Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg
Creators: name: Oladeinde, Adelumola
name: Abdo, Zaid
name: Press, Maximilian
name: Cook, Kimberly
name: Cox, Nelson
name: Zwirzitz, Benjamin
name: Woyda, Reed
name: Lakin, Steven
name: Thomas IV, Jesse
name: Looft, Torey
name: Cosby, Douglas
name: Hinton Jr., Arthur
name: Guard, Jean
name: Line, Eric
name: Rothrock, Michael
name: Berrang, Mark
name: Herrington, Kyler
name: Zock, Gregory
name: Plumblee Lawrence, Jodie
name: Cudnik, Denice
name: House, Sandra
name: Ingram, Kimberly
name: Lariscy, Leah
name: Wagner, Robert
name: Aggrey, Samuel
name: Chai, Lilong
name: Ritz, Casey
Publisher: name: Zenodo
Year: 2021

description: Overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg (SH), a model food pathogen, to test if chicks raised antibiotic-free harbor transferable AR. We challenged chicks with an antibiotic susceptible SH strain using various routes of inoculation and determined if SH isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole genome sequencing (WGS) to show that chicks grown without antibiotics harbored antimicrobial resistant SH population 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing we found that SH infection perturbed the microbiota of broiler chicks and used metagenomics and WGS to confirm commensal Escherichia coli population as the main reservoir of IncI1 plasmid acquired by SH. The carriage of this IncI1 plasmid posed no fitness cost to SH but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of SH and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella.
description: <b>#PBS -S /bin/bash</b> <b>#PBS -N </b> <b>#PBS -q batch</b> <b>#PBS -l nodes=2:ppn=4</b> <b>#PBS -l walltime=</b> <b>#PBS -l mem=40gb</b> <b>#PBS -M </b> <b>#PBS -m ae </b> <b>cd $PBS_O_WORKDIR</b> <b>module load GATK/4.1.2.0-GCCcore-8.2.0-Java-1.8</b> <b>module load SAMtools/1.10-GCC-8.2.0-2.31.1</b> <b>module load BWA/0.7.17-foss-2016b</b> <b>bwa index SH-2813-ancestor.fasta</b> <b>samtools faidx SH-2813-ancestor.fasta</b> <b>bwa mem -k 24 -T 0 -B 100 -O 100 -E 100 -t 8 -R "@RG\tID:IVISII\tSM:SH-isolate-A\tPL:Illumina_Miseq\tLB:PE" SH-2813-ancestor.fasta SH-isolate-A_S11_L001_R1_001.fastq.gz SH-isolate-A-R2_001.fastq.gz &gt; SH-isolate-A.sam</b> <b>samtools view -bS SH-isolate-A.sam &gt; SH-isolate-A.bam</b> <b>samtools sort SH-isolate-A.bam -o SH-isolate-A_sorted.bam</b> <b>samtools rmdup SH-isolate-A_sorted.bam SH-isolate-A_rmdup.bam</b> <b>samtools index -b SH-isolate-A_rmdup.bam &gt; SH-isolate-A</b> <b>gatk HaplotypeCaller -R CP016573.fasta -I SH-isolate-A_rmdup.bam -ploidy 1 -O SH-isolate-A.vcf </b> Funding provided by: University of Georgia Research Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100012483<br>Award Number: 58-6040-6-030Funding provided by: USDA-ARS*<br>Crossref Funder Registry ID: <br>Award Number: 6040‐32000‐010‐00‐DFunding provided by: USDA-ARS<br>Crossref Funder Registry ID: <br>Award Number: 6040‐32000‐010‐00‐D
description: Single nucleotide polymorphisms (SNPs) and indels present in sequenced isolates were determined by aligning raw sequence reads to the chromosome of <em>S</em>. Heidelberg ancestor strain (SH-2813-ancestor) using Burrows-Wheeler Aligner (BWA). SAM file sorting and removal of PCR duplicates were done using SAMtools. Genome Analysis ToolKit with a minimum mapping quality of 30 and a minimum base quality of 30 was used for SNP identification.