<p>Hybrid Genome Assembly and Annotation of a Pandrug-Resistant <em>Klebsiella pneumoniae</em> Strain Using Nanopore and Illumina Sequencing</p>

AbstractBackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.FindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.ConclusionsThe genome and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in detail. The estimated recombination rate will help evolutionary biologist gain a better understanding of commonalities and differences of genomic patterns in insects.

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Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control

10.1101/2021.05.14.444148 ◽

2021 ◽

Author(s):

Sabrina Simon ◽

Thijmen Breeschoten ◽

Hans J Jansen ◽

Ron P Dirks ◽

M. Eric Schranz ◽

...

Keyword(s):

Pest Control ◽

Genome Assembly ◽

Spodoptera Exigua ◽

Control Strategies ◽

Beet Armyworm ◽

Cultivated Plants ◽

Comparative Genomic ◽

Supporting Evidence ◽

Pest Species ◽

Hybrid Genome

Background: The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed from > 130 host plants including several economically important crops. Results: The 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long read data and Illumina short read), a high-quality genome assembly was achieved (N50=1.1 Mb). An official gene set (OGS, 18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq data sets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression in combination with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed potential Spodoptera-specific genes of interest such as mg7 and REPAT46 upregulated during 1st and 3rd instar larval stages for targeted pest-outbreak management. Conclusions: The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provides critical insights into the biology of this devastating polyphagous insect pest species with a worldwide distribution. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.

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Ceftazidime/avibactam resistance is associated with different mechanisms in KPC-producing Klebsiella pneumoniae strains

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2021.01626 ◽

2021 ◽

Author(s):

Sara Cavallini ◽

Ilaria Unali ◽

Anna Bertoncelli ◽

Riccardo Cecchetto ◽

Annarita Mazzariol

Keyword(s):

Amino Acids ◽

Klebsiella Pneumoniae ◽

Illumina Sequencing ◽

Genetic Mutations ◽

Molecular Characterisation ◽

Drug Resistant ◽

Carbapenemase Gene ◽

Resistant Strains

AbstractThis study focused on Klebsiella pneumoniae isolates that were resistant or had low susceptibility to a combination of ceftazidime/avibactam. We aimed to investigate the mechanisms underlying this resistance. A total of 24 multi-drug resistant isolates of K. pneumoniae were included in the study. The phenotypic determination of carbapenemase presence was based on the CARBA NP test. NG-Test CARBA 5 was also performed, and it showed KPC production in 22 out 24 strains. The molecular characterisation of blaKPC carbapenemase gene, ESBL genes (blaCTX-M, blaTEM, and blaSHV) and porin genes ompK35/36 was performed using the PCR. Finally, ILLUMINA sequencing was performed to determine the presence of genetic mutations.Various types of mutations in the KPC sequence, leading to ceftazidime/avibactam resistance, were detected in the analysed resistant strains. We observed that KPC-31 harboured the D179Y mutation, the deletion of the amino acids 167–168, and the mutation of T243M associated with ceftazidime/avibactam resistance. The isolates that did not present carbapenemase alterations were found to have other mechanisms such as mutations in the porins. The mutations both on the KPC-3 enzyme and in the porins confirmed, that diverse mechanisms confer resistance to ceftazidime/avibactam in K. pneumoniae.

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