Whole Genome Sequencing Reveals Virulence-Mobile Element Linkages And Phylogenetic Diversity In Multidrug-Resistant Escherichia Coli From Nigeria

Nubwa Medugu ^1* Mabel Kamweli Aworh ² Kenneth Iregbu ³ Philip Nwajiobi-Princewill ⁴ Dawn Hull ⁵ Lyndy Harden ⁶ Pallavi Singh ⁷ Stephen Obaro ⁸ Abiodun Egwuenu ⁹ Faith Adegboye ¹⁰ Ruth Egah ¹⁰ Leonard Uzairue ¹¹ Yahaya Mohammed ¹² Ifeyinwa Nwafia ¹³ Siddhartha Thakur ⁵

• ¹ Nile University of Nigeria, Abuja, Nigeria
• ² Fayetteville State University, Fayetteville, North Carolina, United States
• ³ National Hospital Abuja, Abuja, Nigeria
• ⁴ National Hospital, Abuja, Nigeria
• ⁵ North Carolina State University, Raleigh, North Carolina, United States
• ⁶ North Carolina Central University, Durham, North Carolina, United States
• ⁷ Northern Illinois University, DeKalb, Illinois, United States
• ⁸ University of Alabama at Birmingham, Birmingham, Alabama, United States
• ⁹ Nigerian Centre for Disease Control (NCDC), Abuja, Nigeria
• ¹⁰ International Foundation Against Infectious Disease in Nigeria, Abuja, Nigeria
• ¹¹ Faculty of Science, Federal University Oye Ekiti, Oye, Ekiti, Nigeria
• ¹² Usmanu Danfodiyo University Teaching Hospital, Sokoto, Sokoto, Nigeria
• ¹³ University of Nigeria, Nsukka, Nsukka, Enugu, Nigeria

Multidrug-resistant Escherichia coli poses a critical public health threat in Nigeria, where limited genomic surveillance hinders the understanding of virulence-resistance interplay. This cross-sectional study employed whole-genome sequencing to characterize 107 MDR-E isolates from a Nigerian tertiary hospital (2019-2020), analysing virulence genes, mobile genetic elements (MGEs), phylogroups, sequence types (STs), pathotypes, and antimicrobial resistance (AMR). We identified 2,021 virulence genes across nine functional categories, dominated by immune evasion (terC, 96.3%), adherence (fimH, 86%), and iron acquisition (fyuA, 63.6%). Strikingly, 81.3% of virulence genes were linked to MGEs, including MITEEc1 (75.7% of isolates) and IS30 (56.1%), with IncFII (17.8%) and Col156 (12.1%) plasmids co-harbouring virulence (e.g., traJ/traT, senB) and AMR genes (e.g., blaTEM-1B). Phylogroup B2 (32.7%) dominated, exhibiting high resistance to ampicillin (97.1%) and emerging meropenem resistance (11.4%). Globally disseminated STs (ST131, ST410, ST648) carried significantly more diverse virulence genes than minor clones (p = 0.028) and were strongly associated with double-serine QRDR mutations (gyrA_S83L: 97.6%, parC_S80I: 97.6%), which correlated with more virulence genes (24.2 vs. 22.3 genes) and resistance (MAR index: 0.7 vs. 0.5) compared to minor clones. Notably, 92% (61/66) of high-risk clones harboured these mutations, versus 57% (21/37)of low-risk clones, suggesting a fitness advantage enabling major clones to sustain larger genetic cargoes. Pathotyping revealed 54.2% as extraintestinal pathogenic E. coli (ExPEC), with 72.4% of these being uropathogenic (UPEC) and 5.2% ExPEC/EAEC hybrids, alongside 43.9% atypical ExPEC strains. Hierarchical clustering demonstrated phylogroup B2's genetic diversity and co-localization of plasmid-borne virulence/AMR genes. These findings underscore Nigeria's MDR-E crisis, driven by MGE-facilitated gene transfer, hybrid pathotypes, and globally disseminated high-risk clones harbouring double-serine QRDR mutations. There is continued need for robust genomic surveillance, stringent infection control measures, enhanced antibiotic stewardship, and exploration of antivirulence strategies (e.g., targeting fimH or yeh) to curb the spread of these highly adaptable pathogens in resource-limited settings and beyond.