Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of nosocomial infections of the bloodstream and urinary tract. Here, we report the draft genome sequences of 48 vancomycin-resistant E. faecium isolates recovered from inpatients exhibiting clinical signs of bacteremia at the University of Arkansas for Medical Sciences (UAMS).
ABSTRACT
Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of nosocomial infections of the bloodstream and urinary tract. Here, we report the draft genome sequences of 48 vancomycin-resistant E. faecium isolates recovered from inpatients exhibiting clinical signs of bacteremia at the University of Arkansas for Medical Sciences (UAMS).
ANNOUNCEMENT
Enterococcus faecium is an opportunistic environmental bacterium with an outstanding adaptive capacity to evolve and transfer antimicrobial-resistant determinants (1). E. faecium can cause persistent infections because of inherent and acquired resistance to common antibiotics, such as ampicillin and vancomycin (2). Vancomycin resistance can be conferred by different acquired gene clusters (vanA, vanB, vanD, vanE, vanG, vanL, vanM, and vanN), with vanA and vanB being the most common (3, 4). Decreasing the intestinal domination of vancomycin-resistant Enterococcus faecium (VREfm) in hospitalized patients and reducing the rate of patient-to-patient transmission are still challenging goals. To better understand the mechanisms of antibiotic resistance and the dynamics of transmission of this species in the hospital setting, we sequenced and analyzed 48 VREfm isolates collected from the University of Arkansas for Medical Sciences (UAMS) Hospital.
The VREfm isolates presented here were identified from positive blood and urine cultures (24 each). Identification and antimicrobial susceptibility tests were performed in the UAMS Clinical Microbiology Laboratory using standard microbiology techniques. More specifically, blood cultures were processed on the BacT/Alert 3D (bioMérieux) system. Positive blood cultures were subcultured on blood agar plates. Isolated colonies were then used for identification and susceptibility testing using the Vitek MS and Vitek 2 systems. Vancomycin resistance was confirmed using Etests (bioMérieux). Urine cultures were processed similarly using blood agar plates for the isolation of colonies. Antimicrobial susceptibility test results were interpreted using the M100 CLSI standards (5). Microbial DNA was extracted from pure growth of VREfm. Isolated colonies on the blood agar plates were picked and resuspended into a DNA/RNA shield collection and lysis tube (Zymo Research, Irvine, CA). Genomic DNA was extracted from the tube using the Quick-DNA fungal/bacterial kit (Zymo Research, Irvine, CA). The purity of extracted DNA was determined using a NanoDrop spectrophotometer by measuring the A260/280 and A260/230 ratios. DNA integrity and quantity were determined using an Agilent 2200 TapeStation and a Qubit 3.0 assay, respectively. Paired-end 150-bp libraries were constructed using the Kapa HyperPlus kit (Roche) with enzymatic fragmentation for 10 min. The resulting genomic libraries of the 48 E. faecium isolates were sequenced using the Illumina NextSeq 550 platform at the University of Arkansas for Medical Sciences Myeloma Center.
Adapters from the reads were trimmed using default parameters of fastp v0.19.5 (6) software, and poor-quality bases were removed using Trimmomatic v0.38 (7) with the following parameters: headcrop, 15; leading, 20; trailing, 20; slidingwindow, 5:20; and minlen, 50. The quality of the pre- and postprocessed reads was analyzed using the FastQC tool v0.11.8 (8). The resulting high-quality reads were assembled de novo using SPAdes v3.13.0 (9) with the “error-correction” and “careful” options; k-mer sizes of 21, 33, 55, and 77; and a minimum contig size of 500 bp. The draft genome sequences were checked for quality using default settings in QUAST v5.0.2 (10).
The genome sequences were submitted for annotation to the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (11) using the default parameters. All 48 isolates were screened for vancomycin resistance genes, verifying the presence of the vanA gene in all genomes in the study.
Data availability.
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers detailed in Table 1. The versions described in this announcement are the first ones. The GenBank and BioSample accession numbers are given in Table 1. Raw sequence data for this study are available at the Sequence Read Archive under accession number PRJNA520878.
TABLE 1.
Assembly metrics and accession numbers for 48 E. faecium isolates
| Isolate name | No. of contigs | Total length (bp) | GC (%) | No. of reads | N50 (bp) | BioSample no. | GenBank accession no. | No. of ORFsa |
|---|---|---|---|---|---|---|---|---|
| UAMSEF_02 | 193 | 2,910,878 | 37.80 | 6,839,636 | 36,818 | SAMN10869073 | SEYV00000000 | 3,046 |
| UAMSEF_03 | 198 | 2,911,646 | 37.80 | 7,114,878 | 35,022 | SAMN10869074 | SEYU00000000 | 3,044 |
| UAMSEF_04 | 204 | 2,909,821 | 37.80 | 4,688,460 | 35,022 | SAMN10869075 | SEYT00000000 | 3,047 |
| UAMSEF_05 | 203 | 2,911,291 | 37.80 | 4,881,024 | 34,261 | SAMN10869076 | SEYS00000000 | 3,054 |
| UAMSEF_06 | 199 | 2,915,048 | 37.80 | 5,499,612 | 35,022 | SAMN10869077 | SEYR00000000 | 3,057 |
| UAMSEF_07 | 200 | 2,921,117 | 37.79 | 5,228,072 | 33,402 | SAMN10869078 | SEYQ00000000 | 3,058 |
| UAMSEF_10 | 204 | 3,029,727 | 37.66 | 6,167,912 | 35,022 | SAMN10869079 | SEYP00000000 | 3,208 |
| UAMSEF_11 | 209 | 3,029,905 | 37.66 | 7,152,790 | 35,022 | SAMN10869080 | SEYO00000000 | 3,209 |
| UAMSEF_12 | 209 | 3,030,170 | 37.66 | 7,191,884 | 35,022 | SAMN10869081 | SEYN00000000 | 3,208 |
| UAMSEF_13 | 208 | 3,031,358 | 37.66 | 5,108,778 | 35,022 | SAMN10869082 | SEYL00000000 | 3,210 |
| UAMSEF_14 | 207 | 3,033,907 | 37.66 | 5,789,340 | 35,022 | SAMN10869083 | SEYK00000000 | 3,228 |
| UAMSEF_15 | 208 | 3,030,699 | 37.66 | 5,022,872 | 34,261 | SAMN10869084 | SEYJ00000000 | 3,218 |
| UAMSEF_16 | 213 | 3,029,394 | 37.66 | 5,993,870 | 34,261 | SAMN10869085 | SEYI00000000 | 3,214 |
| UAMSEF_17 | 219 | 3,036,737 | 37.66 | 6,044,830 | 34,261 | SAMN10869086 | SEYH00000000 | 3,227 |
| UAMSEF_18 | 208 | 3,028,651 | 37.66 | 5,560,272 | 34,261 | SAMN10869087 | SEYG00000000 | 3,212 |
| UAMSEF_19 | 213 | 3,030,152 | 37.66 | 7,403,936 | 34,261 | SAMN10869088 | SEYF00000000 | 3,213 |
| UAMSEF_21 | 198 | 2,891,508 | 37.75 | 6,655,902 | 32,987 | SAMN10869089 | SEYE00000000 | 3,031 |
| UAMSEF_22 | 159 | 2,749,498 | 37.95 | 6,867,326 | 42,992 | SAMN10869090 | SEYD00000000 | 2,857 |
| UAMSEF_23 | 123 | 2,758,039 | 37.96 | 6,408,904 | 53,183 | SAMN10869091 | SEYC00000000 | 2,849 |
| UAMSEF_24 | 40 | 2,770,238 | 38.23 | 7,386,962 | 246,941 | SAMN10869092 | SEYB00000000 | 2,792 |
| UAMSEF_25 | 195 | 2,928,194 | 37.71 | 8,757,500 | 33,213 | SAMN10869093 | SEYA00000000 | 3,068 |
| UAMSEF_26 | 29 | 2,664,140 | 37.94 | 4,900,272 | 136,618 | SAMN10869094 | SEXZ00000000 | 2,721 |
| UAMSEF_27 | 222 | 2,902,431 | 37.71 | 5,726,412 | 31,483 | SAMN10869095 | SEXY00000000 | 3,058 |
| UAMSEF_28 | 172 | 2,739,636 | 37.88 | 6,372,790 | 32,818 | SAMN10869096 | SEXX00000000 | 2,835 |
| UAMSEF_29 | 199 | 2,879,498 | 37.75 | 5,414,500 | 31,547 | SAMN10869097 | SEXW00000000 | 3,036 |
| UAMSEF_30 | 225 | 3,101,010 | 37.66 | 10,543,326 | 35,053 | SAMN10869098 | SEXV00000000 | 3,306 |
| UAMSEF_31 | 229 | 3,096,967 | 37.66 | 6,861,760 | 33,476 | SAMN10869099 | SEXU00000000 | 3,313 |
| UAMSEF_32 | 243 | 3,052,772 | 37.61 | 6,171,754 | 30,771 | SAMN10869100 | SEXT00000000 | 3,234 |
| UAMSEF_33 | 202 | 2,880,836 | 37.74 | 7,659,930 | 31,547 | SAMN10869101 | SEXS00000000 | 3,030 |
| UAMSEF_34 | 193 | 2,918,402 | 37.80 | 6,272,742 | 35,022 | SAMN10869102 | SEXR00000000 | 3,073 |
| UAMSEF_35 | 173 | 2,849,207 | 37.74 | 6,435,630 | 40,697 | SAMN10869103 | SEXQ00000000 | 2,981 |
| UAMSEF_36 | 191 | 2,845,779 | 37.74 | 6,167,138 | 40,603 | SAMN10869104 | SEXP00000000 | 2,996 |
| UAMSEF_37 | 221 | 2,975,344 | 37.74 | 7,491,600 | 34,261 | SAMN10869105 | SEXO00000000 | 3,161 |
| UAMSEF_38 | 187 | 2,938,030 | 37.62 | 6,602,994 | 43,049 | SAMN10869106 | SEXN00000000 | 3,097 |
| UAMSEF_39 | 217 | 2,943,498 | 37.59 | 5,659,958 | 32,692 | SAMN10869107 | SEXM00000000 | 3,123 |
| UAMSEF_40 | 172 | 2,846,352 | 37.74 | 6,122,006 | 46,310 | SAMN10869108 | SEXL00000000 | 2,972 |
| UAMSEF_41 | 204 | 2,855,455 | 37.76 | 7,229,612 | 38,111 | SAMN10869109 | SEXK00000000 | 2,997 |
| UAMSEF_42 | 237 | 3,050,710 | 37.61 | 6,845,894 | 30,771 | SAMN10869110 | SEXJ00000000 | 3,235 |
| UAMSEF_43 | 185 | 2,847,828 | 37.73 | 7,869,526 | 40,603 | SAMN10869111 | SEXI00000000 | 2,978 |
| UAMSEF_44 | 215 | 2,904,552 | 37.72 | 6,379,180 | 31,234 | SAMN10869112 | SEXH00000000 | 3,056 |
| UAMSEF_45 | 185 | 2,845,170 | 37.78 | 6,850,388 | 37,403 | SAMN10869113 | SEXG00000000 | 2,971 |
| UAMSEF_46 | 215 | 2,739,355 | 37.89 | 6,831,284 | 36,762 | SAMN10869114 | SEXF00000000 | 2,837 |
| UAMSEF_47 | 216 | 2,927,294 | 37.74 | 6,728,684 | 34,275 | SAMN10869115 | SEYM00000000 | 3,073 |
| UAMSEF_48 | 177 | 2,847,481 | 37.73 | 8,622,512 | 41,250 | SAMN10869116 | SEXE00000000 | 2,977 |
| UAMSEF_49 | 226 | 2,993,736 | 37.58 | 8,560,860 | 32,693 | SAMN10869117 | SEXD00000000 | 3,170 |
| UAMSEF_50 | 171 | 2,831,453 | 37.75 | 6,264,722 | 44,556 | SAMN10869118 | SEXC00000000 | 2,960 |
| UAMSEF_51 | 174 | 2,848,308 | 37.74 | 8,268,752 | 43,050 | SAMN10869119 | SEXB00000000 | 2,975 |
| UAMSEF_52 | 209 | 2,898,662 | 37.76 | 6,504,814 | 32,904 | SAMN10869120 | SEXA00000000 | 3,055 |
ORFs, open reading frames.
ACKNOWLEDGMENTS
This study was approved by the institutional review board (IRB) of the University of Arkansas for Medical Sciences (IRB number 228137).
This work was funded by the University of Arkansas for Medical Sciences College of Medicine Barton Pilot Grant FY19 program (AWD00052801). T.W., P.J., and I.N. are partially supported by the National Institute of General Medical Sciences of the National Institutes of Health award number P20GM125503. Z.U., T.W., P.J., D.U., and A.K. are supported in part by the Helen Adams & Arkansas Research Alliance. D.U. is also supported by NIH/NIGMS grant 1P20GM121293.
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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
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers detailed in Table 1. The versions described in this announcement are the first ones. The GenBank and BioSample accession numbers are given in Table 1. Raw sequence data for this study are available at the Sequence Read Archive under accession number PRJNA520878.
TABLE 1.
Assembly metrics and accession numbers for 48 E. faecium isolates
| Isolate name | No. of contigs | Total length (bp) | GC (%) | No. of reads | N50 (bp) | BioSample no. | GenBank accession no. | No. of ORFsa |
|---|---|---|---|---|---|---|---|---|
| UAMSEF_02 | 193 | 2,910,878 | 37.80 | 6,839,636 | 36,818 | SAMN10869073 | SEYV00000000 | 3,046 |
| UAMSEF_03 | 198 | 2,911,646 | 37.80 | 7,114,878 | 35,022 | SAMN10869074 | SEYU00000000 | 3,044 |
| UAMSEF_04 | 204 | 2,909,821 | 37.80 | 4,688,460 | 35,022 | SAMN10869075 | SEYT00000000 | 3,047 |
| UAMSEF_05 | 203 | 2,911,291 | 37.80 | 4,881,024 | 34,261 | SAMN10869076 | SEYS00000000 | 3,054 |
| UAMSEF_06 | 199 | 2,915,048 | 37.80 | 5,499,612 | 35,022 | SAMN10869077 | SEYR00000000 | 3,057 |
| UAMSEF_07 | 200 | 2,921,117 | 37.79 | 5,228,072 | 33,402 | SAMN10869078 | SEYQ00000000 | 3,058 |
| UAMSEF_10 | 204 | 3,029,727 | 37.66 | 6,167,912 | 35,022 | SAMN10869079 | SEYP00000000 | 3,208 |
| UAMSEF_11 | 209 | 3,029,905 | 37.66 | 7,152,790 | 35,022 | SAMN10869080 | SEYO00000000 | 3,209 |
| UAMSEF_12 | 209 | 3,030,170 | 37.66 | 7,191,884 | 35,022 | SAMN10869081 | SEYN00000000 | 3,208 |
| UAMSEF_13 | 208 | 3,031,358 | 37.66 | 5,108,778 | 35,022 | SAMN10869082 | SEYL00000000 | 3,210 |
| UAMSEF_14 | 207 | 3,033,907 | 37.66 | 5,789,340 | 35,022 | SAMN10869083 | SEYK00000000 | 3,228 |
| UAMSEF_15 | 208 | 3,030,699 | 37.66 | 5,022,872 | 34,261 | SAMN10869084 | SEYJ00000000 | 3,218 |
| UAMSEF_16 | 213 | 3,029,394 | 37.66 | 5,993,870 | 34,261 | SAMN10869085 | SEYI00000000 | 3,214 |
| UAMSEF_17 | 219 | 3,036,737 | 37.66 | 6,044,830 | 34,261 | SAMN10869086 | SEYH00000000 | 3,227 |
| UAMSEF_18 | 208 | 3,028,651 | 37.66 | 5,560,272 | 34,261 | SAMN10869087 | SEYG00000000 | 3,212 |
| UAMSEF_19 | 213 | 3,030,152 | 37.66 | 7,403,936 | 34,261 | SAMN10869088 | SEYF00000000 | 3,213 |
| UAMSEF_21 | 198 | 2,891,508 | 37.75 | 6,655,902 | 32,987 | SAMN10869089 | SEYE00000000 | 3,031 |
| UAMSEF_22 | 159 | 2,749,498 | 37.95 | 6,867,326 | 42,992 | SAMN10869090 | SEYD00000000 | 2,857 |
| UAMSEF_23 | 123 | 2,758,039 | 37.96 | 6,408,904 | 53,183 | SAMN10869091 | SEYC00000000 | 2,849 |
| UAMSEF_24 | 40 | 2,770,238 | 38.23 | 7,386,962 | 246,941 | SAMN10869092 | SEYB00000000 | 2,792 |
| UAMSEF_25 | 195 | 2,928,194 | 37.71 | 8,757,500 | 33,213 | SAMN10869093 | SEYA00000000 | 3,068 |
| UAMSEF_26 | 29 | 2,664,140 | 37.94 | 4,900,272 | 136,618 | SAMN10869094 | SEXZ00000000 | 2,721 |
| UAMSEF_27 | 222 | 2,902,431 | 37.71 | 5,726,412 | 31,483 | SAMN10869095 | SEXY00000000 | 3,058 |
| UAMSEF_28 | 172 | 2,739,636 | 37.88 | 6,372,790 | 32,818 | SAMN10869096 | SEXX00000000 | 2,835 |
| UAMSEF_29 | 199 | 2,879,498 | 37.75 | 5,414,500 | 31,547 | SAMN10869097 | SEXW00000000 | 3,036 |
| UAMSEF_30 | 225 | 3,101,010 | 37.66 | 10,543,326 | 35,053 | SAMN10869098 | SEXV00000000 | 3,306 |
| UAMSEF_31 | 229 | 3,096,967 | 37.66 | 6,861,760 | 33,476 | SAMN10869099 | SEXU00000000 | 3,313 |
| UAMSEF_32 | 243 | 3,052,772 | 37.61 | 6,171,754 | 30,771 | SAMN10869100 | SEXT00000000 | 3,234 |
| UAMSEF_33 | 202 | 2,880,836 | 37.74 | 7,659,930 | 31,547 | SAMN10869101 | SEXS00000000 | 3,030 |
| UAMSEF_34 | 193 | 2,918,402 | 37.80 | 6,272,742 | 35,022 | SAMN10869102 | SEXR00000000 | 3,073 |
| UAMSEF_35 | 173 | 2,849,207 | 37.74 | 6,435,630 | 40,697 | SAMN10869103 | SEXQ00000000 | 2,981 |
| UAMSEF_36 | 191 | 2,845,779 | 37.74 | 6,167,138 | 40,603 | SAMN10869104 | SEXP00000000 | 2,996 |
| UAMSEF_37 | 221 | 2,975,344 | 37.74 | 7,491,600 | 34,261 | SAMN10869105 | SEXO00000000 | 3,161 |
| UAMSEF_38 | 187 | 2,938,030 | 37.62 | 6,602,994 | 43,049 | SAMN10869106 | SEXN00000000 | 3,097 |
| UAMSEF_39 | 217 | 2,943,498 | 37.59 | 5,659,958 | 32,692 | SAMN10869107 | SEXM00000000 | 3,123 |
| UAMSEF_40 | 172 | 2,846,352 | 37.74 | 6,122,006 | 46,310 | SAMN10869108 | SEXL00000000 | 2,972 |
| UAMSEF_41 | 204 | 2,855,455 | 37.76 | 7,229,612 | 38,111 | SAMN10869109 | SEXK00000000 | 2,997 |
| UAMSEF_42 | 237 | 3,050,710 | 37.61 | 6,845,894 | 30,771 | SAMN10869110 | SEXJ00000000 | 3,235 |
| UAMSEF_43 | 185 | 2,847,828 | 37.73 | 7,869,526 | 40,603 | SAMN10869111 | SEXI00000000 | 2,978 |
| UAMSEF_44 | 215 | 2,904,552 | 37.72 | 6,379,180 | 31,234 | SAMN10869112 | SEXH00000000 | 3,056 |
| UAMSEF_45 | 185 | 2,845,170 | 37.78 | 6,850,388 | 37,403 | SAMN10869113 | SEXG00000000 | 2,971 |
| UAMSEF_46 | 215 | 2,739,355 | 37.89 | 6,831,284 | 36,762 | SAMN10869114 | SEXF00000000 | 2,837 |
| UAMSEF_47 | 216 | 2,927,294 | 37.74 | 6,728,684 | 34,275 | SAMN10869115 | SEYM00000000 | 3,073 |
| UAMSEF_48 | 177 | 2,847,481 | 37.73 | 8,622,512 | 41,250 | SAMN10869116 | SEXE00000000 | 2,977 |
| UAMSEF_49 | 226 | 2,993,736 | 37.58 | 8,560,860 | 32,693 | SAMN10869117 | SEXD00000000 | 3,170 |
| UAMSEF_50 | 171 | 2,831,453 | 37.75 | 6,264,722 | 44,556 | SAMN10869118 | SEXC00000000 | 2,960 |
| UAMSEF_51 | 174 | 2,848,308 | 37.74 | 8,268,752 | 43,050 | SAMN10869119 | SEXB00000000 | 2,975 |
| UAMSEF_52 | 209 | 2,898,662 | 37.76 | 6,504,814 | 32,904 | SAMN10869120 | SEXA00000000 | 3,055 |
ORFs, open reading frames.