Field entomology data from Ethiopian trachoma population survey and laboratory transmission experiments for Musca sorbens and Chlamydia trachomatis – Codebook

Permanent identifier

https://doi.org/10.17037/DATA.00003114

Description

A population-based survey of 247 households was conducted in Shashemane district, Oromia Region, Ethiopia, between April and June 2018. Households were positively selected to include at least one child aged 1–9 years, resident on the day of enumeration. These datasets contain entomology from this survey; including fly-eye contact data, fly positivity for Chlamydia trachomatis and other entomological data (fly species, sex). Experiments were also conducted in the London School of Hygiene & Tropical Medicine to investigate transmission of Chlamydia trachomatis by Musca sorbens, those data are reported here.

Codebook

The dataset contains 14 tables, saved in MS Excel (.xlsx) and tab-delimited (.txt) format. The cell content of the Excel and tab-delimited files are the same. The Excel version contains colour coding that was applied during development.

1_field_fly_spp_sex

The ‘1_field_fly_spp_sex’ table lists all flies caught during the field survey.

Variable Name Variable Label Answer Label Answer Code Variable Type
flynumber Order of flies caught per individual. up to a maximum of 10 flies   1 - 10 Numeric
fly_present Fly present at identification     String
    Yes Yes  
    No No  
    . Not completed  
fly_species Fly species     String
    Musca domestica Musca domestica  
    Musca sorbens Musca sorbens  
    Unknown/Squashed Unknown/Squashed  
    Other Other  
fly_sex Fly sex     String
    Female Female  
    Male Male  
    . Not completed  
label_no Label number for processing     Numeric

2_field_hh28_person_info

The ‘2_field_hh28_person_info’ dataset contains person information (age and sex) for previously studied and reported 28 households.

Variable Name Variable Label Answer Label Answer Code Variable Type
oc_pos_hh Household contained at least one ocular positive individual     Numeric
    0 No  
    1 Yes  
oc_sex Sex of individual     String
    female Female  
    male Male  
    . Not completed  
oc_age_years Age of individual     Numeric

3_field_ocneghh_posflies_ct

The ‘3_field_ocneghh_posflies_ct’ dataset contains Ct omcB and plasmid copies for all positive flies caught in ocular negative households.

Variable Name Variable Label Answer Label Answer Code Variable Type
Fly fly (of 29 positive flies found in ocular negative households)     Numeric
omcb_copies omcB copies per uL recovered from whole fly     Numeric
plasmid_copies plasmid copies per uL recovered from whole fly.     Numeric

4_field_ocneghh_flies_tested

The ‘4_field_ocneghh_flies_tested’ dataset contains number of flies per person that were tested for Ct for all ocular negative households (not including 28hh dataset).

Variable Name Variable Label Answer Label Answer Code Variable Type
total_flies Number of flies tested ‘whole’ (as entire flies) for Ct DNA from ocular negative households, per person     Numeric

5_field_dissections_id

The ‘5_field_dissections_id’ dataset contains Fly information for field caught dissected flies.

Variable Name Variable Label Answer Label Answer Code Variable Type
label_no Label number for processing     Numeric
hh28_diss_body_part Number of dissected body parts   2-4 Numeric
hh28_diss_either_pos Number of dissected body parts positive for Ct   0 - 3 Numeric
flynumber Order of flies caught per individual up to a maximum of 10 flies     Numeric
fly_present Fly present at identification or not     String
    Yes Yes  
    No No  
    . Not completed  
fly_species Fly species     String
    Musca domestica Musca domestica  
    Musca sorbens Musca sorbens  
    Unknown/Squashed Unknown/Squashed  
fly_sex Fly sex     String
    Female Female  
    Male Male  

6_field_dissections_ct

The ‘6_field_dissections_ct’ dataset contains Ct recovery from field caught dissected flies.

Variable Name Variable Label Answer Label Answer Code Variable Type
label_no Label number for processing     Number
body_part Fly body part     String
    L Leg  
    B Body (thorax and abdomen)  
    H Head  
est_omcb_copies_ul Estimated omcB copies per uL   0 - 64 Numeric
omcb_Ct omcB Ct value   30 - 37 Numeric
est_plasmid_copies_ul Estimated plasmid copies per uL   0 – 50 Numeric
plasmid_Ct Plasmid Ct value   31 - 39 Numeric
est_RPP30_copies_ul Estimated RPP30 copies per uL     Numeric
RPP30_Ct RPP30 Ct value     Numeric
omcb_pos omcB positive as binary value     Numeric
    0 Negative  
    1 Positive  
    . Not completed  
plasmid_pos plasmid positive as binary value     Numeric
    0 Negative  
    1 Positive  
    . Not completed  
either_pos Either target positive as binary value     Numeric
    0 Negative  
    1 Positive  
    . Not completed  

7_field_all_pos_flies_id

The ‘7_field_all_pos_flies_id’ dataset contains all positive flies Ct recovery, species and sex.

Variable Name Variable Label Answer Label Answer Code Variable Type
label_no Label number for processing     Numeric
Ct_positive Ct status of household where fly was caught     Numeric
    0 No  
    1 Yes  
omcb_copies Estimated omcB copies per uL     Numeric
omcb_Ct omcB Ct value     Numeric
omcb_pos omcB positive as binary value      
    0 No Numeric
    1 Yes  
plasmid_copies Estimated plasmid copies per uL      
plasmid_Ct Plasmid Ct value     Numeric
plasmidpos plasmid positive as binary value     Numeric
    0 No  
    1 Yes  
either_pos Either target positive as binary value     Numeric
    0 No  
    1 Yes  
fly_sex Fly sex     String
    Female Female  
    Male Male  
fly_species Fly species     String
      Musca domestica  
      Musca sorbens  
      Unknown/Squashed  

8_field_flyeye_data

The ‘8_field_flyeye_data’ contains clinical and fly eye data for phase 1 field study.

Variable Name Variable Label Answer Label Answer Code Variable Type
oc_sex Person sex     String
    Female Female  
    Male Male  
agegroup Person age group     String
    7-9 yrs 7-9 years  
    4-6 yrs 4-6 years  
    1-3 yrs 1-3 years  
    10-17 yrs 10-17 years  
    18+ yrs 18+ years  
oc_tf_or_ti Ocular TF or TI status     String
    Yes Yes  
    No No  
    . Not completed  
oc_ocular_discharge Ocular discharge present     String
    Yes Yes  
    No No  
    . Not completed  
oc_nasal_discharge Nasal discharge present     String
    Yes Yes  
    No No  
    . Not completed  
oc_ct_positive Ocular swab Ct positive     String
    Yes Yes  
    No No  
    . Not completed  
oc_ct_pos_hh Number of people in the household with Ct positive ocular swab      
    0 0  
    1 1  
    2 2  
    3 3  
FE_month Month of fly-eye contact     String
    Apr April  
    May May  
    Jun June  
FE_month_num Month (numerical) of fly-eye contact     String
    4 April  
    5 May  
    6 June  
FE_field_tymp_temp Tympanic temperature     Numeric
FE_field_weight Body weight     Numeric
FE_field_amb_temp Ambient humidity at time of fly-eye contact     Numeric
FE_field_rel_humidity Relative humidity at time of fly-eye contact     Numeric
FE_field_light_intensity Light intensity at time of fly-eye contact     Numeric
FE_light_100 Light intensity/100     Numeric
FE_light_1thous Light intensity/1000     Numeric
FE_field_fly_eye_contacts Fly eye contacts in 10 minutes     Numeric
FE_field_fly_nose_contacts Fly nose contacts in 10 minutes     Numeric
FE_field_fly_mouth_contacts Fly mouth contacts in 10 minutes     Numeric
FE_field_wind_cond Wind conditions at time of fly-eye contact     String
    Yes Yes  
    No No  
FE_field_rain_cond Rain conditions at time of fly-eye contact     String
    Yes Yes  
    No No Numeric
fly_pos_binary If Ct positive fly was caught from individual (binary yes/no)      
    0    
    1    

9_field_28hh_geospatial

The ‘9_field_28hh_geospatial’ dataset contains fly positivity for previously studied and reported 28 households.

Variable Name Variable Label Answer Label Answer Code Variable Type
ocular_pos Ct status of household     Numeric
    0 No  
    1 Yes  
pos_flies Number of Ct positive flies     Numeric
total_flies Total flies caught at household     Numeric
perc_pos Proportion (%) of flies caught at household Ct positive     Numeric

10_field_ocneghh_pos_flies

The ‘10_field_ocneghh_pos_flies’ dataset contains fly positivity for all ocular negative households (not including 28hh dataset).

Variable Name Variable Label Answer Label Answer Code Variable Type
Ct_positive Ct status of household (all negative)     Numeric
pos_flies Number of Ct positive flies     Numeric
total_flies Total flies caught at household     Numeric
perc_pos Proportion (%) of flies caught at household Ct positive     Numeric

10_field_survey_geospatial

The ‘10_field_survey_geospatial’ dataset contains minimum distance to ocular positive household for all households in study.

Variable Name Variable Label Answer Label Answer Code Variable Type
Ct_positive Ct status of household (all negative)     Numeric
pos_flies Number of Ct positive flies     Numeric
total_flies Total flies caught at household     Numeric
perc_pos Proportion (%) of flies caught at household Ct positive     Numeric

11_geospatial_minimum_distance

Variable Name Variable Label Answer Label Answer Code Variable Type
ocular_pos Ct status of household     Numeric
pos_flies Number of Ct positive flies     Numeric
total_flies Total flies caught at household     Numeric
perc_pos Proportion (%) of flies caught at household Ct positive     Numeric
min_dis_km_cat3 Minimum distance to ocular positive household in categories of 100m     Numeric
min_dis Minimum distance to ocular positive household in metres     Numeric
min_dis_km Minimum distance to ocular positive household in kilometers     Numeric
min_dis_100m Minimum distance to ocular positive household in 100-metres     Numeric
dis_sq Minimum distance squared (quadratic term) in metres     Numeric
dis_sq_km Minimum distance squared (quadratic term) in kilometers     Numeric
dis_sq_100m Minimum distance squared (quadratic term) in 100-metres     Numeric

12_lab_feeding_1

The ‘12_lab_feeding_1’ dataset Contains Laboratory feeding experiments, first experiment, 6 female flies.

Variable Name Variable Label Answer Label Answer Code Variable Type
sample_name Sample ID     String
sample_type Type of sample     String
    Body Body  
    Control Control  
    Head Head  
    Wash Wash  
sample_number Sample number     String
time_point Time point of testing     String
    T0 0 minutes  
    T60 60 minutes post feed  
flysex omcB Ct value     String
    Female Female  
    Male Male  
omcb_Ct omcb_Ct     Numeric
est_omcb_copies_ul Estimated omcB copies per uL     Numeric
plasmid_Ct Plasmid Ct value     Numeric
est_plasmid_copies_ul Estimated plasmid copies per uL      
log_est_omcb_copies_ul Log of estimated omcB copies per uL      
log_est_plasmid_copies_ul Log of estimated plasmid copies per uL      

13_lab_feeding_2

The ‘13_lab_feeding_2’ dataset contains Laboratory feeding experiments, second experiment, 6 male flies.

Variable Name Variable Label Answer Label Answer Code Variable Type
sample_name Sample ID     String
sample_type Type of sample     String
    Body Body  
    Control Control  
    Head Head  
    Wash Wash  
sample_number Sample number     String
time_point Time point of testing     String
    T0 0 minutes  
    T60 60 minutes post feed  
flysex Fly sex     String
    Female Female  
    Male Male  
omcb_Ct omcB Ct value     Numeric
est_omcb_copies_ul Estimated omcB copies per uL     Numeric
plasmid_Ct Plasmid Ct value     Numeric
est_plasmid_copies_ul Estimated plasmid copies per uL     Numeric
log_est_plasmid_copies_ul Log of estimated omcB copies per uL     Numeric
log_est_omcb_copies_ul Log of estimated plasmid copies per uL     Numeric

14_lab_feeding_3

The ‘14_lab_feeding_3’ dataset contains Laboratory feeding experiments, third experiment, 6 male and 6 female flies.

Variable Name Variable Label Answer Label Answer Code Variable Type
sample_name Sample ID     String
sample_type Type of sample     String
    Body Body  
    Control Control  
    Head Head  
    Wash Wash  
sample_number Sample number     String
time_point Time point of testing     String
    T0 0 minutes  
      T60 60 minutes post feed  
flysex Fly sex     String
    Female Female  
    Male Male  
omcb_Ct omcB Ct value     Numeric
est_omcb_copies_ul Estimated omcB copies per uL     Numeric
plasmid_Ct Plasmid Ct value     Numeric
est_plasmid_copies_ul Estimated plasmid copies per uL     Numeric
log_est_omcb_copies_ul Log of estimated omcB copies per uL     Numeric
log_est_plasmid_copies_ul Log of estimated plasmid copies per uL     Numeric