Genomic analysis of antibiotic-resistant and susceptible Escherichia coli isolated from bovine sources in Maputo, Mozambique

Authors: TAVIANI, ELISA - Eduardo Mondlane University; MUCHONGO, ARSENIO - Eduardo Mondlane University; KIM, SEON WOO - US Department Of Agriculture (USDA); Van Kessel, Jo Ann; Haley, Bradd

Submitted to: Foodborne Pathogens and Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/8/2021
Publication Date: 6/3/2021
Citation: Taviani, E., Muchongo, A., Kim, S., Van Kessel, J.S., Haley, B.J. 2021. Genomic analysis of antibiotic-resistant and susceptible Escherichia coli isolated from bovine sources in Maputo, Mozambique. Foodborne Pathogens and Disease. https://doi.org/10.1089/fpd.2020.2901.
DOI: https://doi.org/10.1089/fpd.2020.2901

Interpretive Summary: Escherichia coli are part of the normal flora of the mammalian gut, but a small subset of can be occasional human and animal pathogens. Additionally, antimicrobial-resistant E. coli (pathogenic and non-pathogenic) have been commonly identified in the fecal populations from farm animals. The goal of this study was to explore the characteristics of E. coli from bovine production systems around Maputo, Mozambique. This study reports the draft genomes (DNA sequences) of 35 E. coli isolates recovered from 25 bovine fecal composite samples collected from 4 different production units in Maputo City and around Maputo Province, Mozambique. The genomes of these isolates were analyzed to determine the presence of antibiotic resistance genes, genetic relatedness (by classification into phylogroups), and presence of virulence factors that impact the pathogenicity of the bacteria. The majority of the isolates (82%) were identified as members of a single phylogenetic group (B1), with fewer isolates identified as members of group A, and a single isolate identified as group E/Clade I. Seven different antibiotic resistance genes were identified, with tet(B) being the most frequently detected. This gene generally imparts resistance to tetracycline, a common antibiotic. In total, 51 different virulence factors were identified among the genomes. This study demonstrates that E. coli from bovine sources in Mozambique encoded multiple antibiotic resistance elements, plasmids, and virulence factors. To the best of our knowledge this is the first genomic description of antibiotic-resistant E. coli isolated from bovine sources in Mozambique. This work will help researchers assess the public health risk of antibiotic-resistant and pathogenic E. coli to the residents interacting with these animals or using them as sources of food.

Technical Abstract: This study reports the draft genomes of 35 Escherichia coli isolates recovered from 25 bovine fecal composite samples collected from 4 different production units in Maputo City and around Maputo Province, Mozambique. The genomes of these isolates were analyzed to determine the presence of antibiotic resistance genes, genetic relatedness, and presence of virulence factors. Whole genome sequencing was conducted on a subset of isolates using an Illumina NextSeq 500 sequencing platform. The genomes were analyzed using BLAST for the presence of antibiotic resistance genes and virulence factors, as well as to determine their phylotypes, sequence types (ST), and ST complexes (ST Cplx). The majority of the isolates (82%) were identified as members of phylogenetic group B1, with fewer isolates identified as members of group A, and a single isolate identified as group E/Clade I. Sixteen different STs and five ST Cplx were identified. Seven different antibiotic resistance genes were identified, with tet(B) being the most frequently detected followed by aph(3'')-Ib, aph(6)-Id, and sul2. The resistance genes aadA1, blaTEM-1B, and dfrA1 were identified in three isolates carrying IncQ1 plasmids. In total, 51 different virulence factors were identified among the genomes. This study demonstrates that E. coli from bovine sources in Mozambique encoded multiple antibiotic resistance elements, plasmids, and virulence factors. To the best of our knowledge this is the first genomic description of antibiotic-resistant E. coli isolated from bovine sources in Mozambique.