ABSTRACT
A subset of Vibrio spp. isolated from fresh Canadian mollusks (2014 to 2018) were selected for sequencing based on antimicrobial resistance profiles. The resulting de novo draft genomes include 38 Vibrio alginolyticus, 32 V. diabolicus, 10 V. parahaemolyticus, 1 V. cholerae, 1 V. ordalii, and 1 Vibrio sp. isolate.
ANNOUNCEMENT
Vibrio spp. are a diverse group of Gram-negative bacteria ubiquitously present in marine environments (1). Consumption of raw or undercooked mollusks such as oysters, mussels, and clams contaminated with pathogenic Vibrio spp. can lead to severe gastrointestinal infections in humans (1, 2). In Canada’s maritime provinces, the risk of foodborne illness from Vibrio spp. increases during the warmer months, when these pathogens are most abundant in the marine environment (3, 4). Antimicrobial resistance (AMR) in Vibrio spp. has been an increasing concern due to horizontal gene transfer and exposure to AMR bacteria (1, 4).
Mollusk samples were collected during the harvest season (May to October) of 2014 through 2018. Freshly harvested samples (n = 47) were immediately stored on ice, shipped, and processed within 48 h of harvest as described elsewhere (5). Briefly, 10 to 20 shucked mollusks per sample were homogenized in a blender; 50 g of homogenate was mixed with 450 mL alkaline peptone water (1% Bacto peptone, 2% NaCl; pH 8.5) and equilibrated for 1 h at 21°C before overnight enrichment at 35°C. Selective agars (Thiosulfate-Citrate-Bile Salts-Sucrose, CHROMagar, and mCC10 or CC400) were used for both pre-enrichment (100 μL) and postenrichment (10 μL) plating. After 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, USA) for molecular/biochemical Vibrio confirmation (5) and for storage as −80°C stocks (one 10-μL loopful per Microbank vial) (VWR, Mississauga, Ontario, Canada). AMR phenotype relative 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 83 isolates were selected for sequencing (Table 1).
TABLE 1.
Metadata and genome assembly metrics for 83 Vibrio isolates from fresh mollusks harvested in Canada from 2014 to 2018 (NCBI BioProject PRJNA839006)
| Isolate | Sample | Yr | Sampling locationa | AMR profileb | Taxonomy ID (Mash) | Genome size (bp) | % GC | Coverage (×) | No. of reads | No. of contigs | N50 (bp) | No. of genes | Accession no. |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BioSample | GenBank | SRA | |||||||||||||
| HS-1-2 | Clam | 2014 | Smith's Cove, NS | AMP, PIP, KF | V. alginolyticus | 5,279,810 | 44.5 | 81 | 1,742,704 | 58 | 246,583 | 4,929 | SAMN28494979 | JAMQAF000000000 | SRR19505466 |
| HS-3-10 | Oyster | 2014 | Eel Lake, NS | AMP, PIP, KF | V. alginolyticus | 5,296,870 | 44.5 | 36 | 768,012 | 70 | 176,384 | 4,886 | SAMN28494980 | JAMQAE000000000 | SRR19505465 |
| HS-6-2 | Clam | 2014 | Gaspé, QC | AMP, PIP, KF | V. alginolyticus | 5,181,727 | 44.6 | 53 | 1,075,070 | 58 | 231,692 | 4,812 | SAMN28494981 | JAMQAD000000000 | SRR19505454 |
| HS-6-3 | Clam | 2014 | Gaspé, QC | AMP, KF, S | V. parahaemolyticus | 5,035,607 | 45.4 | 28 | 586,672 | 79 | 137,596 | 4,638 | SAMN28494982 | JAMQAC000000000 | SRR19505443 |
| HS-7-2 | Clam | 2014 | Smith's Cove, NS | AMP, KF, S, E | V. parahaemolyticus | 4,942,691 | 45.4 | 39 | 803,332 | 60 | 194,100 | 4,562 | SAMN28494983 | JAMQAB000000000 | SRR19505432 |
| HS-9-7 | Clam | 2014 | Gaspé, QC | AMP, PIP, KF, S, PB, E | V. alginolyticus | 5,247,640 | 44.7 | 41 | 860,084 | 89 | 124,394 | 4,808 | SAMN28494984 | JAMQAA000000000 | SRR19505421 |
| HS-9-13 | Clam | 2014 | Gaspé, QC | AMP, PIP, KF (E, OT) | V. alginolyticus | 5,170,302 | 44.6 | 55 | 1,283,154 | 62 | 231,641 | 4,751 | SAMN28494985 | JAMPZZ000000000 | SRR19505410 |
| HS-11-6A | Oyster | 2014 | Eel Lake, NS | AMP, PIP, KF | V. alginolyticus | 5,167,959 | 44.6 | 90 | 1,787,684 | 81 | 151,557 | 4,801 | SAMN28494986 | JAMPZY000000000 | SRR19505399 |
| HS-14-8 | Oyster | 2014 | Eel Lake, NS | AMP, KF, K | V. alginolyticus | 5,209,924 | 44.6 | 36 | 763,220 | 77 | 112,952 | 4,761 | SAMN28494987 | JAMPZX000000000 | SRR19505388 |
| HS-21-9A | Oyster | 2014 | Eel Lake, NS | AMP, PIP, KF | V. alginolyticus | 5,190,156 | 44.6 | 23 | 540,284 | 153 | 73,880 | 4,784 | SAMN28494988 | JAMPZW000000000 | SRR19505384 |
| HS-23-8 | Clam | 2014 | Gaspé, QC | AMP, PIP, KF | V. alginolyticus | 5,074,093 | 44.5 | 109 | 2,204,816 | 44 | 281,992 | 4,697 | SAMN28494989 | JAMPZV000000000 | SRR19505464 |
| HS-25-4 | Clam | 2015 | Smith's Cove, NS | AMP, PIP, KF | V. alginolyticus | 5,253,555 | 44.5 | 41 | 914,232 | 59 | 225,898 | 4,842 | SAMN28494990 | JAMPZU000000000 | SRR19505463 |
| HS-26-7 | Clam | 2015 | Gaspé, QC | AMP (KF, E, ENO, OT) | V. diabolicus | 5,276,346 | 44.8 | 55 | 1,197,486 | 47 | 402,198 | 4,856 | SAMN28494991 | JAMQRO000000000 | SRR19505462 |
| HS-27-4 | Clam | 2015 | Smith's Cove, NS | AMP, PIP, KF | V. diabolicus | 5,159,751 | 44.8 | 128 | 2,580,938 | 45 | 367,116 | 4,715 | SAMN28494992 | JAMQRN000000000 | SRR19505461 |
| HS-28-5 | Clam | 2015 | Gaspé, QC | AMP, KF, OX | V. alginolyticus | 5,394,800 | 44.6 | 66 | 1,429,102 | 64 | 243,159 | 4,950 | SAMN28494993 | JAMPZT000000000 | SRR19505460 |
| HS-29-8 | Clam | 2015 | Smith's Cove, NS | AMP, PIP, KF, SF, OX | V. diabolicus | 5,148,699 | 44.7 | 44 | 915,460 | 58 | 346347 | 4819 | SAMN28494994 | JAMQRM000000000 | SRR19505459 |
| HS-30-8 | Clam | 2015 | Gaspé, QC | AMP, PIP, KF, SF | V. alginolyticus | 5,173,808 | 44.6 | 50 | 1,095,278 | 46 | 248,013 | 4,775 | SAMN28494997 | JAMPZQ000000000 | SRR19505456 |
| HS-30-11 | Clam | 2015 | Gaspé, QC | AMP, PIP, KF, SF | V. alginolyticus | 5,171,704 | 44.6 | 66 | 1,556,322 | 38 | 455,773 | 4,760 | SAMN28494995 | JAMPZS000000000 | SRR19505458 |
| HS-30-16 | Clam | 2015 | Gaspé, QC | AMP, PIP, KF, SF | V. alginolyticus | 5,135,833 | 44.7 | 52 | 980,026 | 142 | 73,597 | 4,727 | SAMN28494996 | JAMPZR000000000 | SRR19505457 |
| HS-31-7 | Clam | 2015 | Smith's Cove, NS | AMP, PIP, SF, OX | V. diabolicus | 5,073,771 | 44.7 | 77 | 1,542,468 | 59 | 233,837 | 4,758 | SAMN28494998 | JAMQRL000000000 | SRR19505455 |
| HS-31-9 | Clam | 2015 | Smith's Cove, NS | AMP, PIP, SF, OX | V. diabolicus | 5,153,063 | 44.7 | 72 | 1,475,488 | 59 | 220,846 | 4,835 | SAMN28494999 | JAMQRK000000000 | SRR19505453 |
| HS-32-1 | Clam | 2015 | Gaspé, QC | AMP, KF (IPM, E, OT) | V. ordalii | 4,016,157 | 44.6 | 165 | 2,608,402 | 85 | 368,741 | 3,667 | SAMN28495000 | JAMQRJ000000000 | SRR19505452 |
| HS-32-2 | Clam | 2015 | Gaspé, QC | AMP, PIP, KF | V. alginolyticus | 5,250,985 | 44.6 | 46 | 1,007,826 | 40 | 330,647 | 4,838 | SAMN28495001 | JAMPZP000000000 | SRR19505451 |
| HS-32-5 | Clam | 2015 | Gaspé, QC | AMP, KF, SF, OX | V. diabolicus | 4,942,772 | 45.0 | 43 | 729,456 | 265 | 35,098 | 4,577 | SAMN28495002 | JAMQRI000000000 | SRR19505450 |
| HS-32-8 | Clam | 2015 | Gaspé, QC | AMP, PIP, SF, OX | V. diabolicus | 5,247,686 | 44.8 | 38 | 993,638 | 59 | 257,008 | 4,895 | SAMN28495003 | JAMQRH000000000 | SRR19505449 |
| HS-32-9 | Clam | 2015 | Gaspé, QC | AMP, KF, OX | V. diabolicus | 5,068,562 | 44.9 | 44 | 999,746 | 57 | 206,822 | 4,679 | SAMN28495004 | JAMQRG000000000 | SRR19505448 |
| HS-34-5 | Clam | 2015 | Gaspé, QC | AMP, PIP, KF | V. alginolyticus | 5,302,700 | 44.5 | 28 | 641,034 | 116 | 103,790 | 4,877 | SAMN28495005 | JAMPZO000000000 | SRR19505447 |
| HS-34-6 | Clam | 2015 | Gaspé, QC | AMP, PIP, KF, SF | V. alginolyticus | 5,314,580 | 44.5 | 75 | 1,587,218 | 48 | 385,246 | 4,977 | SAMN28495006 | JAMPZN000000000 | SRR19505446 |
| HS-35-11 | Oyster | 2015 | Eel Lake, NS | AMP, PIP, OX | V. alginolyticus | 5,236,535 | 44.6 | 53 | 1,212,078 | 64 | 198,011 | 4,813 | SAMN28495007 | JAMPZM000000000 | SRR19505445 |
| HS-36-4 | Clam | 2015 | NS | AMP, KF, S | V. parahaemolyticus | 5,011,762 | 45.3 | 62 | 1,217,808 | 58 | 228,589 | 4,628 | SAMN28495008 | JAMPZL000000000 | SRR19505444 |
| HS-36-5 | Clam | 2015 | NS | AMP, PIP, OX | V. diabolicus | 5,197,981 | 44.7 | 139 | 2,756,570 | 49 | 552,486 | 4,887 | SAMN28495009 | JAMQRF000000000 | SRR19505442 |
| HS-37-7 | Oyster | 2015 | Eel Lake, NS | AMP, KF, SF, OX | V. diabolicus | 5,347,404 | 44.7 | 107 | 2,502,662 | 50 | 344,809 | 4,980 | SAMN28495010 | JAMQRE000000000 | SRR19505441 |
| HS-39-7 | Oyster | 2015 | Eel Lake, NS | AMP, PIP, KF | V. alginolyticus | 5,112,278 | 44.5 | 55 | 1,207,080 | 47 | 254,573 | 4,686 | SAMN28495011 | JAMPZK000000000 | SRR19505440 |
| HS-40-3 | Clam | 2015 | Smith's Cove, NS | AMP, PIP, KF, OX | V. diabolicus | 5,170,365 | 44.8 | 76 | 1,525,590 | 44 | 301,603 | 4,779 | SAMN28495012 | JAMQRD000000000 | SRR19505439 |
| HS-41-4 | Clam | 2015 | Gaspé, QC | AMP, PIP, KF, SF | V. alginolyticus | 5,230,739 | 44.6 | 73 | 1,574,962 | 61 | 442,486 | 4,837 | SAMN28495013 | JAMPZJ000000000 | SRR19505438 |
| HS-41-6 | Clam | 2015 | Gaspé, QC | AMP, PIP, S | V. alginolyticus | 5,247,006 | 44.5 | 61 | 1,431,306 | 46 | 338,496 | 4,848 | SAMN28495014 | JAMPZI000000000 | SRR19505437 |
| HS-43-1 | Oyster | 2016 | Metcalfe Bay, BC | AMP, PIP, OX | V. diabolicus | 5,321,336 | 44.8 | 58 | 1,347,776 | 61 | 251,182 | 4,930 | SAMN28495015 | JAMQRC000000000 | SRR19505436 |
| HS-43-2 | Oyster | 2016 | Metcalfe Bay, BC | AMP, PIP, OX | V. diabolicus | 5,163,393 | 44.8 | 143 | 3,885,228 | 36 | 446,110 | 4,775 | SAMN28495016 | JAMQRB000000000 | SRR19505435 |
| HS-43-3 | Oyster | 2016 | Metcalfe Bay, BC | AMP, PIP, OX | V. diabolicus | 5,251,744 | 44.7 | 110 | 2,612,064 | 41 | 356,719 | 4,861 | SAMN28495017 | JAMQRA000000000 | SRR19505434 |
| HS-43-5 | Oyster | 2016 | Metcalfe Bay, BC | AMP, PIP, KF, OX | V. diabolicus | 6,124,036 | 43.5 | 95 | 2,361,022 | 59 | 404,856 | 5,974 | SAMN28495018 | JAMQQZ000000000 | SRR19505433 |
| HS-43-6 | Oyster | 2016 | Metcalfe Bay, BC | AMP, PIP, KF, OX | V. diabolicus | 6,124,301 | 43.7 | 80 | 2,043,750 | 57 | 457,829 | 6,056 | SAMN28495019 | JAMQQY000000000 | SRR19505431 |
| HS-43-7A | Oyster | 2016 | Metcalfe Bay, BC | AMP, KF (PIP, CTX, CEF, E, ENO, OX, OT) | V. diabolicus | 5,940,983 | 43.7 | 82 | 1,978,856 | 58 | 357,386 | 5,747 | SAMN28495020 | JAMQQX000000000 | SRR19505430 |
| HS-43-7B | Oyster | 2016 | Metcalfe Bay, BC | AMP, KF, OT | V. alginolyticus | 5,368,506 | 44.4 | 25 | 554,486 | 166 | 85,447 | 5,051 | SAMN28495021 | JAMPZH000000000 | SRR19505429 |
| HS-46-5 | Oyster | 2016 | Parksville, BC | AMP, PIP, KF | V. alginolyticus | 5,396,729 | 44.5 | 129 | 3,050,086 | 48 | 433,779 | 5,025 | SAMN28495022 | JAMPZG000000000 | SRR19505428 |
| HS-47-7 | Oyster | 2016 | Eel Lake, NS | AMP, PIP, KF, OX | V. diabolicus | 5,008,741 | 44.8 | 30 | 689,282 | 95 | 115,568 | 4,657 | SAMN28495023 | JAMQQW000000000 | SRR19505427 |
| HS-50-1 | Oyster | 2016 | Parksville, BC | AMP, PIP, KF, OX | Vibrio spp. | 5,289,568 | 44.8 | 152 | 3,266,532 | 49 | 441,934 | 4,943 | SAMN28495024 | JAMPZF000000000 | SRR19505426 |
| HS-50-2 | Oyster | 2016 | Parksville, BC | AMP, PIP, KF, SF, OX | V. diabolicus | 5,194,668 | 44.8 | 67 | 1,314,048 | 41 | 436,139 | 4,818 | SAMN28495025 | JAMQQV000000000 | SRR19505425 |
| HS-50-3 | Oyster | 2016 | Parksville, BC | AMP, PIP, KF | V. alginolyticus | 5,272,228 | 44.5 | 180 | 3,430,338 | 46 | 237,442 | 4,847 | SAMN28495026 | JAMPZE000000000 | SRR19505424 |
| HS-50-4 | Oyster | 2016 | Parksville, BC | AMP, PIP, KF, OX, OT | V. diabolicus | 5,354,891 | 44.6 | 59 | 1,246,740 | 45 | 428,472 | 4,976 | SAMN28495027 | JAMQQU000000000 | SRR19505423 |
| HS-51-4 | Clam | 2016 | Smith's Cove, NS | AMP, KF (CEF, E, ENO, OX, OT) | V. diabolicus | 5,260,487 | 44.8 | 59 | 1,187,042 | 38 | 406,357 | 4,842 | SAMN28495028 | JAMQQT000000000 | SRR19505422 |
| HS-51-5 | Clam | 2016 | Smith's Cove, NS | AMP (KF, E, ENO) | V. alginolyticus | 5,327,807 | 44.5 | 76 | 1,567,682 | 62 | 233,100 | 4,925 | SAMN28495029 | JAMPZD000000000 | SRR19505420 |
| HS-52-6 | Clam | 2016 | BC | AMP, KF, OX | V. diabolicus | 5,197,446 | 44.8 | 178 | 3,344,254 | 49 | 462,455 | 4,820 | SAMN28495030 | JAMQQS000000000 | SRR19505419 |
| HS-53-2 | Oyster | 2016 | Eel Lake, NS | AMP, KF, S | V. diabolicus | 5,398,014 | 44.6 | 81 | 1,564,256 | 44 | 365,596 | 5,026 | SAMN28495032 | JAMQQR000000000 | SRR19505417 |
| HS-53-10 | Oyster | 2016 | Eel Lake, NS | AMP, PIP, OX | V. parahaemolyticus | 5,032,476 | 45.2 | 43 | 878,212 | 55 | 264,514 | 4,674 | SAMN28495031 | JAMPZC000000000 | SRR19505418 |
| HS-56-5 | Clam | 2016 | Smith's Cove, NS | AMP, PIP, KF | V. alginolyticus | 5,228,619 | 44.6 | 80 | 1,558,618 | 43 | 317,697 | 4,804 | SAMN28495033 | JAMPZB000000000 | SRR19505416 |
| HS-57-1 | Oyster | 2016 | Parksville, BC | AMP, KF, OX | V. diabolicus | 5,157,215 | 44.9 | 165 | 3,065,612 | 39 | 399,323 | 4,747 | SAMN28495034 | JAMQQQ000000000 | SRR19505415 |
| HS-57-7 | Oyster | 2016 | Parksville, BC | AMP, PIP, KF, SF | V. diabolicus | 5,273,448 | 44.7 | 105 | 1,995,998 | 57 | 408,030 | 4,946 | SAMN28495035 | JAMQQP000000000 | SRR19505414 |
| HS-57-10 | Oyster | 2016 | Parksville, BC | AMP, PIP, KF, SF, OX | V. diabolicus | 5,043,465 | 44.8 | 68 | 1,484,814 | 63 | 197,073 | 4,737 | SAMN28495036 | JAMQQO000000000 | SRR19505413 |
| HS-58-1 | Clam | 2016 | Gaspé, QC | AMP, PIP, KF | V. alginolyticus | 5,269,803 | 44.6 | 112 | 2,120,760 | 53 | 221,952 | 4,904 | SAMN28495037 | JAMPZA000000000 | SRR19505412 |
| HS-58-3 | Clam | 2016 | Gaspé, QC | AMP, PIP, KF | V. alginolyticus | 5,188,730 | 44.5 | 80 | 1,542,860 | 55 | 221,952 | 4,807 | SAMN28495038 | JAMPYZ000000000 | SRR19505411 |
| HS-59-6 | Clam | 2016 | Smith's Cove, NS | AMP, PIP, KF, OX | V. diabolicus | 5,101,415 | 44.8 | 76 | 1,477,328 | 34 | 435,153 | 4,704 | SAMN28495039 | JAMQQN000000000 | SRR19505409 |
| HS-60-3 | Oyster | 2016 | Eel Lake, NS | AMP, PIP, KF | V. diabolicus | 5,089,027 | 44.8 | 84 | 1,779,960 | 48 | 463,036 | 4,739 | SAMN28495041 | JAMQQM000000000 | SRR19505407 |
| HS-60-11 | Oyster | 2016 | Eel Lake, NS | AMP, PIP, KF, SF, OX | V. parahaemolyticus | 5,148,398 | 45.2 | 121 | 2,222,476 | 47 | 257,051 | 4,740 | SAMN28495040 | JAMPYY000000000 | SRR19505408 |
| HS-61-1 | Clam | 2016 | Gaspé, QC | AMP, PIP, KF, SF | V. alginolyticus | 5,262,756 | 44.6 | 53 | 1,044,406 | 51 | 222,598 | 4,839 | SAMN28495042 | JAMPYX000000000 | SRR19505406 |
| HS-61-11C | Clam | 2016 | Gaspé, QC | AMR, KF (CTX, CEF, E, ENO, OT) | V. parahaemolyticus | 5,085,472 | 45.3 | 26 | 572,568 | 87 | 130,613 | 4,719 | SAMN28495043 | JAMPYW000000000 | SRR19505405 |
| HS-61-3 | Clam | 2016 | Gaspé, QC | AMP, PIP, KF | V. alginolyticus | 5,317,358 | 44.5 | 53 | 1,194,060 | 69 | 215,779 | 4,909 | SAMN28495044 | JAMPYV000000000 | SRR19505404 |
| HS-62-8 | Oyster | 2016 | Parksville, BC | AMP, PIP, OX | V. diabolicus | 5,070,117 | 44.8 | 104 | 2,346,012 | 48 | 567,202 | 4,756 | SAMN28495045 | JAMQQL000000000 | SRR19505403 |
| HS-62-9 | Oyster | 2016 | Parksville, BC | AMP, KF, SF | V. parahaemolyticus | 5,283,549 | 45.3 | 121 | 2,417,766 | 68 | 194,545 | 4,850 | SAMN28495046 | JAMPYU000000000 | SRR19505402 |
| HS-63-3 | Mussel | 2016 | BC | AMP, PIP, KF | V. alginolyticus | 5,202,885 | 44.6 | 76 | 1,575,390 | 47 | 422,893 | 4,764 | SAMN28495047 | JAMPYT000000000 | SRR19505401 |
| HS-63-7 | Mussel | 2016 | BC | AMP, PIP, OX | V. diabolicus | 5,191,291 | 44.9 | 138 | 2,632,458 | 44 | 815,460 | 48,20 | SAMN28495048 | JAMQQK000000000 | SRR19505400 |
| HS-63-8 | Mussel | 2016 | BC | AMP, PIP, KF | V. alginolyticus | 5,200,087 | 44.5 | 129 | 2,536,190 | 44 | 226,658 | 4,763 | SAMN28495049 | JAMPYS000000000 | SRR19505398 |
| HS-64-4 | Clam | 2016 | Smith's Cove, NS | AMP, PIP, SF, OX | V. diabolicus | 5,172,367 | 44.7 | 39 | 1,019,306 | 83 | 157,536 | 4,847 | SAMN28495050 | JAMQQJ000000000 | SRR19505397 |
| HS-64-5 | Clam | 2016 | Smith's Cove, NS | AMP, KF, OX | V. diabolicus | 5,113,674 | 44.8 | 97 | 2,130,112 | 45 | 423,139 | 4,670 | SAMN28495051 | JAMQQI000000000 | SRR19505396 |
| HS-65-4 | Oyster | 2016 | Eel Lake, NS | AMP, PIP, KF, OX | V. alginolyticus | 5,254,705 | 44.6 | 59 | 1,316,926 | 56 | 225,355 | 4,834 | SAMN28495052 | JAMPYR000000000 | SRR19505395 |
| HS-66-3 | Oyster | 2016 | Metcalfe Bay, BC | AMP, PIP, KF, SF | V. alginolyticus | 5,258,746 | 44.6 | 80 | 1,650,180 | 40 | 508,914 | 4,823 | SAMN28495053 | JAMPYQ000000000 | SRR19505394 |
| HS-66-6 | Oyster | 2016 | Metcalfe Bay, BC | AMP, PIP, KF | V. alginolyticus | 5,369,146 | 44.5 | 61 | 1,261,890 | 62 | 263,734 | 4,953 | SAMN28495054 | JAMPYP000000000 | SRR19505393 |
| HS-67-6 | Oyster | 2016 | NB | AMP, PIP, KF | V. alginolyticus | 5,399,019 | 44.5 | 138 | 2,695,004 | 63 | 325,897 | 5,029 | SAMN28495055 | JAMPYO000000000 | SRR19505392 |
| HS-67-7 | Oyster | 2016 | NB | AMP, PIP, KF | V. parahaemolyticus | 5,121,474 | 45.2 | 68 | 1,401,988 | 36 | 384,982 | 4,771 | SAMN28495056 | JAMPYN000000000 | SRR19505391 |
| HS-67-8 | Oyster | 2016 | NB | AMP, PIP, KF | V. alginolyticus | 5,047,512 | 44.6 | 95 | 1,707,472 | 36 | 435,643 | 4,502 | SAMN28495057 | JAMPYM000000000 | SRR19505390 |
| HS-69-5 | Clam | 2016 | Gaspé, QC | AMP, PIP, KF, SF | V. alginolyticus | 5,342,446 | 44.5 | 58 | 1,169,740 | 70 | 178,422 | 5,068 | SAMN28495058 | JAMPYL000000000 | SRR19505389 |
| HS-80-7 | Oyster | 2017 | Eel Lake, NS | AMP (KF, CTX, E, ENO, OX) | V. parahaemolyticus | 4,909,992 | 45.5 | 96 | 1,800,744 | 134 | 82,946 | 4,570 | SAMN28495059 | JAMPYK000000000 | SRR19505387 |
| HS-92-7 | Oyster | 2017 | Eel Lake, NS | None | V. parahaemolyticus | 5,872,986 | 44.2 | 89 | 1,870,694 | 114 | 123,462 | 5,740 | SAMN28495060 | JAMPYJ000000000 | SRR19505386 |
| HS-119-4 | Clam | 2018 | Gaspé, QC | None | V. cholerae | 4,120,304 | 47.5 | 65 | 968,146 | 155 | 83,542 | 3,884 | SAMN28495061 | JAMPYI000000000 | SRR19505385 |
BC, British Columbia; NB, New Brunswick; NS, Nova Scotia; QC, Québec.
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, sulfamethoxazole-trimethoprim; TE, tetracycline; None, no resistance. Parentheses indicate intermediate resistance.
For sequencing, frozen stocks were streaked onto TSA-2N (Difco BD, Franklin Lakes, NJ, USA) and incubated at 35°C overnight. An isolated colony was used to inoculate 5 mL tryptic soy broth with 2% NaCl (TSB-2N) at 35°C for 24 h, and DNA was extracted using the Maxwell 16 SEV cell DNA purification kit (Promega, Madison, WI, USA). Paired-end Illumina sequencing was performed using indexed Nextera XT libraries run on a MiSeq instrument (2 × 300 cycles, v3 chemistry) according to the manufacturer (Illumina, San Diego, CA, USA).
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, Pilon v1.22) (9), gene prediction (NCBI PGAP v6.1; best-placed reference protein set; GeneMarkS-2+) (10), and metrics 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 that were >0.8 (excluding hits containing the words “phage” or “plasmid”) using reference 13 and www.ncbi.nlm.nih.gov/genome for Vibrio diabolicus classification. Analysis tools were used with default settings unless noted otherwise.
Isolate and genome details are listed in Table 1. Genome assemblies included 34 to 265 contigs and coverage depths of 23-fold to 180-fold. Total genome sizes ranged from 4.0 Mbp to 6.1 Mbp and contained 3,667 to 6,056 predicted genes. This resulted in draft de novo genomes for 38 Vibrio alginolyticus, 32 V. diabolicus, 10 V. parahaemolyticus, 1 V. cholerae, and 3 V. ordalii isolates and 1 unclassified Vibrio isolate.
Data availability.
Data from this study have been deposited in NCBI under BioProject PRJNA839006; raw read SRA and GenBank accession numbers are listed in Table 1.
ACKNOWLEDGMENTS
Samples were collected by the Canadian Food Inspection Agency and Merinov and/or Ministère de l'Agriculture, des Pêcheries et de l'Alimentation du Québec (MAPAQ). Technical support was provided by various Vibrio lab staff at the Bureau of Microbiological Hazards at Health Canada. We thank 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@hc-sc.gc.ca.
Swapan K. Banerjee, Email: sbanerjee2825@gmail.com.
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 from this study have been deposited in NCBI under BioProject PRJNA839006; raw read SRA and GenBank accession numbers are listed in Table 1.