Dryad
Published June 23, 2021 | Version v1
Other Open

Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg

Authors/Creators

  • 1. University of Georgia
  • 2. Colorado State University
  • 3. Phase Genomics Inc*
  • 4. USDA-ARS*
  • 5. University of Veterinary Medicine Vienna
  • 6. Centers for Disease Control and Prevention
  • 7. Medical College of Georgia*

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.

Notes

#PBS -S /bin/bash

#PBS -N 

#PBS -q batch

#PBS -l nodes=2:ppn=4

#PBS -l walltime=

#PBS -l mem=40gb

#PBS -M 

#PBS -m ae 

cd $PBS_O_WORKDIR

module load GATK/4.1.2.0-GCCcore-8.2.0-Java-1.8

module load SAMtools/1.10-GCC-8.2.0-2.31.1

module load BWA/0.7.17-foss-2016b

bwa index SH-2813-ancestor.fasta

samtools faidx SH-2813-ancestor.fasta

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 > SH-isolate-A.sam

samtools view -bS SH-isolate-A.sam > SH-isolate-A.bam

samtools sort SH-isolate-A.bam -o SH-isolate-A_sorted.bam

samtools rmdup SH-isolate-A_sorted.bam SH-isolate-A_rmdup.bam

samtools index -b SH-isolate-A_rmdup.bam > SH-isolate-A

gatk HaplotypeCaller -R CP016573.fasta -I SH-isolate-A_rmdup.bam -ploidy 1 -O SH-isolate-A.vcf 

Funding provided by: University of Georgia Research Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100012483
Award Number: 58-6040-6-030

Funding provided by: USDA-ARS*
Crossref Funder Registry ID:
Award Number: 6040‐32000‐010‐00‐D

Funding provided by: USDA-ARS
Crossref Funder Registry ID:
Award Number: 6040‐32000‐010‐00‐D

Files

Fig.S10.tif

Files (2.5 MB)

Name Size Download all
md5:077da39c3efed2c694ca99b41f9f613a
431.8 kB Preview Download
md5:47b37ea9f4968baed90c0a9cf46a06af
598.2 kB Preview Download
md5:9455203f8a2f366022f952277b655c00
236.8 kB Preview Download
md5:96b8cfbfa750d2721ecae6fee74d8076
543.4 kB Preview Download
md5:5fc935ab54396365d9e10e4d89114498
15.2 kB Download
md5:eb0722350dc032b8f3695ca0aa62a5ea
29.6 kB Preview Download
md5:9cbf2e0d2d9cd3c4dcb203ac3fd6ca29
21.4 kB Download
md5:3e9acdb20af3baec3732f27df112ff63
579.5 kB Preview Download
md5:f0c6d62cf6b2785240e6331292e05264
19.9 kB Download
md5:deb80708fb848e2e02b8dbd7458444cf
20.8 kB Download

Additional details

Related works

Is cited by
10.1101/2021.02.25.432983 (DOI)
Is derived from
10.5061/dryad.4tmpg4f8d (DOI)