A comprehensive genomic study of 208 neonatal Escherichia coli isolates collected from 2012 to 2021 at a major hospital in Blantyre, Malawi found extensive diversity in sequence types (STs), O‑antigens, and H‑antigens among strains causing invasive disease . Genomes from 169 isolates passed quality control and revealed 71 distinct STs, including 11 previously unreported types; over half of STs were observed only once . Among common lineages, ST69, ST131, ST10, and ST410 were most frequent, with ST410 highly enriched in cerebrospinal fluid samples suggesting invasive potential .
Researchers also catalogued 63 O‑antigen types—none exceeding 10% prevalence—and 34 H‑types, with only a handful appearing in more than one year. Notably, serotypes O15, O25B, and O8 appeared most often but no type dominated across years .
Using theoretical vaccine coverage models, the study shows that existing vaccine candidates like EXPEC4V or EXPEC9V would leave a large proportion of isolates unprotected. Crucially, the removal of O8 from some vaccine formulations could significantly reduce coverage in this setting .
Additionally, high resistance rates were observed: over 90% of strains demonstrated resistance to co‑trimoxazole, and many were multidrug resistant; yet meropenem resistance remained rare. Only amikacin and carbapenems remained reliable options in severe cases .
Implications for vaccine design in sub‑Saharan Africa: The extraordinary antigenic diversity among neonatal E. coli in Malawi presents a significant obstacle to one‑size‑fits‑all O‑antigen vaccines. The authors recommend vaccine strategies tailored to local serotype ecology and genetic surveillance integrated into design efforts.
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