Mutations upstream of fabI in triclosan resistant Staphylococcus aureus strains are associated with elevated fabI gene expression

Resistance or tolerance? Highlighting the need for precise terminology in the field of disinfection

The terms 'resistance' and 'tolerance' are well defined in the context of antibiotic research. However, in the field of disinfection, these terms are often used synonymously, which creates ambiguity and can lead to misunderstandings and misconceptions. In addition, this inconsistency in terminology makes it difficult to assess the risk of a disinfectant resistance. This general review aims to discuss existing definitions of the terms 'adaptation', 'susceptibility', 'tolerance', 'persistence' and 'resistance' in the light of disinfectants. The most ambiguity is found between tolerance and resistance. Whereas the former describes the not necessarily heritable survival of transient exposure to usually lethal concentrations, resistance is the strictly heritable ability to survive otherwise lethal concentrations of an antimicrobial agent, regardless of exposure time. A simple transfer of experience from antibiotic research is not recommended when assessing the risk of resistance to disinfectants, as there are important differences between antibiotics and disinfectants, although both are antimicrobials: (i) disinfectants are usually applied at concentrations that exceed the minimum inhibitory concentration by orders of magnitude, (ii) the exposure times of disinfectants are in the range of seconds, minutes, or a few hours, (iii) the mode of action of disinfectants is less specific, and (iv) disinfectants often contain more than one active agent with additive or synergistic effects. It is important to recognize that disinfectants, like other antimicrobial agents such as antibiotics, have a dualistic nature and should be used correctly and with caution.

The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates

The increasing frequency of antibiotic-resistant bacteria is a constant threat to global human health. Therefore, the pathogens of the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp.) are among the most relevant causes of hospital infections responsible for millions of deaths every year. However, little has been explored about the danger of microorganisms resistant to biocides such as antiseptics and disinfectants. Widely used in domestic, industrial, and hospital environments, these substances reach the environment and can cause selective pressure for resistance genes and induce cross-resistance to antibiotics, further aggravating the problem. Therefore, it is necessary to use innovative and efficient strategies to monitor the spread of genes related to resistance to biocides. Whole genome sequencing and bioinformatics analysis aiming to search for sequences encoding resistance mechanisms are essential to help monitor and combat these pathogens. Thus, this work describes the construction of a bioinformatics tool that integrates different databases to identify gene sequences that may confer some resistance advantage about biocides. Furthermore, the tool analyzed all the genomes of Brazilian ESKAPE isolates deposited at NCBI and found a series of different genes related to resistance to benzalkonium chloride, chlorhexidine, and triclosan, which were the focus of this work. As a result, the presence of resistance genes was identified in different types of biological samples, environments, and hosts. Regarding mobile genetic elements (MGEs), around 52% of isolates containing genes related to resistance to these compounds had their genes identified in plasmids, and 48.7% in prophages. These data show that resistance to biocides can be a silent, underestimated danger spreading across different environments and, therefore, requires greater attention.

Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages

The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.

Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis

BACKGROUND

Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.

RESULTS

In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models' performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.

CONCLUSIONS

Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.

A platform for detecting cross-resistance in antibacterial drug discovery

Background

To address the growing antibiotic resistance problem, new antibacterial drugs must exert activity against pathogens resistant to agents already in use. With a view to providing a rapid means for deselecting antibacterial drug candidates that fail to meet this requirement, we report here the generation and application of a platform for detecting cross-resistance between established and novel antibacterial agents.

Methods

This first iteration of the cross-resistance platform (CRP) consists of 28 strains of defined resistance genotype, established in a uniform genetic background (the SH1000 strain of the clinically significant pathogen Staphylococcus aureus). Most CRP members were engineered through introduction of constitutively expressed resistance determinants on a low copy-number plasmid, with a smaller number selected as spontaneous resistant mutants.

Results

Members of the CRP collectively exhibit resistance to many of the major classes of antibacterial agent in use. We employed the CRP to test two antibiotics that have been proposed in the literature as potential drug candidates: γ-actinorhodin and batumin. No cross-resistance was detected for γ-actinorhodin, whilst a CRP member resistant to triclosan exhibited a 32-fold reduction in susceptibility to batumin. Thus, a resistance phenotype that already exists in clinical strains mediates profound resistance to batumin, implying that this compound is not a promising antibacterial drug candidate.

Conclusions

By detecting cross-resistance between established and novel antibacterial agents, the CRP offers the ability to deselect compounds whose activity is substantially impaired by existing resistance mechanisms. The CRP therefore represents a useful addition to the antibacterial drug discovery toolbox.

Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance

Understanding the dynamics and mechanisms of acquired drug resistance across major classes of antibiotics and bacterial pathogens is of critical importance for the optimization of current anti-infective therapies and the development of novel ones. To systematically address this challenge, we developed a workflow combining experimental evolution in a morbidostat continuous culturing device with deep genomic sequencing of population samples collected in time series. This approach was applied to the experimental evolution of six populations of Escherichia coli BW25113 towards acquiring resistance to triclosan (TCS), an antibacterial agent in various consumer products. This study revealed the rapid emergence and expansion (up to 100% in each culture within 4 days) of missense mutations in the fabI gene, encoding enoyl-acyl carrier protein reductase, the known TCS molecular target. A follow-up analysis of isolated clones showed that distinct amino acid substitutions increased the drug IC₉₀ in a 3-16-fold range, reflecting their proximity to the TCS-binding site. In contrast to other antibiotics, efflux-upregulating mutations occurred only rarely and with low abundance. Mutations in several other genes were detected at an earlier stage of evolution. Most notably, three distinct amino acid substitutions were mapped in the C-terminal periplasmic domain of CadC protein, an acid stress-responsive transcriptional regulator. While these mutations do not confer robust TCS resistance, they appear to play a certain, yet unknown, role in adaptation to relatively low drug pressure. Overall, the observed evolutionary trajectories suggest that the FabI enzyme is the sole target of TCS (at least up to the ~50 µm level), and amino acid substitutions in the TCS-binding site represent the main mechanism of robust TCS resistance in E. coli. This model study illustrates the potential utility of the established morbidostat-based approach for uncovering resistance mechanisms and target identification for novel drug candidates with yet unknown mechanisms of action.

Nonactive-Site Mutations in S. aureus FabI That Induce Triclosan Resistance

The wide use of the antimicrobial agent/biocide, triclosan, promotes triclosan-resistant bacterial strains, including Staphylococcus aureus, as well as leads to accumulation in the aquatic and terrestrial environments. Knowledge of the molecular actions of triclosan on S. aureus is needed to understand the consequence of triclosan resistance and environmental accumulation of triclosan on S. aureus resistant strains, as well as to develop biphenyl ether analogs as antibiotic candidates. Triclosan inhibits an essential enzyme in the fatty acid biosynthetic pathway, the reduced nicotinamide adenine dinucleotide (NADH)/reduced nicotinamide adenine dinucleotide phosphate (NADPH)-dependent enoyl-acyl carrier protein (enoyl-ACP) reductase, or FabI. In this study, we used error-prone polymerase chain reaction (epPCR) to generate mutations in the S. aureus FabI enzyme. Instead of using an elaborate FabI enzyme activity assay that involves ACP-linked substrates to determine whether triclosan inhibits the enzyme activities of individual FabI mutants, we used an efficient and economical assay that we developed, based on thermal shift principles, to screen for triclosan binding to FabI mutants in cells. We identified four active-site mutations. More interestingly, we also identified nine triclosan-resistant mutations distant from the active site (G113V, Y123H, S166N, N220I, G227C, A230T, V241I, F252I, and H253P) but located in disparate positions in the monomer-monomer and dimer-dimer interface regions in S. aureus FabI. We suggest that these sites may serve as potential allosteric sites for designing potential therapeutic inhibitors that offer advantages in selectivity since allosteric sites are less evolutionarily conserved.

A comprehensive review of bacterial osteomyelitis with emphasis on Staphylococcus aureus

Osteomyelitis, a significant infection of bone tissue, gives rise to two main groups of infection: acute and chronic. These groups are further categorized in terms of the duration of infection. Usually, children and adults are more susceptible to acute and chronic infections, respectively. The aforementioned groups of osteomyelitis share almost 80% of the corresponding bacterial pathogens. Among all bacteria, Staphylococcus aureus (S. aureus) is a significant pathogen and is associated with a high range of osteomyelitis symptoms. S. aureus has many strategies for interacting with host cells including Small Colony Variant (SCV), biofilm formation, and toxin secretion. In addition, it induces an inflammatory response and causes host cell death by apoptosis and necrosis. However, any possible step to take in this respect is dependent on the conditions and host responses. In the absence of any immune responses and antibiotics, bacteria actively duplicate themselves; however, in the presence of phagocytic cell and harassing conditions, they turn into a SCV, remaining sustainable for a long time. SCV is characterized by notable advantages such as (a) intracellular life that mediates a dam against immune cells and (b) low ATP production that mediates resistance against antibiotics.

Construction of a Bacillus subtilis and Escherichia coli shuttle vector harboring the fabL gene as a triclosan selection marker

A new plasmid containing a mutated fabL gene from Bacillus subtilis as a triclosan selection marker was developed as a useful B. subtilis/E. coli shuttle vector. The pHT-FabL40 plasmid is stable in both gram-positive and gram-negative hosts with increased plasmid DNA yield in E. coli.

Susceptibility of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) to chlorhexidine digluconate, octenidine dihydrochloride, polyhexanide, PVP-iodine and triclosan in comparison to hospital-acquired MRSA (HA-MRSA) and community-aquired MRSA (CA-MRSA): a standardized comparison

Background

Recent publications have raised concerns of reduced susceptibilities of clinical bacterial isolates towards biocides. This study presents a comparative investigation of the susceptibility of livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA), hospital-acquired MRSA (HA-MRSA) and community-aquired MRSA (CA-MRSA) to the commonly used antiseptics chlorhexidine (CHX), octenidine (OCT), polyhexanide (PHMB), PVP-iodine (PVP-I) and triclosan (TCX) based on internationally accepted standards.

Methods

In total, 28 (18 LA-, 5 HA- and 5 CA) genetically characterized MRSA strains representing a broad spectrum of hosts, clonal complexes and spa-types, as well as the reference methicillin-sensitive Staphylococcus aureus (MSSA) strain ATCC 6538, were selected. Minimal inhibitory concentration (MIC) and minimal microbicidal concentration (MBC) were determined in accordance with DIN 58940-7, 58940-8 and DIN EN ISO 20776-1. The microbicidal efficacy was determined in accordance with DIN EN 1040.

Results

Results from the MIC/MBC and quantitative suspension tests revealed differences between antiseptic substances but not between epidemiological groups of MRSA strains. OCT and PHMB were the most active substances with a minimal MIC of 1 mg/L, followed by CHX (2 mg/L), TCX (32 mg/L) and finally PVP-I (1024 mg/L). The MSSA reference strain showed a tendency to a higher susceptibility compared to the MRSA strains.

Conclusions

This investigation of the susceptibility of a range of LA-, HA- and CA-MRSA strains using standardized conditions gave no indication that LA-MRSA strains are less susceptible to commonly used antiseptics compared to HA- and CA-MRSA strains.

Current and Emerging Topical Antibacterials and Antiseptics: Agents, Action, and Resistance Patterns

Bacterial skin infections represent some of the most common infectious diseases globally. Prevention and treatment of skin infections can involve application of a topical antimicrobial, which may be an antibiotic (such as mupirocin or fusidic acid) or an antiseptic (such as chlorhexidine or alcohol). However, there is limited evidence to support the widespread prophylactic or therapeutic use of topical agents. Challenges involved in the use of topical antimicrobials include increasing rates of bacterial resistance, local hypersensitivity reactions (particularly to older agents, such as bacitracin), and concerns about the indiscriminate use of antiseptics potentially coselecting for antibiotic resistance. We review the evidence for the major clinical uses of topical antibiotics and antiseptics. In addition, we review the mechanisms of action of common topical agents and define the clinical and molecular epidemiology of antimicrobial resistance in these agents. Moreover, we review the potential use of newer and emerging agents, such as retapamulin and ebselen, and discuss the role of antiseptic agents in preventing bacterial skin infections. A comprehensive understanding of the clinical efficacy and drivers of resistance to topical agents will inform the optimal use of these agents to preserve their activity in the future.

Dissemination of Novel Antimicrobial Resistance Mechanisms through the Insertion Sequence Mediated Spread of Metabolic Genes

The widely used biocide triclosan selectively targets FabI, the NADH-dependent trans-2-enoyl-acyl carrier protein (ACP) reductase, which is also an important target for the development of narrow spectrum antibiotics. The analysis of triclosan resistant Staphylococcus aureus isolates had previously shown that in about half of the strains, the mechanism of triclosan resistance consists on the heterologous duplication of the triclosan target gene due to the acquisition of an additional fabI allele derived from Staphylococcus haemolyticus (sh-fabI). In the current work, the genomic sequencing of 10 of these strains allowed the characterization of two novel composite transposons TnSha1 and TnSha2 involved in the spread of sh-fabI. TnSha1 harbors one copy of IS1272, whereas TnSha2 is a 11.7 kb plasmid carrying TnSha1 present either as plasmid or in an integrated form generally flanked by two IS1272 elements. The target and mechanism of integration for IS1272 and TnSha1 are novel and include targeting of DNA secondary structures, generation of blunt-end deletions of the stem-loop and absence of target duplication. Database analyses showed widespread occurrence of these two elements in chromosomes and plasmids, with TnSha1 mainly in S. aureus and with TnSha2 mainly in S. haemolyticus and S. epidermidis. The acquisition of resistance by means of an insertion sequence-based mobilization and consequent duplication of drug-target metabolic genes, as observed here for sh-fabI, is highly reminiscent of the situation with the ileS2 gene conferring mupirocin resistance, and the dfrA and dfrG genes conferring trimethoprim resistance both of which are mobilized by IS257. These three examples, which show similar mechanisms and levels of spread of metabolic genes linked to IS elements, highlight the importance of this genetic strategy for recruitment and rapid distribution of novel resistance mechanisms in staphylococci.