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. 2021 Sep 16;10(37):e00449-21. doi: 10.1128/MRA.00449-21

Genome Sequences of Community Carriage Strains of Staphylococcus aureus from Yuma, Arizona

Talima Pearson a,b,✉, Crystal Hepp b,c, Robert T Trotter II b,d, Mimi Mbegbu a, Benjamin Russakoff a, David Panisello Yagüe a, Colin Wood a, Kara Tucker-Morgan e, Kathya Ceniceros e, Cristina Padilla e, Shari Kyman a, Francisco Villa e
Editor: Steven R Gillf
PMCID: PMC8444984  PMID: 34528818

ABSTRACT

Staphylococcus aureus exists as a pathogen and commensal. Individuals with asymptomatic carriage serve as a reservoir for transmission and are at increased risk of infecting themselves. In order to characterize the genomic diversity of S. aureus circulating in the community, we sequenced 166 genomes collected from individuals in Yuma, AZ.

ANNOUNCEMENT

Staphylococcus aureus is a Gram-positive bacterium that lives in close association with humans as both a commensal and pathogen (1). S. aureus is a common cause of skin, soft tissue, bone, joint, respiratory, and endovascular infections that occur when these bacteria penetrate the outer layers of skin or mucosa (2–7). Methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) infections have historically been considered a health care-acquired (HA) phenomenon; however, new lineages, and even traditionally HA strains, are circulating at an increased rate in the community (1, 8–11). Controlling this MSSA/MRSA epidemic is particularly challenging because of a large community-based reservoir; about 19 to 55% of the general population are colonized in the nares by S. aureus, with 1.5% being carriers of MRSA (3, 12). Colonization usually precedes infection and is therefore the major risk factor for disease (2, 5, 13–16).

Ethnic minorities and those with less education are typically at greater risk for a variety of infectious diseases. National data suggest that S. aureus carriage in Hispanics is not significantly different than for non-Hispanic whites, but people born in Mexico and those with higher levels of education have a lower risk of colonization (17). Our data from near the binational U.S./Mexico border in Yuma, AZ, show very high carriage rates, no educational or other socioeconomic gradient on S. aureus colonization, but a nominally lower colonization rate in Hispanics compared to non-Hispanics (18). To more fully understand the genomic aspects of community carriage in this predominantly Hispanic population, we collected and sequenced strains of S. aureus from participants in Yuma, AZ (19). All samples were collected as part of project 1116783, approved by the Northern Arizona University Institutional Review Board. Here, we present the genome sequences of isolates collected from March through June 2019. We used BBL CultureSwab swabs to sample three body sites (the anterior nares, throat, and palm) of each participant, cultured samples on CHROMagar Staph aureus medium, and selected mauve colonies for DNA extraction and sequencing (19). For DNA extraction, we used Qiagen DNeasy blood and tissue kits with added lysostaphin at a final concentration of 0.75 U/μl and an incubation time of 1 h. We constructed libraries using 500 to 1,000 ng genomic DNA (gDNA) with the Kapa HyperPrep kit (Roche Diagnostics) and conducted mechanical shearing on the QSonica Q800R3 sonicator. Double-sided size selection was performed using AMPure XP paramagnetic beads (Beckman Coulter) for 600- to 700-bp fragments. The libraries were pooled equimolar using the KAPA library quantification kit (Roche Diagnostics). DNA from 166 colonies was sequenced on an Illumina NextSeq 500 instrument using a 150-cycle 500/550 high-output kit v2.5. Assembly, error correction, and quality trimming were performed using SPAdes v2.0 (20), and contigs shorter than 500 bp were removed. The average genome coverage was calculated using BBMap (21), and the Prokaryotic Genome Annotation Pipeline (PGAP) was used for annotation (22).

The multilocus sequence type and staphylococcal cassette chromosome mec (SCCmec) type were determined for each genome using MLST v2.0 and SCCmecFinder v1.2 (23). Default settings were used for all software unless otherwise specified. The genome metrics and isolation source information are provided in Table 1.

TABLE 1.

Characteristics and accession numbers for 166 S. aureus genomes

Isolatea SCCmec STb N50 (bp) No. of contigs Size (bp) Coverage (×) GC content (%) No. of reads GenBank accession no.
2a2005n1 MSSA 30 62,943 126 2,758,377 123.726 0.3272 4,584,868 JAGRXT000000000
2a2005t1 MSSA 30 62,943 118 2,756,207 112.034 0.3272 4,167,611 JAGRXS000000000
2a2009n1 MSSA 5 187,277 72 2,788,303 670.834 0.3274 12,611,705 JAGRXR000000000
2a2009t1 MSSA 5 53,193 100 2,760,346 41.312 0.3326 2,647,703 JAGRXQ000000000
2a2010t1 MSSA 188 80,305 73 2,721,189 150.941 0.3268 5,538,066 JAGRXP000000000
2a2015t1 MSSA 5d 81,690 79 2,718,012 117.74 0.327 4,263,633 JAGRXO000000000
2a2017n1 MSSA 30 65,351 103 2,741,214 118.954 0.3271 4,373,292 JAGRXN000000000
2a2023n1 MSSA 30 58,969 111 2,794,809 115.499 0.3272 4,465,014 JAGRXM000000000
2a2024n1 MSSA 30 61,394 104 2,782,339 55.534 0.3284 2,290,514 JAGRXL000000000
2a2024p1 MSSA 30 54,206 111 2,781,358 38.434 0.3305 2,178,584 JAGRXK000000000
2a2024t1 MSSA 30 51,415 116 2,780,566 28.615 0.3342 1,220,699 JAGRXJ000000000
2a2026n1 MSSA 8 96,971 75 2,747,384 150.708 0.3267 5,577,335 JAGRXI000000000
2a2027n1 MSSA 30 65,368 113 2,743,712 131.177 0.3271 4,863,836 JAGRXH000000000
2a2027t1 MSSA 30 66,081 114 2,744,916 158.258 0.3272 5,797,055 JAGRXG000000000
2a2029n1 MSSA 398 71,211 74 2,662,941 127.571 0.3282 4,584,259 JAGRXF000000000
2a2031t1 MSSA U 14,768 482 2,865,289 115.47 0.3271 4,759,290 JAGRXE000000000
2a2036t1 MSSA U 79,805 81 2,684,634 32.237 0.3293 1,504,102 JAGRXD000000000
2a2043n1 MSSA 15 51,742 103 2,706,404 56.862 0.3276 2,269,209 JAGRXC000000000
2a2043t1 MSSA 15 46,199 106 2,656,310 33.421 0.3308 1,302,761 JAGRXB000000000
2a2048n1 MSSA 30 61,993 125 2,817,267 80.866 0.3277 3,425,204 JAGRXA000000000
2a2048t1 MSSA 87 54,033 99 2,678,932 56.111 0.3279 2,009,529 JAGRWZ000000000
2a2049n1 IVg(2B) 5 67,593 97 2,836,262 132.995 0.3278 5,038,467 JAGRWY000000000
2a2049t1 IVg(2B) 5 67,509 93 2,836,243 144.04 0.3279 5,439,365 JAGRWX000000000
2a2050n1 MSSA 582 50,864 114 2,683,760 44.349 0.3278 1,619,432 JAGRWW000000000
2a2050p1 MSSA 582 61,484 95 2,687,584 127.061 0.3275 4,595,761 JAGRWV000000000
2a2051n1 MSSA 582 94,535 54 2,680,589 893.164 0.328 15,895,551 JAGRWU000000000
2a2055t1 MSSA 45 75,685 65 2,696,835 133.122 0.3285 4,791,738 JAGRWT000000000
2a2071t1 MSSA 5 61,800 89 2,721,622 39.798 0.3283 1,495,182 JAGRWS000000000
2a2074n1 MSSA 6 59,828 96 2,746,279 131.777 0.3276 4,839,566 JAGRWR000000000
2a2074t1 MSSA 6 44,465 106 2,745,419 34.919 0.3276 1,474,447 JAGRWQ000000000
2a3002n1 MSSA 8d 87,379 84 2,752,739 123.692 0.327 4,624,050 JAGRWP000000000
2a3005n1 MSSA 97 47,296 101 2,749,588 122.317 0.3272 4,598,588 JAGRWO000000000
2a3007t1 MSSA 188 73,083 83 2,701,956 127.269 0.3269 4,636,473 JAGRWN000000000
2a3015n1 MSSA 45 268,476 26 2,746,283 691.144 0.328 12,635,772 JAGRWM000000000
2a3015p1 MSSA 45 67,650 73 2,735,213 152.045 0.3289 5,723,059 JAGRWL000000000
2a3017n1 MSSA 30 65,233 109 2,764,946 130.212 0.3274 4,843,563 JAGRWK000000000
2a3017t1 MSSA 30 66,082 108 2,764,440 114.524 0.3274 4,269,372 JAGRWJ000000000
2a3037t1 MSSA 109 53,182 86 2,717,649 145.335 0.3269 5,265,909 JAGRWI000000000
2a3067n1 MSSA 15 50,823 99 2,684,656 103.896 0.3274 3,786,964 JAGRWH000000000
2a4019t1 MSSA 5 61,501 83 2,667,243 104.215 0.3281 4,072,000 JAGRWG000000000
2a4022t1 MSSA 4234 78,283 84 2,739,662 158.357 0.328 6,223,001 JAGRWF000000000
2a4023n1 MSSA 30 65,350 119 2,810,922 107.137 0.3274 4,049,446 JAGRWE000000000
2a4023p1 MSSA 30 65,350 118 2,811,110 121.371 0.3275 4,563,129 JAGRWD000000000
2a4023t1 MSSA 30 85,855 84 2,828,195 486.489 0.3273 9,146,412 JAGRWC000000000
2a4024n1 MSSA 5 84,809 78 2,778,721 245.289 0.3271 9,179,810 JAGRWB000000000
2a4026n1 MSSA 30 101,596 59 2,833,877 560.695 0.3273 10,541,369 JAGRWA000000000
2a4033n1 MSSA U 7,486 603 2,694,337 25.919 0.3276 999,908 JAGRVZ000000000
2a4034n1 MSSA 6 112,046 62 2,798,572 645.84 0.3275 11,997,034 JAGRVY000000000
2a4039t1 MSSA 97 49,252 92 2,691,456 127.338 0.3273 4,626,272 JAGRVX000000000
2a4042n1 MSSA 30 65,287 133 2,797,542 109.999 0.329 4,210,149 JAGRVW000000000
2a4047n1 MSSA 8 145,241 59 2,714,836 709.128 0.3263 12,936,127 JAGRVV000000000
2a4060n1 MSSA 30d 66,081 99 2,758,104 124.841 0.3275 4,590,729 JAGRVU000000000
2a4060p1 MSSA 30d 65,237 112 2,794,717 99.698 0.3277 3,753,463 JAGRVT000000000
2a4060t1 MSSA 30d 65,237 111 2,795,489 123.422 0.3277 4,660,746 JAGRVS000000000
2a4064n1 MSSA 8c,d 46,659 110 2,709,980 23.515 0.3314 992,389 JAGRVR000000000
2a5044t1 MSSA 5 72,413 79 2,711,121 77.622 0.3272 2,830,095 JAGRVQ000000000
2a5058n1 MSSA 15c,d 8,147 559 2,647,664 21.36 0.3269 795,963 JAGRVP000000000
2a5062p1 MSSA 97 49,252 91 2,689,012 130.171 0.3274 4,694,918 JAGRVO000000000
2a5062t1 MSSA 97 48,945 97 2,689,173 98.019 0.3274 3,584,907 JAGRVN000000000
2a5064n1 MSSA 5 78,282 83 2,696,476 285.543 0.3276 10,285,666 JAGRVM000000000
2a5066n1 MSSA 5d 72,401 82 2,689,836 75.379 0.3305 3,126,770 JAGRVL000000000
2a5067n1 MSSA 45 82,767 67 2,684,802 31.373 0.3305 1,280,727 JAGRVK000000000
2a5067t1 MSSA 45 17,272 257 2,680,081 22.812 0.3277 893,379 JAGRVJ000000000
2b2003t1 MSSA 5d 75,537 81 2,717,214 108.973 0.327 3,944,772 JAGRVI000000000
2b2004t1 MSSA 30 49,583 144 2,775,085 26.806 0.3326 1,435,359 JAGRVH000000000
2b2015n1 MSSA 30 65,287 114 2,812,352 88.929 0.3274 3,386,929 JAGRVG000000000
2b2015t1 MSSA 5 79,876 83 2,729,458 132.229 0.3269 4,831,563 JAGRVF000000000
2b2024t1 MSSA 30 108,461 63 2,795,850 495.985 0.3272 9,194,168 JAGRVE000000000
2b2027n1 MSSA 6 80,528 85 2,703,882 107.351 0.3281 4,548,896 JAGRVD000000000
2b2027p1 MSSA 6 82,878 88 2,702,738 129.609 0.3272 4,679,989 JAGRVC000000000
2b2027t1 MSSA 6 70,596 87 2,702,646 119.361 0.3271 4,333,009 JAGRVB000000000
2b2036t1 MSSA U 77,767 80 2,685,105 40.066 0.3286 1,720,471 JAGRVA000000000
2b2037t1 MSSA 15 41,150 119 2,641,280 30.562 0.3293 1,358,863 JAGRUZ000000000
2b2039n1 MSSA 5d 88,186 80 2,709,869 130.281 0.3273 4,933,848 JAGRUY000000000
2b2041t1 MSSA 291 50,411 99 2,690,148 26.866 0.3318 1,326,414 JAGRUX000000000
2b2042t1 MSSA 188 74,109 77 2,696,551 348.13 0.3272 12,530,947 JAGRUW000000000
2b2044n1 MSSA 5 14,293 334 2,686,667 23.799 0.3266 864,275 JAGRUV000000000
2b2044p1 MSSA 5 62,109 84 2,697,345 162.483 0.3271 6,135,231 JAGRUU000000000
2b2044t1 MSSA 5 61,502 85 2,693,572 42.598 0.3279 1,584,996 JAGRUT000000000
2b2045n1 MSSA 6 63,783 88 2,757,627 132.062 0.3274 4,871,947 JAGRUS000000000
2b2050p1 MSSA 582 61,484 104 2,683,757 46.385 0.3287 2,192,845 JAGRUR000000000
2b2050t1 MSSA 582 109,343 53 2,700,985 757.844 0.3274 13,594,931 JAGRUQ000000000
2b2054t1 MSSA 87 67,173 90 2,690,298 186.92 0.3277 6,711,788 JAGRUP000000000
2b2056n1 MSSA 27 74,666 76 2,693,190 156.334 0.3269 5,676,539 JAGRUO000000000
2b2057t1 MSSA 398 71,326 86 2,692,776 103.615 0.3285 3,724,537 JAGRUN000000000
2b2058t1 MSSA 45 45,685 122 2,695,612 18.384 0.3372 907,536 JAGRUM000000000
2b2068t1 MSSA 97 49,252 96 2,689,283 112.84 0.3275 4,156,542 JAGRUL000000000
2b2071n1 MSSA 5 72,413 91 2,771,743 140.065 0.3271 5,180,223 JAGRUK000000000
2b3002t1 MSSA 8 88,190 80 2,752,615 141.534 0.3271 5,214,623 JAGRUJ000000000
2b3005t1 MSSA 45 83,096 62 2,659,432 141.283 0.3284 5,063,498 JAGRUI000000000
2b3015n1 MSSA 45 62,499 75 2,720,112 143.28 0.3284 5,192,706 JAGRUH000000000
2b3020t1 MSSA 8 59,267 99 2,721,444 53.859 0.327 2,178,330 JAGRUG000000000
2b3028t1 IV(2B) 5 55,008 89 2,770,872 31.635 0.3299 1,587,011 JAGRUF000000000
2b3034n1 MSSA 5 72,469 88 2,746,936 150.28 0.3279 5,513,845 JAGRUE000000000
2b3034t1 MSSA 5d 14,848 345 2,740,670 21.742 0.3272 837,284 JAGRUD000000000
2b3045n1 MSSA 45 62,492 81 2,778,381 138.767 0.3291 5,642,311 JAGRUC000000000
2b3045t1 MSSA 45 72,175 75 2,694,988 27.714 0.3326 1,080,157 JAGRUB000000000
2b3048n1 MSSA 30 65,917 94 2,799,166 136.285 0.3272 5,093,361 JAGRUA000000000
2b3048t1 MSSA 30 65,917 94 2,797,777 153.266 0.3271 5,791,938 JAGRTZ000000000
2b3049t1 MSSA 4302 8,205 577 2,691,828 13.78 0.3275 898,469 JAGRTY000000000
2b3067n1 MSSA U 171,989 45 2,725,736 505.288 0.3278 9,121,432 JAGRTX000000000
2b3070n1 MSSA 15c,d 51,967 104 2,662,144 140.3 0.3269 5,029,884 JAGRTW000000000
2b3070p1 MSSA 15c,d 55,659 101 2,661,648 122.61 0.327 4,364,407 JAGRTV000000000
2b3070t1 MSSA 15c,d 55,633 104 2,660,629 120.194 0.327 4,367,431 JAGRTU000000000
2b3074n1 MSSA 30d 8,211 558 2,792,658 11.183 0.3269 602,805 JAGRTT000000000
2b3074t1 MSSA 30 53,121 137 2,839,270 46.81 0.3335 2,404,170 JAGRTS000000000
2b4022n1 MSSA 5 72,469 88 2,746,346 127.745 0.3281 4,721,229 JAGRTR000000000
2b4022t1 MSSA 97 48,755 98 2,691,791 101.319 0.3293 4,067,469 JAGRTQ000000000
2b4024n1 MSSA 188 73,065 88 2,700,452 119.163 0.3271 4,323,271 JAGRTP000000000
2b4024t1 MSSA 188 69,232 86 2,700,751 125.062 0.3271 4,516,234 JAGRTO000000000
2b4027n1 MSSA 121 65,074 89 2,776,827 142.093 0.3276 5,332,504 JAGRTN000000000
2b4027t1 MSSA 121 52,515 89 2,777,144 114.892 0.3276 4,266,895 JAGRTM000000000
2b4034p1 MSSA 6 71,551 101 2,781,861 54.936 0.3285 2,513,929 JAGRTL000000000
2b4034t1 MSSA 5d 70,571 83 2,688,692 59.111 0.3321 2,358,983 JAGRTK000000000
2b4042t1 MSSA 45 23,425 211 2,761,436 17.722 0.3294 838,633 JAGRTJ000000000
2b4047n1 MSSA 30 61,920 100 2,819,896 238.065 0.3276 8,979,682 JAGRTI000000000
2b4049p1 MSSA 188 75,493 81 2,703,129 159.8 0.3275 7,035,277 JAGRTH000000000
2b5018n1 MSSA 6 62,625 114 2,771,464 117.266 0.3277 4,356,217 JAGRTG000000000
2b5066n1 MSSA 30 66,929 89 2,777,231 83.516 0.3286 3,419,491 JAGRTF000000000
2c3015n1 MSSA 30 61,920 119 2,823,029 135.415 0.3277 5,124,348 JAGRTE000000000
2c3025n1 MSSA 30 61,993 117 2,813,001 115.522 0.3275 4,386,941 JAGRTD000000000
2c3025t1 MSSA 30 61,993 120 2,812,900 100.235 0.3274 3,891,931 JAGRTC000000000
2c3030n1 MSSA 1821 53,240 117 2,724,369 136.603 0.3256 4,973,804 JAGRTB000000000
2c3041t1 MSSA 8 52,751 87 2,787,640 90.25 0.3268 3,434,811 JAGRTA000000000
2c3057p1 MSSA 106 80,824 87 2,738,220 142.275 0.3277 5,250,575 JAGRSZ000000000
2c4024n1 MSSAc 944 99,112 57 2,745,750 136.994 0.3268 5,005,694 JAGRSY000000000
2c4024t1 MSSAc 944 99,671 55 2,745,833 137.143 0.3268 5,006,024 JAGRSX000000000
2c4027n1 MSSA 30 62,983 111 2,774,672 102.927 0.3275 3,859,238 JAGRSW000000000
2c4027t1 MSSA 30 65,287 110 2,775,568 145.036 0.3275 5,383,842 JAGRSV000000000
2c4042t1 MSSA 45 63,886 84 2,782,623 102.745 0.3283 3,897,755 JAGRSU000000000
2c4044n1 MSSA 97 50,474 92 2,686,005 132.317 0.3275 4,829,497 JAGRST000000000
2c4064t1 MSSA 188 55,148 109 2,791,340 59.428 0.3277 2,485,190 JAGRSS000000000
2c5016t1 MSSA 45d 72,744 66 2,723,492 40.083 0.3285 1,458,565 JAGRSR000000000
2c5053n1 MSSA 182d 207,252 47 2,784,661 437.821 0.3268 8,103,136 JAGRSQ000000000
2c5053p1 MSSAc 182d 87,946 85 2,796,278 194.882 0.3267 7,266,336 JAGRSP000000000
2c5058n1 MSSAc 182d 97,369 56 2,771,715 109.234 0.327 4,037,138 JAGRSO000000000
2c5062n1 MSSA 8 86,210 80 2,761,633 114.358 0.327 4,236,363 JAGRSN000000000
2c5062t1 MSSA 8 86,210 76 2,760,480 130.597 0.327 4,864,229 JAGRSM000000000
2c6023n1 MSSA 5 62,107 79 2,709,038 144.606 0.3282 5,226,099 JAGRSL000000000
2c6023p1 MSSA 5 62,107 79 2,709,408 124.925 0.3282 4,523,923 JAGRSK000000000
2c6027n1 MSSA 20 55,344 96 2,710,726 116.982 0.3271 4,245,848 JAGRSJ000000000
2d4008n1 MSSA 30d 59,006 113 2,825,854 133.957 0.3276 5,051,298 JAGRSI000000000
2d4019n1 MSSA 5 72,525 82 2,668,760 144.552 0.3277 5,219,833 JAGRSH000000000
2d4019t1 MSSA 5 106,868 51 2,710,442 402.459 0.327 7,215,947 JAGRSG000000000
2d4026p1 MSSA 582 48,670 113 2,712,976 146.263 0.3268 5,336,331 JAGRSF000000000
2d4026t1 MSSA 8 86,471 75 2,716,950 122.055 0.3267 4,436,880 JAGRSE000000000
2d4044n1 MSSA 45 72,743 65 2,655,305 164.239 0.3281 5,812,401 JAGRSD000000000
2d4047t1 MSSA 8 36,286 158 2,749,649 22.197 0.334 920,513 JAGRSC000000000
2d4064t1 MSSA 121 50,853 109 2,714,807 21.989 0.3284 1,039,925 JAGRSB000000000
2d4067n1 MSSA 97 48,938 97 2,690,260 43.313 0.3341 1,699,501 JAGRSA000000000
2d4072n1 MSSA 30 66,076 87 2,726,537 206.714 0.3275 7,546,788 JAGRRZ000000000
2d5017n1 MSSA 15 72,774 68 2,754,631 94.439 0.3279 3,519,597 JAGRRY000000000
2d5044n1 MSSA 97 44,317 107 2,633,073 27.209 0.3311 1,449,531 JAGRRX000000000
2d5058n1 MSSA 508 76,890 69 2,706,767 130.345 0.3279 4,710,403 JAGRRW000000000
2d5058t1 MSSA 508 75,567 71 2,705,362 46.968 0.3308 1,952,900 JAGRRV000000000
2d5066t1 MSSA 30 65,350 97 2,821,246 117.842 0.3276 4,484,517 JAGRRU000000000
2e5017n1 MSSA 15 50,905 116 2,722,037 123.819 0.3272 4,540,994 JAGRRT000000000
2e5018t1 MSSA 25c,d 87,659 71 2,705,734 138.923 0.3269 5,016,178 JAGRRS000000000
2e5053n1 MSSA 30 52,179 134 2,776,357 29.303 0.3298 1,397,474 JAGRRR000000000
2e5053p1 MSSA 30 87,946 85 2,796,278 554.642 0.3272 10,281,371 JAGRRQ000000000
2e5053t1 MSSA 30 52,923 138 2,814,956 30.356 0.3306 1,652,949 JAGRRP000000000
2e5062n1 MSSA 30 63,699 88 2,767,914 102.402 0.3276 3,846,202 JAGRRO000000000
2e6023n1 MSSA 72 83,834 76 2,660,285 393.925 0.3274 14,017,959 JAGRRN000000000
2e6027t1 MSSA U 60,584 78 2,754,672 110.934 0.3276 4,081,324 JAGRRM000000000
2f6027n1 MSSA 6 62,626 90 2,698,531 116.987 0.3273 4,256,944 JAGRRL000000000
A MSSA 30 110,216 83 2,782,411 149.833 0.3276 6,177,316 JAGRRK000000000
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a

For each isolate, the individual person is indicated by the first 6 characters, and the source is indicated by n (nares), p (palm), or t (throat) as the 8th character.

b

U, unknown.

c

Alleles with less than 100% coverages found.

d

Alleles with less than 100% identity found.

Data availability.

The genome sequences are available in GenBank under BioProject accession no. PRJNA660486.

ACKNOWLEDGMENTS

This work was supported by the NAU Southwest Health Equities Research Collaborative, which is funded by the National Institute on Minority Health and Health Disparities at the National Institutes of Health (U54MD012388). Support was also provided by the National Institute of Allergy and Infectious Diseases at the National Institutes of Health (R15AI156771). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Contributor Information

Talima Pearson, Email: talima.pearson@nau.edu.

Steven R. Gill, University of Rochester School of Medicine and Dentistry

REFERENCES

  • 1.Chambers HF, DeLeo FR. 2009. Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat Rev Microbiol 7:629–641. doi: 10.1038/nrmicro2200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Williams REO. 1963. Healthy carriage of Staphylococcus aureus: its prevalence and importance. Bacteriol Rev 27:56–71. doi: 10.1128/br.27.1.56-71.1963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Kluytmans J, van Belkum A, Verbrugh H. 1997. Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks. Clin Microbiol Rev 10:505–520. doi: 10.1128/CMR.10.3.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Wertheim HFL, Melles DC, Vos MC, van Leeuwen W, van Belkum A, Verbrugh HA, Nouwen JL. 2005. The role of nasal carriage in Staphylococcus aureus infections. Lancet Infect Dis 5:751–762. doi: 10.1016/S1473-3099(05)70295-4. [DOI] [PubMed] [Google Scholar]
  • 5.von Eiff C, Becker K, Machka K, Stammer H, Peters G. 2001. Nasal carriage as a source of Staphylococcus aureus bacteremia. N Engl J Med 344:11–16. doi: 10.1056/NEJM200101043440102. [DOI] [PubMed] [Google Scholar]
  • 6.Lina G, Piemont Y, Godail-Gamot F, Bes M, Peter M-O, Gauduchon V, Vandenesch F, Etienne J. 1999. Involvement of Panton-Valentine leukocidin–producing Staphylococcus aureus in primary skin infections and pneumonia. Clin Infect Dis 29:1128–1132. doi: 10.1086/313461. [DOI] [PubMed] [Google Scholar]
  • 7.Pannaraj PS, Hulten KG, Gonzalez BE, MasonEO, Jr, Kaplan SL. 2006. Infective pyomyositis and myositis in children in the era of community‐acquired, methicillin‐resistant Staphylococcus aureus infection. Clin Infect Dis 43:953–960. doi: 10.1086/507637. [DOI] [PubMed] [Google Scholar]
  • 8.Gorak EJ, Yamada SM, Brown JD. 1999. Community-acquired methicillin-resistant Staphylococcus aureus in hospitalized adults and children without known risk factors. Clin Infect Dis 29:797–800. doi: 10.1086/520437. [DOI] [PubMed] [Google Scholar]
  • 9.Gonzalez BE, Rueda AM, ShelburneSA, III, Musher DM, Hamill RJ, Hulten KG. 2006. Community-associated strains of methicillin-resistant Staphylococccus aureus as the cause of healthcare-associated infection. Infect Control Hosp Epidemiol 27:1051–1056. doi: 10.1086/507923. [DOI] [PubMed] [Google Scholar]
  • 10.Kennedy LA, Gill JA, Schultz ME, Irmler M, Gordin FM. 2010. Inside-out: the changing epidemiology of methicillin-resistant Staphylococcus aureus. Infect Control Hosp Epidemiol 31:983–985. doi: 10.1086/655837. [DOI] [PubMed] [Google Scholar]
  • 11.David MZ, Cadilla A, Boyle-Vavra S, Daum RS. 2014. Replacement of HA-MRSA by CA-MRSA infections at an academic medical center in the Midwestern United States, 2004–5 to 2008. PLoS One 9:e92760. doi: 10.1371/journal.pone.0092760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Gorwitz RJ, Kruszon‐Moran D, McAllister SK, McQuillan G, McDougal LK, Fosheim GE, Jensen BJ, Killgore G, Tenover FC, Kuehnert MJ. 2008. Changes in the prevalence of nasal colonization with Staphylococcus aureus in the United States, 2001–2004. J Infect Dis 197:1226–1234. doi: 10.1086/533494. [DOI] [PubMed] [Google Scholar]
  • 13.Wertheim HFL, Vos MC, Ott A, van Belkum A, Voss A, Kluytmans JAJW, van Keulen PHJ, Vandenbroucke-Grauls CMJE, Meester MHM, Verbrugh HA. 2004. Risk and outcome of nosocomial Staphylococcus aureus bacteraemia in nasal carriers versus non-carriers. Lancet 364:703–705. doi: 10.1016/S0140-6736(04)16897-9. [DOI] [PubMed] [Google Scholar]
  • 14.Kluytmans JAJW, Mouton JW, Ijzerman EPF, Vandenbroucke-Grauls CMJE, Maat AWPM, Wagenvoort JHT, Verbrugh HA. 1995. Nasal carriage of Staphylococcus aureus as a major risk factor for wound infections after cardiac surgery. J Infect Dis 171:216–219. doi: 10.1093/infdis/171.1.216. [DOI] [PubMed] [Google Scholar]
  • 15.Kalmeijer MD, van Nieuwland-Bollen E, Bogaers-Hofman D, de Baere GAJ, Kluytmans JAJW. 2000. Nasal carriage of Staphylococcus aureus: is a major risk factor for surgical-site infections in orthopedic surgery. Infect Control Hosp Epidemiol 21:319–323. doi: 10.1086/501763. [DOI] [PubMed] [Google Scholar]
  • 16.Huang SS, Platt R. 2003. Risk of methicillin‐resistant Staphylococcus aureus infection after previous infection or colonization. Clin Infect Dis 36:281–285. doi: 10.1086/345955. [DOI] [PubMed] [Google Scholar]
  • 17.GrahamPL, III, Lin SX, Larson EL. 2006. A US population-based survey of Staphylococcus aureus colonization. Ann Intern Med 144:318–325. doi: 10.7326/0003-4819-144-5-200603070-00006. [DOI] [PubMed] [Google Scholar]
  • 18.Barger SD, Lininger MR, TrotterRT, Jr, Wayment HA, Mbegbu M, Kyman S, Pearson T. 2020. Educational attainment and Staphylococcus aureus colonization in a Hispanic border community: testing fundamental cause theory. mSphere 5:e00623-20. doi: 10.1128/mSphere.00623-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Pearson T, Barger SD, Lininger M, Wayment H, Hepp C, Villa F, Tucker-Morgan K, Kyman S, Cabrera M, Hurtado K, Menard A, Fulbright K, Wood C, Mbegbu M, Zambrano Y, Fletcher A, Medina-Rodriguez S, Manone M, Aguirre A, Milner T, TrotterRT, Jr.. 2019. Health disparities in Staphylococcus aureus transmission and carriage in a border region of the United States based on cultural differences in social relationships: protocol for a survey study. JMIR Res Protoc 8:e14853. doi: 10.2196/14853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Bushnell B. 2014. BBMap. https://sourceforge.net/projects/bbmap/.
  • 22.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]
  • 23.Center for Genomic Epidemiology. http://www.genomicepidemiology.org/.

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome sequences are available in GenBank under BioProject accession no. PRJNA660486.

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