Whole-Genome Shotgun Sequence of Drug-Resistant Staphylococcus aureus Strain SA9, Isolated from a Slaughterhouse Chicken Carcass in South Africa

Here, we describe the genomic sequence of a drug-resistant Staphylococcus aureus sequence type 239 (ST239) strain, SA9, isolated from a slaughterhouse chicken carcass in South Africa, including information about its antibiotic resistome, virulome, efflux genes, clonal lineage, and mobilome. This genomic information offers vital insights for the control of drug-resistant S. aureus.

S taphylococcus aureus is an important opportunistic pathogen of humans and animals and a leading global cause of foodborne disease (1). Poultry as a potential reservoir for the zoonotic transmission of drug-resistant S. aureus to humans has been well documented (2). Despite the apparent threat, the genomics of antibioticresistant S. aureus in food animals appear to be neglected in Africa (3,4). Toward this end, S. aureus SA9, isolated from a slaughterhouse chicken carcass in South Africa, was subjected to whole-genome sequencing (WGS). Antimicrobial susceptibility testing utilizing the broth microdilution method revealed its multidrugresistant profile.
Strain SA9 was isolated and confirmed using HiCrome Aureus agar base (HiMedia Laboratories, Mumbai, India) and an API Staph kit (bioMérieux, Marcy-l'Etoile, France), respectively. It was streaked onto Mueller-Hinton agar (MHA) plates and incubated at 37°C for 24 h. Following incubation, genomic DNA was extracted from 1 CFU of a visibly pure culture of the isolate using the GenElute bacterial genomic DNA kit (Sigma-Aldrich, St. Louis, MO, USA), quantified with a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA). A paired-end (2 ϫ 300-bp) library was prepared using an Illumina Nextera XT DNA sample preparation kit and sequenced on a MiSeq machine (Illumina, USA). The generated sequenced reads (1,448,958 reads) were quality assessed and trimmed using the next-generation sequencing (NGS) core tools in the CLC Genomics Workbench version 11.0.1 (CLC bio, Qiagen, Aarhus, Denmark). Default parameters were used for all software unless otherwise specified. The genome was de novo assembled using SPAdes version 3.11 (5), and 477 contigs (99ϫ coverage) were obtained, the longest being 79,480 bp, with an N 50 value of 35,831 bp. The CheckM tool (6), using lineage-specific marker sets from other genetically well-characterized, closely related S. aureus strains, was used to verify that the sequence reads were not from mixed species. The NCBI Prokaryotic Genome Annotation Pipeline (PGAP; version 4.3) (7) and Rapid Annotations using Subsystems Technology (RAST) server (version 2.0) (8) were used for annotation. The genome features were as follows: genome size, 3,055,359 bp; GC content, 33.50%; total number of genes, 3,565; total number of coding sequences (CDS), 3,506; number of coding genes, 3,332; number of RNA genes, 59; number of rRNAs, 13; and number of tRNAs, 42.
Data availability. This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. RQTC00000000. The version described here is the first version, RQTC01000000. The raw reads have been submitted to the SRA under accession no. SRR8583490.

ACKNOWLEDGMENTS
We are grateful to the South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation of South Africa (grant 98342).
Sabiha Y. Essack is the chairperson of the Global Respiratory Infection Partnership, which is sponsored by an unrestricted educational grant from Reckitt and Benckiser. All other authors declare that they have no competing interests regarding the publication of this paper.
Ethical approval was received from the Animal Research Ethics Committee (reference no. AREC 073/016PD) and the Biomedical Research Ethics Committee (reference no. BCA444/16) of the University of KwaZulu-Natal. The study was further registered with the South African National Department of Agriculture, Forestry and Fisheries [reference no. 12/11/1/5 (879)].