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Title: Genotype–Phenotype Correlation of β-Lactamase-Producing Uropathogenic Escherichia coli (UPEC) Strains from Bangladesh
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Authors: Maqsud Hossain, Tahmina Tabassum, Aura Rahman, Arman Hossain, Tamanna Afroze, Abdul Mueed Ibne Momen, Abdus Sadique, Mrinmoy Sarker, Fariza Shams, Ahmed Ishtiaque, Abdul Khaleque, Munirul Alam, Anwar Huq, Gias U.Ahsan & Rita R. Colwell
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This file introduces the original paper, explains the technical details of the replication analyses, and summarizes the replication of the original results.
- The original study conducted by Hossain et al. (2020) represents the first comparative analysis of the draft genome sequences of 11 uropathogenic Escherichia coli (UPEC) strains isolated from tertiary hospitals in Dhaka and Sylhet, Bangladesh.
- The study focused on comparing the genomic characteristics of these strains to each other and to other available UPEC strains.
- The strains belong to sequence types ST59, ST131, ST219, ST361, ST410, ST448, and ST4204.
- Identification of antibiotic resistance genes blaNDM-5, blaNDM-7, blaCTX-M-15, and blaOXA-1.
- Significant heterogeneity was observed within UPEC phylogroups in terms of virulence.
- A porition of the original data was reproduced and analysed.
- The replication focused on verifying the original findings and exploring the genotype-phenotype correlations using updated bioinformatics tools and methods.
- The analyses were replicated using the accession numbers from the original paper in conjuction with the latest online databases to generate raw data.
- The generated raw data was analysed using Iowa State HPC nova cluster using unix commands to reproduce Table 3.
- Python and R programming were used to reproduce the heatmaps.
- The replication study (confirmed a portion of the) original findings and provided additional insights into the distribution of virulence factors and antibiotic resistance genes among the UPEC strains.
- Table 3 illustrated the some slight variations between the original findings and reproduced data.
- The heatmaps facilitated a clear visual contrast between the original and reproduced data.
- The replication study supports the original conclusions drawn by Hossain et al. (2020) and underscores the importance of continuous surveillance of UPEC strains for a better understanding of their evolution and spread of resistance.