ABSTRACT
Vibrio spp. isolated from fresh retail mollusk samples were selected for sequencing based on their antimicrobial resistance burden. The de novo genomes include those for Vibrio alginolyticus (n = 48), V. diabolicus (n = 15), V. parahaemolyticus (n = 3), V. cholerae (n = 2), V. metoecus (n = 1), V. vulnificus (n = 1), V. fluvialis (n = 1), and unidentified Vibrio spp. (n = 4).
ANNOUNCEMENT
Vibrio spp. represent a diverse group of Gram-negative human bacterial pathogens responsible for the majority of foodborne illnesses associated with seafood (1, 2). Illness resulting from these bacteria arises primarily from consuming raw or undercooked mollusks contaminated with pathogenic Vibrio during warmer months of the year (1, 3). There is growing concern that marine pathogens, including Vibrio spp., which are exposed to antimicrobial resistant (AMR) bacteria, may themselves become resistant to standard antibiotic treatment (4). The present study sequenced the genomes of a subset (n = 75) of Vibrio isolates from fresh retail mollusks available in Canada (2014 to 2018) based on AMR profiles.
Single colonies from fresh retail mollusk samples (n = 45) were isolated as described (5). Briefly, 10 to 20 shucked mollusks per sample were homogenized in a blender; a total of 50 g of homogenate was mixed with 450 mL alkaline peptone water (1% Bacto-peptone and 2% NaCl [pH 8.5]) and equilibrated 1 h at 21°C before overnight enrichment at 35°C. Selective agars (thiosulfate-citrate-bile salts-sucrose [TCBS], CHROMagar, and mCC10 or CC400) were used for both pre-enrichment (100 μL) and postenrichment (10 μL) plating. After a 35°C overnight incubation, presumptive Vibrio colonies were grown at 35°C overnight on tryptic soy agar with 2% NaCl (TSA-2N) (Difco BD, Franklin Lakes, NJ) for molecular/biochemical Vibrio confirmation (5) and −80°C stock preparation (10 μL loopful/Microbank vial) (VWR, Mississauga, Ontario, Canada). The AMR phenotype to 23 antibiotics (Oxoid Ltd., Basingstoke, UK) was determined for isolates using the Kirby-Bauer disk diffusion method and published guidelines (6–8); a subset of isolates with AMR profiles ranging from no resistance to multidrug resistance was selected for sequencing (Table 1).
TABLE 1.
Metadata and genome assembly metrics for 75 Vibrio sp. isolates collected from fresh retail mollusks available in Canada from 2014 to 2018
| Isolate | Mollusk type | Yr | Retail locationa | Taxonomic IDb (Mash) | AMR profilec | Genome size (bp) | GC content (%) | Coverage (×) | No. of contigs | No. of reads | N50 (bp) | No. of genes | BioSample accession | Assembly accession | GenBank accession | SRA accession |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RM-6-1 | Mussel | 2014 | PEI | V. alginolyticus | AMP, PIP, S | 5,139,382 | 44.6 | 57 | 65 | 1,086,716 | 225,218 | 4,694 | SAMN28767208 | GCA_024744935.1 | JAMQVD000000000 | SRR19544305 |
| RM-11-1 | Oyster | 2014 | PEI | V. alginolyticus | AMP (KF, E) | 5,237,869 | 44.6 | 58 | 76 | 1,123,262 | 446,189 | 4,876 | SAMN28767209 | GCA_024744915.1 | JAMQVE000000000 | SRR19544304 |
| RM-14-4 | Mussel | 2014 | PEI | V. alginolyticus | AMP, PIP, KF | 5,227,775 | 44.6 | 63 | 71 | 1,188,912 | 249,827 | 4,832 | SAMN28767210 | GCA_024744895.1 | JAMQVF000000000 | SRR19544293 |
| RM-15-5 | Oyster | 2014 | BC | V. alginolyticus | AMP, PIP, KF | 5,126,382 | 44.9 | 70 | 53 | 1,035,206 | 405,367 | 4,635 | SAMN28767211 | GCA_024744855.1 | JAMQVG000000000 | SRR19544282 |
| RM-15-6 | Oyster | 2014 | BC | V. alginolyticus | AMP, PIP, KF | 5,118,101 | 44.5 | 63 | 65 | 1,335,228 | 221,239 | 4,703 | SAMN28767212 | GCA_024744835.1 | JAMQVH000000000 | SRR19544247 |
| RM-15-9 | Oyster | 2014 | BC | V. alginolyticus | AMP, PIP, KF | 5,128,533 | 44.5 | 50 | 50 | 1,246,452 | 379,764 | 4,707 | SAMN28767213 | GCA_024744815.1 | JAMQVI000000000 | SRR19544236 |
| RM-15-10 | Oyster | 2014 | BC | V. diabolicus | AMP, PIP, OX | 5,054,262 | 44.5 | 56 | 41 | 908,836 | 347,902 | 4,702 | SAMN28767214 | GCA_024744845.1 | JAMQVJ000000000 | SRR19544273 |
| RM-16-10 | Mussel | 2014 | PEI | V. alginolyticus | AMP, PIP, KF | 5,271,750 | 44.6 | 58 | 40 | 1,112,442 | 385,123 | 4,788 | SAMN28767215 | GCA_024744795.1 | JAMQVK000000000 | SRR19544262 |
| RM-16-11 | Mussel | 2014 | PEI | V. alginolyticus | AMP, PIP, KF | 5,178,540 | 44.6 | 80 | 51 | 1,574,650 | 290,945 | 4,786 | SAMN28767216 | GCA_024744755.1 | JAMQVL000000000 | SRR19544256 |
| RM-17-4 | Clam | 2014 | BC | V. alginolyticus | AMP, PIP, KF | 5,142,659 | 44.6 | 49 | 54 | 917,938 | 364,175 | 4,672 | SAMN28767217 | GCA_024744735.1 | JAMQVM000000000 | SRR19544255 |
| RM-17-5 | Clam | 2014 | BC | V. alginolyticus | AMP, PIP, KF | 5,138,442 | 44.6 | 45 | 53 | 866,500 | 290,122 | 4,665 | SAMN28767218 | GCA_024744775.1 | JAMQVN000000000 | SRR19544303 |
| RM-18-1 | Oyster | 2014 | PEI | V. alginolyticus | AMP, PIP, KF | 5,218,565 | 44.6 | 53 | 56 | 1,028,156 | 248,131 | 4,844 | SAMN28767219 | GCA_024744715.1 | JAMQVO000000000 | SRR19544302 |
| RM-18-3 | Oyster | 2014 | PEI | V. alginolyticus | AMP, PIP, KF | 5,217,942 | 44.6 | 55 | 48 | 1,027,504 | 442,486 | 4,833 | SAMN28767220 | GCA_024744695.1 | JAMQVP000000000 | SRR19544301 |
| RM-20-4 | Mussel | 2014 | PEI | V. alginolyticus | AMP, PIP, KF | 5,513,473 | 44.6 | 44 | 53 | 882,848 | 422,698 | 5,141 | SAMN28767221 | GCA_024744655.1 | JAMQVQ000000000 | SRR19544300 |
| RM-30-9 | Clam | 2015 | MB | V. diabolicus | AMP, SF, KF, OX | 5,051,443 | 44.7 | 49 | 54 | 881,366 | 336,942 | 4,727 | SAMN28767222 | GCA_024744635.1 | JAMQVR000000000 | SRR19544299 |
| RM-31-4 | Mussel | 2015 | PEI | V. alginolyticus | AMP, PIP, KF | 5,269,051 | 44.6 | 42 | 52 | 790,774 | 230,154 | 4,873 | SAMN28767223 | GCA_024744615.1 | JAMQVS000000000 | SRR19544298 |
| RM-32-1 | Oyster | 2015 | BC | V. alginolyticus | AMP (PIP, KF, E) | 5,264,157 | 44.5 | 113 | 62 | 2,214,222 | 240,981 | 4,869 | SAMN28767224 | GCA_024744645.1 | JAMQVT000000000 | SRR19544297 |
| RM-32-14 | Oyster | 2015 | BC | V. alginolyticus | AMP, PIP, KF, SF | 5,287,414 | 44.5 | 72 | 97 | 1,402,938 | 159,185 | 4,867 | SAMN28767225 | GCA_024744595.1 | JAMQVU000000000 | SRR19544296 |
| RM-33-1 | Mussel | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,305,958 | 44.5 | 42 | 46 | 816,680 | 440,386 | 4,867 | SAMN28767226 | GCA_024744575.1 | JAMQVV000000000 | SRR19544295 |
| RM-35-7 | Mussel | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,252,659 | 44.5 | 39 | 57 | 733,334 | 315,487 | 4,824 | SAMN28767227 | GCA_024744545.1 | JAMQVW000000000 | SRR19544294 |
| RM-35-9 | Mussel | 2015 | BC | V. diabolicus | AMP, KF, OX | 5,064,064 | 44.8 | 34 | 47 | 596,670 | 428,425 | 4,648 | SAMN28767228 | GCA_024744525.1 | JAMQVX000000000 | SRR19544292 |
| RM-36-7 | Clam | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,145,530 | 44.4 | 35 | 72 | 656,786 | 171,080 | 4,655 | SAMN28767229 | GCA_024744515.1 | JAMQVY000000000 | SRR19544291 |
| RM-38-7 | Clam | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,263,704 | 44.6 | 60 | 38 | 1,158,522 | 286,398 | 4853 | SAMN28767230 | GCA_024744495.1 | JAMQVZ000000000 | SRR19544290 |
| RM-39-4 | Clam | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,239,905 | 44.6 | 76 | 50 | 1,659,760 | 368,966 | 4,879 | SAMN28767231 | GCA_024744475.1 | JAMQWA000000000 | SRR19544289 |
| RM-39-6 | Clam | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,289,632 | 44.5 | 84 | 69 | 1,703,254 | 196,839 | 4,864 | SAMN28767232 | GCA_024744455.1 | JAMQWB000000000 | SRR19544288 |
| RM-41-2A | Oyster | 2015 | BC | Vibrio spp. | AMP, PIP, OX | 5,203,605 | 44.8 | 82 | 108 | 1,572,494 | 116,867 | 4,788 | SAMN28767233 | GCA_024744435.1 | JAMQWC000000000 | SRR19544287 |
| RM-41-2B | Oyster | 2015 | BC | Vibrio spp. | AMP, PIP, KF, OX | 5,213,084 | 44.8 | 49 | 57 | 925,380 | 276,740 | 4,780 | SAMN28767234 | GCA_024744415.1 | JAMQWD000000000 | SRR19544286 |
| RM-41-6 | Oyster | 2015 | BC | V. alginolyticus | AMP, KF (PIP, CTX, E, ENO) | 5,590,557 | 44.4 | 110 | 87 | 2,453,644 | 193,719 | 5,245 | SAMN28767235 | GCA_024744395.1 | JAMQWE000000000 | SRR19544285 |
| RM-42-4 | Clam | 2015 | BC | V. diabolicus | AMP, PIP, OX | 5,296,987 | 44.7 | 56 | 68 | 1,088,760 | 223,223 | 4,926 | SAMN28767236 | GCA_024744375.1 | JAMQWF000000000 | SRR19544284 |
| RM-44-2 | Oyster | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,352,218 | 44.6 | 51 | 85 | 998,750 | 178,940 | 5,005 | SAMN28767237 | GCA_024744355.1 | JAMQWG000000000 | SRR19544283 |
| RM-44-3 | Oyster | 2015 | BC | Vibrio spp. | AMP, PIP, KF, SF, OX | 5,203,331 | 44.8 | 85 | 131 | 1,630,898 | 99,981 | 4,802 | SAMN28767238 | GCA_024744335.1 | JAMQWH000000000 | SRR19544281 |
| RM-46-1 | Clam | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,146,619 | 44.6 | 42 | 66 | 773,280 | 219,393 | 4,795 | SAMN28767239 | GCA_024744305.1 | JAMQWI000000000 | SRR19544280 |
| RM-47-7 | Mussel | 2015 | BC | V. alginolyticus | AMP, PIP, KF, SF, OX | 5,234,538 | 44.6 | 60 | 92 | 1,159,622 | 112,517 | 4,798 | SAMN28767240 | GCA_024744285.1 | JAMQWJ000000000 | SRR19544279 |
| RM-48-6 | Mussel | 2015 | PEI | V. alginolyticus | AMP, PIP, KF | 5,139,195 | 44.5 | 97 | 83 | 1,931,742 | 165,239 | 4,728 | SAMN28767241 | GCA_024744275.1 | JAMQWK000000000 | SRR19544254 |
| RM-49-4 | Oyster | 2015 | NB | V. alginolyticus | AMP, PIP, OX | 5,290,784 | 44.5 | 29 | 97 | 565,670 | 109,439 | 4,890 | SAMN28767242 | GCA_024744255.1 | JAMQWL000000000 | SRR19544253 |
| RM-49-5 | Oyster | 2015 | NB | V. alginolyticus | AMP, PIP, OT | 5,138,153 | 44.6 | 38 | 109 | 750,646 | 97,040 | 4,680 | SAMN28767243 | GCA_024744235.1 | JAMQWM000000000 | SRR19544252 |
| RM-49-6 | Oyster | 2015 | NB | V. alginolyticus | AMP, PIP, KF, OX | 5,174,447 | 44.5 | 64 | 73 | 1,232,382 | 186,688 | 4,816 | SAMN28767244 | GCA_024744215.1 | JAMQWN000000000 | SRR19544251 |
| RM-50-2 | Mussel | 2015 | BC | V. diabolicus | AMP, PIP, OX | 5,120,376 | 44.8 | 51 | 160 | 1,416,472 | 68,872 | 4,834 | SAMN28767245 | GCA_024744195.1 | JAMQWO000000000 | SRR19544250 |
| RM-50-3 | Mussel | 2015 | BC | V. diabolicus | AMP, PIP, OX | 5,139,456 | 44.8 | 34 | 91 | 953,844 | 150,209 | 4,840 | SAMN28767246 | GCA_024744175.1 | JAMQWP000000000 | SRR19544249 |
| RM-51-4 | Clam | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,335,949 | 44.5 | 36 | 92 | 715,712 | 161,255 | 4,946 | SAMN28767247 | GCA_024744155.1 | JAMQWQ000000000 | SRR19544248 |
| RM-51-5 | Clam | 2015 | BC | V. alginolyticus | AMP, PIP, KF | 5,336,320 | 44.5 | 55 | 68 | 1,183,996 | 215,337 | 4,949 | SAMN28767248 | GCA_024744105.1 | JAMQWR000000000 | SRR19544246 |
| RM-53-1 | Oyster | 2015 | QC | V. diabolicus | AMP, PIP, KF, SF, OX | 5,179,548 | 44.8 | 46 | 108 | 1,007,130 | 87,078 | 4,759 | SAMN28767249 | GCA_024744135.1 | JAMQWS000000000 | SRR19544245 |
| RM-53-2 | Oyster | 2015 | QC | V. diabolicus | AMP, PIP, KF, OX | 5,184,243 | 44.7 | 39 | 75 | 721,366 | 121,173 | 4,770 | SAMN28767250 | GCA_024744095.1 | JAMQWT000000000 | SRR19544244 |
| RM-54-2 | Oyster | 2015 | NB | V. diabolicus | AMP, PIP, OX | 5,043,200 | 44.8 | 67 | 51 | 1,313,972 | 230,783 | 4,620 | SAMN28767251 | GCA_024744055.1 | JAMQWU000000000 | SRR19544243 |
| RM-54-3 | Oyster | 2015 | NB | V. diabolicus | AMP, PIP, KF, OX | 5,051,438 | 44.8 | 78 | 45 | 1,552,654 | 389,118 | 4,623 | SAMN28767252 | GCA_024744075.1 | JAMQWV000000000 | SRR19544242 |
| RM-55-3 | Oyster | 2015 | QC | V. diabolicus | AMP, PIP, KF, SF, OX | 5,102,463 | 44.9 | 74 | 41 | 1,349,826 | 363,436 | 4,781 | SAMN28767253 | GCA_024744025.1 | JAMQWW000000000 | SRR19544241 |
| RM-58-1 | Mussel | 2015 | NL | V. alginolyticus | AMP, PIP, KF, SF | 5,195,584 | 44.6 | 154 | 45 | 2,987,352 | 285,387 | 4,737 | SAMN28767254 | GCA_024744015.1 | JAMQWX000000000 | SRR19544240 |
| RM-58-2 | Mussel | 2015 | NL | V. alginolyticus | AMP, PIP, KF, PB, OX | 5,194,433 | 44.6 | 48 | 52 | 1,140,158 | 346,030 | 4,746 | SAMN28767255 | GCA_024743995.1 | JAMQWY000000000 | SRR19544239 |
| RM-59-1 | Oyster | 2015 | PEI | V. alginolyticus | AMP, PIP, KF, SF | 5,223,928 | 44.6 | 47 | 224 | 929,392 | 58,091 | 4,830 | SAMN28767256 | GCA_024743975.1 | JAMQWZ000000000 | SRR19544238 |
| RM-59-2 | Oyster | 2015 | PEI | V. alginolyticus | AMP, PIP, KF, SF | 5,223,283 | 44.6 | 42 | 209 | 816,194 | 52,452 | 4,823 | SAMN28767257 | GCA_024743955.1 | JAMQXA000000000 | SRR19544237 |
| RM-62-1 | Oyster | 2015 | QC | V. alginolyticus | AMP, PIP, KF | 5,266,495 | 44.6 | 41 | 93 | 813,524 | 106,402 | 4,787 | SAMN28767258 | GCA_024743935.1 | JAMQXB000000000 | SRR19544235 |
| RM-62-3 | Oyster | 2015 | QC | V. alginolyticus | AMP, PIP, KF | 5,264,540 | 44.6 | 124 | 50 | 2,500,242 | 30,3236 | 4,782 | SAMN28767259 | GCA_024743875.1 | JAMQXC000000000 | SRR19544234 |
| RM-63-1 | Mussel | 2015 | PEI | V. alginolyticus | AMP, PIP, KF, SF | 5,198,355 | 44.7 | 30 | 243 | 549,986 | 44,441 | 4,835 | SAMN28767260 | GCA_024743895.1 | JAMQXD000000000 | SRR19544233 |
| RM-63-2 | Mussel | 2015 | PEI | V. alginolyticus | AMP, PIP, KF, SF | 5,244,519 | 44.6 | 55 | 81 | 1,031,798 | 149,576 | 4,854 | SAMN28767261 | GCA_024743915.1 | JAMQXE000000000 | SRR19544232 |
| RM-65-3 | Clam | 2015 | NB | V. diabolicus | AMP, KF, OX | 5,034,284 | 44.8 | 43 | 65 | 772,454 | 146,395 | 4,605 | SAMN28767262 | GCA_024743855.1 | JAMQXF000000000 | SRR19544231 |
| RM-67-1 | Mussel | 2015 | PEI | V. alginolyticus | AMP, PIP, KF | 5,244,311 | 44.6 | 36 | 289 | 1,051,714 | 43,360 | 4,897 | SAMN28767263 | GCA_024743835.1 | JAMQXG000000000 | SRR19544278 |
| RM-67-3 | Mussel | 2015 | PEI | V. alginolyticus | AMP, PIP, KF | 5,276,861 | 44.5 | 59 | 157 | 1,115,426 | 85,282 | 4,912 | SAMN28767264 | GCA_024743805.1 | JAMQXH000000000 | SRR19544277 |
| RM-69-4 | Oyster | 2015 | NB | Vibrio spp.d | AMP, KF, IPM, DOR (ETP, E, ENO, OT) | 4,036,806 | 44.5 | 317 | 98 | 4,749,982 | 237,730 | 3,687 | SAMN28767265 | GCA_024743775.1 | JAMQXI000000000 | SRR19544276 |
| RM-69-5 | Oyster | 2015 | NB | V. alginolyticus | AMP, PIP, KF | 5,177,717 | 44.6 | 58 | 87 | 1,128,036 | 131,966 | 4,806 | SAMN28767266 | GCA_024743795.1 | JAMQXJ000000000 | SRR19544275 |
| RM-69-8 | Oyster | 2015 | NB | V. alginolyticus | AMP, PIP, KF | 5,178,556 | 44.6 | 46 | 85 | 871,556 | 131,184 | 4,808 | SAMN28767267 | GCA_024743745.1 | JAMQXK000000000 | SRR19544274 |
| RM-75-1 | Oyster | 2015 | NB | V. diabolicus | AMP, PIP, KF, OX | 5,211,380 | 44.8 | 57 | 119 | 1,067,426 | 85,122 | 4,846 | SAMN28767268 | GCA_024743735.1 | JAMQXL000000000 | SRR19544272 |
| RM-75-2 | Oyster | 2015 | NB | V. diabolicus | AMP, KF, OX | 5,220,945 | 44.8 | 47 | 64 | 934,704 | 262,542 | 4,834 | SAMN28767269 | GCA_024743715.1 | JAMQXM000000000 | SRR19544271 |
| RM-80-5B2 | Oyster | 2016 | NB | V. fluvialis | AMP, PIP, KF, CTX, CEF (ETP, IMP, SF, E, OT) | 4,848,434 | 49.7 | 86 | 58 | 1,581,876 | 218,439 | 4,575 | SAMN28767270 | GCA_024743695.1 | JAMQXN000000000 | SRR19544270 |
| RM-85-1 | Mussel | 2016 | BC | V. alginolyticus | AMP, PIP, KF | 5,420,155 | 44.6 | 54 | 65 | 1,054,496 | 301,057 | 5,064 | SAMN28767271 | GCA_024743675.1 | JAMQXO000000000 | SRR19544269 |
| RM-86-11 | Oyster | 2016 | PEI | V. parahaemolyticus | AMP, PIP, KF | 5,019,268 | 45.3 | 70 | 30 | 1,297,124 | 371,872 | 4,618 | SAMN28767272 | GCA_024743635.1 | JAMQXP000000000 | SRR19544268 |
| RM-89-5 | Oyster | 2016 | BC | V. alginolyticus | AMP, PIP, KF | 5,260,117 | 44.6 | 38 | 136 | 1,478,570 | 89,166 | 4,901 | SAMN28767273 | GCA_024743655.1 | JAMQXQ000000000 | SRR19544267 |
| RM-89-6 | Oyster | 2016 | BC | V. parahaemolyticus | AMP, PIP, KF | 5,268,074 | 45.2 | 45 | 54 | 850,322 | 336,059 | 4,891 | SAMN28767274 | GCA_024743615.1 | JAMQXR000000000 | SRR19544266 |
| RM-92-1 | Mussel | 2016 | PEI | V. alginolyticus | AMP, KF | 5,371,879 | 44.6 | 61 | 71 | 1,165,112 | 196,890 | 4,897 | SAMN28767275 | GCA_024743565.1 | JAMQXS000000000 | SRR19544265 |
| RM-92-2 | Mussel | 2016 | PEI | V. alginolyticus | AMP, KF (PIP, E, OT) | 5,375,628 | 44.6 | 31 | 80 | 596,688 | 138,897 | 4,908 | SAMN28767276 | GCA_024743595.1 | JAMQXT000000000 | SRR19544264 |
| RM-160-1 | Mussel | 2018 | NS | V. cholerae | (DOR, IPM) | 4,081,390 | 47.6 | 177 | 50 | 2,741,848 | 648,558 | 3,750 | SAMN28767277 | GCA_024743535.1 | JAMQXU000000000 | SRR19544263 |
| RM-195-1 | No data | 2018 | NS | V. cholerae | NONE | 3,994,309 | 47.6 | 85 | 77 | 1,295,286 | 245,400 | 3,680 | SAMN28767278 | GCA_024743545.1 | JAMQXV000000000 | SRR19544261 |
| RM-195-2 | No data | 2018 | NS | V. metoecus | AMP, PIP, S | 3,995,805 | 47.0 | 106 | 109 | 1,536,338 | 77,829 | 3,776 | SAMN28767279 | GCA_024743495.1 | JAMQXW000000000 | SRR19544260 |
| RM-195-3 | No data | 2018 | NS | V. vulnificus | S, SXT, SF, OT (TE) | 5,205,873 | 46.6 | 69 | 63 | 1,337,300 | 414,924 | 4,744 | SAMN28767280 | GCA_024743455.1 | JAMQXX000000000 | SRR19544259 |
| RM-211-4 | Mussel | 2018 | NS | V. parahaemolyticus | S, SXT, SF, OT (PB, TE) | 4,922,914 | 45.4 | 59 | 67 | 1,096,816 | 203,583 | 4,564 | SAMN28767281 | GCA_024743475.1 | JAMQXY000000000 | SRR19544258 |
| RM-214-3 | No data | 2018 | NS | V. diabolicus | AMP, PIP, KF, CTX, CEF (E) | 5,342,114 | 44.9 | 115 | 143 | 2,270,098 | 86,108 | 4,975 | SAMN28767282 | GCA_024743515.1 | JAMQXZ000000000 | SRR19544257 |
Canadian provinces: BC, British Columbia; MB, Manitoba; NB, New Brunswick; NL, Newfoundland; NS, Nova Scotia; PEI, Prince Edward Island; QC, Québec.
ID, identifier.
Antibiotics: AMP, ampicillin; CEF, ceftiofur; CTX, cefotaxime; C, chloramphenicol; CIP, ciprofloxacin; DOR, doripenem; ETP, ertapenem; E, erythromycin; ENO, enrofloxacin; GN, gentamicin; IPM, imipenem; K, kanamycin; KF, cephalothin; MEM, meropenem; NOR, norfloxacin; OT, oxytetracycline; OX, oxolinic acid; PIP, piperacillin; PB, polymyxin B; S, streptomycin; SF, sulfisoxazole; SXT, sulphamethoxazole-trimethoprim; TE, tetracycline. Brackets, intermediate resistance; NONE, no resistance.
V. anguillarum/V. ordalii.
For sequencing, stocks were streaked onto TSA-2N and incubated at 35°C overnight. Single-colony inoculates (5 mL tryptic soy broth with 2% NaCl [TSB-2N]) were grown for 24 h at 35°C, and DNA was extracted using the Maxwell 16 SEV cell DNA purification kit (Promega, Madison, WI, USA). Paired-end Illumina whole-genome sequencing (WGS) was performed using indexed NexteraXT libraries run on a MiSeq instrument (2 × 300-bp cycles, v3 chemistry) according to the manufacturer (Illumina, San Diego, CA). Reads were trimmed to remove adapters, quality filtered, and error corrected (BBMap v38.26 [BBDuk and Tadpole]) (https://sourceforge.net/projects/bbmap) for de novo assembly (SKESA v2.3 and Pilon v1.22) (9), gene prediction (NCBI PGAP v6.1; best-placed reference protein set; GeneMarkS-2+) (10), and metric reporting (QUAST v5.0.0) (11). Mash (v2.2.1; Mash Screen) (12) was used for taxonomic assignment of assemblies based on the highest RefSeq (v93; https://www.ncbi.nlm.nih.gov/refseq) identities of >0.8 (excluding hits containing the words phage or plasmid) and cross-referencing to V. diabolicus classifications (13) (http://www.ncbi.nlm.nih.gov/genome). Analysis tools were used with default settings unless noted.
Isolate and genome details are listed in Table 1. Genome assemblies included 30 to 289 contigs and coverage depths of 29-fold to 317-fold. Total genome sizes ranged from 4.0 Mbp to 5.6 Mbp and contained 3,508 to 5,138 predicted genes. Taxonomic classification of the de novo genomes identified 48 V. alginolyticus, 15 V. diabolicus, 3 V. parahaemolyticus, 2 V. cholerae, 1 V. metoecus, 1 V. vulnificus, 1 V. fluvialis, and 4 unclassified Vibrio spp.
Data availability.
Data for this study have been deposited in NCBI under BioProject PRJNA843722; raw reads and genome accession numbers are listed in Table 1.
ACKNOWLEDGMENTS
Technical support was provided by various Vibrio lab staff at the Bureau of Microbiological Hazards at Health Canada. The Canadian Food Inspection Agency collected retail samples for testing. Thanks to Nicholas Petronella (Bureau of Food Surveillance and Science Integration, Health Canada) and the Bioinformatics team for providing data infrastructure support.
This study was supported by Genomics Research and Development Initiative (GRDI)-AMR (phase VI) grant to S.K.B. (shared with other federal scientists) and Health Canada A-Base funding to K.W. and S.K.B.
Contributor Information
Kelly Weedmark, Email: kelly.weedmark@canada.ca.
Irene L. G. Newton, Indiana University, Bloomington
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
Data for this study have been deposited in NCBI under BioProject PRJNA843722; raw reads and genome accession numbers are listed in Table 1.