Project Title
The influence of tuberculosis treatment on the emergence of antimicrobial resistance amongst the ESKAPE bacteria (ESKAPE-TB)
EDCTP Project
TMA2019CDF-2738
EDCTP Project Call
Career Development Fellowship (CDF)
Project Objectives
Aim 1: To evaluate the relative abundance of ESKAPE bacteria (16S rRNA sequencing) and ESKAPE AMR associated genes (N-GARD assay) in stool of TB cases during treatment (first-line: n=50, second-line
treatment: n=14).
Sub-Aim 1.1: To measure the relative abundance of ESKAPE bacteria at baseline (pre-treatment initiation),
during treatment (2 months and 6 months) and up to one-year post-treatment in stool of TB cases on first-line treatment and second-line treatment.
Sub-aim 1.2: To evaluate, at the same timepoints, the relative frequency of AMR-associated genes (carbapenem, quinolones, aminoglycosides, trimethoprim-sulfamethoxazole, tetracycline, streptomycin,
chloramphenicol, fosfomycin, and colistin).
Aim 2: To compare relative abundances of ESKAPE taxa, AMR frequency, and associated risk factors in cases
on either regimen over time.
Sub-Aim 2.1: To compare relative abundances of ESKAPE bacteria and AMR related genes between cases on
the first-line TB regimen vs. the second-line TB regimen.
Sub-Aim 2.2: To identify demographic and clinical (HIV status, previous antibiotic exposure, drug side effects
e.g. gastrointestinal disturbances) risk factors of AMR acquisition, stratified by regimen.
Project Summary
Globally, the emergence of antimicrobial resistance (AMR) due to antibiotic usage is considered one of the most pressing future health problems. Tuberculosis (TB), which kills more people worldwide than any other infectious disease, requires hundreds-to-thousands of doses of antibiotics to achieve cure. TB treatment is prescribed to millions of individuals yearly, and after cure these individuals often develop recurrent post-TB complications. There is little information
exists at the intersection of TB and AMR (i.e., resistance in microbes other than M. tuberculosis
complex). The ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae,
Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) are considered key taxa in AMR acquisition. These are important residents in our bodies, but cause most drug-resistant
opportunistic infections, especially in critically ill and immunocompromised individuals, such as
HIV-positive individuals. We aimed to evaluate the relative abundance of ESKAPE bacteria (16S rRNA sequencing) and ESKAPE AMR-associated genes (N-GARD assay) in stool of TB cases during
treatment (first-line: n=50, second-line treatment: n=14). Additionally, we compare relative
abundances of ESKAPE taxa, AMR frequency, and associated risk factors in cases on either regimen
over time. In this study, we evaluated longitudinally the impact of 6 months of standard TB treatment and the
longer drug resistant TB treatment on ESKAPE AMR emergence within the stool microbiome. We used the Next-Gen Antimicrobial Resistance Detection (N-GARD) assay, a novel, multiplex,
sequencing technique to profile AMR associated strains and genes present in stool of drug-susceptible and drug-resistant TB cases longitudinally (n=42 at pre-treatment; n= 37 at month-2; n=39 at month-6 during treatment; n=19 at month 12 and n=12-month 18 post treatment) and
drug-resistant (n=8 at w1; n=8 at w10; n=8 at w16; n=8 at w24; n=7 at pm06 and n=8 at pm12).
The aim of the study was to evaluate the relative abundance of ESKAPE bacteria (16S rRNA
sequencing) and ESKAPE AMR-associated genes (N-GARD assay) in stool of TB cases during
treatment. Preliminary findings showed significant longitudinal decreases in Escherichia coli and trends of longitudinal increases in AMR-related strains; Enterobacter cloacae, Klebsiella pnemoniae, Klebsiella
varicola in the drug susceptible cohort. Additionally, the drug susceptible cohort showed
fluctuations in tetD, strB and trends of increased FosA, qnrD, qnrA, Sul3 and SaM2 were seen. The
drug-resistant cohort showed significant increase in npmA and trends of longitudinal increases of ermA and sul1. Overall, the drug-resistant cohort had more significant changes in AMR-associated genes compared to drug susceptible cohort. These changes in the resistome during TB treatment require future investigation and future studies will involve more targeted analysis of identified trends.
http://www.sun.ac.za/english/faculty/healthsciences/Molecular_Biology_Human_Genetics/clinical_mycobacteriology_epidemiology/Pages
/THE-ESKAPE-TB-STUDY.aspx
Results & Outcomes
Preliminary findings of drug-susceptible and drug-resistant TB cases longitudinally (n=42 at pretreatment; n= 37 at month-2; n=39 at month-6 during treatment; n=19 at month 12 and n=12-month 18 post treatment) and drug-resistant (n=8 at w1; n=8 at w10; n=8 at w16; n=8 at w24; n=7 at pm06 and n=8 at pm12) showed significant longitudinal decreases in Escherichia coli and trends of
longitudinal increases in AMR-related strains; Enterobacter cloacae, Klebsiella pnemoniae, Klebsiella varicola in the drug susceptible cohort. Additionally, the drug susceptible cohort showed fluctuations in tetD, strB and trends of increased FosA, qnrD, qnrA, Sul3 and SaM2 were seen. The drug-resistant cohort showed significant increase in npmA and trends of longitudinal increases of ermA and sul1. Overall, the drug-resistant cohort had more significant changes in AMR-associated genes compared to drug susceptible cohort. The trends of resistance seen in this study were not only to drugs used in the TB regimens and this adds valuable information that could be used to identify vulnerable community of
individuals that have prior resistance to antibiotics. More indepth studies of this nature could impact the preservation of current antibiotics and highlight mechanisms of resistance acquisition not previously explored. These changes in the resistome during TB treatment require future investigation and future studies will involve more targeted analysis of identified trends.
