Team Montes de Oca

List of participants and affiliations:

• Marco Montes de Oca
• Weilong Hao
• Mackenzie Wilke
• Joe Wirth
• Axl Cepeda

Project Goals

This project aims to investigate the relationship between insertion sequences and antibiotic resistance phenotypes by analyzing draft and complete genomes. The goal is to identify patterns in insertion sequence distribution among susceptible and resistant isolates and visualize the findings.

Approach

The approach involves comparing coding sequences from each isolate against databases using BLAST. These databases may include AMRFinder NCBI Database, to identify genes associated with antibiotic resistance, as well as IS Finder, to identify insertion sequences. Once the insertion sequences and resistance genes are identified, the team will compare the insertion sequence profile between resistant and susceptible isolates. A code to start finding these elements is here. The output tables obtained from the script have the following format:

Output from approach n°1

A table file including the following columns:

• qseqid: query sequence id, usually the contig name from a given draft genome
• sseqid: subject sequence id, the antibiotic resistance gene sequence name
• pident: identity percentage
• ppos: similarity percentage
• len: BLAST alignment length
• qstart: query sequence start position
• qend: query sequence end position
• sstart: subject sequence start position
• send: subject sequence end position
• evalue: BLAST alignment evalue
• scov: subject coverage percentage

Steps

• Collect reference porin sequences to build a local BLAST database
  • Use the ones in Table 1 from this paper
  • Could search NCBI Gene or Nucleotide for these porin sequences (filter by E.coli)
• Find porin coding sequences in our 163 isolates with BLAST
  • Made Blast DB with porin coding sequences and then blasted our 163 isolates against it
  • Trying to differeniate which queries are S or R (as we did them in a batch)
• Find indels within porin coding sequences
• Identify insertion sequences within those porin sequences

Results

Future Work

NCBI Codeathon Disclaimer

This software was created as part of an NCBI codeathon, a hackathon-style event focused on rapid innovation. While we encourage you to explore and adapt this code, please be aware that NCBI does not provide ongoing support for it.

For general questions about NCBI software and tools, please visit: NCBI Contact Page