Bacterial and genetic features of raw retail pork meat : integrative analysis of antibiotic susceptibility, whole-genome sequencing, and metagenomics

Show simple item record

dc.contributor.author Lowe, Michelle
dc.contributor.author Strasheim, Wilhelmina
dc.contributor.author Chan, Wai Yin
dc.contributor.author Perovic, Olga
dc.date.accessioned 2024-10-02T12:58:03Z
dc.date.available 2024-10-02T12:58:03Z
dc.date.issued 2024-08
dc.description DATA AVAILABITY STATEMENT: The assembled genome files were deposited in the National Center for Biotechnology Information GenBank and are available under the following BioProject numbers: PRJNA1006163 and PRJNA1137389. The Supplementary Materials contain additional data. en_US
dc.description.abstract The global antibiotic resistance crisis, driven by overuse and misuse of antibiotics, is multifaceted. This study aimed to assess the microbiological and genetic characteristics of raw retail pork meat through various methods, including the isolation, antibiotic susceptibility testing (AST), wholegenome sequencing (WGS) of selected indicator bacteria, antibiotic residue testing, and metagenomic sequencing. Samples were purchased from 10 pre-selected retail stores in Gauteng, South Africa. The samples were aseptically separated, with portions sent to an external laboratory for isolating indicator bacteria and testing for antibiotic residues. Identification of the isolated bacteria was reconfirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). AST was performed using the Microscan Walkaway system (Beckman Coulter, Brea, CA, USA). WGS and metagenomic sequencing were performed using the Illumina NextSeq 550 instrument (San Diego, CA, USA). The isolated E. coli and E. faecalis exhibited minimal phenotypic resistance, with WGS revealing the presence of tetracycline resistance genes. Both the isolated bacteria and meat samples harboured tetracycline resistance genes and the antibiotic residue concentrations were within acceptable limits for human consumption. In the metagenomic context, most identified bacteria were of food/meat spoilage and environmental origin. The resistome analysis primarily indicated beta-lactam, tetracycline and multidrug resistance genes. Further research is needed to understand the broader implications of these findings on environmental health and antibiotic resistance. en_US
dc.description.department Biochemistry, Genetics and Microbiology (BGM) en_US
dc.description.department Forestry and Agricultural Biotechnology Institute (FABI) en_US
dc.description.sdg SDG-03:Good heatlh and well-being en_US
dc.description.sdg SDG-12:Responsible consumption and production en_US
dc.description.sponsorship The South African Medical Research Council (SAMRC), a Fogarty International Center Global Infectious Disease research-training grant and the University of Pittsburgh and the National Institute for Communicable Diseases. en_US
dc.description.uri https://www.mdpi.com/journal/antibiotics en_US
dc.identifier.citation Lowe, M.; Strasheim, W.; Chan, W.Y.; Perovic, O. Bacterial and Genetic Features of Raw Retail Pork Meat: Integrative Analysis of Antibiotic Susceptibility, Whole-Genome Sequencing, and Metagenomics. Antibiotics 2024, 13, 700. https://doi.org/10.3390/antibiotics13080700. en_US
dc.identifier.issn 2079-6382 (online)
dc.identifier.other 10.3390/antibiotics13080700
dc.identifier.uri http://hdl.handle.net/2263/98450
dc.language.iso en en_US
dc.publisher MDPI en_US
dc.rights © 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). en_US
dc.subject Metagenomics en_US
dc.subject Retail pork meat en_US
dc.subject Whole-genome sequencing (WGS) en_US
dc.subject Antibiotic susceptibility testing (AST) en_US
dc.subject South Africa (SA) en_US
dc.subject SDG-03: Good health and well-being en_US
dc.subject SDG-12: Responsible consumption and production en_US
dc.title Bacterial and genetic features of raw retail pork meat : integrative analysis of antibiotic susceptibility, whole-genome sequencing, and metagenomics en_US
dc.type Article en_US


Files in this item

This item appears in the following Collection(s)

Show simple item record