Complete genome arrangement revealed the emergence of a poultry origin superbug Citrobacter portucalensis strain NR-12.

Abstract

Citrobacter spp. are part of normal human and animal intestinal flora. Citrobacter portucalensis (C. portucalensis) is closely related to Citrobacter freundii, which is an emerging opportunistic nosocomial pathogen. The aim of this study was to retrieve colistin-resistant Citrobacter spp. from poultry in Bangladesh. The C. portucalensis strain NR-12 was isolated from poultry droppings and subjected to antibiotic susceptibility testing. Complete genome analysis of NR-12 was performed followed by bioinformatics. It is believed that this is one of first reports of its kind of complete genome sequence of multidrug-resistant (MDR) C. portucalensis isolated from veterinary samples. The C. portucalensis strain NR-12 showed resistance to polymyxin, sulfonamide, tetracycline, fluoroquinolone, and macrolide. Its complete genome revealed 13 acquired antimicrobial resistance gene markers (AMRs) conferring resistance to eight different antibiotic groups: dfrA12 (trimethoprim); sul1 and sul2 (sulfonamide); mph (A) (macrolide); tet (A) (tetracycline); qnrS1 and qnrB13 (fluoroquinolone); blaCMY-39 (extended-spectrum β-lactamase (ESBL)), blaTEM-176 (non-ESBL) and aadA2, aph (3')-Ia, aph (3″)-Ib, aph (3')-Ic, aph (3')-Id, strA, strB) (aminoglycoside). The genome possessed a class 1 integron (IntI1) gene cassette harbouring four different antibiotic resistance genes (dfrA12, aadA2, sul1, mph (A)). The organisation of class 1 integron (IntI1) carrying MDR determinants in C. portucalensis strain NR-12 was also first reported here. Colistin-resistant genes such as mgrB, phoP, phoQ, pmrA, pmrB, eptB and arnB were also present within NR-12. C. portucalensis NR-12 was resistant to eight different antibiotics from six antimicrobial groups. To formulate a control strategy, it is important to understand this resistant mechanism.