Draft Genome Sequence of the Multidrug-Resistant Citrobacter freundii 132-2 Strain Isolated from a Domestic Duck in Bangladesh

ABSTRACT We sequenced a multidrug-resistant strain of Citrobacter freundii, 132-2, isolated from a cloacal swab sample of a domestic duck. The whole genome of the C. freundii 132-2 strain had a length of 5,097,592 bp, 62 contigs, two plasmids, and an average G+C content of 51.85%, with a 105.0× genome coverage.

T he extensive and inappropriate use of antimicrobial agents has resulted in the emergence of antimicrobial resistance in bacteria, leading to various multidrug-resistant (MDR) clones, which have become a major global public health concern (1, 2). Ducks have the potential to harbor antimicrobial-resistant and MDR pathogens that could transfer to humans due to their interactions with them (3). Citrobacter freundii is commonly found in the environment, soil, water, human clinical samples, and intestinal tracts of animals (4). C. freundii can be transmitted from ducks to humans through various means, such as contact with infected eggs, raw or undercooked meat, and the handling of duck carcasses at the slaughterhouse (3,5). In humans, C. freundii isolates can cause bacteremia and severe neurological symptoms such as extreme cognitive impairment, seizures, and hemiparesis, and, in some cases, even death in children, so that it represents a considerable threat to human health (6,7).
The genome coverage of Citrobacter freundii 132-2 was 105.0Â, and a total of 62 contigs were obtained. Our assembled genome had a total length of 5,097,592 bp, a GC content of 51.85%, and an N 50 value of 536,796 bp. This assembled genome identified two important plasmid replicons, i.e., IncFIB(pHCM2) (110,089 bp with a 98.51% identity to AL513384) and IncR (16,190 bp with a 100% identity to DQ449578). Moreover, this genome consists of a sequence type of ST18 (using MLST 2.0) and a probability of being a pathogen for humans of 89.6% (using PathogenFinder 1.1). The strain carried 45 predicted ARGs under 19 antimicrobial categories and 83 predicted virulence genes under more than 12 predicted virulence factors. Moreover, Citrobacter freundii 132-2 contained 395 subsystems (having 2,298 genes) with 33% coverage, 5,024 protein-coding sequences, and 81 RNA genes.
The Animal Welfare and Experimentation Ethical Committee, which is the institutional ethics committee of Bangladesh Agricultural University in Mymensingh, granted approval for the procedures and protocols associated with this research under the reference number of AWEEC/BAU/2020 (10).
Data availability. The whole-genome sequencing (WGS) shotgun study for Citrobacter freundii 132-2 was submitted to NCBI/GenBank with accession number JAPQWA000000000, and the raw reads were deposited under SRA accession number SRR24848516 (BioProject accession number PRJNA907483). The current version referred to this paper is identified as JAPQWA010000000.

ACKNOWLEDGMENTS
We acknowledge the Bangladesh Agricultural Research Council for providing funds through the National Agricultural Technology Program Phase II project for the in-country Ph.D. scholarship (P149553) to facilitate this study.
We extend our appreciation to the Department of Livestock Services, the Ministry of Fisheries and Livestock of Bangladesh, for their assistance in conducting this research.