Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum

Abstract

Background: Tuberculous sputum provides a sample of bacilli that must be eliminated by chemotherapy and that may go on to transmit infection. A preliminary observation that Mycobacterium tuberculosis cells contain triacylglycerol lipid bodies in sputum, but not when growing in vitro, led us to investigate the extent of this phenomenon and its physiological basis.

Methods and findings: Microscopy-positive sputum samples from the UK and The Gambia were investigated for their content of lipid body-positive mycobacteria by combined Nile red and auramine staining. All samples contained a lipid body-positive population varying from 3% to 86% of the acid-fast bacilli present. The recent finding that triacylglycerol synthase is expressed by mycobacteria when they enter in vitro nonreplicating persistence led us to investigate whether this state was also associated with lipid body formation. We found that, when placed in laboratory conditions inducing nonreplicating persistence, two M. tuberculosis strains had lipid body levels comparable to those found in sputum. We investigated these physiological findings further by comparing the M. tuberculosis transcriptome of growing and nonreplicating persistence cultures with that obtained directly from sputum samples. Although sputum has traditionally been thought to contain actively growing tubercle bacilli, our transcript analyses refute the hypothesis that these cells predominate. Rather, they reinforce the results of the lipid body analyses by revealing transcriptional signatures that can be clearly attributed to slowly replicating or nonreplicating mycobacteria. Finally, the lipid body count was highly correlated (R(2) = 0.64, p < 0.03) with time to positivity in diagnostic liquid cultures, thereby establishing a direct link between this cytological feature and the size of a potential nonreplicating population.

Conclusion: As nonreplicating tubercle bacilli are tolerant to the cidal action of antibiotics and resistant to multiple stresses, identification of this persister-like population of tubercle bacilli in sputum presents exciting and tractable new opportunities to investigate both responses to chemotherapy and the transmission of tuberculosis.

Figure 1. Lipid Bodies in Tuberculous Sputum Samples

Auramine/Nile red-fixed sputum smears [5] and aerobic M. tuberculosis growth. Variation in lipid bodies per cell: (A) none, (B) three, (C) five, and (D) eight. Samples are shown with (E) low and (F) high proportions of lipid body–positive cells. (G) Aerobically grown mid-log M. tuberculosis H37Rv contained negligible lipid bodies. Scale bar 2μm.

Figure 2. Display of Genes Differentially Regulated in Sputum and NRP versus Aerobic Culture

Clustering of 648 genes significantly differentially expressed in either sputum, NRP1, NRP2, or a 70:30 mix of aerobic:NRP2 compared to aerobic growth. Biological and technical replicates of conditions are displayed as columns, genes as rows. Red represents the induction of gene expression relative to aerobic growth, green repression. Asterisked columns mark the conditions in which genes were identified as significantly differentially expressed compared to aerobic growth. Boxes 1 and 2 highlight clusters of genes similarly regulated in NRP2 and sputum.

Figure 3. Genes Required for Aerobic Respiration and Ribosomal Function Show Decreased Expression in Sputum Compared with Aerobic Growth while Genes Involved in Lipid Metabolism Were Induced

Box and whisker plots showing the distribution of expression ratios (log2 scale) of (A) 21 aerobic respiration genes and (B) 45 ribosomal genes in NRP2 and sputum relative to aerobic growth using functional classifications defined by Cole et al., 1998 [24]; also (C) 64 genes that may be involved in cholesterol catabolism [38] and (D) 45 genes in the fadB, echA, fadE, and fadA families, which may be involved in the β-oxidation of fatty acids. *Significant difference (p < 0.01) between NRP2 or sputum compared to aerobic; ^#Significant difference (p < 0.01) between NRP2 and sputum.

Figure 4. Gene Expression Signatures Representative of Slow Growth and the M. tuberculosis In Vivo Phenotype Were Identified in the Sputum Transcriptome

The distribution of expression ratios (log2 scale) of (A) 129 genes repressed and (B) 127 genes induced by slow growth [53]; (C) 106 genes repressed and (D) 85 genes induced by NRP2 compared to aerobic growth (this report); (E) 111 genes repressed and (F) 339 genes induced on murine macrophage infection [12]. In all plots the y-axis denotes fold change, boxes encompass the 25th and 75th percentiles, whiskers have been set at 1.5× the range between these values, and only outliers are shown as individual points. *Significant difference (p < 0.01) between NRP2 or sputum compared to aerobic; ^#Significant difference (p < 0.01) between NRP2 and sputum.

Figure 5. Specific Transcript Ratios for tgs1, hspX, icl1, nuoB, qcrC, and ctaD in AFB-Positive Sputum Samples Determined by qRT-PCR and Normalized to Values for Aerobically Grown Mid-Log M. tuberculosis H37Rv

Individual target gene transcript copy numbers were normalized against transcript copy numbers of sigA in the samples concerned. Numbers on the abscissa refer to the designated sputum sample numbers.

Figure 6. Time to Positivity in BACTEC 960 Cultures Related to Lipid Body Counts Determined in the Samples from Which the Cultures Were Prepared

Analysis was confined to samples graded 3+ by microscopy to minimize the effect of varying bacterial inoculum on time to positivity.