Introduction: Co-infection pneumonia with Mycobacterium abscessus  (M. abscessus ) and Pneumocystis jirovecii  (P. jirovecii ) is rarely reported in previously healthy patients without HIV infection. The diagnosis of pneumonia of M. abscessus  and P. jirovecii  remains challenging due to its nonspecific clinical presentation and the inadequate performance of conventional diagnostic methods.
Case Report: We report the case of a 44-year-old previously healthy male transferred to our hospital in February 2020 with a 4-month history of productive cough and one month of intermittent fever. At local hospital, the metagenomic next-generation sequencing(mNGS) detected P. jirovecii  sequences in blood; with the antifungal therapy (Caspofungin, trimethoprim–sulfamethoxazole [TMP-SMX] and methylprednisolone [MP]), the patient still had hypoxemia, cough and fever. Then he was transferred to our hospital, the mNGS of bronchoalveolar lavage fluid (BALF) detected the sequences of M. abscessus  and P. jirovecii . CD4+ T-lymphocytopenia in the peripheral blood cells was presented and HIV serology was negative. Caspofungin, TMP-SMX, clindamycin and MP were used to treat P. jirovecii  pneumonia (PJP). Moxifloxacin, imipenem cilastatin and linezolid were used to treat M. abscessus  infection. Clinical progress was satisfactory following antifungal combined with anti-M. abscessus  therapy.
Conclusion: Co-infection pneumonia with M. abscessus  and P. jirovecii  as reported here is exceptionally rare. mNGS is a powerful tool for pathogen detection. M. abscessus  infection could be a risk factor for P. jirovecii  infection. This case report supports the value of mNGS in diagnosing of M. abscessus  and P. jirovecii , and highlights the inadequacies of conventional diagnostic methods.
Keywords: Pneumocystis jiroveci , Mycobacterium abscessus , mNGS, co-infection, HIV negative