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Breedt G, Korsten L, Gokul JK. Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield. Curr Microbiol 2024; 81:170. [PMID: 38734822 PMCID: PMC11088555 DOI: 10.1007/s00284-024-03685-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/01/2024] [Indexed: 05/13/2024]
Abstract
As a primary nutrient in agricultural soils, phosphorus plays a crucial but growth-limiting role for plants due to its complex interactions with various soil elements. This often results in excessive phosphorus fertilizer application, posing concerns for the environment. Agri-research has therefore shifted focus to increase fertilizer-use efficiency and minimize environmental impact by leveraging plant growth-promoting rhizobacteria. This study aimed to evaluate the in-field incremental effect of inorganic phosphate concentration (up to 50 kg/ha/P) on the ability of two rhizobacterial isolates, Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), from the previous Breedt et al. (Ann Appl Biol 171:229-236, 2017) study on maize in enhancing the yield of commercially grown Duzi® cultivar wheat. Results obtained from three seasons of field trials revealed a significant relationship between soil phosphate concentration and the isolates' effectiveness in improving wheat yield. Rhizospheric samples collected at flowering during the third season, specifically to assess phosphatase enzyme activity at the different soil phosphate levels, demonstrated a significant decrease in soil phosphatase activity when the phosphorus rate reached 75% for both isolates. Furthermore, in vitro assessments of inorganic phosphate solubilization by both isolates at five increments of tricalcium phosphate-amended Pikovskaya media found that only isolate T19 was capable of solubilizing tricalcium at concentrations exceeding 3 mg/ml. The current study demonstrates the substantial influence of inorganic phosphate on the performance of individual rhizobacterial isolates, highlighting that this is an essential consideration when optimizing these isolates to increase wheat yield in commercial cultivation.
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Affiliation(s)
- Gerhardus Breedt
- Limpopo Department of Agriculture and Rural Development, Towoomba ADC, Private Bag X1615, Bela-Bela, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa
- Department of Science and Innovation - National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Jarishma Keriuscia Gokul
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa.
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Private Bag X20, Pretoria, South Africa.
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Viviers SA, Richter L, du Plessis EM, Korsten L. Microbiological quality of irrigation water on highly diverse fresh produce smallholder farms: elucidating environmental routes of contamination. J Appl Microbiol 2024; 135:lxae091. [PMID: 38632044 DOI: 10.1093/jambio/lxae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/12/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
AIM To evaluate the microbiological safety, potential multidrug-resistant bacterial presence and genetic relatedness (DNA fingerprints) of Escherichia coli isolated from the water-soil-plant nexus on highly diverse fresh produce smallholder farms. METHODS AND RESULTS Irrigation water (n = 44), soil (n = 85), and fresh produce (n = 95) samples from six smallholder farms with different production systems were analysed for hygiene indicator bacterial counts and the presence of shigatoxigenic E. coli and Salmonella spp. using standard microbiological methods. Identities of isolates were confirmed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and the genetic relatedness of the E. coli isolates determined using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) analysis. Irrigation water E. coli levels ranged between 0 and 3.45 log MPN/100 ml-1 with five farms having acceptable levels according to the World Health Organization limit (3 log MPN/100 ml-1). Fresh produce samples on four farms (n = 65) harboured E. coli at low levels (<1 log CFU/g-1) except for one sample from kale, spring onion, green pepper, onion, and two tomato samples, which exceeded international acceptable limits (100 CFU/g-1). Only one baby carrot fresh produce sample tested positive for Salmonella spp. Of the 224 samples, E. coli isolates were identified in 40% (n = 90) of all water, soil, and fresh produce types after enrichment. Additionally, the DNA fingerprints of E. coli isolates from the water-soil-plant nexus of each respective farm clustered together at high similarity values (>90%), with all phenotypically characterized as multidrug-resistant. CONCLUSIONS The clustering of E. coli isolated throughout the water-soil-plant nexus, implicated irrigation water in fresh produce contamination. Highlighting the importance of complying with irrigation water microbiological quality guidelines to limit the spread of potential foodborne pathogens throughout the fresh produce supply chain.
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Affiliation(s)
- Sheldon A Viviers
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0001, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0001, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0001, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0001, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, University of Pretoria, Hatfield, Pretoria 0028, South Africa
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de Bruin W, van Zijl MC, Aneck-Hahn NH, Korsten L. Quality and safety of South African hand sanitisers during the COVID-19 pandemic. Int J Environ Health Res 2024; 34:719-731. [PMID: 36652575 DOI: 10.1080/09603123.2023.2166020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Health agencies recommend using hand sanitisers as protection against the coronavirus. Thus far, the emphasis on hand sanitiser studies is limited to an analysis of disinfectant content only. This study aims to provide an extended analysis of 60 off-the-shelf alcohol-based hand sanitisers by using gas chromatography to report on alcohol content and the presence of impurities, a recombinant yeast estrogen screen to assess estrogenic activity, and an investigation into labelling compliance with the South African National Standard. Fifty hand sanitisers had an alcohol content of ≥60% v/v alcohol; however, most contained skin irritants and substances that could harm human and environmental health. Estrogenic activity was detected in 29 hand sanitisers and none of the products complied with all the labelling requirements. Since off-the-shelf hand sanitisers in South Africa are not regulated and monitored, evidence-based public awareness programmes on hand sanitiser quality and safety should become a priority.
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Affiliation(s)
- W de Bruin
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M C van Zijl
- Environmental Chemical Pollution and Health Research Unit, University of Pretoria, Pretoria, South Africa
| | - N H Aneck-Hahn
- Environmental Chemical Pollution and Health Research Unit, University of Pretoria, Pretoria, South Africa
| | - L Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
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Kgoale DM, Duvenage S, Du Plessis EM, Gokul JK, Korsten L. Serotype Distribution, Antimicrobial Resistance, Virulence Genes, and Genetic Diversity of Salmonella spp. Isolated from small-scale Leafy Green Vegetable Supply Chains in South Africa. J Food Prot 2024; 87:100195. [PMID: 37977503 DOI: 10.1016/j.jfp.2023.100195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/27/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Salmonella have been implicated in foodborne disease outbreaks globally and is a pressing concern in the South African small-scale sector due to inadequate hygiene standards and limited regulatory oversight, leading to a higher risk of foodborne diseases. By investigating irrigation water and leafy green vegetables produced by small-scale growers and sold through unregulated supply chains, this study was able to determine the presence, serotype distribution, virulence gene profiles, antibiotic resistance, and genetic diversity of Salmonella isolated from these sources. From 426 samples, 21 Salmonella-positive samples were identified, providing 53 Salmonella isolates. Of these, six different Salmonella serotypes and sequence types (STs) were identified, including Salmonella II 42:r: ST1208 (33.96%; n = 18), Salmonella Enteritidis: ST11 (22.64%; n = 12), Salmonella II 42:z29: ST4395 (16.98%; n = 9), Salmonella Havana: ST1524 (15.09%; n = 8), Salmonella Typhimurium: ST19 (9.43%; n = 5), and Salmonella IIIb 47:i:z: ST7890 (1.89%; n = 1). A total of 92.45% of the isolates were found to be multidrug-resistant, showing high rates of resistance to aztreonam (88.68%; n = 47), ceftazidime (86.79%; n = 46), nalidixic acid (77.36%; n = 41), cefotaxime (75.47%; n = 40), cefepime (71.70%; n = 38), and streptomycin (69.81%; n = 37). All isolates possessed the aac(6')-Iaa antimicrobial resistance gene, with a range of between 9 and 256 virulence genes. Eleven cluster patterns were observed from Enterobacterial Repetitive Intergenic Consensus sequence analyses, demonstrating high diversity among the Salmonella spp., with water and fresh produce isolates clustering, suggesting water as a potential contamination source. Plasmid replicon types were identified in 41.51% (n = 22) of the isolates, including Col(pHAD28) in Salmonella Havana (5.66%; n = 3), Col156 in Salmonella II 42:z29:- (1.89%; n = 1) and both IncFIB(S) and IncFII(S) in Salmonella Enteritidis (22.64; n = 12), Salmonella Typhimurium (9.43%; n = 5), and Salmonella Havana (1.89%; n = 1). This study highlights the presence of multidrug-resistant and multivirulent Salmonella spp. in the small-scale leafy green vegetable supply chains, underscoring the need for the development of a "fit-for-purpose" food safety management system within this system.
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Affiliation(s)
- Degracious M Kgoale
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
| | - Stacey Duvenage
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa; Food and Markets Department, Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Erika M Du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
| | - Jarishma K Gokul
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa.
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Msimango T, Duvenage S, Du Plessis EM, Korsten L. Microbiological quality assessment of fresh produce: Potential health risk to children and urgent need for improved food safety in school feeding schemes. Food Sci Nutr 2023; 11:5501-5511. [PMID: 37701226 PMCID: PMC10494634 DOI: 10.1002/fsn3.3506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/02/2023] [Accepted: 05/31/2023] [Indexed: 09/14/2023] Open
Abstract
About 388 million school-going children worldwide benefit from school feeding schemes, which make use of fresh produce to prepare meals. Fresh produce including leafy greens and other vegetables were served at 37% and 31% of school feeding programs, respectively, in Africa. This study aimed at assessing the microbiological quality of fresh produce grown onsite or supplied to South African schools that are part of the national school feeding programs that benefit over 9 million school-going children. Coliforms, Escherichia coli, Enterobacteriaceae, and Staphylococcus aureus were enumerated from fresh produce (n = 321) samples. The occurrence of E. coli, Listeria monocytogenes, Salmonella spp., and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae was determined. Presumptive pathogens were tested for antimicrobial resistance. E. coli was further tested for diarrheagenic virulence genes. Enterobacteriaceae on 62.5% of fresh produce samples (200/321) exceeded previous microbiological guidelines for ready-to-eat food, while 86% (276/321 samples) and 31.6% (101/321 samples) exceeded coliform and E. coli criteria, respectively. A total of 76 Enterobacteriaceae were isolated from fresh produce including E. coli (n = 43), Enterobacter spp. (n = 15), and Klebsiella spp. (n = 18). Extended-spectrum β-lactamase production was confirmed in 11 E. coli, 13 Enterobacter spp., and 17 Klebsiella spp. isolates. No diarrheagenic virulence genes were detected in E. coli isolates. However, multidrug resistance (MDR) was found in 60.5% (26/43) of the E. coli isolates, while all (100%; n = 41) of the confirmed ESBL and AmpC Enterobacteriaceae showed MDR. Our study indicates the reality of the potential health risk that contaminated fresh produce may pose to school-going children, especially with the growing food safety challenges and antimicrobial resistance crisis globally. This also shows that improved food safety approaches to prevent foodborne illness and the spread of foodborne pathogens through the food served by school feeding schemes are necessary.
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Affiliation(s)
- Thabang Msimango
- Department of Plant and Soil SciencesUniversity of PretoriaPretoriaSouth Africa
- Department of Science and Innovation‐National Research Foundation Centre of Excellence in Food SecurityPretoriaSouth Africa
| | - Stacey Duvenage
- Natural Resources Institute, Faculty of Engineering and ScienceUniversity of GreenwichLondonUK
| | - Erika M. Du Plessis
- Department of Plant and Soil SciencesUniversity of PretoriaPretoriaSouth Africa
- Department of Science and Innovation‐National Research Foundation Centre of Excellence in Food SecurityPretoriaSouth Africa
| | - Lise Korsten
- Department of Plant and Soil SciencesUniversity of PretoriaPretoriaSouth Africa
- Department of Science and Innovation‐National Research Foundation Centre of Excellence in Food SecurityPretoriaSouth Africa
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Iwu CD, Nontongana N, Iwu-Jaja CJ, Anyanwu BO, du Plessis E, Korsten L, Okoh AI. Spatial diarrheal disease risks and antibiogram diversity of diarrheagenic Escherichia coli in selected access points of the Buffalo River, South Africa. PLoS One 2023; 18:e0288809. [PMID: 37616257 PMCID: PMC10449160 DOI: 10.1371/journal.pone.0288809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/04/2023] [Indexed: 08/26/2023] Open
Abstract
Freshwater sources, often used for domestic and agricultural purposes in low- and middle-income countries are repositories of clinically significant bacterial pathogens. These pathogens are usually diversified in their antibiogram profiles posing public health threats. This study evaluated the spatial diarrhoeal disease risk and antibiogram diversity of diarrheagenic Escherichia coli (DEC) in four access points of the Buffalo River, Eastern Cape Province, South Africa using standard epidemiological, culture, and molecular methods. The diarrhoeal disease risk was characterised using the Monte Carlo simulation, while the antibiogram diversity was assessed using the species observed Whittaker's single alpha-diversity modelling. E. coli mean count was highest in King William's Town dam [16.0 × 102 CFU/100ml (SD: 100.0, 95% CI: 13.5 × 102 to 18.5 × 102)]. Enterohemorrhagic E. coli (stx1/stx2) was the most prevalent DEC pathotype across the study sites. A high diarrhoeal disease risk of 25.0 ×10-2 exceeding the World Health Organization's standard was recorded across the study sites. The average single and multiple antimicrobial resistance indices of the DEC to test antimicrobials were highest in the Eluxolzweni dam [0.52 (SD: 0.25, 95% CI: 0.37 to 0.67)] and King William's Town dam [0.42 (SD: 0.25, 95% CI: 0.27 to 0.57)] respectively. The prevalent antibiotic resistance genes detected were tetA, blaFOX and blaMOX plasmid-mediated AmpC, blaTEM and blaSHV extended-spectrum β-lactamases, which co-occurred across the study sites on network analysis. The phenotypic and genotypic resistance characteristics of the DEC in Maden dam (r = 0.93, p<0.00), Rooikrantz dam (r = 0.91, p<0.00), King William's Town dam (r = 0.83, p = 0.0), and Eluxolzweni dam (r = 0.91, p<0.00) were strongly correlated. At least, three phylogenetic clades of the DEC with initial steep descent alpha-diversity curves for most of the test antimicrobials were observed across the study sites, indicating high diversity. The occurrence of diversified multi drug resistant DEC with diarrhoeal disease risks in the Buffalo River substantiates the role surface water bodies play in the dissemination of drug-resistant bacterial pathogens with public health implications.
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Affiliation(s)
- Chidozie Declan Iwu
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
| | | | - Brilliance Onyinyechi Anyanwu
- Centre for Occupational Health, Safety and Environment, University of Port Harcourt, Port Harcourt, Rivers State, Nigeria
| | - Erika du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
- Department of Science and Technology-National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
- Department of Science and Technology-National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Anthony Ifeanyin Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
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Richter L, Du Plessis EM, Duvenage S, Korsten L. Prevalence of extended-spectrum β-lactamase producing Enterobacterales in Africa's water-plant-food interface: A meta-analysis (2010–2022). Front Sustain Food Syst 2023. [DOI: 10.3389/fsufs.2023.1106082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
BackgroundMultidrug-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacterales is regarded as a critical health issue, yet, surveillance in the water-plant-food interface remains low, especially in Africa.ObjectivesThe objective of the study was to elucidate the distribution and prevalence of antimicrobial resistance in clinically significant members of the Enterobacterales order isolated from the water-plant-food interface in Africa.MethodsA literature search was conducted using six online databases according to the PRISMA guidelines. All available published studies involving phenotypic and genotypic characterization of ESBL-producing Enterobacterales from water, fresh produce or soil in Africa were considered eligible. Identification and characterization methods used as well as a network analysis according to the isolation source and publication year were summarized. Analysis of Escherichia coli, Salmonella spp. and Klebsiella pneumoniae included the calculation of the multiple antibiotic resistance (MAR) index according to isolation sources and statistical analysis was performed using RStudio.ResultsOverall, 51 studies were included for further investigation. Twelve African countries were represented, with environmental AMR surveillance studies predominantly conducted in South Africa. In 76.47% of the studies, occurrence of antimicrobial resistant bacteria was investigated in irrigation water samples, while 50.98% of the studies included fresh produce samples. Analysis of bacterial phenotypic antimicrobial resistance profiles were reported in 94.12% of the studies, with the disk diffusion method predominantly used. When investigating the MAR indexes of the characterized Escherichia coli, Klebsiella pneumoniae and Salmonella spp., from different sources (water, fresh produce or soil), no significant differences were seen across the countries. The only genetic determinant identified using PCR detection in all the studies was the blaCTX − M resistance gene. Only four studies used whole genome sequence analysis for molecular isolate characterization.DiscussionGlobally, AMR surveillance programmes recognize ESBL- and carbapenemase-producing Enterobacterales as vectors of great importance in AMR gene dissemination. However, in low- and middle-income countries, such as those in Africa, challenges to implementing effective and sustainable AMR surveillance programmes remain. This review emphasizes the need for improved surveillance, standardized methods and documentation of resistance gene dissemination across the farm-to-fork continuum in Africa.
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Korsten L, Jansen F, Lissenberg-Witte B, Vergeer M, Brakenhoff R, Leemans R, Verdonck-de Leeuw I. O2.1 The course of health-related quality of life from diagnosis to two years follow-up in patients with oropharyngeal cancer: does HPV status matter? Oral Oncol 2022. [DOI: 10.1016/j.oraloncology.2022.106172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bill M, Gokul JK, Viljoen F, Korsten L. Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions. J Appl Microbiol 2022; 133:1905-1918. [PMID: 35776004 DOI: 10.1111/jam.15693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/27/2022]
Abstract
AIM OF THE STUDY To characterise the baseline microbial population of the avocado carposphere and understand shifts in community structure from the harvest to ready-to-eat stages. METHODS AND RESULTS The changes in surface or stem-end fungal microbiomes at the postharvest stage of avocado fruit were studied using next-generation sequencing of the internal transcribed spacer (ITS) region. Avocado fructoplane and stem-end pulp fungal richness differed significantly between postharvest stages with a decline following prochloraz dip treatments. Known postharvest decay-causing genera, Colletotrichum, Fusarium, Alternaria, Epicoccum, Penicillium and Neofusicoccum were detected, with Papiliotrema, Meyerozyma and Aureobasidium confirmed as the most dominant potentially beneficial genera. Postharvest interventions such as prochloraz had a negative non-target effect on the presence of Papiliotrema flavescens on the avocado fructoplane. CONCLUSION Our findings reveal a core community of beneficial and pathogenic taxa in the avocado fructoplane, and further highlights the reduction of pathogenic fungi as a consequence of fungicide use. SIGNIFICANCE AND IMPACT OF THE STUDY The current study provides important baseline data for further exploration of fungal population shifts in avocado fruit driven by chemical (fungicide) as well as physical (cold storage) interventions.
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Affiliation(s)
- Malick Bill
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
| | | | - Francois Viljoen
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
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Baloyi T, Duvenage S, Du Plessis E, Villamizar-Rodríguez G, Korsten L. Multidrug resistant Escherichia coli from fresh produce sold by street vendors in South African informal settlements. Int J Environ Health Res 2022; 32:1513-1528. [PMID: 33706630 DOI: 10.1080/09603123.2021.1896681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study was to assess the prevalence of commensal and pathogenic Escherichia coli on informally sold fresh produce in South Africa, who harbour and express antimicrobial resistance genes and therefore pose indirect risks to public health. The majority (85.71%) of E. coli isolates from spinach, apples, carrots, cabbage and tomatoes, were multidrug resistant (MDR). Resistance to Aminoglycoside (94.81%), Cephalosporin (93.51%), Penicillin (93.51%) and Chloramphenicol (87.01%) antibiotic classes were most prevalent. Antibiotic resistance genes detected included blaTEM (89.29%), tetA (82.14%), tetB (53.57%), tetL (46.43%), sulI (41.07%), sulII (51.79%), aadA1a (58.93%) and strAB (51.79%). A single isolate was found to harbour eae virulence factor. Moreover, E. coli isolates were grouped into the intra-intestinal infectious phylogenetic group E (28.57%), the rare group C (26.79%), the generalist group B1 (21.43%) and the human commensal group A (16.07%). Presence of MDR E. coli represents a transmission route and significant human health risk.
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Affiliation(s)
- Tintswalo Baloyi
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Erika Du Plessis
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Germán Villamizar-Rodríguez
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Lise Korsten
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
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Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang QJ, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany JL, Liu C, Zeng ZQ, Zhuang WY, Yu ZH, Thines M. Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Syst Evol 2022; 9:161-200. [PMID: 35978986 PMCID: PMC9355104 DOI: 10.3114/fuse.2022.09.08] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/14/2022] [Indexed: 11/07/2022] Open
Abstract
Seven Fusarium species complexes are treated, namely F. aywerte species complex (FASC) (two species), F. buharicum species complex (FBSC) (five species), F. burgessii species complex (FBURSC) (three species), F. camptoceras species complex (FCAMSC) (three species), F. chlamydosporum species complex (FCSC) (eight species), F. citricola species complex (FCCSC) (five species) and the F. concolor species complex (FCOSC) (four species). New species include Fusicolla elongata from soil (Zimbabwe), and Neocosmospora geoasparagicola from soil associated with Asparagus officinalis (Netherlands). New combinations include Neocosmospora akasia, N. awan, N. drepaniformis, N. duplosperma, N. geoasparagicola, N. mekan, N. papillata, N. variasi and N. warna. Newly validated taxa include Longinectria gen. nov., L. lagenoides, L. verticilliforme, Fusicolla gigas and Fusicolla guangxiensis. Furthermore, Fusarium rosicola is reduced to synonymy under N. brevis. Finally, the genome assemblies of Fusarium secorum (CBS 175.32), Microcera coccophila (CBS 310.34), Rectifusarium robinianum (CBS 430.91), Rugonectria rugulosa (CBS 126565), and Thelonectria blattea (CBS 952.68) are also announced here. Citation: Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang Q-J, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany J-L, Liu C, Zeng Z-Q, Zhuang W-Y, Yu Z-H, Thines M (2022). Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Systematics and Evolution 9: 161-200. doi: 10.3114/fuse.2022.09.08.
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Affiliation(s)
- P W Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.,Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M M Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - J Z Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - A L van Iperen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M Starink-Willemse
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M Hernández-Restrepo
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - H Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B Ulaszewski
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - W de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Soil Biology Group, Wageningen University, Wageningen, Netherlands
| | - A M Abdel-Azeem
- Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - J Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - A Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022 Kharkiv, Ukraine
| | - M Bakhshi
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - J D P Bezerra
- Setor de Micologia / Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Rua 235 - s/n - Setor Universitário - CEP: 74605-050, Universidade Federal de Goiás / Federal University of Goiás, Goiânia, Brasil / Goiânia, Brazil
| | - C S Bhunjun
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - M P S Câmara
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - P Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, Costa Rica
| | - W A S Vieira
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - C A Decock
- Mycothèque de l'Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute - ELIM - Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348 Louvain-la-Neuve, Belgium
| | - E Gaya
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - J Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d'Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201 Reus, Spain
| | - J Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d'Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201 Reus, Spain
| | - D Gramaje
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC)-University of La Rioja-Government of La Rioja, Logroño 26007, Spain
| | - M Grube
- Institut für Biologie, Karl-Franzens-Universität Graz, Holteigasse 6, 8010 Graz, Austria
| | - V K Gupta
- Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.,Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - V Guarnaccia
- Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - R Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Y Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - K D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - R S Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - R Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
| | - Ž Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ 08077, USA
| | - L Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P. Bag X20 Hatfield, Pretoria 0002, South Africa
| | - S C Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch 7599, Western Cape, South Africa
| | - L Lombard
- Dutch General Inspection Service for agricultural seeds and seed potatoes (NAK), Randweg 14, 8304 AS, Emmeloord, The Netherlands
| | - S S N Maharachchikumbura
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People's Republic of China
| | - G Polizzi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - K C Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Group, Agharkar Research Institute, Pune, Maharashtra 411 004, India
| | - C Salgado-Salazar
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Bldg. 010A, Rm. 212, BARC-West, 10300 Baltimore Ave. Beltsville, MD 20705, USA
| | - Q-J Shang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People's Republic of China
| | - R G Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba 4350, Queensland, Australia
| | - R C Summerbell
- Sporometrics, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - G Y Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - W J Swart
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Y P Tan
- Centre for Crop Health, University of Southern Queensland, Toowoomba 4350, Queensland, Australia.,Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, Queensland 4102, Australia
| | - A Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125 Torino, Italy
| | - J W Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - R Zare
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - C D González
- Lab. Salud de Bosques, Fac. de Ciencias Forestales y RRNN, Universidad Austral de Chile, Chile
| | - T Iturriaga
- Curator, Cornell University Plant Pathology Herbarium, Ithaca, NY, USA
| | - O Savary
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - M Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - E Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - J-L Jany
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - C Liu
- College of Life Sciences, Yangtze University, Jingzhou, Hubei 434025, China
| | - Z-Q Zeng
- College of Life Sciences, Yangtze University, Jingzhou, Hubei 434025, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - W-Y Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Z-H Yu
- College of Life Sciences, Yangtze University, Jingzhou, Hubei 434025, China
| | - M Thines
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
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12
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Wassermann B, Abdelfattah A, Müller H, Korsten L, Berg G. The microbiome and resistome of apple fruits alter in the post-harvest period. Environ Microbiome 2022; 17:10. [PMID: 35256002 PMCID: PMC8900306 DOI: 10.1186/s40793-022-00402-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/06/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing. RESULTS All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing. CONCLUSION Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, Republic of South Africa
- DSI-NRF Centre of Excellence in Food Security, Pretoria, Republic of South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, 14476 Potsdam OT Golm, Germany
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13
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Savary S, Waddington S, Akter S, Almekinders CJM, Harris J, Korsten L, Rötter RP, Van den Broeck G. Revisiting food security in 2021: an overview of the past year. Food Secur 2022; 14:1-7. [PMID: 35529169 PMCID: PMC9061970 DOI: 10.1007/s12571-022-01266-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Articles published in Food Security in 2021 are reviewed, showing a wide range of topics covered. Many articles are directly linked with "food" and associated terms such as "nutritive", "nutrition", "dietary", and "health". Another important group is linked with (food) "production" and a range of connected terms including: "irrigation", "cultivated", "organic", "varieties", "crop", "vegetable", and "land". A third group of terms refers to the scales at which food security is considered: "household", "farmer", "farm", "smallholder", "community", "nation" and "region". A few themes of Food Security are considered: (1) food supply and demand, food prices, and global trade; (2) food security in households; (3) food production; (4) value chains and food systems; (5) the evolution of the concept of food security; and (6) global nutrition. In a last section, perspectives for Food Security are discussed along four lines of thoughts: the level of inter-disciplinary research published in Food Security; the importance of the Social Sciences for food security as a collective good underpinned by other collective goods within food systems; the balance between the Global South and the Global North in Food Security; and a warning that urgent global challenges that vitally interact with food security may be left unattended as a result of the current public health emergency.
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Affiliation(s)
- Serge Savary
- Editor-in-Chief, Food Security, INRAE, Auzeville, France
| | | | - Sonia Akter
- Senior Editor, Lee Kuan Yew School of Public Policy, National University of Singapore, Food Security, Bukit Timah, Singapore
| | - Conny J. M. Almekinders
- Senior Editor, Knowledge, Technology and Innovation, WUR, Food Security, Wageningen, The Netherlands
| | - Jody Harris
- Senior Editor, Thailand and Institute of Development Studies, Food Security, World Vegetable Center, Chiang Mai, UK
| | - Lise Korsten
- Senior Editor, Food Security, Department of Science and Technology/National Research Foundation, Centre of Excellence Food Security at the University of Pretoria, Pretoria, South Africa
| | - Reimund P. Rötter
- Senior Editor, Food Security, Chair, Tropical Plant Production and Agrosystems Modelling (TROPAGS), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Goedele Van den Broeck
- Senior Editor, Food Security, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
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14
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Ratshilingano MT, du Plessis EM, Duvenage S, Korsten L. Characterization of Multidrug-Resistant Escherichia coli Isolated from Two Commercial Lettuce and Spinach Supply Chains. J Food Prot 2022; 85:122-132. [PMID: 34324673 DOI: 10.4315/jfp-21-125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/24/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Leafy green vegetables have increasingly been reported as a reservoir of multidrug-resistant pathogenic Enterobacteriaceae, with Shiga toxin-producing Escherichia coli frequently implicated in disease outbreaks worldwide. This study examined the presence and characteristics of antibiotic resistance, diarrheagenic virulence genes, and phylogenetic groupings of E. coli isolates (n = 51) from commercially produced lettuce and spinach from farms, through processing, and at the point of sale. Multidrug resistance was observed in 33 (64.7%) of the 51 E. coli isolates, with 35.7% (10 of 28) being generic and 100% (23 of 23) being extended-spectrum β-lactamase/AmpC producing. Resistance of E. coli isolates was observed against neomycin (51 of 51, 100%), ampicillin (36 of 51, 70.6%), amoxicillin (35 of 51, 68.6%), tetracycline (23 of 51, 45%), trimethoprim-sulfamethoxazole (22 of 51, 43%), chloramphenicol (13 of 51, 25.5%), Augmentin (6 of 51, 11.8%), and gentamicin (4 of 51, 7.8%), with 100% (51 of 51) susceptibility to imipenem. Virulence gene eae was detected in two E. coli isolates from irrigation water sources only, whereas none of the other virulence genes for which we tested were detected. Most of the E. coli strains belonged to phylogenetic group B2 (25.5%; n = 13), B1 (19.6%; n = 10), and A (17.6%; n = 9), with D (5.9%; n = 3) less distributed. Although diarrheagenic E. coli was not detected, antibiotic resistance in E. coli prevalent in the supply chain was evident. In addition, a clear link between E. coli isolates from irrigation water sources and leafy green vegetables through DNA fingerprinting was established, indicating the potential transfer of E. coli from irrigation water to minimally processed leafy green vegetables. HIGHLIGHTS
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Affiliation(s)
- Muneiwa T Ratshilingano
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
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15
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Duvenage S, Rossouw W, Villamizar-Rodríguez G, du Plessis EM, Korsten L. Antibiotic resistance profiles of Staphylococcus spp. from white button mushrooms and handlers. S AFR J SCI 2021. [DOI: 10.17159/sajs.2021/8667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The presence of Staphylococcus spp. has increasingly been reported in food products and poses a public health threat. The aim of this study was to determine the diversity of Staphylococcus spp. and the antibiotic resistance profiles of isolates obtained from freshly harvested and packed ready-to-eat mushrooms (n=432) and handlers’ hands (n=150). A total of 56 Staphylococcus isolates [46.4% (n=26) from hands and 53.6% (n=30) from mushrooms] were recovered belonging to 10 species. Staphylococcus succinus isolates (n=21) were the most prevalent, of which 52.4% came from mushrooms and 47.6% from hands. This was followed by S. equorum isolates [n=12; 91.7% (n=11) from mushrooms and 8.3% (n=1) from hands] and S. saprophyticus [n=9; 66.7% (n=6) from mushrooms and 33.3% (n=3) from hands]. Six isolates that were characterised as multidrug resistant were isolated from hands of handlers. Most (83.9%; n=47) of the 56 isolates were resistant to penicillin [53.2% (n=25) from mushrooms and 46.8% (n=22) from hands] and 14.3% (n=8) were resistant to cephalosporin classes [25% (n=2) from mushrooms and 75% (n=6) from hands], both of which are used to treat staphylococcal infections. Antibiotic resistance genes blaZ [25.0% (n=14) of all isolates of which 71.4% (n=10) were from hands and 28.57% (n=4) from mushrooms], tetL and tetK [both 1.8% (n=1) from hands], mecA [5.4% (n=3) from hands] and ermA [1.8% (n=1) from mushrooms] were detected from the 56 isolates. Only two (25.0%) of the eight methicillin-resistant staphylococci harboured the mecA gene, while only 11 (23%) of the 47 penicillin-resistant isolates harboured the blaZ gene [36.4% (n=4) from mushrooms and 63.6% (n=7) from hands]. Our results demonstrate that food handlers and harvested and packed ready-to-eat mushrooms could be a source of diverse Staphylococcus spp. that exhibit antimicrobial resistance. Clinically relevant S. aureus was only detected on one handler’s hand; however, the isolate was not multidrug resistant. The presence of diverse Staphylococcus spp. on mushrooms and the hands of handlers is a potential public health concern due to their potential to cause opportunistic infections.
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Affiliation(s)
- Stacey Duvenage
- DSI–NRF Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria
| | - Werner Rossouw
- DSI–NRF Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria
| | - Germán Villamizar-Rodríguez
- DSI–NRF Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria
| | - Erika M. du Plessis
- DSI–NRF Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria
| | - Lise Korsten
- DSI–NRF Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria
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16
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Richter L, du Plessis EM, Duvenage S, Korsten L. Microbiological safety of spinach throughout commercial supply chains in Gauteng Province, South Africa and characterization of isolated multidrug-resistant Escherichia coli. J Appl Microbiol 2021; 132:2389-2409. [PMID: 34767685 DOI: 10.1111/jam.15357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/28/2021] [Accepted: 11/02/2021] [Indexed: 01/02/2023]
Abstract
AIM To investigate the microbiological quality, potential foodborne pathogen presence, and to phenotypically (antimicrobial resistance [AMR] profiles) and genotypically (DNA fingerprints and diarrhoeagenic genes) characterize Escherichia coli isolated throughout spinach production systems from farm-to-sale. METHODS AND RESULTS Samples (n = 288) were collected from two commercial supply chains using either river or borehole irrigation water. E. coli was enumerated throughout the chain where river water was directly used for overhead irrigation at levels between 0.00 and 3.22 log colony forming unit (CFU) g-1 . Following enrichment, isolation and matrix-assisted laser desorption ionization time-of-flight mass spectrometry identification, E. coli was isolated from 22.57% (n = 65/288) of all samples. Salmonella spp. were isolated from 3% (n = 9/288) of river and irrigation water samples on one farm, and no Listeria monocytogenes was detected throughout the study. Of the 80 characterized E. coli isolates, one harboured the stx2 virulence gene, while 43.75% (n = 35) were multidrug resistant. Overall, 26.30% of the multidrug-resistant E. coli isolates were from production scenario one that used river irrigation water, and 17.50% from the second production scenario that used borehole irrigation water. A greater percentage of resistance phenotypes were from water E. coli isolates (52.50%), than isolates from spinach (37.50%). E. coli isolates from spinach and irrigation water clustered together at high similarity values (>90%) using enterobacterial repetitive intergenic consensus-polymerase chan reaction analysis. CONCLUSIONS This study reported the presence of multidrug-resistant environmental E. coli throughout spinach production from farm, during processing and up to retail. Furthermore, the similarity of multi-drug resistant E. coli isolates suggests transfer from irrigation water to spinach in both scenarios, reiterating that irrigation water for vegetables consumed raw, should comply with standardized microbiological safety guidelines. SIGNIFICANCE AND IMPACT OF STUDY Multidrug-resistant E. coli presence throughout spinach production emphasizes the necessity of increased surveillance of AMR in fresh produce and the production environment within a One Health paradigm to develop AMR mitigation strategies.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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17
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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18
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Hinsenveld FJ, Boormans JL, van der Poel HG, van der Schoot DKE, Vis AN, Aben KKH, Arends TJ, Ausems PJ, Baselmans D, Berger C, Berrens A, Bickerstaffe H, Bos SD, Braam M, Buddingh KT, Claus S, Dekker K, van Doeveren T, Einerhand S, Fossion L, van Gennep EJ, van Ginkel N, Palacios LAG, Hermans T, Hobijn MM, van Huystee SH, Jaspers-Valentijn M, Klaver OS, Koldewijn EL, Korsten L, Lenting A, Lentjes KJ, Luiting HB, van der Meer S, Nieuwenhuijzen JA, Noordzij MA, Nooter RI, Notenboom C, Oomen R, van Roermund J, de Rooij J, Roshani H, Schrier BP, van der Slot MA, Somford DM, Stelwagen PJ, Stroux A, van der West A, Wijsman BP, Windt W, van Zanten P, van Beek SC. Intermediate-term survival of robot-assisted versus open radical cystectomy for muscle-invasive and high-risk non-muscle invasive bladder cancer in The Netherlands. Urol Oncol 2021; 40:60.e1-60.e9. [PMID: 34303597 DOI: 10.1016/j.urolonc.2021.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/31/2021] [Accepted: 06/21/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND Radical cystectomy with pelvic lymph node dissection is the recommended treatment in non-metastatic muscle-invasive bladder cancer (MIBC). In randomised trials, robot-assisted radical cystectomy (RARC) showed non-inferior short-term oncological outcomes compared with open radical cystectomy (ORC). Data on intermediate and long-term oncological outcomes of RARC are limited. OBJECTIVE To assess the intermediate-term overall survival (OS) and recurrence-free survival (RFS) of patients with MIBC and high-risk non-MIBC (NMIBC) who underwent ORC versus RARC in clinical practice. METHODS AND MATERIALS A nationwide retrospective study in 19 Dutch hospitals including patients with MIBC and high-risk NMIBC treated by ORC (n = 1086) or RARC (n = 386) between January 1, 2012 and December 31, 2015. Primary and secondary outcome measures were median OS and RFS, respectively. Survival outcomes were estimated using Kaplan-Meier curves. A multivariable Cox regression model was developed to adjust for possible confounders and to assess prognostic factors for survival including clinical variables, clinical and pathological disease stage, neoadjuvant therapy and surgical margin status. RESULTS The median follow-up was 5.1 years (95% confidence interval ([95%CI] 5.0-5.2). The median OS after ORC was 5.0 years (95%CI 4.3-5.6) versus 5.8 years after RARC (95%CI 5.1-6.5). The median RFS was 3.8 years (95%CI 3.1-4.5) after ORC versus 5.0 years after RARC (95%CI 3.9-6.0). After multivariable adjustment, the hazard ratio for OS was 1.00 (95%CI 0.84-1.20) and for RFS 1.08 (95%CI 0.91-1.27) of ORC versus RARC. Patients who underwent ORC were older, had higher preoperative serum creatinine levels and more advanced clinical and pathological disease stage. CONCLUSION ORC and RARC resulted in similar intermediate-term OS and RFS in a cohort of almost 1500 MIBC and high-risk NMIBC.
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Affiliation(s)
- Florentien J Hinsenveld
- Department of Urology, Amsterdam University Medical Centres location Vrije University Medical Centre, Amsterdam, The Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands.
| | - Henk G van der Poel
- Department of Urology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - André N Vis
- Department of Urology, Amsterdam University Medical Centres location Vrije University Medical Centre, Amsterdam, The Netherlands
| | - Katja K H Aben
- Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - T J Arends
- Department of Urology, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - P J Ausems
- Department of Urology, HagaZiekenuis, Den Haag, The Netherlands
| | - D Baselmans
- Department of Urology, Máxima Medical Centre, Veldhoven, The Netherlands
| | - Cpam Berger
- Department of Urology, Haaglanden Medical Centre, Den Haag, The Netherlands
| | - A Berrens
- Department of Urology, Franciscus Hospital, Rotterdam, The Netherlands
| | - H Bickerstaffe
- Department of Urology, Bravis Hospital, Bergen op Zoom, Roosendaal, The Netherlands
| | - S D Bos
- Department of Urology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - M Braam
- Department of Urology, Martini Hospital, Groningen, The Netherlands
| | - K T Buddingh
- Department of Urology, HagaZiekenuis, Den Haag, The Netherlands
| | - S Claus
- Department of Urology, Catharina Hospital, Eindhoven, The Netherlands
| | - K Dekker
- Department of Urology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - T van Doeveren
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Smh Einerhand
- Department of Urology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lmcl Fossion
- Department of Urology, Máxima Medical Centre, Veldhoven, The Netherlands
| | - E J van Gennep
- Department of Urology, Leiden University Medical Centre, Leiden, The Netherlands
| | - N van Ginkel
- Department of Urology, Spaarne Gasthuis, Haarlem, Hoofddorp, The Netherlands
| | | | - Tjn Hermans
- Department of Urology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - M M Hobijn
- Department of Urology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - S H van Huystee
- Department of Urology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - M Jaspers-Valentijn
- Department of Urology, Bravis Hospital, Bergen op Zoom, Roosendaal, The Netherlands
| | - O S Klaver
- Department of Urology, Maasstad Hospital, Rotterdam, The Netherlands
| | - E L Koldewijn
- Department of Urology, Catharina Hospital, Eindhoven, The Netherlands
| | - L Korsten
- Department of Urology, Elisabeth TweeSteden Hospital, Tilburg, The Netherland
| | - A Lenting
- Department of Urology, Franciscus Hospital, Rotterdam, The Netherlands
| | - K J Lentjes
- Department of Urology, Leiden University Medical Centre, Leiden, The Netherlands
| | - H B Luiting
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - S van der Meer
- Department of Urology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - J A Nieuwenhuijzen
- Department of Urology, Amsterdam University Medical Centres location Vrije University Medical Centre, Amsterdam, The Netherlands
| | - M A Noordzij
- Department of Urology, Spaarne Gasthuis, Haarlem, Hoofddorp, The Netherlands
| | - R I Nooter
- Department of Urology, Franciscus Hospital, Rotterdam, The Netherlands
| | - Caw Notenboom
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Rja Oomen
- Department of Urology, Elisabeth TweeSteden Hospital, Tilburg, The Netherland
| | - Jgh van Roermund
- Department of Urology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - J de Rooij
- Department of Urology, Máxima Medical Centre, Veldhoven, The Netherlands
| | - H Roshani
- Department of Urology, HagaZiekenuis, Den Haag, The Netherlands
| | - B P Schrier
- Department of Urology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - M A van der Slot
- Department of Urology, Maasstad Hospital, Rotterdam, The Netherlands
| | - D M Somford
- Department of Urology, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - P J Stelwagen
- Department of Urology, Amsterdam University Medical Centres location Vrije University Medical Centre, Amsterdam, The Netherlands
| | - Ama Stroux
- Department of Urology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - A van der West
- Department of Urology, Spaarne Gasthuis, Haarlem, Hoofddorp, The Netherlands
| | - B P Wijsman
- Department of Urology, Elisabeth TweeSteden Hospital, Tilburg, The Netherland
| | - Wakm Windt
- Department of Urology, Martini Hospital, Groningen, The Netherlands
| | - P van Zanten
- Department of Urology, HagaZiekenuis, Den Haag, The Netherlands
| | - Sytse C van Beek
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
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19
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Loots M, Chidamba L, Korsten L. Microbial Load and Prevalence of Escherichia coli and Salmonella spp. in Macadamia Nut Production Systems. J Food Prot 2021; 84:1088-1096. [PMID: 33508076 DOI: 10.4315/jfp-20-238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022]
Abstract
ABSTRACT This study evaluated the potential impact of environmental factors and harvesting practices on the microbial load of macadamia nuts. Three farms located in primary macadamia nut production regions, the Mbombela (A), Barberton (B) and White River (C) areas in Mpumalanga Province, South Africa, were sampled over a 2-year period. A total of 264 irrigation water (54), soil (30), and macadamia nut (180) samples were collected and evaluated for microbial load. All water samples had mean Escherichia coli loads below 1,000 MPN/100 mL, which is the standard regulatory requirement for agricultural water considered fit for irrigation in South Africa. Mean total aerobic plate counts of nut-in-husk on-tree samples (3.91 log CFU/g; n = 60) were higher after harvesting (5.98 log CFU/g; n = 60) but were lower after dehusking (to 4.89 log CFU/g; n = 60) on nut-in-shell samples. Salmonella spp. were only detected in water samples from farm B (67%; n = 18) and farm C (15%; n = 18). Neither Listeria monocytogenes nor Salmonella spp. were detected in the soil samples. E. coli was only detected in 20% (n = 10) of soil samples collected from two farms (farms A and B). None of the E. coli isolated in this study was positive for the eae, stx1, and stx2 enterohemorrhagic E. coli virulence genes. This study provides basic data that can be used in the development of macadamia nut-specific hazard assessment tools within primary production environments. HIGHLIGHTS
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Affiliation(s)
- Maike Loots
- Department of Plant and Soil Sciences, University of Pretoria, Lynnwood Road, Pretoria 0001, South Africa, and Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - Lizyben Chidamba
- Department of Plant and Soil Sciences, University of Pretoria, Lynnwood Road, Pretoria 0001, South Africa, and Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Lynnwood Road, Pretoria 0001, South Africa, and Private Bag X20, Hatfield, Pretoria 0028, South Africa
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20
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Crous P, Lombard L, Sandoval-Denis M, Seifert K, Schroers HJ, Chaverri P, Gené J, Guarro J, Hirooka Y, Bensch K, Kema G, Lamprecht S, Cai L, Rossman A, Stadler M, Summerbell R, Taylor J, Ploch S, Visagie C, Yilmaz N, Frisvad J, Abdel-Azeem A, Abdollahzadeh J, Abdolrasouli A, Akulov A, Alberts J, Araújo J, Ariyawansa H, Bakhshi M, Bendiksby M, Ben Hadj Amor A, Bezerra J, Boekhout T, Câmara M, Carbia M, Cardinali G, Castañeda-Ruiz R, Celis A, Chaturvedi V, Collemare J, Croll D, Damm U, Decock C, de Vries R, Ezekiel C, Fan X, Fernández N, Gaya E, González C, Gramaje D, Groenewald J, Grube M, Guevara-Suarez M, Gupta V, Guarnaccia V, Haddaji A, Hagen F, Haelewaters D, Hansen K, Hashimoto A, Hernández-Restrepo M, Houbraken J, Hubka V, Hyde K, Iturriaga T, Jeewon R, Johnston P, Jurjević Ž, Karalti İ, Korsten L, Kuramae E, Kušan I, Labuda R, Lawrence D, Lee H, Lechat C, Li H, Litovka Y, Maharachchikumbura S, Marin-Felix Y, Matio Kemkuignou B, Matočec N, McTaggart A, Mlčoch P, Mugnai L, Nakashima C, Nilsson R, Noumeur S, Pavlov I, Peralta M, Phillips A, Pitt J, Polizzi G, Quaedvlieg W, Rajeshkumar K, Restrepo S, Rhaiem A, Robert J, Robert V, Rodrigues A, Salgado-Salazar C, Samson R, Santos A, Shivas R, Souza-Motta C, Sun G, Swart W, Szoke S, Tan Y, Taylor J, Taylor P, Tiago P, Váczy K, van de Wiele N, van der Merwe N, Verkley G, Vieira W, Vizzini A, Weir B, Wijayawardene N, Xia J, Yáñez-Morales M, Yurkov A, Zamora J, Zare R, Zhang C, Thines M. Fusarium: more than a node or a foot-shaped basal cell. Stud Mycol 2021; 98:100116. [PMID: 34466168 PMCID: PMC8379525 DOI: 10.1016/j.simyco.2021.100116] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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Key Words
- Apiognomonia platani (Lév.) L. Lombard
- Atractium ciliatum Link
- Atractium pallidum Bonord.
- Calloria tremelloides (Grev.) L. Lombard
- Cephalosporium sacchari E.J. Butler
- Cosmosporella cavisperma (Corda) Sand.-Den., L. Lombard & Crous
- Cylindrodendrum orthosporum (Sacc. & P. Syd.) L. Lombard
- Dialonectria volutella (Ellis & Everh.) L. Lombard & Sand.-Den.
- Fusarium aeruginosum Delacr.
- Fusarium agaricorum Sarrazin
- Fusarium albidoviolaceum Dasz.
- Fusarium aleyrodis Petch
- Fusarium amentorum Lacroix
- Fusarium annuum Leonian
- Fusarium arcuatum Berk. & M.A. Curtis
- Fusarium aridum O.A. Pratt
- Fusarium armeniacum (G.A. Forbes et al.) L.W. Burgess & Summerell
- Fusarium arthrosporioides Sherb.
- Fusarium asparagi Delacr.
- Fusarium batatas Wollenw.
- Fusarium biforme Sherb.
- Fusarium buharicum Jacz. ex Babajan & Teterevn.-Babajan
- Fusarium cactacearum Pasin. & Buzz.-Trav.
- Fusarium cacti-maxonii Pasin. & Buzz.-Trav.
- Fusarium caudatum Wollenw.
- Fusarium cavispermum Corda
- Fusarium cepae Hanzawa
- Fusarium cesatii Rabenh.
- Fusarium citriforme Jamal.
- Fusarium citrinum Wollenw.
- Fusarium citrulli Taubenh.
- Fusarium clavatum Sherb.
- Fusarium coccinellum Kalchbr.
- Fusarium cromyophthoron Sideris
- Fusarium cucurbitae Taubenh.
- Fusarium cuneiforme Sherb.
- Fusarium delacroixii Sacc.
- Fusarium dimerum var. nectrioides Wollenw.
- Fusarium echinatum Sand.-Den. & G.J. Marais
- Fusarium epicoccum McAlpine
- Fusarium eucheliae Sartory, R. Sartory & J. Mey.
- Fusarium fissum Peyl
- Fusarium flocciferum Corda
- Fusarium gemmiperda Aderh.
- Fusarium genevense Dasz.
- Fusarium graminearum Schwabe
- Fusarium graminum Corda
- Fusarium heterosporioides Fautrey
- Fusarium heterosporum Nees & T. Nees
- Fusarium idahoanum O.A. Pratt
- Fusarium juruanum Henn.
- Fusarium lanceolatum O.A. Pratt
- Fusarium lateritium Nees
- Fusarium loncheceras Sideris
- Fusarium longipes Wollenw. & Reinking
- Fusarium lyarnte J.L. Walsh, Sangal., L.W. Burgess, E.C.Y. Liew & Summerell
- Fusarium malvacearum Taubenh.
- Fusarium martii f. phaseoli Burkh.
- Fusarium muentzii Delacr.
- Fusarium nigrum O.A. Pratt
- Fusarium oxysporum var. asclerotium Sherb.
- Fusarium palczewskii Jacz.
- Fusarium palustre W.H. Elmer & Marra
- Fusarium polymorphum Matr.
- Fusarium poolense Taubenh.
- Fusarium prieskaense G.J. Marais & Sand.-Den.
- Fusarium prunorum McAlpine
- Fusarium pusillum Wollenw.
- Fusarium putrefaciens Osterw.
- Fusarium redolens Wollenw.
- Fusarium reticulatum Mont.
- Fusarium rhizochromatistes Sideris
- Fusarium rhizophilum Corda
- Fusarium rhodellum McAlpine
- Fusarium roesleri Thüm.
- Fusarium rostratum Appel & Wollenw.
- Fusarium rubiginosum Appel & Wollenw.
- Fusarium rubrum Parav.
- Fusarium samoense Gehrm.
- Fusarium scirpi Lambotte & Fautrey
- Fusarium secalis Jacz.
- Fusarium spinaciae Hungerf.
- Fusarium sporotrichioides Sherb.
- Fusarium stercoris Fuckel
- Fusarium stilboides Wollenw.
- Fusarium stillatum De Not. ex Sacc.
- Fusarium sublunatum Reinking
- Fusarium succisae Schröt. ex Sacc.
- Fusarium tabacivorum Delacr.
- Fusarium trichothecioides Wollenw.
- Fusarium tritici Liebman
- Fusarium tuberivorum Wilcox & G.K. Link
- Fusarium tumidum var. humi Reinking
- Fusarium ustilaginis Kellerm. & Swingle
- Fusarium viticola Thüm.
- Fusarium werrikimbe J.L. Walsh, L.W. Burgess, E.C.Y. Liew & B.A. Summerell
- Fusarium willkommii Lindau
- Fusarium xylarioides Steyaert
- Fusarium zygopetali Delacr.
- Fusicolla meniscoidea L. Lombard & Sand.-Den.
- Fusicolla quarantenae J.D.P. Bezerra, Sand.-Den., Crous & Souza-Motta
- Fusicolla sporellula Sand.-Den. & L. Lombard
- Fusisporium andropogonis Cooke ex Thüm.
- Fusisporium anthophilum A. Braun
- Fusisporium arundinis Corda
- Fusisporium avenaceum Fr.
- Fusisporium clypeaster Corda
- Fusisporium culmorum Wm.G. Sm.
- Fusisporium didymum Harting
- Fusisporium elasticae Thüm.
- Fusisporium episphaericum Cooke & Ellis
- Fusisporium flavidum Bonord.
- Fusisporium hordei Wm.G. Sm.
- Fusisporium incarnatum Roberge ex Desm.
- Fusisporium lolii Wm.G. Sm.
- Fusisporium pandani Corda
- Gibberella phyllostachydicola W. Yamam.
- Hymenella aurea (Corda) L. Lombard
- Hymenella spermogoniopsis (Jul. Müll.) L. Lombard & Sand.-Den.
- Luteonectria Sand.-Den., L. Lombard, Schroers & Rossman
- Luteonectria albida (Rossman) Sand.-Den. & L. Lombard
- Luteonectria nematophila (Nirenberg & Hagedorn) Sand.-Den. & L. Lombard
- Macroconia bulbipes Crous & Sand.-Den.
- Macroconia phlogioides Sand.-Den. & Crous
- Menispora penicillata Harz
- Multi-gene phylogeny
- Mycotoxins
- Nectriaceae
- Neocosmospora
- Neocosmospora epipeda Quaedvl. & Sand.-Den.
- Neocosmospora floridana (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora merkxiana Quaedvl. & Sand.-Den.
- Neocosmospora neerlandica Crous & Sand.-Den.
- Neocosmospora nelsonii Crous & Sand.-Den.
- Neocosmospora obliquiseptata (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora pseudopisi Sand.-Den. & L. Lombard
- Neocosmospora rekana (Lynn & Marinc.) L. Lombard & Sand.-Den.
- Neocosmospora tuaranensis (T. Aoki et al.) L. Lombard & Sand.-Den.
- Nothofusarium Crous, Sand.-Den. & L. Lombard
- Nothofusarium devonianum L. Lombard, Crous & Sand.-Den.
- Novel taxa
- Pathogen
- Scolecofusarium L. Lombard, Sand.-Den. & Crous
- Scolecofusarium ciliatum (Link) L. Lombard, Sand.-Den. & Crous
- Selenosporium equiseti Corda
- Selenosporium hippocastani Corda
- Selenosporium sarcochroum Desm
- Selenosporium urticearum Corda.
- Setofusarium (Nirenberg & Samuels) Crous & Sand.-Den.
- Setofusarium setosum (Samuels & Nirenberg) Sand.-Den. & Crous.
- Sphaeria sanguinea var. cicatricum Berk.
- Sporotrichum poae Peck.
- Stylonectria corniculata Gräfenhan, Crous & Sand.-Den.
- Stylonectria hetmanica Akulov, Crous & Sand.-Den.
- Taxonomy
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Affiliation(s)
- P.W. Crous
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - L. Lombard
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - K.A. Seifert
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - H.-J. Schroers
- Plant Protection Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000, Ljubljana, Slovenia
| | - P. Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- Escuela de Biología and Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, Costa Rica
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - J. Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - Y. Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, 184-8584, Japan
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - G.H.J. Kema
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - S.C. Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, Western Cape, South Africa
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - A.Y. Rossman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, 97330, USA
| | - M. Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - J.W. Taylor
- Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA, 94720-3102, USA
| | - S. Ploch
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - A.M. Abdel-Azeem
- Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - J. Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - A. Abdolrasouli
- Department of Medical Microbiology, King's College Hospital, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - A. Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022, Kharkiv, Ukraine
| | - J.F. Alberts
- Department of Food Science and Technology, Cape Peninsula University of Technology, P.O. Box 1906, Bellville, 7535, South Africa
| | - J.P.M. Araújo
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - H.A. Ariyawansa
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 106, Taiwan, ROC
| | - M. Bakhshi
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - M. Bendiksby
- Natural History Museum, University of Oslo, Norway
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - A. Ben Hadj Amor
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - J.D.P. Bezerra
- Setor de Micologia/Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Rua 235 - s/n – Setor Universitário - CEP: 74605-050, Universidade Federal de Goiás/Federal University of Goiás, Goiânia, Brazil
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M.P.S. Câmara
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - M. Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina – Universidad de la República, Av. A. Navarro 3051, Montevideo, Uruguay
| | - G. Cardinali
- Department of Pharmaceutical Science, University of Perugia, Via Borgo 20 Giugno, 74 Perugia, Italy
| | - R.F. Castañeda-Ruiz
- Instituto de Investigaciones Fundamentales en Agricultura Tropical Alejandro de Humboldt (INIFAT), Académico Titular de la Academia de Ciencias de, Cuba
| | - A. Celis
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, 111711, Colombia
| | - V. Chaturvedi
- Mycology Laboratory, New York State Department of Health Wadsworth Center, Albany, NY, USA
| | - J. Collemare
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, CH-2000, Neuchatel, Switzerland
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806, Görlitz, Germany
| | - C.A. Decock
- Mycothèque de l'Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute – ELIM – Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348, Louvain-la-Neuve, Belgium
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - X.L. Fan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - N.B. Fernández
- Laboratorio de Micología Clínica, Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - E. Gaya
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - C.D. González
- Laboratorio de Salud de Bosques y Ecosistemas, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, casilla 567, Valdivia, Chile
| | - D. Gramaje
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC)-University of La Rioja-Government of La Rioja, Logroño, 26007, Spain
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Grube
- Institut für Biologie, Karl-Franzens-Universität Graz, Holteigasse 6, 8010, Graz, Austria
| | - M. Guevara-Suarez
- Applied genomics research group, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - V.K. Gupta
- Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - V. Guarnaccia
- Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, 10095, Grugliasco, TO, Italy
| | | | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, 35 K.L. Ledeganckstraat, 9000, Ghent, Belgium
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - K. Hansen
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - A. Hashimoto
- Microbe Division/Japan Collection of Microorganisms RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - K.D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chaing Rai, 57100, Thailand
| | - T. Iturriaga
- Cornell University, 334 Plant Science Building, Ithaca, NY, 14850, USA
| | - R. Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
| | - P.R. Johnston
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Ž. Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ, 08077, USA
| | - İ. Karalti
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Yeditepe University, Turkey
| | - L. Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P. Bag X20 Hatfield, Pretoria, 0002, South Africa
| | - E.E. Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - I. Kušan
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - R. Labuda
- University of Veterinary Medicine, Vienna (VetMed), Institute of Food Safety, Food Technology and Veterinary Public Health, Veterinaerplatz 1, 1210 Vienna and BiMM – Bioactive Microbial Metabolites group, 3430 Tulln a.d. Donau, Austria
| | - D.P. Lawrence
- University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - H.B. Lee
- Department of Agricultural Biological Chemistry, College of Agriculture & Life Sciences, Chonnam National University, Yongbong-Dong 300, Buk-Gu, Gwangju, 61186, South Korea
| | - C. Lechat
- Ascofrance, 64 route de Chizé, 79360, Villiers-en-Bois, France
| | - H.Y. Li
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Y.A. Litovka
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - S.S.N. Maharachchikumbura
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Y. Marin-Felix
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - B. Matio Kemkuignou
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - N. Matočec
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - A.R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, G.P.O. Box 267, Brisbane, 4001, Australia
| | - P. Mlčoch
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - L. Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology section, University of Florence, P.le delle Cascine 28, 50144, Firenze, Italy
| | - C. Nakashima
- Graduate school of Bioresources, Mie University, Kurima-machiya 1577, Tsu, Mie, 514-8507, Japan
| | - R.H. Nilsson
- Gothenburg Global Biodiversity Center at the Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
| | - S.R. Noumeur
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences, University of Batna 2, Batna, 05000, Algeria
| | - I.N. Pavlov
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - M.P. Peralta
- Laboratorio de Micodiversidad y Micoprospección, PROIMI-CONICET, Av. Belgrano y Pje. Caseros, Argentina
| | - A.J.L. Phillips
- Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Campo Grande, 1749-016, Lisbon, Portugal
| | - J.I. Pitt
- Microbial Screening Technologies, 28 Percival Rd, Smithfield, NSW, 2164, Australia
| | - G. Polizzi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - W. Quaedvlieg
- Phytopathology, Van Zanten Breeding B.V., Lavendelweg 15, 1435 EW, Rijsenhout, the Netherlands
| | - K.C. Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Group, Agharkar Research Institute, Pune, Maharashtra, 411 004, India
| | - S. Restrepo
- Laboratory of Mycology and Phytopathology – (LAMFU), Department of Chemical and Food Engineering, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - A. Rhaiem
- Plant Pathology and Population Genetics, Laboratory of Microorganisms, National Gene Bank, Tunisia
| | | | - V. Robert
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - C. Salgado-Salazar
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Bldg. 010A, Rm. 212, BARC-West, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.C.S. Santos
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - R.G. Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
| | - C.M. Souza-Motta
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - G.Y. Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - W.J. Swart
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | | | - Y.P. Tan
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, Queensland, 4102, Australia
| | - J.E. Taylor
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom
| | - P.W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - P.V. Tiago
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - K.Z. Váczy
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300, Eger, Hungary
| | | | - N.A. van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - W.A.S. Vieira
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - A. Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125, Torino, Italy
| | - B.S. Weir
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - N.N. Wijayawardene
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - J.W. Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - M.J. Yáñez-Morales
- Fitosanidad, Colegio de Postgraduados-Campus Montecillo, Montecillo-Texcoco, 56230 Edo. de Mexico, Mexico
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36, Uppsala, Sweden
| | - R. Zare
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - C.L. Zhang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
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Richter L, Plessis ED, Duvenage S, Korsten L. High prevalence of multidrug resistant Escherichia coli isolated from fresh vegetables sold by selected formal and informal traders in the most densely populated Province of South Africa. J Food Sci 2020; 86:161-168. [PMID: 33294974 DOI: 10.1111/1750-3841.15534] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 01/26/2023]
Abstract
Contaminated fresh produce has increasingly been implicated in foodborne disease outbreaks. As microbiological safety surveillance in South Africa is limited, a total of 545 vegetable samples (spinach, tomato, lettuce, cucumber, and green beans) were purchased from retailers, street traders, trolley vendors and farmers' markets. Escherichia coli, coliforms and Enterobacteriaceae were enumerated and the prevalence of Escherichia coli, Salmonella spp. and Listeria monocytogenes determined. E. coli isolates were characterized phenotypically (antibiotic resistance) and genotypically (diarrheagenic virulence genes). Coliforms, E. coli and Enterobacteriaceae counts were mostly not significantly different between formal and informal markets, with exceptions noted on occasion. When compared to international standards, 90% to 98% tomatoes, 70% to 94% spinach, 82% cucumbers, 93% lettuce, and 80% green bean samples, had satisfactory (≤ 100 CFU/g) E. coli counts. Of the 545 vegetable samples analyzed, 14.86% (n = 81) harbored E. coli, predominantly from leafy green vegetables. Virulence genes (lt, st, bfpA, eagg, eaeA, stx1, stx2, and ipaH) were not detected in the E. coli isolates (n = 67) characterized, however 40.30% were multidrug-resistant. Resistance to aminoglycosides (neomycin, 73.13%; gentamycin, < 10%), penicillins (ampicillin, 38.81%; amoxicillin, 41.79%; augmentin, < 10%), sulfonamides (cotrimoxazole, 22.39%), tetracycline (19.4%), chloramphenicol (11.94%), cephalosporins (cefepime, 34.33%), and carbapenemases (imipenem, < 10%) were observed. This study highlights the need for continued surveillance of multidrug resistant foodborne pathogens in fresh produce retailed formally and informally for potential consumer health risks. PRACTICAL APPLICATION: The results indicate that the microbiological quality of different vegetables were similar per product type, regardless of being purchased from formal retailers or informal street traders, trolley vendors or farmers' markets. Although no pathogenic bacteria (diarrheagenic E. coli, Salmonella spp. or L. monocytogenes) were isolated, high levels of multidrug-resistance was observed in the generic E. coli isolates. These findings highlight the importance of microbiological quality surveillance of fresh produce in formal and informal markets, as these products can be a reservoir of multidrug resistant bacteria harboring antibiotic resistance and virulence genes, potentially impacting human health.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, 0001, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Cape Town, South Africa
| | - Erika Du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, 0001, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, 0001, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Cape Town, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, 0001, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Cape Town, South Africa
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22
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Kusstatscher P, Cernava T, Abdelfattah A, Gokul J, Korsten L, Berg G. Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables. FEMS Microbiol Ecol 2020; 96:5857999. [PMID: 32542314 DOI: 10.1093/femsec/fiaa119] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/14/2020] [Indexed: 01/07/2023] Open
Abstract
Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.
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Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Jarishma Gokul
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
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Broekman A, Steyn WJ, Steyn JLP, Bill M, Korsten L. smAvo and smaTo: A fruity odyssey of smart sensor platforms in Southern Africa. HardwareX 2020; 8:e00156. [PMID: 35498247 PMCID: PMC9041179 DOI: 10.1016/j.ohx.2020.e00156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/24/2020] [Accepted: 10/28/2020] [Indexed: 06/14/2023]
Abstract
Avocado and tomato production are key agricultural sectors for many economies including South Africa. The quality of avocadoes and tomatoes that reach consumers is directly dependent on the handling at the postharvest stage. The fruit undergoes an extensive journey, and subsequently stress, comprised of several steps, including harvesting, application of postharvest treatments, packaging and transportation by road and sea to reach the export markets. To date, the quantification of these external stresses on a discrete fruit has not been measured in detail, primarily due to a lack of compatible instrumentation. This paper demonstrates a low cost, stand-alone, open source data acquisition system, termed smAvo and smaTo, that can be introduced effortlessly to monitor agricultural processing facilities and transportation networks. The miniaturised Arduino sensor platform is enclosed within a waterproof enclosure and surrounded by a 3D printed shell manufactured from morphologically compatible materials. The software is customisable to the needs of the research project or individual transportation phases under study, providing both extensive environmental data and high-frequency tri-axis acceleration measurements that are crucial to understanding the dynamic processes that directly affect the final quality of the fruit. Four successful field trials demonstrate the fidelity of both the smAvo and smaTo platforms.
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Affiliation(s)
- André Broekman
- Department of Civil Engineering, University of Pretoria, Pretoria, South Africa
| | - Wynand JvdM Steyn
- Department of Civil Engineering, University of Pretoria, Pretoria, South Africa
| | - Johannes LP Steyn
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, South Africa
| | - Malick Bill
- Department of Plant and Soil Sciences, University of Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, South Africa
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24
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Iwu CD, du Plessis EM, Korsten L, Nontongana N, Okoh AI. Antibiogram Signatures of Some Enterobacteria Recovered from Irrigation Water and Agricultural Soil in two District Municipalities of South Africa. Microorganisms 2020; 8:microorganisms8081206. [PMID: 32784678 PMCID: PMC7463487 DOI: 10.3390/microorganisms8081206] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/15/2022] Open
Abstract
This study was undertaken to evaluate the antibiogram fingerprints of some Enterobacteria recovered from irrigation water and agricultural soil in two District Municipalities of the Eastern Cape Province, South Africa using standard culture-based and molecular methods. The prevalent resistance patterns in the isolates follow the order: Salmonella enterica serovar Typhimurium [tetracycline (92.3%), ampicillin (69.2%)]; Enterobacter cloacae [amoxicillin/clavulanic acid (77.6%), ampicillin (84.5%), cefuroxime (81.0%), nitrofurantoin (81%), and tetracycline (80.3%)]; Klebsiella pneumoniae [amoxicillin/clavulanic acid (80.6%), ampicillin (88.9%), and cefuroxime (61.1%)]; and Klebsiella oxytoca [chloramphenicol (52.4%), amoxicillin/clavulanic acid (61.9%), ampicillin (61.9%), and nitrofurantoin (61.9%)]. Antibiotic resistance genes detected include tetC (86%), sulII (86%), and blaAmpC (29%) in Salmonella enterica serovar Typhimurium., tetA (23%), tetB (23%), tetC (12%), sulI (54%), sulII (54%), catII (71%), blaAmpC (86%), blaTEM (43%), and blaPER (17%) in Enterobacter cloacae., tetA (20%), tetC (20%), tetD (10%), sulI (9%), sulII (18%), FOX (11%) and CIT (11%)-type plasmid-mediated AmpC, blaTEM (11%), and blaSHV (5%) in Klebsiella pneumoniae and blaAmpC (18%) in Klebsiella oxytoca. Our findings document the occurrence of some antibiotic-resistant Enterobacteria in irrigation water and agricultural soil in Amathole and Chris Hani District Municipalities, Eastern Cape Province of South Africa, thus serving as a potential threat to food safety.
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Affiliation(s)
- Chidozie Declan Iwu
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
- Correspondence:
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (E.M.d.P.); (L.K.)
| | - Lise Korsten
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (E.M.d.P.); (L.K.)
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
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Abstract
This opinion article results from a collective analysis by the Editorial Board of Food Security. It is motivated by the ongoing covid-19 global epidemic, but expands to a broader view on the crises that disrupt food systems and threaten food security, locally to globally. Beyond the public health crisis it is causing, the current global pandemic is impacting food systems, locally and globally. Crises such as the present one can, and do, affect the stability of food production. One of the worst fears is the impacts that crises could have on the potential to produce food, that is, on the primary production of food itself, for example, if material and non-material infrastructure on which agriculture depends were to be damaged, weakened, or fall in disarray. Looking beyond the present, and not minimising its importance, the covid-19 crisis may turn out to be the trigger for overdue fundamental transformations of agriculture and the global food system. This is because the global food system does not work well today: the number of hungry people in the world has increased substantially, with the World Food Programme warning of the possibility of a "hunger pandemic". Food also must be nutritious, yet unhealthy diets are a leading cause of death. Deepening crises impoverish the poorest, disrupt food systems, and expand "food deserts". A focus on healthy diets for all is all the more relevant when everyone's immune system must react to infection during a global pandemic. There is also accumulating and compelling evidence that the global food system is pushing the Earth system beyond the boundaries of sustainability. In the past twenty years, the growing demand for food has increasingly been met through the destruction of Earth's natural environment, and much less through progress in agricultural productivity generated by scientific research, as was the case during the two previous decades. There is an urgent need to reduce the environmental footprint of the global food system: if its performances are not improved rapidly, the food system could itself be one main cause for food crises in the near future. The article concludes with a series of recommendations intended for policy makers and science leaders to improve the resilience of the food system, global to local, and in the short, medium and long term.
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Affiliation(s)
- Serge Savary
- UMR AGIR (AGroécologie, Innovations et teRritoires), INRAE, Institut National Polytechnique de Toulouse, INP-EI Purpan, Université de Toulouse, Castanet Tolosan, France
| | - Sonia Akter
- Lee Kuan Yew School of Public Policy, The National University of Singapore, Singapore, Singapore
| | - Conny Almekinders
- Knowledge, Technology and Innovation, Social Sciences, Wageningen University, Hollandseweg 1, 6706 KN Wageningen, The Netherlands
| | | | - Lise Korsten
- Department of Plant and Soil Sciences, Centre of Excellence Food Security, University of Pretoria, Pretoria, 0002 South Africa
| | - Reimund Rötter
- TROPAGS, Department of Crop Sciences, University of Göttingen, Grisebachstr. 6, 37077 Göttingen, Germany
| | | | - Derrill Watson
- Department of Accounting, Finance, and Economics, Tarleton State University, Stephenville, TX 76401 USA
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26
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Iwu CD, Korsten L, Okoh AI. The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health. Microbiologyopen 2020; 9:e1035. [PMID: 32710495 PMCID: PMC7520999 DOI: 10.1002/mbo3.1035] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of antibiotics in the veterinary, agricultural, and medical sectors. This results in the selective pressure for the intrinsic and extrinsic development of the antimicrobial resistance phenomenon, especially within the aquaculture‐animal‐manure‐soil‐water‐plant nexus. The existence of antimicrobial resistance in the environment has been well documented in the literature. However, the possible transmission routes of antimicrobial agents, their resistance genes, and naturally selected antibiotic‐resistant bacteria within and between the various niches of the agricultural environment and humans remain poorly understood. This study, therefore, outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; transmission routes of antimicrobial resistance in the agro‐ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro‐ecosystem; and possible ways to curtail the menace of antimicrobial resistance.
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Affiliation(s)
- Chidozie D Iwu
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
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27
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Kusstatscher P, Cernava T, Abdelfattah A, Gokul J, Korsten L, Berg G. Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables. FEMS Microbiol Ecol 2020. [PMID: 32542314 DOI: 10.1093/femsec/fiaa1119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.
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Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Jarishma Gokul
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
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Kusstatscher P, Cernava T, Abdelfattah A, Gokul J, Korsten L, Berg G. Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables. FEMS Microbiol Ecol 2020. [PMID: 32542314 DOI: 10.1093/femsec/fiaa119/5857999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.
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Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Jarishma Gokul
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
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Richter L, du Plessis EM, Duvenage S, Korsten L. Occurrence, Phenotypic and Molecular Characterization of Extended-Spectrum- and AmpC- β-Lactamase Producing Enterobacteriaceae Isolated From Selected Commercial Spinach Supply Chains in South Africa. Front Microbiol 2020; 11:638. [PMID: 32351477 PMCID: PMC7176360 DOI: 10.3389/fmicb.2020.00638] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase-producing Enterobacteriaceae in health care systems, the environment and fresh produce is a serious concern globally. Production practices, processing and subsequent consumption of contaminated raw fruit and vegetables represent a possible human transmission route. The purpose of this study was to determine the presence of ESBL/AmpC-producing Enterobacteriaceae in complete spinach supply chains and to characterize the isolated strains phenotypically (antimicrobial resistance profiles) and genotypically (ESBL/AmpC genetic determinants, detection of class 1, 2, and 3 integrons). Water, soil, fresh produce, and contact surface samples (n = 288) from two commercial spinach production systems were screened for ESBL/AmpC-producing Enterobacteriaceae. In total, 14.58% (42/288) of the samples were found to be contaminated after selective enrichment, plating onto chromogenic media and matrix-assisted laser desorption ionization time-of-flight mass spectrometry identity confirmation of presumptive ESBL/AmpC isolates. This included 15.28% (11/72) water and 12.12% (16/132) harvested- and processed spinach, while 25% (15/60) retail spinach samples were found to be contaminated with an increase in isolate abundance and diversity in both scenarios. Dominant species identified included Serratia fonticola (45.86%), Escherichia coli (20.83%), and Klebsiella pneumoniae (18.75%). In total, 48 (81.36%) isolates were phenotypically confirmed as ESBL/AmpC-producing Enterobacteriaceae of which 98% showed a MDR phenotype. Genotypic characterization (PCR of ESBL/AmpC resistance genes and integrons) further revealed the domination of the CTX-M Group 1 ESBL type, followed by TEM and SHV; whilst the CIT-type was the only plasmid-mediated AmpC genetic determinant detected. Integrons were detected in 79.17% (n = 38) of the confirmed ESBL/AmpC-producing isolates, of which we highlight the high prevalence of class 3 integrons, detected in 72.92% (n = 35) of the isolates, mostly in S. fonticola. Class 2 integrons were not detected in this study. This is the first report on the prevalence of ESBL/AmpC-producing Enterobacteriaceae isolated throughout commercial spinach production systems harboring class 1 and/or class 3 integrons in Gauteng Province, South Africa. The results add to the global knowledge base regarding the prevalence and characteristics of ESBL/AmpC-producing Enterobacteriaceae in fresh vegetables and the agricultural environment required for future risk analysis.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Technology-National Research Foundation Centre of Excellence in Food Security, Bellville, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Technology-National Research Foundation Centre of Excellence in Food Security, Bellville, South Africa
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de Bruin W, Kritzinger Q, Bornman R, Korsten L. Occurrence, fate and toxic effects of the industrial endocrine disrupter, nonylphenol, on plants - A review. Ecotoxicol Environ Saf 2019; 181:419-427. [PMID: 31220782 DOI: 10.1016/j.ecoenv.2019.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/16/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
Nonylphenol (NP) and its detrimental effects on the environment, humans, wildlife, fish and birds is an increasingly important global research focus. The number of investigations on the toxicity and metabolic fate of NP in plants is however limited. This paper reviews the prevalence and source of NP in plants and the effect it has on its morphological, physiological and ultrastructural status. Fruit and vegetables have been found to contain levels of NP that is twenty-fold exceeding the no observable effect level (NOEL) of freshwater algae. Apart from the potential risk this poses to the health of consumers, it can overburden the plant's natural defence system, leading to growth disorders. Plants exposed to NP show signs of overall growth reduction, changes in organelle structure and oxidative damage. These adverse effects may exacerbate the food security dilemma faced by many countries and impede their progress towards attaining the sustainable development goals.
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Affiliation(s)
- Willeke de Bruin
- Department of Plant and Soil Sciences, Department of Science and Technology and National Research Foundation: Centre of Excellence in Food Security, University of Pretoria, Pretoria, 0002, South Africa
| | - Quenton Kritzinger
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0002, South Africa
| | - Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Private Bag X323, Pretoria, 0001, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, Department of Science and Technology and National Research Foundation: Centre of Excellence in Food Security, University of Pretoria, Pretoria, 0002, South Africa.
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31
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Boatemaa S, Barney M, Drimie S, Harper J, Korsten L, Pereira L. Awakening from the listeriosis crisis: Food safety challenges, practices and governance in the food retail sector in South Africa. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Louw JP, Korsten L. Impact of Postharvest Storage on the Infection and Colonization of Penicillium digitatum and Penicillium expansum on Nectarine. Plant Dis 2019; 103:1584-1594. [PMID: 31025905 DOI: 10.1094/pdis-08-18-1475-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Very few studies have investigated the host-pathogen interaction of Penicillium spp. on nectarine. Penicillium digitatum was identified as pathogenic and highly aggressive on nectarine. A strong association was made with host age/ripeness. This points to a new mechanism or life strategy used by P. digitatum to infect and colonize previously thought nonhosts. The aim of this study was to determine the effect of postharvest storage of nectarine on the infection and colonization of P. digitatum and Penicillium expansum at molecular and physical (firmness and pH) levels. The impact of environmental conditions (cold storage) and pathogen pressure (inoculum load) was also investigated. Although disease incidence was much lower, lesions caused by P. digitatum were similar in size to those caused by P. expansum on freshly harvested nectarine. Disease incidence and lesion diameter significantly increased (larger than P. expansum) on longer stored fruit. Cold storage had the largest effect on P. digitatum. Inoculum load had a meaningful effect on both Penicillium spp. Storage significantly affected pH modulation and gene expression. The pathogens not only decreased but also, increased and maintained (similar to initial pH of the host) pH of infected tissue. The polygalacturonase (PG) gene and creA were upregulated by P. digitatum on 7-day postharvest fruit (other genes were unaffected). It partly explains the larger lesions on older or riper fruit. A different expression profile was observed from P. expansum: strong downregulation in PG and slight upregulation in pacC. Very different life strategies were used by the two Penicillium spp. when infecting nectarine. Unlike what is known on citrus, P. digitatum showed an opportunistic lifestyle that takes advantage of specific host and environmental conditions. It is largely still unclear (gene expression) what specifically triggers the increase in disease incidence (infection) and lesion diameter (colonization) of P. digitatum on older or riper fruit. The differences between in vivo and in vitro studies make it difficult to directly correlate results. Additional research is still needed to differentiate and understand the infection and colonization of these pathogens on the same host.
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Affiliation(s)
- Johannes Petrus Louw
- 1 Department of Plant and Soil Sciences, University of Pretoria, Hillcrest 0083, South Africa
- 2 University of Pretoria, Pretoria 0028, South Africa
| | - Lise Korsten
- 1 Department of Plant and Soil Sciences, University of Pretoria, Hillcrest 0083, South Africa
- 2 University of Pretoria, Pretoria 0028, South Africa
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Richter L, Du Plessis EM, Duvenage S, Korsten L. Occurrence, Identification, and Antimicrobial Resistance Profiles of Extended-Spectrum and AmpC β-Lactamase-Producing Enterobacteriaceae from Fresh Vegetables Retailed in Gauteng Province, South Africa. Foodborne Pathog Dis 2019; 16:421-427. [PMID: 30785775 DOI: 10.1089/fpd.2018.2558] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase-producing Enterobacteriaceae are no longer restricted to the health care system, but represent increased risks related to environmental integrity and food safety. Fresh produce has been increasingly reported to constitute a reservoir of multidrug-resistant (MDR) potential human pathogenic Enterobacteriaceae. This study aimed to detect, identify, and characterize the antimicrobial resistance of ESBL/AmpC-producing Enterobacteriaceae isolates from fresh vegetables at point of sale. Vegetable samples (spinach, tomatoes, lettuce, cucumber, and green beans; n = 545) were purchased from retailers in Gauteng, the most densely populated province in South Africa. These included street vendors, trolley vendors, farmers' market stalls, and supermarket chain stores. Selective enrichment, plating onto chromogenic media, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) confirmation of isolate identities showed that 17.4% (95/545) vegetable samples analyzed were contaminated with presumptive ESBL/AmpC-producing Enterobacteriaceae. Dominant species identified included Escherichia coli, Enterobacter cloacae, Enterobacter asburiae, and Klebsiella pneumoniae. Phenotypic antibiotic resistance analysis showed that 96.1% of 77 selected isolates were MDR, while resistance to aminoglycoside (94.8%), chloramphenicol (85.7%), and tetracycline (53.2%) antibiotic classes was most prevalent. Positive phenotypic analysis for ESBL production was shown in 61 (79.2%) of the 77 isolates, and AmpC production in 41.6% of the isolates. PCR and sequencing confirmed the presence of β-lactamase genes in 75.3% isolates from all vegetable types analyzed, mainly in E. coli, Enterobacter spp., and Serratia spp. isolates. CTX-M group 9 (32.8%) was the dominant ESBL type, while EBC (24.1%) was the most prevalent plasmidic type AmpC β-lactamase. Our findings document for the first time the presence of MDR ESBL/AmpC-producing Enterobacteriaceae in raw vegetables sold at selected retailers in Gauteng Province, South Africa.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Erika M Du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
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Carmichael PC, Siyoum N, Chidamba L, Korsten L. Characterization of fungal communities of developmental stages in table grape grown in the northern region of South Africa. J Appl Microbiol 2018; 123:1251-1262. [PMID: 28862786 DOI: 10.1111/jam.13577] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/25/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
AIMS To determine fungal communities that characterize table grapes during berry development. METHODS AND RESULTS Two agro-ecologically different table grape commercial farms (site A and B) were used in this study. Samples were collected at full bloom, pea size and mature stages, from three positions (inside centre, eastern and western peripheral ends) per site. Total DNA extraction, Illumina sequencing and analysis of 18 pooled samples for fungal diversity targeting ITS1-2 generated a total of 2 035 933 high-quality sequences. The phylum Ascomycota (77.0%) and Basidiomycota (23.0%) were the most dominant, while the genera, Alternaria (33.1%) and Cladosporium (24.2%) were the overall dominant postharvest decay causing fungi throughout the developmental stages. Inside centre of site A were more diverse at full bloom (3.82) than those at the peripheral ends (<3.8), while at site B, the peripheral ends showed better diversity, particularly the eastern part at both full bloom (3.3) and pea size (3.7). CONCLUSION Fungal population diversity varies with different phenological table grape growth stages and is further influenced by site and vine position within a specific vineyard. SIGNIFICANCE AND IMPACT OF THE STUDY The information on fungal diversity and succession in table grapes during preharvest growth stages is critical in the development of a more targeted control strategy, to improve postharvest quality of table grapes.
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Affiliation(s)
- P C Carmichael
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
| | - N Siyoum
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
| | - L Chidamba
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
| | - L Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
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Chidamba L, Korsten L. Relative proportions of E. coli and Enterococcus spp. may be a good indicator of potential health risks associated with the use of roof harvested rainwater stored in tanks. Environ Monit Assess 2018; 190:177. [PMID: 29488034 DOI: 10.1007/s10661-018-6554-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
A total of 285 water samples were collected from 71 roof harvested rainwater tanks from four villages in different provinces over a two-year (2013-2014) period during the early (October to December) and late (January to March) rainy season. Water quality was evaluated based on Escherichia coli, faecal coliforms and Enterococcus spp. prevalence using the IDEXX Quanti-Tray quantification system. Real-Time PCR was used to analyse a subset of 168 samples for the presence of Shigella spp., Salmonella spp. and E. coli virulence genes (stx1, stx2 and eaeA). Escherichia coli were detected in 44.1% of the samples, Enterococcus spp. in 57.9% and faecal coliforms in 95.7%. The most prevalent E. coli concentrations in harvested rainwater were observed in 29.1% of samples and 22.5% for Enterococcus spp. and, were within 1-10 cfu/100 ml and 10-100 cfu/100 ml, respectively, whereas those for faecal coliforms (36.6%) were within 100-1000 cfu/100 ml. On average 16.8% of the samples had neither E. coli nor Enterococcus spp. detected, while 33.9% had only Enterococcus spp. and 23.7% had only E. coli. E. coli and Enterococcus spp. were detected together in 25.5% of the samples. Evaluation of samples for potential pathogenic bacteria showed all tested samples to be negative for the Shigella spp. ipaH gene, while five tested positive for Salmonella ipaB gene. None of the samples tested positive for the stx1 and stx2 genes, and only two tested positive for the eaeA gene. These findings are potentially useful in the development of a simplified risk assessment strategy based on the concentrations of indicator bacteria.
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Affiliation(s)
- Lizyben Chidamba
- Research Group for Plant Health and Food Safety, Department of Plant and Soil Sciences, University of Pretoria, Room: 2-18, Hatfield Campus, Agriculture Building, Private Bag X20, Hatfield/Pretoria, South Africa
| | - Lise Korsten
- Research Group for Plant Health and Food Safety, Department of Plant and Soil Sciences, University of Pretoria, Room: 2-18, Hatfield Campus, Agriculture Building, Private Bag X20, Hatfield/Pretoria, South Africa.
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Plessis EMD, Govender S, Pillay B, Korsten L. Exploratory Study into the Microbiological Quality of Spinach and Cabbage Purchased from Street Vendors and Retailers in Johannesburg, South Africa. J Food Prot 2017; 80:1726-1733. [PMID: 28922029 DOI: 10.4315/0362-028x.jfp-16-540] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Knowledge of the microbiological quality and prevalence of antibiotic resistance and virulence genes in bacterial isolates from leafy green vegetables supplied by formal suppliers (retailers) and informal suppliers (street vendors) in South Africa is limited. Because leafy vegetables have been implicated in foodborne disease outbreaks worldwide, 180 cabbage and spinach samples were collected from three major retailers and nine street vendors in Johannesburg, South Africa. Escherichia coli and coliforms were enumerated using Petrifilm plates. The prevalence of Listeria monocytogenes, Salmonella, and Shigella was determined using real-time PCR analysis. Identities of presumptive E. coli isolates from the fresh produce were confirmed using matrix-assisted laser desorption-ionization time of flight mass spectroscopy. Isolates were characterized using phenotypic (antibiotic resistance) and genotypic (phylogenetic and virulence gene) analysis. Hygiene indicator bacteria levels on spinach from formal and informal retailers exceeded the maximum level specified by the Department of Health guidelines for fresh fruit and vegetables. E. coli counts for street vendor spinach were higher (P < 0.0789) than those for retailer spinach. E. coli was present in only two cabbage samples, at 0.0035 CFU/g. L. monocytogenes and Salmonella were detected in 7.2 and 5% of the 180 samples, respectively, based on real-time PCR analysis; Shigella was not detected. Of the 29 spinach E. coli isolates, 37.9% were multidrug resistant. Virulence genes eae and stx1 were present in 14 and 3% of the spinach E. coli isolates, respectively; the stx2 gene was not detected. Eighty-six percent of these isolates belonged to phylogroup A, 3% belonged to group C, 7% belonged to group E, and 3% belonged to clade 1. The results from the current exploratory study on the microbiological quality of spinach bought from selected retailers highlight the need for continued surveillance on a larger scale, especially in the informal sector, to characterize the potential health risks to the consumer.
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Affiliation(s)
- Erika M du Plessis
- 1 Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa; and
| | - Sarasha Govender
- 2 Department of Microbiology, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X 54001, Durban 4000, South Africa
| | - Bala Pillay
- 2 Department of Microbiology, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X 54001, Durban 4000, South Africa
| | - Lise Korsten
- 1 Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa; and
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Jongman M, Chidamba L, Korsten L. Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing. J Appl Microbiol 2017; 123:1043-1053. [PMID: 28795469 DOI: 10.1111/jam.13558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/14/2017] [Accepted: 07/24/2017] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the influence of irrigation water microbial quality on leafy green vegetables produced in commercial and small-scale farms as well as homestead gardens using pyrosequencing. METHODS AND RESULTS Next generation sequencing analysis of the V1-V3 hypervariable region of bacterial 16S rDNA was used to compare bacterial diversity in irrigation water sources and on leafy vegetables. In all samples (12) analysed, the phylum Proteobacteria (64·5%), class Gammaproteobacteria (56·6%) and genus Aeromonas (14·4%) were found to be dominant. Of the total Escherichia sequences detected in tested samples, lettuce (16·3%) from the one commercial farm harboured more sequences than cabbage from the small-scale farm (1·3%) or homestead gardens (1·9%). Escherichia sequences were detected in both irrigation water (4·6%) and on cabbage (1·3%) samples from the small-scale farm. The genus Salmonella was absent in borehole water but was detected in the holding dam water (<1%) from commercial farm A. Salmonella sequences were present in river water (<1%) and on cabbages (1·9%) from the small-scale farm but were not detected on cabbage samples from the one commercial farm or the homestead gardens. CONCLUSION Water sources quality used for irrigation greatly influences the microbial dynamics of the irrigated crop. SIGNIFICANCE AND IMPACT OF THE STUDY Microbial biomes in irrigation water and on leafy greens were described with pyrosequencing and revealed insights into prevalence of potential and opportunistic pathogens across different production systems.
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Affiliation(s)
- M Jongman
- Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa
| | - L Chidamba
- Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa
| | - L Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa
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Rossouw W, Korsten L. Cultivable microbiome of fresh white button mushrooms. Lett Appl Microbiol 2017; 64:164-170. [PMID: 27930823 DOI: 10.1111/lam.12698] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/22/2016] [Accepted: 12/02/2016] [Indexed: 11/29/2022]
Abstract
Microbial dynamics on commercially grown white button mushrooms is of importance in terms of food safety assurance and quality control. The purpose of this study was to establish the microbial profile of fresh white button mushrooms. The total microbial load was determined through standard viable counts. Presence and isolation of Gram-negative bacteria including coagulase-positive Staphylococci were performed using a selective enrichment approach. Dominant and presumptive organisms were confirmed using molecular methods. Total mushroom microbial counts ranged from 5·2 to 12·4 log CFU per g, with the genus Pseudomonas being most frequently isolated (45·37% of all isolations). In total, 91 different microbial species were isolated and identified using Matrix-assisted laser desorption ionization-time of flight mass spectrophotometry, PCR and sequencing. Considering current food safety guidelines in South Africa for ready-to-eat fresh produce, coliform counts exceeded the guidance specifications for fresh fruit and vegetables. Based on our research and similar studies, it is proposed that specifications for microbial loads on fresh, healthy mushrooms reflect a more natural microbiome at the point-of-harvest and point-of-sale. SIGNIFICANCE AND IMPACT OF THE STUDY Presence and persistence of micro-organisms within the microbiome of fresh produce is important when identifying a potential niche for foodborne pathogens. Most foodborne outbreaks can be attributed to microbial imbalances or lack of diversity within the associated host surface and residing microbial population. Agaricus bisporus samples analysed during this study showed a higher microbial load (5·2 up to 12·4 log CFU per g) compared to known values for other fresh produce. These mushrooms were considered to carry microbial loads representing a healthy and safe product, fit for consumption, despite showing a high indicator incidence. Although foodborne pathogens may be associated on occasion with fresh mushrooms, it remains a low-risk commodity; therefore, this study provides insight and experimental evidence identifying microbial population dynamics of fresh and packed mushrooms.
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Affiliation(s)
- W Rossouw
- Department of Plant and Crop Sciences, University of Pretoria, Pretoria, South Africa
| | - L Korsten
- Department of Plant and Crop Sciences, University of Pretoria, Pretoria, South Africa
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Jongman M, Korsten L. Irrigation water quality and microbial safety of leafy greens in different vegetable production systems: A review. Food Reviews International 2017. [DOI: 10.1080/87559129.2017.1289385] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mosimanegape Jongman
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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Gomba A, Chidamba L, Korsten L. Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides. J Food Saf 2017. [DOI: 10.1111/jfs.12357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- A. Gomba
- Department of Plant and Soil Sciences; University of Pretoria; Hatfield 0028 South Africa
| | - L. Chidamba
- Department of Plant and Soil Sciences; University of Pretoria; Hatfield 0028 South Africa
| | - L. Korsten
- Department of Plant and Soil Sciences; University of Pretoria; Hatfield 0028 South Africa
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Duvenage FJ, Duvenage S, Du Plessis EM, Volschenk Q, Korsten L. Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane. J Sci Food Agric 2017; 97:1185-1192. [PMID: 27300139 DOI: 10.1002/jsfa.7847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 05/20/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Knowledge on the culturable bacteria and foodborne pathogen presence on pears is important for understanding the impact of postharvest practices on food safety assurance. Pear fruit bacteria were investigated from the point of harvest, following chlorine drenching and after controlled atmosphere (CA) storage to assess the impact on natural bacterial populations and potential foodborne pathogens. RESULTS Salmonella spp. and Listeria monocytogenes were detected on freshly harvested fruit in season one. During season one, chemical drenching and CA storage did not have a significant effect on the bacterial load of orchard pears, except for two farms where the populations were lower 'after CA storage'. During season two, bacterial populations of orchard pears from three of the four farms increased significantly following drenching; however, the bacterial load decreased 'after CA storage'. Bacteria isolated following enumeration included Enterobacteriaceae, Microbacteriaceae, Pseudomonadaceae and Bacillaceae, with richness decreasing 'after drench' and 'after CA storage'. CONCLUSION Salmonella spp. and L. monocytogenes were not detected after postharvest practices. Postharvest practices resulted in decreased bacterial species richness. Understanding how postharvest practices have an impact on the viable bacterial populations of pear fruit will contribute to the development of crop-specific management systems for food safety assurance. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Francois J Duvenage
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Stacey Duvenage
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Erika M Du Plessis
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Quinton Volschenk
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Lise Korsten
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
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Gomba A, Chidamba L, Korsten L. Effect of postharvest practices including degreening on citrus carpoplane microbial biomes. J Appl Microbiol 2017; 122:1057-1070. [PMID: 28052466 DOI: 10.1111/jam.13396] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/23/2016] [Accepted: 12/13/2016] [Indexed: 01/04/2023]
Abstract
AIMS To investigate the effect of commercial citrus packhouse processing steps on the fruit surface microbiome of Clementines and Palmer navel oranges. METHODS AND RESULTS Viable bacteria, yeast and fungi counts, and the pyrosequencing analysis of the 16S rRNA and ITS were used to evaluate the community structure and population dynamics of phylloepiphytic bacteria and fungi associated with commercial postharvest processing. Drenching significantly reduced microbial counts in all cases except for yeasts on navels, while the extent of degreening effects varied between the citrus varieties. Pyrosequencing analysis showed a total of 4409 bacteria and 5792 fungi nonchimeric unique sequences with an average of 1102 bacteria and 1448 fungi reads per sample. Dominant phyla on the citrus carpoplane were Proteobacteria (53·5%), Actinobacteria (19·9%), Bacteroidetes (5·6%) and Deinococcus-Thermus (5·4%) for bacteria and Ascomycota (80·5%) and Basidiomycota (9·8%) for fungi. Beginning with freshly harvested fruit fungal diversity declined significantly after drenching, but had little effect on bacteria and populations recovered during degreening treatments, including those for Penicillium sp. CONCLUSION Packhouse processing greatly influences microbial communities on the citrus carpoplane. SIGNIFICANCE AND IMPACT OF THE STUDY A broad orange biome was described with pyrosequencing and gave insight into the likely survival and persistence of pathogens, especially as they may affect the quality and safety of the packed product. A close examination of the microbiota of fruit and the impact of intervention strategies on the ecological balance may provide a more durable approach to reduce losses and spoilage.
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Affiliation(s)
- A Gomba
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
| | - L Chidamba
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
| | - L Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
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de Bruin W, van der Merwe C, Kritzinger Q, Bornman R, Korsten L. Ultrastructural and developmental evidence of phytotoxicity on cos lettuce (Lactuca sativa) associated with nonylphenol exposure. Chemosphere 2017; 169:428-436. [PMID: 27889509 DOI: 10.1016/j.chemosphere.2016.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 10/04/2016] [Accepted: 11/05/2016] [Indexed: 05/02/2023]
Abstract
It has long been understood that the presence of endocrine disrupter chemicals (EDCs) in water can affect the reproductive, behavioural and regulatory systems of different types of mammals. Thus far, only a handful of studies have examined its impact on plant systems. Present research is limited to the potential uptake of these chemicals by plants and the general phytotoxic effects it can elicit. The aim of this study was to determine what effect an EDC has on developing plant and cell organelles and how it affects it. In this study, cos lettuce plants were exposed to different concentrations of nonylphenol (NP), an EDC, in a static hydroponic system. Changes in plant morphology, mass and length, chlorophyll content, as well as electrolyte leakage were examined. Furthermore an in-depth investigation of the plant cell ultrastructure was carried out with transmission electron microscopy. Results indicated that cos lettuce growth was severely restricted, chlorophyll content was reduced, leakage of electrolytes increased and roots were stunted especially after ≥3200 μg/l NP exposures. The structure of the rough endoplasmic reticulum, vacuole and chloroplast were also changed. This study emphasizes the importance of water quality management, since the presence of an EDC, like NP, can negatively impact the yield and internal structure of one of the world's most significant salad crops, namely lettuce.
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Affiliation(s)
- Willeke de Bruin
- Department of Plant and Soil Sciences, Department of Science and Technology and National Research Foundation: Centre of Excellence Food Security, University of Pretoria, Pretoria, 0002, South Africa
| | - Chris van der Merwe
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0002, South Africa
| | - Quenton Kritzinger
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0002, South Africa.
| | - Riana Bornman
- School of Health Systems and Public Health, Institute for Food, Nutrition and Well-being, University of Pretoria, Private Bag X323, Pretoria, 0001, South Africa.
| | - Lise Korsten
- Department of Plant and Soil Sciences, Department of Science and Technology and National Research Foundation: Centre of Excellence Food Security, University of Pretoria, Pretoria, 0002, South Africa.
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Jongman M, Korsten L. Microbial quality and suitability of roof-harvested rainwater in rural villages for crop irrigation and domestic use. J Water Health 2016; 14:961-971. [PMID: 27959874 DOI: 10.2166/wh.2016.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The study aimed at assessing the microbiological quality and suitability of roof-harvested rainwater (RHRW) for crop irrigation and domestic use. In total, 80 rainwater tanks (246 samples) across three rural villages (Ga-Molepane, Jericho and Luthngele) were visited. Culture-based techniques were used to isolate bacterial microbes and identities were confirmed using matrix-assisted laser desorption/ionization time of flight (MALDI-TOF-MS). Uncultured fungal populations were also identified using pyrosequencing. Salmonella spp. (3%), Listeria monocytogenes (22%), total coliforms (57.7%), Escherichia coli (30.5%), Enterococcus spp. (48.8%), Pseudomonas spp. (21.5%) were detected in RHRW samples after rainfall. Fungal sequences belonging to species known to cause fever, coughing and shortness of breath in humans (Cryptococcus spp.) were identified. This study indicates that RHRW quality can be affected by external factors such as faecal material and debris on rooftops. The use of untreated RHRW could pose a potential health risk if used for irrigation of crops or domestic use, especially in the case of a relative high population of immunocompromised individuals. This study does not dispute the fact that RHRW is an alternative irrigation water source but it recommends treatment before use for domestic purposes or for watering crops.
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Affiliation(s)
- Mosimanegape Jongman
- Department of Plant and Soil Sciences, University of Pretoria, Lynwood Road, Pretoria 0082, South Africa E-mail:
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Lynwood Road, Pretoria 0082, South Africa E-mail:
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Affiliation(s)
- Mosimanegape Jongman
- Faculty of Natural and Agricultural Sciences, Department of Plant and Soil Sciences; University of Pretoria; Private bag X20, Hatfield Pretoria 0082 South Africa
| | - Lise Korsten
- Faculty of Natural and Agricultural Sciences, Department of Plant and Soil Sciences; University of Pretoria; Private bag X20, Hatfield Pretoria 0082 South Africa
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Duvenage S, Korsten L. Effect of Temperature and Nutrient Concentration on Survival of Foodborne Pathogens in Deciduous Fruit Processing Environments for Effective Hygiene Management. J Food Prot 2016; 79:1959-1964. [PMID: 28221909 DOI: 10.4315/0362-028x.jfp-16-050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Temperature and good sanitation practices are important factors for controlling growth of microorganisms. Fresh produce is stored at various temperatures to ensure quality and to prolong shelf life. When foodborne pathogens survive and grow on fresh produce at storage temperatures, then additional control strategies are needed to inactivate these pathogens. The aim of this study was to determine how temperatures associated with deciduous fruit processing and storage facilities (0.5, 4, and 21°C) affect the growth and/or survival of Escherichia coli O157:H7, Listeria monocytogenes , Salmonella enterica subsp. enterica serovar Typhimurium, and Staphylococcus aureus under different nutrient conditions (nutrient rich and nutrient poor) and on simulated contact surfaces (vinyl coupons). Information on the growth and survival of foodborne pathogens at specific deciduous fruit processing and storage temperatures (0.5°C) is not available. All pathogens except E. coli O157:H7 were able to survive on vinyl coupons at all temperatures. L. monocytogenes proliferated under both nutrient conditions independent of temperature. S. aureus was the pathogen least affected by nutrient conditions. The survival of foodborne pathogens on the vinyl coupons, a model system for studying surfaces in fruit preparation and storage environments, indicates the potential for cross-contamination of deciduous fruit products under poor sanitation conditions. Foodborne pathogens that can proliferate and survive at various temperatures under different nutrient conditions could lead to fruit cross-contamination. Temperature mismanagement, which could allow pathogen proliferation in contaminated fruit packing houses and storage environments, is a concern. Therefore, proper hygiene and sanitation practices, removal of possible contaminants, and proper food safety management systems are needed to ensure food safety.
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Affiliation(s)
- Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Lynnwood Road, Pretoria, South Africa 0001
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Lynnwood Road, Pretoria, South Africa 0001
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Abstract
Foodborne disease outbreaks linked to contaminated irrigation water and fresh produce are a public health concern. The presence of Escherichia coli isolates from irrigation water and leafy green vegetables in different food production systems (large commercial farms, small-scale farms, and homestead gardens) was investigated. The prevalence of antibiotic resistance and virulence in these isolates was further assessed, and links between water source and irrigated crops were identified using antimicrobial and genotypic analyses. Presumptive E. coli isolates were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy, and identities were confirmed by PCR using the uidA gene. Antimicrobial susceptibility was evaluated with the Kirby Bauer disk diffusion test; the presence of virulence genes was determined with enterobacterial repetitive intergenic consensus PCR assays. Of the 130 E. coli isolates from water (n =60) and leafy green vegetables (n =70), 19 (14.6%) were resistant to one antibiotic (tetracycline) and 92 (70.7%) were resistant to various antibiotics (including ampicillin, cefoxitin, and nalidixic acid). All E. coli isolates were susceptible to ceftriaxone and gentamicin. The virulence gene stx2 was detected in E. coli isolates from irrigation water (8 [13.3%] of 60 isolates) and cabbages (3 [7.5%] of 40), but the virulence genes eae and stx1 were not detected in any tested isolates from irrigation water and fresh produce samples. The prevalence of multidrug-resistant E. coli was lower in isolates from GLOBALG.A.P.-certified farms than in isolates from noncertified commercial and small-scale farms and homestead gardens. A link between the E. coli isolates from irrigation water sources and leafy green vegetables was established with phenotypic (antimicrobial) and genotypic (DNA fingerprinting) analyses. However, a link between virulence genes and the prevalence of antimicrobial resistance could not be established.
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Affiliation(s)
- Mosimanegape Jongman
- Department of Plant Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0082, South Africa
| | - Lise Korsten
- Department of Plant Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0082, South Africa
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Gomba A, Chidamba L, Korsten L. Prevalence and serovar diversity of Salmonella spp. in primary horticultural fruit production environments. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.04.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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