Abstract

We would like to correct the sample description in our original paper. The clinical samples stated in the paper should be urine samples spiked with pathogens from clinical isolates. The detailed corrections are listed below. In the Abstract, "⋯from both bacteria spiked urine and clinical infected urine samples⋯ " should be replaced with "from human urine specimens spiked with lab strain E. coli (ATCC 43888) and an E. coli strain isolated from a clinical urine sample". On page 6315, in the Experimental Section, Materials, "Unfiltered human urine samples (Lot BRH1041997) and E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) were purchased from Bioreclamation IVT Co. and Fisher Scientific, respectively." should be replaced with "Unfiltered pooled human urine specimens from multiple healthy individuals (Lot BRH1041997) were purchased from Bioreclamation IVT Co. and were stored at -80 °C immediately after receiving and thawed prior to the experiment. E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) was purchased from Fisher Scientific and was stored at -80 °C immediately after receiving and thawed prior to the experiment." On page 6316, Experimental Section, "Clinical Sample Preparation and Testing. This study was approved by Arizona State University's Institutional Review Board. All urine clinical samples were stored at 4 °C and detected within 2 h after collection. The raw urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells." should be replaced with "Preparation of Standardized Urine Samples Spiked with a Clinical Bacterial Isolate. Deidentified excess urine specimens from clinical testing were obtained from Microbiology Lab, Mayo Clinic Hospital, Phoenix, AZ, U.S. 24 h after collection. The specimens (100 μL) were streaked onto LB agar and incubated overnight at 37 °C to obtain isolated colonies. An isolated bacterial colony from a positive specimen was then subcultured and spiked into filtered normal urine samples (from IVT) following the same procedure described in Growth and Preparation of E. coli (ATCC 43888) of the Experimental Section. The spiked urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells." On page 6317, Figure 3, the label for the horizontal axis of the plot at the right side of Figure 3a should be "C". On page 6319, Table 1, the "MIC (μg/mL) BMDb" should be replaced with "MIC in 16 h (μg/mL) BMDb)" On page 6319, in the Results and Discussion, "Clinical Testing. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with clinically collected urine samples. Midstream urine samples from 10 patients with UTI symptoms were obtained at the Mayo Clinic Hospital, in Phoenix, AZ, U.S. Before AST, we first evaluated bacterial infection in each sample by automatic cell counting in the phase contrast microscopic images. Among the 10 samples, 1 case was confirmed positive for bacterial infection, and the other 9 cases were confirmed negative because few bacterial cells were observed. This evaluation corresponds well to laboratory results from isolation culture performed separately, and the pathogen in the positive case was identified to be E. coli, the most common pathogen in UTI." should be replaced with "Testing of a Clinical Isolate. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with normal urine spiked with E. coli isolated from a clinical urine specimen (No. 20170824E1) obtained from the Mayo Clinic. The specimen was analyzed by the Mayo Clinic Hospital using standard microbiological methodology and was confirmed to be positive for E. coli, the most common pathogen in UTI." On page 6319, Results and Discussion, the second paragraph in the Clinical Testing section, "⋯within 30 min, and standard BMD methods in 12 h" should be replaced with "⋯within 30 min, and standard BMD methods in 16 h" On page 6320, Figure 6 caption, "DLVM-AST results of the five antibiotics against the pathogens in the clinical samples, including (a) polymyxin B, (b) streptomyxin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin." should be replaced with "DLVM-AST results of the five antibiotics, (a) polymyxin B, (b) streptomycin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin, tested against the E. coli clinical isolate incubated in normal urine samples." On page 6321, Table 2 caption, "⋯Clinical Urine Samples (Caused by E. coli)⋯" should be replaced with "Urine samples spiked with an isolate of E. coli from a clinical specimen.".

Original languageEnglish (US)
Number of pages1
JournalAnalytical Chemistry
Volume90
Issue number12
DOIs
StatePublished - Jun 19 2018

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Escherichia coli
Microscopes
Testing
Chemical analysis
Pathogens
Shiga Toxin 1
Shiga Toxin 2
Aztreonam
Polymyxin B
Ampicillin
Ciprofloxacin
Deep learning
Blood
Genes
Cells
Anti-Bacterial Agents
Membranes
Microbiology
Streptomycin
Agar

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Correction to : Phenotypic antimicrobial susceptibility testing with deep learning video microscope (Analytical Chemistry (2018) 90: 10 (6314-6322) DOI: 10.1021/acs.analchem.8b01128). / Yu, Hui; Jing, Wenwen; Iriya, Rafael; Yang, Yunze; Syal, Karan; Mo, Manni; Grys, Thomas E.; Haydel, Shelley; Wang, Shaopeng; Tao, Nongjian.

In: Analytical Chemistry, Vol. 90, No. 12, 19.06.2018.

Research output: Contribution to journalComment/debate

@article{1e7e3aa1073b4aa79b1d51999a0e7ec5,
title = "Correction to: Phenotypic antimicrobial susceptibility testing with deep learning video microscope (Analytical Chemistry (2018) 90: 10 (6314-6322) DOI: 10.1021/acs.analchem.8b01128)",
abstract = "We would like to correct the sample description in our original paper. The clinical samples stated in the paper should be urine samples spiked with pathogens from clinical isolates. The detailed corrections are listed below. In the Abstract, {"}⋯from both bacteria spiked urine and clinical infected urine samples⋯ {"} should be replaced with {"}from human urine specimens spiked with lab strain E. coli (ATCC 43888) and an E. coli strain isolated from a clinical urine sample{"}. On page 6315, in the Experimental Section, Materials, {"}Unfiltered human urine samples (Lot BRH1041997) and E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) were purchased from Bioreclamation IVT Co. and Fisher Scientific, respectively.{"} should be replaced with {"}Unfiltered pooled human urine specimens from multiple healthy individuals (Lot BRH1041997) were purchased from Bioreclamation IVT Co. and were stored at -80 °C immediately after receiving and thawed prior to the experiment. E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) was purchased from Fisher Scientific and was stored at -80 °C immediately after receiving and thawed prior to the experiment.{"} On page 6316, Experimental Section, {"}Clinical Sample Preparation and Testing. This study was approved by Arizona State University's Institutional Review Board. All urine clinical samples were stored at 4 °C and detected within 2 h after collection. The raw urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells.{"} should be replaced with {"}Preparation of Standardized Urine Samples Spiked with a Clinical Bacterial Isolate. Deidentified excess urine specimens from clinical testing were obtained from Microbiology Lab, Mayo Clinic Hospital, Phoenix, AZ, U.S. 24 h after collection. The specimens (100 μL) were streaked onto LB agar and incubated overnight at 37 °C to obtain isolated colonies. An isolated bacterial colony from a positive specimen was then subcultured and spiked into filtered normal urine samples (from IVT) following the same procedure described in Growth and Preparation of E. coli (ATCC 43888) of the Experimental Section. The spiked urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells.{"} On page 6317, Figure 3, the label for the horizontal axis of the plot at the right side of Figure 3a should be {"}C{"}. On page 6319, Table 1, the {"}MIC (μg/mL) BMDb{"} should be replaced with {"}MIC in 16 h (μg/mL) BMDb){"} On page 6319, in the Results and Discussion, {"}Clinical Testing. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with clinically collected urine samples. Midstream urine samples from 10 patients with UTI symptoms were obtained at the Mayo Clinic Hospital, in Phoenix, AZ, U.S. Before AST, we first evaluated bacterial infection in each sample by automatic cell counting in the phase contrast microscopic images. Among the 10 samples, 1 case was confirmed positive for bacterial infection, and the other 9 cases were confirmed negative because few bacterial cells were observed. This evaluation corresponds well to laboratory results from isolation culture performed separately, and the pathogen in the positive case was identified to be E. coli, the most common pathogen in UTI.{"} should be replaced with {"}Testing of a Clinical Isolate. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with normal urine spiked with E. coli isolated from a clinical urine specimen (No. 20170824E1) obtained from the Mayo Clinic. The specimen was analyzed by the Mayo Clinic Hospital using standard microbiological methodology and was confirmed to be positive for E. coli, the most common pathogen in UTI.{"} On page 6319, Results and Discussion, the second paragraph in the Clinical Testing section, {"}⋯within 30 min, and standard BMD methods in 12 h{"} should be replaced with {"}⋯within 30 min, and standard BMD methods in 16 h{"} On page 6320, Figure 6 caption, {"}DLVM-AST results of the five antibiotics against the pathogens in the clinical samples, including (a) polymyxin B, (b) streptomyxin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin.{"} should be replaced with {"}DLVM-AST results of the five antibiotics, (a) polymyxin B, (b) streptomycin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin, tested against the E. coli clinical isolate incubated in normal urine samples.{"} On page 6321, Table 2 caption, {"}⋯Clinical Urine Samples (Caused by E. coli)⋯{"} should be replaced with {"}Urine samples spiked with an isolate of E. coli from a clinical specimen.{"}.",
author = "Hui Yu and Wenwen Jing and Rafael Iriya and Yunze Yang and Karan Syal and Manni Mo and Grys, {Thomas E.} and Shelley Haydel and Shaopeng Wang and Nongjian Tao",
year = "2018",
month = "6",
day = "19",
doi = "10.1021/acs.analchem.8b02212",
language = "English (US)",
volume = "90",
journal = "Analytical Chemistry",
issn = "0003-2700",
publisher = "American Chemical Society",
number = "12",

}

TY - JOUR

T1 - Correction to

T2 - Phenotypic antimicrobial susceptibility testing with deep learning video microscope (Analytical Chemistry (2018) 90: 10 (6314-6322) DOI: 10.1021/acs.analchem.8b01128)

AU - Yu, Hui

AU - Jing, Wenwen

AU - Iriya, Rafael

AU - Yang, Yunze

AU - Syal, Karan

AU - Mo, Manni

AU - Grys, Thomas E.

AU - Haydel, Shelley

AU - Wang, Shaopeng

AU - Tao, Nongjian

PY - 2018/6/19

Y1 - 2018/6/19

N2 - We would like to correct the sample description in our original paper. The clinical samples stated in the paper should be urine samples spiked with pathogens from clinical isolates. The detailed corrections are listed below. In the Abstract, "⋯from both bacteria spiked urine and clinical infected urine samples⋯ " should be replaced with "from human urine specimens spiked with lab strain E. coli (ATCC 43888) and an E. coli strain isolated from a clinical urine sample". On page 6315, in the Experimental Section, Materials, "Unfiltered human urine samples (Lot BRH1041997) and E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) were purchased from Bioreclamation IVT Co. and Fisher Scientific, respectively." should be replaced with "Unfiltered pooled human urine specimens from multiple healthy individuals (Lot BRH1041997) were purchased from Bioreclamation IVT Co. and were stored at -80 °C immediately after receiving and thawed prior to the experiment. E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) was purchased from Fisher Scientific and was stored at -80 °C immediately after receiving and thawed prior to the experiment." On page 6316, Experimental Section, "Clinical Sample Preparation and Testing. This study was approved by Arizona State University's Institutional Review Board. All urine clinical samples were stored at 4 °C and detected within 2 h after collection. The raw urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells." should be replaced with "Preparation of Standardized Urine Samples Spiked with a Clinical Bacterial Isolate. Deidentified excess urine specimens from clinical testing were obtained from Microbiology Lab, Mayo Clinic Hospital, Phoenix, AZ, U.S. 24 h after collection. The specimens (100 μL) were streaked onto LB agar and incubated overnight at 37 °C to obtain isolated colonies. An isolated bacterial colony from a positive specimen was then subcultured and spiked into filtered normal urine samples (from IVT) following the same procedure described in Growth and Preparation of E. coli (ATCC 43888) of the Experimental Section. The spiked urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells." On page 6317, Figure 3, the label for the horizontal axis of the plot at the right side of Figure 3a should be "C". On page 6319, Table 1, the "MIC (μg/mL) BMDb" should be replaced with "MIC in 16 h (μg/mL) BMDb)" On page 6319, in the Results and Discussion, "Clinical Testing. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with clinically collected urine samples. Midstream urine samples from 10 patients with UTI symptoms were obtained at the Mayo Clinic Hospital, in Phoenix, AZ, U.S. Before AST, we first evaluated bacterial infection in each sample by automatic cell counting in the phase contrast microscopic images. Among the 10 samples, 1 case was confirmed positive for bacterial infection, and the other 9 cases were confirmed negative because few bacterial cells were observed. This evaluation corresponds well to laboratory results from isolation culture performed separately, and the pathogen in the positive case was identified to be E. coli, the most common pathogen in UTI." should be replaced with "Testing of a Clinical Isolate. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with normal urine spiked with E. coli isolated from a clinical urine specimen (No. 20170824E1) obtained from the Mayo Clinic. The specimen was analyzed by the Mayo Clinic Hospital using standard microbiological methodology and was confirmed to be positive for E. coli, the most common pathogen in UTI." On page 6319, Results and Discussion, the second paragraph in the Clinical Testing section, "⋯within 30 min, and standard BMD methods in 12 h" should be replaced with "⋯within 30 min, and standard BMD methods in 16 h" On page 6320, Figure 6 caption, "DLVM-AST results of the five antibiotics against the pathogens in the clinical samples, including (a) polymyxin B, (b) streptomyxin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin." should be replaced with "DLVM-AST results of the five antibiotics, (a) polymyxin B, (b) streptomycin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin, tested against the E. coli clinical isolate incubated in normal urine samples." On page 6321, Table 2 caption, "⋯Clinical Urine Samples (Caused by E. coli)⋯" should be replaced with "Urine samples spiked with an isolate of E. coli from a clinical specimen.".

AB - We would like to correct the sample description in our original paper. The clinical samples stated in the paper should be urine samples spiked with pathogens from clinical isolates. The detailed corrections are listed below. In the Abstract, "⋯from both bacteria spiked urine and clinical infected urine samples⋯ " should be replaced with "from human urine specimens spiked with lab strain E. coli (ATCC 43888) and an E. coli strain isolated from a clinical urine sample". On page 6315, in the Experimental Section, Materials, "Unfiltered human urine samples (Lot BRH1041997) and E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) were purchased from Bioreclamation IVT Co. and Fisher Scientific, respectively." should be replaced with "Unfiltered pooled human urine specimens from multiple healthy individuals (Lot BRH1041997) were purchased from Bioreclamation IVT Co. and were stored at -80 °C immediately after receiving and thawed prior to the experiment. E. coli (ATCC 43888; Biosafety Level 1 organism that does not produce either Shiga-like I or II toxins and lacks the genes for these toxins) was purchased from Fisher Scientific and was stored at -80 °C immediately after receiving and thawed prior to the experiment." On page 6316, Experimental Section, "Clinical Sample Preparation and Testing. This study was approved by Arizona State University's Institutional Review Board. All urine clinical samples were stored at 4 °C and detected within 2 h after collection. The raw urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells." should be replaced with "Preparation of Standardized Urine Samples Spiked with a Clinical Bacterial Isolate. Deidentified excess urine specimens from clinical testing were obtained from Microbiology Lab, Mayo Clinic Hospital, Phoenix, AZ, U.S. 24 h after collection. The specimens (100 μL) were streaked onto LB agar and incubated overnight at 37 °C to obtain isolated colonies. An isolated bacterial colony from a positive specimen was then subcultured and spiked into filtered normal urine samples (from IVT) following the same procedure described in Growth and Preparation of E. coli (ATCC 43888) of the Experimental Section. The spiked urine samples were filtered by a 5 μm filter membrane, which removes large substances such as epithelial cells and blood cells." On page 6317, Figure 3, the label for the horizontal axis of the plot at the right side of Figure 3a should be "C". On page 6319, Table 1, the "MIC (μg/mL) BMDb" should be replaced with "MIC in 16 h (μg/mL) BMDb)" On page 6319, in the Results and Discussion, "Clinical Testing. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with clinically collected urine samples. Midstream urine samples from 10 patients with UTI symptoms were obtained at the Mayo Clinic Hospital, in Phoenix, AZ, U.S. Before AST, we first evaluated bacterial infection in each sample by automatic cell counting in the phase contrast microscopic images. Among the 10 samples, 1 case was confirmed positive for bacterial infection, and the other 9 cases were confirmed negative because few bacterial cells were observed. This evaluation corresponds well to laboratory results from isolation culture performed separately, and the pathogen in the positive case was identified to be E. coli, the most common pathogen in UTI." should be replaced with "Testing of a Clinical Isolate. To evaluate the effectiveness of the proposed approach, we then performed DLVM-AST with normal urine spiked with E. coli isolated from a clinical urine specimen (No. 20170824E1) obtained from the Mayo Clinic. The specimen was analyzed by the Mayo Clinic Hospital using standard microbiological methodology and was confirmed to be positive for E. coli, the most common pathogen in UTI." On page 6319, Results and Discussion, the second paragraph in the Clinical Testing section, "⋯within 30 min, and standard BMD methods in 12 h" should be replaced with "⋯within 30 min, and standard BMD methods in 16 h" On page 6320, Figure 6 caption, "DLVM-AST results of the five antibiotics against the pathogens in the clinical samples, including (a) polymyxin B, (b) streptomyxin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin." should be replaced with "DLVM-AST results of the five antibiotics, (a) polymyxin B, (b) streptomycin, (c) ciprofloxacin, (d) aztreonam, and (e) ampicillin, tested against the E. coli clinical isolate incubated in normal urine samples." On page 6321, Table 2 caption, "⋯Clinical Urine Samples (Caused by E. coli)⋯" should be replaced with "Urine samples spiked with an isolate of E. coli from a clinical specimen.".

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