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Gana J, Gcebe N, Pierneef RE, Chen Y, Moerane R, Adesiyun AA. Genomic Characterization of Listeria innocua Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa. Pathogens 2023; 12:1062. [PMID: 37624022 PMCID: PMC10457781 DOI: 10.3390/pathogens12081062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Whole-genome sequencing (WGS) was used for the genomic characterization of one hundred and ten strains of Listeria innocua (L. innocua) isolated from twenty-three cattle farms, eight beef abattoirs, and forty-eight retail outlets in Gauteng province, South Africa. In silico multilocus sequence typing (MLST) was used to identify the isolates' sequence types (STs). BLAST-based analyses were used to identify antimicrobial and virulence genes. The study also linked the detection of the genes to the origin (industries and types of samples) of the L. innocua isolates. The study detected 14 STs, 13 resistance genes, and 23 virulence genes. Of the 14 STs detected, ST637 (26.4%), ST448 (20%), 537 (13.6%), and 1085 (12.7%) were predominant, and the frequency varied significantly (p < 0.05). All 110 isolates of L. innocua were carriers of one or more antimicrobial resistance genes, with resistance genes lin (100%), fosX (100%), and tet(M) (30%) being the most frequently detected (p < 0.05). Of the 23 virulence genes recognized, 13 (clpC, clpE, clpP, hbp1, svpA, hbp2, iap/cwhA, lap, lpeA, lplA1, lspA, oatA, pdgA, and prsA2) were found in all 110 isolates of L. innocua. Overall, diversity and significant differences were detected in the frequencies of STs, resistance, and virulence genes according to the origins (source and sample type) of the L. innocua isolates. This, being the first genomic characterization of L. innocua recovered from the three levels/industries (farm, abattoir, and retail) of the beef production system in South Africa, provides data on the organism's distribution and potential food safety implications.
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Affiliation(s)
- James Gana
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; (J.G.); (R.M.)
- Agricultural Education, Federal College of Education, Kontagora 923101, Nigeria
| | - Nomakorinte Gcebe
- Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa;
| | - Rian Ewald Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa;
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria 0001, South Africa
- Microbiome@UP, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria 0001, South Africa
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 5001 Campus Dr. Room 4E-007/Mailstop HFS-710, College Park, MD 20740, USA;
| | - Rebone Moerane
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; (J.G.); (R.M.)
| | - Abiodun Adewale Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; (J.G.); (R.M.)
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine 685509, Trinidad and Tobago
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Moabelo KC, Gcebe N, Gana J, Ngoshe YB, Adesiyun AA. Contamination of beef and beef products by
Listeria
spp. and molecular characterization of
L. monocytogenes
in Mpumalanga, South Africa. J Food Saf 2023. [DOI: 10.1111/jfs.13055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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Draft genome sequence of Cronobacter sakazakii strain MEZCS99 sequence type 3 isolated from chicken in South Africa. J Glob Antimicrob Resist 2022; 31:292-294. [PMID: 36049732 DOI: 10.1016/j.jgar.2022.08.016] [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: 03/16/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Cronobacter sakazakii is an emerging opportunistic foodborne pathogen that is frequently associated with life-threatening infections such as infantile septicemia, meningitis, and necrotizing enterocolitis. The emergence of antimicrobial-resistant, livestock-associated C. sakazakii is a great public health concern. Here, we report on the first draft genome sequence of C. sakazakii strain MEZCS99 sequence type 3 (ST3) isolated from feces from a healthy chicken in KwaZulu-Natal Province, South Africa. METHODS The genomic DNA of C. sakazakii was sequenced using an Illumina MiSeq platform (Illumina Inc., San Diego, CA). Generated reads were trimmed and de novo assembled. The assembled contigs were analyzed for virulence and antimicrobial resistance genes, extra-chromosomal plasmids, and multilocus sequence type (MLST). To compare the sequenced strains to other previously sequenced C. sakazakii strains, available raw read sequences of C. sakazakii were downloaded and all sequence files were treated identically to generate a core genome phylogenetic tree. RESULTS Intrinsic beta-lactam resistance gene blaCSA-1 was detected in MEZCS99. No colistin or other antibiotic resistance genes were detected. MEZCS99 belonged to ST3 and harbored an extra-chromosomal plasmid (IncFIB (pCTU3)). The genome of MEZCS99 strain showed two CRISPR/Cas cluster arrays of I-E (n = 1) and I-F (n = 1) type. CONCLUSION The genome sequence of strain MEZCS99 will serve as a reference point for molecular epidemiological studies of livestock-associated C. sakazakii in Africa. In addition, this study allows in-depth analysis of the genomic structure and will provide valuable information that helps understand the pathogenesis and antimicrobial resistance of livestock-associated C. sakazakii.
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Mafuna T, Matle I, Magwedere K, Pierneef RE, Reva ON. Comparative Genomics of Listeria Species Recovered from Meat and Food Processing Facilities. Microbiol Spectr 2022; 10:e0118922. [PMID: 36066257 PMCID: PMC9604131 DOI: 10.1128/spectrum.01189-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/12/2022] [Indexed: 12/30/2022] Open
Abstract
Listeria species (spp.) are contaminants that can survive in food, on equipment, and on food processing premises if appropriate hygiene measures are not used. Homologous stress tolerance genes, virulence gene clusters such as the prfA cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic Listeria spp. To enhance understanding of the genome evolution of virulence and virulence-associated properties, a comparative genome approach was used to analyze 41 genome sequences belonging to L. innocua and L. welshimeri isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette bcrABC and Tn6188_qac_1 disinfectant resistance determinant, and stress survival islets. These disinfectant-resistant genes were more frequently found in L. innocua (12%) than in L. welshimeri (2%). Several isolates representing the presumed nonpathogenic L. innocua still carried virulence-associated genes, including LGI2, LGI3, LIPI-3, and LIPI-4 which were absent in all L. welshimeri isolates. The mobile genetic elements identified were plasmids (pLGUG1 and J1776) and prophages (PHAGE_Lister_vB_LmoS_188, PHAGE_Lister_LP_030_3, PHAGE_Lister_A118, PHAGE_Lister_B054, and PHAGE_Lister_vB_LmoS_293). The results suggest that the presumed nonpathogenic isolates especially L. innocua can carry genes relevant to the strain's virulence and stress tolerance in the food and food processing facilities. IMPORTANCE This study provides genomic insights into the recently expanded genus in order to gain valuable information about the evolution of the virulence and stress tolerance properties of the genus Listeria and the distribution of these genetic elements pertinent to the pathogenic potential across Listeria spp. and clonal lineages in South Africa (SA).
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Affiliation(s)
- T. Mafuna
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - I. Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - K. Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - R. E. Pierneef
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - O. N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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El Zowalaty ME, Moura A, Lecuit M, Zishiri OT. Draft Genome Sequence of Listeria innocua Strain MEZLIS29, Isolated from a Cow in South Africa. Microbiol Resour Announc 2022; 11:e0112221. [PMID: 35225692 PMCID: PMC8928759 DOI: 10.1128/mra.01122-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Here, we report the draft genome sequence of Listeria innocua strain MEZLIS29, which was isolated from a healthy cow in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,805,865 bp, with a G+C content of 37.5% and 2,783 coding DNA sequences, 58 tRNAs, 4 noncoding RNAs, and 8 rRNA genes.
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Affiliation(s)
- Mohamed E. El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexandra Moura
- Institut Pasteur, National Reference Center and World Health Organization Collaborating Center for Listeria, Paris, France
- Institut Pasteur, Université de Paris, INSERM U1117, Biology of Infection Unit, Paris, France
| | - Marc Lecuit
- Institut Pasteur, National Reference Center and World Health Organization Collaborating Center for Listeria, Paris, France
- Institut Pasteur, Université de Paris, INSERM U1117, Biology of Infection Unit, Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris, France
| | - Oliver T. Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering, and Science, University of KwaZulu-Natal, Durban, South Africa
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Kaszoni-Rückerl I, Mustedanagic A, Muri-Klinger S, Brugger K, Wagner KH, Wagner M, Stessl B. Predominance of Distinct Listeria Innocua and Listeria Monocytogenes in Recurrent Contamination Events at Dairy Processing Facilities. Microorganisms 2020; 8:E234. [PMID: 32050536 PMCID: PMC7074772 DOI: 10.3390/microorganisms8020234] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/24/2020] [Accepted: 02/06/2020] [Indexed: 12/25/2022] Open
Abstract
: The genus Listeria now comprises up to now 21 recognized species and six subspecies, with L. monocytogenes and L. innocua as the most prevalent sensu stricto associated species. Reports focusing on the challenges in Listeria detection and confirmation are available, especially from food-associated environmental samples. L. innocua is more prevalent in the food processing environment (FPE) than L. monocytogenes and has been shown to have a growth advantage in selective enrichment and agar media. Until now, the adaptive nature of L. innocua in FPEs has not been fully elucidated and potential persistence in the FPE has not been observed. Therefore, the aim of this study is to characterize L. innocua (n = 139) and L. monocytogenes (n = 81) isolated from FPEs and cheese products collected at five dairy processing facilities (A-E) at geno- and phenotypic levels. Biochemical profiling was conducted for all L. monocytogenes and the majority of L. innocua (n = 124) isolates and included a rhamnose positive reaction. L. monocytogenes isolates were most frequently confirmed as PCR-serogroups 1/2a, 3a (95%). Pulsed-field gel electrophoresis (PFGE)-typing, applying the restriction enzymes AscI, revealed 33 distinct Listeria PFGE profiles with a Simpson's Index of Diversity of 0.75. Multi-locus sequence typing (MLST) resulted in 27 STs with seven new L. innocua local STs (ST1595 to ST1601). L. innocua ST1597 and ST603 and L. monocytogenes ST121 and ST14 were the most abundant genotypes in dairy processing facilities A-E over time. Either SSI-1 (ST14) or SSI-2 (ST121, all L. innocua) were present in successfully FPE-adapted strains. We identified housekeeping genes common in Listeria isolates and L. monocytogenes genetic lineage III. Wherever there are long-term contamination events of L. monocytogenes and other Listeria species, subtyping methods are helpful tools to identify niches of high risk.
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Affiliation(s)
- Irene Kaszoni-Rückerl
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
- Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Azra Mustedanagic
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFOQSI), Technopark C, 3430 Tulln, Austria;
| | - Sonja Muri-Klinger
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
| | - Katharina Brugger
- Unit of Veterinary Public Health and Epidemiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria;
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Martin Wagner
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFOQSI), Technopark C, 3430 Tulln, Austria;
| | - Beatrix Stessl
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department of Farm Animal and Public Health in Veterinary Medicine Department of Veterinary Public Health and Food Science, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (I.K.-R.); (S.M.-K.); (M.W.)
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