Whole-Genome Sequencing of Multidrug-Resistant Gram-Negative Bacteria Isolated from Clinical Samples in Liberia Using Oxford Nanopore Technology

Multidrug resistance (MDR) is a key driver of antimicrobial resistance (AMR) in all of sub-Saharan Africa; however, genomic AMR data from Liberia are unavailable. To fill the gap, this study utilized Oxford Nanopore long-read sequencing to produce draft genomes of seven multidrug-resistant isolates from four bacterial species ( Escherichia coli, Enterobacter hormaechei, Proteus mirabilis , and Shigella flexneri ) of diarrheal samples at Liberia’s National Public Health Reference Laboratory (NPHRL). The sequencing was of moderate quality (8–13×), long reads and BUSCO coverage (75 to 93 percent), thus enabling relevant de novo assembly and standardized annotation through PGAP. In the isolates, AMR determinants were found to confer resistance to β-lactams (including blaTEM variants and blaACT -16), fluoroquinolones ( qnrS 1 and mutations in gyr A, gyr B, par C and par E), aminoglycosides, sulfonamides, tetracyclines, phencyclines, and polymyxins, as well as RND/MFS efflux systems and global regulatory genes, including marA, soxS and mdtE. PlasmidFinder found IncFIA, IncFIB(K), and Col-type replicons in two isolates but no plasmid-encoded AMR genes, which suggests that the resistance of this collection is mainly chromosomally located. MLST showed that only partial allele profiles and the nearest-sequence-type matches were possible, indicating a great quantity of genetic diversity and region-specific E. coli lineages circulating in Liberia. These findings provide the initial genomic baseline of MDR Gram-negative pathogens in Liberia and show that whole-genome sequencing with Nanopores can be successfully performed in portable technology, which is likely to increase the need to consider higher-resolution genomic surveillance to direct stewardship and public health interventions.