Genomic Characterization of an Emerging Enterobacteriaceae Species: the First Case of Co-infection With a Typical Pathogen in a Human Patient

Abstract

Background Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a novel species strain of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient of with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause. Results The isolate grows grew very slowly but confers conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumonia pneumoniae . As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis , and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains respectively isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like As its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural wild environment and animal host, tens of over 30 mobile genetic mobile elements, and a plasmid bearing bla CTX-M-3 gene, indicating its ability to disseminate antimicrobial - resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18 , which could serve as targets for novel antimicrobial strategies. Conclusions Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes i n transferring antibiotic determinants , which highlights the need for continuous monitoring for this novel species and efforts to develop controlling treatment strategies.