Left, who noted he has been short Mallinckrodt "on and off" in recent years, questioned whether the company misrepresented the effectiveness of H.P. Acthar Gel, its high-priced specialty drug. He contended sales of the drug, which is used for infantile spasms and some autoimmune conditions, show Mallinckrodt may have problems with reimbursement from insurance companies.
Mallinckrodt shares were 7 percent higher Tuesday afternoon following Left's remarks.
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Mallinckrodt CEO Mark Trudeau rebutted Left's argument Tuesday afternoon, telling CNBC that "the facts he quoted were mostly, if not completely wrong."
"The main takeaway is that Andrew really put out a whole variety of different speculations and allegations and not very many facts," Trudeau said in a statement.
Earlier on Tuesday, he defended the company's business model and downplayed concerns about payment for Acthar. On CNBC's "Squawk Box," he contended Acthar is "very effective for a variety of autoimmune conditions" and will "drive value."
Mallinckrodt in August reported net sales of $965 million for its fiscal 2015 third quarter, a nearly 50 percent increase driven by its inclusion of Acthar. On Tuesday, Trudeau declined to disclose the profit margin for Acthar, which The New York Times said went from $40 a vial to more than $28,000 over a decade.
Left called Mallinckrodt the "poster child" for price gouging.
Mallinckrodt is the latest drugmaker hit by Citron after it published a scathing report about Valeant's practices last month. Since then, Valeant shares have lost about half their value.
Left noted his Valeant short position is "significantly scaled down" from its initial size.
— CNBC's Tae Kim, Tom DiChristopher and Meg Tirrell contributed to this report