Tracking Antibiotic-Resistant Bacteria in the Field with Bento Lab and MinION

Antibiotic-resistant bacteria are a major global threat to human health. Tracking the emergence of resistance can provide valuable information to help fight its spread, but how do you track different resistance variants in remote hospital settings, or where molecular laboratory resources may be limited?

As a step towards answering this question, in 2017 a team of researchers investigated the potential of using Bento Lab and MinION as a portable laboratory to genetically identify antibiotic-resistant bacteria. 

The idea was that by using more portable workflows bacterial strains could be identified at the point of infection even where molecular facilities were otherwise lacking. Genomic and sequence data could be rapidly produced and compared with national and international datasets. These data could then help indicate the presence of common antibiotic-resistance strains and genes between and within countries, suggesting possible routes of spread, and potentially give public health officials the information needed to help prevent rising infections.

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The team — a collaboration between the National Institute of Public Health (NIPH) in Phnom Penh, Cambodia, and the  National Institute of Infectious Diseases and Juntendo University School of Medicine, Tokyo, Japan — focused on bacteria resistant to a group of drugs known as carbapenems, one of the last-resort antibiotics for bacterial infections, during a five day visit to NIPH.

Carbapenems are critical to human health because they have a broad spectrum of activity and can treat infections when other antibiotics fail. However, since their introduction as a drug in the 1980s a rising number of resistant bacteria have been found. The mechanism of resistance is the production of enzymes called carbapenemases — these degrade carbapenems and make the treatments ineffective. And once all antibiotic options are exhausted then infections have a high mortality rate, and other treatment options are limited.

The team first successfully used Bento Lab to do multiplex PCR assays to amplify and visualise different carpapenamase-producing genes from clinical bacterial isolates. The researchers then performed library prep with Bento Lab for whole genome sequencing of three isolates using Oxford Nanopore MinION. Samples were taken back to Japan to resequence using Illumina genome sequencing  for validation purposes. Genome and plasmid sequences were assembled, and strain genomes and plasmids sequences were compared with those present in public sequence databases.

This collaborative effort using Bento Lab and MinION was the first glimpse into the epidemiology of carbapenemase-producing gram-negative bacteria in Cambodia. Despite the portable laboratory setup and short duration of the visit,  the researchers identified several high-risk clones reported from other countries. The team also found clinically relevant carbapenamase genes on plasmids and mobile gene elements (which can pass from bacterium to bacterium) with very  high sequence identity to those from other countries. The on-site MinION genome assemblies were sufficient to detect antibiotic-resistance genes and where they were located.

The researchers also concluded that Bento Lab and MinION could be useful for similar genomic analysis and surveillance of clinically important bacteria in hospitals and research centres with limited facilities.

The paper is open-access and available to read here:

Hirabayashi et al. (2021). On-site genomic epidemiological analysis of antimicrobial-resistant bacteria in Cambodia with portable laboratory equipment. Frontiers in microbiology, 12, 675463.

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