Trial Outcomes & Findings for Antibiotic Resistance and Microbiome in Children Aged 6-59 Months in Nouna, Burkina Faso (NCT NCT03187834)

Results Overview

The primary outcome of the study was pre-specified as α-diversity (inverse Simpson's) at the genus level, expressed in effective number. Simpson's Alpha Diversity were obtained at Baseline and Post-treatment in this study. The minimum of Simpson's index of diversity is 0, there is no maximum. Higher Simpson's index of diversity means more diverse. There are no subscales.

Recruitment status

COMPLETED

Study phase

PHASE4

Target enrollment

252 participants

Primary outcome timeframe

Baseline and Day 9

Results posted on

2023-03-02

Participant Flow

Unit of analysis: household

Participant milestones

Participant milestones
Measure	Amoxicillin Households Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin Households Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin Households - Antibiotic: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole Households Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. In placebo households, both children received placebo.
Overall Study STARTED	62 31	62 31	62 31	62 31
Overall Study Receive Antibiotic	31 31	31 31	31 31	31 31
Overall Study Receive Placebo	31 31	31 31	31 31	31 31
Overall Study COMPLETED	57 30	58 31	56 31	58 31
Overall Study NOT COMPLETED	5 1	4 0	6 0	4 0

Reasons for withdrawal

Reasons for withdrawal
Measure	Amoxicillin Households Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin Households Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin Households - Antibiotic: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole Households Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. In placebo households, both children received placebo.
Overall Study Lost to Follow-up	0	1	2	2
Overall Study Had invalid anthropometric measurements	5	3	4	2

Baseline Characteristics

Race and Ethnicity were not collected from any participant.

Baseline characteristics by cohort

Baseline characteristics by cohort
Measure	Amoxicillin Households - Antibiotic n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Amoxicillin Households - Placebo n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Amoxicillin Households - Placebo: Children in this arm will receive Placebo.	Azithromycin Households - Antibiotic n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin Households - Antibiotic: Children in this arm will receive Azithromycin once a day.	Azithromycin Households - Placebo n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Azithromycin Households - Placebo: Children in this arm will receive Placebo.	Cotrimoxazole Households - Antibiotic n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Cotrimoxazole Households - Placebo n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Cotrimoxazole Households - Placebo: Children in this arm will receive Placebo.	Placebo n=62 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. In placebo households, both children received placebo.	Total n=248 Participants Total of all reporting groups
Age, Continuous	35 months n=31 Participants	36 months n=31 Participants	29 months n=31 Participants	42 months n=31 Participants	37 months n=31 Participants	40 months n=31 Participants	38 months n=62 Participants	37 months n=248 Participants
Sex: Female, Male Female	14 Participants n=31 Participants	18 Participants n=31 Participants	18 Participants n=31 Participants	12 Participants n=31 Participants	20 Participants n=31 Participants	19 Participants n=31 Participants	24 Participants n=62 Participants	125 Participants n=248 Participants
Sex: Female, Male Male	17 Participants n=31 Participants	13 Participants n=31 Participants	13 Participants n=31 Participants	19 Participants n=31 Participants	11 Participants n=31 Participants	12 Participants n=31 Participants	38 Participants n=62 Participants	123 Participants n=248 Participants
Race and Ethnicity Not Collected	—	—	—	—	—	—	—	0 Participants Race and Ethnicity were not collected from any participant.
Wasted	2 Participants n=31 Participants	3 Participants n=31 Participants	2 Participants n=31 Participants	3 Participants n=31 Participants	2 Participants n=31 Participants	7 Participants n=31 Participants	6 Participants n=62 Participants	25 Participants n=248 Participants
Stunted	8 Participants n=31 Participants	7 Participants n=31 Participants	8 Participants n=31 Participants	7 Participants n=31 Participants	4 Participants n=31 Participants	11 Participants n=31 Participants	7 Participants n=62 Participants	52 Participants n=248 Participants
Underweight	5 Participants n=31 Participants	3 Participants n=31 Participants	4 Participants n=31 Participants	4 Participants n=31 Participants	3 Participants n=31 Participants	10 Participants n=31 Participants	6 Participants n=62 Participants	35 Participants n=248 Participants
Visited healthcare facility in past 30 days	6 Participants n=31 Participants	2 Participants n=31 Participants	4 Participants n=31 Participants	2 Participants n=31 Participants	6 Participants n=31 Participants	8 Participants n=31 Participants	14 Participants n=62 Participants	42 Participants n=248 Participants

PRIMARY outcome

Timeframe: Baseline and Day 9

Population: 248 children in 124 households were enrolled and randomized to 1 of the 3 antibiotic regimens or placebo. Of these, 124 children were randomized within their household to receive treatment and are included in this analysis. Of these children, 9 children were lost to follow-up. The samples from Amoxicillin Households - Placebo, Azithromycin Households - Placebo, Cotrimoxazole Households - Placebo and half of placebo (31 participants) were not collected and analyzed, due to limited budget.

The primary outcome of the study was pre-specified as α-diversity (inverse Simpson's) at the genus level, expressed in effective number. Simpson's Alpha Diversity were obtained at Baseline and Post-treatment in this study. The minimum of Simpson's index of diversity is 0, there is no maximum. Higher Simpson's index of diversity means more diverse. There are no subscales.

Outcome measures

Outcome measures
Measure	Amoxicillin n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
Simpson's Index of Diversity (Alpha Diversity) in Intestinal Microbiome Baseline	10.2 Index score Interval 8.8 to 11.5	8.8 Index score Interval 7.5 to 10.1	9.7 Index score Interval 8.2 to 11.2	9.6 Index score Interval 8.6 to 10.7
Simpson's Index of Diversity (Alpha Diversity) in Intestinal Microbiome Post-treatment	8.3 Index score Interval 7.0 to 9.6	6.6 Index score Interval 5.5 to 7.8	8.3 Index score Interval 6.9 to 9.7	9.8 Index score Interval 8.7 to 10.9

SECONDARY outcome

Timeframe: Day 9

Population: rectal samples were not analyzed due to limited budget - samples were collected but not analyzed and never will be analyzed

Direct and indirect effect of antibiotics on alpha diversity from rectal samples

Outcome measures

Outcome data not reported

SECONDARY outcome

Timeframe: Day 35

Population: In Amoxicillin, Azithromycin, Cotrimoxazole households, children assigned to receive antibiotic and placebo were analyzed separately, showed in different row below.

Nutritional status as determined by weight-for-height Z-score vs. Placebo household Weight-for-height Z-score in each antibiotic group compared with placebo 4 weeks after last antibiotic dose Weight-for-height Z (WHZ) scores were calculated based on the 2006 World Health Organization (WHO) standards. The mean of the 2006 population standards is 0. Lower standard deviations = worse outcomes. A cutoff of \< -2 means moderately wasted (WHZ). A cutoff of \< -3 means wasted (WHZ).

Outcome measures

Outcome measures
Measure	Amoxicillin n=57 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=56 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
Weight-for-height Z-score Children who received Antibiotic	-0.24 z score Standard Deviation 0.92	-0.71 z score Standard Deviation 0.98	-0.27 z score Standard Deviation 0.91	—
Weight-for-height Z-score Children who received Placebo	-0.52 z score Standard Deviation 1.05	-0.17 z score Standard Deviation 0.85	-0.49 z score Standard Deviation 1.11	-0.28 z score Standard Deviation 1.00

SECONDARY outcome

Timeframe: Day 35

Population: In Amoxicillin, Azithromycin, Cotrimoxazole households, children assigned to receive antibiotic and placebo were analyzed separately, showed in different row below.

Nutritional status as determined by height-for-age Z-score Height-for-age Z-score in each antibiotic group compared with placebo 4 weeks after last antibiotic dose Height-for-age Z (HAZ) score were calculated based on the 2006 World Health Organization (WHO) standards. The mean of the 2006 population standards is 0. Lower standard deviations = worse outcomes. A cutoff of \< -2 means moderately stunted (HAZ). A cutoff of \< -3 means severely stunted (HAZ).

Outcome measures

Outcome measures
Measure	Amoxicillin n=57 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=56 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
Height-for-age Z-score Children who received Antibiotic	-0.80 z score Standard Deviation 1.19	-0.92 z score Standard Deviation 1.13	-0.69 z score Standard Deviation 1.00	—
Height-for-age Z-score Children who received Placebo	-0.73 z score Standard Deviation 1.11	-1.16 z score Standard Deviation 1.34	-1.38 z score Standard Deviation 0.94	-0.59 z score Standard Deviation 1.08

SECONDARY outcome

Timeframe: Day 35

Population: In Amoxicillin, Azithromycin, Cotrimoxazole households, children assigned to receive antibiotic and placebo were analyzed separately, showed in different row below.

Nutritional status as determined by weight-for-age Z-score vs. Placebo household Weight-for-age Z-score in each antibiotic group compared with placebo 4 weeks after last antibiotic dose Weight-for-age Z-score (WAZ) scores were calculated based on the 2006 World Health Organization (WHO) standards. The mean of the 2006 population standards is 0. Lower standard deviations = worse outcomes. A cutoff of \< -2 means moderately underweight (WAZ). A cutoff of \< -3 means severely underweight (WAZ).

Outcome measures

Outcome measures
Measure	Amoxicillin n=57 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=56 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
Weight-for-age Z-score Children who received Antibiotic	-0.60 Z score Standard Deviation 0.87	-1.01 Z score Standard Deviation 0.95	-0.58 Z score Standard Deviation 0.94	—
Weight-for-age Z-score Children who received Placebo	-0.78 Z score Standard Deviation 0.89	-0.78 Z score Standard Deviation 1.02	-1.12 Z score Standard Deviation 1.04	-0.53 Z score Standard Deviation 0.97

SECONDARY outcome

Timeframe: Day 35

Population: In Amoxicillin, Azithromycin, Cotrimoxazole households, children assigned to receive antibiotic and placebo were analyzed separately, showed in different row below.

Nutritional status as determined by mid-upper arm circumference in each antibiotic group compared with placebo 4 weeks after last antibiotic dose Mid-upper arm circumference (MUAC) in each antibiotic group compared with placebo 4 weeks after last antibiotic dose. MUAC is a measure to assess nutritional status. It is measured on a straight left arm, mid-way between the tip of the shoulder and the tip of the elbow. It identifies acute malnutrition and is commonly used in children 6-59 months of age as well as pregnant women. MUAC less than 115 mm indicates severe wasting or severe acute malnutrition (SAM). MUAC greater than or equal to 115 mm and less than 125 mm indicates moderate wasting or moderate acute malnutrition (MAM).

Outcome measures

Outcome measures
Measure	Amoxicillin n=57 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=56 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=58 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
Mid-upper Arm Circumference Children who received Antibiotic	15.01 mm Standard Deviation 0.92	14.53 mm Standard Deviation 1.11	15.49 mm Standard Deviation 0.98	—
Mid-upper Arm Circumference Children who received Placebo	14.90 mm Standard Deviation 1.10	15.15 mm Standard Deviation 1.01	14.83 mm Standard Deviation 1.36	15.23 mm Standard Deviation 1.23

SECONDARY outcome

Timeframe: Baseline and Day 9 (Post- Treatment)

Population: 248 children in 124 households were enrolled and randomized to 1 of the 3 antibiotic regimens or placebo. Of these, 124 children were randomized within their household to receive treatment and are included in this analysis. Of these children, 9 children were lost to follow-up. The samples for children who received placebo in Amoxicillin Households, Azithromycin Households, Cotrimoxazole Households and half of placebo (31 participants) were not collected and analyzed, due to limited budget.

Shannon's Alpha Diversity at Baseline and Post-treatment. combines richness and diversity. Shannon's index of diversity (alpha diversity) measures both the number of species and the inequality between species abundances. A large value is given by the presence of many species with well balanced abundances.

Outcome measures

Outcome measures
Measure	Amoxicillin n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
Shannon's Index of Diversity (Alpha Diversity) in Intestinal Microbiome Baseline	16.6 Index score Interval 14.5 to 18.7	14.6 Index score Interval 13.0 to 16.2	15.6 Index score Interval 13.4 to 17.8	15.4 Index score Interval 14.1 to 16.7
Shannon's Index of Diversity (Alpha Diversity) in Intestinal Microbiome Post-treatment	13.9 Index score Interval 12.1 to 15.8	11.0 Index score Interval 9.3 to 12.7	13.5 Index score Interval 11.6 to 15.4	16.0 Index score Interval 14.3 to 17.8

SECONDARY outcome

Timeframe: Day 9

Population: Nasopharyngeal samples were not analyzed, due to limited budget - samples were collected but not analyzed and never will be analyzed

Direct and indirect effects of antibiotics on Shannon's index of bacterial diversity

Outcome measures

Outcome data not reported

SECONDARY outcome

Timeframe: Baseline and Day 9 (Post- Treatment)

Population: 248 children in 124 households were enrolled and randomized to 1 of the 3 antibiotic regimens or placebo. Of these, 124 children were randomized within their household to receive treatment and are included in this analysis. Of these children, 9 children were lost to follow-up. The samples for children who received placebo in Amoxicillin Households, Azithromycin Households, Cotrimoxazole Households and half of placebo (31 participants) were not collected and analyzed, due to limited budget.

L1-norm distance on bacterial reads (intestinal) - L1 norm is equivalent to Shannon's diversity. Shannon's Alpha Diversity combines richness and diversity. Shannon's index of diversity (alpha diversity) measures both the number of species and the inequality between species abundances. A large value is given by the presence of many species with well balanced abundances.

Outcome measures

Outcome measures
Measure	Amoxicillin n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
L1-norm Distance on Bacterial Reads (Intestinal) Baseline	16.6 Index score Interval 14.5 to 18.7	14.6 Index score Interval 13.0 to 16.2	15.6 Index score Interval 13.4 to 17.8	15.4 Index score Interval 14.1 to 16.7
L1-norm Distance on Bacterial Reads (Intestinal) Post-treatment	13.9 Index score Interval 12.1 to 15.8	11.0 Index score Interval 9.3 to 12.7	13.5 Index score Interval 11.6 to 15.4	16.0 Index score Interval 14.3 to 17.8

SECONDARY outcome

Timeframe: Day 9

Population: Nasopharyngeal samples were not analyzed due to limited budget- samples were collected but not analyzed and never will be analyzed

L1-norm distance on bacterial reads (nasopharyngeal)

Outcome measures

Outcome data not reported

SECONDARY outcome

Timeframe: Baseline and Day 9 (Post- Treatment)

Population: 248 children in 124 households were enrolled and randomized to 1 of the 3 antibiotic regimens or placebo. Of these, 124 children were randomized within their household to receive treatment and are included in this analysis. Of these children, 9 children were lost to follow-up. Indirect effect (antibiotic household - placebo) was not analyzed. we will not analyzed these biological specimens because no funding are available for this. Only direct effect of treatment is analyzed.

L2-norm distance on bacterial reads (intestinal) - L2 norm is equivalent to Simpson's diversity. Simpson's Alpha Diversity were obtained at Baseline and Post-treatment in this study. The minimum of Simpson's index of diversity is 0, there is no maximum. Higher Simpson's index of diversity means more diverse. There are no subscales.

Outcome measures

Outcome measures
Measure	Amoxicillin n=31 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo n=31 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
L2-norm Distance on Bacterial Reads (Intestinal) Baseline	10.2 Index score Interval 8.8 to 11.5	8.8 Index score Interval 7.5 to 10.1	9.7 Index score Interval 8.2 to 11.2	9.6 Index score Interval 8.6 to 10.7
L2-norm Distance on Bacterial Reads (Intestinal) Post-treatment	8.3 Index score Interval 7.0 to 9.6	6.6 Index score Interval 5.5 to 7.8	8.3 Index score Interval 6.9 to 9.7	9.8 Index score Interval 8.7 to 10.9

SECONDARY outcome

Timeframe: Day 9

Population: Nasopharyngeal samples were not analyzed due to limited budget. these samples were collected but won't be analyzed.

L2-norm distance on bacterial reads (nasopharyngeal)

Outcome measures

Outcome data not reported

SECONDARY outcome

Timeframe: 2 years

Population: The outcome is limited to children randomized to placebo in azithromycin households and to the placebo-treated child control in placebo households. A direct effect of antibiotics on the resistome was only observed among children receiving azithromycin compared with placebo; we were unable to process samples from the other study arms due to cost constraints. According to study design, only placebo treated children in these two arms were analyzed.

Prevalence of macrolide resistance genes measured using DNA-seq from rectal swabs.

Outcome measures

Outcome measures
Measure	Amoxicillin n=30 Participants Households were randomized in a 1:1:1:1 fashion to a 5-day course of amoxicillin, azithromycin, cotrimoxazole, or placebo. Within each antibiotic household, one child was randomly assigned to receive placebo. Children will receive treatment everyday, twice a day as is: Amoxicillin: 25 mg/kg/day, divided into twice daily doses for Days 1-5 Amoxicillin Households - Antibiotic: Children in this arm will receive Amoxicillin twice a day.	Azithromycin n=28 Participants Comparison of nasopharyngeal and rectal microbiome in children receiving Azithromycin versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm and treated for 5 days. Children will receive treatment everyday, once a day as is: Azithromycin: 10 mg/kg once daily on Day 1, then 5 mg/kg once daily Days 2-5 Azithromycin: Children in this arm will receive Azithromycin once a day.	Cotrimoxazole Comparison of nasopharyngeal and rectal microbiome in children receiving Cotri-moxazole versus children receiving placebo Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive treatment everyday, once a day as is: Co-trimoxazole: 240 mg daily for Days 1-5 Cotrimoxazole: Children in this arm will receive co-trimoxazole once a day.	Placebo Comparison of nasopharyngeal and rectal microbiome in children receiving placebo versus children receiving antibiotics Children aged 6 months to 59 months will be measured and weighed then, they will be randomized to one of the study arm. Children will receive Placebo everyday, once a day. Placebo: Children in this arm will receive Placebo once a day.
Number of Participants With Macrolide Resistance Genes	12 Participants	9 Participants	—	—

SECONDARY outcome

Timeframe: 2 years

Population: The intestinal microbiome in rectal swabs were not analyzed due to limited budget. these samples were collected but will not be analyzed

Alpha diversity in the intestinal microbiome using DNA-seq from rectal swabs