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Ramadan H, Al-Ashmawy M, Soliman AM, Elbediwi M, Sabeq I, Yousef M, Algammal AM, Hiott LM, Berrang ME, Frye JG, Jackson CR. Whole-genome sequencing of Listeria innocua recovered from retail milk and dairy products in Egypt. Front Microbiol 2023; 14:1160244. [PMID: 37234542 PMCID: PMC10206011 DOI: 10.3389/fmicb.2023.1160244] [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: 02/06/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023] Open
Abstract
The similarity of the Listeria innocua genome with Listeria monocytogenes and their presence in the same niche may facilitate gene transfer between them. A better understanding of the mechanisms responsible for bacterial virulence requires an in-depth knowledge of the genetic characteristics of these bacteria. In this context, draft whole genome sequences were completed on five L. innocua isolated from milk and dairy products in Egypt. The assembled sequences were screened for antimicrobial resistance and virulence genes, plasmid replicons and multilocus sequence types (MLST); phylogenetic analysis of the sequenced isolates was also performed. The sequencing results revealed the presence of only one antimicrobial resistance gene, fosX, in the L. innocua isolates. However, the five isolates carried 13 virulence genes involved in adhesion, invasion, surface protein anchoring, peptidoglycan degradation, intracellular survival, and heat stress; all five lacked the Listeria Pathogenicity Island 1 (LIPI-1) genes. MLST assigned these five isolates into the same sequence type (ST), ST-1085; however, single nucleotide polymorphism (SNP)-based phylogenetic analysis revealed 422-1,091 SNP differences between our isolates and global lineages of L. innocua. The five isolates possessed an ATP-dependent protease (clpL) gene, which mediates heat resistance, on a rep25 type plasmids. Blast analysis of clpL-carrying plasmid contigs showed approximately 99% sequence similarity to the corresponding parts of plasmids of L. monocytogenes strains 2015TE24968 and N1-011A previously isolated from Italy and the United States, respectively. Although this plasmid has been linked to L. monocytogenes that was responsible for a serious outbreak, this is the first report of L. innocua containing clpL-carrying plasmids. Various genetic mechanisms of virulence transfer among Listeria species and other genera could raise the possibility of the evolution of virulent strains of L. innocua. Such strains could challenge processing and preservation protocols and pose health risks from dairy products. Ongoing genomic research is necessary to identify these alarming genetic changes and develop preventive and control measures.
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Affiliation(s)
- Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Maha Al-Ashmawy
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Ahmed M. Soliman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Mohammed Elbediwi
- Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany
- Animal Health Research Institute, Agriculture Research Center, Cairo, Egypt
| | - Islam Sabeq
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Benha University, Tukh, Qalyubia, Egypt
| | - Mona Yousef
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Abdelazeem M. Algammal
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Lari M. Hiott
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Mark E. Berrang
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Jonathan G. Frye
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Charlene R. Jackson
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
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A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility. Microbiol Spectr 2022; 10:e0204522. [PMID: 35980043 PMCID: PMC9603805 DOI: 10.1128/spectrum.02045-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities which persist in food processing facilities may have a detrimental impact on food safety and spoilage. In meat processing, Listeria monocytogenes is an organism of concern due to its ability to cause significant human illnesses and persist in refrigerated environments. The microbial ecology of Listeria spp. in small meat processing facilities has not been well characterized. Therefore, we collected samples from a newly constructed meat processing facility as an opportunity to investigate several research objectives: (i) to determine whether a stable, consistent microbiome develops in a small meat processing facility during the first 18 months of operation, (ii) to evaluate the environmental factors that drive microbial community formation, and (iii) to elucidate the relationship between microbial communities and the presence of Listeria species. We evaluated microbiomes using 16S rRNA gene sequencing and Listeria presence using quantitative PCR. We demonstrated that microbial communities differentiate by the functional room type, which is representative of several environmental differences such as temperature, sources of microbes, and activity. Temperature was an especially important factor; in rooms with low temperatures, communities were dominated by psychotrophs, especially Pseudomonas, while warmer rooms supported greater diversity. A stable core community formed in facility drains, indicating that mechanisms which cause persistence are present in the communities. The overall presence of Listeria in the facility was low but could be tied to specific organisms within a room, and the species of Listeria could be stratified by room function. IMPORTANCE This study provides critical knowledge to improve meat safety and quality from small meat processing facilities. Principally, it demonstrates the importance of facility design and room condition to the development of important microbial communities; temperature, sanitation regimen, and physical barriers all influence the ability of microorganisms to join the stable core community. It also demonstrates a relationship between the microbial community and Listeria presence in the facility, showing the importance of managing facility sanitation plans for not only pathogens, but also the general facility microbiome.
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Parra-Flores J, Holý O, Bustamante F, Lepuschitz S, Pietzka A, Contreras-Fernández A, Castillo C, Ovalle C, Alarcón-Lavín MP, Cruz-Córdova A, Xicohtencatl-Cortes J, Mancilla-Rojano J, Troncoso M, Figueroa G, Ruppitsch W. Virulence and Antibiotic Resistance Genes in Listeria monocytogenes Strains Isolated From Ready-to-Eat Foods in Chile. Front Microbiol 2022; 12:796040. [PMID: 35299835 PMCID: PMC8921925 DOI: 10.3389/fmicb.2021.796040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 01/30/2023] Open
Abstract
Listeria monocytogenes is causing listeriosis, a rare but severe foodborne infection. Listeriosis affects pregnant women, newborns, older adults, and immunocompromised individuals. Ready-to-eat (RTE) foods are the most common sources of transmission of the pathogen This study explored the virulence factors and antibiotic resistance in L. monocytogenes strains isolated from ready-to-eat (RTE) foods through in vitro and in silico testing by whole-genome sequencing (WGS). The overall positivity of L. monocytogenes in RTE food samples was 3.1% and 14 strains were isolated. L. monocytogenes ST8, ST2763, ST1, ST3, ST5, ST7, ST9, ST14, ST193, and ST451 sequence types were identified by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST. Seven isolates had serotype 1/2a, five 1/2b, one 4b, and one 1/2c. Three strains exhibited in vitro resistance to ampicillin and 100% of the strains carried the fosX, lin, norB, mprF, tetA, and tetC resistance genes. In addition, the arsBC, bcrBC, and clpL genes were detected, which conferred resistance to stress and disinfectants. All strains harbored hlyA, prfA, and inlA genes almost thirty-two the showed the bsh, clpCEP, hly, hpt, iap/cwhA, inlA, inlB, ipeA, lspA, mpl, plcA, pclB, oat, pdgA, and prfA genes. One isolate exhibited a type 11 premature stop codon (PMSC) in the inlA gene and another isolate a new mutation (deletion of A in position 819). The Inc18(rep25), Inc18(rep26), and N1011A plasmids and MGEs were found in nine isolates. Ten isolates showed CAS-Type II-B systems; in addition, Anti-CRISPR AcrIIA1 and AcrIIA3 phage-associated systems were detected in three genomes. These virulence and antibiotic resistance traits in the strains isolated in the RTE foods indicate a potential public health risk for consumers.
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Affiliation(s)
- Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - Ondrej Holý
- Science and Research Centre, Faculty of Health Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Fernanda Bustamante
- Environmental and Public Health Laboratory, Regional Secretariat of the Ministry of Health in Maule, Talca, Chile
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | - Claudia Castillo
- School of Nutrition and Dietetics, Universidad del Bío-Bío, Chillán, Chile
| | - Catalina Ovalle
- School of Nutrition and Dietetics, Universidad del Bío-Bío, Chillán, Chile
| | | | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jetsi Mancilla-Rojano
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.,Faculty of Medicine, Biological Sciences Graduate Program, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miriam Troncoso
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Guillermo Figueroa
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
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Lourenco A, Linke K, Wagner M, Stessl B. The Saprophytic Lifestyle of Listeria monocytogenes and Entry Into the Food-Processing Environment. Front Microbiol 2022; 13:789801. [PMID: 35350628 PMCID: PMC8957868 DOI: 10.3389/fmicb.2022.789801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes is an environmentally adapted saprophyte that can change into a human and animal bacterial pathogen with zoonotic potential through several regulatory systems. In this review, the focus is on the occurrence of Listeria sensu stricto and sensu lato in different ecological niches, the detection methods, and their analytical limitations. It also highlights the occurrence of L. monocytogenes genotypes in the environment (soil, water, and wildlife), reflects on the molecular determinants of L. monocytogenes for the saprophytic lifestyle and the potential for antibiotic resistance. In particular, the strain-specific properties with which some genotypes circulate in wastewater, surface water, soil, wildlife, and agricultural environments are of particular interest for the continuously updating risk analysis.
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Affiliation(s)
- Antonio Lourenco
- Department of Food Biosciences, Teagasc Food Research Centre, Co. Cork, Ireland
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Kristina Linke
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Beatrix Stessl
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Genotyping of Listeria monocytogenes isolates by high-resolution melting curve (HRM) analysis of tandem repeat locus. Braz J Infect Dis 2022; 26:102348. [PMID: 35341738 PMCID: PMC9387474 DOI: 10.1016/j.bjid.2022.102348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
Listeria monocytogenes is responsible for causing listeriosis, a type of food poisoning with high mortality. This bacterium is mainly transmitted to humans through the consumption of contaminated foods. Detection of L. monocytogenes through molecular methods is crucial for food safety and clinical diagnosis. Present techniques are characterized by low discrimination power and high cost, as well as being time-consuming and taking several days to give the final result. In our study, MLVA-HRM (Multiple-Locus Variable-number tandem repeats Analysis ‒ High-Resolution Melting) was investigated as an alternative method for a fast and precise method for the genotyping of L. monocytogenes isolates. Forty-eight isolates of L. monocytogenes obtained from the microbial bank of Department of Microbiology, Iran University of Medical Sciences, were typed by MLVA-HRM analysis using five Variable Numbers of Tandem Repeat (VNTR) loci. A total of 43 different types were obtained. This research demonstrated the usefulness of the MLVA-HRMA method and its ability to discriminate L. monocytogenes isolates. Since this method is easier and more efficient than existing methods, it can be widely used in food processing plants and diagnostic laboratories as a fast and accurate method.
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Bespalova TY, Mikhaleva TV, Meshcheryakova NY, Kustikova OV, Matovic K, Dmitrić M, Zaitsev SS, Khizhnyakova MA, Feodorova VA. Novel Sequence Types of Listeria monocytogenes of Different Origin Obtained in the Republic of Serbia. Microorganisms 2021; 9:1289. [PMID: 34204786 PMCID: PMC8231576 DOI: 10.3390/microorganisms9061289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Listeria monocytogenes, the causative agent of listeriosis, is amongst the major food-borne pathogens in the world that affect mammal species, including humans. This microorganism has been associated with both sporadic episodes and large outbreaks of human listeriosis worldwide, with high mortality rates. In this study, the main sequence types (STs) and clonal complexes (CCs) were investigated in all of the 13 L. monocytogenes strains originating from different sources in the Republic of Serbia in 2004-2019 and that were available in the BIGSdb-Lm database. We found at least 13 STs belonging to the phylogenetic lineages I and II. These strains were represented by ST1/ST3/ST9 of CC1/CC3/CC9, which were common in the majority of the European countries and worldwide, as well as by eight novel STs (ST1232/ST1233/ST1234/ST1235/ST1238/ST1236/ST1237/ST1242) of CC19/CC155/CC5/CC21/CC3/CC315/CC37, and the rare ST32 (clonal complex ST32) and ST734 (CC1), reported in the Republic of Serbia, the EU, for the first time. Our study confirmed the association of CC1 with cases of neuroinfection and abortions among small ruminants, and of CC3 and CC9 with food products of animal origin. The strains isolated in 2019 carried alleles of the internalin genes (inlA/inlB/inlC/inlE) characteristic of the most virulent strains from the hypervirulent CC1. These findings demonstrated the genetic relatedness between L. monocytogenes strains isolated in the Republic of Serbia and worldwide. Our study adds further information about the diversity of the L. monocytogenes genotypes of small ruminants and food products, as the strain distribution in these sources in Serbia had not previously been evaluated.
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Affiliation(s)
- Tatiana Yu. Bespalova
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Tatiana V. Mikhaleva
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Nadezhda Yu Meshcheryakova
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Olga V. Kustikova
- Federal Research Center for Virology and Microbiology, Branch in Samara, 443013 Samara, Russia; (T.Y.B.); (T.V.M.); (N.Y.M.); (O.V.K.)
| | - Kazimir Matovic
- Department for Laboratory Diagnostic, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia; (K.M.); (M.D.)
- Department of Food Safety, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia
| | - Marko Dmitrić
- Department for Laboratory Diagnostic, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia; (K.M.); (M.D.)
- Department of Food Safety, Veterinary Specialized Institute Kraljevo, 36000 Kraljevo, Serbia
| | - Sergey S. Zaitsev
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia; (S.S.Z.); (M.A.K.)
| | - Maria A. Khizhnyakova
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia; (S.S.Z.); (M.A.K.)
| | - Valentina A. Feodorova
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia; (S.S.Z.); (M.A.K.)
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