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J Environ Manage

Title:		"Genomic analysis of antibiotic-resistant Enterococcus spp. reveals novel enterococci strains and the spread of plasmid-borne Tet(M), Tet(L) and Erm(B) genes from chicken litter to agricultural soil in South Africa"
Author(s):		Fatoba DO; Amoako DG; Akebe ALK; Ismail A; Essack SY;
Address:		"Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa. Electronic address: dorcas4c@gmail.com. Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa; Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa. Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa. Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa"
Journal Title:		J Environ Manage
Year:		2022
Volume:		20211117
Issue:		Pt B
Page Number:		114101 -
DOI:		10.1016/j.jenvman.2021.114101
ISSN/ISBN:		1095-8630 (Electronic) 0301-4797 (Linking)
Abstract:		"Manure from food animals exposed to antibiotics is often used as soil fertiliser, potentially releasing antibiotic-resistant bacteria (ARB) with diverse antibiotic-resistance genes (ARGs) into the soil. To determine the impact of chicken litter application on the soil resistome, Enterococcus spp. isolated from chicken litter and soil samples collected before and after the soil amendment were characterised, using whole-genome sequencing and bioinformatics tools. Nineteen Enterococcus spp. isolates from the three sources were sequenced on Illumina Miseq platform to ascertain the isolates' resistome, mobilome, virulome, clonality, and phylogenomic relationships. Multilocus sequence typing (MLST) analysis revealed eight novel sequence types (STs) (ST1700, ST1752, ST1753, ST1754, ST1755, ST1756, ST1004, and ST1006). The isolates harboured multiple resistance genes including those conferring resistance to inter alia macrolides-lincosamide-streptogramin (erm(B), lnu(B), lnu(G), lsaA, lsaE, eat(A), msr(C)), tetracycline (tet(M), tet(L), tet(S)), aminoglycosides (aac(6')-Ii, aac(6')-Iih, ant(6)-Ia, aph(3')-III, ant(9)-Ia), fluoroquinolones (efmA, and emeA), vancomycin (VanC VanC-2, VanXY, VanXYC-3, VanXYC-4, VanRC), and chloramphenicol (cat). The litter-amended soil harboured new ARB (particularly E. faecium) and ARGs (ant(6)-Ia, aac(6')-Ii, aph(3')-III), lnu(G), msr(C), and eat(A), efmA) that were not previously detected in the soil. The identified ARGs were associated with diverse mobile genetic elements (MGEs) such as insertion sequences (IS6, ISL3, IS256, IS30), transposons (Tn3 and Tn916) and plasmids (repUS43, repUS1, rep9b, and rep 22). Twenty-eight virulence genes encoding adherence/biofilm formation (ebpA, ebpB, ebpC), antiphagocytosis (elrA) and bacterial sex pheromones (Ccf10, cOB1, cad, and camE), were detected in the genomes of the isolates. Phylogenomic analysis revealed a close relationship between a few isolates from litter-amended soil and the chicken litter isolates. The differences in the ARG and ARB profiles in the soil before and after the litter amendment and their association with diverse MGEs indicate the mobilisation and transmission of ARGs and ARB from the litter to the soil"
Keywords:		"Angiotensin Receptor Antagonists Angiotensin-Converting Enzyme Inhibitors Animals Anti-Bacterial Agents/pharmacology *Chickens Drug Resistance, Bacterial/genetics *Enterococcus Genomics Microbial Sensitivity Tests Multilocus Sequence Typing Plasmids Soil;"
Notes:		"MedlineFatoba, Dorcas Oladayo Amoako, Daniel Gyamfi Akebe, Abia Luther King Ismail, Arshad Essack, Sabiha Y eng England 2021/11/21 J Environ Manage. 2022 Jan 15; 302(Pt B):114101. doi: 10.1016/j.jenvman.2021.114101. Epub 2021 Nov 17"