The National Antimicrobial Resistance Monitoring System (NARMS) Human Isolate Data makes it easier and quicker to find out how antibiotic resistance has changed over the past 20 years for four bacteria transmitted commonly through food—Campylobacter, E. coli O157, Salmonella, and Shigella.
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The National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS) was established in 1996. NARMS is a collaboration between state and local public health departments, CDC (Centers of Disease Control and Prevention), the U.S. Food and Drug Administration (FDA), and the U.S. Department of Agriculture (USDA). This national public health surveillance system tracks changes in the antimicrobial susceptibility of certain enteric (intestinal) bacteria found in ill people (CDC), retail meats (FDA), and food animals (USDA) in the United States. The NARMS program at CDC helps protect public health by providing information about emerging bacterial resistance, the ways in which resistance is spread, and how resistant infections differ from susceptible infections.
NARMS monitors antibiotic resistance among the following four major foodborne bacteria.
Salmonella:
Non-typhoidal Salmonella enterica is widely dispersed in nature. It can be found in intestinal tracts of vertebrates including wildlife, livestock, domestic pets, and also in environmental sources such as pond water. It is spread through the fecal oral route and through contact with contaminated foods. An estimated 1.2 million people get sick from Salmonella infection in the United States each year. Of these, about 23,000 are hospitalized, and 450 die from their infections. Symptoms include nausea, vomiting, abdominal cramps, diarrhea, fever, headache generally lasting 4 to 7 days with acute symptoms lasting 1-2 days. Serious disease can develop in the very young, the elderly and the immunocompromised. Fluoroquinolones and cephalosporins are used as first-line therapies for the treatment of serious Salmonella infection in adults. Cephalosporins are recommended for the treatment of pediatric infections.
Campylobacter:
Campylobacter is part of the natural gut flora of most food-producing animals such as chickens, turkeys, swine, cattle and sheep. It is estimated to cause over 1.3 million illnesses and 76 deaths in the United States each year. More than 80% of Campylobacter infections are caused by C. jejuni. However, other Campylobacter species, such as C. coli and C. fetus can cause disease in humans. C. coli and C. jejuni cause similar disease symptoms including fever, diarrhea, abdominal cramps, and vomiting lasting anywhere from 2 to 10 days. Most cases of Campylobacter gastroenteritis are self-limited and typically, antibiotic therapy is not needed. When antibiotic therapy is indicated, macrolides and fluoroquinolones are most commonly prescribed. Major food sources linked to C. jejuni infections include improperly handled or undercooked poultry products, raw milk and cheeses made from raw milk, and contaminated water.
Escherichia coli
Escherichia coli Escherichia coli is one of the predominant enteric species in the normal intestinal flora of vertebrates. However, some serotypes of E. coli can cause severe diarrheal diseases in humans. One of these pathogenic strains is E. coli O157, which is monitored for antibiotic resistance by CDC in the human population. More information can be found on the CDC website. USDA and FDA monitor resistance among generic (non-serotyped) E. coli from food animals and retail meats. Generic E. coli are used by NARMS as an indicator organism to detect both emerging resistance patterns and specific resistance genes that could potentially be transferred to other pathogenic gram-negative bacteria, like Salmonella.
Enterococcus
Enterococcus is ubiquitous in nature and can be found in the gastrointestinal tracts, genitourinary tracts, oral cavities, and skin of humans and animals, as well as in insects, plants, soil, and water. Enterococcus is the only gram-positive organism that NARMS routinely monitors. Because it is consistently present in both types of meat and food animals, NARMS uses Enterococcus as an indicator organism to track resistance to antibiotics with activity against gram-positive organisms that may result from antimicrobial use. Enterococcus infection is notable largely as a hospital or community-acquired illness, and not much information is known about its role as a direct cause of foodborne illness. However, it is known that poorly processed meat and milk are among the foods that can transmit it.
About this Dataset
Data Info
Date Created
1996
Last Modified
2022-05-23
Version
2022-05-23
Update Frequency
Annual
Temporal Coverage
1996 - 2022
Spatial Coverage
United States
Source
John Snow Labs; Centers of Disease Control and Prevention(CDC), U.S. Food and Drug Administration (FDA), U.S. Department of Agriculture (USDA);
Source License URL
Source License Requirements
N/A
Source Citation
N/A
Keywords
Human PBMC, Ficoll Separation, Centrifuged Blood, Peripheral Mononuclear, Human Antibiotics, Antibacterial Resistance, Antimicrobial Medicines, Anti Microbial Drugs, Human Isolates, Antimicrobial Resistance
Other Titles
Human PBMC Isolate Data, Human Isolate Data Ficoll Separation, Human Isolate Data Centrifuged Blood, Peripheral Mononuclear Human Isolate Data
Data Fields
Name
Description
Type
Constraints
Specimen_ID
Unique identification number of the specimen.
string
-
NCBI_Accession_Number
Accession number for whole-genome sequence uploaded to NCBI for this isolate (assigned by NCBI).
string
-
Whole_Genome_Sequence_ID
Unique ID assigned by PulseNet for an assembled whole-genome sequence. Used to identify sequences uploaded to NCBI.
string
-
Is_AST_Approved
If yes (true), the isolate was collected for routine surveillance purposes and underwent antimicrobial susceptibly testing (AST) at CDC and AST results are approved by CDC NARMS. If no (false), the isolate was not collected for routine surveillance purposes, or did not undergo antimicrobial susceptibly testing (AST) at CDC, or AST results are not approved by CDC NARMS.
boolean
-
Is_WGS_Approved
If yes (true), the isolate underwent whole genome sequencing (WGS), the WGS data was screened for resistance genes, and results are approved by CDC NARMS. If no (false), the isolate did not undergo whole genome sequencing (WGS), or WGS data was not screened for resistance genes, or the results are not approved by CDC NARMS.
Species of the bacterial isolate. This is usually based on what the submitting laboratory reported, but may be updated if identification is performed at CDC and a different species result is obtained. Species is confirmed at CDC for all Campylobacter submitted for NARMS surveillance.
string
-
Serotype_of_Bacterial_Isolate
Serotype of the bacterial isolate. This is usually based on what the submitting laboratory reported, but may be updated if identification is performed at CDC and a different serotype result is obtained.
string
-
Data_Year_of_the_Bacterial_Isolate_Submission
The calendar year for the isolate (i.e. calendar year is assigned based off of specimen collection date).
string
-
Region_Name
HHS (Health & Human Services) Region is the geographic location for the state that submitted the isolate to NARMS.
string
-
Age_Group
Age category (in years: 0-4, 5-9, 10-19, 20-29, 30- 39, 40- 49, 50- 59, 60- 69, 70- 79, 80+)
string
-
Specimen_Source
Type of specimen from which the isolate was obtained (i.e. blood or stool)
string
-
Resistance_Pattern
Antibiotics that were found to be resistant for the isolate; otherwise, will read "No resistance detected"
string
-
Resistance_Determinants
Genes or mutations known to predict resistance found through whole genome sequencing. If none were found, will read "No determinants detected". If whole genome sequencing was not performed on the isolate, will read "Not sequenced". If whole genome sequencing was performed on the isolate, but it has not yet been analyzed for the presence of resistance genes, will read "Not analyzed".
string
-
Predictive_Resistance_Pattern
Predicted resistance pattern based on resistance determinants. If no determinants were found, will read "No determinants detected". If whole genome sequencing was not performed on the isolate, will read "Not sequenced". If whole genome sequencing was performed on the isolate, but it has not yet been analyzed for the presence of resistance genes, will read "Not analyzed".
string
-
Is_Lost_Resistance_On_Retest
If yes (true), the isolate has lost resistance through some mechanism.
boolean
-
Amikacin_Equivalence_Operator
Equivalence operator on the test result for Amikacin
string
-
Amikacin_Result
number
level : Ratio
Amikacin_Conclusion
Value: S,I,R,X
string
-
Amikacin_Conclusion_Predicted
AMI predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Ampicillin_Equivalence_Operator
AMP (or A in Resistance Pattern). Equivalence operator on the test result for Ampicillin
string
-
Ampicillin_Result
number
level : Ratio
Ampicillin_Conclusion
Value: S,I,R,X
string
-
Ampicillin_Conclusion_Predicted
AMP predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Aztreonam_Equivalence_Operator
Equivalence operator on the test result for Aztreonam
string
-
Aztreonam_Result
number
level : Ratio
Aztreonam_Conclusion
Value: S,I,R,X
string
-
Aztreonam_Conclusion_Predicted
ATM predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Amoxicillin_Clavulanic_Acid_Equivalence_Operator
AUG (or Au in Resistance Pattern). Equivalence operator on the test result for Amoxicillin-clavulanic acid
string
-
Amoxicillin_Clavulanic_Acid_Result
number
level : Ratio
Amoxicillin_Clavulanic_Acid_Conclusion
Value: S,I,R,X
string
-
Amoxicillin_Clavulanic_Acid_Conclusion_Predicted
AUG predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Ceftriaxone_Equivalence_Operator
AXO (or Cx in Resistance Pattern). Equivalence operator on the test result for Ceftriaxone
string
-
Ceftriaxone_Result
number
level : Ratio
Ceftriaxone_Conclusion
Value: S,I,R,X
string
-
Ceftriaxone_Conclusion_Predicted
AXO predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Azithromycin_Equivalence_Operator
Equivalence operator on the test result for Azithromycin
string
-
Azithromycin_Result
number
level : Ratio
Azithromycin_Conclusion
Value: S,I,R,X
string
-
Azithromycin_Conclusion_Predicted
AZM predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Ceftazidime_Equivalence_Operator
Equivalence operator on the test result for Ceftazidime
string
-
Ceftazidime_Result
number
level : Ratio
Ceftazidime_Conclusion
Value: S,I,R,X
string
-
Ceftazidime_Conclusion_Predicted
CAZ predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Ceftazidime_Clavulanic_Acid_Equivalence_Operator
Equivalence operator on the test result for Ceftazidime-clavulanic acid
string
-
Ceftazidime_Clavulanic_Acid_Result
number
level : Ratio
Ceftazidime_Clavulanic_Acid_Conclusion
Value: S,I,R,X
string
-
Ceftazidime_Clavulanic_Acid_Conclusion_Predicted
CCV predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Cephalothin_Equivalence_Operator
Equivalence operator on the test result for Cephalothin
string
-
Cephalothin_Result
number
level : Ratio
Cephalothin_Conclusion
Value: S,I,R,X
string
-
Cephalothin_Conclusion_Predicted
CEP predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Cefquinome_Equivalence_Operator
Equivalence operator on the test result for Cefquinome
string
-
Cefquinome_Result
number
level : Ratio
Cefquinome_Conclusion
Value: S,I,R,X
string
-
Cefquinome_Conclusion_Predicted
CEQ predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Chloramphenicol_Equivalence_Operator
CHL (or C in Resistance Pattern). Equivalence operator on the test result for Chloramphenicol
string
-
Chloramphenicol_Result
number
level : Ratio
Chloramphenicol_Conclusion
Value: S,I,R,X
string
-
Chloramphenicol_Conclusion_Predicted
CHL predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Ciprofloxacin_Equivalence_Operator
Equivalence operator on the test result for Ciprofloxacin
string
-
Ciprofloxacin_Result
number
level : Ratio
Ciprofloxacin_Conclusion
Value: S,I,R,X
string
-
Ciprofloxacin_Conclusion_Predicted
CIP predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Clindamycin_Equivalence_Operator
Equivalence operator on the test result for Clindamycin
string
-
Clindamycin_Result
number
level : Ratio
Clindamycin_Conclusion
Value: S,I,R,X
string
-
Clindamycin_Conclusion_Predicted
CLI predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Colistin_Equivalence_Operator
Equivalence operator on the test result for Colistin
string
-
Colistin_Result
number
level : Ratio
Colistin_Conclusion
Value: S,I,R,X
string
-
Colistin_Conclusion_Predicted
COL predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
COT predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Cefotaxime_Clavulanic_Acid_Equivalence_Operator
Equivalence operator on the test result for Cefotaxime-clavulanic acid
string
-
Cefotaxime_Clavulanic_Acid_Result
number
level : Ratio
Cefotaxime_Clavulanic_Acid_Conclusion
Value: S,I,R,X
string
-
Cefotaxime_Clavulanic_Acid_Conclusion_Predicted
CTC predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Cefotaxime_Equivalence_Operator
Equivalence operator on the test result for Cefotaxime
string
-
Cefotaxime_Result
number
level : Ratio
Cefotaxime_Conclusion
Value: S,I,R,X
string
-
Cefotaxime_Conclusion_Predicted
CTX predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Erythromycin_Equivalence_Operator
Equivalence operator on the test result for Erythromycin
string
-
Erythromycin_Result
number
level : Ratio
Erythromycin_Conclusion
Value: S,I,R,X
string
-
Erythromycin_Conclusion_Predicted
ERY predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Cefepime_Equivalence_Operator
Equivalence operator on the test result for Cefepime
string
-
Cefepime_Result
number
level : Ratio
Cefepime_Conclusion
Value: S,I,R,X
string
-
Cefepime_Conclusion_Predicted
FEP predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Florfenicol_Equivalence_Operator
Equivalence operator on the test result for Florfenicol
string
-
Florfenicol_Result
number
level : Ratio
Florfenicol_Conclusion
Value: S,I,R,X
string
-
Florfenico_Conclusion_Predicted
FFN predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Sulfisoxazole_Equivalence_Operator
FIS (or Su in Resistance Pattern). Equivalence operator on the test result for Sulfisoxazole
string
-
Sulfisoxazole_Result
integer
level : Ratio
Sulfisoxazole_Conclusion
Value: S,I,R,X
string
-
Sulfisoxazole_Conclusion_Predicted
FIS predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Cefoxitin_Equivalence_Operator
Equivalence operator on the test result for Cefoxitin
string
-
Cefoxitin_Result
number
level : Ratio
Cefoxitin_Conclusion
Value: S,I,R,X
string
-
Cefoxitin_Conclusion_Predicted
FOX predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Gentamicin_Equivalence_Operator
Equivalence operator on the test result for Gentamicin
string
-
Gentamicin_Result
number
level : Ratio
Gentamicin_Conclusion
Value: S,I,R,X
string
-
Gentamicin_Conclusion_Predicted
GEN predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Imipenem_Equivalence_Operator
Equivalence operator on the test result for Imipenem
string
-
Imipenem_Result
number
level : Ratio
Imipenem_Conclusion
Value: S,I,R,X
string
-
Imipenem_Conclusion_Predicted
IMI predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Kanamycin_Equivalence_Operator
Equivalence operator on the test result for Kanamycin
string
-
Kanamycin_Result
number
level : Ratio
Kanamycin_Conclusion
Value: S,I,R,X
string
-
Kanamycin_Conclusion_Predicted
KAN predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Meropenem_Equivalence_Operator
Equivalence operator on the test result for Meropenem.
string
-
Meropenem_Result
number
level : Ratio
Meropenem_Conclusion
Value: S,I,R,X
string
-
Meropenem_Conclusion_Predicted
MER predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Naladixic_Acid_Equivalence_Operator
Equivalence operator on the test result for Naladixic acid
string
-
Naladixic_Acid_Result
number
level : Ratio
Naladixic_Acid_Conclusion
Value: S,I,R,X
string
-
Naladixic_Conclusion_Predicted
NAL predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Piperacillin_Tazobactam_Equivalence_Operator
Equivalence operator on the test result for Piperacillin-tazobactam
string
-
Piperacillin_Tazobactam_Result
number
level : Ratio
Piperacillin_Tazobactam_Conclusion
Value: S,I,R,X
string
-
Piperacillin_Tazobactam_Conclusion_Predicted
PTZ predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Sulfamethoxazole_Equivalence_Operator
Equivalence operator on the test result for Sulfamethoxazole
string
-
Sulfamethoxazole_Result
integer
level : Ratio
Sulfamethoxazole_Conclusion
Value: S,I,R,X
string
-
Sulfamethoxazole_Conclusion_Predicted
SMX predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Streptomycin_Equivalence_Operator
STR (or S in Resistance Pattern). STR (or S in Resistance Pattern) .Equivalence operator on the test result for Streptomycin
string
-
Streptomycin_Result
number
level : Ratio
Streptomycin_Conclusion
Value: S,I,R,X
string
-
Streptomycin_Conclusion_Predicted
STR predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Telithromycin_Equivalence_Operator
Equivalence operator on the test result for Telithromycin
string
-
Telithromycin_Result
number
level : Ratio
Telithromycin_Conclusion
Value: S,I,R,X
string
-
Telithromycin_Conclusion_Predicted
TEL predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Tetracycline_Equivalence_Operator
TET (or T in Resistance Pattern) .Equivalence operator on the test result for Tetracycline
string
-
Tetracycline_Result
number
level : Ratio
Tetracycline_Conclusion
Value: S,I,R,X
string
-
Tetracycline_Conclusion_Predicted
TET predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
string
-
Ceftiofur_Equivalence_Operator
Equivalence operator on the test result for Ceftiofur
string
-
Ceftiofur_Result
number
level : Ratio
Ceftiofur_Conclusion
Value: S,I,R,X
string
-
Ceftiofur_Conclusion_Predicted
TIO predicted conclusion as determined by genetic sequencing (NPR - No Predicted Resistance, DS - Decreased Susceptibility, or R - Resistant. Will be blank if not sequenced or if not yet analyzed for the presences of resistance genes).
Demos
