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Thesis (MSc Food Sc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Food-borne disease outbreaks caused by Escherichia coli have been linked to the use of faecally-polluted irrigation waters. Thus the overall aim of this research was to evaluate irrigation water and agricultural effluents as sources of antibiotic resistant E. coli in the Western Cape. The aim of the first study was to enumerate and characterise E. coli present in irrigation water and in potential contamination sources. Maximum total coliform and E. coli counts for irrigation sites was log 7.862 and log 5.364 MPN.100 mL-1, respectively. Five out of seven irrigation sites had E. coli counts exceeding national and international guidelines for ‘safe’ irrigation water (<1 000 counts.100 mL-1), making it unsafe for the irrigation of fresh produce. In this study, 46.6% of the E. coli strains were characterised in phylogenetic group B1. It has been shown that E. coli in group B1 have the ability to survive and persist in the external environment. Group B1 was also the most common group among isolates from irrigation sites (79.4%), while isolates from environmental sites grouped mainly in group A0 (54.1%). It was concluded that the wide variation of E. coli types present in irrigation water is a concern that should be further investigated. This raises human health implications since the increased exposure to faecal organisms increases the risk of food-borne outbreaks. The E. coli isolates (n = 120) and the marker (n = 37) and reference strains (n = 6), were evaluated for antibiotic resistance to seven medically-important antibiotics from different classes using the Kirby-Bauer disc diffusion method. Thirty-five strains (35/163 = 21.5%) exhibited resistance to one or more antibiotics. Piggery effluent was found to harbour the most antibiotic resistant E. coli isolates (9/35 = 25.7%). Among the resistant E. coli strains, the highest occurrence of antibiotic resistance was to trimethoprim (2.5 μg) (68.6%), tetracycline (30 μg) (57.1%), ampicillin (10 μg) (45.7%) and chloramphenicol (30 μg) (34.3%). Seventy-four percent (26/35) exhibited multiple antibiotic resistances to two or more antibiotics. The antibiotic resistant E. coli strains were evaluated for the presence of pathotypes using Polymerase Chain Reaction analysis to detect Intestinal Pathogenic E. coli (InPEC) and Extra-intestinal Pathogenic E. coli (ExPEC). Five InPEC strains were characterised as four Entero-Pathogenic E. coli (EPEC) strains resistant to three or four antibiotics and one Entero-Aggregative E. coli (EAEC) strain resistant to trimethoprim. The antibiotic resistant EAEC strain also possessed the ExPEC-related gene iutA. Two E. coli isolated from the Mosselbank River were both resistant to chloramphenicol and trimethoprim and also possessed the ExPEC-related gene iutA. It was concluded that the diverse antibiotic resistances of E. coli pathotypes present in irrigation water is a concern that should be further investigated. / AFRIKAANSE OPSOMMING: Voedselverwante siekte uitbrake wat deur Escherichia coli veroorsaak word, is gekoppel aan die gebruik van fekale besoedelde besproeiingswater. Dus was die hoof doel van die navorsing om besproeiingswater en landbou-afvalwater te evalueer as bronne van antibiotika-weerstandbiedende E. coli in die Wes-kaap. Die doel van die eerste studie was om die getalle en eienskappe van E. coli te bepaal wat in besproeiingswater en in ander potensiële besmettingsbronne teenwoordig is. Maksimum totale koliforme en E. coli-tellings vir besproeiingspunte was onderskeidelik log 7.862 en log 5.364 MPN.100 mL-1. Vyf uit sewe besproeiingspunte het E. coli-tellings gehad wat hoër is as die nasionale en internasionale riglyne vir ‘veilige’ besproeiingswater (<1 000 tellings.100 mL-1). Dit maak dit onveilig vir die besproeiing van vars produkte. In hierdie studie was 46.6% van die E. coli-stamme in filogenetiese groep B1 gegroepeer. Dit is reeds bewys dat E. coli in groep B1 oor die vermoë beskik om in die eksterne omgewing te oorleef en voort te bestaan. Groep B1 was ook die mees algemene groep onder die isolate van besproeiingspunte (79.4%), terwyl isolate van omgewingspunte meestal in groep A0 (54.1%) gegroepeer is. Die breë variasie E. coli tipes in die besproeiingswater is bekommerniswaardig en sal gevolglik verder ondersoek moet word. Dit bring gesondsheidsimplikasies mee vir mense aangesien die verhoogde blootstelling aan fekale organismes die risiko van voedselverwante uitbrake verhoog. Die E. coli isolate (n = 120) en die merker (n = 37) en verwysingsstamme (n = 6), is teen sewe medies belangrike antibiotikas uit verskillende klasse getoets vir antibiotika-weerstandbiedendheid. Die Kirby-Bauer skyfie diffusie metode is gebruik. Vyf-en-dertig stamme (35/163 = 21.5%) het weerstand teen een of meer antibiotika getoon. Dit is gevind dat vark-afvalwater die meeste antibiotika-weerstandbiedende E. coli-isolate (9/35 = 25.7%) bevat. Die weerstandbiedende E. coli-stamme het die hoogste antibiotika-weerstandheid getoon teen "trimethoprim" (2.5 μg) (68.6%), tetrasiklien (30 μg) (57.1%), ampisillien (10 μg) (45.7%) en chloramfenikol (30 μg) (34.3%). Vier-en-sewentig persent (26/35) het meervoudige weerstandbiedheid teen twee of meer antibiotikas getoon. Die antibiotika-weerstandbiedende E. Coli stamme is getoets vir die teenwoordigheid van patogene deur van Polimerase Ketting Reaksie analise gebruik te maak om ‘Intestinal Pathogenic’ E. coli (InPEC) en ‘Extra-intestinal Pathogenic’ E. coli (ExPEC) op te spoor. Vyf InPEC-stamme is geklassifiseer as vier ‘Entero-Pathogenic’ E. coli (EPEC)-stamme wat weerstandbiedend teen drie of vier antibiotika getoon het en een ‘Entero-Aggregative’ E. coli (EAEC)-stam wat weerstandbiedendheid getoon het teen "trimethoprim". Die antibiotika-weerstandbiedende EAEC-stam het ook die ExPEC-verwante geen, iutA, besit. Twee E. coli isolate van die Mosselbankrivier het weerstand teen beide chloramfenikol en "trimethoprim" getoon en het ook die ExPEC-verwante geen, iutA, besit. Daar is tot die gevolgtrekking gekom dat die diverse antibiotika-weerstandbiedenheid van E. coli patogene teenwoordig in besproeiingswaters bekommerniswaardig is en verder ondersoek behoort te word.

Thesis (MSc Food Sc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Fresh produce irrigation water from Western Cape Rivers carries faecal coliforms (FC) (Escherichia coli) at concentrations which often exceed the suggested limit of 1 000 FC per 100 mL and presents a health risk to consumers. On-farm ultraviolet (UV) irradiation presents several advantages for water disinfection but is an uncommon practice in South Africa. The aim of this study was to investigate the use of UV irradiation for river water disinfection prior to irrigation. Escherichia coli (E. coli) strains were exposed to low-pressure (LP) UV (4 mJ.cm-2) and UV/Hydrogen peroxide (H2O2) (4 mJ.cm-2/20 mg.L-1) treatments in Sterile Saline Solution (SSS). Strain variation in reductions was observed and ranged from 1.58 to 3.68 and 1.34 to 3.60 log for the UV and UV/H2O2 treatments, respectively. The UV/H2O2 treatment (4 mJ.cm-2/20 mg.L-1) was more effective, compared to UV singly, against some of the E. coli strains. Selected strains showed increased sensitivity at higher UV doses (8, 10 and 13 mJ.cm-2) and H2O2 concentrations (100 and 200 mg.L-1 with 4 mJ.cm-2) but a 3 log target reduction was not always reached. For all UV and UV/H2O2 treatments maximum resistance was shown by an environmental strain. Reference strains should, therefore, not be used for the optimisation of UV based disinfection parameters. At 10 mJ.cm-2 an American Type Culture Collection (ATCC) reference strain and an environmental strain (ATCC 25922 and F11.2) were both significantly less inactivated in sterilised river water compared to SSS. Enhanced water quality allowed for improved inactivation of the ATCC strain. Also, the efficiency of LP UV (5, 7 and 10 mJ.cm-2) and medium-pressure (MP) UV (13, 17 and 24 mJ.cm-2) radiation was investigated using water from the Plankenburg River. Water was sampled and treated on three respective days (Trials 1 to 3). Physico-chemical and microbiological water quality was always poor. The FC concentration reached a maximum of 6.41 log cfu.100 mL-1 while UV transmission was always below 38%. For LP and MP UV irradiation increased doses resulted in increased disinfection but a 3 log reduction of FC was only attained when MP UV light was used in Trial 1. Disinfection efficiency was dependent on water quality and on the characteristics of the microbial population in the water. Since FC were never reduced to below 3 log cfu.100 mL-1, the water did not adhere to guidelines for produce irrigation. Photo-repair following irradiation was investigated in river water using MP UV doses of 13 and 24 mJ.cm-2 and 3.5 kLux reactivating light, initially. Ultraviolet transmission was close to 50% and total coliform (TC) reduction exceeded 3 log, even at 13 mJ.cm-2. However, TC were reactivated from below 1 000 cfu.100.mL-1 to 3.93 and 4.41 log cfu.100 mL-1 for the 13 and 24 mJ.cm-2 treatments, respectively. A higher MP dose (40 mJ.cm-2) and a different treatment regime (2 x 20 mJ.cm-2) inhibited photo-repair (compared to 13 and 24 mJ.cm-2) but TC were always recovered to a final concentration surpassing 3 log cfu.100 mL-1, even under lower light intensities (1.0 to 2.0 kLux). In the current study UV irradiation did not produce water of acceptable standards for produce irrigation, mainly as a result of extremely poor water quality. However, on farm-scale, UV efficiency could be enhanced by improving water quality before irradiation. Also, stronger lamps that deliver higher UV doses may result in adequate disinfection, irrespective of water quality. Higher UV doses and the use of combination treatments (such as UV/Chlorine and UV/Peracetic acid) should be further investigated also to determine its disinfection efficiency and possible capability to inhibit post-disinfection repair. / AFRIKAANSE OPSOMMING: Varsproduk besproeiingswater vanuit Wes-Kaapse riviere bevat fekale kolivorme (FK) (Escherichia coli) in konsentrasies wat dikwels die voorgestelde limiet van 1 000 FK per 100 mL oorskry en hou `n gesondheidsrisiko vir verbruikers in. Plaasvlak ultraviolet (UV) bestraling bied verskeie voordele met verwysing na water dekontaminering, maar word selde aangewend in Suid-Afrika. Die doel van hierdie studie was om die gebruik van UV bestraling vir die dekontaminering van rivierwater, voor besproeiing, te ondersoek. Escherichia coli (E. coli) isolate is blootgestel aan lae-druk (LD) UV (4 mJ.cm-2) en UV/Waterstofperoksied (H2O2) (4 mJ.cm-2/20 mg.L-1) behandelings in Steriele Sout Oplossing (SSO). Isolaat variasie in reduksies is waargeneem en het gewissel tussen 1.58 tot 3.68 en 1.34 tot 3.60 log vir die UV en UV/H2O2 behandelings, onderskeidelik. In vergelyking met UV bestraling alleen was die UV/H2O2 behandeling (4 mJ.cm-2/20 mg.L-1) meer effektief teen sommige E. coli isolate. Geselekteerde isolate was meer sensitief tot hoër UV dosisse (8, 10 en 13 mJ.cm-2) en H2O2 konsentrasies (100 en 200 mg.L-1 met 4 mJ.cm-2), maar `n 3 log teikenreduksie was nie altyd haalbaar nie. Vir alle UV en UV/H2O2 behandlinge was die meeste weerstand deur `n omgewingsisolaat gebied. Verwysingsisolate behoort daarom nie aangewend te word vir die optimisering van UV-gebaseerde behandelingsparameters nie. By 10 mJ.cm-2 was beide `n ATCC verwysingsisolaat en `n omgewingsisolaat (ATCC 25922 en F11.2) betekenisvol minder gedeaktiveer in rivierwater as in SSO. Verbeterde waterkwaliteit het verhoogde inaktivering van die ATCC isolaat toegelaat. Die doeltreffendheid van LD UV (5, 7 en 10 mJ.cm-2) en medium-druk (MD) UV (13, 17 en 24 mJ.cm-2) bestraling is ook ondersoek deur watermonsters vanuit die Plankenburg Rivier te gebruik. Watermonsters was getrek en behandel op drie verskillende dae (Proewe 1 tot 3). Fisies-chemiese en mikrobiologiese kwaliteit van die water was deurentyd swak. Die FK konsentrasie het `n maksimum van 6.41 log kve.100 mL-1 bereik terwyl UV transmissie altyd laer as 38% was. Vir beide LD en MD UV bestraling het verhoogde dosisse gelei tot verbeterde dekontaminering, maar `n 3 log reduksie is slegs bereik toe MD UV lig gebruik is in Proef 1. Die effektiwiteit van die behandelings was afhanklik van waterkwaliteit en die eienskappe van die mikrobiese populasie in die water. Aangesien FK nooit tot onder 3 log kve.100 mL-1 verminder is nie het die water nie voldoen aan riglyne vir varsproduk-besproeiing nie. Fotoherstel na bestraling was ondersoek in rivierwater deur aanvanklik gebruik te maak van MD UV dosisse van 13 en 24 mJ.cm-2 en 3.5 kLux heraktiverende lig. Ultraviolettransmissie het byna 50% bereik en reduksie van totale kolivorme (TK) het 3 log oorskry, selfs by 13 mJ.cm-2. Totale kolivorme was egter geheraktiveer van onder 1 000 kve.100.mL-1 tot 3.93 en 4.41 log kve.100 mL-1 vir die 13 en 24 mJ.cm-2 behandelings, onderskeidelik. In vergelyking met 13 en 24 mJ.cm-2 het `n hoër MD dosis (40 mJ.cm-2) en `n veranderde bestralingstegniek (2 x 20 mJ.cm-2) fotoherstel onderdruk, maar TK was in elke geval geheraktiveer tot `n finale konsentrasie hoër as 3 log kve.100 mL-1, selfs onder laer intensiteit lig (1.0 tot 2.0 kLux). In hierdie ondersoek het UV bestraling nie water van aanvaarbare standaarde vir varsproduk besproeiing gelewer nie, hoofsaaklik as gevolg van swak waterkwaliteit. Nietemin, op plaasvlak mag die effektiwiteit van UV bestraling verhoog word deur waterkwaliteit voor bestraling te verbeter. Die gebruik van sterker lampe, om hoër UV dosisse te produseer, mag verder bydra tot voldoende dekontaminasie, ongeag van waterkwaliteit. Hoër UV dosisse en die gebruik van kombinasie behandelinge (soos UV/Chloor en UV/Perasynsuur) moet ook verder ondersoek word om die dekontaminasie effektiwiteit, en vermoë daarvan om heraktivering na dekontaminering te onderdruk, vas te stel.

The inappropriate solid waste destination in urban regions create problems in streams flows such as pollution of water sources and obstruction of channels, which can cause flooding, which in addition to economic impacts, can cause severe damage to population human health . With this it is important to have tools that allow the effectiveness evaluation and the action impact in a way to generate benefits to the process of decision making by municipal managers. It is proposed in this work develop a methodology to contain the solid waste carried to Esperança s watershed, quantity and qualify these solid drainage waste SDW according to CONAMA s resolution 275 in relation to total rainfall in each event. The importance of these procedures follows the high risk of environmental damage that solid waste can cause in drainage networks. So, a sub watershed (0,57 Km2) was evaluated in the urban center of Santa Maria city, RS, using a fluviometric station with Parshall flume, where was project a structure to intercept the solid waste carried by the stream flow, it was based in collectors baskets. In accordance whith colors pattern of CONAMAS s resolution 275, it was recognized the main material in inappropriate places for people and is observed throw water resource degradation in the sub watershed. It was verify, in operational term, the efficiency of the solid waste retention strategy in isolated events, allowing people mobilization according to weather forecast. The results concerning the structure of monitoring were satisfactory, as the waste was retained in each precipitation event effectively. Monitoring of solid waste - resulted in 73% of organic matter and 27% of inorganic materials, and highlighted the significant presence of plastic was because of extensive use of this material by the population, represented 14% of the retained and the main constituents were bags groceries and bags of candy and pastries. The classification "others" was also significant, representing 6% from the total quantified and, mostly, was represented by diapers and shoes. The prediction curve of SDW is a parameter for decision to municipal managers in relation to solid waste generated within the urban basin-school, because it relates the SDW in Esperança s watershed in the stream as a function of rainfall. The total SDW loaded in one year corresponded to approximately 10.000kg with a total rainfall for the period of 1.572mm. The analysis of outcomes demonstrates a large amount of inorganic material in water quality degradation thus, questions arise about city s population environmental awareness, show up importance of environmental education actions. The identification of strong human interference reveals the environmental risks that sub watershed Esperança is submitted and results in information to support the process of municipal management of solid waste. / A deposição inadequada de resíduos sólidos em regiões urbanizadas gera problemas em riachos, como a poluição dos mananciais e a obstrução de canais, que podem causar inundações, as quais, além de impactos econômicos, podem causar severos danos à saúde da população. Assim, é importante o desenvolvimento de ferramentas que permitam avaliar a efetividade e o impacto de ações de forma a gerar subsídios ao processo de tomada de decisão pelos gestores municipais. Propõe-se, neste estudo, desenvolver uma metodologia para reter os resíduos sólidos carreados até o arroio Esperança, além de quantificar e qualificar estes resíduos conforme a resolução do CONAMA n.º 275 e relacioná-los com os dados de precipitação pluviométrica. A importância destes procedimentos decorre do elevado risco de danos ambientais que os resíduos sólidos podem causar nas redes de drenagem. Para tanto, foi instrumentada uma pequena bacia (0,57km2) no centro urbano de Santa Maria, RS, com uma estação fluviométrica com calha Parshall, onde projetou-se uma estrutura para a detenção do resíduo sólido carreado pelo riacho, baseada em cestos coletores. Seguindo as normas de padrão de cores da resolução 275 do CONAMA, foram identificados os principais materiais dispostos de forma inadequada pela população e que atingiram o arroio. Comprovou-se, em termos operacionais, a eficiência da estratégia de retenção de resíduos por eventos pluviosos isolados, pois permite a mobilização das pessoas em função de previsões meteorológicas de tempo. Os resultados referentes à estrutura de monitoramento foram satisfatórios, pois os resíduos foram retidos em cada evento de precipitação de forma efetiva. O monitoramento dos resíduos sólidos urbanos - RSD resultou em 73% de matéria orgânica e 27% de materiais inorgânicos, sendo destacada a significativa presença de plástico devido à grande utilização deste material pela população, representando 14% do volume retido e os principais constituintes foram sacolas de supermercado e embalagens de doces e salgados. A classificação outros também foi expressiva, representando 6% do total quantificado e, em sua maioria, foram representados por fraldas descartáveis e calçados. A curva de previsão de RSD é um parâmetro para a tomada de decisão dos gestores municipais em relação aos resíduos sólidos gerados no âmbito da bacia escola urbana, pois relaciona os RSD carreados no arroio Esperança em função da precipitação pluviométrica. O total de RSD carreado, no período de um ano, no arroio Esperança correspondeu a aproximadamente 10.000Kg com uma precipitação total para o período de 1.572mm. Os resultados observados evidenciam a grande quantidade de material inorgânico afetando a qualidade da água da bacia e aflora os questionamentos acerca da sensibilização ambiental da população da cidade, o que denota a importância de ações que visem a educação ambiental. A identificação de forte interferência humana na bacia revela os riscos ambientais a que o arroio Esperança está submetido e gera informações de apoio no processo de gestão municipal de resíduos sólidos.

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