The genome sequences of four antibiotic-resistant Salmonella strains isolated from red meat animals in Australia are presented. Multidrug-resistant Salmonella enterica serovar Heidelberg 329 and Salmonella enterica serovar Typhimurium 2470 harbored an IncHI2 plasmid similar to the multidrug-resistant S. Heidelberg strain N13-01290 plasmid pN13-01290_23 previously isolated in Canada.
ABSTRACT
The genome sequences of four antibiotic-resistant Salmonella strains isolated from red meat animals in Australia are presented. Multidrug-resistant Salmonella enterica serovar Heidelberg 329 and Salmonella enterica serovar Typhimurium 2470 harbored an IncHI2 plasmid similar to the multidrug-resistant S. Heidelberg strain N13-01290 plasmid pN13-01290_23 previously isolated in Canada.
ANNOUNCEMENT
Salmonella enterica is a leading cause of human foodborne bacterial gastroenteritis worldwide (1). The widespread use of antibiotics in animal husbandry has resulted in multiantibiotic-resistant Salmonella strains in many countries, but their presence in Australia is generally low (2).
Forty-nine Salmonella strains consisting of Salmonella enterica serovars Anatum, Bovismorbificans, Heidelberg, Newport, Saintpaul, Typhimurium, and Virchow, isolated from different red meat animals consisting of cattle, sheep, and goats in Australia from 2001 to 2013, were isolated as described previously (3–5). All strains were grown in tryptone soy broth (TSB; Oxoid, UK) at 37°C for 24 h for genomic DNA extraction. Genomic DNA was extracted and purified using the Wizard genomic DNA purification kit (Promega, USA), according to the manufacturer’s instructions. The purity and concentration of the genomic DNA were determined using agarose gel electrophoresis and by a Qubit 2.0 fluorometer. The genomic DNA was fragmented and tagged using a Nextera XT DNA library preparation version 3 600-cycle MiSeq kit, followed by whole-genome sequencing on an Illumina MiSeq V3 sequencer (2 × 300-bp reads). The quality of the reads was determined using the BayesHammer error correction tool to improve the quality of the assembly. Genomes were assembled using SPAdes, and the genome qualities of the final assemblies were confirmed using the Quality Assessment Tool (QUAST) for genome assembly algorithm, followed by annotation using Rapid Annotations using Subsystems Technology (RAST) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (6–8). Antimicrobial resistance genes were determined using ResFinder (9). The genome sequences of three strains of S. Heidelberg (329 and 632 from goat rumen and 2581 from cattle feces) and one strain of S. Typhimurium (2470 from cattle feces), which were the only strains found to have antibiotic resistance genes, are presented here. Plasmid replicons were determined using PlasmidFinder (10). Plasmid contigs were identified using a local BLAST search against a database of known plasmids in PATRIC and mlplasmids (11, 12). Default parameters were used for all software, unless otherwise specified.
Genome features, including the total number of sequence reads, number of contigs, N50, L50, assembly size, GC content, and numbers of coding sequences (CDS), tRNAs, rRNAs, and plasmids across the four Salmonella genomes are shown in Table 1. The sources and dates of isolation of the four Salmonella strains are also shown in Table 1. A 100% orthologous average nucleotide identity was identified between the genomes of S. Heidelberg 329 and S. Typhimurium 2470 and between S. Heidelberg 632 and 2581, using the OrthoANI algorithm (13). This suggests a close phylogenetic relationship between the two sets of strains.
TABLE 1.
Summary of the whole-genome features of S. Heidelberg and S. Typhimurium strains
| Parameter | Data for strain: |
|||
|---|---|---|---|---|
| S. Heidelberg 329 | S. Heidelberg 632 | S. Heidelberg 2581a | S. Typhimurium 2470 | |
| Source | Goat rumen | Goat rumen | Cattle feces | Cattle feces |
| Date of isolation (day/mo/yr) | 13/12/2001 | 27/2/2002 | 27/8/2013 | 26/2/2013 |
| Total no. of sequence reads | 3,047,918 | 1,395,904 | 1,851,866 | 1,790,304 |
| No. of contigs | 69 | 34 | 28 | 63 |
| N50 (bp) | 191,631 | 740,277 | 641,189 | 231,719 |
| L50 | 9 | 2 | 2 | 7 |
| Assembly length (bp) | 5,069,302 | 4,780,505 | 4,685,585 | 5,071,508 |
| GC content (%) | 51.9 | 52.1 | 52.2 | 51.9 |
| No. of CDS | 5,172 | 4,773 | 4,654 | 5,181 |
| No. of tRNAs | 81 | 79 | 79 | 82 |
| No. of rRNAs | 12 | 13 | 13 | 11 |
| No. of plasmids | 3 | 3 | 0 | 2 |
| Accession no. | SWJR01000000 | SWMX00000000 | SWMW00000000 | SWMV00000000 |
| Contig accession no. (plasmid) | SWJR01000007 (p329_1), SWJR01000047 (p329_2), SWJR01000048 (p329_3) | SWMX01000015 (p632_1), SWMX01000017 (p632_2), SWMX01000020 (p632_3) | NA | SWMV01000009 (p2470_1), SWMV01000043 (p2470_2) |
| Sequence Read Archive accession no. | PRJNA534061 | PRJNA540014 | PRJNA540012 | PRJNA540010 |
NA, not applicable.
The S. Heidelberg 329 and S. Typhimurium 2470 plasmids belong to the IncHI2 group and that of S. Heidelberg 632 to the IncII group. IncHI2 is a plasmid lineage associated with the spread of antibiotic-resistant Salmonella spp. (1). S. Heidelberg 329 and S. Typhimurium 2470 harbored a plasmid similar to S. Heidelberg N13-01290/pN13-01290_23 (GenBank accession number CP012931), isolated from turkey meat in Canada (14). A nucleotide BLAST search of specific contigs in S. Heidelberg 329 (p329_1) and S. Typhimurium 2470 (p2470_1) against the pN13-01290_23 sequence revealed 99% identity to both strain contigs with 81% coverage. S. Heidelberg pN13-01290_23 belongs to the IncHI2 group and carries aph(3″)-Ib and aph(6)-Id (aminoglycoside resistance), blaTEM-1B (beta-lactam resistance), sul1 (sulfonamide resistance), and tet(B) (tetracycline resistance) genes. S. Heidelberg 329 and S. Typhimurium 2470 have several antibiotic resistance genes, including aac(6′)-Iaa, aph(3″)-Ib, aph(6)-Id, aadA1, blaTEM-1B, mph(B) (macrolide resistance), sul1 and sul2 (sulfonamide resistance), tet(A) (tetracycline resistance), and dfrA1 (trimethoprim resistance). All of these antibiotic resistance genes were located on the matching contig of pN13-01290_23, with the exception of the beta-lactam resistance gene, which was located in a different contig.
S. Heidelberg 632 and 2581 carry aac(6′)-Iaa (aminoglycoside resistance gene) and fosA7 (fosfomycin resistance gene) only on their chromosomes. A previous study reported that the fosA7 gene was found on the chromosome in S. Heidelberg isolated from poultry in Canada, although this gene is rarely reported among Salmonella spp. (15). Multidrug resistance efflux pump genes, such as acrA and mdfA, were detected on the chromosome in all Salmonella strains used in this study. Further understanding of antibiotic-resistant Salmonella spp. is required.
Data availability.
The whole-genome shotgun project sequences of Salmonella strains 329, 632, 2581, and 2470 have been deposited at DDBJ/ENA/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENT
This work was funded by the Australian Meat Processors Corporation (AMPC). No specific grant number is associated with this funding.
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Associated Data
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Data Availability Statement
The whole-genome shotgun project sequences of Salmonella strains 329, 632, 2581, and 2470 have been deposited at DDBJ/ENA/GenBank under the accession numbers listed in Table 1.