1
|
Overbeek LV. Human Pathogens in Primary Production Systems. Microorganisms 2023; 11:microorganisms11030750. [PMID: 36985323 PMCID: PMC10053829 DOI: 10.3390/microorganisms11030750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 03/16/2023] Open
Abstract
Human pathogenic micro-organisms can contaminate plants [...]
Collapse
Affiliation(s)
- Leo van Overbeek
- Wageningen Plant Research, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
2
|
Aguirre-Sánchez JR, Valdez-Torres JB, Del Campo NC, Martínez-Urtaza J, Del Campo NC, Lee BG, Quiñones B, Chaidez-Quiroz C. Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105380. [PMID: 36283634 DOI: 10.1016/j.meegid.2022.105380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
Abstract
Escherichia coli is a leading cause of human enteric diseases worldwide. The rapid and accurate causal agent identification to a particular source represents a crucial step in the establishment of safety and health measures in the affected human populations and would thus provide insights into the relationship of traits that may contribute for pathogen persistence in a particular reservoir. The objective of the present study was to characterize over two hundred E. coli strains from different isolation sources in Mexico by conducting a correspondence analysis to explore associations with the detected phylogenetic groups. The results indicated that E. coli strains, recovered from distinct sources in Mexico, were classified into phylogroups B1 (35.8%), A (27.8%), and D (12.3%) and were clustered to particular clades according to the predicted phylogroups. The results from correspondence analysis showed that E. coli populations from distinct sources in Mexico, belonging to different phylogroups, were not dispersed randomly and were associated with a particular isolation source. Phylogroup A was strongly associated with human sources, and the phylogroup B1 showed a significant relationship with food sources. Additionally, phylogroup D was also related to human sources. Phylogroup B2 was associated with herbivorous and omnivorous mammals. Moreover, common virulence genes in the examined E. coli strains, assigned to all phylogroups, were identified as essential markers for survival and invasion in the host. Although virulence profiles varied among the detected phylogroups, E. coli strains belonging to phylogroup D, associated with humans, were found to contain the largest virulence gene repertoire conferring for persistence and survival in the host. In summary, these findings provide fundamental information for a better characterization of pathogenic E. coli, recovered from distinct isolation sources in Mexico and would assist in the development of better tools for identifying potential transmission routes of contamination.
Collapse
Affiliation(s)
- José R Aguirre-Sánchez
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - José B Valdez-Torres
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - Nohemí Castro Del Campo
- Facultad de Medicina Veterinaria y Zootecnia de la Universidad Autónoma de Sinaloa, 80260 Culiacán, Sinaloa, Mexico
| | - Jaime Martínez-Urtaza
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Nohelia Castro Del Campo
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - Bertram G Lee
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, United States
| | - Beatriz Quiñones
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, United States
| | - Cristóbal Chaidez-Quiroz
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico.
| |
Collapse
|
3
|
Assessment Impacts of Ozone on Salmonella Typhimurium and Escherichia coli O157:H7 in Liquid Dairy Waste. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12136527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Liquid dairy manure, which is produced in enormous quantities in flush dairy manure management systems, is commonly used as an alternative to chemical fertilizers. It provides nutrient benefits to crops and soils. While dairy waste is a well-accepted and widely used fertilizer, the presence of indicator organisms and human pathogens in manure may lead to pathogen contamination in crops and soils. This study is focused on the examination of ozone gas-based sterilization. In the past, ozone (O3) has been used for sanitizing various foods and solid surfaces, but the potential of O3 for eliminating human pathogens in liquid dairy waste is not studied yet. Pathogens such as Salmonella Typhimurium and Escherichia coli O157:H7 are reported to be present in liquid dairy manure, and this research evaluated the effects of various levels of ozone on the survival of these two pathogens. We designed a continuous type O3 treatment system that has four major components: (1) ozone generator using oxygen; (2) ozone concentration control by mixing with pure air; (3) continuous monitoring of ozone concentrations; and (4) ozone experiment chambers. Various levels of ozone (43.26, 87.40, and 132.46 mg·L−1) were produced in the ozone system, and subsequently, ozone was diffused through liquid manure. Liquid manure was exposed to ozone for multiple durations (30, 60, and 120 min). To determine the effectiveness of O3 in eliminating pathogens, time-series samples were collected and analyzed for determining the levels of S. typhimurium and E. coli O157:H7. Preliminary results showed that ozone concentrations of 132.46 mg/L, and exposure time of 120 min resulted in the reduced levels of E. coli and Salmonella. Low levels of ozone and limited exposure time were found to be less effective in pathogen removal potentially due to high solid contents. Additional studies carrying out experiments to evaluate the impacts of solids in combination with ozone concentrations will provide further insights into developing full-scale ozone-based treatment systems.
Collapse
|
4
|
Withenshaw SM, Smith RP, Davies R, Smith AEO, Gray E, Rodgers J. A systematized review and qualitative synthesis of potential risk factors associated with the occurrence of non‐O157 Shiga toxin‐producing
Escherichia coli
(STEC) in the primary production of cattle. Compr Rev Food Sci Food Saf 2022; 21:2363-2390. [DOI: 10.1111/1541-4337.12929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/22/2022]
Affiliation(s)
- Susan M. Withenshaw
- Department of Epidemiological Sciences Animal and Plant Health Agency – Weybridge New Haw UK
| | - Richard P. Smith
- Department of Epidemiological Sciences Animal and Plant Health Agency – Weybridge New Haw UK
| | - Rob Davies
- Department of Bacteriology Animal and Plant Health Agency – Weybridge New Haw UK
| | - Alice E. O. Smith
- Department of Epidemiological Sciences Animal and Plant Health Agency – Weybridge New Haw UK
| | - Elizabeth Gray
- Department of Epidemiological Sciences Animal and Plant Health Agency – Weybridge New Haw UK
| | - John Rodgers
- Department of Bacteriology Animal and Plant Health Agency – Weybridge New Haw UK
| |
Collapse
|
5
|
Antibiotic resistance and phylogenetic profiling of Escherichia coli from dairy farm soils; organic versus conventional systems. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100088. [PMID: 34977826 PMCID: PMC8688864 DOI: 10.1016/j.crmicr.2021.100088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 12/25/2022] Open
Abstract
First known comparison of antimicrobial resistance traits in E. coli strains from new zealand farms practicing organic and conventional husbandry. Potential extended spectrum β-lactamase producing strains isolated from dairy farm environments. Organic dairy farms tended to harbour fewer resistant isolates than those recovered from conventionally farmed counterparts. Evidence for anthroponotic transmission of resistant strains of human origin to farm environments. Implications for the spread of antimicrobial resistance traits from farm environments discussed.
The prevalence and spread of antimicrobial resistance (AMR) as a result of the persistent use and/or abuse of antimicrobials is a key health problem for health authorities and governments worldwide. A study of contrasting farming systems such as organic versus conventional dairy farming may help to authenticate some factors that may contribute to the prevalence and spread of AMR in their soils. A case study was conducted in organic and conventional dairy farms in the South Canterbury region of New Zealand. A total of 814 dairy farm soil E. coli (DfSEC) isolates recovered over two years were studied. Isolates were recovered from each of two farms practicing organic, and another two practicing conventional husbandries. The E. coli isolates were examined for their antimicrobial resistance (AMR) against cefoxitin, cefpodoxime, chloramphenicol, ciprofloxacin, gentamicin, meropenem, nalidixic acid, and tetracycline. Phylogenetic relationships were assessed using an established multiplex PCR method. The AMR results indicated 3.7% of the DfSEC isolates were resistant to at least one of the eight selected antimicrobials. Of the resistant isolates, DfSEC from the organic dairy farms showed a lower prevalence of resistance to the antimicrobials tested, compared to their counterparts from the conventional farms. Phylogenetic analysis placed the majority (73.7%) of isolates recovered in group B1, itself dominated by isolates of bovine origin. The tendency for higher rates of resistance among strains from conventional farming may be important for future decision-making around farming practices Current husbandry practices may contribute to the prevalence and spread of AMR in the industry.
Collapse
|
6
|
Onyeka LO, Adesiyun AA, Keddy KH, Manqele A, Madoroba E, Thompson PN. Prevalence and patterns of fecal shedding of Shiga toxin–producing
Escherichia coli
by cattle at a commercial feedlot in South Africa. J Food Saf 2021. [DOI: 10.1111/jfs.12961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Libby Obumneke Onyeka
- Department of Production Animal Studies, Faculty of Veterinary Science University of Pretoria Onderstepoort South Africa
- Department of Veterinary Public Health and Preventive Medicine College of Veterinary Medicine, Michael Okpara University of Agriculture Umudike Nigeria
| | - Abiodun A. Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary Science University of Pretoria Onderstepoort South Africa
- Department of Basic Veterinary Sciences School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies St. Augustine Trinidad and Tobago
| | - Karen H. Keddy
- School of Public Health, Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa
| | - Ayanda Manqele
- Department of Production Animal Studies, Faculty of Veterinary Science University of Pretoria Onderstepoort South Africa
- Agricultural Research Council—Onderstepoort Veterinary Research Onderstepoort South Africa
| | - Evelyn Madoroba
- Agricultural Research Council—Onderstepoort Veterinary Research Onderstepoort South Africa
- Department of Biochemistry & Microbiology University of Zululand KwaDlangezwa South Africa
| | - Peter Neil Thompson
- Department of Production Animal Studies, Faculty of Veterinary Science University of Pretoria Onderstepoort South Africa
| |
Collapse
|
7
|
Transmission of Escherichia coli from Manure to Root Zones of Field-Grown Lettuce and Leek Plants. Microorganisms 2021; 9:microorganisms9112289. [PMID: 34835415 PMCID: PMC8622635 DOI: 10.3390/microorganisms9112289] [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: 09/14/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022] Open
Abstract
Pathogenic Escherichia coli strains are responsible for food-borne disease outbreaks upon consumption of fresh vegetables and fruits. The aim of this study was to establish the transmission route of E. coli strain 0611, as proxy for human pathogenic E. coli, via manure, soil and plant root zones to the above-soil plant compartments. The ecological behavior of the introduced strain was established by making use of a combination of cultivation-based and molecular targeted and untargeted approaches. Strain 0611 CFUs and specific molecular targets were detected in the root zones of lettuce and leek plants, even up to 272 days after planting in the case of leek plants. However, no strain 0611 colonies were detected in leek leaves, and only in one occasion a single colony was found in lettuce leaves. Therefore, it was concluded that transmission of E. coli via manure is not the principal contamination route to the edible parts of both plant species grown under field conditions in this study. Strain 0611 was shown to accumulate in root zones of both species and metagenomic reads of this strain were retrieved from the lettuce rhizosphere soil metagenome library at a level of Log 4.11 CFU per g dry soil.
Collapse
|
8
|
Meisner A, Wepner B, Kostic T, van Overbeek LS, Bunthof CJ, de Souza RSC, Olivares M, Sanz Y, Lange L, Fischer D, Sessitsch A, Smidt H. Calling for a systems approach in microbiome research and innovation. Curr Opin Biotechnol 2021; 73:171-178. [PMID: 34479027 DOI: 10.1016/j.copbio.2021.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 12/23/2022]
Abstract
Microbiomes are all around us in natural and cultivated ecosystems, for example, soils, plants, animals and our own body. Microbiomes are essential players of biotechnological applications, and their functions drive human, animal, plant and environmental health. The rapidly developing microbiome research landscape was studied by a global mapping excercise and bibliometric analysis. Although microbiome research is performed in many different science fields, using similar concepts within and across fields, microbiomes are mostly investigated one ecosystem at-a-time. In order to fully understand microbiome impacts and leverage microbial functions, research needs to adopt a systems approach connecting microbiomes and research initiatives in divergent fields to create understanding on how microbiomes can be modulated for desirable functions as a basis of sustainable, circular bioeconomy.
Collapse
Affiliation(s)
- Annelein Meisner
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Beatrix Wepner
- AIT Austrian Institute of Technology, Center for Innovation Systems & Policy, Giefinggasse 4, Vienna, 1210, Austria
| | - Tanja Kostic
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Leo S van Overbeek
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Christine J Bunthof
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Lene Lange
- BioEconomy, Research & Advisory, Karensgade 5, Valby, 2500, Denmark
| | - Doreen Fischer
- Helmholtz Zentrum München, National Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstaedter Landstr. 1, Neuherberg, Munich, D-85764, Germany
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.
| |
Collapse
|
9
|
Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms. Microorganisms 2021; 9:microorganisms9010141. [PMID: 33435450 PMCID: PMC7826917 DOI: 10.3390/microorganisms9010141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/27/2022] Open
Abstract
Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. blaCMY
was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the blaCMY
was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment.
Collapse
|
10
|
S. van Overbeek L, Lombaers-van der Plas C, van der Zouwen P. The Role of Pea ( Pisum sativum) Seeds in Transmission of Entero-Aggregative Escherichia coli to Growing Plants. Microorganisms 2020; 8:microorganisms8091271. [PMID: 32825568 PMCID: PMC7565074 DOI: 10.3390/microorganisms8091271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 11/16/2022] Open
Abstract
Crop plants can become contaminated with human pathogenic bacteria in agro-production systems. Some of the transmission routes of human pathogens to growing plants are well explored such as water, manure and soil, whereas others are less explored such as seeds. Fenugreek seeds contaminated with the entero-hemorrhagic Escherichia coli O104:H4 were suspected to be the principle vectors for transmission of the pathogen to sprouts at the food-borne disease outbreak in Hamburg and surrounding area in 2011. In this study we raised the questions of whether cells of the entero-aggregative E. coli O104:H4 strain 55989 is capable of colonizing developing plants from seeds and if it would be possible that, via plant internalization, these cells can reach the developing embryonic tissue of the next generation of seeds. To address these questions, we followed the fate of strain 55989 and of two other E. coli strains from artificially contaminated seeds to growing plants, and from developing flower tissue to mature seeds upon proximate introductions to the plant reproductive organs. Escherichia coli strains differing in origin, adherence properties to epithelial cells, and virulence profile were used in our experimentation to relate eventual differences in seed and plant colonization to typical E. coli properties. Experiments were conducted under realistic growth circumstances in greenhouse and open field settings. Entero-aggregative E. coli strain 55989 and the two other E. coli strains were able to colonize the root compartment of pea plants from inoculated seeds. In roots and rhizosphere soil, the strains could persist until the senescent stage of plant growth, when seeds had ripened. Colonization of the above-soil parts was only temporary at the start of plant growth for all three E. coli strains and, therefore, the conclusion was drawn that translocation of E. coli cells via the vascular tissue of the stems to developing pea seeds seems unlikely under circumstances realistic for agricultural practices. Proximate introductions of cells of E. coli strains to developing flowers also did not result in internal seed contamination, indicating that internal seed contamination with E. coli is an unlikely event. The fact that all three E. coli strains showed stronger preference for the root-soil zones of growing pea plants than for the above soil plant compartments, in spite of their differences in clinical behaviour and origin, indicate that E. coli in general will colonize root compartments of crop plants in production systems.
Collapse
|