Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China

Abstract

Background To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China. Methods Four Citrobacter spp. strains were isolated from stool samples. Individual fresh stool samples were collected and subsequently diluted in phosphate buffered saline as described previously. The diluted fecal samples were plated on MacConkey agar supplemented with 1 mg/l cefotaxime and incubated for 20 h at 37 °C. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI–TOF–MS) was used for identification. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing was performed on an Illumina Novaseq-6000 platform. Acquired antimicrobial resistance genes and plasmid replicons were detected using ResFinder 4.1 and PlasmidFinder 1.3, respectively. Comparative genomic analysis of 277 Citrobacter genomes was also performed. Results Isolate FF141 was identified as Citrobacter cronae while isolate FF371, isolate FF414, and isolate FF423 were identified as Citrobacter braakii. Of these, three C. braakii isolates were further confirmed to be extended-spectrum β-lactamases (ESBL)-producer. All isolates are all multidrug resistance (MDR) with resistance to multiple antimicrobials. Plasmid of pKPC-CAV1321 belong to incompatibility (Inc) group. Comparative genomics analysis of Citrobacter isolates generated a large core-genome. Genetic diversity was observed in our bacterial collection, which clustered into five main clades. Human, environmental and animal Citrobacter isolates were distributed into five clusters. Conclusions To our knowledge, this is the first investigation of MDR-Citrobacter from Fennec Fox. Our phenotypic and genomic data further underscore the threat of increased ESBL prevalence in wildlife and emphasize that increased effort should be committed to monitoring the potentially rapid dissemination of ESBL-producers with one health perspective.

Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen

“…Moreover, recent studies on the C. werkmanii strain BF-6 have demonstrated that OmpA plays an important role in the regulation of multiple virulence phenotypes, including biofilm formation on distinct surfaces, swimming motility, metal ion responses, and resistance to biocides [ 75 ]. Finally, the virulence typing analyses of C. werkmanii indicated the presence of the siderophore enterobactin genes for the acquisition of iron, an essential nutrient for bacteria growth and the increased virulence potential of Citrobacter [ 76 , 77 ].…”

Dissemination of carbapenemase‐producing Enterobacteriaceae and associated resistance determinants through global food systems

“…can act as a reservoir of AMR and CR genes with the ability to disseminate them to other species. Citrobacter species have been observed carrying MGEs containing genes imparting resistance to aminoglycosides, tetracyclines (TETs), and trimethoprim (Qin et al., 2021). Furthermore, prominent carbapenemase genes, including KPC, NDM, and OXA‐48, have been detected alongside other AMR genes within MGEs found in species of Citrobacter (Yao et al., 2021).…”

Draft Genome Sequence of Citrobacter cronae Awk (Sequence Type 880), Associated with Edible Snails Commercially Available in Awka, Nigeria

“… Citrobacter cronae was first described in 2020, following its isolation from rectal swabs of immunocompromised patients in Germany ( 1 ). Antimicrobial-resistant (AR) strains of C. cronae have been isolated from fennec fox ( Vulpes zerda ) imported into China from Sudan and from termites and fruits in Senegal ( 4 , 5 ).…”

“…Moreover, our strain contained several AR genes, including bla CMY-98 and qnrB12 . C. cronae ST141, isolated from fennec fox, contains bla CMY-98 ( 4 ). No mobile genetic elements were detected.…”