Rapid Detection of Mobilized Colistin Resistance using a Nucleic Acid Based Lab-on-a-Chip Diagnostic System

• Published in: Scientific reports Vol. 10; no. 1; p. 8448
• Main Authors: Rodriguez-Manzano, Jesus, Moser, Nicolas, Malpartida-Cardenas, Kenny, Moniri, Ahmad, Fisarova, Lenka, Pennisi, Ivana, Boonyasiri, Adhiratha, Jauneikaite, Elita, Abdolrasouli, Alireza, Otter, Jonathan A., Bolt, Frances, Davies, Frances, Didelot, Xavier, Holmes, Alison, Georgiou, Pantelis
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21-05-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/2234; 631/1647/277; 692/699/255; 692/700/139; Anti-Bacterial Agents - pharmacology; Antimicrobial agents; Antimicrobial resistance; Bacteria - drug effects; Bacteria - genetics; Bacteria - isolation & purification; Bacterial Infections - diagnosis; Bacterial Infections - drug therapy; Bacterial Infections - genetics; Bacterial Infections - microbiology; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Carbapenemase; Colistin; Colistin - pharmacology; Cross-reactivity; Data acquisition; Deoxyribonucleic acid; DNA; Drug resistance; Drug Resistance, Bacterial; Gene amplification; Genomes; Humanities and Social Sciences; Humans; Infectious diseases; Lab-on-a-chip; Lab-On-A-Chip Devices; multidisciplinary; Nucleic Acids - analysis; Nucleic Acids - genetics; Public health; Science; Science (multidisciplinary); Semiconductors; Statistical analysis; Temperature requirements; Whole genome sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-64612-1

The increasing prevalence of antimicrobial resistance is a serious threat to global public health. One of the most concerning trends is the rapid spread of Carbapenemase-Producing Organisms (CPO), where colistin has become the last-resort antibiotic treatment. The emergence of colistin resistance, including the spread of mobilized colistin resistance (
mcr
) genes, raises the possibility of untreatable bacterial infections and motivates the development of improved diagnostics for the detection of colistin-resistant organisms. This work demonstrates a rapid response for detecting the most recently reported
mcr
gene,
mcr
−9, using a portable and affordable lab-on-a-chip (LoC) platform, offering a promising alternative to conventional laboratory-based instruments such as real-time PCR (qPCR). The platform combines semiconductor technology, for non-optical real-time DNA sensing, with a smartphone application for data acquisition, visualization and cloud connectivity. This technology is enabled by using loop-mediated isothermal amplification (LAMP) as the chemistry for targeted DNA detection, by virtue of its high sensitivity, specificity, yield, and manageable temperature requirements. Here, we have developed the first LAMP assay for
mcr
−9 - showing high sensitivity (down to 100 genomic copies/reaction) and high specificity (no cross-reactivity with other
mcr
variants). This assay is demonstrated through supporting a hospital investigation where we analyzed nucleic acids extracted from 128 carbapenemase-producing bacteria isolated from clinical and screening samples and found that 41 carried
mcr
−9 (validated using whole genome sequencing). Average positive detection times were 6.58 ± 0.42 min when performing the experiments on a conventional qPCR instrument (
n
 = 41). For validating the translation of the LAMP assay onto a LoC platform, a subset of the samples were tested (
n
 = 20), showing average detection times of 6.83 ± 0.92 min for positive isolates (
n
 = 14). All experiments detected
mcr
−9 in under 10 min, and both platforms showed no statistically significant difference (
p
-value > 0.05). When sample preparation and throughput capabilities are integrated within this LoC platform, the adoption of this technology for the rapid detection and surveillance of antimicrobial resistance genes will decrease the turnaround time for DNA detection and resistotyping, improving diagnostic capabilities, patient outcomes, and the management of infectious diseases.