Study maps bed bugs’ genomes in unprecedented detail to find out why they just won’t die

Scientists mapped near-gap-free and near-error-free genomes of a susceptible bed bug strain and a superstrain around 20,000 times more insecticide-resistant, offering the broadest look yet at the full scope of their resistance mutations.

Their findings were published in the journal Insects.

Although there is no evidence that bed bugs transmit diseases to humans, their bites can cause itchy rashes and secondary skin infections. Widespread use of insecticides, including the now-banned DDT, nearly wiped out populations of these blood-sucking insects by the 1960s, making infestations rare. But over the past 20 years, the world has witnessed their resurgence, partly due to resistance mutations they developed against these insecticides.

Resistance can occur through different mechanisms, such as by producing enzymes that detoxify the insecticides (metabolic resistance) or developing thicker outer layers to block the chemicals (penetration resistance). Past studies have identified some of the mutations and gene expressions linked to insecticide resistance. However, the full extent of mutations driving resistance remains unknown as no research has sequenced the whole genome of insecticide-resistant strains.

A research team led by Hidemasa Bono, professor at Hiroshima University’s (HU) Graduate School of Integrated Sciences for Life, mapped genomes of susceptible and resistant bed bug strains from Japan to address this gap. They obtained susceptible strains descended from wild bed bugs (Cimex lectularius) collected 68 years ago in fields at Isahaya City, Nagasaki.

Meanwhile, the resistant strains were bred from specimens collected from a Hiroshima City hotel in 2010. Their tests revealed that the resistant samples had 19,859-fold stronger resistance to pyrethroids—the most commonly used insecticide for bed bug control—exceeding levels seen in many previously identified superstrains. All the specimens were provided by Fumakilla Limited, a Japan-based chemical manufacturing company.

Piecing together the genome puzzle

Sequencing a genome is like assembling a massive jigsaw puzzle, spanning anywhere from about 160,000 to 160 billion pieces. To map the most complete bed bug genomes to date, researchers used the breakthrough method of long-read sequencing, which captures longer stretches of DNA—akin to having entire sections of puzzle pieces put together. Traditional short-read sequencing, by contrast, only covers tiny snippets, often leading to frustrating gaps.

The researchers assembled a near-total picture of the two genomes with just about every piece precisely where it belonged, achieving 97.8% completeness and quality value (QV) of 57.0 for the susceptible strain and 94.9% completeness and QV of 56.9 for the resistant strain. A QV above 30 indicates high-quality sequences with less than a 0.1% error rate. Both also surpassed the N50 value of the existing C. lectularius reference genome, Clec2.1, from a previous sequencing effort, meaning there were fewer gaps and more complete sections of the genome puzzle.

Known, new resistance mutations uncovered

After fully sequencing the genomes, the team identified protein-coding genes, determined their functions, and assessed if they were active through transcriptional analysis. They uncovered 3,938 transcripts with amino acid mismatches. Of these, 729 mutated transcripts were linked to insecticide resistance.

“We determined the genome sequence of insecticide-resistant bed bugs, which exhibited 20,000-fold greater resistance compared to susceptible bed bugs. By comparing the amino acid sequences between the susceptible and resistant bed bugs, we identified 729 transcripts with resistance-specific mutations,” said study first author Kouhei Toga, postdoctoral researcher at the Laboratory of Genome Informatics of HU’s Graduate School of Integrated Sciences for Life.

“These transcripts included genes related to DNA damage response, cell cycle regulation, insulin metabolism, and lysosome functions. This suggests that these molecular pathways may play a role in the development of pyrethroid resistance in bed bugs.”

By drawing on previous insect studies, the researchers confirmed known resistance mutations and discovered new ones that could inform more targeted and effective pest control strategies.

“We identified a large number of genes likely involved in insecticide resistance, many of which have not been previously reported as being associated with resistance in bedbugs. Genome editing of these genes could provide valuable insights into the evolution and mechanisms of insecticide resistance,” Toga said.

“Additionally, this study expands the pool of target genes for monitoring allele distribution and frequency changes, which could contribute significantly to assessing resistance levels in wild populations. This work highlights the potential of genome-wide approaches in understanding insecticide resistance in bed bugs.”

Other research team members include Fumiko Kimoto and Hiroki Fujii.