie Fournier
- Nestle Institute of Health Sciences SA, EPFL Innovation Park, Lausanne, Switzerland
| | - Johan Gimonet
- Nestec Ltd., Nestle Research Center, Lausanne, Switzerland
| | | | | | - Leen Baert
- Nestec Ltd., Nestle Research Center, Lausanne, Switzerland
| |
Collapse
|
35
|
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]
|
36
|
Muhterem-Uyar M, Ciolacu L, Wagner KH, Wagner M, Schmitz-Esser S, Stessl B. New Aspects on Listeria monocytogenes ST5-ECVI Predominance in a Heavily Contaminated Cheese Processing Environment. Front Microbiol 2018; 9:64. [PMID: 29472901 PMCID: PMC5810274 DOI: 10.3389/fmicb.2018.00064] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/10/2018] [Indexed: 01/25/2023] Open
Abstract
The eradication of Listeria monocytogenes from food chains is still a great challenge for the food industry and control authorities since some clonal complexes (CCs) are either better adapted to food processing environments (FPEs) or are globally widespread. In this work, we focus on the in-house evolution of L. monocytogenes genotypes collected from a heavily contaminated FPE whose contamination pattern underwent a massive and yet unexplained change. At the beginning of the sampling in 2010, a high variety of most likely transient L. monocytogenes genotypes was detected belonging to sequence type (ST) 1, ST7, ST21, ST37. After several efforts to intensify the hygiene measures, the variability was reduced to L. monocytogenes ST5 that was dominant in the following years 2011 and 2012. We aimed to elucidate possible genetic mechanisms responsible for the high abundance and persistence of ST5 strains in this FPE. Therefore, we compared the genomes of six L. monocytogenes ST5 strains to the less frequently occurring transient L. monocytogenes ST37 and ST204 from the same FPE as well as the highly abundant ST1 and ST21 isolated in 2010. Whole genome analysis indicated a high degree of conservation among ST5 strains [average nucleotide identity (ANI) 99.93-99.99%; tetranucleotide correlation 0.99998-0.99999]. Slight differences in pulsed field gel electrophoresis (PFGE) patterns of two ST5 isolates could be explained by genetic changes in the tRNA-Arg-TCT prophages. ST5 and ST204 strains harbored virtually identical 91 kbp plasmids related to plasmid group 2 (pLM80 and pLMUCDL175). Interestingly, highly abundant genotypes present in the FPE in 2010 did not harbor any plasmids. The ST5 plasmids harbored an efflux pump system (bcrABC cassette) and heavy metal resistance genes possibly providing a higher tolerance to disinfectants. The pLM80 prototype plasmids most likely provide important genetic determinants for a better survival of L. monocytogenes in the FPE. We reveal short-term evolution of L. monocytogenes strains within the same FPE over a 3 year period and our results suggest that plasmids are important for the persistence of ST5 strains in this FPE.
Collapse
Affiliation(s)
- Meryem Muhterem-Uyar
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Austria.,Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Luminita Ciolacu
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Austria
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Martin Wagner
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Austria
| | - Stephan Schmitz-Esser
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Austria.,Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Beatrix Stessl
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Austria
| |
Collapse
|
37
|
Allard MW, Bell R, Ferreira CM, Gonzalez-Escalona N, Hoffmann M, Muruvanda T, Ottesen A, Ramachandran P, Reed E, Sharma S, Stevens E, Timme R, Zheng J, Brown EW. Genomics of foodborne pathogens for microbial food safety. Curr Opin Biotechnol 2018; 49:224-229. [DOI: 10.1016/j.copbio.2017.11.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/27/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
|
38
|
Salazar JK, Bathija VM, Carstens CK, Narula SS, Shazer A, Stewart D, Tortorello ML. Listeria monocytogenes Growth Kinetics in Milkshakes Made from Naturally and Artificially Contaminated Ice Cream. Front Microbiol 2018; 9:62. [PMID: 29416531 PMCID: PMC5787567 DOI: 10.3389/fmicb.2018.00062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/10/2018] [Indexed: 12/15/2022] Open
Abstract
This study assessed the growth of Listeria monocytogenes in milkshakes made using the process-contaminated ice cream associated with a listeriosis outbreak in comparison to milkshakes made with artificially contaminated ice cream. For all temperatures, growth kinetics including growth rates, lag phases, maximum populations, and population increases were determined for the naturally and artificially derived contaminants at 5, 10, 15, and 25°C storage for 144 h. The artificially inoculated L. monocytogenes presented lower growth rates and shorter lag phases than the naturally contaminated populations at all temperatures except for 5°C, where the reverse was observed. At 25°C, lag phases of the naturally and artificially contaminated L. monocytogenes were 11.6 and 7.8 h, respectively. The highest increase in population was observed for the artificially inoculated pathogen at 15°C after 96 h (6.16 log CFU/mL) of storage. Growth models for both contamination states in milkshakes were determined. In addition, this study evaluated the antimicrobial effectiveness of flavoring agents, including strawberry, chocolate and mint, on the growth of the pathogen in milkshakes during 10°C storage. All flavor additions resulted in decreased growth rates of L. monocytogenes for both contamination states. The addition of chocolate and mint flavoring also resulted in significantly longer lag phases for both contamination states. This study provides insight into the differences in growth between naturally and artificially contaminated L. monocytogenes in a food product.
Collapse
Affiliation(s)
- Joelle K. Salazar
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, Bedford Park, IL, United States
| | - Vriddi M. Bathija
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, United States
| | - Christina K. Carstens
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, Bedford Park, IL, United States
| | - Sartaj S. Narula
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, United States
| | - Arlette Shazer
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, Bedford Park, IL, United States
| | - Diana Stewart
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, Bedford Park, IL, United States
| | - Mary Lou Tortorello
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, Bedford Park, IL, United States
| |
Collapse
|
39
|
Kase JA, Zhang G, Chen Y. Recent foodborne outbreaks in the United States linked to atypical vehicles — lessons learned. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
40
|
Henri C, Leekitcharoenphon P, Carleton HA, Radomski N, Kaas RS, Mariet JF, Felten A, Aarestrup FM, Gerner Smidt P, Roussel S, Guillier L, Mistou MY, Hendriksen RS. An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes. Front Microbiol 2017; 8:2351. [PMID: 29238330 PMCID: PMC5712588 DOI: 10.3389/fmicb.2017.02351] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L. monocytogenes. Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses. Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering. Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories.
Collapse
Affiliation(s)
- Clémentine Henri
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, Maisons-Alfort Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Pimlapas Leekitcharoenphon
- European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Heather A Carleton
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Nicolas Radomski
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, Maisons-Alfort Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Rolf S Kaas
- European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jean-François Mariet
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, Maisons-Alfort Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Arnaud Felten
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, Maisons-Alfort Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Frank M Aarestrup
- European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Gerner Smidt
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sophie Roussel
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, Maisons-Alfort Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Laurent Guillier
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, Maisons-Alfort Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - Michel-Yves Mistou
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, Maisons-Alfort Laboratory for Food Safety, University Paris-Est, Maisons-Alfort, France
| | - René S Hendriksen
- European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
41
|
Timme RE, Rand H, Shumway M, Trees EK, Simmons M, Agarwala R, Davis S, Tillman GE, Defibaugh-Chavez S, Carleton HA, Klimke WA, Katz LS. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ 2017; 5:e3893. [PMID: 29372115 PMCID: PMC5782805 DOI: 10.7717/peerj.3893] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/15/2017] [Indexed: 11/20/2022] Open
Abstract
Background As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. Methods We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and “known” phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Results Our “outbreak” benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) and one simulated dataset where the “known tree” can be accurately called the “true tree”. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. Discussion These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations. Our work is part of a global effort to provide collaborative infrastructure for sequence data and analytic tools—we welcome additional benchmark datasets in our recommended format, and, if relevant, we will add these on our GitHub site. Together, these datasets, dataset format, and the underlying GitHub infrastructure present a recommended path for worldwide standardization of phylogenomic pipelines.
Collapse
Affiliation(s)
- Ruth E Timme
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
| | - Hugh Rand
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
| | - Martin Shumway
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, United States of America
| | - Eija K Trees
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Mustafa Simmons
- Food Safety and Inspection Service, US Department of Agriculture, Athens, GA, United States of America
| | - Richa Agarwala
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, United States of America
| | - Steven Davis
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
| | - Glenn E Tillman
- Food Safety and Inspection Service, US Department of Agriculture, Athens, GA, United States of America
| | - Stephanie Defibaugh-Chavez
- Food Safety and Inspection Service, US Department of Agriculture, Wahington, D.C., United States of America
| | - Heather A Carleton
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - William A Klimke
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, United States of America
| | - Lee S Katz
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America.,Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, United States of America
| |
Collapse
|
42
|
Whole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, United States, 2013. Appl Environ Microbiol 2017; 83:AEM.00633-17. [PMID: 28550058 PMCID: PMC5514676 DOI: 10.1128/aem.00633-17] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/17/2017] [Indexed: 12/21/2022] Open
Abstract
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS 3 months later revealed that the equipment purchased by company B from company A yielded an environmental isolate highly similar to all outbreak isolates. The whole genome and core genome multilocus sequence typing and single nucleotide polymorphism (SNP) analyses results were compared to demonstrate the maximum discriminatory power obtained by using multiple analyses, which were needed to differentiate outbreak-associated isolates from a PFGE-indistinguishable isolate collected in a nonimplicated food source in 2012. This unrelated isolate differed from the outbreak isolates by only 7 to 14 SNPs, and as a result, the minimum spanning tree from the whole genome analyses and certain variant calling approach and phylogenetic algorithm for core genome-based analyses could not provide differentiation between unrelated isolates. Our data also suggest that SNP/allele counts should always be combined with WGS clustering analysis generated by phylogenetically meaningful algorithms on a sufficient number of isolates, and the SNP/allele threshold alone does not provide sufficient evidence to delineate an outbreak. The putative prophages were conserved across all the outbreak isolates. All outbreak isolates belonged to clonal complex 5 and serotype 1/2b and had an identical inlA sequence which did not have premature stop codons. IMPORTANCE In this outbreak, multiple analytical approaches were used for maximum discriminatory power. A PFGE-matched, epidemiologically unrelated isolate had high genetic similarity to the outbreak-associated isolates, with as few as 7 SNP differences. Therefore, the SNP/allele threshold should not be used as the only evidence to define the scope of an outbreak. It is critical that the SNP/allele counts be complemented by WGS clustering analysis generated by phylogenetically meaningful algorithms to distinguish outbreak-associated isolates from epidemiologically unrelated isolates. Careful selection of a variant calling approach and phylogenetic algorithm is critical for core-genome-based analyses. The whole-genome-based analyses were able to construct the highly resolved phylogeny needed to support the findings of the outbreak investigation. Ultimately, epidemiologic evidence and multiple WGS analyses should be combined to increase confidence levels during outbreak investigations.
Collapse
|
43
|
Li Z, Pérez-Osorio A, Wang Y, Eckmann K, Glover WA, Allard MW, Brown EW, Chen Y. Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State. BMC Microbiol 2017; 17:134. [PMID: 28619007 PMCID: PMC5472956 DOI: 10.1186/s12866-017-1043-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/03/2017] [Indexed: 11/25/2022] Open
Abstract
Background In 2015, in addition to a United States multistate outbreak linked to contaminated ice cream, another outbreak linked to ice cream was reported in the Pacific Northwest of the United States. It was a hospital-acquired outbreak linked to milkshakes, made from contaminated ice cream mixes and milkshake maker, served to patients. Here we performed multiple analyses on isolates associated with this outbreak: pulsed-field gel electrophoresis (PFGE), whole genome single nucleotide polymorphism (SNP) analysis, species-specific core genome multilocus sequence typing (cgMLST), lineage-specific cgMLST and whole genome-specific MLST (wgsMLST)/outbreak-specific cgMLST. We also analyzed the prophages and virulence genes. Results The outbreak isolates belonged to sequence type 1038, clonal complex 101, genetic lineage II. There were no pre-mature stop codons in inlA. Isolates contained Listeria Pathogenicity Island 1 and multiple internalins. PFGE and multiple whole genome sequencing (WGS) analyses all clustered together food, environmental and clinical isolates when compared to outgroup from the same clonal complex, which supported the finding that L. monocytogenes likely persisted in the soft serve ice cream/milkshake maker from November 2014 to November 2015 and caused 3 illnesses, and that the outbreak strain was transmitted between two ice cream production facilities. The whole genome SNP analysis, one of the two species-specific cgMLST, the lineage II-specific cgMLST and the wgsMLST/outbreak-specific cgMLST showed that L. monocytogenes cells persistent in the milkshake maker for a year formed a unique clade inside the outbreak cluster. This clustering was consistent with the cleaning practice after the outbreak was initially recognized in late 2014 and early 2015. Putative prophages were conserved among prophage-containing isolates. The loss of a putative prophage in two isolates resulted in the loss of the AscI restriction site in the prophage, which contributed to their AscI-PFGE banding pattern differences from other isolates. Conclusions The high resolution of WGS analyses allowed the differentiation of epidemiologically unrelated isolates, as well as the elucidation of the microevolution and persistence of isolates within the scope of one outbreak. We applied a wgsMLST scheme which is essentially the outbreak-specific cgMLST. This scheme can be combined with lineage-specific cgMLST and species-specific cgMLST to maximize the resolution of WGS.
Collapse
Affiliation(s)
- Zhen Li
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - Ailyn Pérez-Osorio
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - Yu Wang
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Kaye Eckmann
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - William A Glover
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - Marc W Allard
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA.
| |
Collapse
|