Tigres UANL midfielder Flores, 22, was injured in last month's CONCACAF Champions Cup final.
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"Austin FC’s Jayden Nelson has been selected to replace Tigres UANL's Marcelo Flores on #CANMNT's roster for the upcoming FIFA World Cup 2026," Canada Soccer posted on X.
The 23-year-old Nelson has netted three goals in 14 appearances for Canada.
World Cup co-hosts Canada will open their campaign against Bosnia and Herzegovina on June 12th in Toronto, before taking on Qatar and Switzerland in Group B.