Browsing by Author "Rahman, Abdur"

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    Comparative Genomic Analysis of a Panton–Valentine Leukocidin-Positive ST22 Community-Acquired Methicillin-Resistant Staphylococcus aureus from Pakistan
    (MDPI, 2022-04-08) Ullah, Nimat; Nasir, Samavi; Ishaq, Zaara; Anwer, Farha; Raza, Tanzeela; Rahman, Moazur; Alshammari, Abdulrahman; Alharbi, Metab; Bae, Taeok; Rahman, Abdur; Ali, Amjad; Microbiology and Immunology, School of Medicine
    Staphylococcus aureus (S. aureus) ST22 is considered a clinically important clone because an epidemic strain EMRSA-15 belongs to ST22, and several outbreaks of this clone have been documented worldwide. We performed genomic analysis of an S. aureus strain Lr2 ST22 from Pakistan and determined comparative analysis with other ST22 strains. The genomic data show that Lr2 belongs to spa-type t2986 and harbors staphylococcal cassette chromosome mec (SCCmec) type IVa(2B), one complete plasmid, and seven prophages or prophage-like elements. The strain harbors several prophage-associated virulence factors, including Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin (TSST). The single nucleotide polymorphism (SNPs)-based phylogenetic relationship inferred from whole genome and core genome revealed that strain Lr2 exhibits the nearest identities to a South African community-acquired methicillin-resistant S. aureus (CA-MRSA) ST22 strain and makes a separate clade with an Indian CA-MRSA ST22 strain. Although most ST22 strains carry blaZ, mecA, and mutations in gyrA, the Lr2 strain does not have the blaZ gene but, unlike other ST22 strains, carries the antibiotic resistance genes erm(C) and aac(6')-Ie-aph(2″)-Ia. Among ST22 strains analyzed, only the strain Lr2 possesses both PVL and TSST genes. The functional annotation of genes unique to Lr2 revealed that mobilome is the third-largest Cluster of Orthologous Genes (COGs) category, which encodes genes associated with prophages and transposons. This possibly makes methicillin-resistant S. aureus (MRSA) Lr2 ST22 strain highly virulent, and this study would improve the knowledge of MRSA ST22 strains in Pakistan. However, further studies are needed on a large collection of MRSA to comprehend the genomic epidemiology and evolution of this clone in Pakistan.
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    Genomic Investigation of Methicillin-Resistant Staphylococcus aureus ST113 Strains Isolated from Tertiary Care Hospitals in Pakistan
    (MDPI, 2021-09-17) Ullah, Nimat; Dar, Hamza Arshad; Naz, Kanwal; Andleeb, Saadia; Rahman, Abdur; Saeed, Muhammad Tariq; Hanan, Fazal; Bae, Taeok; Ali, Amjad; Microbiology and Immunology, School of Medicine
    Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant and opportunistic pathogen. The emergence of new clones of MRSA in both healthcare settings and the community warrants serious attention and epidemiological surveillance. However, epidemiological data of MRSA isolates from Pakistan are limited. We performed a whole-genome-based comparative analysis of two (P10 and R46) MRSA strains isolated from two provinces of Pakistan to understand the genetic diversity, sequence type (ST), and distribution of virulence and antibiotic-resistance genes. The strains belong to ST113 and harbor the SCCmec type IV encoding mecA gene. Both the strains contain two plasmids, and three and two complete prophage sequences are present in P10 and R46, respectively. The specific antibiotic resistance determinants in P10 include two aminoglycoside-resistance genes, aph(3')-IIIa and aad(6), a streptothrin-resistance gene sat-4, a tetracycline-resistance gene tet(K), a mupirocin-resistance gene mupA, a point mutation in fusA conferring resistance to fusidic acid, and in strain R46 a specific plasmid associated gene ant(4')-Ib. The strains harbor many virulence factors common to MRSA. However, no Panton-Valentine leucocidin (lukF-PV/lukS-PV) or toxic shock syndrome toxin (tsst) genes were detected in any of the genomes. The phylogenetic relationship of P10 and R46 with other prevailing MRSA strains suggests that ST113 strains are closely related to ST8 strains and ST113 strains are a single-locus variant of ST8. These findings provide important information concerning the emerging MRSA clone ST113 in Pakistan and the sequenced strains can be used as reference strains for the comparative genomic analysis of other MRSA strains in Pakistan and ST113 strains globally.
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    In silico designed Staphylococcus aureus B-cell multi-epitope vaccine did not elicit antibodies against target antigens suggesting multi-domain approach
    (Elsevier, 2022) Ullah, Nimat; Anwer, Farha; Ishaq, Zaara; Siddique, Abubakar; Shah, Majid Ali; Rahman, Moazur; Rahman, Abdur; Mao, Xinrui; Jiang, TingTing; Lee, Bok Luel; Bae, Taeok; Ali, Amjad; Microbiology and Immunology, School of Medicine
    The vaccine development strategies have evolved from using an entire organism as an immunogen to a single antigen and further towards an epitope. Since an epitope is a relatively tiny and immunologically relevant part of an antigen, it has the potential to stimulate more robust and specific immune responses while causing minimal adverse effects. As a result, the recent focus of vaccine development has been to develop multi-epitope vaccines that can target multiple virulence mechanisms. Accordingly, we designed multi-epitope vaccine candidates B (multi-B-cell epitope immunogen) and CTB-B (an adjuvant - cholera toxin subunit B (CTB) - attached to immunogen B) against S. aureus by employing immunoinformatics approaches. The designed vaccines are composed of B-cell epitope segments (20-mer) of the eight well-characterized S. aureus virulence factors, namely ClfB, FnbpA, Hla, IsdA, IsdB, LukE, SdrD, and SdrE connected in series. The designed vaccines were expressed, purified, and administered to C57BL/6 mice with Freund adjuvant to evaluate the immunogenicity and protective efficacy. The results revealed that the immunized mice showed high IgG titers for the immunogen, and the antibody titers increased significantly following the second immunization. However, the generated antibodies did not protect the mice from infection. The interaction of anti-B antibodies with source virulence factors showed that the generated antibodies have no binding affinity with any of the corresponding virulence factors. Our results demonstrate the limitation of the in silico designed B-cell multi-epitope vaccine and suggest that a protein domain carrying both linear and conformational B-cell epitopes might be a better choice for developing an effective multi-epitope vaccine against S. aureus.