Subject of charges remains unclear, after earlier case over congressional testimony was dismissed

• US politics live – latest updates

• Sign up for the Breaking News US newsletter email

The justice department filed new criminal charges against James Comey, the former FBI director, on Tuesday, according to a person familiar with the matter.

Comey was charged over a picture he posted on Instagram last year in which sea shells were arranged to say “86 47”, CNN and the Associated Press reported. The post was taken as a threat to Donald Trump. The number 86 can be used as shorthand for getting rid of something, and Trump is the 47th president. Comey subsequently deleted the post and apologized, saying he didn’t realize the numbers were associated with violence. “It never occurred to me, but I oppose violence of any kind so I took the post down,” he wrote on Instagram.

Todd Blanche announces 11-count indictment over payments to informants in extremist groups including Ku Klux Klan

• Sign up for the Breaking News US email to get newsletter alerts in your inbox

The Southern Poverty Law Center, the prominent civil rights organization, has been indicted on federal fraud charges related to past payments it made to confidential informants to infiltrate extremist groups including the Ku Klux Klan, the justice department has announced.

In a statement, Bryan Fair, the SPLC’s chief executive, called the allegations “false” and said the justice department’s actions “will not shake our resolve to fight for justice and ensure the promise of the civil rights movement becomes a reality for all”.

Pugilistic presence has laid waste to civil rights decision – her take-no-prisoners approach has alarmed legal experts but earned president’s plaudits

When Donald Trump abruptly fired Pam Bondi earlier this month, he made it clear that an unmistakable priority for the justice department would be using the nation’s top law enforcement agency to seek retribution against his political rivals.

For months, Trump pressured Bondi to move ahead with prosecutions against James Comey, Letitia James, Adam Schiff and other rivals, even publicly venting his frustration with Bondi in October. The justice department eventually did secure indictments against Comey and James, but the cases later collapsed. Trump fired Bondi on 2 April, reportedly because he was angered by the department’s lack of progress in prosecuting enemies. Todd Blanche, the acting attorney general, has since said Trump has the “right” to direct investigations at the justice department.

Maria Medetis Long had expressed doubts over case of John Brennan, whose agency said Russia boosted Trump in 2016

• Sign up for the Breaking News US email to get newsletter alerts in your inbox

A federal prosecutor leading the investigation into former CIA director John Brennan is no longer working on the case after expressing reservations about it, according to a person familiar with the matter.

The prosecutor, Maria Medetis Long, informed attorneys involved in the case she was no longer handling it, according to CNN, which first reported she was leaving the case. Medetis Long is a career attorney serving as the chief of the national security division in the US attorney’s office for the southern district of Florida. The Department of Justice did not immediately respond to a request for comment.