Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii

Insecticide resistance is a major threat to gains in malaria control, which have been stalling and potentially reversing since 2015. Studies into the causal mechanisms of insecticide resistance are painting an increasingly complicated picture, underlining the need to design and implement targeted studies on this phenotype. In this study, we compare three populations of the major malaria vector An. coluzzii: a susceptible and two resistant colonies with the same genetic background. The original colonised resistant population rapidly lost resistance over a 6-month period, a subset of this population was reselected with pyrethroids, and a third population of this colony that did not lose resistance was also available. The original resistant, susceptible and re-selected colonies were subject to RNAseq and whole genome sequencing, which identified a number of changes across the transcriptome and genome linked with resistance. Firstly, an increase in the expression of genes within the oxidative phosphorylation pathway were seen in both resistant populations compared to the susceptible control; this translated phenotypically through an increased respiratory rate, indicating that elevated metabolism is linked directly with resistance. Genome sequencing highlighted several blocks clearly associated with resistance, including the 2Rb inversion. Finally, changes in the microbiome profile were seen, indicating that the microbial composition may play a role in the resistance phenotype. Taken together, this study reveals a highly complicated phenotype in which multiple transcriptomic, genomic and microbiome changes combine to result in insecticide resistance.

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Integration of whole genome sequencing and transcriptomics reveals a complex picture of insecticide resistance in the major malaria vector Anopheles coluzzii

10.1101/2021.08.21.457189 ◽

2021 ◽

Author(s):

Victoria A Ingham ◽

Jacob A Tennessen ◽

Eric R Lucas ◽

Sara Elg ◽

Henrietta Carrington-Yates ◽

...

Keyword(s):

Insecticide Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Malaria Vector ◽

Anopheles Coluzzii ◽

Whole Genome ◽

Microbial Composition ◽

Expression Of Genes ◽

Oxidative Phosphorylation Pathway ◽

Major Malaria Vector

Insecticide resistance is a major threat to gains in malaria control, which have been stalling and potentially reversing since 2015. Studies into the causal mechanisms of insecticide resistance are painting an increasingly complicated picture, underlining the need to design and implement targeted studies on this phenotype. In this study, we compare three populations of the major malaria vector An. coluzzii: a susceptible and two resistant colonies with the same genetic background. The original colonised resistant population rapidly lost resistance over a 6-month period, a subset of this population was reselected with pyrethroids a third population of this colony that did not lose resistance was also available. The original resistant, susceptible and re-selected colonies were subject to RNAseq and whole genome sequencing, which identified a number of changes across the transcriptome and genome linked with resistance. Firstly, an increase in the expression of genes within the oxidative phosphorylation pathway were seen in both resistant populations compared to the susceptible control; this translated phenotypically through an increased respiratory rate, indicating that elevated metabolism is linked directly with resistance. Genome sequencing highlighted several blocks clearly associated with resistance, including the 2Rb inversion. Finally, changes in the microbiome profile were seen, indicating that the microbial composition may play a role in the resistance phenotype. Taken together, this study reveals a highly complicated phenotype in which multiple transcriptomic, genomic and microbiome changes combine to result in insecticide resistance.

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Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species

BMC Genomics ◽

10.1186/s12864-019-5877-9 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 7

Author(s):

Sonia Hussain ◽

Muhammad Farooq ◽

Hassan Jamil Malik ◽

Imran Amin ◽

Brian E. Scheffler ◽

...

Keyword(s):

Insecticide Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Virus Transmission ◽

Whole Genome ◽

Genetic Variances ◽

Asia Ii 1

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High Plasmodium infection and multiple insecticide resistance in a major malaria vector Anopheles coluzzii from Sahel of Niger Republic

Malaria Journal ◽

10.1186/s12936-019-2812-0 ◽

2019 ◽

Vol 18 (1) ◽

Cited By ~ 1

Author(s):

Sulaiman S. Ibrahim ◽

Muhammad M. Mukhtar ◽

Helen Irving ◽

Rabiou Labbo ◽

Michael O. Kusimo ◽

...

Keyword(s):

Insecticide Resistance ◽

Malaria Vector ◽

Anopheles Coluzzii ◽

Plasmodium Infection ◽

Major Malaria Vector

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Whole genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes

10.1101/399568 ◽

2018 ◽

Cited By ~ 2

Author(s):

Eric R. Lucas ◽

Alistair Miles ◽

Nicholas J. Harding ◽

Chris S. Clarkson ◽

Mara K. N. Lawniczak ◽

...

Keyword(s):

Insecticide Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Copy Number ◽

Gene Families ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Metabolic Resistance ◽

Extended Haplotype

AbstractBackgroundPolymorphisms in the copy number of a genetic region can influence gene expression, coding sequence and zygosity, making them powerful actors in the evolutionary process. Copy number variants (CNVs) are however understudied, being more difficult to detect than single nucleotide polymorphisms. We take advantage of the intense selective pressures on the major malaria vector Anopheles gambiae, caused by the widespread use of insecticides for malaria control, to investigate the role of CNVs in the evolution of insecticide resistance.ResultsUsing the whole-genome sequencing data from 1142 samples in the An. gambiae 1000 genomes project, we identified 1557 independent increases in copy number, encompassing a total of 267 genes, which were enriched for gene families linked to metabolic insecticide resistance. The five major candidate genes for metabolic resistance were all found in at least one CNV, and were often the target of multiple independent CNVs, reaching as many as 16 CNVs in Cyp9k1. These CNVs have furthermore been spreading due to positive selection, indicated by high local CNV frequencies and extended haplotype homozygosity.ConclusionsOur results demonstrate the importance of CNVs in the response to selection, with CNVs being closely associated with genes involved in the evolution of resistance to insecticides, highlighting the urgent need to identify their relative contributions to resistance and to track their spread as the application of insecticide in malaria endemic countries intensifies. Our detailed descriptions of CNVs found across the species range provides the tools to do so.

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Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing

Journal of Clinical Medicine ◽

10.3390/jcm8030351 ◽

2019 ◽

Vol 8 (3) ◽

pp. 351 ◽

Cited By ~ 2

Author(s):

Jyun-Hong Lin ◽

Zong-Yen Wu ◽

Liang Gong ◽

Chee-Hong Wong ◽

Wen-Cheng Chao ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Brain Abscess ◽

Genome Sequencing ◽

Antibiotic Resistance Genes ◽

Taxonomic Diversity ◽

Whole Genome ◽

Metagenomic Sequencing ◽

Microbial Composition ◽

Culture Independent ◽

Virus Communities

Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.

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