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This study detected methicillin-resistant Staphylococcus aureus (MRSA) isolates circulating in poultry and farm workers at an intensive poultry production system in uMgungundlovu, South Africa and established the genetic relatedness and characteristics of the isolates using whole genome sequencing (WGS). A total of 145 S. aureus were isolated from poultry (120) and occupational workers (25) in the "farm to fork" continuum (farm, transport, slaughterhouse, and retail points). Twelve MRSA (12/145; 8.3%) isolates were found in the poultry food-chain. MRSA isolates were subjected to antibiotic susceptibility testing against a panel of 20 antibiotics using the broth dilution method and their whole genome was sequenced via the Illumina MiSeq. All the MRSA isolates were multi-drug resistant (MDR) and carried the mecA gene on the SCCmec mobile genetic element (MGE). The majority (11/12) of the MRSA isolates circulating between humans and animals in the continuum belonged to a human-associated clone, ST612-CC8-t1257-SCCmec_IVd (2B), previously reported in South Africa. Other MGEs present in the isolates included: plasmid replicons based on Rep 7 and 20, insertion sequences (IS1182), and prophages (phi2958PVL). Genomic analysis identified a distinct acquired antibiotic resistome in the clone, which accurately predicted the phenotypic antibiograms. Phylogenetic analysis clustered the isolates within the major cluster (I), suggesting the spread of the local dominant multidrug resistance MRSA clone ST612-CC8-t1257-SCCmec_IVd (2B) between humans and animals along the 'farm to fork' continuum. The findings of this study suggest the need to establish appropriate control measures to curb the spread of MDR-MRSA in the food chain.

Anaerobic ammonium oxidation (ANAMMOX) represents an efficient, cost-effective, but sensitive nitrogen removal process for wastewater treatment. Different reactor configurations have been used in full-scale applications but each configuration has unique characteristics, which could influence process performance and community dynamics. The objective of this study is thus to analyze the impact of mixing conditions on nitrogen removal and community structures in a hybrid up-flow anaerobic sludge blanket reactor (H-UASB), moving bed biofilm reactor (MBBR) and gas-lift reactor (GLR). Community dynamics were studied through shotgun sequencing, while concentrations of NH4+, NO3- and NO2- were determined colorimetrically. During the study, MBBR displayed the highest average nitrogen removal efficiency (NRE) (67%) followed by H-UASB (63%), and then GLR (54%). The relative abundance of AMX in the suspended biomass was consistently higher in H-UASB than in MBBR and GLR, while that of nitrite-oxidizing bacteria (NOB) and complete ammonia-oxidizing bacteria (CMX) was higher in MBBR than in GLR and H-UASB. It was observed that the relative abundance of ammonia-oxidizing bacteria (AOB) in the suspended biomass fluctuated across the reactors. The relative abundance of CMX and Nitrospira in the biofilms in H-UASB and GLR was higher than in the suspended biomass, while comparable abundance was observed in MBBR. On the contrary, the relative abundance of AMX in the suspended biomass in H-UASB and MBBR was higher than in the biofilms, whereas it was comparable in the GLR. It was thus concluded that the mixing conditions in the three reactors influenced process performance and community dynamics.

Objectives Here we describe the draft genome sequence of a clinical Acinetobacter haemolyticus isolate (A109R1B4) from a rectal swab of a hospitalised patient in South Africa. Methods Genomic DNA from the isolate was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antimicrobial resistance genes and sequence type were identified. Results The genome comprised 281 contigs with a total assembly length of 3 371 389 bp, a G + C content of 39.9% and an N50 value of 58 196 bp, and reference coverage was 93.08 while the coverage was 88.08. A total of 3387 genes, 3292 coding sequences (CDS), 3175 coding genes and 95 RNA genes were detected. The antimicrobial resistance genes blaOXA-264 and aac(6ʹ)-Ig were detected. Conclusion The genome sequence reported will serve as a reference point for molecular epidemiological studies of antibiotic-resistant A. haemolyticus in Africa.

Objectives Here we report the draft genome sequence of a methicillin-resistant Staphylococcus epidermidis strain (sequence type 59) isolated from a pooled rectal sample from pigs collected in an abattoir in South Africa. Methods Genomic DNA of S. epidermidis PR246B0 was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using CLC Genomics Workbench (QIAGEN). The assembled contigs were annotated and antimicrobial resistance genes, plasmids and the sequence type were identified. Results The genome comprised a circular chromosome of 2 537 769 bp, with a G-C content of 32.32% and various antimicrobial resistance genes associated with resistance to β-lactams, fluoroquinolones, aminoglycosides, fosfomycin, macrolides, lincosamides and tetracycline. Genome analysis also revealed the presence of seven plasmid replicon types. Conclusion The genome sequence reported herein will provide useful information for a better understanding of the genetic structure of the S. epidermidis genome in Africa.