Applied Biology and Biochemistry Publications

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Browsing Applied Biology and Biochemistry Publications by Author "Abia, A.L."

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    Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study
    (MDPI, 2024-08-23) Hetsa, B.A.; Asante, J.; Mbanga, J.; Ismail, A.; Abia, A.L.; Amoako, D.G.; Essack, S.Y.
    Staphylococcus aureus is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of S. aureus isolates from patients with bloodstream infections in KwaZulu-Natal, South Africa, to gain insights into their resistance mechanisms, virulence factors, and clonal and phylogenetic relationships. Six multidrug-resistant (MDR) S. aureus isolates, comprising three methicillin-resistant S. aureus (MRSA) and three methicillin-susceptible S. aureus (MSSA), underwent whole genome sequencing and bioinformatics analysis. These isolates carried a range of resistance genes, including blaZ, aac(6′)-aph(2″), ant(9)-Ia, ant(6)-Ia, and fosB. The mecA gene, which confers methicillin resistance, was detected only in MRSA strains. The isolates exhibited six distinct spa types (t9475, t355, t045, t1265, t1257, and t7888) and varied in virulence gene profiles. Panton–Valentine leukocidin (Luk-PV) was found in one MSSA isolate. Two SCCmec types, IVd(2B) and I(1B), were identified, and the isolates were classified into four multilocus sequence types (MLSTs), with ST5 (n = 3) being the most common. These sequence types clustered into two clonal complexes, CC5 and CC8. Notably, two MRSA clones were identified: ST5-CC5-t045-SCCmec_I(1B) and the human-associated endemic clone ST612-CC8-t1257-SCCmec_IVd(2B). Phylogenomic analysis revealed clustering by MLST, indicating strong genetic relationships within clonal complexes. These findings highlight the value of genomic surveillance in guiding targeted interventions to reduce treatment failures and mortality.
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    Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa
    (Frontiers in Veterinary Science, 2021-02-26) Mbanga, J.; Amoako, D.G.; Abia, A.L.; Allam, M.; Ismail, A.; Essack, S. Y.
    There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the blaTEM1B gene and a single isolate the blaCTX−M−14 and blaCTX−M−55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.
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    Whole genome sequencing reveals insights into antibiotic resistant Klebsiella grimontii novel sequence type ST350 isolated from a wastewater source in South Africa
    (Journal of Biotech Research, 2022) Mbanga, J.; Amoako, D.G.; Abia, A.L.; Fatoba, D.; Essack, S.
    Klebsiella grimontii is a recently identified species that has been implicated in clinical infections. Few or no reports on environmental K. grimontii exist from Africa. This study was part of a broader longitudinal research that aimed to assess the distribution, antibiotic resistance patterns, and genomics of Enterobacterales obtained from raw and treated wastewater and the associated river water of a wastewater treatment plant (WWTP) in KwaZulu-Natal, South Africa. We reported the genomics of an antibiotic resistant Klebsiella grimontii isolate obtained from the raw influent of the WWTP. Following phenotypic characterisation and antibiotic susceptibility testing, the isolate was sequenced on an Illumina MiSeq machine. Raw reads were assembled de novo by using SPAdes (v3. 6.2) prior to bioinformatics analysis. The assembled K. grimontii INF139 genome was 6,369,878 bp, with 113 contiguous sequences (> 200 bp) and 55.4% GC content. The isolate was assigned a novel sequence type ST350. Genomic analysis revealed the presence of chromosomally encoded β-lactamase (blaOXY-6-1) and fluoroquinolone (oqxB) resistance genes. Virulence factors encoding antiphagocytic, iron acquisition, and Intracellular survival properties were identified. Mobilome analysis revealed the presence of plasmid replicons (ColRNAI, FIA (pBK30683), IncFII, IncFII (Yp)) and insertion sequences (ISIX2, ISSen9, ISIS, IS1A). To our knowledge, this is the first description of antibiotic resistant K. grimontii from the water environment from Africa. The presence of this antibiotic resistant and potentially pathogenic isolate in the water environment is worrying as it may be disseminated into river systems used by informal settlements.