Emergence of Canonical and Noncanonical Genomic Variants following In Vitro Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine

In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible (fbiD: del555GCT) or rifampicin mono-resistant (fbiA: 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678, glpK, nuoG, and uvrD1. Genes with variants in the bedaquiline resistant mutants included atpE, fadE28, truA, mmpL5, glnH, and pks8, while clofazimine-resistant mutants displayed ppsD, fbiA, fbiD, mutT3, fadE18, Rv0988, and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.

Percutaneous left atrial appendage occlusion: impact on left atrial deformation indices

Background

Percutaneous left atrial appendage occlusion (LAAO) is an accepted alternative to thromboprophylaxis in atrial fibrillation (AF) patients who are: i) intolerant to oral anticoagulation (OAC) (e.g. life-threatening haemorrhage), ii) non-adherent to OAC, or iii) at a high bleeding risk with OAC. Improvement in LA mechanics was shown post-LAAO in the LAFIT-LARIAT study, using the Lariat device (SentreHEART, Redwood City, CA, USA). No significant change was seen in LA mechanics after LAAO with the Watchman device (Boston Scientific, St. Paul, MN, USA) in the LAFIT-Watchman study. The impact of LAAO with the Amplatz or Amulet device (Abbot Vascular, St. Paul, MN, USA) on LA deformation mechanics, has not been investigated.

Purpose

To evaluate the impact of LAAO with the Amplatz or Amulet device on echocardiographic LA deformation indices.

Methods

All patients undergoing percutaneous LAAO from 2013 to 2021 at a single centre were included from an ongoing clinical registry. LA reservoir, conduit and contractile strain and strain rate were assessed with two-dimensional speckle tracking echocardiography from an apical four-chamber view. Conduit and contractile strain and strain rates were only recorded for patients without AF at the time of echocardiography. Changes in LA deformation indices over time were compared with a linear mixed model.

Results

32 LAAO recipients (mean age 72±12 years, 63% male) were analysed. 5 (16%) patients had AF pre- or post-procedure. After a mean follow-up of 17 months, the mean LA reservoir strain increased from 11.8±7.7% to 12.9±9.1% (P=0.49), the mean LA conduit strain increased from 6.8±6.0% to 8.0±7.4% (P=0.42) and the mean LA contractile strain decreased from 5.7±5.2% to 5.3±5.4% (P=0.77). During the same time interval, the mean LA reservoir strain rate decreased from 0.68±0.44/s to 0.64±0.47/s (P=0.70), the mean LA conduit strain rate increased from −0.52±0.43/s to −0.44±0.32/s (P=0.42) and the mean LA contractile strain rate decreased from −0.77±0.55/s to −0.83±0.53/s (P=0.66).

Conclusions

No statistically significant improvement in LA mechanical function was seen after LAAO with the Amplatz or Amulet device, although a trend towards improved strain was observed for reservoir and conduit strain, with a worsening in contractile strain. Different LAAO devices therefore appear to have divergent effects on LA deformation, the clinical implications of which require further study.

Funding Acknowledgement

Type of funding sources: None.

EMERGENCE OF BEDAQUILINE RESISTANCE AFTER COMPLETION OF BEDAQUILINE-BASED DRUGRESISTANT TB TREATMENT: A CASE STUDY FROM SOUTH AFRICA

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WHOLE GENOME SEQUENCING SHEDS LIGHT ON THE TRANSMISSION DYNAMICS OF A MULTIDRUG RESISTANT MYCOBACTERIUM TUBERCULOSIS OUTBREAK OVER 23 YEARS IN A HIGH INCIDENCE SETTING

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Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

BACKGROUND

Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis.

METHODS

Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline.

RESULTS

Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30% to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event.

CONCLUSIONS

Our study demonstrated true levels of genetic diversity within an M. tuberculosis population and showed that genetic diversity may be re-defined when a selective pressure, such as drug exposure, is imposed on M. tuberculosis populations during the course of infection. This suggests that the genome of M. tuberculosis is more dynamic than previously thought, suggesting preparedness to respond to a changing environment.

Interferon-gamma release assays for the detection of Mycobacterium tuberculosis infection in children with cancer

SETTING

The paediatric oncology unit at Tygerberg Children's Hospital, South Africa.

OBJECTIVES

To assess the use of the tuberculin skin test (TST) and two commercial interferon-gamma release assays (IGRAs) for the detection of Mycobacterium tuberculosis infection in children with cancer before initiating chemotherapy treatment.

DESIGN

Prospective hospital-based study, including children newly diagnosed with cancer; all underwent TST and IGRA testing.

RESULTS

Of the 34 children enrolled, seven (17.6%) tested positive with either test: TST (3/7, 8.8%), T-SPOT.TB (n = 6, 17.6%) and QuantiFERON-TB Gold In-Tube (QFT-G; n = 3, 8.8%). T-SPOT.TB assay results were negative in 17 (50.0%) and indeterminate in four (11.8%) children. Six T-SPOT.TB tests could not be completed due to low cell counts (<100,000 per well), and one clotted. QFT-G results were negative in 26 (76.5%) and indeterminate in five (14.7%).

CONCLUSIONS

TST and IGRAs were frequently discordant, with fewer positive results than expected. T-SPOT.TB produced more positive results, but inadequate cell counts were a particular problem. The sample size was too small to comment with confidence on test accuracy. All latent TB infection tests appear to perform sub-optimally in this group of children, and therefore none of them can be used in isolation to confirm or disprove TB infection.

Improved outcome in South African children of mixed ethnicity treated for all

A historical cohort study with an analytical component was conducted to determine whether risk-appropriate chemotherapy can improve survival in children of mixed ethnicity with ALL. Eighty-one coloured children treated for ALL in South Africa were divided into 2 groups: group A (n = 39), treated prior to 1992, and group B (n = 42), treated after 1992. A comparison was made of survival, treatment complications, and supportive measures. The two groups were comparable. The mean nadirs of the white cell count (p < .01), platelet count (p = .01), and hemoglobin value (p < .01) were significantly lower in group B. The survival rate of 37% in group A improved to 66% in group B (p = .025). The results show that a risk-adapted regimen increased survival in children of mixed ethnicity in the Western Cape, despite increased hematological toxicity and episodes of febrile neutropenia.