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Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing
Thesis (MScFoodSc)--Stellenbosch University, 2023.
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Stellenbosch : Stellenbosch University
2023
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| access_status_str | Open Access |
| author | Lambrechts, Karlene |
| author2 | Rip, Diane |
| author_browse | Lambrechts, Karlene Rip, Diane |
| author_facet | Rip, Diane Lambrechts, Karlene |
| author_sort | Lambrechts, Karlene |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScFoodSc)--Stellenbosch University, 2023. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/129412 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:42:12.448Z |
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| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
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| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/129412 Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing Lambrechts, Karlene Rip, Diane Gouws, Pieter Stellenbosch University. Faculty of Agrisciences. Dept. of Food Science. Listeria monocytogenes -- South Africa -- Western Cape Fish trade -- South Africa -- Western Cape Listeria monocytogenes -- Genetics Food -- Safety measures Food contamination Food industry and trade -- Environmental aspects Whole genome sequencing -- Technique UCTD Thesis (MScFoodSc)--Stellenbosch University, 2023. ENGLISH ABSTRACT: Numerous global outbreaks have been linked to various fish products, emphasising the importance of studying Listeria monocytogenes. The bacterium presents a significant challenge in both fish and the fish food processing environment (FPE), yet there is limited information in South African literature regarding its lineage distribution, resistance mechanisms and survival determinants. Understanding these aspects is crucial for food safety. This research focusses on the investigation of L. monocytogenes from fish products, the fish FPE, and clinical cases from the Western Cape, South Africa. It addresses the lineage distribution, presence of sanitiser resistance genes, antibiotic resistance, and survival mechanisms of these isolates giving insight to the pathogenicity and ability to survive and persist. In this study, forty-six (n=46) L. monocytogenes isolates were examined, originating from fish products (n=32) and the FPE (n=6) (e.g. salmon, smoked trout, fresh hake, and oysters) as well as clinical cases (n=8). These fish isolates came from seven different factories (Factory A-G) that process and package various fish products. The findings indicated that all clinical isolates belonged to lineage I, while the majority of fish and FPE isolates were categorised into lineage II (p<0.01). Whole genome sequencing (WGS) further categorised twenty-four L. monocytogenes isolates into sequence types (STs), serotypes, and clonal complexes (CCs). The WGS data identified three serogroups (1/2a, 1/2b and 4b), eight CCs (CC1, CC3, CC5, CC54, CC87, CC121, CC155, CC204) and ten different STs (ST1, ST3, ST5, ST54, ST87, ST121, ST155, ST204, ST515, ST876), with all clinical isolates belonging to serogroup 4b, CC1, which is a hypervirulent CC of L. monocytogenes. In contrast, the isolates from fish products and the FPE were distributed across eight STs and eight different CCs, with CC121 being the most prevalent. Interestingly, one fish isolate carried a hypervirulent, CC1(ST515) strain. Additionally, a persistent strain was identified within two factories (Factory A; ST121 and C; ST204). All isolates, (n=24) were found to carry Listeria pathogenicity island (LIPI) 1 and 2. Additionally, LIPI-3 was detected in 50% of the isolates, specifically those belonging to lineage I (ST1, ST3, ST54, ST515, and ST876), which were isolated from both fish products and all clinical cases. LIPI-4, on the other hand, was identified in one fish isolate, which was from lineage I, serotype 4b, ST87. Five isolates from fish and the FPE exhibited phenotypic resistance to antibiotics, including tetracycline (n=2), sulphamethoxazole/trimethoprim (n=2), erythromycin (n=1), and chloramphenicol (n=1). Three clinical isolates showed resistance to sulphamethoxazole/trimethoprim. None of the isolated showed multidrug-resistance. Furthermore, four intrinsic antibiotic resistance genes (fosX, mprF, norB, and sul) were present in all 24 isolates. Stress survival islets (SSI) were identified, with SSI-2 found in all five ST121 (serotype 1/2a) isolates from fish products. SSI-1 was identified in 44% of fish and fish FPE isolates, including various STs (ST3, ST5, ST155, and ST204) across different serotypes and lineages. SSIs confer growth advantages to L. monocytogenes during various environmental stresses routinely encountered in the FPE. Aside from the bcrABC gene cassette (benzalkonium chloride resistance cassette) and emrC (efflux- mediated resistance gene C) genes identified using PCR, WGS data revealed that 42% of the isolates (n=10) harboured the Tn1688_qac (ermC) transposon, which provides tolerance to quaternary ammonium compounds (QACs). Five distinct plasmids were identified in 13 isolates from fish products and their FPE: pLM5578, pLGUG1, N1011A plasmid, pLM33, and Dop1. It is worth noting that all ST121(CC121) isolates in this study carried SSI-2, pLM5778, and the Tn6188 transposon. These plasmids play a pivotal role in enhanced tolerance to various stresses encountered in the FPE, thereby facilitating the survival of these strains in their environment. Comparing the CCs and STs found in this study to global reports on clinical cases highlights the potential risk posed by these fish products to immunocompromised individuals. The presence of major virulence genes in these isolates (LIPI-1, LIPI-2, LIPI-3 and LIPI-4) is particularly concerning, especially given that many of these products are ready-to-eat. The ability of L. monocytogenes to survive and grow in refrigeration temperatures increases the risk of these foods even more. The findings underscore the importance of understanding the risk associated with these foods and provides insights into the reasons behind L. monocytogenes survival and persistence. Furthermore, as no prior research on L. monocytogenes in fish products in South Africa exists, this study offers valuable baseline information for future investigations and food safety considerations. AFRIKAANSE OPSOMMING: Verskeie globale uitbrake is aan visprodukte gekoppel, wat die belangrikheid van die bestudering van Listeria monocytogenes beklemtoon. Hierdie bakterium stel 'n beduidende uitdaging in beide vis en die vis- prosseseringsomgewing voor, maar daar is beperkte inligting in die Suid-Afrikaanse literatuur oor L. monocytogenes se genetiese diversiteit, weerstandbiedende meganismes en oorlewingsbepalers. Begrip van hierdie aspekte is noodsaaklik vir voedselveiligheid. Hierdie waarnemingstudie het gefokus op die ondersoek van L. monocytogenes vanaf visprodukte, die vis-prosseseringsomgewing en kliniese gevalle vanuit die Wes-Kaap, Suid-Afrika. Dit hou verband met die genetiese diversiteit, teenwoordigheid van weerstandsgene teen kwaternêre ammoniumverbindings (ontsmettingsmiddels), antibiotiese weerstandbiedendheid en oorlewingsmeganismes van hierdie isolate, wat insig gee in die patogeniteit en die vermoë om te kan oorleef in die prosseseringsomgewing. In hierdie studie is ses-en-veertig (n=46) L. monocytogenes isolate ondersoek, afkomstig van visprodukte (n=32) en die vis-prosseseringsomgewing (n=6) (bv. salmon, gerookte forel, vars snoek en oesters), sowel as kliniese gevalle (n=8). Hierdie isolate vanaf visprodukte kom van sewe verskillende fabrieke (Fabriek A-G) wat verskeie visprodukte verwerk en verpak. Die bevindinge dui aan dat alle kliniese isolate behoort tot stam I, terwyl die meeste vis- en -prosseseringsomgewing isolate geval het onder stam II (p<0.01). WGS het verder L. monocytogenes isolate in STs, serotipes en CCs ingedeel. Die WGS-data het drie serotipes (1/2a, 1/2b en 4b), agt CCs (CC1, CC3, CC5, CC54, CC87, CC121, CC155, CC204) en tien verskillende ST's (ST1, ST3, ST5, ST54, ST87, ST121, ST155, ST204, ST515, ST876) geïdentifiseer, met al die kliniese isolate wat behoort tot serotipe 4b, CC1, wat 'n hipervirulente CC van L. monocytogenes is. In teenstelling hiermee is die isolate van visprodukte en die vis-prosseseringsomgewing oor agt ST's en agt verskillende CC's versprei, met CC121 wat die mees algemeen was. Interessant genoeg was een visi-isolaat geklassifiseer in die hipervirulente, CC1(ST515) stam. Daarbenewens is 'n volhardende stam geïdentifiseer in twee fabrieke (Fabriek A; ST121 en C; ST204). Al die isolate (n=24) is gevind om Listeria-patogenisiese eiland (LIPI) 1 en 2 te dra. Daarbenewens is LIPI-3 in 50% van die isolate geïdentifiseer, spesifiek dié wat behoort tot stam I (ST1, ST3, ST54, ST515, en ST876), wat uit beide visprodukte en in alle kliniese gevalle geïsoleer was. LIPI-4 is aan die ander kant in een vis-isolaat geïdentifiseer, wat behoort tot stam I, serotipe 4b, ST87. Vyf isolate van vis en die vis-prosseseringsomgewing het fenotipiese weerstand teen antibiotika getoon, insluitend tetrasiklien, sulfametoksasool/trimetoprim, eritromisien en chloramfenikol, getoon. Drie kliniese isolate het weerstand teen sulfametoksasool/trimetoprim getoon. Verder was vier intrinsieke antibiotikaweerstandsgene (fosX, mprF, norB, en sul) in al 24 isolate teenwoordig. Stressoorlewings-eilande (SOE) is geïdentifiseer, met SOE-2 wat in alle (n=5) ST121 (serotipe 1/2a) isolate van visprodukte gevind was. SOE-1 is in 44% van vis- en vis-prosseseringsomgewing -isolate geïdentifiseer, insluitend verskeie ST's (ST3, ST5, ST155, en ST204) oor verskeie serotipes en stamme. SOE's verleen groeivoordele aan L. monocytogenes tydens verskeie omgewingsstresse wat gereeld in die voedselprosseseringsomgewing ondervind word. Afgesien van die bcrABC weerstandbiedende geen en emrC geen wat met PCR geïdentifiseer was, het WGS-data aan die lig gebring dat 42% van die isolate (n=10) die Tn1688_qac (ermC)-transposoon bevat, wat weerstand bied teen kwaternêre ammoniumverbindings ontsmettingsmiddels. Vyf onderskeie plasmiede is in 13 isolate van visprodukte en hul vis-prosseseringsomgewing geïdentifiseer: pLM5578, pLGUG1, N1011A- plasmied, pLM33, en Dop1. Verder, alle ST121(CC121)-isolate in hierdie studie het die SOE-2, pLM5778, en die Tn6188-transposoon teenwoordig gehad. Hierdie plasmiede speel 'n deurslaggewende rol in verhoogde weerstand teen verskeie stresvolle omgewings wat in die voedselprosseseringsomgewing ondervind word, wat die oorlewing van hierdie isolate in hul omgewing fasiliteer. Vergelyking van die CC's en ST's wat in hierdie studie gevind is met globale verslae oor kliniese gevalle beklemtoon die potensiële risiko wat hierdie visprodukte vir individue met verswakte immuun stelsels inhou. Die teenwoordigheid van belangrike virulensie gene in hierdie isolate (LIPI-1, LIPI-2, LIPI-3 en LIPI-4) is veral kommerwekkend, veral as ‘n mens in aanmerking neem dat baie van hierdie vis-produkte gereed is om te eet, en geen verhitting of gaar-maak nodig het nie. Die vermoë van L. monocytogenes om te oorleef en te groei by yskas-temperature, verhoog die risiko van hierdie vis-produkte nog meer. Die bevindings beklemtoon die belangrikheid van die begrip vir die risiko wat met hierdie voedsel gepaard gaan, en bied insig in die redes vir die oorlewing van L. monocytogenes. Verder, aangesien geen voorafgaande navorsing oor L. monocytogenes in visprodukte in Suid-Afrika bestaan nie, bied hierdie studie waardevolle grondslag inligting vir toekomstige ondersoeke en voedselveiligheidsoorwegings. Masters 2023-11-30T08:28:39Z 2024-02-20T10:41:13Z 2023-11-30T08:28:39Z 2024-02-20T10:41:13Z 2023-12 Thesis https://scholar.sun.ac.za/handle/10019.1/129412 en_ZA Stellenbosch University xiv, 98 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Listeria monocytogenes -- South Africa -- Western Cape Fish trade -- South Africa -- Western Cape Listeria monocytogenes -- Genetics Food -- Safety measures Food contamination Food industry and trade -- Environmental aspects Whole genome sequencing -- Technique UCTD Lambrechts, Karlene Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing |
| title | Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing |
| title_full | Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing |
| title_fullStr | Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing |
| title_full_unstemmed | Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing |
| title_short | Genetic diversity of Listeria monocytogenes from the fish products, the fish food processing environment and clinical origin in the Western Cape, South Africa using whole genome sequencing |
| title_sort | genetic diversity of listeria monocytogenes from the fish products the fish food processing environment and clinical origin in the western cape south africa using whole genome sequencing |
| topic | Listeria monocytogenes -- South Africa -- Western Cape Fish trade -- South Africa -- Western Cape Listeria monocytogenes -- Genetics Food -- Safety measures Food contamination Food industry and trade -- Environmental aspects Whole genome sequencing -- Technique UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/129412 |
| work_keys_str_mv | AT lambrechtskarlene geneticdiversityoflisteriamonocytogenesfromthefishproductsthefishfoodprocessingenvironmentandclinicalorigininthewesterncapesouthafricausingwholegenomesequencing |