Thirty Clostridioides difficile isolates collected in 2016 through the Centers for Disease Control and Prevention Emerging Infections Program were selected for reference antimicrobial susceptibility testing and whole-genome sequencing. Here, we present the genetic characteristics of these isolates and announce their availability in the CDC & FDA Antibiotic Resistance Isolate Bank.
ABSTRACT
Thirty Clostridioides difficile isolates collected in 2016 through the Centers for Disease Control and Prevention Emerging Infections Program were selected for reference antimicrobial susceptibility testing and whole-genome sequencing. Here, we present the genetic characteristics of these isolates and announce their availability in the CDC & FDA Antibiotic Resistance Isolate Bank.
ANNOUNCEMENT
Clostridioides difficile infection (CDI) is among the most common health care-associated infections in the United States, linked to approximately 30,000 deaths annually (1). Antibiotic exposure is a risk factor for CDI, and resistance to commonly used antimicrobials may contribute to the evolving epidemiology of C. difficile (1). The Centers for Disease Control and Prevention (CDC) performs surveillance through the Emerging Infections Program (EIP) to monitor CDI in the United States (https://www.cdc.gov/hai/eip/cdiff-tracking.html). We announce a panel of 30 community- and health care-associated EIP CDI isolates, representing the 10 most prevalent PCR ribotypes (RTs) collected in 2016, available through the CDC & FDA Antibiotic Resistance Isolate Bank (AR Isolate Bank, https://wwwn.cdc.gov/ARIsolateBank/).
Strain typing was performed using a standardized high-resolution capillary gel-based PCR ribotyping protocol (2) with an in-house curated standard profile library and 100% similarity threshold (BioNumerics 6.6.11; Applied Maths). Multiplex real-time PCR (3) was used to detect genes encoding cytotoxins A and B (tcdA, tcdB) and binary toxin (cdtA, cdtB). Deletions in anti-sigma factor tcdC were assessed by PCR fragment (3) and whole-genome sequencing (WGS) analysis. For WGS, genomic DNA was extracted from colonies cultured overnight on CDC anaerobic blood agar with vitamin K, hemin, and 5% sheep blood at 37°C under anaerobic conditions from 10% skim milk glycerol stocks. DNA was isolated using the Promega Maxwell 16-cell low elution volume DNA purification kit and the Maxwell 16 MDx instrument (Madison, WI). DNA was sheared using the Covaris ME220 focused ultrasonicator (Woburn, MA), and indexed libraries were prepared using the NuGEN Ovation ultralow system version 2 assay kit (San Carlos, CA) and the PerkinElmer Zephyr G3 next-generation sequencing (NGS) workstation (Waltham, MA). Libraries were analyzed using the standard-sensitivity NGS fragment analysis kit and fragment analyzer system (Agilent Technologies, Santa Clara, CA). Sequencing was performed using the MiSeq reagent kit version 2 (500 cycles) and MiSeq system (Illumina, San Diego, CA), generating 2 × 250-bp paired-end reads. Sequence data were analyzed using the QuAISAR-H pipeline (https://github.com/DHQP/QuAISAR_singularity, version 1.0.2, default settings, accessed May 2019), including removal of phiX reads using BBDuk (BBMap version 37.87, sourceforge.net/projects/bbmap/), removal of adaptors and read trimming using Trimmomatic version 0.36 (4), and de novo assembly using SPAdes version 3.13.0 (5). Sequence types were assigned using the software package MLST version 2.16 (6) and the pubMLST C. difficile multilocus sequence typing scheme (7). Antimicrobial resistance (AR) genes were identified using a nonredundant combined database of the ResFinder (last updated 1 May 2019 and accessed on 20 May 2019) and ARG-ANNOT (last updated in May 2018 and accessed on 20 May 2019) AR databases; 98% sequence identity and 90% sequence coverage were used. A full description of custom scripts and publicly available tools and versions utilized by QuAISAR-H is available at the GitHub site. Assembled genomes were submitted to the NCBI Prokaryotic Genome Annotation Pipeline for annotation. The Clinical and Laboratory Standards Institute (CLSI) agar dilution method (8) was used to determine MICs for clindamycin, ceftriaxone, meropenem, metronidazole, moxifloxacin, and vancomycin. The results are summarized in Table 1.
TABLE 1.
Molecular characteristics and antimicrobial susceptibility profiles for C. difficile isolates in the AR Isolate Banka
| Isolate no. | BioSample no. | RT | MLST | Toxin profile | tcdC mutation(s)b | MIC (μg/ml) for: |
Mutation and/or gene(s) identified by ResFinder and ARG-ANNOTc | No. of reads | Genome size (bp) | No. of contigs | N50 (bp) | GC content (%) | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CRO | CLI | MEM | MTZ | MXF | VAN | ||||||||||||
| AR-1067 | SAMN13029148 | 027 | ST1 | tcdA/B+, cdtA/B+ | 18bp, Δ117 | 64 | >16 | 2 | 1 | >8 | 2 | cfrC, dfrf, ermB, tetM, vanG, vanR, vanS, vanT, vanZ, gyrA (Thr82Ile) | 1,232,466 | 4,243,914 | 301 | 24,052 | 28.7 |
| AR-1068 | SAMN13029149 | 056 | ST34 | tcdA/B+, cdtA/B– | WT | 64 | 4 | 1 | 0.25 | 1 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,520,666 | 4,140,240 | 323 | 27,508 | 28.4 |
| AR-1069 | SAMN13029150 | 015 | ST10 | tcdA/B+, cdtA/B– | 18bp | 32 | 2 | 2 | 0.5 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,155,646 | 4,340,988 | 57 | 227,612 | 28.2 |
| AR-1070 | SAMN13029151 | 002 | ST8 | tcdA/B+, cdtA/B– | WT | 32 | 4 | 1 | 0.25 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,484,766 | 4,272,556 | 231 | 41,015 | 28.4 |
| AR-1071 | SAMN13029152 | 027 | ST1 | tcdA/B+, cdtA/B+ | 18bp, Δ117 | 64 | 8 | 2 | 1 | 8 | 0.5 | vanG, vanR, vanS, vanT, vanZ1, gyrA (Thr82Ile) | 1,409,698 | 4,181,997 | 267 | 34,074 | 28.6 |
| AR-1072 | SAMN13029153 | 027 | ST1 | tcdA/B+, cdtA/B+ | 18bp, Δ117 | 64 | >16 | 2 | 1 | >8 | 2 | cfrC, ermB, vanG, vanR, vanS, vanT, vanZ1, gyrA (Thr82Ile) | 1,826,800 | 4,172,909 | 222 | 38,400 | 28.6 |
| AR-1073 | SAMN13029154 | 020 | ST2 | tcdA/B+, cdtA/B– | WT | 32 | 4 | 2 | 0.5 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,579,584 | 4,177,999 | 117 | 103,880 | 28.6 |
| AR-1074 | SAMN13029155 | 002 | ST8 | tcdA/B+, cdtA/B– | WT | 32 | 8 | 2 | 0.5 | 8 | 0.5 | vanG, vanR, vanS, vanT, vanZ1, gyrA (Thr82Ile) | 1,599,852 | 4,125,816 | 269 | 37,978 | 28.2 |
| AR-1075 | SAMN13029156 | 019 | ST67 | tcdA/B+, cdtA/B+ | WT | 32 | 4 | 2 | 0.5 | 1 | 0.5 | vanZ1 | 1,604,652 | 4,207,539 | 53 | 163,554 | 28.5 |
| AR-1076 | SAMN13029157 | 027 | ST1 | tcdA/B+, cdtA/B+ | 18bp, Δ117 | 64 | 8 | 4 | 0.25 | >8 | 2 | vanG, vanR, vanS, vanT, vanZ1, gyrA (Thr82Ile) | 1,871,410 | 4,107,095 | 47 | 174,380 | 28.5 |
| AR-1077 | SAMN13029158 | 078 | ST11 | tcdA/B+, cdtA/B+ | 39bp, C184T | 32 | 4 | 1 | 0.25 | 1 | 0.5 | ant(6)-ia, spw, tetM | 1,451,232 | 3,918,602 | 121 | 64,610 | 28.5 |
| AR-1078 | SAMN13029159 | 106 | ST42 | tcdA/B+, cdtA/B– | WT | 32 | 8 | 2 | 0.5 | 2 | 1 | vanG, vanR, vanS, vanT, vanZ1 | 1,432,018 | 4,046,102 | 97 | 78,397 | 28.5 |
| AR-1079 | SAMN13029160 | 056 | ST34 | tcdA/B+, cdtA/B– | WT | 32 | 2 | 2 | 0.25 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,540,522 | 4,177,894 | 144 | 70,736 | 28.5 |
| AR-1080 | SAMN13029161 | 020 | ST2 | tcdA/B+, cdtA/B– | WT | 16 | 8 | 1 | 0.25 | 2 | 0.5 | vanG, vanR, vanS, vanT | 1,326,024 | 4,145,293 | 256 | 28,424 | 28.7 |
| AR-1081 | SAMN13029162 | 014 | ST110 | tcdA/B+, cdtA/B– | WT | 32 | 2 | 1 | 0.25 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,596,282 | 4,091,127 | 79 | 125,940 | 28.6 |
| AR-1082 | SAMN13029163 | 054 | ST43 | tcdA/B+, cdtA/B– | WT | 32 | 1 | 2 | 0.5 | 2 | 0.5 | vanG, vanR, vanS, vanT | 1,606,932 | 4,187,731 | 92 | 100,411 | 28.3 |
| AR-1083 | SAMN13029164 | 078 | ST11 | tcdA/B+, cdtA/B+ | 39bp, C184T | 32 | 4 | 1 | 0.25 | 1 | 0.5 | ant(6)-ia, ant(6)-ib, spw, tetM, tet44 | 1,076,082 | 3,964,561 | 153 | 56,789 | 28.5 |
| AR-1084 | SAMN13029165 | 002 | ST8 | tcdA/B+, cdtA/B– | WT | 32 | 2 | 1 | 0.25 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,887,930 | 4,039,601 | 47 | 171,828 | 28.2 |
| AR-1085 | SAMN13029166 | 106 | ST42 | tcdA/B+, cdtA/B– | WT | 64 | 8 | 2 | 0.25 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,514,658 | 4,119,511 | 223 | 42,869 | 28.5 |
| AR-1086 | SAMN13029167 | 015 | ST10 | tcdA/B+, cdtA/B– | 18bp | 32 | 4 | 1 | 0.25 | 1 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,520,910 | 4,319,533 | 122 | 73,649 | 28.3 |
| AR-1087 | SAMN13029168 | 106 | ST42 | tcdA/B+, cdtA/B– | WT | 32 | 2 | 1 | 0.5 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,670,654 | 4,022,519 | 63 | 151,217 | 28.4 |
| AR-1088 | SAMN13029169 | 054 | ST43 | tcdA/B+, cdtA/B– | WT | 32 | 8 | 2 | 0.25 | 1 | 0.5 | vanG, vanR, vanS, vanT | 1,178,682 | 4,094,056 | 100 | 78,787 | 28.3 |
| AR-1089 | SAMN13029170 | 106 | ST42 | tcdA/B+, cdtA/B– | WT | 64 | >16 | 2 | 0.5 | 2 | 0.5 | ermB, vanG, vanR, vanS, vanT, vanZ1 | 2,200,272 | 4,081,462 | 51 | 154,757 | 28.5 |
| AR-1090 | SAMN13029171 | 014 | ST14 | tcdA/B+, cdtA/B– | WT | 32 | >16 | 2 | 0.5 | 2 | 0.5 | ermB, vanG, vanR, vanS, vanT, vanZ1 | 2,200,528 | 4,155,416 | 68 | 119,271 | 28.6 |
| AR-1091 | SAMN13029172 | 014 | ST2 | tcdA/B+, cdtA/B– | WT | 64 | 4 | 2 | 0.5 | 2 | 0.5 | vanG, vanR, vanS, vanT | 2,044,134 | 4,141,305 | 59 | 150,646 | 28.6 |
| AR-1092 | SAMN13029173 | 027 | ST1 | tcdA/B+, cdtA/B+ | 18bp, Δ117 | 64 | >16 | 4 | 1 | >8 | 1 | ermB, vanG, vanR, vanS, vanT, vanZ1, gyrA (Thr82Ile) | 1,720,350 | 4,134,672 | 64 | 122,158 | 28.6 |
| AR-1093 | SAMN13029174 | 106 | ST42 | tcdA/B+, cdtA/B– | WT | 64 | 4 | 2 | 0.5 | 2 | 0.5 | vanG, vanR, vanS, vanT, vanZ1 | 1,201,366 | 4,071,812 | 146 | 62,561 | 28.5 |
| AR-1094 | SAMN13029175 | 019 | ST67 | tcdA/B+, cdtA/B+ | WT | 32 | 4 | 1 | 0.25 | 1 | 0.5 | vanZ1 | 1,935,084 | 4,139,106 | 123 | 74,476 | 28.4 |
| AR-1095 | SAMN13029176 | 027 | ST1 | tcdA/B+, cdtA/B+ | 18bp, Δ117 | 128 | 4 | 2 | 0.5 | >8 | 2 | vanG, vanR, vanS, vanT, vanZ1, gyrA (Thr82Ile) | 925,204 | 4,103,471 | 109 | 91,825 | 28.5 |
| AR-1096 | SAMN13029177 | 020 | ST2 | tcdA/B+, cdtA/B– | WT | 64 | 8 | 2 | 0.5 | 2 | 0.5 | vanG, vanR, vanS, vanT | 1,946,384 | 4,095,571 | 38 | 204,538 | 28.6 |
Abbreviations: CRO, ceftriaxone; CLI, clindamycin; MEM, meropenem; MTZ, metronidazole; MXF, moxifloxacin; VAN, vancomycin; MLST, multilocus sequence type; RT, ribotype; WT, wild type.
tcdC mutations analyzed were Δ117, 18-bp and 39-bp deletions, and the C184T nucleotide point mutation.
The mutations and genes described are for characterization purposes only, and their presence may not predict antimicrobial resistance in C. difficile.
The 10 most prevalent RTs collected in 2016 were 027, 106, 002, 014, 020, 015, 056, 054, 019, and 078. All isolates harbored tcdA and tcdB, and 10/30 (33%) contained cdtA and cdtB. The six RT027 isolates contained an 18-bp deletion and a deletion at nucleotide position 117 in tcdC, resulting in a premature stop codon characteristic of the BI/NAP1/RT027 epidemic strain (9, 10). The two RT078 isolates contained a 39-bp deletion and C184T point mutation in tcdC, resulting in a premature stop codon associated with this hypervirulent ribotype (11).
No isolates displayed elevated MICs to vancomycin based on the CLSI epidemiological cutoff value (wild type, ≤2 μg/ml; non-wild type, ≥4 μg/ml), and all isolates were susceptible to metronidazole (12). No acquired genes conferring resistance to vancomycin or metronidazole were detected. A total of 28 isolates contained genes belonging to the vanG-like gene cluster, which is highly conserved among C. difficile strains, but their presence is not indicative of vancomycin resistance (13). Recently, investigators suggested that mutations in the regulatory genes vanS and vanR may be associated with vancomycin resistance in RT027 isolates (14). No RT027 isolates in this panel contained known mutations in vanS or vanR; however, 3/3 RT002 and 1/3 RT014 (AR-1090) isolates contained the VanS Thr349Ile mutation described by Shen et al. (14) but had a vancomycin MIC of 0.5 μg/ml (Table 1). Five isolates with a clindamycin MIC of >16 μg/ml harbored ermB genes, which are associated with macrolide-lincosamide-streptogramin B resistance (15, 16). Two of these isolates also contained the cfrC gene, which is associated with resistance to phenicols, lincosamides, oxazolidinones, and streptogramins (17, 18). While all isolates contained the wild-type gyrB allele, seven with a moxifloxacin MIC of ≥8 μg/ml harbored an amino acid substitution (Thr82Ile) in the gyrA gene product associated with fluoroquinolone resistance (13).
The “Clostridioides difficile EIP 2016” panel represents the first publicly available resource for highly characterized isolates, and additional panels may be included to provide a growing source of contemporary isolates.
Data availability.
The Clostridioides difficile EIP 2016 panel is available through the CDC & FDA Antibiotic Resistance Isolate Bank (https://wwwn.cdc.gov/ARIsolateBank/). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank, and the first versions are described here. The raw reads were deposited in the Sequence Read Archive (SRA). Assembly and SRA data are available at NCBI under BioProject number PRJNA577141.
ACKNOWLEDGMENTS
Members of the Emerging Infections Program Clostridioides difficile Pathogen Group include Paula Clogher, Christopher Czaja, Ghinwa Dumyati, Scott Fridkin, Dale Gerding, Stacy Holzbauer, Helen Johnston, Amelia Keaton, James Meek, Rebecca Perlmutter, Erin Phipps, Rebecca Pierce, Lucy Wilson, and Lisa Winston. We thank the CDC & FDA Antibiotic Resistance Isolate Bank team members Karlos Crayton, Kenya Enoch, Jennifer Haynie, Justina Ilutsik, Nadine Wilmott, and Brian Yoo for their contributions to the creation of the Clostridioides difficile EIP 2016 panel.
The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention/The Agency for Toxic Substances and Disease Registry. Use of trade names is for identification only and does not imply endorsement by the U.S. Centers for Disease Control and Prevention, the Agency for Toxic Substances and Disease Registry, the Public Health Service, or the U.S. Department of Health and Human Services.
REFERENCES
- 1.McDonald LC, Gerding DN, Johnson S, Bakken JS, Carroll KC, Coffin SE, Dubberke ER, Garey KW, Gould CV, Kelly C, Loo V, Shaklee Sammons J, Sandora TJ, Wilcox MH. 2018. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis 66:987–994. doi: 10.1093/cid/ciy149. [DOI] [PubMed] [Google Scholar]
- 2.Fawley WN, Knetsch CW, MacCannell DR, Harmanus C, Du T, Mulvey MR, Paulick A, Anderson L, Kuijper EJ, Wilcox MH. 2015. Development and validation of an internationally-standardized, high-resolution capillary gel-based electrophoresis PCR-ribotyping protocol for Clostridium difficile. PLoS One 10:e0118150. doi: 10.1371/journal.pone.0118150. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Williams SH, Che X, Paulick A, Guo C, Lee B, Muller D, Uhlemann AC, Lowy FD, Corrigan RM, Lipkin WI. 2018. New York City house mice (Mus musculus) as potential reservoirs for pathogenic bacteria and antimicrobial resistance determinants. mBio 9:e00624-18. doi: 10.1128/mBio.00624-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.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]
- 6.Seemann T. 2016. MLST: scan contig files against PubMLST typing schemes. https://github.com/tseemann/mlst.
- 7.Jolley KA, Bray JE, Maiden MCJ. 2018. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3:124. doi: 10.12688/wellcomeopenres.14826.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.CLSI. 2018. Methods for antimicrobial susceptibility testing of anaerobic bacteria, 9th ed. CLSI standard M11. CLSI, Wayne, PA. [Google Scholar]
- 9.MacCannell DR, Louie TJ, Gregson DB, Laverdiere M, Labbe AC, Laing F, Henwick S. 2006. Molecular analysis of Clostridium difficile PCR ribotype 027 isolates from eastern and western Canada. J Clin Microbiol 44:2147–2152. doi: 10.1128/JCM.02563-05. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.O’Connor JR, Johnson S, Gerding DN. 2009. Clostridium difficile infection caused by the epidemic BI/NAP1/027 strain. Gastroenterology 136:1913–1924. doi: 10.1053/j.gastro.2009.02.073. [DOI] [PubMed] [Google Scholar]
- 11.Goorhuis A, Bakker D, Corver J, Debast SB, Harmanus C, Notermans DW, Bergwerff AA, Dekker FW, Kuijper EJ. 2008. Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078. Clin Infect Dis 47:1162–1170. doi: 10.1086/592257. [DOI] [PubMed] [Google Scholar]
- 12.CLSI. 2020. Performance standards for antimicrobial susceptibility testing, 30th ed. CLSI supplement M100. Clinical and Laboratory Standards Institute, Wayne, PA. [Google Scholar]
- 13.Spigaglia P. 2016. Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection. Ther Adv Infect Dis 3:23–42. doi: 10.1177/2049936115622891. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Shen WJ, Deshpande A, Hevener KE, Endres BT, Garey KW, Palmer KL, Hurdle JG. 2020. Constitutive expression of the cryptic vanGCd operon promotes vancomycin resistance in Clostridioides difficile clinical isolates. J Antimicrob Chemother 75:859–867. doi: 10.1093/jac/dkz513. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Farrow KA, Lyras D, Rood JI. 2001. Genomic analysis of the erythromycin resistance element Tn5398 from Clostridium difficile. Microbiology (Reading) 147:2717–2728. doi: 10.1099/00221287-147-10-2717. [DOI] [PubMed] [Google Scholar]
- 16.Spigaglia P, Carucci V, Barbanti F, Mastrantonio P. 2005. ErmB determinants and Tn916-Like elements in clinical isolates of Clostridium difficile. Antimicrob Agents Chemother 49:2550–2553. doi: 10.1128/AAC.49.6.2550-2553.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Hansen LH, Vester B. 2015. A cfr-like gene from Clostridium difficile confers multiple antibiotic resistance by the same mechanism as the cfr gene. Antimicrob Agents Chemother 59:5841–5843. doi: 10.1128/AAC.01274-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Arias CA, Vallejo M, Reyes J, Panesso D, Moreno J, Castaneda E, Villegas MV, Murray BE, Quinn JP. 2008. Clinical and microbiological aspects of linezolid resistance mediated by the cfr gene encoding a 23S rRNA methyltransferase. J Clin Microbiol 46:892–896. doi: 10.1128/JCM.01886-07. [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
The Clostridioides difficile EIP 2016 panel is available through the CDC & FDA Antibiotic Resistance Isolate Bank (https://wwwn.cdc.gov/ARIsolateBank/). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank, and the first versions are described here. The raw reads were deposited in the Sequence Read Archive (SRA). Assembly and SRA data are available at NCBI under BioProject number PRJNA577141.