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. 2024 Jun 12;13(7):e00132-24. doi: 10.1128/mra.00132-24

Draft genome sequences of 148 Klebsiella pneumoniae species complex members from bovine and human hosts

Bridget O’Brien 1, Alla Yushchenko 1, Jinha Suh 1, Dongyun Jung 1,2,3, Zhangbin Cai 1, Ngoc Sang Nguyen 1, Makeda Semret 4, Simon Dufour 2,3,5, Jennifer Ronholm 1,2,3,✉
Editor: Vanja Klepac-Ceraj6
PMCID: PMC11256802  PMID: 38864639

ABSTRACT

Klebsiella pneumoniae species complex members, particularly K. pnemoniae sensu stricto, are common bovine clinical mastitis pathogens and often the cause of hospital- and community-acquired infections in humans. Here, we present 148 draft genome assemblies and annotations of K. pneumoniae species complex members from bovine and human hosts in Canada.

KEYWORDS: Klebsiella, Bovine Mastitis, Klebsiella pneumoniae sensu stricto

ANNOUNCEMENT

Comprising Klebsiella pneumoniae sensu stricto, Klebsiella quasipneumoniae subsp. quasipneumoniae, K. quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, and K. variicola subsp. tropica, members of the K. pneumoniae species complex (KpSC) cause infections in both humans and dairy cattle (1, 2). K. pneumoniae sensu stricto, herein referred to as K. pneumoniae, is the predominant KpSC isolate in bovine mastitis and human infections, such as pneumonia, bacteremia, and urinary sepsis (2–7). Relatively few KpSC isolates from Canada have been studied, making publicly available KpSC genomes from Canada a valuable resource for further research.

Here, we present draft genome sequences of 148 KpSC isolates from human (n = 78) and bovine (n = 70) hosts. K. pneumoniae sensu strico represented 86% of KpSC isolates (bovine, n = 65; human n = 63), K. variicola subsp. variicola represented 8% (bovine, n = 2; human, n = 10), and both K. quasipneumoniae subsp. quasipneumoniae (bovine, n = 3; human, n = 1) and K. quasipneumoniae subsp. similipneumoniae (human, n = 4) represented 3%.

Bovine isolates were obtained from the Mastitis Pathogen Culture Collection (8). Briefly, these isolates were confirmed as Klebsiella spp. using biochemical tests (lactose positive; indole, citrate, and oxidase negative) after plating 10 µL of raw milk on Columbia agar with 5% sheep blood and MacConkey agar. In accordance with the institutional ethical guidelines at McGill University and the Declaration of Helsinki, up to 10 mL of blood from patients at the McGill University Health Centre was inoculated directly into BACT/ALERT aerobic and anaerobic blood culture bottles (BioMérieux) which contain 40 mL tryptic soy broth (TSB), and placed on the BacT/ALERT automated platform at 35°C for incubation. Bottles flagged as culture-positive were subcultured onto blood and MacConkey agar using one drop of the incubated blood. Following growth, pure colonies were identified as K. pneumoniae using Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS), as described previously (9). Each isolate, stored in a stock solution at −80°C, was thawed, streaked onto tryptic soy agar (TSA), and incubated overnight at 37°C. One colony was picked from the TSA plate, added into 5 mL of TSB, and grown overnight at 37°C under shaking conditions (~200 rpm). DNA was extracted from liquid cultures using DNeasy Ultraclean Microbial kit following manufacturer’s instructions (Qiagen, USA). DNA quality was assessed using the NanoDrop 2,000 spectrophotometer (ThermoScientific), and the concentration was determined using Quant-IT dsDNA High-Sensitivity assay (Invitrogen, USA). Samples with A260/A280 ratio < 1.8 and A260/A230 ratio between 1.8 and 2.2 were included in library preparation using Nextera DNA Flex Prep kit following manufacturer’s instructions (Illumina, USA). Libraries were sequenced using the MiSeq benchtop sequencer (Illumina) and the MiSeq Reagent Kit v3 (2 × 300 bp), yielding a total of 153,632,994 reads. Reads were assembled de novo using ProkaryoteAssembly (v. 0.1.6) (https://github.com/BFSSI-Bioinformatics-Lab/ProkaryoteAssembly) with default parameters, apart from the trimming step in which low-quality sequences with Q-score < 20 were filtered out. Following assembly, contigs with fewer than 1,000 bp were removed. Quality of final assemblies was assessed with QualiMap (v. 2.2.2) (10). Species identification was completed using Kleborate (v. 2.4.0) (11). Gene annotations and predictions were performed using NCBI Prokaryotic Genome Annotation Pipeline (v. 6.6) upon submission to GenBank (Table 1) (12).

TABLE 1.

Genome quality and predications of K. pneumoniae sensu strico, K. variicola subsp. variicola, K. quasipneumoniae subsp. quasipneumoniae, and K. quasipneumoniae subsp. similipneumoniae assemblies

Isolate identification number/name Host Species BioSample accession no. GenBank accession no. SRA accession no.a Draft genome size (bp) Coverage
(X)		 G + C content (%) No. of contigs N50 (bp) No. of CDSb No. of RNAs
10106020 Bovine K. pneumoniae sensu strico SAMN38811387 JAXSFJ000000000 SRR27199061 5,425,478 30 56.43 115 103,101 5,373 92
10106228 Bovine K. pneumoniae sensu strico SAMN38811388 JAXSFI000000000 SRR27199060 5,228,123 46 56.84 87 159,343 5,147 92
10108161 Bovine K. pneumoniae sensu strico SAMN38811389 JAXSFH000000000 SRR27198969 5,232,226 35 56.69 87 148,395 5,155 92
10108963 Bovine K. pneumoniae sensu strico SAMN38811390 JAXSFG000000000 SRR27198958 5,226,237 34 56.84 101 119,473 5,154 87
10116548 Bovine K. pneumoniae sensu strico SAMN38811391 JAXSFF000000000 SRR27198947 5,427,354 32 56.32 104 141,038 5,366 94
10116616 Bovine K. pneumoniae sensu strico SAMN38811392 JAXSFE000000000 SRR27198936 5,371,671 18 56.37 292 40,642 5,449 74
10116623 Bovine K. pneumoniae sensu strico SAMN38811393 JAXSFD000000000 SRR27199021 5,423,477 26 56.46 113 114,031 5,369 90
10116692 Bovine K. pneumoniae sensu strico SAMN38811394 JAXSFC000000000 SRR27199010 5,428,749 33 56.26 101 118,039 5,365 92
10116739 Bovine K. pneumoniae sensu strico SAMN38811395 JAXSFB000000000 SRR27198999 5,435,163 46 56.36 95 148,395 5,373 93
10201992 Bovine K. pneumoniae sensu strico SAMN38811396 JAXSFA000000000 SRR27198924 5,224,805 28 56.7 122 119,474 5,168 95
10202968 Bovine K. pneumoniae sensu strico SAMN38811397 JAXSEZ000000000 SRR27199059 5,230,909 36 56.6 90 159,221 5,150 90
10214985 Bovine K. pneumoniae sensu strico SAMN38811398 JAXSEY000000000 SRR27199048 5,385,679 39 56.59 26 798,846 5,200 94
10216484 Bovine K. pneumoniae sensu strico SAMN38811399 JAXSEX000000000 SRR27199037 5,237,069 39 56.64 88 159,221 5,158 90
10300398 Bovine K. pneumoniae sensu strico SAMN38811400 JAXSEW000000000 SRR27198994 5,658,740 29 56.14 79 182,860 5,563 86
10300862 Bovine K. pneumoniae sensu strico SAMN38811401 JAXSEV000000000 SRR27198983 5,370,163 36 56.51 146 119,659 5,353 92
10302521 Bovine K. pneumoniae sensu strico SAMN38811402 JAXSEU000000000 SRR27198974 5,403,094 57 56.83 50 266,010 5,266 97
10309735 Bovine K. pneumoniae sensu strico SAMN38811403 JAXSET000000000 SRR27198973 5,268,042 48 56.83 88 159,343 5,189 94
10309742 Bovine K. pneumoniae sensu strico SAMN38811404 JAXSES000000000 SRR27198972 5,463,147 59 56.72 40 366,197 5,298 90
10310236 Bovine K. pneumoniae sensu strico SAMN38811405 JAXSER000000000 SRR27198971 5,365,745 15 56.75 309 32,624 5,413 59
10310267 Bovine K. pneumoniae sensu strico SAMN38811406 JAXSEQ000000000 SRR27198970 5,277,068 40 56.59 89 159,343 5,209 90
10400807 Bovine K. pneumoniae sensu strico SAMN38811407 JAXSEP000000000 SRR27198968 5,297,921 59 56.89 39 421,036 5,156 95
10402672 Bovine K. pneumoniae sensu strico SAMN38811408 JAXSEO000000000 SRR27198967 5,292,939 40 56.89 23 506,305 5,164 101
10413500 Bovine K. pneumoniae sensu strico SAMN38811409 JAXSEN000000000 SRR27198966 5,387,201 26 56.23 119 97,898 5,334 91
10415139 Bovine K. pneumoniae sensu strico SAMN38811410 JAXSEM000000000 SRR27198965 5,426,595 25 56.56 105 180,680 5,266 94
10415269 Bovine K. pneumoniae sensu strico SAMN38811411 JAXSEL000000000 SRR27198964 5,481,433 77 56.57 44 297,708 5,355 93
10417423 Bovine K. pneumoniae sensu strico SAMN38811412 JAXSEK000000000 SRR27198963 5,424,186 39 56.26 96 142,713 5,357 94
10417447 Bovine K. pneumoniae sensu strico SAMN38811413 JAXSEJ000000000 SRR27198962 5,472,868 28 56.38 60 239,632 5,344 101
10417843 Bovine K. pneumoniae sensu strico SAMN38811414 JAXSEI000000000 SRR27198961 5,383,914 45 56.02 91 159,343 5,304 93
10418109 Bovine K. pneumoniae sensu strico SAMN38811415 JAXSEH000000000 SRR27198960 5,723,621 49 56.05 64 204,589 5,613 97
10418338 Bovine K. pneumoniae sensu strico SAMN38811416 JAXSEG000000000 SRR27198959 5,713,685 26 56.04 85 158,630 5,648 97
11003939 Bovine K. pneumoniae sensu strico SAMN38811417 JAXSEF000000000 SRR27198957 5,457,274 35 56.6 56 381,920 5,278 97
11005407 Bovine K. pneumoniae sensu strico SAMN38811418 JAXSEE000000000 SRR27198956 5,531,908 34 56.41 51 288,946 5,381 91
11005414 Bovine K. pneumoniae sensu strico SAMN38811419 JAXSED000000000 SRR27198955 5,530,947 38 56.28 44 375,673 5,373 91
11006091 Bovine K. pneumoniae sensu strico SAMN38811420 JAXSEC000000000 SRR27198954 5,526,959 41 56.65 51 288,947 5,372 91
11007937 Bovine K. pneumoniae sensu strico SAMN38811421 JAXSEB000000000 SRR27198953 5,514,281 21 56.23 116 94,010 5,403 91
11007944 Bovine K. pneumoniae sensu strico SAMN38811422 JAXSEA000000000 SRR27198952 5,534,843 45 56.52 43 355,703 5,378 92
11009085 Bovine K. pneumoniae sensu strico SAMN38811423 JAXSDZ000000000 SRR27198951 5,507,594 54 56.58 35 375,690 5,341 92
11009146 Bovine K. pneumoniae sensu strico SAMN38811424 JAXSDY000000000 SRR27198950 5,534,898 53 56.55 42 355,703 5,373 92
11010982 Bovine K. pneumoniae sensu strico SAMN38811425 JAXSDX000000000 SRR27198949 5,524,841 40 56.38 46 383,384 5,364 90
11113904 Bovine K. pneumoniae sensu strico SAMN38811426 JAXSDW000000000 SRR27198948 5,480,810 35 56.21 55 346,188 5,377 96
11114840 Bovine K. pneumoniae sensu strico SAMN38811427 JAXSDV000000000 SRR27198946 5,442,605 49 56.61 47 369,687 5,314 95
11115748 Bovine K. pneumoniae sensu strico SAMN38811428 JAXSDU000000000 SRR27198945 5,525,882 38 56.42 50 269,910 5,370 90
11708612 Bovine K. pneumoniae sensu strico SAMN38811429 JAXSDT000000000 SRR27198944 5,617,391 40 56.39 78 214,765 5,502 93
11912781 Bovine K. pneumoniae sensu strico SAMN38811430 JAXSDS000000000 SRR27198943 5,229,672 36 57.16 29 371,293 5,052 89
21206061 Bovine K. pneumoniae sensu strico SAMN38811431 JAXSDR000000000 SRR27198942 5,626,718 49 56.03 27 387,075 5,499 94
22513373 Bovine K. pneumoniae sensu strico SAMN38811432 JAXSDQ000000000 SRR27198941 5,353,554 80 56.61 42 350,392 5,176 94
22713346 Bovine K. pneumoniae sensu strico SAMN38811433 JAXSDP000000000 SRR27198940 5,380,696 38 56.86 45 304,306 5,238 91
30817180 Bovine K. pneumoniae sensu strico SAMN38811434 JAXSDO000000000 SRR27198939 5,418,896 30 56.75 51 297,910 5,233 97
40400129 Bovine K. pneumoniae sensu strico SAMN38811435 JAXSDN000000000 SRR27198938 5,324,373 46 56.42 60 228,832 5,147 91
40611440 Bovine K. quasipneumoniae subsp. quasipneumoniae SAMN38811436 JAXSDM000000000 SRR27198937 5,380,139 31 57.44 63 256,433 5,161 88
40615929 Bovine K. variicola subsp. variicola SAMN38811437 JAXSDL000000000 SRR27198935 5,485,656 40 57.16 24 483,749 5,231 91
40706870 Bovine K. pneumoniae sensu strico SAMN38811438 JAXSDK000000000 SRR27198934 5,480,982 51 56.65 41 321,408 5,310 98
40706948 Bovine K. pneumoniae sensu strico SAMN38811439 JAXSDJ000000000 SRR27199029 5,458,436 41 56.66 63 350,390 5,293 83
40706993 Bovine K. quasipneumoniae subsp. quasipneumoniae SAMN38811440 JAXSDI000000000 SRR27199028 5,417,015 34 57.3 54 291,465 5,198 98
40709369 Bovine K. pneumoniae sensu strico SAMN38811441 JAXSDH000000000 SRR27199027 5,288,319 46 57.01 45 370,742 5,136 91
40713625 Bovine K. quasipneumoniae subsp. quasipneumoniae SAMN38811442 JAXSDG000000000 SRR27199026 5,416,886 29 57.5 67 216,074 5,180 95
40717173 Bovine K. pneumoniae sensu strico SAMN38811443 JAXSDF000000000 SRR27199025 5,522,691 37 56.58 67 216,982 5,374 101
40718170 Bovine K. pneumoniae sensu strico SAMN38811444 JAXSDE000000000 SRR27199024 5,490,775 42 56.56 48 475,862 5,316 92
40718231 Bovine K. pneumoniae sensu strico SAMN38811445 JAXSDD000000000 SRR27199023 5,455,694 41 56.77 50 769,862 5,316 98
40718651 Bovine K. variicola subsp. variicola SAMN38811446 JAXSDC000000000 SRR27199022 5,707,929 38 56.67 45 389,087 5,549 100
40806273 Bovine K. pneumoniae sensu strico SAMN38811447 JAXSDB000000000 SRR27199020 5,699,707 31 56.36 86 205,377 5,620 89
41006955 Bovine K. pneumoniae sensu strico SAMN38811448 JAXSDA000000000 SRR27199019 5,279,381 48 56.92 34 360,377 5,150 96
41203163 Bovine K. pneumoniae sensu strico SAMN38811449 JAXSCZ000000000 SRR27199018 5,315,776 61 56.32 61 229,224 5,133 87
41508275 Bovine K. pneumoniae sensu strico SAMN38811450 JAXSCY000000000 SRR27199017 5,185,978 52 56.71 80 155,317 4,997 91
41510377 Bovine K. pneumoniae sensu strico SAMN38811451 JAXSCX000000000 SRR27199016 5,420,290 84 56.71 51 323,739 5,262 93
41518175 Bovine K. pneumoniae sensu strico SAMN38811452 JAXSCW000000000 SRR27199015 5,350,680 58 56.53 44 255,820 5,239 97
41518533 Bovine K. pneumoniae sensu strico SAMN38811453 JAXSCV000000000 SRR27199014 5,586,164 87 56.32 72 221,685 5,456 93
41518540 Bovine K. pneumoniae sensu strico SAMN38811454 JAXSCU000000000 SRR27199013 5,454,922 39 56.28 95 155,030 5,291 89
41518854 Bovine K. pneumoniae sensu strico SAMN38811455 JAXSCT000000000 SRR27199012 5,450,089 22 56.39 183 71,321 5,419 90
41519141 Bovine K. pneumoniae sensu strico SAMN38811456 JAXSCS000000000 SRR27199011 5,191,411 60 56.87 83 176,242 5,008 94
HKp1 Human K. pneumoniae sensu strico SAMN38811457 JAXSCR000000000 SRR27199009 5,438,233 34 56.68 43 231,448 5,258 87
HKp10 Human K. pneumoniae sensu strico SAMN38811458 JAXSCQ000000000 SRR27199008 5,263,762 43 56.75 37 295,122 5,044 90
HKp11 Human K. pneumoniae sensu strico SAMN38811459 JAXSCP000000000 SRR27199007 5,274,286 34 56.79 65 212,985 5,071 92
HKp12 Human K. pneumoniae sensu strico SAMN38811460 JAXSCO000000000 SRR27199006 5,605,874 57 56.63 52 231,035 5,513 100
HKp13 Human K. quasipneumoniae subsp. similipneumoniae SAMN38811461 JAXSCN000000000 SRR27199005 5,568,097 28 56.7 67 329,287 5,429 88
HKp14 Human K. pneumoniae sensu strico SAMN38811462 JAXSCM000000000 SRR27199004 5,383,514 63 56.61 39 362,892 5,223 96
HKp15 Human K. variicola subsp. variicola SAMN38811463 JAXSCL000000000 SRR27199003 5,392,356 64 56.88 22 478,496 5,119 100
HKp16 Human K. pneumoniae sensu strico SAMN38811464 JAXSCK000000000 SRR27199002 5,565,637 69 55.79 32 508,313 5,392 99
HKp17 Human K. pneumoniae sensu strico SAMN38811465 JAXSCJ000000000 SRR27199001 5,547,533 80 56.24 36 391,789 5,396 96
HKp18 Human K. pneumoniae sensu strico SAMN38811466 JAXSCI000000000 SRR27199000 5,469,254 61 56.6 32 340,162 5,272 94
HKp19 Human K. pneumoniae sensu strico SAMN38811467 JAXSCH000000000 SRR27198998 5,521,504 32 56.4 41 353,306 5,341 95
HKp2 Human K. pneumoniae sensu strico SAMN38811468 JAXSCG000000000 SRR27198933 5,486,293 41 56.01 56 352,022 5,261 88
HKp20 Human K. pneumoniae sensu strico SAMN38811469 JAXSCF000000000 SRR27198932 5,492,507 34 56.19 59 255,498 5,267 83
HKp21 Human K. quasipneumoniae subsp. similipneumoniae SAMN38811470 JAXSCE000000000 SRR27198931 5,099,859 45 57.68 19 591,100 4,827 93
HKp22 Human K. pneumoniae sensu strico SAMN38811471 JAXSCD000000000 SRR27198930 5,524,670 69 55.69 53 288,852 5,327 96
HKp23 Human K. pneumoniae sensu strico SAMN38811472 JAXSCC000000000 SRR27198929 5,347,731 45 56.67 43 251,342 5,144 95
HKp24 Human K. pneumoniae sensu strico SAMN38811473 JAXSCB000000000 SRR27198928 5,405,787 49 56.24 60 216,924 5,342 98
HKp25 Human K. variicola subsp. variicola SAMN38811474 JAXSCA000000000 SRR27198927 5,356,039 43 57.19 20 482,246 5,106 95
HKp26 Human K. variicola subsp. variicola SAMN38811475 JAXSBZ000000000 SRR27198926 5,496,742 23 56.91 67 141,189 5,248 87
HKp28 Human K. variicola subsp. variicola SAMN38811476 JAXSBY000000000 SRR27198925 5,487,839 47 56.79 27 440,092 5,225 88
HKp29 Human K. pneumoniae sensu strico SAMN38811477 JAXSBX000000000 SRR27198923 5,773,613 51 56.34 38 356,169 5,628 94
HKp3 Human K. quasipneumoniae subsp. similipneumoniae SAMN38811478 JAXSBW000000000 SRR27198922 5,231,235 45 57.15 23 393,992 5,006 89
HKp30 Human K. pneumoniae sensu strico SAMN38811479 JAXSBV000000000 SRR27198921 5,526,729 68 56.03 49 289,601 5,322 98
HKp31 Human K. pneumoniae sensu strico SAMN38811480 JAXSBU000000000 SRR27198920 5,464,356 50 56.76 40 350,419 5,277 89
HKp32 Human K. pneumoniae sensu strico SAMN38811481 JAXSBT000000000 SRR27198919 5,563,033 44 56.71 39 282,176 5,361 96
HKp33 Human K. variicola subsp. variicola SAMN38811482 JAXSBS000000000 SRR27198918 5,492,619 41 56.91 29 440,646 5,229 91
HKp34 Human K. pneumoniae sensu strico SAMN38811483 JAXSBR000000000 SRR27198917 5,191,039 59 57.42 23 433,863 4,987 91
HKp35 Human K. pneumoniae sensu strico SAMN38811484 JAXSBQ000000000 SRR27198916 5,300,781 30 56.18 91 157,144 5,147 85
HKp36 Human K. pneumoniae sensu strico SAMN38811485 JAXSBP000000000 SRR27198915 5,495,317 45 56.98 46 350,109 5,280 95
HKp37 Human K. pneumoniae sensu strico SAMN38811486 JAXSBO000000000 SRR27198914 5,365,006 49 56.81 34 333,153 5,187 95
HKp38 Human K. pneumoniae sensu strico SAMN38811487 JAXSBN000000000 SRR27199058 5,579,148 38 55.77 99 129,962 5,420 97
HKp39 Human K. pneumoniae sensu strico SAMN38811488 JAXSBM000000000 SRR27199057 5,483,494 113 56.43 68 265,340 5,332 88
HKp4 Human K. pneumoniae sensu strico SAMN38811489 JAXSBL000000000 SRR27199056 5,437,624 45 55.98 131 95,856 5,330 94
HKp40 Human K. pneumoniae sensu strico SAMN38811490 JAXSBK000000000 SRR27199055 5,605,006 51 56.43 82 305,637 5,519 100
HKp41 Human K. pneumoniae sensu strico SAMN38811491 JAXSBJ000000000 SRR27199054 5,422,742 42 56.5 55 301,240 5,336 92
HKp42 Human K. variicola subsp. variicola SAMN38811492 JAXSBI000000000 SRR27199053 5,616,842 102 56.88 35 318,729 5,407 93
HKp43 Human K. pneumoniae sensu strico SAMN38811493 JAXSBH000000000 SRR27199052 5,350,440 49 56.93 25 356,104 5,140 87
HKp44 Human K. pneumoniae sensu strico SAMN38811494 JAXSBG000000000 SRR27199051 5,247,822 45 57.25 22 439,392 5,049 95
HKp45 Human K. pneumoniae sensu strico SAMN38811495 JAXSBF000000000 SRR27199050 5,334,273 51 56.82 47 323,114 5,136 90
HKp46 Human K. variicola subsp. variicola SAMN38811496 JAXSBE000000000 SRR27199049 5,506,348 57 57.22 21 404,218 5,230 90
HKp47 Human K. quasipneumoniae subsp. similipneumoniae SAMN38811497 JAXSBD000000000 SRR27199047 5,577,170 35 56.75 95 164,232 5,459 92
HKp48 Human K. pneumoniae sensu strico SAMN38811498 JAXSBC000000000 SRR27199046 5,603,980 66 56.4 68 326,559 5,514 99
HKp49 Human K. pneumoniae sensu strico SAMN38811499 JAXSBB000000000 SRR27199045 5,227,155 63 56.75 60 194,543 5,076 89
HKp5 Human K. pneumoniae sensu strico SAMN38811500 JAXSBA000000000 SRR27199044 5,197,967 84 56.61 39 392,908 4,966 101
HKp50 Human K. pneumoniae sensu strico SAMN38811501 JAXSAZ000000000 SRR27199043 5,525,194 64 56.83 61 266,427 5,410 95
HKp51 Human K. pneumoniae sensu strico SAMN38811502 JAXSAY000000000 SRR27199042 5,415,873 32 56.82 40 378,459 5,223 99
HKp52 Human K. variicola subsp. variicola SAMN38811503 JAXSAX000000000 SRR27199041 5,417,958 56 57.23 15 1,005,355 5,150 97
HKp53 Human K. pneumoniae sensu strico SAMN38811504 JAXSAW000000000 SRR27199040 5,473,219 62 56.98 26 581,574 5,272 94
HKp54 Human K. pneumoniae sensu strico SAMN38811505 JAXSAV000000000 SRR27199039 5,293,626 38 56.69 66 246,509 5,163 94
HKp55 Human K. pneumoniae sensu strico SAMN38811506 JAXSAU000000000 SRR27199038 5,490,231 41 56.46 55 371,210 5,265 91
HKp56 Human K. pneumoniae sensu strico SAMN38811507 JAXSAT000000000 SRR27199036 5,333,990 49 56.93 50 269,909 5,139 92
HKp57 Human K. variicola subsp. variicola SAMN38811508 JAXSAS000000000 SRR27199035 5,507,063 61 57.17 18 462,100 5,228 89
HKp58 Human K. pneumoniae sensu strico SAMN38811509 JAXSAR000000000 SRR27199034 5,387,393 52 56.68 39 333,445 5,229 94
HKp59 Human K. pneumoniae sensu strico SAMN38811510 JAXSAQ000000000 SRR27199033 5,607,908 88 56.31 74 326,559 5,521 99
HKp6 Human K. pneumoniae sensu strico SAMN38811511 JAXSAP000000000 SRR27199032 5,303,782 50 56.06 78 252,845 5,127 87
HKp60 Human K. pneumoniae sensu strico SAMN38811512 JAXSAO000000000 SRR27199031 5,511,978 44 56.6 58 295,498 5,389 92
HKp61 Human K. pneumoniae sensu strico SAMN38811513 JAXSAN000000000 SRR27199030 5,707,669 53 56.17 82 210,766 5,610 98
HKp62 Human K. pneumoniae sensu strico SAMN38811514 JAXSAM000000000 SRR27198997 5,783,949 42 56.1 49 262,494 5,655 93
HKp63 Human K. pneumoniae sensu strico SAMN38811515 JAXSAL000000000 SRR27198996 5,530,438 48 56.7 34 391,677 5,346 98
HKp64 Human K. pneumoniae sensu strico SAMN38811516 JAXSAK000000000 SRR27198995 5,349,402 67 56.99 25 353,558 5,135 90
HKp65 Human K. pneumoniae sensu strico SAMN38811517 JAXSAJ000000000 SRR27198993 5,426,112 96 56.02 67 343,360 5,272 94
HKp66 Human K. pneumoniae sensu strico SAMN38811518 JAXSAI000000000 SRR27198992 5,392,351 30 56.8 47 379,271 5,190 98
HKp67 Human K. pneumoniae sensu strico SAMN38811519 JAXSAH000000000 SRR27198991 5,192,727 56 56.77 33 403,964 4,958 94
HKp68 Human K. pneumoniae sensu strico SAMN38811520 JAXSAG000000000 SRR27198990 5,534,022 30 56.42 80 218,950 5,419 91
HKp69 Human K. pneumoniae sensu strico SAMN38811521 JAXSAF000000000 SRR27198989 5,618,659 77 56.37 54 336,934 5,454 97
HKp7 Human K. pneumoniae sensu strico SAMN38811522 JAXSAE000000000 SRR27198988 5,278,397 45 56.79 62 289,518 5,076 93
HKp70 Human K. quasipneumoniae subsp. quasipneumoniae SAMN38811523 JAXSAD000000000 SRR27198987 5,480,726 49 57.24 27 493,923 5,260 98
HKp72 Human K. pneumoniae sensu strico SAMN38811524 JAXSAC000000000 SRR27198986 5,494,696 54 56.13 53 321,085 5,265 90
HKp73 Human K. pneumoniae sensu strico SAMN38811525 JAXSAB000000000 SRR27198985 5,192,637 51 56.68 33 408,428 4,955 93
HKp74 Human K. variicola subsp. variicola SAMN38811526 JAXSAA000000000 SRR27198984 5,595,544 52 56.99 29 470,508 5,390 95
HKp75 Human K. pneumoniae sensu strico SAMN38811527 JAXRZZ000000000 SRR27198982 5,193,738 45 56.82 30 408,428 4,954 94
HKp76 Human K. pneumoniae sensu strico SAMN38811528 JAXRZY000000000 SRR27198981 5,559,252 56 56.48 48 334,965 5,461 97
HKp77 Human K. pneumoniae sensu strico SAMN38811529 JAXRZX000000000 SRR27198980 5,548,795 30 56.55 57 304,407 5,460 93
HKp78 Human K. pneumoniae sensu strico SAMN38811530 JAXRZW000000000 SRR27198979 5,407,764 78 56.68 37 304,230 5,205 91
HKp79 Human K. pneumoniae sensu strico SAMN38811531 JAXRZV000000000 SRR27198978 5,408,561 44 56.54 37 305,094 5,207 90
HKp8 Human K. pneumoniae sensu strico SAMN38811532 JAXRZU000000000 SRR27198977 5,382,904 59 56.67 39 333,445 5,222 93
HKp80 Human K. pneumoniae sensu strico SAMN38811533 JAXRZT000000000 SRR27198976 5,405,426 47 56.57 39 265,416 5,205 91
HKp9 Human K. pneumoniae sensu strico SAMN38811534 JAXRZS000000000 SRR27198975 5,496,703 32 56.55 49 311,929 5,291 89
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a

"SRA”,Seqeunce Read Archive.

b

"CDS”,Coding Sequence.

ACKNOWLEDGMENTS

We acknowledge the support of the Natural Sciences and Engineering Research Council of Canada (NSERC), (funding reference number ALLRP 576756-22).

Contributor Information

Jennifer Ronholm, Email: jennifer.ronholm@mcgill.ca.

Vanja Klepac-Ceraj, Wellesley College Department of Biological Sciences, Wellesley, Massachusetts, USA.

DATA AVAILABILITY

Raw sequencing reads corresponding to each sample are deposited under BioProject Accession number PRJNA1052047.

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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

Raw sequencing reads corresponding to each sample are deposited under BioProject Accession number PRJNA1052047.

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