Sample Set Annotation Tool: Gene expression patterns in blood leukocytes discriminate patients with acute infections - GSE6269 - GPL96 [Influenza A virus, Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), Streptococcus pneumoniae (S. pneumoniae), Sepsis]

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Each infectious agent represents a unique combination of pathogen-associated molecular patterns that interact with specific pattern-recognition receptors expressed on immune cells. Therefore, we surmised that the blood immune cells of individuals with different infections might bear discriminative transcriptional signatures. Gene expression profiles were obtained for 131 peripheral blood samples from pediatric patients with acute infections caused by influenza A virus, Gram-negative (Escherichia coli) or Gram-positive (Staphylococcus aureus and Streptococcus pneumoniae) bacteria. Thirty-five genes were identified that best discriminate patients with influenza A virus infection from patients with either E coli or S pneumoniae infection. These genes classified with 95% accuracy (35 of 37 samples) an independent set of patients with either influenza A, E coli, or S pneumoniae infection. A different signature discriminated patients with E coli versus S aureus infections with 85% accuracy (34 of 40). Furthermore, distinctive gene expression patterns were observed in patients presenting with respiratory infections of different etiologies. Thus, microarray analyses of patient peripheral blood leukocytes might assist in the differential diagnosis of infectious diseases.

Hypothesis

Experimental Design

Entire study included 144 samples. Only 143 are included in this series because the CHP/CEL file was not available for sample PBMC_Healthy_INF295.

Experimental Variables

Blood infection due to Influenza A virus (2021 ICD-10-CM code* = J10)

Escherichia coli (2021 ICD-10-CM code* = B96.20)

Staphylococcus aureus (2021 ICD-10-CM code* = B95.8)

Streptococcus pneumoniae (2021 ICD-10-CM code* = B95.3)

Sepsis (2021 ICD-10-CM code* = A41)

Controls

Methods

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6269

Expected Samples:

97 Samples Loaded: 97

Species

Human (Homo sapiens)

Sample Source

PBMC

Disease

Blood infection due to Influenza A virus, Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae

Treatment Protocol

Growth Protocol

Extraction Protocol

RNeasy mini

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	Gender	Illness	race	treatment
GSM173178	PBMC_S.aureus_MSSA_INF005	M	Osteomyelitis	Hispanic	Cefazolin
GSM173179	PBMC_S.pneumoniae_INF009	M	Abscess	Caucasian	Cefazolin
GSM173180	PBMC_E.coli_INF012	M	Bacteremia	Black	Ceftriaxone
GSM173181	PBMC_E.coli_INF013	F	UTI	Caucasian	Ceftriaxone
GSM173182	PBMC_S.aureus_MRSA_INF024	M	Osteomyelitis	Black	Vancomycin/Rifampin

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File
sampleset4000198_sampleannotations (1).csv Sample Set Spreadsheet
sampleset4000198_sampleannotations.csv Sample Set Spreadsheet
sampleset4000198_sampleannotations.csv Sample Set Spreadsheet
sampleset4000198_sampleannotations.csv Sample Set Spreadsheet
sampleset4000198_sampleannotations_v1.csv Sample Set Spreadsheet

Samples Viewer / Editor

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Sample ID	!Sample Title	Gender	Illness	Race	Treatment	Grouping	Pathogen	Illness V1	Age V1 (months)
GSM173178	PBMC_S.aureus_MSSA_INF005	M	Osteomyelitis	Hispanic	Cefazolin	S. aureus	S. aureus, MSSA	Non Bacteremia	120
GSM173179	PBMC_S.pneumoniae_INF009	M	Abscess	Caucasian	Cefazolin	S. pneumoniae	S. pneumoniae	Non Bacteremia	4
GSM173180	PBMC_E.coli_INF012	M	Bacteremia	Black	Ceftriaxone	E. coli	E. coli	Bacteremia	5
GSM173181	PBMC_E.coli_INF013	F	UTI	Caucasian	Ceftriaxone	E. coli	E. coli	Non Bacteremia	5
GSM173182	PBMC_S.aureus_MRSA_INF024	M	Osteomyelitis	Black	Vancomycin/Rifampin	S. aureus	S. aureus, MRSA	Non Bacteremia	36
GSM173183	PBMC_S.pneumoniae_INF025	M	Meningitis	Hispanic	Ampicillin/Ceftriaxone	S. pneumoniae	S. pneumoniae	Non Bacteremia	2
GSM173184	PBMC_S.aureus_MRSA_INF030	M	Bacteremia	Black	Vancomycin	S. aureus	S. aureus, MRSA	Bacteremia	180
GSM173185	PBMC_E.coli_INF031	F	UTI	Hispanic	Gentamicin	E. coli	E. coli	Non Bacteremia	3
GSM173186	PBMC_E.coli_INF034	F	Pyelonephritis	Caucasian	Gentamicin	E. coli	E. coli	Non Bacteremia	192
GSM173187	PBMC_S.aureus_MSSA_INF040	M	Osteomyelitis/bacteremia	Caucasian	Cefazolin	S. aureus	S. aureus, MSSA	Bacteremia	144
GSM173188	PBMC_S.pneumoniae_INF041	F	Pneumonia/Empyema	Caucasian	Ceftriaxone	S. pneumoniae	S. pneumoniae	Non Bacteremia	23
GSM173189	PBMC_S.aureus_MRSA_INF043	M	Hip abscess/bacteremia	Black	Vancomycin/Rifampin	S. aureus	S. aureus, MRSA	Bacteremia	84
GSM173190	PBMC_E.coli_INF048	M	UTI	Caucasian	Ampicillin/ceftriaxone	E. coli	E. coli	Non Bacteremia	2
GSM173191	PBMC_InfluenzaA_INF055	M	Resp distress	Hispanic	Cefuroxime	Influenza	Influenza A	Non Bacteremia	11
GSM173192	PBMC_E.coli_INF057	F	UTI/bacteremia	Black	Gentamicin	E. coli	E. coli	Bacteremia	3
GSM173193	PBMC_S.aureus_MRSA_INF062	M	Osteomyelitis	Caucasian	Clindamycin	S. aureus	S. aureus, MRSA	Non Bacteremia	24
GSM173194	PBMC_S.pneumoniae_INF064	F	Meningitis/Bacteremia	Caucasian	Vancomycin/Ceftriaxone	S. pneumoniae	S. pneumoniae	Bacteremia	10
GSM173195	PBMC_S.aureus_MRSA_INF066	F	Pneumonia	Black	Vancomycin/Gentamicin	S. aureus	S. aureus, MRSA	Non Bacteremia	3
GSM173196	PBMC_S.aureus_MRSA_INF067	F	Osteomyelitis/bacteremia	Caucasian	Vancomycin/Rifampin	S. aureus	S. aureus, MRSA	Bacteremia	84
GSM173197	PBMC_S.aureus_MSSA_INF069	M	Lung abscess	Hispanic	Vancomycin/Cefazolin	S. aureus	S. aureus, MSSA	Non Bacteremia	9
GSM173198	PBMC_S.aureus_MRSA_INF070	F	Abscess	Caucasian	Vancomycin	S. aureus	S. aureus, MRSA	Non Bacteremia	15
GSM173199	PBMC_E.coli_INF074	F	UTI/bacteremia	Hispanic	Ceftriaxone	E. coli	E. coli	Bacteremia	4
GSM173200	PBMC_E.coli_INF082	M	UTI	Hispanic	Ampicillin/Ceftriaxone	E. coli	E. coli	Non Bacteremia	2
GSM173201	PBMC_S.aureus_MSSA_INF084	F	Abcess	Black	Cefazolin	S. aureus	S. aureus, MSSA	Non Bacteremia	216
GSM173202	PBMC_E.coli_INF086	M	UTI	Hispanic	Ceftriaxone	E. coli	E. coli	Non Bacteremia	3
GSM173203	PBMC_InfluenzaA_INF087	F	Fever	Caucasian	Cefuroxime	Influenza	Influenza A	Non Bacteremia	19
GSM173204	PBMC_S.aureus_MRSA_INF088	M	Osteomyelitis/bacteremia	Hispanic	Vancomycin	S. aureus	S. aureus, MRSA	Bacteremia	11
GSM173205	PBMC_S.aureus_MRSA_INF089	F	Abcess	Black	Clindamycin	S. aureus	S. aureus, MRSA	Non Bacteremia	4
GSM173206	PBMC_S.aureus_MSSA_INF090	M	Septic arthiritis/bacteremia	Black	Oxacillin	S. aureus	S. aureus, MSSA	Bacteremia	8
GSM173207	PBMC_InfluenzaA_INF092	F	Fever	Hispanic	Ampicillin/Ceftriaxone	Influenza	Influenza A	Non Bacteremia	1
GSM173208	PBMC_InfluenzaA_INF095	M	Fever	Hispanic	None	Influenza	Influenza A	Non Bacteremia	48
GSM173209	PBMC_S.pneumoniae_INF096	M	Pneumonia/Empyema	Hispanic	Ceftriaxone/Azithromycin	S. pneumoniae	S. pneumoniae	Non Bacteremia	16
GSM173211	PBMC_InfluenzaA_INF101	M	Fever	Hispanic	Cefuroxime/Oseltamivir	Influenza	Influenza A	Non Bacteremia	4
GSM173212	PBMC_InfluenzaA_INF104	M	Fever	Hispanic	Ceftriaxone	Influenza	Influenza A	Non Bacteremia	17
GSM173213	PBMC_InfluenzaA_INF105	F	Fever	Hispanic	Ceftriaxone/Acyclovir/Oseltamivir	Influenza	Influenza A	Non Bacteremia	48
GSM173214	PBMC_InfluenzaA_INF107	M	Fever	Asian	Ampicillin/Ceftriaxone	Influenza	Influenza A	Non Bacteremia	1.5
GSM173215	PBMC_InfluenzaA_INF108	M	Fever	Hispanic	Ceftriaxone	Influenza	Influenza A	Non Bacteremia	5
GSM173216	PBMC_InfluenzaA_INF112	M	Fever	Hispanic	Ampicillin/Gentamicin	Influenza	Influenza A	Non Bacteremia	1
GSM173217	PBMC_S.pneumoniae_INF113	F	Septic arthritis	Hispanic	Ceftriaxone/Clindamycin	S. pneumoniae	S. pneumoniae	Bacteremia	7
GSM173218	PBMC_InfluenzaA_INF114	F	Fever	Black	Cefuroxime/Oseltamivir	Influenza	Influenza A	Non Bacteremia	18
GSM173219	PBMC_InfluenzaA_INF115	M	Seizures	Caucasian	Amoxicillin	Influenza	Influenza A	Non Bacteremia	20
GSM173220	PBMC_InfluenzaA_INF116	M	Fever	Caucasian	Cefuroxime/Clindamycin	Influenza	Influenza A	Non Bacteremia	24
GSM173221	PBMC_InfluenzaA_INF117	F	Fever	Caucasian	None	Influenza	Influenza A	Non Bacteremia	288
GSM173222	PBMC_E.coli_INF118	M	UTI	Caucasian	Gentamicin/Ampicillin	E. coli	E. coli	Non Bacteremia	1.5
GSM173223	PBMC_E.coli_INF120	M	UTI	Hispanic	Ampicillin/Ceftriaxone	E. coli	E. coli	Non Bacteremia	1.5
GSM173224	PBMC_InfluenzaA_INF128	F	Fever	Hispanic	Cefuroxime	Influenza	Influenza A	Non Bacteremia	11
GSM173225	PBMC_Healthy_INF12N	M	Healthy	Caucasian		Healthy	None	Healthy	22
GSM173226	PBMC_InfluenzaA_INF132	M	Resp distress	Caucasian	Oxacillin/Tobramycin	Influenza	Influenza A	Non Bacteremia	6
GSM173227	PBMC_E.coli_INF133	M	UTI	Hispanic	Ceftriaxone	E. coli	E. coli	Non Bacteremia	2
GSM173228	PBMC_E.coli_INF139	M	UTI	Hispanic	Ampicillin/Ceftriaxone	E. coli	E. coli	Non Bacteremia	1
GSM173229	PBMC_E.coli_INF148	F	UTI	Hispanic	Ceftriaxone	E. coli	E. coli	Non Bacteremia	96
GSM173230	PBMC_S.aureus_MRSA_INF150	F	Osteomyelitis/bacteremia	Black	Vancomycin/Rifampin	S. aureus	S. aureus, MRSA	Bacteremia	108
GSM173231	PBMC_E.coli_INF151	M	UTI	Hispanic	Gentamicin/Ampicillin	E. coli	E. coli	Non Bacteremia	1.5
GSM173232	PBMC_E.coli_INF152	M	Bactermia	Black	Ceftriaxone/Gentamicin	E. coli	E. coli	Bacteremia	2.5
GSM173233	PBMC_E.coli_INF154	M	UTI	Hispanic	Ceftriaxone	E. coli	E. coli	Non Bacteremia	2
GSM173234	PBMC_S.pneumoniae_INF155	M	Meningitis	Hispanic	Ceftriaxone/Vancomycin	S. pneumoniae	S. pneumoniae	Non Bacteremia	3
GSM173235	PBMC_E.coli_INF161	M	UTI	Hispanic	Ampicillin/Ceftriaxone	E. coli	E. coli	Non Bacteremia	1.7
GSM173236	PBMC_E.coli_INF168	F	UTI	Caucasian	Ceftriaxone	E. coli	E. coli	Non Bacteremia	3
GSM173237	PBMC_E.coli_INF171	F	UTI	Hispanic	Ceftriaxone	E. coli	E. coli	Non Bacteremia	3
GSM173238	PBMC_E.coli_INF175	F	UTI/bacteremia	Hispanic	Ceftriaxone	E. coli	E. coli	Bacteremia	0.5
GSM173239	PBMC_S.aureus_MSSA_INF179	M	Endocarditis/bacteremia	Caucasian	Oxacillin/Gentamicin/Rifampin	S. aureus	S. aureus, MSSA	Bacteremia	144
GSM173240	PBMC_E.coli_INF180	M	UTI/bacteremia	Hispanic	Gentamicin/Ampicillin	E. coli	E. coli	Bacteremia	1
GSM173241	PBMC_E.coli_INF183	M	UTI	Hispanic	Ampicillin/Gentamicin/Ceftriaxone	E. coli	E. coli	Non Bacteremia	1.5
GSM173242	PBMC_E.coli_INF184	F	UTI/bacteremia	Caucasian	Gentamicin/Ampicillin	E. coli	E. coli	Bacteremia	0.5
GSM173243	PBMC_E.coli_INF188	M	UTI	Caucasian	Ampicillin/Gentamicin/Ceftriaxone	E. coli	E. coli	Non Bacteremia	1.5
GSM173244	PBMC_E.coli_INF197	M	UTI	Caucasian	Gentamicin/Ampicillin	E. coli	E. coli	Non Bacteremia	1.25
GSM173245	PBMC_Healthy_INF19N	M	Healthy	Hispanic		Healthy	None	Healthy	4
GSM173246	PBMC_Healthy_INF204	M	Healthy	Caucasian		Healthy	None	Healthy	24
GSM173247	PBMC_S.aureus_MRSA_INF205	M	Pneumonia/Bacteremia	Hispanic	Vancomycin	S. aureus	S. aureus, MRSA	Bacteremia	84
GSM173248	PBMC_S.aureus_MSSA_INF206	F	Abscess	Hispanic	Clindamycin	S. aureus	S. aureus, MSSA	Non Bacteremia	12
GSM173249	PBMC_S.aureus_MRSA_INF208	F	Osteomyelitis/bacteremia/Pneumonia	Caucasian	Vancomycin/Clindamycin/Rifampin	S. aureus	S. aureus, MRSA	Bacteremia	120
GSM173250	PBMC_Healthy_INF20N	M	Healthy	Hispanic		Healthy	None	Healthy	11
GSM173251	PBMC_S.aureus_MRSA_INF216	F	Osteomyelitis/bacteremia	Hispanic	Vancomycin/Rifampin	S. aureus	S. aureus, MRSA	Bacteremia	120
GSM173252	PBMC_E.coli_INF219	F	UTI/bacteremia	Caucasian	Ceftriaxone	E. coli	E. coli	Bacteremia	5
GSM173253	PBMC_S.aureus_MSSA_INF220	M	Osteomyelitis/bacteremia	Hispanic	Cefazolin/Rifampin	S. aureus	S. aureus, MSSA	Bacteremia	132
GSM173254	PBMC_S.aureus_MRSA_INF221	F	Osteomyelitis/bacteremia	Black	Vancomycin/Rifampin	S. aureus	S. aureus, MRSA	Bacteremia	72
GSM173255	PBMC_E.coli_INF222	F	UTI/bacteremia	Hispanic	Ceftriaxone/Gentamicin	E. coli	E. coli	Bacteremia	3
GSM173256	PBMC_S.aureus_MSSA_INF224	M	Osteomyelitis/bacteremia	Caucasian	Oxacillin/Rifampin	S. aureus	S. aureus, MSSA	Bacteremia	120
GSM173257	PBMC_E.coli_INF229	F	UTI/bacteremia	Hispanic	Ceftriaxone	E. coli	E. coli	Bacteremia	4
GSM173258	PBMC_S.aureus_MRSA_INF241	F	Pneumonia/Bacteremia	Black	Vancomycin/Rifampin	S. aureus	S. aureus, MRSA	Bacteremia	11
GSM173259	PBMC_S.aureus_MRSA_INF242	M	Pneumonia/Bacteremia	Black	Clindamycin	S. aureus	S. aureus, MRSA	Bacteremia	13
GSM173260	PBMC_S.aureus_MSSA_INF258	F	Osteomyelitis/bacteremia	Caucasian	Cefazolin	S. aureus	S. aureus, MSSA	Bacteremia	96
GSM173261	PBMC_InfluenzaA_INF259	F	Pneumonia	Hispanic	None	Influenza	Influenza A	Non Bacteremia	3
GSM173262	PBMC_Healthy_INF25N	F	Healthy	Hispanic		Healthy	None	Healthy	11
GSM173263	PBMC_S.pneumoniae_INF261	M	Meningitis	Caucasian	Ceftriaxone/Vancomycin	S. pneumoniae	S. pneumoniae	Non Bacteremia	156
GSM173264	PBMC_S.aureus_MRSA_INF262	M	Skin/Soft Tissue Abscess/Bacteremia	Hispanic	Clindamycin	S. aureus	S. aureus, MRSA	Bacteremia	156
GSM173265	PBMC_S.aureus_MSSA_INF264	M	Suppurative arthritis	Black	Vancomycin/Cefazolin/Gentamicin	S. aureus	S. aureus, MSSA	Non Bacteremia	156
GSM173267	PBMC_S.pneumoniae_INF265_j7657238	F	Pneumonia/Empyema	Caucasian	Ceftriaxone/Vancomycin	S. pneumoniae	S. pneumoniae	Non Bacteremia	24
GSM173268	PBMC_InfluenzaA_INF266	F	Fever	Caucasian	None	Influenza	Influenza A	Non Bacteremia	432
GSM173270	PBMC_S.pneumoniae_INF268_j5294684	M	Pneumonia/Empyema	Hispanic	Ceftriaxone/Clindamycin	S. pneumoniae	S. pneumoniae	Non Bacteremia	36
GSM173271	PBMC_S.aureus_MSSA_INF271	M	Osteomyelitis	Black	Clindamycin	S. aureus	S. aureus, MSSA	Non Bacteremia	156
GSM173273	PBMC_S.pneumoniae_INF277_j4695042	M	Pneumonia/Empyema	Caucasian	Ceftriaxone/Vancomycin	S. pneumoniae	S. pneumoniae	Non Bacteremia	192
GSM173274	PBMC_Healthy_INF27N	M	Healthy	Caucasian		Healthy	None	Healthy	10
GSM173275	PBMC_S.aureus_MRSA_INF281	F	Osteomyelitis	Caucasian	Clindamycin	S. aureus	S. aureus, MRSA	Non Bacteremia	36
GSM173277	PBMC_S.pneumoniae_INF287_j8790090	F	Pneumonia/Bacteremia	Caucasian	Ceftriaxone/Vancomycin	S. pneumoniae	S. pneumoniae	Bacteremia	36
GSM173280	PBMC_S.pneumoniae_INF289_j6962833	M	Pneumonia/Empyema	Hispanic	Ceftriaxone/Vancomycin	S. pneumoniae	S. pneumoniae	Non Bacteremia	24
GSM173284	PBMC_S.aureus_MRSA_INF315	F	Cellulitis	Hispanic	Vancomycin	S. aureus	S. aureus, MRSA	Non Bacteremia	36

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