结核分枝杆菌基因表达与氟喹诺酮类耐药和外排泵抑制相关。

Mycobacterium tuberculosis Gene Expression Associated With Fluoroquinolone Resistance and Efflux Pump Inhibition.

机构信息

Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

出版信息

J Infect Dis. 2023 Aug 16;228(4):469-478. doi: 10.1093/infdis/jiad112.

DOI:10.1093/infdis/jiad112

PMID:37079382

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10428193/

Abstract

BACKGROUND

We evaluated the relationship between response to efflux pump inhibition in fluoroquinolone-resistant Mycobacterium tuberculosis (Mtb) isolates and differences in gene expression and expression quantitative trait loci (eQTL).

METHODS

We determined ofloxacin minimum inhibitory concentration (MIC) for ofloxacin-resistant and -susceptible Mtb isolates without and with the efflux pump inhibitor verapamil. We performed RNA sequencing (RNA-seq), whole genome sequencing (WGS), and eQTL analysis, focusing on efflux pump, transport, and secretion-associated genes.

RESULTS

Of 42 ofloxacin-resistant Mtb isolates, 27 had adequate WGS coverage and acceptable RNA-seq quality. Of these 27, 7 had >2-fold reduction in ofloxacin MIC with verapamil; 6 had 2-fold reduction, and 14 had <2-fold reduction. Five genes (including Rv0191) had significantly increased expression in the MIC fold change >2 compared to <2 groups. Among regulated genes, 31 eQTLs (without ofloxacin) and 35 eQTLs (with ofloxacin) had significant allele frequency differences between MIC fold change >2 and <2 groups. Of these, Rv1410c, Rv2459, and Rv3756c (without ofloxacin) and Rv0191 and Rv3756c (with ofloxacin) have previously been associated with antituberculosis drug resistance.

CONCLUSIONS

In this first reported eQTL analysis in Mtb, Rv0191 had increased gene expression and significance in eQTL analysis, making it a candidate for functional evaluation of efflux-mediated fluoroquinolone resistance in Mtb.

摘要

背景

我们评估了氟喹诺酮类药物耐药结核分枝杆菌（Mtb）分离株对流出泵抑制的反应与基因表达和表达数量性状基因座（eQTL）差异之间的关系。

方法

我们确定了氟喹诺酮耐药和敏感 Mtb 分离株的氧氟沙星最小抑菌浓度（MIC），而没有和有流出泵抑制剂维拉帕米。我们进行了 RNA 测序（RNA-seq）、全基因组测序（WGS）和 eQTL 分析，重点关注流出泵、转运和分泌相关基因。

结果

在 42 株氧氟沙星耐药 Mtb 分离株中，有 27 株具有足够的 WGS 覆盖度和可接受的 RNA-seq 质量。在这 27 株中，有 7 株用维拉帕米后氧氟沙星 MIC 降低了 2 倍以上；6 株降低了 2 倍，14 株降低了不到 2 倍。与 MIC 变化<2 相比，MIC 变化>2 时，有 5 个基因（包括 Rv0191）的表达显著增加。在受调控的基因中，有 31 个 eQTL（无氧氟沙星）和 35 个 eQTL（有氧氟沙星）在 MIC 变化>2 和<2 组之间的等位基因频率差异有统计学意义。其中，Rv1410c、Rv2459 和 Rv3756c（无氧氟沙星）和 Rv0191 和 Rv3756c（有氧氟沙星）以前与抗结核药物耐药有关。