Dataset DOI: 10.5061/dryad.k98sf7mnv

Description of the data and file structure

All data was generated from human monocyte derived macrophages infected with Mycobacterium avium subsp. hominissuis 104 (MAH 104) strain.

Files and variables

File: Thong_JID_DRYAD_File_2026.xlsx

The data is presented in an Excel file. All data was anonymised and relabelled after analysis starting at Donor 1 etc. and as such any data from a given donor can be matched throughout the data set. It is highly recommended to read the Excel file in conjunction with the associated paper. The data has been organised based on the layout of figures in the associated paper published in the Journal of Infectious Disease.

For the Excel file the outputs are listed in columns F or AA. These outputs correspond to subparts of figure 1, i.e. Fig 1A, 1B etc. in the accompanying paper in the Journal of Infectious Disease. The Excel workbook preserves the original figure-oriented layout used for the associated manuscript for ease of cross referencing for readers of the manuscript.

Corresponding CSV files contain the same underlying data in machine-readable format for reuse and re-analysis. Labelled Thong JID DRYAD File 2026 Fig1A, Thong JID DRYAD File 2026 Fig1B etc.

All cells used to generate the data are human monocyte derived macrophages and are infected with Mycobacterium avium subsp. hominissuis 104.

Excel Sheet 1 (Figure 1):

Data is derived from human monocyte derived macrophages (MDM) that were treated with vehicle control (VC; ethanol 0.02%) or dexamethasone (0.5 or 5 µM) for 20 min prior to infection with M. avium and analysis in the Seahorse XFe24 Analyzer using a glycolytic rate assay (A-F). Alternatively, human MDM were treated with VC or dexamethasone for 1 hours, infected with M. avium lysed and RNA extracted. The expression of mRNA transcripts of metabolic enzymes were assessed to support the functional metabolic data (G-J). Mycobacterial growth was examined in dexamethasone treated macrophages by colony forming unit assay (K-L). Cell death was assessed in uninfected or M. avium infected MDM in the absence or presence of dexamethasone (N). Finally, ability of dexamethasone to alter the secretion of cytokines TNF, IL-6, IL-8, IL-1β and IL-10 was assessed in supernatants from M. avium infected MDM (O-S). The expression of mRNA transcripts of NADPH oxidase subunits were assessed to support the CFU data (T-W).

Outputs within the data:

Glyco Proton Extrusion Rate (GlycoPER; pmol/min), a marker of glycolysis. This output relates to Figure 1A, 1B, 1C, and 1D of the associated paper.

Oxygen Consumption Rate (OCR, pmol/min), a surrogate marker of oxidative phosphorylation. This output relates to Figure 1E, and 1F of the associated paper.

Gene expression relative to 18S (fold change to infected control) for PFKFB3, GAPDH and PKM2. These are genes encoding for glycolytic enzymes. This output relates to Figure 1G-I of the associated paper.

Gene expression relative to 18S (fold change to infected control) for ATP5B. This is a gene encoding an enzyme required for oxidative phosphorylation. This output relates to Figure 1J of the associated paper.

Colony Forming Units (CFU) per mL (CFU/mL) were used to measure bacterial growth from infected macrophages. This output relates to Figures 1K, 1L and 1M of the associated paper. 

Cell Death calculated as a percentage (%) of total cells. This output relates to Figure 1N of the associated paper.

Secreted levels of TNF, IL-6, IL-8, IL-1β and IL-10 are reported as picogram per mL (pg/mL) and were assayed by ELISA. This output relates to Figure 1O-R of the associated paper.

Gene expression relative to 18S (fold change to infected control) for CYBB, CYBA, NCF1 and NCF2. These genes encode for subunits of the NADPH oxidase enzyme complex. This output relates to Figure 1T-W of the associated paper.

Figure 1A

• Thong_JID_DRYAD_File_2026_Fig1A.csv

Time-course of a Seahorse glycolytic rate assay measuring GlycoPER of human monocyte-derived macrophages (MDM) treated with vehicle control (VC), dexamethasone 0.5 μM, or dexamethasone 5 μM and infected in realtime with M. avium after the 4^th reading during the assay. GlycoPER (pmol/min) is a measure of cellular glycolytic activity.

Figure 1B

• Thong_JID_DRYAD_File_2026_Fig1B.csv

Average induced glycolysis was calculated from the Seahorse time-course in Figure 1A, post infection with M. avium and prior to the addition of inhibitors to conduct the glycolytic rate assay. Values are reported as GlycoPER (pmol/min).

Figure 1C

• Thong_JID_DRYAD_File_2026_Fig1C.csv

Maximum induced glycolysis was derived from the final reading before the addition of inhibitors to conduct the glycolytic rate assay in Figure 1A. Values are reported as GlycoPER (pmol/min).

Figure 1D

• Thong_JID_DRYAD_File_2026_Fig1D.csv

Compensatory glycolysis calculated from the Seahorse Glycolytic Rate Assay shown in Figure 1A. Compensatory glycolysis represents the ability of cells to increase glycolysis in response to loss of mitochondrial ATP production by blockade using rotenone and antimycin A during the Glycolytic Rate Assay. Values are reported as GlycoPER (pmol/min).

Figure 1E

• Thong_JID_DRYAD_File_2026_Fig1E.csv

Induced oxygen consumption rate (OCR) was calculated from the reading post infection with M. avium to the reading immediately prior to addition of inhibitors to conduct the glycolytic rate assay. Data is derived from the time-course in figure 1F. OCR is a surrogate measure of oxidative phosphorylation and is reported in pmol/min.

Figure 1F

• Thong_JID_DRYAD_File_2026_Fig1F.csv

Time-course OCR measurements obtained during Seahorse analysis. OCR is reported in pmol/min.

Figure 1G

• Thong_JID_DRYAD_File_2026_Fig1G.csv

Expression of the glycolytic enzyme gene PFKFB3 in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Figure 1H

• Thong_JID_DRYAD_File_2026_Fig1H.csv

Expression of the glycolytic enzyme gene GAPDH in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Figure 1I

• Thong_JID_DRYAD_File_2026_Fig1I.csv

Expression of the glycolytic enzyme gene PKM2 in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Figure 1J

• Thong_JID_DRYAD_File_2026_Fig1J.csv

Expression of ATP5B, a gene involved in oxidative phosphorylation, in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Figure 1K

• Thong_JID_DRYAD_File_2026_Fig1K.csv

Bacterial burden measured as colony-forming units per millilitre (CFU/mL) at 3 h, 48 h and 120 h after M. avium infection in the presence or absence of dexamethasone.

Figure 1L

• Thong_JID_DRYAD_File_2026_Fig1L.csv

CFU/mL values at 48 h post-infection extracted from Figure 1K for statistical comparison.

Figure 1M

• Thong_JID_DRYAD_File_2026_Fig1M.csv

CFU/mL values at 120 h post-infection extracted from Figure 1K for statistical comparison.

Figure 1N

• Thong_JID_DRYAD_File_2026_Fig1N.csv

Percentage cell death in uninfected or Mycobacterium avium-infected macrophages treated with vehicle control or dexamethasone.

Figure 1O

• Thong_JID_DRYAD_File_2026_Fig1O.csv

TNF secretion in supernatants of uninfected or Mycobacterium avium-infected human MDM, in the presence or absence of dexamethasone measured by ELISA. The data is reported as pg/mL.

Figure 1P

• Thong_JID_DRYAD_File_2026_Fig1P.csv

IL-6 secretion in supernatants of uninfected or Mycobacterium avium-infected human MDM, in the presence or absence of dexamethasone measured by ELISA. The data is reported as pg/mL.

Figure 1Q

• Thong_JID_DRYAD_File_2026_Fig1Q.csv

IL-8 secretion in supernatants of uninfected or Mycobacterium avium-infected human MDM, in the presence or absence of dexamethasone measured by ELISA. The data is reported as pg/mL.

Figure 1R

• Thong_JID_DRYAD_File_2026_Fig1R.csv

IL-1β secretion in supernatants of uninfected or Mycobacterium avium-infected human MDM, in the presence or absence of dexamethasone measured by ELISA. The data is reported as pg/mL.

Figure 1S

• Thong_JID_DRYAD_File_2026_Fig1S.csv

IL-10 secretion in supernatants of uninfected or Mycobacterium avium-infected human MDM, in the presence or absence of dexamethasone measured by ELISA. The data is reported as pg/mL.

Figure 1T

• Thong_JID_DRYAD_File_2026_Fig1T.csv

Expression of the NADPH oxidase subunit CYBB in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Figure 1U

• Thong_JID_DRYAD_File_2026_Fig1U.csv

Expression of the NADPH oxidase subunit CYBA in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Figure 1V

• Thong_JID_DRYAD_File_2026_Fig1V.csv

Expression of the NADPH oxidase subunit NCF1 in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Figure 1W

• Thong_JID_DRYAD_File_2026_Fig1W.csv

Expression of the NADPH oxidase subunit NCF2 in M. avium infected human MDM treated with dexamethasone and measured by qPCR. The data is reported as fold change relative to M. avium infected controls.

Abbreviations

• VC: Vehicle Control
• Dex: Dexamethasone
• MDM: Monocyte-Derived Macrophages
• MAH: Mycobacterium avium subsp. hominissuis
• GlycoPER: Glycolytic Proton Efflux Rate
• OCR: Oxygen Consumption Rate
• CFU: Colony Forming Unit
• TNF: Tumour Necrosis Factor
• IL: Interleukin
• qPCR: Quantitative Polymerase Chain Reaction

Human subjects data

All individuals provided written informed consent and were made aware that collective results arising from samples given would be published. Each donor was assigned an anonymized, sequential identification number (starting at 1) after data analysis and graphing. These identifiers are arbitrary and cannot be linked to any personal information, ensuring complete anonymisation.