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Abstract : The most important complications that can be observed with Covid-19 cases is secondary bacterial infections that are chief causes of increase human morbidity and mortality rates. The current study was conducted from three hospitals in Baghdad city through a period from January to June 2021. Five hundred specimens (sputum and bronchial fluids) were obtained from patients who suffered from Covid-19 infection. Opportunistic performance of Stenotrophomonas maltophilia isolates were diagnosed as secondary bacterial through bacterial culture and confirmed the identification by API 20 strep system (Analytical Profile Index and Vitek-2 system. Antibiotic susceptibility pattern of Stenotrophomonas maltophilia isolates against nine antibiotics (Levofloxacin, Azithromycin, Imipenem, Vancomycin, Ceftriaxone, Gentamicin, Amoxicillin/Clavulanate, Amikacin and Tobramycin) was tested by Vitek-2 system methods. In addition, Molecular detection of 16Sr RNA gene of isolated Stenotrophomonas maltophilia used through polymerase Chain Reaction (PCR). Results explained that the distribution of 500 study specimens included 490 (98%) sputum and 10 (2%) were bronchial fluids with statistical differences (P≤0.01). 233 (46.6%) specimens were presented positive bacterial culture and able to grow on; blood, MacConkey and chocolate agar, so that all these results were confirmed by analytical assays API 20 test and VITEK 2 system. Results of isolation and identification appeared that there were 15 types Gram-negative isolates and 8 types Gram-positive isolates. While Stenotrophomonas maltophilia isolated with 3(1.29%). Antibiotics susceptibility pattern that obtained by VITEK-2 system methods of Stenotrophomonas maltophilia isolates showed different susceptibility pattern to the antibiotics that used. The PCR amplification assays of the region of 16S rRNA gene of Stenotrophomonas maltophilia isolates were documented the isolation and identification of bacterial culture and VITEK 2 system. Study concluded that Stenotrophomonas maltophilia bacterium occurred in severe Covid-19 cases specially in hospital’s patients. In addition, this bacterium appeared resistance for different types of antibiotics which used in treatment protocol of Covid-19 cases which lead to increase the mortality among these patients and had no significant impact on patient’s survival alive.

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