DOI: 10.5061/dryad.4tmpg4f8d
title: Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg

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: 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. 
description: <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -S /bin/bash</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -N </b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -q batch</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -l nodes=2:ppn=4</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -l walltime=</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -l mem=40gb</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -M </b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">#PBS -m ae </b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">cd $PBS_O_WORKDIR</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">module load GATK/4.1.2.0-GCCcore-8.2.0-Java-1.8</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">module load SAMtools/1.10-GCC-8.2.0-2.31.1</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">module load BWA/0.7.17-foss-2016b</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">bwa index SH-2813-ancestor.fasta</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">samtools faidx SH-2813-ancestor.fasta</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">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 id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">samtools view -bS SH-isolate-A.sam &gt; SH-isolate-A.bam</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">samtools sort SH-isolate-A.bam -o SH-isolate-A_sorted.bam</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">samtools rmdup SH-isolate-A_sorted.bam SH-isolate-A_rmdup.bam</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">samtools index -b SH-isolate-A_rmdup.bam &gt; SH-isolate-A</b> <b id="docs-internal-guid-cbcbf801-7fff-6493-c9f5-6dbdbf5dbd98">gatk HaplotypeCaller -R CP016573.fasta -I SH-isolate-A_rmdup.bam -ploidy 1 -O SH-isolate-A.vcf </b>