Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield.

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.

Microbiological quality of irrigation water on highly diverse fresh produce smallholder farms: elucidating environmental routes of contamination.

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.

Serotype Distribution, Antimicrobial Resistance, Virulence Genes, and Genetic Diversity of Salmonella spp. Isolated from small-scale Leafy Green Vegetable Supply Chains in South Africa.

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.

Microbiological quality assessment of fresh produce: Potential health risk to children and urgent need for improved food safety in school feeding schemes.

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 ß-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 ß-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.

Spatial diarrheal disease risks and antibiogram diversity of diarrheagenic Escherichia coli in selected access points of the Buffalo River, South Africa.

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 ß-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.

Occurrence and Molecular Characterization of Multidrug-Resistant Vegetable-Borne Listeria monocytogenes Isolates.

Fresh vegetables play a significant role in the human diet. However, ready-to-eat (RTE) vegetables have been associated with increasing foodborne outbreaks including L. monocytogenes, which is a common human pathogen associated with foodborne infections resulting in listeriosis. This study aims to assess the resistance of vegetable-borne L. monocytogenes to antibiotics. L. monocytogenes was isolated and molecularly characterized using polymerase chain reaction (PCR) from 17 RTE vegetable samples. The confirmed L. monocytogenes was further assessed for phenotypic and genotypic antibiotic resistance using the disc diffusion test and PCR primers targeting six antibiotic classes and thirty-one related antibiotic resistance genes (ARGs), respectively. The results revealed that Listeria counts ranged from 1.60 to 3.44 log10 CFU/g in the samples. The isolates exhibited high resistance against penicillin G, erythromycin, vancomycin, tetracycline, trimethoprim-sulfamethoxazole, and nitrofurantoin among the 108 isolates tested. A total of 71 multiple antibiotic resistance (MAR) phenotypes were observed in the isolates, which ranged from resistance to 3 to 13 antibiotics. The MAR index was ˃0.2 in 97% of the isolates. Some of the highly detected ARG subtypes included SulI (100%), TEM (76.9%), tetA (59%), and tetM (54.7%). The findings show a high occurrence of multidrug-resistant L. monocytogenes and clinical ARGs in fresh vegetables, which constitutes an immediate danger for the health security of the public.

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions.

AIM OF THE STUDY: The aim was to characterize 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 (SE) fungal microbiomes at the postharvest stage of avocado fruit were studied using next-generation sequencing of the internal transcribed spacer region. Avocado fructoplane and SE 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 highlight 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.

Revisiting food security in 2021: an overview of the past year.

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.

The microbiome and resistome of apple fruits alter in the post-harvest period.

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.

Characterization of Multidrug-Resistant Escherichia coli Isolated from Two Commercial Lettuce and Spinach Supply Chains.

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 ß-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.

Multidrug resistant Escherichia coli from fresh produce sold by street vendors in South African informal settlements.

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.

Microbiological safety of spinach throughout commercial supply chains in Gauteng Province, South Africa and characterization of isolated multidrug-resistant Escherichia coli.

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.

Whole Genome Sequencing of Extended-Spectrum- and AmpC- ß-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa.

The increasing occurrence of multidrug-resistant (MDR) extended-spectrum ß-lactamase- (ESBL) and/or AmpC ß-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 ß-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.

Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves.

Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine's resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.

Microbial Load and Prevalence of Escherichia coli and Salmonella spp. in Macadamia Nut Production Systems.

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.

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.

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.

Antibiogram Signatures of Some Enterobacteria Recovered from Irrigation Water and Agricultural Soil in two District Municipalities of South Africa.

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.

Mapping disruption and resilience mechanisms in food systems.

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.

The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health.

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.

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables.

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.