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. 2022 Nov 14;11(12):e00750-22. doi: 10.1128/mra.00750-22

Draft Genomes of 92 Vibrio Isolates from Warm-Water Shrimps Imported into Canada between 2009 and 2019

Januana S Teixeira a, Forest Dussault b, Emily Hoover a, Julie A Shay b, Kelly Weedmark a,✉, Swapan K Banerjee a
Editor: Irene L G Newtonc
PMCID: PMC9753665  PMID: 36374081

ABSTRACT

Vibrio spp. were isolated from raw shrimps imported into Canada (2009 to 2019). A total of 92 isolates with various multidrug resistance profiles were sequenced, including 59 V. parahaemolyticus, 12 V. diabolicus, 10 V. cholerae, 7 V. alginolyticus, 1 V. campbellii, 1 V. harveyi, 1 V. owensii, and 1 V. vulnificus isolate.

ANNOUNCEMENT

Vibrio spp. are Gram-negative bacterial pathogens ubiquitous in aquatic and marine environments (1). They can cause severe gastrointestinal infection in humans from ingestion of water or raw/partially cooked seafood contaminated with pathogenic Vibrio spp. (2). The majority of human illnesses associated with Vibrio spp. are caused by V. cholerae, V. parahaemolyticus, V. vulnificus, and V. alginolyticus (1). Given a propensity for horizontal gene transfer among Vibrio spp. and the presence of antimicrobial-resistant (AMR) bacteria in marine ecosystems (2–4), Vibrio spp. have the potential to acquire resistance to antibiotic treatment (4). This study sequenced and identified 92 Vibrio isolates present in raw shrimp imported to Canada that were selected based on their antibiotic resistance profiles.

Single colonies from imported raw shrimp samples (n = 54, fresh or frozen) were isolated as in reference 5. Briefly, shrimps (50 g/sample) were homogenized in a blender 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 salt sucrose [TCBS], 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 and biochemical Vibrio confirmation (5) and −80°C stocks (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 92 isolates was selected for sequencing (Table 1).

TABLE 1.

Genome assembly metrics for 92 vibrio species isolates from raw shrimp imported to Canada (NCBI BioProject PRJNA843723)

Isolate yr Country of origin Taxonomic ID (MASH) AMR profilea Genome size (bp) GC (%) Coverage (×) No. of contigs No. of reads N50 (bp) No. of genes BioSample accession no. Assembly accession no. WGS GenBank accession no. SRA accession no.
ISF-4-2 2009 Thailand V. parahaemolyticus AMP (KF, SXT, E) 5,031,302 45.4 57 74 1,153,170 155,980 4,701 SAMN28767292 GCA_024746775 JANFVC000000000 SRR19513301
ISF-8-6 2009 China V. parahaemolyticus AMP (KF, CIP, OX) 4,917,741 45.5 105 38 1,873,986 353,627 4,548 SAMN28767293 GCA_024746735 JANFVB000000000 SRR19513300
ISF-10-3 2009 Vietnam V. alginolyticus AMP, PIP, KF 5,126,989 44.6 42 90 950,138 148,213 4,711 SAMN28767294 GCA_024746755 JANFVA000000000 SRR19513289
ISF-15-1 2009 Mexico V. diabolicus AMP, PIP, OX 5,159,569 44.9 82 44 1,635,904 214,849 4,795 SAMN28767295 GCA_024746715 JANFUZ000000000 SRR19513278
ISF-15-4 2009 Mexico V. parahaemolyticus AMP, PIP, KF, OX 5,145,313 45.2 107 62 1,997,334 193,197 4,732 SAMN28767296 GCA_024746695 JANFUY000000000 SRR19513267
ISF-24-5 2009 Ecuador V. parahaemolyticus AMP, PIP, KF 4,951,092 45.4 79 51 1,463,684 315,201 4,564 SAMN28767297 GCA_024746655 JANFUX000000000 SRR19513256
ISF-29-3 2009 Ecuador V. parahaemolyticus AMP, SF, TE, OT 5,320,303 45 28 140 713,474 108,977 4,951 SAMN28767298 GCA_024746635 JANFUW000000000 SRR19513225
ISF-29-4 2009 Ecuador V. diabolicus AMP, KF, OX 5,060,319 44.8 116 57 2,140,656 199,367 4,728 SAMN28767299 GCA_024746645 JANFUV000000000 SRR19513214
ISF-36-1 2010 Peru V. diabolicus AMP, PIP, OX 5,017,756 44.8 47 55 1,029,532 294,177 4,633 SAMN28767300 GCA_024746585 JANFUU000000000 SRR19513247
ISF-38-2 2010 Thailand V. alginolyticus AMP, PIP, KF 5,204,850 44.5 25 150 512,020 78,737 4,777 SAMN28767301 GCA_024746615 JANFUT000000000 SRR19513236
ISF-49-4 2011 India V. parahaemolyticus AMP, KF, OX 5,085,405 45.3 63 84 128,0358 202,791 4,759 SAMN28767302 GCA_024746555 JANFUS000000000 SRR19513299
ISF-49-9 2011 India V. parahaemolyticus AMP, KF, SF, OX 5,011,927 45.4 96 29 2,029,078 461,187 4,598 SAMN28767303 GCA_024746575 JANFUR000000000 SRR19513298
ISF-49-12 2011 India V. diabolicus AMP, PIP, SF, OX 5,096,250 44.8 35 98 700,098 208,287 4781 SAMN28767304 GCA_024746535 JANFUQ000000000 SRR19513297
ISF-50-4 2011 Philippines V. parahaemolyticus AMP, PIP, KF 5,007,265 45.4 80 34 1598,182 404,666 4,673 SAMN28767305 GCA_024746515 JANFUP000000000 SRR19513296
ISF-50-6 2011 Philippines V. parahaemolyticus AMP, PIP, KF 4,967,225 45.4 51 46 919,352 259,902 4,622 SAMN28767306 GCA_024746495 JANFUO000000000 SRR19513295
ISF-50-9 2011 Philippines V. parahaemolyticus AMP, PIP, KF, SF 4,972,944 45.4 54 38 1,102,162 258,794 4,607 SAMN28767307 GCA_024746475 JANFUN000000000 SRR19513294
ISF-56-4 2011 Thailand V. parahaemolyticus AMP, SXT, SF, TE, OT 5,061,529 45.3 47 71 949,142 201,099 4,727 SAMN28767308 GCA_024746455 JANFUM000000000 SRR19513293
ISF-56-5 2011 Thailand V. parahaemolyticus AMP, SXT, SF, OT (KF, E, ENO, TE) 5,075,302 45.3 38 79 756,372 200,930 4,765 SAMN28767309 GCA_024746415 JANFUL000000000 SRR19513292
ISF-56-8 2011 Thailand V. parahaemolyticus SXT, KF, SF, TE, OT (E) 5,059,887 45.4 56 110 1,087,546 124,670 4,729 SAMN28767310 GCA_024746425 JANFUK000000000 SRR19513291
ISF-56-10 2011 Thailand V. parahaemolyticus AMP, SXT, SF, TE, OT (KF, E, C) 5,062,302 45.4 101 50 1,841,494 377,044 4,721 SAMN28767311 GCA_024746355 JANFUJ000000000 SRR19513290
ISF-57-5 2011 Vietnam V. diabolicus AMP, PIP, OX 5,083,437 44.9 89 50 1,710,478 210,412 4,722 SAMN28767312 GCA_024746195 JANFUI000000000 SRR19513288
ISF-61-5 2011 USA V. alginolyticus AMP, PIP, KF 5,291,624 44.6 49 130 967,808 111,346 4,922 SAMN28767313 GCA_024746395 JANFUH000000000 SRR19513287
ISF-63-5 2011 Vietnam V. parahaemolyticus AMP, PIP, KF 4,991,923 45.4 55 65 1,048,406 191,317 4,648 SAMN28767314 GCA_024746375 JANFUG000000000 SRR19513286
ISF-64-3 2011 Thailand V. parahaemolyticus AMP, PIP, KF 5,121,081 45.4 113 40 2,085,744 359,986 4,798 SAMN28767315 GCA_024746335 JANFUF000000000 SRR19513285
ISF-69-8 2011 Mexico V. owensii AMP, SXT, SF, TE, OT (PIP, E) 6,030,242 45.4 98 67 2,247,260 252,192 5,448 SAMN28767316 GCA_024746155 JANFUE000000000 SRR19513284
ISF-74-1 2012 India V. alginolyticus AMP, PIP, KF 5,157,601 44.7 109 80 2,006,056 169,653 4,694 SAMN28767317 GCA_024746315 JANFUD000000000 SRR19513283
ISF-77-1 2012 Indonesia V. parahaemolyticus AMP, PIP, KF 5,008,845 45.3 95 51 1,756,968 404,200 4,590 SAMN28767318 GCA_024746295 JANFUC000000000 SRR19513282
ISF-77-7 2012 Indonesia V. cholerae AMP (PIP) 4,007,917 47.6 57 96 799,370 194,054 3,722 SAMN28767319 GCA_024746215 JANFUB000000000 SRR19513281
ISF-82-2 2012 Indonesia V. diabolicus AMP, PIP, KF 5,005,844 44.9 63 57 1,183,816 207,104 4,590 SAMN28767320 GCA_024746275 JANFUA000000000 SRR19513280
ISF-85-1 2012 India V. diabolicus AMP, PIP, KF 5,097,833 44.9 83 48 1,605,808 317,856 4,708 SAMN28767321 GCA_024746235 JANFTZ000000000 SRR19513279
ISF-88-1 2012 Thailand V. parahaemolyticus AMP (KF, E) 5,254,276 45.2 110 81 2,321,878 216,128 4,957 SAMN28767322 GCA_024746175 JANFTY000000000 SRR19513277
ISF-93-4 2012 Vietnam V. diabolicus AMP, PIP, KF 5,027,740 44.9 30 93 618,270 155,061 4,643 SAMN28767323 GCA_024746245 JANFTX000000000 SRR19513276
ISF-94-3 2012 Bangladesh V. parahaemolyticus AMP, PIP, KF 5,036,542 45.3 224 36 4,255,404 526,057 4,677 SAMN28767324 GCA_024746135 JANFTW000000000 SRR19513275
ISF-94-4 2012 Bangladesh V. alginolyticus AMP, PIP, KF 5,244,137 44.5 34 101 748,274 125,444 4,832 SAMN28767325 GCA_024746095 JANFTV000000000 SRR19513274
ISF-99-2 2012 Indonesia V. parahaemolyticus AMP, PIP, KF 5,351,538 45.3 26 208 541,802 78,827 5,114 SAMN28767326 GCA_024746105 JANFTU000000000 SRR19513273
ISF-104-5 2012 Thailand V. parahaemolyticus AMP, PIP, KF 4,996,778 45.4 66 34 1,329,562 378,528 4,564 SAMN28767327 GCA_024746075 JANFTT000000000 SRR19513272
ISF-113-8 2013 Mexico V. diabolicus AMP (KF, E) 5,162,038 44.6 56 69 1,097,316 168,689 4,778 SAMN28767328 GCA_024746045 JANFTS000000000 SRR19513271
ISF-113-9 2013 Mexico V. diabolicus AMP (KF, SF, SXT, E) 5,168,988 44.6 95 38 2,141,496 397,363 4,784 SAMN28767329 GCA_024746035 JANFTR000000000 SRR19513270
ISF-128-1 2013 India V. campbellii AMP, PIP, OX 5,963,364 45.3 57 102 1,221,224 145,273 5,551 SAMN28767330 GCA_024746015 JANFTQ000000000 SRR19513269
ISF-128-2 2013 India V. parahaemolyticus AMP (OX) 5,173,068 45.2 112 34 2,033,516 553,726 4,858 SAMN28767331 GCA_024745995 JANFTP000000000 SRR19513268
ISF-131-2 2013 India V. parahaemolyticus AMP, TE, SF, OT (KF) 5,168,805 45.2 82 52 1,499,022 268,606 4,856 SAMN28767332 GCA_024745975 JANFTO000000000 SRR19513266
ISF-136-11 2013 Ecuador V. parahaemolyticus AMP, TE, OT 5,289,134 45 42 55 903,106 234,466 4,893 SAMN28767333 GCA_024745955 JANFTN000000000 SRR19513265
ISF-180-2 2014 India V. cholerae None 4,019,634 47.6 183 77 3,157,838 278,041 3,749 SAMN28767334 GCA_024745935 JANFTM000000000 SRR19513264
ISF-184-12 2014 India V. parahaemolyticus AMP, PIP, KF 5,528,471 44.9 62 98 1,333,060 190,987 5,185 SAMN28767335 GCA_024745915 JANFTL000000000 SRR19513263
ISF-184-13 2014 India V. parahaemolyticus AMP, KF (CTX, CEF, E) 5512,355 45.0 56 201 1,430,228 62,934 5,180 SAMN28767336 GCA_024745895 JANFTK000000000 SRR19513262
ISF-188-12 2014 No data V. parahaemolyticus AMP, PIP, KF, S, SXT, SF, OT 5,231,654 45.2 98 92 1,827,276 163,660 4,923 SAMN28767337 GCA_024745875 JANFTJ000000000 SRR19513261
ISF-189-3 2015 Mexico V. parahaemolyticus AMP, KF, PB, E, TE, OT 5,158,166 45.2 36 74 805,380 185,319 4,773 SAMN28767338 GCA_024745835 JANFTI000000000 SRR19513260
ISF-189-4 2015 Mexico V. alginolyticus AMP, PIP, KF 5,257,285 44.6 60 116 1,188,410 101,010 4,829 SAMN28767339 GCA_024745855 JANFTH000000000 SRR19513259
ISF-189-5 2015 Mexico V. alginolyticus AMP, PIP, KF 5,046,083 44.6 46 62 1,078,388 213,662 4,667 SAMN28767340 GCA_024745815 JANFTG000000000 SRR19513258
ISF-199-1 2015 Vietnam V. parahaemolyticus AMP, KF, SF, TE, OT (CTX, CEF, E, ENO, OX) 5,330,197 45.3 39 78 881,938 269,650 5,001 SAMN28767341 GCA_024745795 JANFTF000000000 SRR19513257
ISF-199-2 2015 Vietnam V. parahaemolyticus AMP, SXT, SF, CIP, OX, OT (KF, S, E, ENO, NOR) 5,062,936 45.4 57 98 1,039,018 126,520 4,655 SAMN28767342 GCA_024745755 JANFTE000000000 SRR19513255
ISF-199-3 2015 Vietnam V. parahaemolyticus AMP, SF, TE, OT 5,335,527 45 76 86 1,477,046 528,927 4,966 SAMN28767343 GCA_024745775 JANFTD000000000 SRR19513254
ISF-199-4 2015 Vietnam V. parahaemolyticus AMP, KF, SF, TE, OT (CTX, CEF, E, ENO, OX) 5,333,116 45.3 30 146 670,782 103,872 5,025 SAMN28767344 GCA_024745735 JANFTC000000000 SRR19513233
ISF-199-5 2015 Vietnam V. parahaemolyticus AMP, SXT, SF, CIP, ENO, NOR, OX, TE, OT (KF) 5,038,673 45.5 30 238 578,680 54,328 4,655 SAMN28767345 GCA_024745715 JANFTB000000000 SRR19513232
ISF-199-6 2015 Vietnam V. vulnificus CIP, ENO, NOR, OX, TE, OT 4,942,439 46.8 27 161 497,672 80,843 4,537 SAMN28767346 GCA_024745695 JANFTA000000000 SRR19513231
ISF-199-7 2015 Vietnam V. parahaemolyticus AMP, SF, TE, OT (KF, CTX, CEF, E, CIP, ENO, OX) 5,340,468 45.3 32 101 677,388 146,316 5,020 SAMN28767347 GCA_024745655 JANFSZ000000000 SRR19513230
ISF-200-6 2015 Vietnam V. harveyi AMP, SXT, SF, OX, TE, OT (PIP, S, E, CIP, ENO) 5,819,105 45.0 93 45 1926336 284289 5,375 SAMN28767348 GCA_024745675 JANFSY000000000 SRR19513229
ISF-200-8 2015 Vietnam V. parahaemolyticus AMP, KF, SXT, SF, TE, OT (CTX, E) 5,164,514 45.3 123 58 2,523,256 220,941 4,744 SAMN28767349 GCA_024745635 JANFSX000000000 SRR19513228
ISF-203-4 2015 India V. parahaemolyticus AMP, KF, OX 5,284,022 45.2 35 79 864,710 258,208 4,867 SAMN28767350 GCA_024745615 JANFSW000000000 SRR19513227
ISF-203-5 2015 India V. parahaemolyticus AMP, KF, OX 5,286,444 45.2 83 54 1,946,386 458,527 4,868 SAMN28767351 GCA_024745535 JANFSV000000000 SRR19513226
ISF-208-1 2016 Thailand V. cholerae K, OX (S, E) 4,470,139 47.3 73 86 1,207,970 152,725 4,285 SAMN28767352 GCA_024745555 JANFSU000000000 SRR19513224
ISF-208-2 2016 Thailand V. cholerae AMP, PIP, KF, CTX, CEF, K, OX (S, SF, E) 4,441,697 47.3 68 88 1,100,812 163,543 4,237 SAMN28767353 GCA_024745565 JANFST000000000 SRR19513223
ISF-208-5 2016 Thailand V. cholerae AMP, PIP, KF, CTX, CEF, K, E, OX (S, ENO) 4,477,917 47.4 106 80 1,739,866 152,725 4,308 SAMN28767354 GCA_024745585 JANFSS000000000 SRR19513222
ISF-208-8 2016 Thailand V. cholerae AMP, PIP, KF, CTX, CEF, K, S, OX (SF, E, CIP) 4,472,093 47.4 114 80 1,874,806 214,953 4,286 SAMN28767355 GCA_024745515 JANFSR000000000 SRR19513221
ISF-209-3 2016 Vietnam V. parahaemolyticus AMP, PIP, KF, SF 5,198,526 45.2 53 52 1,152,550 282,081 4,820 SAMN28767356 GCA_024745495 JANFSQ000000000 SRR19513220
ISF-209-5 2016 Vietnam V. parahaemolyticus AMP, PIP, KF, SF 5,210,137 45.2 46 59 916,300 228,194 4,834 SAMN28767357 GCA_024745475 JANFSP000000000 SRR19513219
ISF-209-6 2016 Vietnam V. diabolicus AMP, SF, TE, OT (SXT, E) 5,062,782 44.7 155 44 2,856,634 269,099 4,652 SAMN28767358 GCA_024745435 JANFSO000000000 SRR19513218
ISF-210-7 2016 Vietnam V. parahaemolyticus AMP, S, OX (K, E, CIP, ENO) 5,134,186 45.3 41 80 805,448 182,090 4,712 SAMN28767359 GCA_024745445 JANFSN000000000 SRR19513217
ISF-210-8 2016 Vietnam V. parahaemolyticus AMP, KF, CIP, OX (ENO) 5,147,064 45.3 109 35 2,090,122 447,148 4,723 SAMN28767360 GCA_024745415 JANFSM000000000 SRR19513216
ISF-211-7 2016 Thailand V. parahaemolyticus AMP, PIP, KF, CTX, CEF (SXT, E, ENO) 5,230,424 45.3 67 133 1,251,372 89,406 4,839 SAMN28767361 GCA_024745375 JANFSL000000000 SRR19513215
ISF-214-8 2016 Thailand V. parahaemolyticus AMP, PIP, KF 5,252,400 45.2 45 53 994,428 258,124 4,821 SAMN28767362 GCA_024745395 JANFSK000000000 SRR19513213
ISF-221-5 2016 Cuba V. parahaemolyticus AMP, KF, TE, OT (PIP, CTX, CEF, E, ENO) 5,352,130 45.3 114 58 2,428,508 390,904 5,042 SAMN28767363 GCA_024745355 JANFSJ000000000 SRR19513212
ISF-221-6 2016 Cuba V. parahaemolyticus AMP, PIP, KF, TE, OT 5,346,813 45 68 82 1,451,948 248,879 4,995 SAMN28767364 GCA_024745305 JANFSI000000000 SRR19513211
ISF-232-1 2016 Thailand V. parahaemolyticus AMP, KF, CTX, CEF (E) 5,109,422 45.3 30 129 636,700 116,289 4,709 SAMN28767365 GCA_024745335 JANFSH000000000 SRR19513210
ISF-234-6 2016 India V. parahaemolyticus AMP, TE, OT 5,479,698 45 30 190 625,694 71,806 5,081 SAMN28767366 GCA_024745265 JANFSG000000000 SRR19513253
ISF-235-5 2016 India V. parahaemolyticus AMP, TE, OT 5,525,342 45.0 80 138 1,757,450 91,505 5,175 SAMN28767367 GCA_024745255 JANFSF000000000 SRR19513252
ISF-237-6 2016 India V. cholerae (IPM, E, OT) 4,078,171 47.5 105 82 1,578,896 348,811 3,810 SAMN28767368 GCA_024745295 JANFSE000000000 SRR19513251
ISF-237-7B 2016 India V. parahaemolyticus AMP, KF (CTX, CEF, E, ENO) 5,564,410 45.2 85 89 1,732,466 205,604 5,207 SAMN28767369 GCA_024745215 JANFSD000000000 SRR19513250
ISF-242-5 2017 Thailand V. parahaemolyticus AMP, KF, CTX, CEF, K (E) 5,529,472 45.0 93 107 1,894,620 216,134 5,214 SAMN28767370 GCA_024745225 JANFSC000000000 SRR19513249
ISF-242-6 2017 Thailand V. parahaemolyticus AMP, KF, CTX, CEF (K, E, OT) 5,245,179 45.2 107 62 2,054,414 306,059 4,870 SAMN28767371 GCA_024745155 JANFSB000000000 SRR19513248
ISF-242-7 2017 Thailand V. parahaemolyticus AMP, PIP, KF, CTX, CEF, K (E) 5,811,791 44.8 68 86 1,639,176 205,369 5,442 SAMN28767372 GCA_024745175 JANFSA000000000 SRR19513246
ISF-242-8 2017 Thailand V. parahaemolyticus AMP, KF, CTX, CEF, SF,(PIP, S, SXT, E, OX) 5,594,092 45.0 34 148 753,934 106,759 5,268 SAMN28767373 GCA_024745165 JANFRZ000000000 SRR19513245
ISF-242-9 2017 Thailand V. parahaemolyticus AMP, KF, CTX, CEF (K, E) 5,246,136 45.2 151 50 2,943,230 331,149 4,872 SAMN28767374 GCA_024745115 JANFRY000000000 SRR19513244
ISF-242-10B 2017 Thailand V. parahaemolyticus AMP, PIP, KF, CTX, CEF (E, ENO) 5,214,000 45.3 27 111 596,650 109,782 4,820 SAMN28767375 GCA_024745135 JANFRX000000000 SRR19513243
ISF-243-9 2017 India V. cholerae (IPM) 4,041,506 47.5 97 101 1,441,966 254,697 3,763 SAMN28767376 GCA_024745065 JANFRW000000000 SRR19513242
ISF-256-8 2017 Thailand V. cholerae None 3,907,993 47.6 188 76 2,819,586 247,517 3,635 SAMN28767377 GCA_024745095 JANFRV000000000 SRR19513241
ISF-270-13 2017 Ecuador V. parahaemolyticus AMP, TE, OT 5,192,289 45.2 34 135 923,272 119,550 4,826 SAMN28767378 GCA_024745055 JANFRU000000000 SRR19513240
ISF-271-2 2017 India V. cholerae None 4,169,508 47.5 73 132 1,103,922 216,279 3,938 SAMN28767379 GCA_024744955 JANFRT000000000 SRR19513239
ISF-318-1 2018 Ecuador V. parahaemolyticus AMP, KF, TE, OT (CEF, E) 5,091,952 45.2 53 62 979,238 288,964 4,723 SAMN28767380 GCA_024744985 JANFRS000000000 SRR19513238
ISF-328-1 2019 Mexico V. diabolicus AMP, S, SXT, SF, TE, OT (ENO, OX) 5,139,724 44.9 79 72 1,434,814 130,541 4,708 SAMN28767381 GCA_024744965 JANFRR000000000 SRR19513237
ISF-331-1 2019 Bangladesh V. parahaemolyticus None 5,398,934 45.4 62 183 1,206,868 61,297 5,067 SAMN28767382 GCA_024744975 JANFRQ000000000 SRR19513235
ISF-332-2 2019 Vietnam V. parahaemolyticus AMP, SXT, SF, OT (TE) 5,088,365 45.4 54 93 998,334 128,214 4,750 SAMN28767383 GCA_024745005 JANFRP000000000 SRR19513234
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a

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. Brackets, intermediate resistance; none, no resistance.

For sequencing, stocks were streaked onto TSA-2N and incubated overnight at 35°C; a single 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 whole-genome sequencing (WGS) 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 (Prodigal [commit fe80417]) (10), and metrics reporting (QUAST v5.0.0) (11). Mash (v2.2; Mash Screen) (12) was used for taxonomic assignment of assemblies based on the highest RefSeq (v93; https://www.ncbi.nlm.nih.gov/refseq) identities >0.8 (excluding hits containing the words “phage” or “plasmid”) with V. diabolicus designated according to reference 13 and www.ncbi.nlm.nih.gov/genome. Analysis tools were used with default settings unless noted.

Isolate and genome details are listed in Table 1. In alignment with reference 14, the de novo genome assemblies reported here comprised 29 to 238 contigs and coverage depths of 25-fold to 223-fold. Total genome size ranged from 3.9 Mbp to 6.0 Mbp, containing 3,442 to 5,391 predicted genes. The 92 genomes were analyzed and identified as V. parahaemolyticus (n = 59), V. diabolicus (n = 12), V. cholerae (n = 10), V. alginolyticus (n = 7), V. campbellii (n = 1), V. harveyi (n = 1), V. owensii (n = 1), and V. vulnificus (n = 1).

Data availability.

Data for this study have been deposited in NCBI under BioProject accession number PRJNA843723; 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.

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.

Irene L. G. Newton, Indiana University, Bloomington

REFERENCES

  • 1.Faruque SM, Nair GB. 2006. Epidemiology, p 383–398. In Thompson FL, Austin B, Swings J (ed), The biology of vibrios. ASM Press, Washington, DC. [Google Scholar]
  • 2.Baker-Austin C, Oliver JD, Alam M, Ali A, Waldor MK, Qadri F, Martinez-Urtaza J. 2018. Vibrio spp. infections. Nat Rev Dis Primers 4:8–8. doi: 10.1038/s41572-018-0005-8. [DOI] [PubMed] [Google Scholar]
  • 3.Baker-Austin C, Trinanes J, Gonzalez-Escalona N, Martinez-Urtaza J. 2017. Non-cholera vibrios: the microbial barometer of climate change. Trends Microbiol 25:76–84. doi: 10.1016/j.tim.2016.09.008. [DOI] [PubMed] [Google Scholar]
  • 4.Baquero F, Martínez JL, Cantón R, Baquero F, Martinez JL, Canton R. 2008. Antibiotics and antibiotic resistance in water environments. Curr Opin Biotechnol 19:260–265. doi: 10.1016/j.copbio.2008.05.006. [DOI] [PubMed] [Google Scholar]
  • 5.Banerjee SK, Farber JM. 2017. Detection, enumeration, and isolation of Vibrio parahaemolyticus and V. vulnificus from seafood: development of a multidisciplinary protocol. J AOAC Int 100:445–453. doi: 10.5740/jaoacint.16-0290. [DOI] [PubMed] [Google Scholar]
  • 6.Ronholm J, Petrunka LJ, Banerjee SK. 2015. Antimicrobial resistance in Vibrio spp. isolated from Canadian imported shrimp, 2009–2014. Int J Antimicrob Agents 46:475–476. doi: 10.1016/j.ijantimicag.2015.05.009. [DOI] [PubMed] [Google Scholar]
  • 7.Bauer AW, Kirby WM, Sherris JC, Turck M. 1966. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496. doi: 10.1093/ajcp/45.4_ts.493. [DOI] [PubMed] [Google Scholar]
  • 8.Clinical and Laboratory Standards Institute. 2015. Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated or fastidious bacteria, 3rd ed. CLSI M45. Clinical and Laboratory Standards Institute, Wayne, PA. [DOI] [PubMed] [Google Scholar]
  • 9.Souvorov A, Agarwala R, Lipman DJ. 2018. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 19:153. doi: 10.1186/s13059-018-1540-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. 2019. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biol 20:232. doi: 10.1186/s13059-019-1841-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Turner JW, Tallman JJ, Macias A, Pinnell LJ, Elledge NC, Nasr Azadani D, Nilsson WB, Paranjpye RN, Armbrust EV, Strom MS. 2018. Comparative genomic analysis of Vibrio diabolicus and six taxonomic synonyms: a first look at the distribution and diversity of the expanded species. Front Microbiol 9:1893. doi: 10.3389/fmicb.2018.01893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Teixeira JS, Weedmark K, Dussault F, Banerjee S. 2022. Whole-genome sequences of Vibrio species from warm-water shrimps imported into Canada: detection of genetic elements associated with antimicrobial resistance and potential mobilizing capacities. Microbiol Resour Announc 11:e01014-21. doi: 10.1128/mra.01014-21. [DOI] [PMC free article] [PubMed] [Google Scholar]

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 accession number PRJNA843723; raw reads and genome accession numbers are listed in Table 1.

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