Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa

Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data

Staphylococcus aureus is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on S. aureus pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approach that alleviates wastage of resources and redundancy in experiments. The current review covers how big data bioinformatics has been used in the analysis of S. aureus from publicly available -omics data to uncover mechanisms of infection and inhibition. Particularly, advances in the past two decades in biomarker discovery, host responses, phenotype identification, consolidation of information, and drug development are discussed highlighting the challenges and shortcomings. Overall, the review summarizes the diverse aspects of scrupulous re-analysis of S. aureus proteomic and transcriptomic expression datasets retrieved from public repositories in terms of the efforts taken, benefits offered, and follow-up actions. The detailed review thus serves as a reference and aid for (i) Computational biologists by briefing the approaches utilized for bacterial omics re-analysis concerning S. aureus and (ii) Experimental biologists by elucidating the potential of bioinformatics in biological research to generate reliable postulates in a prompt and economical manner.

Prevalence and Characteristics of Staphylococcus aureus Associated with Meat and Meat Products in African Countries: A Review

Antimicrobial resistance has been increasing globally, which negatively affects food safety, veterinary, and human medicine. Ineffective antibiotics may cause treatment failure, which results in prolonged hospitalisation, increased mortality, and consequently, increased health care costs. Staphylococcus aureus causes a diverse range of infections including septicaemia and endocarditis. However, in food, it mainly causes food poisoning by the production of enterotoxins. With the discovery of methicillin-resistant S. aureus strains that have a separate reservoir in livestock animals, which were termed as livestock-associated methicillin-resistant S. aureus (LA-MRSA) in 2005, it became clear that animals may pose another health risk. Though LA-MRSA is mainly transferred by direct contact, food transmission cannot be excluded. While the current strains are not very pathogenic, mitigation is advisable, as they may acquire new virulence genes, becoming more pathogenic, and may transfer their resistance genes. Control of LA-MRSA poses significant problems, and only Norway has an active mitigation strategy. There is limited information about LA-MRSA, MRSA in general, and other S. aureus infections from African countries. In this review, we discuss the prevalence and characteristics of antimicrobial susceptible and resistant S. aureus (with a focus on MRSA) from meat and meat products in African countries and compare it to the situation in the rest of the world.

Staphylococcus aureus in Intensive Pig Production in South Africa: Antibiotic Resistance, Virulence Determinants, and Clonality

Although Staphylococcus aureus is a major threat to the veterinary, agricultural, and public health sectors because of its zoonotic potential, studies on its molecular characterisation in intensive animal production are rare. We phenotypically and genotypically characterised antibiotic-resistant S. aureus in intensive pig production in South Africa, using the farm-to-fork approach. Samples (n = 461) were collected from the farm, transport vehicles, and the abattoir using the World Health Organisation on Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR) sampling protocol. Bacteria were isolated using selective media and identified using biochemical tests and polymerase chain reaction (PCR). Phenotypic resistance was determined using the disk diffusion method. Selected resistance and virulence genes were investigated using PCR. Clonality among the isolates was determined using the repetitive element sequence-PCR. In all, 333 presumptive staphylococcal isolates were obtained, with 141/333 (42.3%) identified as staphylococci biochemically. Ninety-seven (97; 68.8%) were confirmed as S. aureus using PCR, 52.6% of which were identified as methicillin-resistant S. aureus (MRSA) through the mecA gene. All the 97 S. aureus isolates (100%) were resistant to at least one of the antibiotics tested, with the highest resistance observed against erythromycin and clindamycin (84.50% each), and the lowest observed against amikacin (2.10%); 82.47% (80/97) were multidrug-resistant with an average multiple antibiotic resistance index of 0.50. Most of the phenotypically resistant isolates carried at least one of the corresponding resistance genes tested, ermC being the most detected. hla was the most detected virulence gene (38.14%) and etb was the least (1.03%). Genetic fingerprinting revealed diverse MRSA isolates along the farm-to-fork continuum, the major REP types consisting of isolates from different sources suggesting a potential transmission along the continuum. Resistance to antibiotics used as growth promoters was evidenced by the high prevalence of MDR isolates with elevated multiple antibiotic resistance indices >0.2, specifically at the farm, indicating exposure to high antibiotic use environments, necessitating antibiotic stewardship and proper infection control measures in pig husbandry and intensive pig production.

First genome sequence of Aeromonas hydrophilia novel sequence type 658 strain isolated from livestock in South Africa

OBJECTIVES

The underlying resistance mechanisms, defence systems, mobilome, virulome, clonality and global phylogenetic relationship of a novel sequence type (ST) 658 Aeromonas hydrophilia (A34a) isolated from a pig abattoir in South Africa was determined using whole-genome sequence (WGS) technology.

METHODS

Following isolation on chromogenic agar (CHROMID® CARBA SMART), microbial identification and antibiotic susceptibility testing were performed using a VITEK®2 platform. Genotyping involved WGS performed with an Illumina MiSeq platform.

RESULTS

The antibiotic resistome agreed with the resistance phenotype of the isolate and included antibiotic resistance determinants for β-lactams (bla_CPHA3 and bla_OXA-724). BLASTn analysis of resistome-encoding contigs affirmed chromosomally-mediated resistance. BURST algorithmic analysis identified the novel ST658 as a satellite variant. Virulome analysis predicted virulence genes of Aeromonas whose expression are critical for establishing infection in the host. Global phylogenomic analyses showed strain A34a is closely related to two international isolates from Sri Lanka (Ae25) and the USA (RU34A), although there is little to suggest that it was imported from abroad.

CONCLUSION

This is the first report on the genomic analysis of a novel ST658 A. hydrophilia, offering useful insights into its pathogenicity and global phylogenetics.

Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (bla_CPHA3 and bla_OXA-12) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (P_score ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium.

Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana

Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (P_score ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.

Diversity of SCCmec elements and spa types in South African Staphylococcus aureus mecA-positive blood culture isolates

BACKGROUND

The prevalence of Staphylococcus aureus varies depending on the healthcare facility, region and country. To understand its genetic diversity, transmission, dissemination, epidemiology and evolution in a particular geographical location, it is important to understand the similarities and variations in the population being studied. This can be achieved by using various molecular characterisation techniques. This study aimed to provide detailed molecular characterisation of South African mecA-positive S. aureus blood culture isolates by describing the SCCmec types, spa types and to lesser extent, the sequence types obtained from two consecutive national surveillance studies.

METHODS

S. aureus blood culture isolates from a national laboratory-based and enhanced surveillance programme were identified and antimicrobial susceptibility testing was performed using automated systems. A real-time PCR assay confirmed the presence of the methicillin-resistance determinant, mecA. Conventional PCR assays were used to identify the SCCmec type and spa type, which was subsequently analysed using the Ridom StaphType™ software. Multilocus sequence typing was performed on selected isolates using conventional methods. MRSA clones were defined by their sequence type (ST), SCCmec type and spa type.

RESULTS

A detailed description of findings is reported in this manuscript. SCCmec type III predominated overall followed by type IV. A total of 71 different spa types and 24 novel spa types were observed. Spa type t037 was the most common and predominated throughout followed by t1257. Isolates were multidrug resistant; isolates belonging to all SCCmec types were resistant to most of the antibiotics with the exception of type I; isolates with spa type t045 showed resistance to all antibiotics except vancomycin. The most diverse SCCmec-spa type complex was composed of the SCCmec type IV element and 53 different spa types.

CONCLUSION

Although ST data was limited, thereby limiting the number of clones that could be identified, the circulating clones were relatively diverse.

Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a blaNDM-1 Carbapenemase in South Africa

Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (P_score ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the bla_NDM-1 encoding contig (00022) and its flanking sequences revealed the bla_NDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing bla_NDM-1, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.