Abstract
BackgroundOpportunistic 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 strain of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient 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.ResultsThe isolate grew very slowly but conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella 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 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 its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural environment and animal host, over 30 mobile genetic elements, and a plasmid bearing blaCTX-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.ConclusionsOur findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes, which highlights the need for continuous monitoring for this novel species and efforts to develop treatment strategies.
Highlights
Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections
We isolated from a patient with a biliary infection a novel strain of unknown taxonomy accompanying an infectious Klebsiella pneumoniae strain, which we designated as AF18
We find that AF18 is a strain of an undefined novel species in the family Enterobacteriaceae, and that sensitive K. pneumoniae can survive when co-cultured with AF18 in Luria-Bertani broth containing 8 μg/mL ceftriaxone
Summary
Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. 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. Growing surveillances based on genomic sequencing of microbes from the natural environment, human settlements, and clinical settings have been conducted worldwide to investigate the evolution and transfer of antibiotic resistance genes (ARGs) [2,3,4]. The ecoevolutionary feedback loops between ecological and evolutionary dynamics have been increasingly recognized, where spillover of antibiotic use to natural and seminatural environments may have profound implications on the distribution of ARGs in natural bacterial populations which serve as environmental reservoirs of resistance determinants [5, 6]. Understanding the dynamics of the continuous feedback loops from clinical to nature and back may prove critical for preventing and controlling the problem of antibiotic resistance
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