ID

45691

Description

Principal Investigator: Sarah Highlander, PhD, J Craig Venter Institute, La Jolla, CA, USA MeSH: Diarrhea,Escherichia coli,Salmonella,Campylobacter,Norovirus,Astroviridae,Adenoviridae,Gastroenteritis,Rotavirus https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001260 The study of antimicrobial resistance (AMR) in infectious diarrhea has generally been limited to cultivation, antimicrobial susceptibility testing and targeted PCR assays. When individual strains of significance are identified, whole genome shotgun (WGS) sequencing of important clones and clades is performed. Genes that encode resistance to antibiotics have been detected in environmental, insect, human and animal metagenomes and are known as "resistomes". While metagenomic datasets have been mined to characterize the healthy human gut resistome in the Human Microbiome Project and MetaHIT and in a Yanomani Amerindian cohort, directed metagenomic sequencing has not been used to examine the epidemiology of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate antibiotic resistance elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple antibiotic resistance in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia. We propose to use deep metagenomic sequencing and genome level assembly to study the epidemiology of AMR in stools of children suffering from diarrhea. Here the epidemiology component will be surveillance and analysis of the microbial composition (to the bacterial species/strain level where possible) and its constituent antimicrobial resistance genetic elements (such as plasmids, integrons, transposons and other mobile genetic elements, or MGEs) in samples from a cohort where diarrhea is prevalent and antibiotic exposure is endemic. The goal will be to assess whether consortia of specific mobile antimicrobial resistance elements associate with species/strains and whether their presence is enhanced or amplified in diarrheal microbiomes and in the presence of antibiotic exposure. This work could potentially identify clonal complexes of organisms and MGEs with enhanced resistance and the potential to transfer this resistance to other enteric pathogens. We have performed WGS, metagenomic assembly and gene/protein mapping to examine and characterize the types of AMR genes and transfer elements (transposons, integrons, bacteriophage, plasmids) and their distribution in bacterial species and strains assembled from DNA isolated from diarrheal and non-diarrheal stools. The samples were acquired from a cohort of pediatric patients and controls from Colombia, South America where antibiotic use is prevalent. As a control, the distribution and abundance of AMR genes can be compared to published studies where resistome gene lists from healthy cohort sequences were compiled. Our approach is more epidemiologic in nature, as we plan to identify and catalogue antimicrobial elements on MGEs capable of spread through a local population and further we will, where possible, link mobile antimicrobial resistance elements with specific strains within the population.

Link

dbGaP study = phs001260

Keywords

Versions (1)
  1. 5/5/23 5/5/23 - Simon Heim
Copyright Holder

Sarah Highlander, PhD, J Craig Venter Institute, La Jolla, CA, USA

Uploaded on

May 5, 2023

DOI

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License

Creative Commons BY 4.0
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dbGaP phs001260 Metagenomic Epidemiology of Antibiotic Resistance in Infectious Diarrhea

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
*Cases:* *Inclusion criteria:*
Description

*Cases:* *Inclusion criteria:*

Data type

boolean

Alias
UMLS CUI [1,1]
C1706256
UMLS CUI [1,2]
C1512693
Children less than 5 years
Description

Children less than 5 years

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C0001779
Child is not currently enrolled as a case (not previously enrolled for diarrhea within the last 60 days)
Description

Child is not currently enrolled as a case (not previously enrolled for diarrhea within the last 60 days)

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C5239242
Presence of acute, moderate-to-severe diarrhea and/or vomiting within the past 10 days. Diarrhea is defined by the WHO as three or more liquid stools in a 24 hour period.
Description

Presence of acute, moderate-to-severe diarrhea and/or vomiting within the past 10 days. Diarrhea is defined by the WHO as three or more liquid stools in a 24 hour period.

Data type

boolean

Alias
UMLS CUI [1,1]
C0546816
UMLS CUI [1,2]
C1299393
UMLS CUI [1,3]
C0740441
UMLS CUI [1,4]
C0332185
UMLS CUI [2,1]
C0679227
UMLS CUI [2,2]
C0043237
UMLS CUI [2,3]
C0011991
Diarrhea is moderate to severe, and must meet at least one of the following criteria. <dl><dd>- Sunken eyes, confirmed by parent/caretaker</dd> <dd>- Loss of skin turgor by skin pinch (≤2s slow, or >2 very slow)</dd> <dd>- IV rehydration prescribed or administered</dd> <dd>- Dysentery (1 or more bloody stools)</dd> <dd>- Evaluated in the Emergency Department or admitted to the hospital for diarrhea</dd></dl>
Description

Diarrhea is moderate to severe, and must meet at least one of the following criteria. <dl><dd>- Sunken eyes, confirmed by parent/caretaker</dd> <dd>- Loss of skin turgor by skin pinch (≤2s slow, or >2 very slow)</dd> <dd>- IV rehydration prescribed or administered</dd> <dd>- Dysentery (1 or more bloody stools)</dd> <dd>- Evaluated in the Emergency Department or admitted to the hospital for diarrhea</dd></dl>

Data type

boolean

Alias
UMLS CUI [1,1]
C0011991
UMLS CUI [1,2]
C1299393
UMLS CUI [1,3]
C0679228
UMLS CUI [2,1]
C0423224
UMLS CUI [2,2]
C0521093
UMLS CUI [2,3]
C0030551
UMLS CUI [2,4]
C4554594
UMLS CUI [3,1]
C4264625
UMLS CUI [3,2]
C1123023
UMLS CUI [3,3]
C0427081
UMLS CUI [4,1]
C0348016
UMLS CUI [4,2]
C0034997
UMLS CUI [4,3]
C0278329
UMLS CUI [4,4]
C0806914
UMLS CUI [5,1]
C0277526
UMLS CUI [6,1]
C0220825
UMLS CUI [6,2]
C0562508
UMLS CUI [6,3]
C0184666
Children will still be eligible for enrollment even if they have received antibiotics within the last 14 days.
Description

Children will still be eligible for enrollment even if they have received antibiotics within the last 14 days.

Data type

boolean

Alias
UMLS CUI [1,1]
C1548635
UMLS CUI [1,2]
C1516879
UMLS CUI [1,3]
C0003232
UMLS CUI [1,4]
C0420210
UMLS CUI [1,5]
C0332185
Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs including the municipalities of: Girón, Floridablanca y Piedecuesta. *Exclusion criteria*
Description

Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs including the municipalities of: Girón, Floridablanca y Piedecuesta. *Exclusion criteria*

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C0237096
UMLS CUI [1,3]
C3245499
UMLS CUI [1,4]
C0557849
UMLS CUI [1,5]
C055775
UMLS CUI [1,6]
C0557755
UMLS CUI [2,1]
C0680251
Children older than 60 months of age
Description

Children older than 60 months of age

Data type

boolean

Alias
UMLS CUI [1,1]
C0001779
UMLS CUI [1,2]
C0008059
Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.
Description

Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.

Data type

boolean

Alias
UMLS CUI [1,1]
C0401151
UMLS CUI [1,2]
C1275743
UMLS CUI [1,3]
C0010346
UMLS CUI [1,4]
C0009324
Children with URI symptoms including: runny nose, sneezing, cough, congestion, sore throat, and ear ache.
Description

Children with URI symptoms including: runny nose, sneezing, cough, congestion, sore throat, and ear ache.

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C0041912
UMLS CUI [1,3]
C1457887
UMLS CUI [1,4]
C0242429
UMLS CUI [1,5]
C0010200
UMLS CUI [1,6]
C1260880
UMLS CUI [1,7]
C0497339
UMLS CUI [1,8]
C0013456
Children who live outside of Bucaramanga and its surrounding suburbs.
Description

Children who live outside of Bucaramanga and its surrounding suburbs.

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C0237096
UMLS CUI [1,3]
C0557849
UMLS CUI [1,4]
C0557755
*Healthy Controls:* *Inclusion criteria:*
Description

*Healthy Controls:* *Inclusion criteria:*

Data type

boolean

Alias
UMLS CUI [1,1]
C0009932
UMLS CUI [1,2]
C1512693
Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs: Girón, Floridablanca y Piedecuesta.
Description

Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs: Girón, Floridablanca y Piedecuesta.

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C0237096
UMLS CUI [1,3]
C3245499
UMLS CUI [1,4]
C0557849
UMLS CUI [1,5]
C055775
UMLS CUI [1,6]
C0557755
Matched to cases for age. Age matching is ±2 months for 0-11 months, ±4months for 12-59 months. (Cannot exceed the stratum boundaries of the case). *Exclusion criteria:*
Description

Matched to cases for age. Age matching is ±2 months for 0-11 months, ±4months for 12-59 months. (Cannot exceed the stratum boundaries of the case). *Exclusion criteria:*

Data type

boolean

Alias
UMLS CUI [1,1]
C0150103
UMLS CUI [1,2]
C0001779
UMLS CUI [1,3]
C5453780
Diarrhea, as defined by the WHO, in the previous 7 days (regardless of whether they develop diarrhea after enrollment).
Description

Diarrhea, as defined by the WHO, in the previous 7 days (regardless of whether they develop diarrhea after enrollment).

Data type

boolean

Alias
UMLS CUI [1,1]
C0011991
UMLS CUI [1,2]
C0679227
UMLS CUI [1,3]
C0332185
Children older than 60 months of age
Description

Children older than 60 months of age

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C0001779
Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.
Description

Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.

Data type

boolean

Alias
UMLS CUI [1,1]
C0401151
UMLS CUI [1,2]
C1275743
UMLS CUI [1,3]
C0010346
UMLS CUI [1,4]
C0009324
Children who live outside of Bucaramanga and its surrounding suburbs.
Description

Children who live outside of Bucaramanga and its surrounding suburbs.

Data type

boolean

Alias
UMLS CUI [1,1]
C0008059
UMLS CUI [1,2]
C0557849
UMLS CUI [1,3]
C0557755
UMLS CUI [1,4]
C0237096
*Rationale for Exclusion/Inclusion Criteria:* Children from outlying municipalities will be included in this study because the volume of children with diarrhea at the central study site, Universidad de Santander, is not sufficient for the purposes of this study to not utilize outlying health care facilities. The population distribution is equitable between these two locations in terms of socioeconomic factors and there is not transportation limitation between the two. The suburbs have access to pediatricians and health clinics, so no sampling bias will be introduced by including this population.
Description

*Rationale for Exclusion/Inclusion Criteria:* Children from outlying municipalities will be included in this study because the volume of children with diarrhea at the central study site, Universidad de Santander, is not sufficient for the purposes of this study to not utilize outlying health care facilities. The population distribution is equitable between these two locations in terms of socioeconomic factors and there is not transportation limitation between the two. The suburbs have access to pediatricians and health clinics, so no sampling bias will be introduced by including this population.

Data type

boolean

Alias
UMLS CUI [1,1]
C2827031
UMLS CUI [1,2]
C0008059
UMLS CUI [1,3]
C0600182
UMLS CUI [1,4]
C1512693
UMLS CUI [1,5]
C4035618
UMLS CUI [1,6]
C0018704
UMLS CUI [2,1]
C0032666
UMLS CUI [2,2]
C0205163
UMLS CUI [2,3]
C0037464
UMLS CUI [2,4]
C1298908
UMLS CUI [2,5]
C4534518
UMLS CUI [3,1]
C0557755
UMLS CUI [3,2]
C0444454
UMLS CUI [3,3]
C0237433
UMLS CUI [3,4]
C0035960
UMLS CUI [3,5]
C1298908
UMLS CUI [3,6]
C0005349
UMLS CUI [3,7]
C1512693
UMLS CUI [3,8]
C1257890
In prior studies, antibiotic use has been used as exclusion criteria for cases. The rationale for this has been primarily for the benefit of the research team. That is, in patients with prior antibiotic use bacterial species, such as E. coli, are very difficult to culture (and thus may skew the data). However, the most commonly used antibiotics in Colombia are older and include ampicillin, bactrim, and first generation penicillins. Since there is high resistance among E. coli strains for these antibiotics, we feel that their use will not necessarily prevent use from recovering these bacteria in laboratory culture.
Description

In prior studies, antibiotic use has been used as exclusion criteria for cases. The rationale for this has been primarily for the benefit of the research team. That is, in patients with prior antibiotic use bacterial species, such as E. coli, are very difficult to culture (and thus may skew the data). However, the most commonly used antibiotics in Colombia are older and include ampicillin, bactrim, and first generation penicillins. Since there is high resistance among E. coli strains for these antibiotics, we feel that their use will not necessarily prevent use from recovering these bacteria in laboratory culture.

Data type

boolean

Alias
UMLS CUI [1,1]
C0332152
UMLS CUI [1,2]
C0240320
UMLS CUI [1,3]
C0003232
UMLS CUI [1,4]
C2828389
UMLS CUI [2,1]
C0814225
UMLS CUI [2,2]
C0035168
UMLS CUI [2,3]
C0871489
UMLS CUI [2,4]
C3695179
UMLS CUI [3,1]
C0002680
UMLS CUI [3,2]
C0591139
UMLS CUI [3,3]
C0030842
UMLS CUI [4,1]
C0949669
UMLS CUI [4,2]
C0430402
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Similar models

Eligibility Criteria

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
*Cases:* *Inclusion criteria:*
Item
*Cases:* *Inclusion criteria:*
boolean
C1706256 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
Children less than 5 years
Item
Children less than 5 years
boolean
C0008059 (UMLS CUI [1,1])
C0001779 (UMLS CUI [1,2])
Child is not currently enrolled as a case (not previously enrolled for diarrhea within the last 60 days)
Item
Child is not currently enrolled as a case (not previously enrolled for diarrhea within the last 60 days)
boolean
C0008059 (UMLS CUI [1,1])
C5239242 (UMLS CUI [1,2])
Presence of acute, moderate-to-severe diarrhea and/or vomiting within the past 10 days. Diarrhea is defined by the WHO as three or more liquid stools in a 24 hour period.
Item
Presence of acute, moderate-to-severe diarrhea and/or vomiting within the past 10 days. Diarrhea is defined by the WHO as three or more liquid stools in a 24 hour period.
boolean
C0546816 (UMLS CUI [1,1])
C1299393 (UMLS CUI [1,2])
C0740441 (UMLS CUI [1,3])
C0332185 (UMLS CUI [1,4])
C0679227 (UMLS CUI [2,1])
C0043237 (UMLS CUI [2,2])
C0011991 (UMLS CUI [2,3])
Diarrhea is moderate to severe, and must meet at least one of the following criteria. <dl><dd>- Sunken eyes, confirmed by parent/caretaker</dd> <dd>- Loss of skin turgor by skin pinch (≤2s slow, or >2 very slow)</dd> <dd>- IV rehydration prescribed or administered</dd> <dd>- Dysentery (1 or more bloody stools)</dd> <dd>- Evaluated in the Emergency Department or admitted to the hospital for diarrhea</dd></dl>
Item
Diarrhea is moderate to severe, and must meet at least one of the following criteria. <dl><dd>- Sunken eyes, confirmed by parent/caretaker</dd> <dd>- Loss of skin turgor by skin pinch (≤2s slow, or >2 very slow)</dd> <dd>- IV rehydration prescribed or administered</dd> <dd>- Dysentery (1 or more bloody stools)</dd> <dd>- Evaluated in the Emergency Department or admitted to the hospital for diarrhea</dd></dl>
boolean
C0011991 (UMLS CUI [1,1])
C1299393 (UMLS CUI [1,2])
C0679228 (UMLS CUI [1,3])
C0423224 (UMLS CUI [2,1])
C0521093 (UMLS CUI [2,2])
C0030551 (UMLS CUI [2,3])
C4554594 (UMLS CUI [2,4])
C4264625 (UMLS CUI [3,1])
C1123023 (UMLS CUI [3,2])
C0427081 (UMLS CUI [3,3])
C0348016 (UMLS CUI [4,1])
C0034997 (UMLS CUI [4,2])
C0278329 (UMLS CUI [4,3])
C0806914 (UMLS CUI [4,4])
C0277526 (UMLS CUI [5,1])
C0220825 (UMLS CUI [6,1])
C0562508 (UMLS CUI [6,2])
C0184666 (UMLS CUI [6,3])
Children will still be eligible for enrollment even if they have received antibiotics within the last 14 days.
Item
Children will still be eligible for enrollment even if they have received antibiotics within the last 14 days.
boolean
C1548635 (UMLS CUI [1,1])
C1516879 (UMLS CUI [1,2])
C0003232 (UMLS CUI [1,3])
C0420210 (UMLS CUI [1,4])
C0332185 (UMLS CUI [1,5])
Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs including the municipalities of: Girón, Floridablanca y Piedecuesta. *Exclusion criteria*
Item
Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs including the municipalities of: Girón, Floridablanca y Piedecuesta. *Exclusion criteria*
boolean
C0008059 (UMLS CUI [1,1])
C0237096 (UMLS CUI [1,2])
C3245499 (UMLS CUI [1,3])
C0557849 (UMLS CUI [1,4])
C055775 (UMLS CUI [1,5])
C0557755 (UMLS CUI [1,6])
C0680251 (UMLS CUI [2,1])
Children older than 60 months of age
Item
Children older than 60 months of age
boolean
C0001779 (UMLS CUI [1,1])
C0008059 (UMLS CUI [1,2])
Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.
Item
Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.
boolean
C0401151 (UMLS CUI [1,1])
C1275743 (UMLS CUI [1,2])
C0010346 (UMLS CUI [1,3])
C0009324 (UMLS CUI [1,4])
Children with URI symptoms including: runny nose, sneezing, cough, congestion, sore throat, and ear ache.
Item
Children with URI symptoms including: runny nose, sneezing, cough, congestion, sore throat, and ear ache.
boolean
C0008059 (UMLS CUI [1,1])
C0041912 (UMLS CUI [1,2])
C1457887 (UMLS CUI [1,3])
C0242429 (UMLS CUI [1,4])
C0010200 (UMLS CUI [1,5])
C1260880 (UMLS CUI [1,6])
C0497339 (UMLS CUI [1,7])
C0013456 (UMLS CUI [1,8])
Children who live outside of Bucaramanga and its surrounding suburbs.
Item
Children who live outside of Bucaramanga and its surrounding suburbs.
boolean
C0008059 (UMLS CUI [1,1])
C0237096 (UMLS CUI [1,2])
C0557849 (UMLS CUI [1,3])
C0557755 (UMLS CUI [1,4])
*Healthy Controls:* *Inclusion criteria:*
Item
*Healthy Controls:* *Inclusion criteria:*
boolean
C0009932 (UMLS CUI [1,1])
C1512693 (UMLS CUI [1,2])
Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs: Girón, Floridablanca y Piedecuesta.
Item
Children who reside within the catchment area of the city Bucaramanga, Colombia and its surrounding suburbs: Girón, Floridablanca y Piedecuesta.
boolean
C0008059 (UMLS CUI [1,1])
C0237096 (UMLS CUI [1,2])
C3245499 (UMLS CUI [1,3])
C0557849 (UMLS CUI [1,4])
C055775 (UMLS CUI [1,5])
C0557755 (UMLS CUI [1,6])
Matched to cases for age. Age matching is ±2 months for 0-11 months, ±4months for 12-59 months. (Cannot exceed the stratum boundaries of the case). *Exclusion criteria:*
Item
Matched to cases for age. Age matching is ±2 months for 0-11 months, ±4months for 12-59 months. (Cannot exceed the stratum boundaries of the case). *Exclusion criteria:*
boolean
C0150103 (UMLS CUI [1,1])
C0001779 (UMLS CUI [1,2])
C5453780 (UMLS CUI [1,3])
Diarrhea, as defined by the WHO, in the previous 7 days (regardless of whether they develop diarrhea after enrollment).
Item
Diarrhea, as defined by the WHO, in the previous 7 days (regardless of whether they develop diarrhea after enrollment).
boolean
C0011991 (UMLS CUI [1,1])
C0679227 (UMLS CUI [1,2])
C0332185 (UMLS CUI [1,3])
Children older than 60 months of age
Item
Children older than 60 months of age
boolean
C0008059 (UMLS CUI [1,1])
C0001779 (UMLS CUI [1,2])
Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.
Item
Presence of chronic diarrhea (>10 days) or other co-morbid conditions such as Crohn's disease or ulcerative colitis.
boolean
C0401151 (UMLS CUI [1,1])
C1275743 (UMLS CUI [1,2])
C0010346 (UMLS CUI [1,3])
C0009324 (UMLS CUI [1,4])
Children who live outside of Bucaramanga and its surrounding suburbs.
Item
Children who live outside of Bucaramanga and its surrounding suburbs.
boolean
C0008059 (UMLS CUI [1,1])
C0557849 (UMLS CUI [1,2])
C0557755 (UMLS CUI [1,3])
C0237096 (UMLS CUI [1,4])
*Rationale for Exclusion/Inclusion Criteria:* Children from outlying municipalities will be included in this study because the volume of children with diarrhea at the central study site, Universidad de Santander, is not sufficient for the purposes of this study to not utilize outlying health care facilities. The population distribution is equitable between these two locations in terms of socioeconomic factors and there is not transportation limitation between the two. The suburbs have access to pediatricians and health clinics, so no sampling bias will be introduced by including this population.
Item
*Rationale for Exclusion/Inclusion Criteria:* Children from outlying municipalities will be included in this study because the volume of children with diarrhea at the central study site, Universidad de Santander, is not sufficient for the purposes of this study to not utilize outlying health care facilities. The population distribution is equitable between these two locations in terms of socioeconomic factors and there is not transportation limitation between the two. The suburbs have access to pediatricians and health clinics, so no sampling bias will be introduced by including this population.
boolean
C2827031 (UMLS CUI [1,1])
C0008059 (UMLS CUI [1,2])
C0600182 (UMLS CUI [1,3])
C1512693 (UMLS CUI [1,4])
C4035618 (UMLS CUI [1,5])
C0018704 (UMLS CUI [1,6])
C0032666 (UMLS CUI [2,1])
C0205163 (UMLS CUI [2,2])
C0037464 (UMLS CUI [2,3])
C1298908 (UMLS CUI [2,4])
C4534518 (UMLS CUI [2,5])
C0557755 (UMLS CUI [3,1])
C0444454 (UMLS CUI [3,2])
C0237433 (UMLS CUI [3,3])
C0035960 (UMLS CUI [3,4])
C1298908 (UMLS CUI [3,5])
C0005349 (UMLS CUI [3,6])
C1512693 (UMLS CUI [3,7])
C1257890 (UMLS CUI [3,8])
In prior studies, antibiotic use has been used as exclusion criteria for cases. The rationale for this has been primarily for the benefit of the research team. That is, in patients with prior antibiotic use bacterial species, such as E. coli, are very difficult to culture (and thus may skew the data). However, the most commonly used antibiotics in Colombia are older and include ampicillin, bactrim, and first generation penicillins. Since there is high resistance among E. coli strains for these antibiotics, we feel that their use will not necessarily prevent use from recovering these bacteria in laboratory culture.
Item
In prior studies, antibiotic use has been used as exclusion criteria for cases. The rationale for this has been primarily for the benefit of the research team. That is, in patients with prior antibiotic use bacterial species, such as E. coli, are very difficult to culture (and thus may skew the data). However, the most commonly used antibiotics in Colombia are older and include ampicillin, bactrim, and first generation penicillins. Since there is high resistance among E. coli strains for these antibiotics, we feel that their use will not necessarily prevent use from recovering these bacteria in laboratory culture.
boolean
C0332152 (UMLS CUI [1,1])
C0240320 (UMLS CUI [1,2])
C0003232 (UMLS CUI [1,3])
C2828389 (UMLS CUI [1,4])
C0814225 (UMLS CUI [2,1])
C0035168 (UMLS CUI [2,2])
C0871489 (UMLS CUI [2,3])
C3695179 (UMLS CUI [2,4])
C0002680 (UMLS CUI [3,1])
C0591139 (UMLS CUI [3,2])
C0030842 (UMLS CUI [3,3])
C0949669 (UMLS CUI [4,1])
C0430402 (UMLS CUI [4,2])
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