PT  - JOURNAL ARTICLE
AU  - Peter J. Diebold
AU  - Felicia N. New
AU  - Michael Hovan
AU  - Michael J. Satlin
AU  - Ilana L. Brito
TI  - Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR
AID  - 10.1101/2021.01.22.427834
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.22.427834
4099  - http://biorxiv.org/content/early/2021/01/23/2021.01.22.427834.short
4100  - http://biorxiv.org/content/early/2021/01/23/2021.01.22.427834.full
AB  - The horizonal transfer of plasmid-encoded genes allows bacteria to adapt to constantly shifting environmental pressures, bestowing functional advantages to their bacterial hosts such as antibiotic resistance, metal resistance, virulence factors, and polysaccharide utilization. However, common molecular methods such as short- and long-read sequencing of microbiomes cannot associate extrachromosomal plasmids with the genome of the host bacterium. Alternative methods to link plasmids to host bacteria are either laborious, expensive or prone to contamination. Here we present the One-step Isolation and Lysis PCR (OIL-PCR) method, which molecularly links target ARGs with the bacterial 16S rRNA gene via fusion PCR performed within an emulsion. After validating this method, we apply it to identify the bacterial hosts of three clinically relevant beta-lactamases in a neutropenic patient population who are particularly vulnerable multidrug-resistant infections. We detect novel associations of two low-abundance genera, Romboutsia and Agathobacter, with a multi-drug resistant plasmid harbored by Klebsiella pneumoniae. We put forth a robust, accessible, and high-throughput platform for sensitively surveying the bacterial hosts of mobile genes in complex microbial communities.Competing Interest StatementM.J.S has received grant funding from BioFire Diagnostics, Allergan, and Merck and has received consulting fees from Shionogi and Achaogen. All other authors declare that they have no conflicts of interest.