Three-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance

Antibiofilm approaches as a new paradigm for treating infections

The lack of effective antibiotics for drug-resistant infections has led the World Health Organization to declare antibiotic resistance a global priority. Most bacterial infections are caused by microbes growing in structured communities called biofilms. Bacteria growing in biofilms are less susceptible to antibiotics than their planktonic counterparts. Despite their significant clinical implications, bacterial biofilms have not received the attention they warrant, with no approved antibiotics specifically designed for their eradication. In this paper, we aim to shed light on recent advancements in antibiofilm strategies that offer compelling alternatives to traditional antibiotics. Additionally, we will briefly explore the potential synergy between computational approaches, including the emerging field of artificial intelligence, and the accelerated design and discovery of novel antibiofilm molecules in the years ahead.

Cellulase Promotes Mycobacterial Biofilm Dispersal in Response to a Decrease in the Bacterial Metabolite Gamma-Aminobutyric Acid

Biofilm dispersal contributes to bacterial spread and disease transmission. However, its exact mechanism, especially that in the pathogen Mycobacterium tuberculosis, is unclear. In this study, the cellulase activity of the M. tuberculosis Rv0062 protein was characterized, and its effect on mycobacterial biofilm dispersal was analyzed by observation of the structure and components of Rv0062-treated biofilm in vitro. Meanwhile, the metabolite factors that induced cellulase-related biofilm dispersal were also explored with metabolome analysis and further validations. The results showed that Rv0062 protein had a cellulase activity with a similar optimum pH (6.0) and lower optimum temperature (30 °C) compared to the cellulases from other bacteria. It promoted mycobacterial biofilm dispersal by hydrolyzing cellulose, the main component of extracellular polymeric substrates of mycobacterial biofilm. A metabolome analysis revealed that 107 metabolites were significantly altered at different stages of M. smegmatis biofilm development. Among them, a decrease in gamma-aminobutyric acid (GABA) promoted cellulase-related biofilm dispersal, and this effect was realized with the down-regulation of the bacterial signal molecule c-di-GMP. All these findings suggested that cellulase promotes mycobacterial biofilm dispersal and that this process is closely associated with biofilm metabolite alterations.

Three-Dimensional Rotary Culture to Model Mycobacterial Biofilms in Low-Shear Detergent-Free Liquid Suspension

In vitro biofilm models have allowed researchers to investigate the role biofilms play in the pathogenesis, virulence, and antimicrobial drug susceptibility of a wide range of bacterial pathogens. Rotary cell culture systems create three-dimensional cellular structures, primarily applied to eukaryotic organoids, that better capture characteristics of the cells in vivo. Here, we describe how to apply a low-shear, detergent-free rotary cell culture system to generate biofilms of Mycobacterium bovis BCG. The three-dimensional biofilm model forms mycobacterial cell aggregates in suspension as surface-detached biomass, without severe nutrient starvation or environmental stress, that can be harvested for downstream experiments. Mycobacterium bovis BCG derived from cell clusters display antimicrobial drug tolerance, presence of an extracellular matrix, and evidence of cell wall remodeling, all features of biofilm-associated bacteria that may be relevant to the treatment of tuberculosis.

Impaired ESX-3 Induces Bedaquiline Persistence in Mycobacterium abscessus Growing Under Iron-Limited Conditions

ESX-3 is a secretion pathway which is essential for mycobactin-mediated iron acquisition under iron-limited conditions. Although present in all Mycobacterium sp., ESX-3 remains to be elucidated in Mycobacterium abscessus. In the study reported here, impaired ESX-3 seriously restricts the growth of M. abscesses under iron-limited conditions; growth is salvaged by functional ESX-3 or iron supplementation. Notably, impaired ESX-3 does not kill M. abscesses when environmental iron is insufficient but induces persistence to bedaquiline, a diarylquinoline class antibiotic used to treat multidrug-resistant mycobacteria. One potential mechanism contributing to persistence is the iron deficiency due to impaired ESX-3 suppressing succinate dehydrogenase activity, which dysregulates the tricarboxylic acid cycle and inactivates bedaquiline. Experiments conducted here also demonstrate that the regulator, MtrA, can bind ESX-3 and promote the survival of M. abscessus. As such, this study suggests that a novel pathway involving MtrA, ESX-3, iron metabolism, and the TCA cycle contributes to bedaquiline persistence in M. abscesses growing under iron-limited conditions.

Mucispirillum schaedleri: Biofilm Architecture and Age-Dependent Pleomorphy

Round bodies in spirochete cultures have been a controversial subject since their description seven decades ago. We report the existence of round bodies (spherical cells) in cultures of Mucispirillum schaedleri, a spiral bacterium phylogenetically distant from spirochetes. Furthermore, when grown in biofilms, M. schaedleri demonstrates a unique morphology known as cording, which has been previously described only in mycobacteria. Thus, M. schaedleri has two distinct features, each previously thought to be unique to two different phylogenetically distant groups of bacteria.

In vitro and ex vivo proteomics of Mycobacterium marinum biofilms and the development of biofilm-binding synthetic nanobodies

The antibiotic-tolerant biofilms present in tuberculous granulomas add an additional layer of complexity when treating mycobacterial infections, including tuberculosis (TB). For a more efficient treatment of TB, the biofilm forms of mycobacteria warrant specific attention. Here, we used Mycobacterium marinum (Mmr) as a biofilm-forming model to identify the abundant proteins covering the biofilm surface. We used biotinylation/streptavidin-based proteomics on the proteins exposed at the Mmr biofilm matrices in vitro to identify 448 proteins and ex vivo proteomics to detect 91 Mmr proteins from the mycobacterial granulomas isolated from adult zebrafish. In vitro and ex vivo proteomics data are available via ProteomeXchange with identifier PXD033425 and PXD039416, respectively. Data comparisons pinpointed the molecular chaperone GroEL2 as the most abundant Mmr protein within the in vitro and ex vivo proteomes, while its paralog, GroEL1, with a known role in biofilm formation, was detected with slightly lower intensity values. To validate the surface exposure of these targets, we created in-house synthetic nanobodies (sybodies) against the two chaperones and identified sybodies that bind the mycobacterial biofilms in vitro and those present in ex vivo granulomas. Taken together, the present study reports a proof-of-concept showing that surface proteomics in vitro and ex vivo proteomics combined are a valuable strategy to identify surface-exposed proteins on the mycobacterial biofilm. Biofilm-surface-binding nanobodies could be eventually used as homing agents to deliver biofilm-targeting treatments to the sites of persistent biofilm infection.

Biofilms in tuberculosis: What have we learnt in the past decade and what is still unexplored?

Elucidating how Mycobacterium tuberculosis produces biofilms, and its impact for tuberculosis (TB) pathogenesis is gaining momentum. Here, we discuss recent findings reported over the last decade, which help us gain insights into the association between biofilm formation and TB pathogenesis. A new appreciation of extracellular TB phenotypes found in lung lesions will drive drug and vaccine discovery forward to new possibilities.