Whole-genome sequencing of antimicrobial-resistant Salmonella enterica isolates from a Cairina moschata carcass

Salmonella enterica is one of the most common agents of foodborne bacterial illness with poultry being an important reservoir. The indiscriminate use of antimicrobial compounds in poultry farming increasingly leads to antimicrobial-resistant (AMR) which threatens the health of both animals and humans. Antimicrobial-resistant Salmonella enterica from the poultry can spread to human through the direct contact with infected poultry or fecal contaminated environments. Antimicrobial-resistant S. enterica, especially fluoroquinolone-resistant nontyphoidal Salmonella is in the list of global health concern stated by the World Health Organization (WHO). Here we report the whole-genome sequencing data and de novo genome assemble of antimicrobial-resistant S. enterica strains S8 and S9 from the C. moschata carcass collected in Vietnam. Genomic DNA of S. enterica were extracted and subjected to whole-genome sequencing using Illumina MiSeq platform. The genome size of antimicrobial-resistant S. enterica strain S8 is 4,707,459 bp with a GC-content of 52.38%, containing 10 antimicrobial resistant genes. The genome size of antimicrobial-resistant Samonella enterica strain S9 is 4,923,944 bp with a GC-content of 52,39%, containing 10 antimicrobial resistance genes. Our data provided the insights on antimicrobial resistant genes of S. enterica isolates from the C. moschata carcass, which help to understand the infection mechanism of antimicrobial-resistant S. enterica in human.


a b s t r a c t
Salmonella enterica is one of the most common agents of foodborne bacterial illness with poultry being an important reservoir. The indiscriminate use of antimicrobial compounds in poultry farming increasingly leads to antimicrobialresistant (AMR) which threatens the health of both animals and humans. Antimicrobial-resistant Salmonella enterica from the poultry can spread to human through the direct contact with infected poultry or fecal contaminated environments. Antimicrobial-resistant S. enterica, especially fluoroquinoloneresistant nontyphoidal Salmonella is in the list of global health concern stated by the World Health Organization (WHO). Here we report the whole-genome sequencing data and de novo genome assemble of antimicrobial-resistant S. enterica strains S8 and S9 from the C. moschata carcass collected in Vietnam. Genomic DNA of S. enterica were extracted and subjected to whole-genome sequencing using Illumina MiSeq platform. The genome size of antimicrobial-resistant S. enterica strain S8 is 4,707,459 bp with a GC-content of 52.38%, containing 10 antimicrobial resistant genes. The genome size of antimicrobial-resistant Samonella enterica strain S9 is 4,923,944 bp with a GC-content of 52,39%, containing 10 antimicrobial resistance genes. Our data provided the insights on antimicrobial resistant genes of S. enterica isolates from the C. moschata carcass, which help to understand the infection mechanism of antimicrobial-resistant S. enterica in human. ©

Value of the Data
• The data provides the information of whole genome sequence of antimicrobial-resistant Salmonella enterica S8 and S9 isolates from the C. moschata carcass collected in Vietnam. • Whole-genome sequence data of antimicrobial-resistant S. enterica provides insights on antimicrobial resistance genes in S. enterica genome The data enables further understanding of the mechanism and treatment of diseases caused by antimicrobial-resistant S. enterica in human. • Whole genome sequence data are available in the gene bank for the biomedical community and can be applied to develop the effective test kits based on the information of antimicrobial resistance genes.

Objective
Among Salmonella genus, Salmonella enterica is the common factor that causes foodborne outbreaks. Salmonella enterica consists of 6 subspecies, which compose of more than 2600 serovars. S. enterica subsp. enterica is responsible for more than 99% of human salmonellosis globally. In Vietnam, due to the expansion in antimicrobial resistance of pathogenic bacteria and increased availability of whole-genome sequencing tools, publications of whole-genome sequencing data of pathogenic Salmonella in Vietnam have risen in recent years [1][2][3][4][5][6] . Here we isolated the antimicrobial-resistant Salmonella S8 and S9 isolates from Cairina moschata carcasses (commonly called Muscovy duck) carcasses collected from several wet markets in Hanoi, Vietnam. The Salmonella S8 and S9 isolates were classified as Salmonella enterica serovar Muenster and serovar Infantis, respectively. Both antimicrobial-resistant S. enterica S8 and S9 isolates have not been published in databases related to pathogenic bacteria in Vietnam. Thus, in this study, we analyzed the whole genome sequencing of S. enterica serovar Muenster S8 and S. enterica serovar Infantis S9 strains to give insights into antimicrobial resistance genes of Samonella isolates from C. moschata carcasses.

Data Description
Here we reported the whole genome sequencing of S. enterica serovar Muenster S8 and S. enterica serovar Infantis S9 together with antimicrobial resistant genes.
The assembled genome size of antimicrobial-resistant S. enterica S8 strain was 4,707,459 bp with a GC content of 52,38%. While antimicrobial-resistant S. enterica strain S9 accounted for a genome size of 4,923,944 bp and a GC content of 52,39% ( Table 1 ). The genomes dataset of strain S8 and S9 were assigned as ST-321 and ST-32 in the public databases for molecular typing and microbial genome diversity (PubMLST), respectively. The screening results for contigs of antimicrobial resistant genes suggested that both genomes of S. enterica S8 and S9 strains contained a number of antimicrobial resistant genes against multiple antibiotics, including tetracycline, quinolone, gentamicin, beta-lactam, streptomycin, extended-spectrum beta-lactamases (ESBLs). Mass screening for contigs of antimicrobial resistant or virulence genes (ABRicate) identified all the antibiotic resistant genes in Tables 2 and 3 .

Genomic DNA extraction and sequencing
S. enterica S8 and S9 strains were cultured in Brain Heart Ìnfusion broth (BHI broth, Merck, Germany) at 37 °C for 18 -24 hours. 1mL of overnight culture was centrifuged at 2,0 0 0 rpm for 10 minutes at room temperature and harversted cells were applied for genomic DNA extraction. The DNA extraction procedure was executed by using PureLink TM Genomic DNA Mini Kit (Invitrogen, Thermofisher scientific) according to the manufacturer's protocol. A library was prepared for sequencing using Nextera XT DNA Library Preparation Kit (Nextera XT, Illumina, San Diego, CA, USA) and WGS sequencing was performed using the Illumina MiSeq system (Illumina, San Diego, CA, USA), as described by the respective manufacturers.

Genome assembly, annotation and comparative genomic analysis
Read trimming was carried out using Trimmomatic removing the sequence adaptor [7] . Quality control was conducted with FastQC ( https://www.bioinformatics.babra-ham.ac.uk/projects/ fastqc/ ). De novo assembly was performed using SPAdes 3.15 [8] . Contigs were ordered against a Salmonella enterica sbsps . enterica serovar Typhimurium strain ATCC 14028 using ABACAS v1.3.1 with -dmbc setting [9] . Whole genome sequencing data of both isolates were then identified by using Serotype (SISTR1 + SeqSero2) web tool from the EnteroBase website ( http: //enterobase.warwick.ac.uk/ ), the database used for analysis is based on Salmonella In Silico Typing Resource (SISTR) platform [10] . Abricate was applied for screening of the antibiotic resistant genes, plasmid replicons and virulence genes [11] . The antibiotic resistant genes were identified by screening of the draft genome against NCBI ARM finderPlus databases [12] . The search of plasmid replicons was conducted by screening of the draft genome against PlasmidFinder database [13] . The virulence genes were detected by screening of the draft genome against Virulence Factors Data Base [14] .

Ethics Statements
This work did not involve studies with animals and humans.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.