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Elcheninov AG, Zayulina KS, Klyukina AA, Kremneva MK, Kublanov IV, Kochetkova TV. Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia. Microorganisms 2023; 12:16. [PMID: 38276185 PMCID: PMC10819033 DOI: 10.3390/microorganisms12010016] [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: 11/18/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.
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Affiliation(s)
- Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Kseniya S. Zayulina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Mariia K. Kremneva
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia;
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
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2
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Putnam NE, Youn JH, Wallace MA, Luethy PM, Burnham CAD, Butler-Wu S, Dekker JP, Lau AF. Comparative Evaluation of Current Biochemical-, Sequencing-, and Proteomic-Based Identification Methods for the Streptococcus bovis Group. J Clin Microbiol 2023; 61:e0171222. [PMID: 36912659 PMCID: PMC10117079 DOI: 10.1128/jcm.01712-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/05/2023] [Indexed: 03/14/2023] Open
Abstract
The Streptococcus bovis group (previously group D streptococci) consists of seven distinct species and subspecies. Definitive identification within the group is important, as certain organisms have been associated with gastrointestinal carcinoma, bacteremia, infective endocarditis, meningitis, biliary tract disease, and carcinoma, among others. Definitive identification, however, remains elusive due to limitations and inconsistencies across commonly used identification platforms in the United States. Here, we compared the performance of standard biochemical (Trek Gram-positive identification [GPID] plate, Vitek 2 GPID), sequencing (16S rDNA, sodA) databases (NCBI, RDP, CDC MicrobeNet), and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) platforms (Vitek MS, Bruker Biotyper MS) using a set of eight type strains representing all seven strains within the S. bovis group. Despite the evaluation of contemporary methods, no single platform was able to definitively identify all type strains within the S. bovis group. Vitek MS (85.7%, 7/8) provided the most accurate definitive identifications, followed by sodA sequencing (75%, 6/8). Vitek 2 and Bruker Biotyper RUO platforms performed the next best (62.5%, 5/8). All remaining platforms failed to adequately differentiate type strains within the S. bovis group (range, 0 to 37.5%). Laboratorians and clinicians should be aware of the identification limitations of routine testing algorithms and incorporate reflex testing, when appropriate, to platforms such as Vitek MS and/or sodA sequencing that are more able to definitively identify S. bovis group organisms. Further clinical evaluation was conducted using 65 clinical isolates from three geographically distinct U.S. institutions. Future improvements in identification platforms may reveal new clinical and epidemiological trends for members of the S. bovis group.
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Affiliation(s)
- Nicole E. Putnam
- Clinical Microbiology, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jung-Ho Youn
- Clinical Microbiology, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Paul M. Luethy
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Susan Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - John P. Dekker
- Clinical Microbiology, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anna F. Lau
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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3
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Ammoun I, Kothe CI, Mohellibi N, Beal C, Yaacoub R, Renault P. Lebanese fermented goat milk products: From tradition to meta-omics. Food Res Int 2023; 168:112762. [PMID: 37120212 DOI: 10.1016/j.foodres.2023.112762] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.
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Affiliation(s)
- I Ammoun
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France; Lebanese Agricultural Research Institute (LARI), Milk and Milk Products Department, Fanar, Lebanon
| | - C I Kothe
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France; Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - N Mohellibi
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France
| | - C Beal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120, Palaiseau, France
| | - R Yaacoub
- Lebanese University, Faculty of Agricultural and Veterinary Sciences, Food Science and Technology Department, Dekwaneh, Lebanon
| | - P Renault
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France.
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Todorov SD, Popov I, Weeks R, Chikindas ML. Use of Bacteriocins and Bacteriocinogenic Beneficial Organisms in Food Products: Benefits, Challenges, Concerns. Foods 2022; 11:foods11193145. [PMID: 36230222 PMCID: PMC9563261 DOI: 10.3390/foods11193145] [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] [Received: 09/18/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
This review’s objective was to critically revisit various research approaches for studies on the application of beneficial organisms and bacteriocins as effective biopreservatives in the food industry. There are a substantial number of research papers reporting newly isolated bacterial strains from fermented food products and their application as potential probiotics, including partial characterization of bacteriocins produced by these microorganisms. Most of these studies follow scientific community-accepted standard procedures and propose various applications of the studied strains and bacteriocins as potential biopreservatives for the food industry. A few investigations go somewhat further, performing model studies, exploring the application of expressed bacteriocins in a designed food product, or trying to evaluate the effectiveness of the studied potential probiotics and bacteriocins against foodborne pathogens. Some authors propose applications of bacteriocin producers as starter cultures and are exploring in situ bacteriocin production to aid in the effective control of foodborne pathogens. However, few studies have evaluated the possible adverse effects of bacteriocins, such as toxicity. This comes from well-documented reports on bacteriocins being mostly non-immunogenic and having low cytotoxicity because most of these proteinaceous molecules are small peptides. However, some studies have reported on bacteriocins with noticeable cytotoxicity, which may become even more pronounced in genetically engineered or modified bacteriocins. Moreover, their cytotoxicity can be very specific and is dependent on the concentration of the bacteriocin and the nature of the targeted cell. This will be discussed in detail in the present review.
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Affiliation(s)
- Svetoslav Dimitrov Todorov
- ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
- Correspondence: ; Tel.: +359-88-9583119
| | - Igor Popov
- Center for Agrobiotechnology, Don State Technical University, 344002 Rostov-on-Don, Russia
| | - Richard Weeks
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ 08904, USA
| | - Michael Leonidas Chikindas
- Center for Agrobiotechnology, Don State Technical University, 344002 Rostov-on-Don, Russia
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ 08904, USA
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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5
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Jans C, Wambui J, Stevens MJA, Tasara T. Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore. Front Microbiol 2022; 13:923080. [PMID: 36046020 PMCID: PMC9421002 DOI: 10.3389/fmicb.2022.923080] [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: 04/18/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus infection is considered to be a neglected tropical disease with huge impact on human and animal health alike. Dairy production in sub-Saharan Africa (SSA) relies heavily on various animals such as cows, goats, and camels, depending on the region. S. aureus causes mastitis and exhibits high prevalence in raw milk. The population structure including genotypic and phenotypic traits of dairy S. aureus in relation to animal and human isolates is, however, unknown for SSA. In this work, 20 S. aureus dairy isolates from East and West Africa were selected for comparative genomics and phenotypic analysis. Comparing their population structure revealed a large diversity of different origins suggesting milk to be a reservoir for human and animal strains alike. Furthermore, a novel putative siderophore was detected in multiple strains in a distinct animal-clade with strains of global origin. This putative siderophore shares a high genetic identity with that from Streptococcus equi suggesting possible horizontal gene transfer. These findings combined with the virulence genes harbored by these dairy-derived strains such as pvl, human evasion factor scn, various enterotoxin, leucocidin and antibiotic resistance genes, stresses the need for an integrative One Health approach to tackle the problem of S. aureus infections in animals and humans in sub-Saharan Africa.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Switzerland
| | - Joseph Wambui
- Institute of Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Marc J. A. Stevens
- Institute of Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Taurai Tasara
- Institute of Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
- *Correspondence: Taurai Tasara,
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6
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Güley Z, Fallico V, Cabrera-Rubio R, Cotter PD, Beresford T. Identification of Streptococcus infantarius subsp. infantarius as the species primarily responsible for acid production in Izmir Brined Tulum Cheese from the Aegean Region of Türkiye. Food Res Int 2022; 160:111707. [DOI: 10.1016/j.foodres.2022.111707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/02/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022]
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7
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Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics. Food Res Int 2022; 157:111265. [DOI: 10.1016/j.foodres.2022.111265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 01/02/2023]
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8
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Özkan ER, Öztürk Hİ, Demirci T, Akın N. Detection of biofilm formation, virulence factor genes, antibiotic-resistance, adherence properties, and some beneficial properties of cheese origin S. infantarius, S. gallolyticus, and S. lutetiensis strains belonging to the S. bovis/S. equinus complex. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Lactic acid bacteria diversity and dynamics during ripening of traditional Turkish goatskin Tulum cheese produced in Mut region assessed by culturing and PCR-DGGE. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110701] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Hess C, Jandreski-Cvetkovic D, Liebhart D, Bilic I, Hess M. Outbreaks of Streptococcus gallolyticus subsp. pasteurianus in Goslings Characterized by Central Nervous Symptoms. Avian Dis 2020; 65:165-170. [PMID: 34339136 DOI: 10.1637/aviandiseases-d-20-00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/06/2020] [Indexed: 11/05/2022]
Abstract
The present report describes outbreaks of Streptococcus gallolyticus subsp. pasteurianus in young geese flocks in Austria. The flocks, comprising 160-1450 goslings of 2-3 wk of age, experienced increased mortalities The clinical signs were characterized by severe central nervous symptoms, namely leg paddling and torticollis. The postmortem investigation revealed hepatitis, splenitis, and a low amount of liquid fluid in the coelomic cavity. Livers were of fragile texture, with white necrotic areas. The latter were also found in spleens. No macroscopic lesions were seen in brains. Bacteriologic investigation followed by bacterial identification by matrix-assisted laser desorption time-of-flight mass spectrometry and phylogenetic analysis of the partial 16S rRNA region revealed the presence in heart, liver, spleen, and brain of S. gallolyticus subsp. pasteurianus. Histologic investigation revealed multifocal necrosis in liver and spleen samples together with infiltration of mononuclear cells and heterophilic granulocytes. Furthermore, in the lesions, coccoid bacteria could be identified. No histopathologic changes were observed in brain samples from goslings, except in one bird in which accumulation of coccoid bacteria in blood vessels of the brain samples was present. Antibiotic sensitivity tests revealed identical profiles for all strains, which were susceptible to penicillins, cephalosporins, chloramphenicol, imipenem, and tylosin. However, resistance was found against quinolones, aminoglycosides, tetracycline, and trimethoprim-sulfamethoxazole, which are commonly used to treat infections with gram-positive bacteria.
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Affiliation(s)
- C Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria,
| | - D Jandreski-Cvetkovic
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - D Liebhart
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - I Bilic
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - M Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
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11
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Silva A, Silva SA, Lourenço-Lopes C, Jimenez-Lopez C, Carpena M, Gullón P, Fraga-Corral M, Domingues VF, Barroso MF, Simal-Gandara J, Prieto MA. Antibacterial Use of Macroalgae Compounds against Foodborne Pathogens. Antibiotics (Basel) 2020; 9:E712. [PMID: 33080894 PMCID: PMC7603221 DOI: 10.3390/antibiotics9100712] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The search for food resources is a constant in human history. Nowadays, the search for natural and safe food supplies is of foremost importance. Accordingly, there is a renewed interest in eco-friendly and natural products for substitution of synthetic additives. In addition, microbial contamination of food products during their obtaining and distribution processes is still a sanitary issue, and an important target for the food industry is to avoid food contamination and its related foodborne illnesses. These diseases are fundamentally caused by certain microorganisms listed in this review and classified according to their Gram negative or positive character. Algae have proven to possess high nutritional value and a wide variety of biological properties due to their content in active compounds. Among these capabilities, macroalgae are recognized for having antimicrobial properties. Thus, the present paper revises the actual knowledge of microbial contaminants in the food industry and proposes antimicrobial algal compounds against those pathogenic bacteria responsible for food contamination as valuable molecules for its growth inhibition. The capacity of algae extracts to inhibit some major food pathogen growth was assessed. Moreover, the main applications of these compounds in the food industry were discussed while considering their favorable effects in terms of food safety and quality control.
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Affiliation(s)
- Aurora Silva
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Rua Dr António Bernardino de Almeida 431, 4200-072 Porto, Portugal; (V.F.D.); (M.F.B.)
| | - Sofia A. Silva
- Departamento de Química, Universidade de Aveiro, 3810-168 Aveiro, Portugal;
| | - C. Lourenço-Lopes
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
| | - C. Jimenez-Lopez
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolonia, 5300-253 Bragança, Portugal
| | - M. Carpena
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
| | - P. Gullón
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
| | - M. Fraga-Corral
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolonia, 5300-253 Bragança, Portugal
| | - V. F. Domingues
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Rua Dr António Bernardino de Almeida 431, 4200-072 Porto, Portugal; (V.F.D.); (M.F.B.)
| | - M. Fátima Barroso
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Rua Dr António Bernardino de Almeida 431, 4200-072 Porto, Portugal; (V.F.D.); (M.F.B.)
| | - J. Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
| | - M. A. Prieto
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain; (A.S.); (C.L.-L.); (C.J.-L.); (M.C.); (P.G.); (M.F.-C.)
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12
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Yasir M, Bibi F, Hashem AM, Azhar EI. Comparative metagenomics and characterization of antimicrobial resistance genes in pasteurized and homemade fermented Arabian laban. Food Res Int 2020; 137:109639. [PMID: 33233218 DOI: 10.1016/j.foodres.2020.109639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 11/25/2022]
Abstract
The aim of this study was to investigate bacterial diversity and function in a fermented milk drink called laban, which is traditionally served in the Middle East, Africa, and Indian subcontinent. Pasteurized laban (LBP) and unpasteurized, homemade, raw laban (LBR) underwent 16S rRNA gene amplicon and shotgun sequencing to analyze their bacterial community, presence of antimicrobial resistance genes (ARGs), and metabolic pathways. This study highlighted relatively greater diversity in LBR bacterial populations compared to LBP, despite containing similar major taxa that consisted primarily of Firmicutes followed by Proteobacteria, Bacteroidetes, and Actinobacteria. The dominant species, Streptococcus thermophilus, was relatively more abundant in LBP (80.7%) compared to LBR (47.9%). LBR had increased diversity and higher relative abundance of several known probiotic bacteria, such as Streptococcus salivarius and Lactococcus lactis, whereas Lactobacillus acidophilus was detected at a higher abundance in LBP. Pathogens like Acinetobacter baumannii, Streptococcus pneumoniae, Streptococcus pyogenes, and Escherichia coli had lower abundance in LBP compared to LBR. Thirty-three ARGs were detected in LBR compared to nine in LBP and are responsible for resistance to 11 classes of antibiotics. A significant proportion of the metagenomes from both types of laban were assigned to housekeeping functions, such as amino acid metabolism, translation, membrane transport, and carbohydrate metabolism. LBR demonstrated increased diversity in probiotics and metabolic functions compared to LBP. However, the relatively high diversity of pathogenic and opportunistic bacteria and ARGs in LBR raises safety concerns and highlights the need for a more hygienic environment for the processing of homemade fermented dairy foods.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia; Vaccines and Immunnotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Traditional milk transformation schemes in Côte d'Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products. PLoS One 2020; 15:e0233132. [PMID: 32413097 PMCID: PMC7228116 DOI: 10.1371/journal.pone.0233132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) and possibly Streptococcus infantarius subsp. infantarius (Sii) are associated with human and animal diseases. Sii predominate in spontaneously fermented milk products with unknown public health effects. Sii/SBSEC prevalence data from West Africa in correlation with milk transformation practices are limited. Northern Côte d'Ivoire served as study area due to its importance in milk production and consumption and to link a wider Sudano-Sahelian pastoral zone of cross-border trade. We aimed to describe the cow milk value chain and determine Sii/SBSEC prevalence with a cross-sectional study. Dairy production practices were described as non-compliant with basic hygiene standards. The system is influenced by secular sociocultural practices and environmental conditions affecting product properties. Phenotypic and molecular analyses identified SBSEC in 27/43 (62.8%) fermented and 26/67 (38.8%) unfermented milk samples. Stratified by collection stage, fermented milk at producer and vendor levels featured highest SBSEC prevalence of 71.4% and 63.6%, respectively. Sii with 62.8% and 38.8% as well as Streptococcus gallolyticus subsp. macedonicus with 7.0% and 7.5% were the predominant SBSEC species identified among fermented and unfermented milk samples, respectively. The population structure of Sii/SBSEC isolates seems to reflect evolving novel dairy-adapted, non-adapted and potentially pathogenic lineages. Northern Côte d'Ivoire was confirmed as area with high Sii presence in dairy products. The observed production practices and the high diversity of Sii/SBSEC supports in-depth investigations on Sii ecology niche, product safety and related technology in the dairy value chain potentially affecting large population groups across sub-Saharan Africa.
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Domínguez-Ramírez LL, Rodríguez-Sanoja R, Tecante A, García-Garibay M, Sainz T, Wacher C. Tolerance to acid and alkali by Streptococcus infantarius subsp. infantarius strain 25124 isolated from fermented nixtamal dough: Pozol. Studies in APT broth. Food Microbiol 2020; 90:103458. [PMID: 32336375 DOI: 10.1016/j.fm.2020.103458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/10/2019] [Accepted: 02/10/2020] [Indexed: 01/21/2023]
Abstract
Pozol is a beverage prepared with maize dough made after boiling the kernels in limewater. This pretreatment could act as a selective force that shapes the starter microbiota, with microorganisms able to survive the fermentation. Since Streptococcus infantarius subsp. infantarius (Sii) dominates in pozol, we evaluated the effect of acid and alkali stresses on strain Sii-25124 in commercial APT broth as a first attempt to assess its adaptation capacity. Results suggest that Sii-25124 has adaptative advantages to pH changes that possibly contribute to its persistence even after the acidification of the dough. Its cardinal pH values were 4.0 and 11.0, with an optimum between 6.6 and 8.0. It showed alkali tolerance unlike other pozol Sii strains. Adaptation at pH 4.0, 10.0 and 11.0, compared with non-adapted cells, induced acid tolerance enhancing survival at pH 3.6 (P < 0.05); a 2 min heat shock at 62 °C induced alkali tolerance response enhancing survival at pH 10.5 (P < 0.05). The up-regulation of dnaK, groEL, ptsG and atpB was observed during 5 h of exposition at pH 3.6, 4.0 and 10.0, showing similar expression rates after induction by acid shock or alkaline stress. Changes of atpB were more evident having almost five-fold induction during long-term stress.
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Affiliation(s)
- Lila Lubianka Domínguez-Ramírez
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Coyoacán, C.P., 04510, Mexico City, Mexico.
| | - Romina Rodríguez-Sanoja
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Coyoacán, C.P., 04510, Mexico City, Mexico; Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Coyoacán, C.P., 04510, Mexico City, Mexico.
| | - Alberto Tecante
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Coyoacán, C.P., 04510, Mexico City, Mexico
| | - Mariano García-Garibay
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Coyoacán, C.P., 04510, Mexico City, Mexico; Departamento de Biotecnología/Departamento de Ciencias de La Alimentación, Universidad Autónoma Metropolitana-Iztapalapa/Lerma. Av. San Rafael Atlixco 186, Colonia Vicentina, Iztapalapa, C.P., 09340, Mexico City, Mexico.
| | - Teresita Sainz
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Coyoacán, C.P., 04510, Mexico City, Mexico; Departamento de Sistemas Biológicos de La División de CBS, Universidad Autónoma Metropolitana-Xochimilco. Calzada Del Hueso 1100, Colonia Villa Quietud, Coyoacán, C.P, 04969, Mexico City, Mexico.
| | - Carmen Wacher
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Coyoacán, C.P., 04510, Mexico City, Mexico.
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15
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Exploring Beneficial/Virulence Properties of Two Dairy-Related Strains of Streptococcus infantarius subsp. infantarius. Probiotics Antimicrob Proteins 2020; 12:1524-1541. [DOI: 10.1007/s12602-020-09637-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Alexandraki V, Kazou M, Blom J, Pot B, Papadimitriou K, Tsakalidou E. Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. Front Microbiol 2019; 10:2916. [PMID: 31956321 PMCID: PMC6951406 DOI: 10.3389/fmicb.2019.02916] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.
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Affiliation(s)
- Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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17
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Gboko KDT, Traoré SG, Sanhoun AR, Kirioua J, Otaru N, Kurt F, Jaeger FN, Isenring J, Kaindi DWM, Kreikemeyer B, Renault P, Hattendorf J, Meile L, Jans C, Nguetta R, Bonfoh B. Risk factors for the carriage of Streptococcus infantarius subspecies infantarius isolated from African fermented dairy products. PLoS One 2019; 14:e0225452. [PMID: 31774832 PMCID: PMC6881063 DOI: 10.1371/journal.pone.0225452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023] Open
Abstract
Streptococcus infantarius subsp. infantarius (Sii) has been identified as predominant lactic acid bacteria in spontaneously fermented dairy products (FDPs) in sub-Saharan Africa including Côte d'Ivoire. However, Sii belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Most SBSEC members are assumed to be involved as opportunistic pathogens in serious diseases in both humans and animals. A population-based cross-sectional survey, including 385 participants was conducted in Korhogo, northern Côte d'Ivoire, to identify risk factors for Sii fecal carriage, including consumption of local FDPs. A structured questionnaire was used to gather participant's socio-demographic and economic characteristics, their relation to livestock and dietary habits. In addition, fresh stool and milk samples were collected. The identification of Sii was done using a SBSEC-specific PCR assay targeting 16S rRNA and groEL genes. The overall prevalence of SBSEC and Sii carriage was 23.2% (confidence interval CI 95% = 18.9-27.5) and 12.0% (CI 95% = 8.4-15.5) for stool, respectively. Prevalence of Sii was significantly higher in consumers of artisanal butter compared with non-consumers (57.1% vs 10.1%, odds ratio OR: 11.9, 95% CI: 3.9-36.6), as well as in persons handling livestock (OR = 3.9; 95% CI = 1.6-9.3) and livestock primary products (OR = 5.7; 95% CI = 2.3-14.3). The closer contact with livestock was a risk factor for Sii fecal carriage. Sii strains were isolated from fresh and fermented milk products with a prevalence of 30.4% and 45.4%, respectively. Analysis of Sii population structure through the SBSEC multi locus sequence typing assay revealed a close relationship across human and dairy isolates, possibly linked to a Kenyan human isolate. All these outcomes underline the interest of in-depth investigations on the ecology, potential reservoirs and pathways of contamination by Sii at the human-animal-environment interface in comparison to yet to be collected data from Europe, Asia and the Americas to further elucidate the various roles of Sii.
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Affiliation(s)
- Kossia D T Gboko
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire
| | - Sylvain G Traoré
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,University of Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Aimé R Sanhoun
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,University of Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Jérôme Kirioua
- University of Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Nize Otaru
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Fabienne Kurt
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Fabienne N Jaeger
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Julia Isenring
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Dasel W M Kaindi
- Department of Food Science, Nutrition and Technology, University of Nairobi, Nairobi, Kenya
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre Rostock, Germany
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, Jouy-en-Josas, France
| | - Jan Hattendorf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Roland Nguetta
- Institut de cardiologie d'Abidjan (ICA), Abidjan, Côte d'Ivoire.,Université Felix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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18
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Wambui J, Njage PMK, Tasara T, Buys EM. Meta-Analysis and Meta-Regression Indicate Dynamic Prevalence and Moderators of Foodborne Pathogens in African Indigenous Fermented Milk. Microorganisms 2019; 7:microorganisms7110563. [PMID: 31739578 PMCID: PMC6921058 DOI: 10.3390/microorganisms7110563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 11/16/2022] Open
Abstract
As more microbiological data for indigenous fermented milk (IFM) becomes available, concern about their microbial safety becomes eminent. Nonetheless, these data are highly fragmented, and a tool is required to integrate existing data and to provide a basis for data-driven decision making for IFM’s safety. Therefore, meta-analysis and meta-regression were conducted to estimate the prevalence of foodborne pathogens in IFM and to determine factors influencing the estimated values. Using Africa as a case, searches were systematically made for published data and relevant grey literature. Data from 18 studies in 15 countries were analyzed. Staphylococcus aureus (37%), pathogenic Escherichia coli (16%), Listeria monocytogenes (6%), and Salmonella spp. (3%) were the most prevalent pathogens with a pooled prevalence estimate of 12%. Heterogeneity among prevalence estimates was attributed to sampling point and microbial group but could be moderated by publication year, country cluster, and methods for microbial confirmation. The pooled prevalence estimates increased over time as more studies became available, whereby the odds were higher in studies from 2010 onwards than studies before 2010. From the analyses, S. aureus presented the greatest safety concern in African IFM. Future microbiological studies should take into consideration different IFM sampling points and advanced analytical methods to identify pathogens.
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Affiliation(s)
- Joseph Wambui
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland;
- Correspondence: (J.W.); (E.M.B.); Tel.: +41-44-635-86-51; Fax: +41-44-635-89-08 (J.W.)
| | - Patrick Murigu Kamau Njage
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kongens Lyngby, Denmark;
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland;
| | - Elna Maria Buys
- Department of Consumer and Food Sciences, University of Pretoria, Lynwood Road, Pretoria 0002, South Africa
- Correspondence: (J.W.); (E.M.B.); Tel.: +41-44-635-86-51; Fax: +41-44-635-89-08 (J.W.)
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19
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Correlation between Streptococcus bovis bacteremia and density of cows in Galicia, northwest of Spain. Infection 2018; 47:399-407. [PMID: 30498902 DOI: 10.1007/s15010-018-1254-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
Abstract
BACKGROUND There are few data on the epidemiology of infections caused by Streptococcus bovis (Sb). Some studies suggest that both residence in rural areas and contact with livestock could be potential risk factors. METHODS We performed a retrospective study for the period 2005-2016 of all cases of bacteremia caused by Sb in Galicia (a region in the northwest of Spain). The association between the incidence rate of Sb bacteremia and the number of cattle by province and district was analyzed. RESULTS 677 cases were included with a median age of 76 years, 69.3% males. The most frequent infections were endocarditis (234 cases, 34.5%), primary bacteremia (213 cases, 31.5%) and biliary infection (119 cases, 17.5%). In 252 patients, colon neoplasms were detected (37.2%). S. gallolyticus subsp. gallolyticus was the predominant species (52.3%). Mortality was 15.5% (105 cases). The annual incidence rate was 20.2 cases/106 inhabitants and was correlated with the density of cattle (p < 0.001), but not with rurality. When comparing the two provinces with a strong predominance of rural population, but with important differences in the number of cattle, such as Orense and Lugo, with 6% and 47.7% of Galician cattle, respectively, the rates were very different: 15.8 and 43.6 cases/106, respectively, with an RR of 2.7 (95% CI, 2.08-3.71). Some districts of the province of Lugo had rates higher than 100 cases/106 inhabitants. CONCLUSIONS Our study shows a significant correlation between the rates of Sb bacteremia and cattle density, suggesting a possible transmission of Sb from cows to people.
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20
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Kaindi DWM, Kogi-Makau W, Lule GN, Kreikemeyer B, Renault P, Bonfoh B, Otaru N, Schmid T, Meile L, Hattendorf J, Jans C. Colorectal cancer-associated Streptococcus infantarius subsp. infantarius differ from a major dairy lineage providing evidence for pathogenic, pathobiont and food-grade lineages. Sci Rep 2018; 8:9181. [PMID: 29907746 PMCID: PMC6003927 DOI: 10.1038/s41598-018-27383-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
Streptococcus infantarius subsp. infantarius (Sii), a member of the Streptococcus bovis/Streptococcus equinus complex (SBSEC), predominates as dairy-adapted and non-adapted variants in fermented dairy products (FDP) in East and West Africa. Epidemiologic data suggest an association with colorectal cancer for most SBSEC members, including Sii from Kenyan patients. Phylogenetic relationships of East African human (EAH) isolates to those of dairy and pathogenic origin were analysed to better estimate potential health implications via FDP consumption. The MLST-derived population structure was also evaluated to provide host, disease, geography and dairy adaptation associations for 157 SBSEC isolates, including 83 novel Sii/SBSEC isolates of which 40 originated from Kenyan colonoscopy patients. Clonal complex (CC) 90 was delineated as potential pathogenic CC for Sii. Single EAH, West African dairy (WAD), food and animal Sii isolates clustered within CC-90, suggesting a potential link to pathogenic traits for CC-90. The majority of EAH and WAD Sii were clustered in a shared clade distinct from CC-90 and East African dairy (EAD) isolates. This indicates shared ancestry for the EAH and WAD clade and limitations to translate disease associations of EAH and CC-90 to EAD Sii, which could support the separation of pathogenic, pathobiont/commensal and food lineages.
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Affiliation(s)
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, University of Nairobi, Nairobi, Kenya
| | | | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre Rostock, Rostock, Germany
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, Jouy-en-Josas, France
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Adiopodoume, Ivory Coast
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nize Otaru
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Thomas Schmid
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland
| | - Jan Hattendorf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, ETH Zurich, Zurich, Switzerland.
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21
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El Hatmi H, Jrad Z, Oussaief O, Nasri W, Sbissi I, Khorchani T, Canabady-Rochelle LL. Fermentation of dromedary camel (Camelus dromedarius) milk by Enterococcus faecium, Streptococcus macedonicus as a potential alternative of fermented cow milk. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.12.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Kaindi DWM, Kogi-Makau W, Lule GN, Kreikemeyer B, Renault P, Bonfoh B, Schelling E, Zinsstag J, Lacroix C, Meile L, Jans C, Hattendorf J. Investigating the association between African spontaneously fermented dairy products, faecal carriage of Streptococcus infantarius subsp. infantarius and colorectal adenocarcinoma in Kenya. Acta Trop 2018; 178:10-18. [PMID: 29079186 PMCID: PMC5766739 DOI: 10.1016/j.actatropica.2017.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 12/22/2022]
Abstract
Consumption of traditional fermented dairy products (tFDP) in Africa leads to the ingestion of up to 108Streptococcus infantarius subspecies infantarius (Sii) per millilitre of spontaneously fermented milk. Sii is a member of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) for which some members are associated particularly with colorectal cancer or endocarditis. The extent of health risks to tFDP consumers is largely unknown. A hospital-based unmatched case-control study was conducted at Kenyatta National Hospital, Nairobi (Kenya) on 80 cases and 193 controls that were selected exhaustively from patients attending colonoscopy at the hospital. Logistic regression models adjusted for age, sex and residency were used in the statistical analysis. Consumption of tFDP was not associated with CRC (odds ratio (OR) 1.4; 95% Confidence interval (CI) 0.7-2.7; p=0.34). Risk factors associated with CRC included age above 40 years, and consumption of processed meat and alcohol. Faecal carriage of Sii was significantly higher in persons with colon tumours and polyps compared to controls (8.4% vs 21.6%: OR: 4.6; CI 1.3-15.9). Patients with haemorrhoids represented an unexpected carrier group with significantly higher Sii faecal carriage (30.4%, CI: 17.7-45.8). Consumption of tFDP does not represent risk factors for CRC whereas Sii seems to be associated with CRC. However, there is urgent need to assess this finding also in the general population, investigate the causality of SBSEC, Sii and CRC as well as compare the phylogenetic, functional and genomic relationship between human and dairy Sii with regards to the ongoing application of Sii in FDP production.
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Affiliation(s)
- Dasel W M Kaindi
- Department of Food Science, Nutrition and Technology, University of Nairobi, P. O. Box 29053 - 00625, Nairobi, Kenya.
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, University of Nairobi, P. O. Box 29053 - 00625, Nairobi, Kenya.
| | - Godfrey N Lule
- School of Medicine, University of Nairobi, P. O. Box 19676, Nairobi, Kenya.
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Schillingallee 70, 18055 Rostock, Germany.
| | - Pierre Renault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Km 17, Adiopodoumé, Rte Dabou, 01 BP 1303 Abidjan 01, Cote d'Ivoire; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland.
| | - Esther Schelling
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland.
| | - Jakob Zinsstag
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland.
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Jan Hattendorf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland.
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Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks. Appl Environ Microbiol 2017. [PMID: 28625983 DOI: 10.1128/aem.01144-17] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization.IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products.
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Bacterial diversity of the Colombian fermented milk "Suero Costeño" assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. Food Microbiol 2017; 68:129-136. [PMID: 28800820 DOI: 10.1016/j.fm.2017.07.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/13/2017] [Accepted: 07/16/2017] [Indexed: 11/22/2022]
Abstract
"Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC.
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Jans C, Meile L, Kaindi DWM, Kogi-Makau W, Lamuka P, Renault P, Kreikemeyer B, Lacroix C, Hattendorf J, Zinsstag J, Schelling E, Fokou G, Bonfoh B. African fermented dairy products - Overview of predominant technologically important microorganisms focusing on African Streptococcus infantarius variants and potential future applications for enhanced food safety and security. Int J Food Microbiol 2017; 250:27-36. [PMID: 28364623 DOI: 10.1016/j.ijfoodmicro.2017.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/17/2022]
Abstract
Milk is a major source of nutrients, but can also be a vehicle for zoonotic foodborne diseases, especially when raw milk is consumed. In Africa, poor processing and storage conditions contribute to contamination, outgrowth and transmission of pathogens, which lead to spoilage, reduced food safety and security. Fermentation helps mitigate the impact of poor handling and storage conditions by enhancing shelf life and food safety. Traditionally-fermented sour milk products are culturally accepted and widely distributed in Africa, and rely on product-specific microbiota responsible for aroma, flavor and texture. Knowledge of microbiota and predominant, technologically important microorganisms is critical in developing products with enhanced quality and safety, as well as sustainable interventions for these products, including Africa-specific starter culture development. This narrative review summarizes current knowledge of technologically-important microorganisms of African fermented dairy products (FDP) and raw milk, taking into consideration novel findings and taxonomy when re-analyzing data of 29 publications covering 25 products from 17 African countries. Technologically-important lactic acid bacteria such as Lactococcus lactis and Streptococcus infantarius subsp. infantarius (Sii), Lactobacillus spp. and yeasts predominated in raw milk and FDP across Africa. Re-analysis of data also suggests a much wider distribution of Sii and thus a potentially longer history of use than previously expected. Therefore, evaluating the role and safety of African Sii lineages is important when developing interventions and starter cultures for FDP in Africa to enhance food safety and food security. In-depth functional genomics, epidemiologic investigations and latest identification approaches coupled with stakeholder involvement will be required to evaluate the possibility of African Sii lineages as novel food-grade Streptococcus lineage.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Dasel Wambua Mulwa Kaindi
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, 00625 Nairobi, Kenya
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, 00625 Nairobi, Kenya
| | - Peter Lamuka
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, 00625 Nairobi, Kenya
| | - Pierre Renault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Schillingallee 70, 18055 Rostock, Germany
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food Nutrition and Health, Department of Health Science and Technology, ETH Zurich, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Jan Hattendorf
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Esther Schelling
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Gilbert Fokou
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Km 17, Adiopodoumé, Rte Dabou, 01 BP 1303 Abidjan 01, Côte d'Ivoire
| | - Bassirou Bonfoh
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Km 17, Adiopodoumé, Rte Dabou, 01 BP 1303 Abidjan 01, Côte d'Ivoire.
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Jans C, Merz A, Johler S, Younan M, Tanner SA, Kaindi DWM, Wangoh J, Bonfoh B, Meile L, Tasara T. East and West African milk products are reservoirs for human and livestock-associated Staphylococcus aureus. Food Microbiol 2017; 65:64-73. [PMID: 28400021 DOI: 10.1016/j.fm.2017.01.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/12/2017] [Accepted: 01/29/2017] [Indexed: 12/13/2022]
Abstract
Staphylococcus aureus frequently isolated from milk products in sub-Saharan Africa (SSA) is a major pathogen responsible for food intoxication, human and animal diseases. SSA hospital-derived strains are well studied but data on the population structure of foodborne S. aureus required to identify possible staphylococcal food poisoning sources is lacking. Therefore, the aim was to assess the population genetic structure, virulence and antibiotic resistance genes associated with milk-derived S. aureus isolates from Côte d'Ivoire, Kenya and Somalia through spa-typing, MLST, and DNA microarray analysis. Seventy milk S. aureus isolates from the three countries were assigned to 27 spa (7 new) and 23 (12 new) MLST sequence types. Milk-associated S. aureus of the three countries is genetically diverse comprising human and livestock-associated clonal complexes (CCs) predominated by the CC5 (n = 10) and CC30 (n = 9) isolates. Panton-Valentine leukocidin, toxic shock syndrome toxin and enterotoxin encoding genes were predominantly observed among human-associated CCs. Penicillin, fosfomycin and tetracycline, but not methicillin resistance genes were frequently detected. Our findings indicate that milk-associated S. aureus in SSA originates from human and animal sources alike highlighting the need for an overarching One Health approach to reduce S. aureus disease burdens through improving production processes, animal care and hygienic measures.
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Affiliation(s)
- Christoph Jans
- ETH Zurich, Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Axel Merz
- University of Zurich, Institute of Food Safety and Hygiene, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Sophia Johler
- University of Zurich, Institute of Food Safety and Hygiene, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Mario Younan
- Vétérinaires Sans Frontières Germany, P.O. Box 25653, 00603 Nairobi, Kenya
| | - Sabine A Tanner
- ETH Zurich, Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Dasel Wambua Mulwa Kaindi
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, PO Box 29053, Nairobi, Kenya
| | - John Wangoh
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, PO Box 29053, Nairobi, Kenya
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), KM 17 route de Dabou, Adiopodoumé Yopougon, Abidjan - 01, B.P. 1303 Abidjan, Cote d'Ivoire
| | - Leo Meile
- ETH Zurich, Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Taurai Tasara
- University of Zurich, Institute of Food Safety and Hygiene, Winterthurerstrasse 272, 8057 Zurich, Switzerland.
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Jans C, de Wouters T, Bonfoh B, Lacroix C, Kaindi DWM, Anderegg J, Böck D, Vitali S, Schmid T, Isenring J, Kurt F, Kogi-Makau W, Meile L. Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme. BMC Microbiol 2016; 16:117. [PMID: 27329036 PMCID: PMC4915170 DOI: 10.1186/s12866-016-0735-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
Background The Streptococcus bovis/Streptococcus equinus complex (SBSEC) comprises seven (sub)species classified as human and animal commensals, emerging opportunistic pathogens and food fermentative organisms. Changing taxonomy, shared habitats, natural competence and evidence for horizontal gene transfer pose difficulties for determining their phylogeny, epidemiology and virulence mechanisms. Thus, novel phylogenetic and functional classifications are required. An SBSEC overarching multi locus sequence type (MLST) scheme targeting 10 housekeeping genes was developed, validated and combined with host-related properties of adhesion to extracellular matrix proteins (ECM), activation of the immune responses via NF-KB and survival in simulated gastric juice (SGJ). Results Commensal and pathogenic SBSEC strains (n = 74) of human, animal and food origin from Europe, Asia, America and Africa were used in the MLST scheme yielding 66 sequence types and 10 clonal complexes differentiated into distinct habitat-associated and mixed lineages. Adhesion to ECMs collagen I and mucin type II was a common characteristic (23 % of strains) followed by adhesion to fibronectin and fibrinogen (19.7 %). High adhesion abilities were found for East African dairy and human blood isolate branches whereas commensal fecal SBSEC displayed low adhesion. NF-KB activation was observed for a limited number of dairy and blood isolates suggesting the potential of some pathogenic strains for reduced immune activation. Strains from dairy MLST clades displayed the highest relative survival to SGJ independently of dairy adaptation markers lacS/lacZ. Conclusion Combining phylogenetic and functional analyses via SBSEC MLST enabled the clear delineation of strain clades to unravel the complexity of this bacterial group. High adhesion values shared between certain dairy and blood strains as well as the behavior of NF-KB activation are concerning for specific lineages. They highlighted the health risk among shared lineages and establish the basis to elucidate (zoonotic-) transmission, host specificity, virulence mechanisms and enhanced risk assessment as pathobionts in an overarching One Health approach. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0735-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Tomas de Wouters
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), KM 17 route de Dabou, Adiopodoumé Yopougon, Abidjan - 01B.P. 1303, Abidjan, Côte d'Ivoire
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Dasel Wambua Mulwa Kaindi
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, Nairobi, Kenya
| | - Janine Anderegg
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Désirée Böck
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Sabrina Vitali
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Thomas Schmid
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Julia Isenring
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Fabienne Kurt
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Wambui Kogi-Makau
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053, Nairobi, Kenya
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
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Corredoira J, Grau I, Garcia-Rodriguez JF, Alonso-Garcia P, Garcia-Pais MJ, Rabuñal R, Garcia-Garrote F, Ardanuy C, Coira A, Lopez-Alvarez MJ, Pallares R. The clinical epidemiology and malignancies associated with Streptococcus bovis biotypes in 506 cases of bloodstream infections. J Infect 2015; 71:317-25. [PMID: 25982024 DOI: 10.1016/j.jinf.2015.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 05/06/2015] [Accepted: 05/09/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To determine the incidence of Streptococcus bovis (Sb) biotypes causing bacteraemia and associated malignancies. METHODS This is a retrospective analysis of patients with Sb bacteraemia, pulled out from a prospective surveillance protocol of bacteraemia cases, in three areas of Spain (1990-2013): a cattle area (Lugo), a fishing area (Ferrol) and an urban area (Barcelona). Colonoscopy and Sb biotypes (Sb-I and Sb-II) were determined in most cases. RESULTS 506 patients with Sb bacteraemia; mean age 68.1 (±14.1) years, and 66.2% were males. The cattle area, compared with the fishing and urban areas, had higher incidence of bacteraemia by SbI (40.29 vs 9.38 vs 6.15 cases/10(6) person-years, P < 0.001) and bacteraemia by Sb-II (29.07 vs 9.84 vs 13.37 cases/10(6) person-years, P < 0.001). The Sb-I cases (n = 224), compared with Sb-II cases (n = 270), had greater rates of endocarditis (77.6% vs 9.6%, P < 0.001) and colorectal neoplasm (CRN) (50.9% vs 16.6%, P < 0.001), and smaller rates of biliary tract infection (2.2% vs 29.6%, P < 0.001) and non-colorectal malignancy (8.9% vs 31.4%, P < 0.001). CONCLUSION There was a link between the cattle area and higher incidence of Sb bacteraemia. Sb-I differed from Sb-II cases in clinical findings and associated malignancies. Colonoscopy is mandatory in cases of endocarditis or bacteraemia caused by Sb-I.
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Affiliation(s)
- Juan Corredoira
- Infectious Disease Unit and Microbiology Departments, Hospital Lugo "Lucus Augusti", Lugo, Spain.
| | - Imma Grau
- Infectious Disease and Microbiology Departments, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, L'Hospitalet, Barcelona, Spain.
| | | | - Pilar Alonso-Garcia
- Infectious Disease Unit and Microbiology Departments, Hospital Lugo "Lucus Augusti", Lugo, Spain.
| | - M J Garcia-Pais
- Infectious Disease Unit and Microbiology Departments, Hospital Lugo "Lucus Augusti", Lugo, Spain.
| | - Ramon Rabuñal
- Infectious Disease Unit and Microbiology Departments, Hospital Lugo "Lucus Augusti", Lugo, Spain.
| | - Fernando Garcia-Garrote
- Infectious Disease Unit and Microbiology Departments, Hospital Lugo "Lucus Augusti", Lugo, Spain.
| | - Carmen Ardanuy
- Infectious Disease and Microbiology Departments, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, L'Hospitalet, Barcelona, Spain.
| | - Amparo Coira
- Infectious Disease Unit and Microbiology Departments, Hospital Lugo "Lucus Augusti", Lugo, Spain.
| | - M J Lopez-Alvarez
- Infectious Disease Unit and Microbiology Departments, Hospital Lugo "Lucus Augusti", Lugo, Spain.
| | - Roman Pallares
- Infectious Disease and Microbiology Departments, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, L'Hospitalet, Barcelona, Spain.
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Papadimitriou K, Anastasiou R, Maistrou E, Plakas T, Papandreou NC, Hamodrakas SJ, Ferreira S, Supply P, Renault P, Pot B, Tsakalidou E. Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One 2015; 10:e0116337. [PMID: 25584532 PMCID: PMC4293149 DOI: 10.1371/journal.pone.0116337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 12/05/2014] [Indexed: 12/22/2022] Open
Abstract
Background Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex. Methodology/Principal Findings We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198’s acquisition is not a recent event. Conclusions/Significance Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- * E-mail:
| | - Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Eleni Maistrou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Thomas Plakas
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Nikos C. Papandreou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stavros J. Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stéphanie Ferreira
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
| | - Philip Supply
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Pierre Renault
- INRA, UMR1319 Micalis, Jouy-en-Josas, F-78352, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, F-78352, France
| | - Bruno Pot
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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Jans C, Meile L, Lacroix C, Stevens MJA. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC). INFECTION GENETICS AND EVOLUTION 2014; 33:419-36. [PMID: 25233845 DOI: 10.1016/j.meegid.2014.09.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 02/07/2023]
Abstract
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are pivotal for strain performance during fermentation. Comparative genomics is a powerful tool to identify acquired pathogenic functions, but there is still an urgent need for more physiological and epidemiological data to understand SBSEC-specific traits.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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