Table 2 Summary of the major attributes of the 2022–2023 and historical V. cholerae isolates in Malawi

Species

V. cholerae

V. cholerae

Serogroup, serotype, and biotype

Mostly O1 Ogawa and a minority of O1 Inaba El Tor and sporadic non-O1/O139

All O1 Ogawa El Tor

Pandemic strain

Pandemic

Pandemic

ST or clone

Mostly ST69 (7PET; outbreak); also, ST40 and ST635 (sporadic)

All ST69 (7PET)

Genomic wave

Late wave 3

Early wave 3

Genetic markers

ctxB7

ctxB3

AMR profile

DOX^S/TET^S, CIP^I, SXT^R/SXZ^R, STR^R, CRO^R, AMP^R, CAZ^R, CAR^R, CEP^R, CPM^R, MER^S, NA^R, NIT^R, STR^R, TMP^R, FZD^R, and CHL^R

DOX^S/TET^S, CIP^S, SXT^S/SXZ^S, STR^R, CRO^R, AMP^R, CAZ^R, CAR^R, CEP^R, CPM^R, MER^S, NA^R, NIT^R, STR^R, TMP^S, FZD^S, and CHL^S

Horizontally acquired AMR-conferring ICEs

ICE^GEN/ICEVchHai1/ICEVchind5 SXT-like ICEs

None

Bacteriophages

CTXφ

CTXφ

Pathogenicity islands

VPI-1, VPI-2, and VSP–II^a

VPI-1, VPI-2, and VSP-II^b