Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis

Transcriptomic signature of bacteria exposed to benzalkonium chloride

The COVID-19 pandemic has highlighted our reliance on biocides, the increasing prevalence of resistance to biocides is a risk to public health. Bacterial exposure to the biocide, benzalkonium chloride (BAC), resulted in a unique transcriptomic profile, characterised by both a short and long-term response. Differential gene expression was observed in four main areas: motility, membrane composition, proteostasis, and the stress response. A metabolism shift to protect the proteome and the stress response were prioritised suggesting these are main resistance mechanisms. Whereas "well-established" mechanisms, such as biofilm formation, were not found to be differentially expressed after exposure to BAC.

Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance

Quinolone resistance presents a growing global health threat. We employed word-based GWAS to explore genomic data, aiming to enhance our understanding of this phenomenon. Unlike traditional variant-based GWAS analyses, this approach simultaneously captures multiple genomic factors, including single and interacting resistance mutations and genes. Analyzing a dataset of 92 genomic E. coli samples from a wastewater treatment plant in Dresden, we identified 54 DNA unitigs significantly associated with quinolone resistance. Remarkably, our analysis not only validated known mutations in gyrA and parC genes and the results of our variant-based GWAS but also revealed new (mutated) genes such as mdfA, the AcrEF-TolC multidrug efflux system, ptrB, and hisI, implicated in antibiotic resistance. Furthermore, our study identified joint mutations in 14 genes including the known gyrA gene, providing insights into potential synergistic effects contributing to quinolone resistance. These findings showcase the exceptional capabilities of word-based GWAS in unraveling the intricate genomic foundations of quinolone resistance.

Quaternary ammonium compounds of emerging concern: Classification, occurrence, fate, toxicity and antimicrobial resistance

Amplified hygiene and precautionary measures are of utmost importance to control the spread of COVID-19 and future infection; however, these changes in practice are projected to trigger a rise in the purchase, utilisation and hence, discharge of many disinfectants into the environment. While alcohol-based, hydrogen peroxide-based, and chlorine-based compounds have been used widely, quaternary ammonium compounds (QACs) based disinfectants are of significant concern due to their overuse during this pandemic. This review presents the classification of disinfectants and their mechanism of action, focusing on QACs. Most importantly, the occurrence, fate, toxicity and antimicrobial resistance due to QACs are covered in this paper. Here we collated evidence from multiple studies and found rising trends of concern, including an increase in the mass load of QACs at a wastewater treatment plant (WWTP) by 331% compared to before the COVID-19 pandemic, as well as an increases in the concentration of 62% in residential dust, resulting in high concentrations of QACs in human blood and breast milk and suggesting that these could be potential sources of persistent QACs in infants. In addition to increased toxicity to human and aquatic life, increased use of QACs and accelerated use of antibiotics and antimicrobials during the COVID-19 pandemic could multiply the threat to antimicrobial resistance.

Impact of benzalkonium chloride, benzethonium chloride and chloroxylenol on bacterial antimicrobial resistance

This review examined 3655 articles on benzalkonium chloride (BKC), benzethonium chloride (BZT) and chloroxylenol (CHO) aiming to understand their impact on antimicrobial resistance. Following the application of inclusion/exclusion criteria, only 230 articles were retained for analysis; 212 concerned BKC, with only 18 for CHO and BZT. Seventy-eight percent of studies used MIC to measure BKC efficacy. Very few studies defined the term 'resistance' and 85% of studies defined 'resistance' as <10-fold increase (40% as low as 2-fold) in MIC. Only a few in vitro studies reported on formulated products and when they did, products performed better. In vitro studies looking at the impact of BKC exposure on bacterial resistance used either a stepwise training protocol or exposure to constant BKC concentrations. In these, BKC exposure resulted in elevated MIC or/and MBC, often associated with efflux, and at time, a change in antibiotic susceptibility profile. The clinical relevance of these findings was, however, neither reported nor addressed. Of note, several studies reported that bacterial strains with an elevated MIC or MBC remained susceptible to the in-use BKC concentration. BKC exposure was shown to reduce bacterial diversity in complex microbial microcosms, although the clinical significance of such a change has not been established. The impact of BKC exposure on the dissemination of resistant genes (notably efflux) remains speculative, although it manifests that clinical, veterinary and food isolates with elevated BKC MIC carried multiple efflux pump genes. The correlation between BKC usage and gene carriage, maintenance and dissemination has also not been established. The lack of clinical interpretation and significance in these studies does not allow to establish with certainty the role of BKC on AMR in practice. The limited literature and BZT and CHO do not allow to conclude that these will impact negatively on emerging bacterial resistance in practice.

MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks

Thanks to recent advances in sequencing and computational technologies, many researchers with biological and/or medical backgrounds are now producing multiple data sets with an embedded temporal dimension. Multi-modalities enable researchers to explore and investigate different biological and physico-chemical processes with various technologies. Motivated to explore multi-omics data and time-series multi-omics specifically, the exploration process has been hindered by the separation introduced by each omics-type. To effectively explore such temporal data sets, discover anomalies, find patterns, and better understand their intricacies, expertise in computer science and bioinformatics is required. Here we present MOVIS, a modular time-series multi-omics exploration tool with a user-friendly web interface that facilitates the data exploration of such data. It brings into equal participation each time-series omic-type for analysis and visualization. As of the time of writing, two time-series multi-omics data sets have been integrated and successfully reproduced. The resulting visualizations are task-specific, reproducible, and publication-ready. MOVIS is built on open-source software and is easily extendable to accommodate different analytical tasks. An online version of MOVIS is available under https://movis.mathematik.uni-marburg.de/ and on Docker Hub (https://hub.docker.com/r/aanzel/movis).

Persistence against benzalkonium chloride promotes rapid evolution of tolerance during periodic disinfection

Biocides used as disinfectants are important to prevent the transmission of pathogens, especially during the current antibiotic resistance crisis. This crisis is exacerbated by phenotypically tolerant persister subpopulations that can survive transient antibiotic treatment and facilitate resistance evolution. Here, we show that E. coli displays persistence against a widely used disinfectant, benzalkonium chloride (BAC). Periodic, persister-mediated failure of disinfection rapidly selects for BAC tolerance, which is associated with reduced cell surface charge and mutations in the lpxM locus, encoding an enzyme for lipid A biosynthesis. Moreover, the fitness cost incurred by BAC tolerance turns into a fitness benefit in the presence of antibiotics, suggesting a selective advantage of BAC-tolerant mutants in antibiotic environments. Our findings highlight the links between persistence to disinfectants and resistance evolution to antimicrobials.

In vitro virulence potential, surface attachment and transcriptional response of sublethally injured Listeria monocytogenes following exposure to peracetic acid

The disinfectant Peracetic acid (PAA) can cause high levels of sublethal injury to L. monocytogenes. This study aims to evaluate phenotypic and transcriptional characteristics concerning surface attachment and virulence potential of sublethally injured L. monocytogenes ScottA and EGDe after exposure to 0.75 ppm PAA for 90 min at 4°C and subsequent incubation in TSBY at 4°C. Results showed that injured L. monocytogenes cells (99% of total population) were able to attach (after 2 and 24h) on stainless steel coupons at 4°C and 20°C. In vitro virulence assays using human intestinal epithelial Caco-2 cells showed that injured L. monocytogenes could invade host cells but could not proliferate intracellularly. In vitro virulence response was strain-dependent; injured ScottA was more invasive than EGDe. Assessment of PAA-injury at the transcriptional level showed upregulation of genes (motB, flaA) involved in flagellum motility and surface attachment. The transcriptional response of L. monocytogenes EGDe and ScottA was different; only injured ScottA demonstrated upregulation of the virulence genes inlA and plcA. Downregulation of the stress-related genes fri and kat, and upregulation of lmo0669 was observed in injured ScottA. The obtained results indicate that sublethally-injured L. monocytogenes cells may retain part of their virulence properties as well as their ability to adhere on food processing surfaces. Transmission to food products and introduction of these cells in the food chain is therefore a plausible scenario that is worth taking into consideration in terms of risk assessment. Importance L. monocytogenes is the causative agent of listeriosis a serious food-borne illness. Antimicrobial practices, such as disinfectants used for the elimination of this pathogen in food industry can produce a sublethally injured population fraction. Injured cells of this pathogen, that may survive an antimicrobial treatment, may pose a food safety-risk. Nevertheless, knowledge regarding how sublethal injury may impact important cellular traits and phenotypic responses of this pathogen is limited. This work suggests that sublethally injured L. monocytogenes cells maintain the virulence and surface attachment potential and highlights the importance of the occurrence of sublethally injured cells regarding food safety.

Transcriptomic Response Analysis of Escherichia coli to Palladium Stress

Palladium (Pd), due to its unique catalytic properties, is an industrially important heavy metal especially in the form of nanoparticles. It has a wide range of applications from automobile catalytic converters to the pharmaceutical production of morphine. Bacteria have been used to biologically produce Pd nanoparticles as a new environmentally friendly alternative to the currently used energy-intensive and toxic physicochemical methods. Heavy metals, including Pd, are toxic to bacterial cells and cause general and oxidative stress that hinders the use of bacteria to produce Pd nanoparticles efficiently. In this study, we show in detail the Pd stress-related effects on E. coli. Pd stress effects were measured as changes in the transcriptome through RNA-Seq after 10 min of exposure to 100 μM sodium tetrachloropalladate (II). We found that 709 out of 3,898 genes were differentially expressed, with 58% of them being up-regulated and 42% of them being down-regulated. Pd was found to induce several common heavy metal stress-related effects but interestingly, Pd causes unique effects too. Our data suggests that Pd disrupts the homeostasis of Fe, Zn, and Cu cellular pools. In addition, the expression of inorganic ion transporters in E. coli was found to be massively modulated due to Pd intoxication, with 17 out of 31 systems being affected. Moreover, the expression of several carbohydrate, amino acid, and nucleotide transport and metabolism genes was vastly changed. These results bring us one step closer to the generation of genetically engineered E. coli strains with enhanced capabilities for Pd nanoparticles synthesis.

Prevalence and Risk Factors for ESBL/AmpC-E. coli in Pre-Weaned Dairy Calves on Dairy Farms in Germany

The objectives of this study were to ascertain the fecal ESBL/AmpC-E. coli prevalence and to detect risk factors for their occurrence in young pre-weaned calves and their dams on large dairy farms in Germany. From 2018-2019 we investigated 2816 individual fecal samples from pre-weaned dairy calves and their dams, representing seventy-two farms (mean = 667 milking cows) from eight German federal states. To assess possible risk factors associated with ESBL/AmpC-E. coli prevalence in calves and dams, a questionnaire was performed, collecting management data. We observed an ESBL/AmpC-E. coli prevalence of 63.5% (95% CI: 57.4-69.5) among the sampled calves and 18.0% (95% CI: 12.5-23.5) among the dams. On all farms, at least one positive sample was obtained. To date, this is the highest ESBL/AmpC-E. coli prevalence observed in dairy herds in Europe. Feeding with waste milk was identified as a significant risk factor for a high prevalence of ESBL/AmpC-E. coli in calves. Many calves at large dairies in Germany are fed with waste milk due to the large amounts generated as a result of antibiotic dry-off routines and mastitis treatment with antibiotics. Other notable risk factors for high ESBL/AmpC-E. coli in calves were the general fitness/health of dams and calves, and the quality of farm hygiene. Taken together, these findings suggest that new or improved approaches to animal health management, for example, antibiotic dry cow management (selective dry cow therapy) and mastitis treatment (high self-recovery), as well as farm hygiene, should be researched and implemented.

Are There Effective Intervention Measures in Broiler Production against the ESBL/AmpC Producer Escherichia coli?

Extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase (AmpC) producing Enterobacteriaceae occur frequently in livestock animals and the subsequent stages of the meat production chain and are therefore considered a risk for human health. Strict biosecurity measures and optimal farm management should reduce or even prevent poultry flock colonization at farm level. This review summarizes and evaluates published information on the effectiveness of specific intervention measures and farm management factors aiming to reduce the occurrence and spread of ESBL/AmpC producing or commensal or pathogenic E. coli in broiler chicken farms. In this systematic literature review, a total of 643 publications were analyzed, and 14 studies with significant outcome about the effectiveness of specific measures against E. coli and ESBL/AmpC producing E. coli in broiler chicken farms were found. Different feed additives seem to have an impact on the occurrence of those microorganisms. The measures ‘cleaning and disinfection’ and ‘competitive exclusion’ showed strong effects in prevention in some studies. In summary, some intervention measures showed potential to protect against or eliminate ESBL/AmpC-producing, commensal or pathogenic E. coli at farm level. Due to the high variability in the outcome of the studies, more specific, detailed investigations are needed to assess the potential of the individual intervention measures.

Biocide-Induced Emergence of Antibiotic Resistance in Escherichia coli

Biocide use is essential and ubiquitous, exposing microbes to sub-inhibitory concentrations of antiseptics, disinfectants, and preservatives. This can lead to the emergence of biocide resistance, and more importantly, potential cross-resistance to antibiotics, although the degree, frequency, and mechanisms that give rise to this phenomenon are still unclear. Here, we systematically performed adaptive laboratory evolution of the gut bacteria Escherichia coli in the presence of sub-inhibitory, constant concentrations of ten widespread biocides. Our results show that 17 out of 40 evolved strains (43%) also decreased the susceptibility to medically relevant antibiotics. Through whole-genome sequencing, we identified mutations related to multidrug efflux proteins (mdfA and acrR), porins (envZ and ompR), and RNA polymerase (rpoA and rpoBC), as mechanisms behind the resulting (cross)resistance. We also report an association of several genes (yeaW, pyrE, yqhC, aes, pgpA, and yeeP-isrC) and specific mutations that induce cross-resistance, verified through mutation repairs. A greater capacity for biofilm formation with respect to the parent strain was also a common feature in 11 out of 17 (65%) cross-resistant strains. Evolution in the biocides chlorophene, benzalkonium chloride, glutaraldehyde, and chlorhexidine had the most impact in antibiotic susceptibility, while hydrogen peroxide and povidone-iodine the least. No cross-resistance to antibiotics was observed for isopropanol, ethanol, sodium hypochlorite, and peracetic acid. This work reinforces the link between exposure to biocides and the potential for cross-resistance to antibiotics, presents evidence on the underlying mechanisms of action, and provides a prioritized list of biocides that are of greater concern for public safety from the perspective of antibiotic resistance.

SIGNIFICANCE STATEMENT

Bacterial resistance and decreased susceptibility to antimicrobials is of utmost concern. There is evidence that improper biocide (antiseptic and disinfectant) use and discard may select for bacteria cross-resistant to antibiotics. Understanding the cross-resistance emergence and the risks associated with each of those chemicals is relevant for proper applications and recommendations. Our work establishes that not all biocides are equal when it comes to their risk of inducing antibiotic resistance; it provides evidence on the mechanisms of cross-resistance and a risk assessment of the biocides concerning antibiotic resistance under residual sub-inhibitory concentrations.