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ID

45691

Descrição

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

Palavras-chave

Versões (1)
  1. 05/05/2023 05/05/2023 - Simon Heim
Titular dos direitos

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

Transferido a

5 de maio de 2023

DOI

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Licença

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

    Inglês

    Eligibility Criteria

    5 Formulários  
    Inclusion and exclusion criteria
    Descrição

    Inclusion and exclusion criteria

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

    *Cases:* *Inclusion criteria:*

    Tipo de dados

    boolean

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

    Children less than 5 years

    Tipo de dados

    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)
    Descrição

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

    Tipo de dados

    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.
    Descrição

    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.

    Tipo de dados

    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>
    Descrição

    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>

    Tipo de dados

    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.
    Descrição

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

    Tipo de dados

    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*
    Descrição

    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*

    Tipo de dados

    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
    Descrição

    Children older than 60 months of age

    Tipo de dados

    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.
    Descrição

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

    Tipo de dados

    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.
    Descrição

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

    Tipo de dados

    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.
    Descrição

    Children who live outside of Bucaramanga and its surrounding suburbs.

    Tipo de dados

    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:*
    Descrição

    *Healthy Controls:* *Inclusion criteria:*

    Tipo de dados

    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.
    Descrição

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

    Tipo de dados

    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:*
    Descrição

    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:*

    Tipo de dados

    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).
    Descrição

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

    Tipo de dados

    boolean

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

    Children older than 60 months of age

    Tipo de dados

    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.
    Descrição

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

    Tipo de dados

    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.
    Descrição

    Children who live outside of Bucaramanga and its surrounding suburbs.

    Tipo de dados

    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.
    Descrição

    *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.

    Tipo de dados

    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.
    Descrição

    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.

    Tipo de dados

    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 Formulários
    Name
    Tipo
    Description | Question | Decode (Coded Value)
    Tipo de dados
    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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