Prevalence, characterisation and potential origin of Escherichia coli found in surface and ground waters utilized for irrigation of fresh produce

Schoeman, Nika Anna (2013-03)

Thesis (MSc Food Sc)--Stellenbosch University, 2013.

Thesis

ENGLISH ABSTRACT: Over the past two decades, there has been an increase in the use of water sources for irrigation, as well as an increase in Escherichia coli outbreaks linked to fresh produce. The full extent and type of E. coli contamination present in natural water sources is unknown and the contamination sources have also not been confirmed. The aim of this study was to enumerate and characterise E. coli from both irrigation water and potential contamination source sites. Total coliform and E. coli counts found in contamination source sites were as high as log 7.114 and log 6.912 MPN.100 mL-1, respectively. Total coliform and E. coli counts for irrigation sites were lower, with maximum counts of log 5.788 and log 5.768 MPN.100 mL-1, respectively. It was found that more than one third (5/14 = 35.71%) of the irrigation sites had E. coli counts exceeding the guidelines (<1 000 counts.100 mL-1) for ‘safe’ irrigation water for fresh produce (<1 000 counts.100 mL-1) as set by the Department of Water Affairs (DWA) and World Health Organisation (WHO), making the water unsuitable for the irrigation of fresh produce. Phylogenetic subgroups (A0, A1, B1, B22, B23, D1 and D2) and the MALDI Biotyper system (PCA dendrogram) were used to create a fingerprint of each E. coli isolated from the environment. These were then used to link E. coli strains from irrigation water to their most probable contamination origin. Escherichia coli population structure was found in this study, to be better suited for linking E. coli strains from irrigation water to their most likely source, than just applying the phylogenetic grouping. The MALDI Biotyper data in combination with the phylogenetic subgroup assignment was then used to group similar strains and link E. coli from irrigation water to their contamination sources by comparing population structures. Strains isolated from surface and groundwater showed similar distribution patterns, but groundwater strains showed a population structure more indicative of porcine and bovine origin, while surface water showed population characteristics which could not be used to make conclusive links between the irrigation water and suspected contamination sources. When investigating the population structures of individual sample sites, it was found that phylogenetic subgroups A0, A1 and B1 frequently made up the bulk of the E. coli population. It was also found that linking individual irrigation sites to contamination sources was successful, as irrigation site Berg-2 was found to have a similar population structure to contamination source site Plank-1 which represents human pollution from an informal settlement. This led to the conclusion that Berg-2 was being contaminated by human pollution, most probably from an informal settlement. Upon further investigation it was found that Berg-2 is downstream of an informal settlement, proving that E. coli population structure is a successful means of microbial source tracking (MST). Virulence factors of the 153 E. coli isolated during the study were identified and the potential risk associated with using the investigated irrigation water for irrigation of fresh produce, was determined. Two enteropathogenic E. coli (EPEC) strains were isolated from the irrigation water, one from the Plankenburg River water, and the other from a borehole in the Drakenstein area. The latter indicates that borehole water is not as safe as was once thought, and that there are bacterial contaminants finding their way into groundwater. The occurrence of an EPEC strain in river water shows that neither ground nor surface water is guaranteed to be safe, and that treatment of water being used for the irrigation of fresh produce should be implemented.

AFRIKAANSE OPSOMMING: Oor die afgelope twee dekades was daar nie net 'n toename in die gebruik van alternatiewe waterbronne vir besproeiing nie, maar ook 'n toename in uitbrake van Escherichia coli uitbrake wat aan vars produkte gekoppel kan word. Die tipe E. coli-besmetting wat in natuurlike waterbronne teenwoordig is, is onbekend en die besmettingsbron is ook nog nie bevestig nie. Daarom was die doel van hierdie studie om die voorkomssyfer van E. coli van beide besproeiingswater en potensiële kontaminasiebronne te bepaal, asook om die E. coli te karakteriseer. Totale kolivorme en E. coli-tellings wat in kontaminasiebronne gevind is, het ‘n maksimum van log 7,114 en log 6,912 MPN.100 mL-1 onderskeidelik bereik, terwyl die totale kolivorme en E. coli-tellings vir besproeiingswater laer was, met 'n maksimum van log 5,788 en 5,768 MPN.100 mL-1, onderskeidelik. Dit is bevind dat meer as 1/3 (5/14 = 35,71%) van die besproeiingswaterbronne meer E. coli bevat as wat toegelaat word in die riglyne vir "veilige" besproeiingswater vir vars produkte (<1 000 fekale koliforme.100 mL-1) wat deur die Departement Waterwese (DWA) en die Organisasie vir Wêreldgesondheid (WHO) aanbeveel word. Filogenetiese subgroepe (A0, A1, B1, B22, B23, D1 en D2) en die ‘MALDI Biotyper’-stelsel (PKA dendrogram) is gebruik om unieke profiele vir elke geïsoleerde E. coli te skep. Dié profiele is daarna gebruik om E. coli-stamme van besproeiingswater te koppel aan die mees waarskynlike oorsprong van kontaminasie. Daar is in hierdie studie bevind dat die E. coli-populasiestruktuur beter geskik was vir die koppeling van E. coli-stamme van besproeiingswater na hul mees waarskynlikste bron, as net die toepassing van die filogenetiese groepering. Dit was toe gevind dat E. coli wat uit oppervlak- en grondwater geïsoleer is, soortgelyke verspreidingspatrone het, maar grondwaterstamme se bevolkingstruktuur is meer aanduidend van fekale besmetting deur varke en beeste, terwyl oppervlakwater se bevolkingseienskappe nie duidelik genoeg was om ‘n gevolgtrekking oor moontlike bronne van besmetting te maak nie. Toe die populasiestruktuur van die individuele bemonsteringspunte ondersoek is, is daar bevind dat die filogenetiese subgroepe A0, A1 en B1 dikwels die meeste tot die E. coli bevolking bydra. Daar is ook bevind dat die koppeling van isolate in individuele besproeiingswaterbronne met hul mees waarskynlike bronne van kontaminasie suksesvol was. Besproeiingswater van Berg-2 het 'n soortgelyke populasiestruktuur as Plank-1 wat beskou is as ‘n kontaminasiebron. Dit het gelei tot die gevolgtrekking dat Berg-2 heel waarskynlik deur menslike besoedeling beïnvloed word, soos Plank-1, en dat daar moontlik ook ‘n informele nedersetting by Berg-2 betrokke is. Na verdere ondersoek is gevind dat Berg-2 inderdaad ook stroomaf van 'n ander informele nedersetting geleë is, wat bewys dat die E. coli-populasiestruktuur 'n suksesvolle manier is om E. coli kontaminasie te verbind met besproeiingswater. Patogeniese faktore, wat in E. coli voorkom en maagkieme veroorsaak, is vooraf getoets in elkeen van die 153 E. coli-isolate wat tydens die studie geïdentifiseer is. Twee ‘enteropathogenic’ E. coli (EPEC)-stamme is uit die besproeiingswater geïsoleer: een uit die Plankenburgrivier (Plank-3), en die ander uit 'n boorgat in die Drakenstein-gebied (Boorgat A1). Hierdie inligting dui aan dat boorgatwater nie so veilig is as wat voorheen vermoed is nie, en dat bakteriese kontaminasie wel vookom wat nie alleen die grondwater besmet nie, maar ook daarin oorleef. Die voorkoms van die EPEC-stamme in hierdie studie is ‘n aanduiding dat beide grond- en opppervlakwater ewe gevaarlik kan wees, en dat daar dus geen waarborg vir die veiligheid van die water is nie. Die behandeling van grond- en oppervlakwater, wat vir die besproeiing van vars produkte gebruik word, moet daarom ernstig oorweeg word om moontlike uitbrake van E. coli op vars produkte te verhoed.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/79801
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