Comparative genomics of Listeria species isolated from the meat processing chain in South Africa

English; This thesis, Comparative genomics of Listeria species isolated from the meat processing chain in South Africa, explores the applications of Whole Genome Sequencing (WGS) of meat products isolated from food and food processing facilities to enhance understanding of the overall distribution of genomic elements that contribute toward the pathogenicity and survival of Listeria spp. including L. monocytogenes, L. innocua, and L. welshimeri in food and food processing environments. The work in this thesis adds to the exponentially increasing body of evidence on the pathogen surveillance application of WGS in food industries. This study is to date the largest to report baseline data on the presence of Listeria spp. including L. monocytogenes, L. innocua, and L. welshimeri’s serogroups, lineages, Sequence Types, and Clonal Complexes across the meat value chain in SA. This study further highlights the association of multiple STs of Listeria spp. to different meat products in SA and their resistance and virulence traits as well as genetic mutations of certain subgroups found in food products. This study also showed how these pathogens thrive in different environments and conditions by developing tolerance and resistance against such factors. This thesis further explores the development of a rapid online tool for sequence typing of Listeria spp. from Next Generation Sequencing raw data The insights from this work directly informed the incorporation of WGS into the national surveillance of Listeria spp. and the information generated here can be used in food safety risk assessment, management, and protection public health. Afrikaans: Hierdie proefskrif, Vergelykende genomika van Listeria-spesies geïsoleer uit die vleisverwerkingsketting in Suid-Afrika, ondersoek die toepassings van volledige genoomvolgordebepaling (WGS) van vleisprodukte geïsoleer uit voedsel en voedselverwerkingsfasiliteite om die begrip van die algehele verspreiding van genomiese elemente wat bydra tot die patogenisiteit en oorlewing van Listeria spp., insluitend L. monocytogenes, L. innocua en L. welshimeri in voedsel- en voedselverwerkingsomgewings, te verbeter. Die werk in hierdie proefskrif dra by tot die eksponensieel toenemende aantal bewyse oor die patogeenmoniteringstoepassing van WGS in voedselbedrywe. Hierdie studie is tot op hede die grootste wat basislyndata oor die teenwoordigheid van Listeria spp., insluitend L. monocytogenes, L. innocua en L. welshimeri serogroepe, afstammelinge, volgordetipes en klonale komplekse oor die vleiswaardeketting in SA, gerapporteer het. Hierdie studie beklemtoon verder die assosiasie van veelvuldige ST's van Listeria spp. aan verskillende vleisprodukte in SA en hul weerstand- en virulensie-eienskappe, sowel as genetiese mutasies van sekere subgroepe wat in voedselprodukte voorkom. Hierdie studie het ook getoon hoe hierdie patogene in verskillende omgewings en toestande floreer deur toleransie en weerstand teen sulke faktore te ontwikkel. Hierdie proefskrif ondersoek verder die ontwikkeling van 'n vinnige aanlyn hulpmiddel vir volgordetipering van Listeria spp. vanaf ''Next Generation Sequencing'' rou data. Die insigte uit hierdie werk het direk die insluiting van WGS in die nasionale toesig van Listeria spp. beïnvloed, en die inligting wat hier gegenereer word, kan gebruik word in voedselveiligheidsrisikobepaling, -bestuur en -beskerming vir openbare gesondheid. IsiZulu: Lolu cwaningo, lwesifundo sokuqhathanisa izakhi zofuzo zezinhlobo ze-Listeriya ezihlukaniswe neketango lokucubungula inyama eNingizimu Afrika, ihlola ukusetshenziswa kwe-Whole Genome Sequencing (i-WGS) yemikhiqizo yenyama ehlukanisiwe ekudleni kanye nasezindaweni zokucubungula ukudla ukuze kuthuthukiswe ukuqonda kokusatshalaliswa okuphelele kwezakhi zofuzo ezifaka isandla ekuguleni nasekusindeni kwe-Listeriya spp. Kubandakanya nama--L. monocytogene, i-L. innocua , kanye ne-L. welshimeri ezindaweni zokucubungula ukudla kanye nasekudleni. Umsebenzi okulolu cwaningo wengeza endikimbeni yobufakazi obuba buningi ngokubhekwa kokusetshenziswa kwe-pathogen ye-WGS ezimbonini zokudla. Lolu cwaningo kuze kube manje yilo olukhulu kunazo zonke olubike ngemininingwane eyisisekelo ngobukhona be-Listeriya spp. okubandakanya ama-L. monocytogene, i-L. innocua , kanye namaqembu e-sero e-L. welshimeri , ukuhlobana, izinhlobo zokulandelana, kanye ne-Clonal Complexes kulo lonke uchungechunge lwenani lenyama e-SA. Lolu cwaningo luphinde futhi lugqamise ukuhlangana kwama-ST amaningi e-Listeriya spp. emikhiqizweni yenyama ehlukene e-SA kanye nezici zayo zokungazweli nobungozi kanye nokuguqulwa kofuzo kwamaqembu amancane athile atholakala emikhiqizweni yokudla. Lolu cwaningo luphinde lwabonisa ukuthi lawa magciwane akhula kanjani ezindaweni nezimo ezihlukahlukene ngokuthuthukisa ukubekezelelana nokumelana maqondana nezinto ezinjalo. Lolu cwaningo luphinde luhlole ukuthuthukiswa kwethuluzi elisheshayo eliku-inthanethi lokuthayipha ngokulandelana kwe-Listeriya spp. kusukela esizukulwaneni ukulandelanisa imininingwane eluhlaza Imininingwane evela kulo msebenzi yazisa ngokuqondile ukufakwa kwama-WGS ekugadweni kukazwelonke kwe-Listeriya spp. kanye nolwazi olukhiqizwa lapha lungasetshenziswa ekuhloleni ubungozi bokuphepha kokudla, ekulawuleni nasekuvikeleni impilo yomphakathi.

Grantor dc:publisher

University of Pretoria

Year dc:date.issued

2022

Advisor dc:contributor.advisor

• Reva, Oleg N.

• UCTD
• Comparative genomics
• Listeria
• Meat processing chain
• Food industry
• Whole genome sequencing (WGS)

Statement dc:rights

• © 2022 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria.

Language dc:language.iso

en

DOI

https://doi.org/10.25403/UPresearchdata.21682877

Identifier URI

DOI: https://doi.org/10.25403/UPresearchdata.21682877

Dc Identifier Other

A2023

OAI identifier oai:identifier

oai:repository.up.ac.za:2263/88689