Exposure to Quaternary Ammonium Compounds Selects Resistance to Ciprofloxacin in Listeria monocytogenes

Challenges of quaternary ammonium antimicrobial agents: Mechanisms, resistance, persistence and impacts on the microecology

Quaternary ammonium compounds (QACs) served as broad spectrum antimicrobial agents are widely applied for surface disinfection, skin and mucous disinfection, and mouthwash. The daily applications of QACs have significantly increased, especially during the COVID-19 pandemic. However, the environmental residues of QACs have demonstrated harmful impacts on the environment, leading to an increase in environmental contamination, resistant microbes and disruption of microecology. The actions of QACs were related to their cationic character, which can impact the negatively charged cell membranes, but the details are still unclear. Moreover, bacteria with lower sensitivity and resistant pathogens have been detected in clinics and environments, while QACs were also reported to induce the formation of bacterial persisters. Even worse, the resistant bacteria even showed co-resistance and cross-resistance with traditional antibiotics, decreasing therapeutic effectiveness, and disrupting the microecology homeostasis. Unfortunately, the resistance and persistence mechanisms of QACs and the effects of QACs on microecology are still not clear, which even neglected during their daily usages. Therefore, we summarized and discussed current understandings on the antimicrobial actions, resistance, persistence and impacts on the microecology to highlight the challenges in the QACs applications and discuss the possible strategies for overcoming their drawbacks.

Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits

One of the main challenges in food microbiology is to prevent the risk of outbreaks by avoiding the distribution of food contaminated by bacteria. This requires constant monitoring of the circulating strains throughout the food production chain. Bacterial genomes contain signatures of natural evolution and adaptive markers that can be exploited to better understand the behavior of pathogen in the food industry. The monitoring of foodborne strains can therefore be facilitated by the use of these genomic markers capable of rapidly providing essential information on isolated strains, such as the source of contamination, risk of illness, potential for biofilm formation, and tolerance or resistance to biocides. The increasing availability of large genome datasets is enhancing the understanding of the genetic basis of complex traits such as host adaptation, virulence, and persistence. Genome-wide association studies have shown very promising results in the discovery of genomic markers that can be integrated into rapid detection tools. In addition, machine learning has successfully predicted phenotypes and classified important traits. Genome-wide association and machine learning tools have therefore the potential to support decision-making circuits intending at reducing the burden of foodborne diseases. The aim of this chapter review is to provide knowledge on the use of these two methods in food microbiology and to recommend their use in the field.

Investigations of microbial adaptation to singular, binary, and fully formulated quaternary ammonium compounds

The study was conducted to inform risk assessments concerning microbial exposure to quaternary ammonium biocides (QUATs) by investigating their effects on 10 microbial strains of hygiene relevance. Biocides were divided into three categories: simple aqueous solutions, biocide mixtures, and formulated biocides. Organisms were grown in the presence of biocides for 10 generations and then subsequently for another 10 generations in biocide-free media. Control organisms were passaged 20 times in biocide-free media. Strains were then assessed for biocide and antibiotic susceptibility, changes in growth dynamics, and single nucleotide polymorphisms (SNPs). Biocide mixtures demonstrated greater antimicrobial potency than singular and formulated biocides. Susceptibility changes of under twofold were observed for all biocides tested. Susceptibility decreased significantly for organisms passaged with singular biocides (1.29- to 4.35-fold) and biocide mixtures (1.4- to 1.5-fold), but not for formulated biocides (1.3- to 1.84-fold) compared to controls. Antibiotic susceptibility both increased and decreased in passaged organisms, with heightened susceptibility occurring more frequently in the singular biocide group. Changes in susceptibility and growth dynamics were similar in the passaged and unexposed controls for fitness measures of adapted bacteria; there were no significant differences between biocide groups, but significantly lower generation and doubling times in organisms exposed to singular biocides. Similar frequencies in SNPs occurred for the three biocide groups and unexposed controls. While some adaptations occurred, particularly with singular biocides, the impact on antibiotic resistance and genomic mutations was limited. These findings suggest that the use of formulated QUATs may pose a comparatively lower risk for antimicrobial resistance.IMPORTANCEBiocides are used globally to control microbial growth and effective assessment of the risks and benefits of their use is therefore a high priority. Much of the data used to assess risk has been based on sub-lethal exposure of bacteria to singular biocides in simple aqueous solutions. This work builds on limited prior realism-based studies to demonstrate enhanced potency in biocidal mixtures; the mitigation of resistance selection by formulations and inconsistent cross-resistance effects with both increases and decreases in susceptibility for a wide range of antibiotics. These data can be used to better inform risk assessments of biocide deployment.

Differential Selection for Survival and for Growth in Adaptive Laboratory Evolution Experiments With Benzalkonium Chloride

Biocides are used to control microorganisms across different applications, but emerging resistance may pose risks for those applications. Resistance to biocides has commonly been studied using adaptive laboratory evolution (ALE) experiments with growth at subinhibitory concentrations linked to serial subculturing. It has been shown recently that Escherichia coli adapts to repeated lethal stress imposed by the biocide benzalkonium chloride (BAC) by increased survival (i.e., tolerance) and not by evolving the ability to grow at increased concentrations (i.e., resistance). Here, we investigate the contributions of evolution for tolerance as opposed to resistance for the outcome of ALE experiments with E. coli exposed to BAC. We find that BAC concentrations close to the half maximal effective concentration (EC50, 4.36 μg mL-1) show initial killing (~40%) before the population resumes growth. This indicates that cells face a two-fold selection pressure: for increased survival and for increased growth. To disentangle the effects of both selection pressures, we conducted two ALE experiments: (i) one with initial killing and continued stress close to the EC50 during growth and (ii) another with initial killing and no stress during growth. Phenotypic characterization of adapted populations showed that growth at higher BAC concentrations was only selected for when BAC was present during growth. Whole genome sequencing revealed distinct differences in mutated genes across treatments. Treatments selecting for survival-only led to mutations in genes for metabolic regulation (cyaA) and cellular structure (flagella fliJ), while treatments selecting for growth and survival led to mutations in genes related to stress response (hslO and tufA). Our results demonstrate that serial subculture ALE experiments with an antimicrobial at subinhibitory concentrations can select for increased growth and survival. This finding has implications for the design of ALE experiments to assess resistance risks of antimicrobials in different scenarios such as disinfection, preservation, and environmental pollution.

Biofilm formation by Listeria monocytogenes from the meat processing industry environment and the use of different combinations of detergents, sanitizers, and UV-A radiation to control this microorganism in planktonic and sessile forms

This study aimed to evaluate the ability of biofilm formation by L. monocytogenes from the meat processing industry environment, as well as the use of different combinations of detergents, sanitizers, and UV-A radiation in the control of this microorganism in the planktonic and sessile forms. Four L. monocytogenes isolates were evaluated and showed moderate ability to form biofilm, as well as carried genes related to biofilm production (agrB, agrD, prfA, actA, cheA, cheY, flaA, sigB), and genes related to tolerance to sanitizers (lde and qacH). The biofilm-forming isolates of L. monocytogenes were susceptible to quaternary ammonium compound (QAC) and peracetic acid (PA) in planktonic form, with minimum inhibitory concentrations of 125 and 75 ppm, respectively, for contact times of 10 and 5 min. These concentrations are lower than those recommended by the manufacturers, which are at least 200 and 300 ppm for QAC and PA, respectively. Biofilms of L. monocytogenes formed from a pool of isolates on stainless steel and polyurethane coupons were subjected to 14 treatments involving acid and enzymatic detergents, QAC and PA sanitizers, and UV-A radiation at varying concentrations and contact times. All treatments reduced L. monocytogenes counts in the biofilm, indicating that the tested detergents, sanitizers, and UV-A radiation exhibited antimicrobial activity against biofilms on both surface types. Notably, the biofilm formed on polyurethane showed greater tolerance to the evaluated compounds than the biofilm on stainless steel, likely due to the material's surface facilitating faster microbial colonization and the development of a more complex structure, as observed by scanning electron microscopy. Listeria monocytogenes isolates from the meat processing industry carry genes associated with biofilm production and can form biofilms on both stainless steel and polyurethane surfaces, which may contribute to their persistence within meat processing lines. Despite carrying sanitizer tolerance genes, QAC and PA effectively controlled these microorganisms in their planktonic form. However, combinations of detergent (AC and ENZ) with sanitizers (QAC and PA) at minimum concentrations of 125 ppm and 300 ppm, respectively, were the most effective.

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.

Chemical mutagenesis of Listeria monocytogenes for increased tolerance to benzalkonium chloride shows independent genetic underpinnings and off-target antibiotic resistance

Listeria monocytogenes, a potentially fatal foodborne pathogen commonly found in food processing facilities, creates a significant economic burden that totals more than $2 billion annually in the United States due to outbreaks. Quaternary ammonium compounds (QACs), including benzalkonium chloride (BAC), are among the most widely used sanitizers to inhibit the growth and spread of L. monocytogenes from food processing facilities. However, resistance to QACs has been increasing in L. monocytogenes and different genetic mechanisms conferring resistance have been discovered. Here, we used ethyl methanesulfonate (EMS) to chemically mutagenize the BAC-susceptible strain, L. monocytogenes FSL-N1-304. We isolated two mutants with increased tolerance to BAC compared to the parental strain. Next, we assessed the off-target effect of increased tolerance to BAC by measuring the minimum inhibitory concentrations (MICs) of a diverse set of antibiotics, revealing that mut-1 and mut-2 displayed significantly increased resistance to fluoroquinolone antibiotics compared to the parental strain. A hemolysis assay was then used to investigate a potential correlation between BAC tolerance and virulence. Interestingly, mut-1 and mut-2 both exhibited significantly higher hemolysis percentage than the parental strain. We then sequenced the genomes of the parental strain and both mutants to identify mutations that may be involved in the increased resistance to BAC. We identified 3 and 29 mutations in mut-1 and mut-2, respectively. mut-1 contained nonsynonymous mutations in dagK (a diacylglycerol kinase), lmo2768 (a permease-encoding gene), and lmo0186 (resuscitation promoting factor). mut-2 contained a nonsense mutation in the nucleotide excision repair enzyme UvrABC system protein B encoding gene, uvrB, which likely accounts for the higher number of mutations observed. Transcriptome analysis in the presence of BAC revealed that genes related to the phosphotransferase system and internalins were up-regulated in both mutants, suggesting their significance in the BAC stress response. These two mutants provide insights into alternative mechanisms for increased BAC tolerance and could further our understanding of how L. monocytogenes persists in the food processing environment.

Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?

The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Phenotypic and genotypic antimicrobial resistance of Listeria monocytogenes: an observational study in France

Background

Large-scale studies are needed to clarify antimicrobial resistance in the foodborne pathogen Listeria monocytogenes (Lm) and the effectiveness of listeriosis treatment options. Here we examined the antimicrobial resistance patterns in Lm over time and assessed genotype-phenotype concordances.

Methods

We analyzed 5339 Lm isolates (2908 clinical and 2431 food isolates) collected in France and overseas territories, between 2012 and 2019. Whole genome sequencing was performed for all isolates and antimicrobial resistance profiles inferred from draft assemblies. Antimicrobial susceptibility towards 22 antimicrobials was determined for all clinical isolates, and in food isolates with acquired resistance genes.

Findings

All tested isolates were resistant to at least 3 different classes of antimicrobials, consistent with Lm intrinsic traits. Acquired antimicrobial resistance in Lm was rare (2.23% isolates) and more prevalent in food (mainly lineage II) compared to clinical isolates (mainly lineage I) (3.74% vs 0.98%, p < 0.0001), and in isolates with disinfectants or stress resistance traits (e.g. bcrABC, 20.20% vs 7.20%, p < 0.0001), suggesting co-selection of resistance in food-production environments. Acquired antimicrobial resistance could be predicted from genomes with high accuracy (>99%), except for ciprofloxacin. Acquired antimicrobial phenotypes were towards tetracyclines (mostly due to tetM), trimethoprim (dfrD), lincosamides (lnuG), macrolides (ermB, mphB) and phenicols (fexA).

Interpretation

The reference treatment for listeriosis (aminopenicillins/aminoglycosides) remains effective, with no acquired resistance observed. Continuous surveillance of antimicrobial resistance in clinical and food isolates is crucial to detect the emergence of novel resistance.

Funding

Institut Pasteur, INSERM, Santé Publique France, Investissement d'Avenir program Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62-IBEID).

Polyhexamethylene biguanide promotes adaptive cross-resistance to gentamicin in Escherichia coli biofilms

Antimicrobial resistance is a critical public health issue that requires a thorough understanding of the factors that influence the selection and spread of antibiotic-resistant bacteria. Biocides, which are widely used in cleaning and disinfection procedures in a variety of settings, may contribute to this resistance by inducing similar defense mechanisms in bacteria against both biocides and antibiotics. However, the strategies used by bacteria to adapt and develop cross-resistance remain poorly understood, particularly within biofilms -a widespread bacterial habitat that significantly influences bacterial tolerance and adaptive strategies. Using a combination of adaptive laboratory evolution experiments, genomic and RT-qPCR analyses, and biofilm structural characterization using confocal microscopy, we investigated in this study how Escherichia coli biofilms adapted after 28 days of exposure to three biocidal active substances and the effects on cross-resistance to antibiotics. Interestingly, polyhexamethylene biguanide (PHMB) exposure led to an increase of gentamicin resistance (GenR) phenotypes in biofilms formed by most of the seven E. coli strains tested. Nevertheless, most variants that emerged under biocidal conditions did not retain the GenR phenotype after removal of antimicrobial stress, suggesting a transient adaptation (adaptive resistance). The whole genome sequencing of variants with stable GenR phenotypes revealed recurrent mutations in genes associated with cellular respiration, including cytochrome oxidase (cydA, cyoC) and ATP synthase (atpG). RT-qPCR analysis revealed an induction of gene expression associated with biofilm matrix production (especially curli synthesis), stress responses, active and passive transport and cell respiration during PHMB exposure, providing insight into potential physiological responses associated with adaptive crossresistance. In addition, confocal laser scanning microscopy (CLSM) observations demonstrated a global effect of PHMB on biofilm architectures and compositions formed by most E. coli strains, with the appearance of dense cellular clusters after a 24h-exposure. In conclusion, our results showed that the PHMB exposure stimulated the emergence of an adaptive cross-resistance to gentamicin in biofilms, likely induced through the activation of physiological responses and biofilm structural modulations altering gradients and microenvironmental conditions in the biological edifice.

Adaptation mechanisms of Listeria monocytogenes to quaternary ammonium compounds

Listeria monocytogenes is ubiquitously found in nature and can easily enter food-processing facilities due to contaminations of raw materials. Several countermeasures are used to combat contamination of food products, for instance, the use of disinfectants that contain quaternary ammonium compounds, such as benzalkonium chloride (BAC) and cetyltrimethylammonium bromide (CTAB). In this study, we assessed the potential of the commonly used wild-type strain EGD-e to adapt to BAC and CTAB under laboratory growth conditions. All BAC-tolerant suppressors exclusively carried mutations in fepR, encoding a TetR-like transcriptional regulator, or its promoter region, likely resulting in the overproduction of the efflux pump FepA. In contrast, CTAB tolerance was associated with mutations in sugR, which regulates the expression of the efflux pumps SugE1 and SugE2. L. monocytogenes strains lacking either FepA or SugE1/2 could still acquire tolerance toward BAC and CTAB. Genomic analysis revealed that the overproduction of the remaining efflux system could compensate for the deleted one, and even in the absence of both efflux systems, tolerant strains could be isolated, which all carried mutations in the diacylglycerol kinase-encoding gene lmo1753 (dgkB). DgkB converts diacylglycerol to phosphatidic acid, which is subsequently reused for the synthesis of phospholipids, suggesting that alterations in membrane composition could be the third adaptation mechanism. IMPORTANCE Survival and proliferation of Listeria monocytogenes in the food industry are ongoing concerns, and while there are various countermeasures to combat contamination of food products, the pathogen still successfully manages to withstand the harsh conditions present in food-processing facilities, resulting in reoccurring outbreaks, subsequent infection, and disease. To counteract the spread of L. monocytogenes, it is crucial to understand and elucidate the underlying mechanism that permits their successful evasion. We present various adaptation mechanisms of L. monocytogenes to withstand two important quaternary ammonium compounds.

Mechanisms of Listeria monocytogenes Disinfection with Benzalkonium Chloride: From Molecular Dynamics to Kinetics of Time-Kill Curves

Unravelling the mechanisms of action of disinfectants is essential to optimise dosing regimes and minimise the emergence of antimicrobial resistance. In this work, we examined the mechanisms of action of a commonly used disinfectant-benzalkonium chloride (BAC)-over a significant pathogen-L. monocytogenes-in the food industry. For that purpose, we used modelling at multiple scales, from the cell membrane to cell population inactivation. Molecular modelling revealed that the integration of the BAC into the membrane requires three phases: (1) the approaching of BAC to the cellular membrane, (2) the absorption of BAC to its surface, and (3) the integration of the compound into the lipid bilayer, where it remains at least for several nanoseconds, probably destabilising the membrane. We hypothesised that the equilibrium of adsorption, although fast, was limiting for sufficiently large BAC concentrations, and a kinetic model was derived to describe time-kill curves of a large population of cells. The model was tested and validated with time series data of free BAC decay and time-kill curves of L. monocytogenes at different inocula and BAC dose concentrations. The knowledge gained from the molecular simulation plus the proposed kinetic model offers the means to design novel disinfection processes rationally.

Quaternary ammonium disinfectants and antiseptics: tolerance, resistance and potential impact on antibiotic resistance

BACKGROUND

Due to the substantial increase in the use of disinfectants containing quaternary ammonion compounds (QACs) in healthcare and community settings during the COVID-19 pandemic, there is increased concern that heavy use might cause bacteria to develop resistance to QACs or contribute to antibiotic resistance. The purpose of this review is to briefly discuss the mechanisms of QAC tolerance and resistance, laboratory-based evidence of tolerance and resistance, their occurrence in healthcare and other real-world settings, and the possible impact of QAC use on antibiotic resistance.

METHODS

A literature search was conducted using the PubMed database. The search was limited to English language articles dealing with tolerance or resistance to QACs present in disinfectants or antiseptics, and potential impact on antibiotic resistance. The review covered the period from 2000 to mid-Jan 2023.

RESULTS

Mechanisms of QAC tolerance or resistance include innate bacterial cell wall structure, changes in cell membrane structure and function, efflux pumps, biofilm formation, and QAC degradation. In vitro studies have helped elucidate how bacteria can develop tolerance or resistance to QACs and antibiotics. While relatively uncommon, multiple episodes of contaminated in-use disinfectants and antiseptics, which are often due to inappropriate use of products, have caused outbreaks of healthcare-associated infections. Several studies have identified a correlation between benzalkonium chloride (BAC) tolerance and clinically-defined antibiotic resistance. The occurrence of mobile genetic determinants carrying multiple genes that encode for QAC or antibiotic tolerance raises the concern that widespread QAC use might facilitate the emergence of antibiotic resistance. Despite some evidence from laboratory-based studies, there is insufficient evidence in real-world settings to conclude that frequent use of QAC disinfectants and antiseptics has promoted widespread emergence of antibiotic resistance.

CONCLUSIONS

Laboratory studies have identified multiple mechanisms by which bacteria can develop tolerance or resistance to QACs and antibiotics. De novo development of tolerance or resistance in real-world settings is uncommon. Increased attention to proper use of disinfectants is needed to prevent contamination of QAC disinfectants. Additional research is needed to answer many questions and concerns related to use of QAC disinfectants and their potential impact on antibiotic resistance.

Characterization and Antibiotic Resistance of Listeria monocytogenes Strains Isolated from Greek Myzithra Soft Whey Cheese and Related Food Processing Surfaces over Two-and-a-Half Years of Safety Monitoring in a Cheese Processing Facility

Listeriosis is a serious infectious disease with one of the highest case fatality rates (ca. 20%) among the diseases manifested from bacterial foodborne pathogens in humans, while dairy products are often implicated as sources of human infection with Listeria monocytogenes. In this study, we characterized phenotypically and genetically by whole-genome sequencing (WGS) 54 L. monocytogenes strains isolated from Myzithra, a traditional Greek soft whey cheese (48 isolates), and swabs collected from surfaces of a cheese processing plant (six isolates) in the Epirus region of Greece. All but one strain of L. monocytogenes belonged to the polymerase chain reaction (PCR) serogroups IIa (16.7%) and IIb (81.5%), corresponding to serotypes 1/2a, 3a and 1/2b, 3b, 7, respectively. The latter was identified as a PCR-serogroup IVb strain (1.8%) of serotypes 4b, 4d, 4e. Bioinformatics analysis revealed the presence of five sequence types (STs) and clonal complexes (CCs); ST1, ST3, ST121, ST 155, ST398 and CC1, CC3, CC121, CC155, CC398 were thus detected in 1.9, 83.3, 11.0, 1.9, and 1.9% of the L. monocytogenes isolates, respectively. Antibiograms of the pathogen against a panel of seven selected antibiotics (erythromycin, tetracycline, benzylpenicillin, trimethoprim-sulfamethoxazole, ampicillin, ciprofloxacin, and meropenem) showed that 50 strains (92.6%), the six surface isolates also included, were intermediately resistant to ciprofloxacin and susceptible to the rest of the six antimicrobial agents tested, whereas strong resistance against the use of a single from three implicated antibiotics was recorded to four strains (7.4%) of the pathogen isolated from Myzithra cheese samples. Thence, the minimum inhibitory concentrations (MICs) were determined for erythromycin (MIC = 0.19 μg/mL), ciprofloxacin (MIC ≥ 0.19 μg/mL), and meropenem (MIC = 0.64 μg/mL), and finally, just one strain was deemed resistant to the latter antibiotic. The phylogenetic positions of the L. monocytogenes strains and their genetic variability were determined through WGS, whilst also stress response and virulence gene analysis for the isolates was conducted. Findings of this work should be useful as they could be utilized for epidemiological investigations of L. monocytogenes in the food processing environment, revealing possible contamination scenarios, and acquired antimicrobial resistance along the food production chain.

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.

The effectiveness of newly synthesized quaternary ammonium salts differing in chain length and type of counterion against priority human pathogens

Quaternary ammonium salts (QAS) commonly occur as active substances in disinfectants. QAS have the important property of coating abiotic surfaces, which prevents adhesion of microorganisms, thus inhibiting biofilm formation. In this study, a group of nine monomeric QAS, differing in the structure and length of the aliphatic chain (C12, C14, C16) and the counterion (methylcarbonate, acetate, bromide), were investigated. The study included an analysis of their action against planktonic forms as well as bacterial biofilms. The compounds were tested for their anti-adhesion properties on stainless steel, polystyrene, silicone and glass surfaces. Moreover, mutagenicity analysis and evaluation of hemolytic properties were performed. It was found that compounds with 16-carbon hydrophobic chains were the most promising against both planktonic forms and biofilms. Tested surfactants (C12, C14, C16) showed anti-adhesion activity but it was dependent on the type of the surface and strain used. The tested compounds at MIC concentrations did not cause hemolysis of sheep blood cells. The type of counterion was not as significant for the activity of the compound as the length of the hydrophobic aliphatic chain.

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.

Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence

Background

Quaternary ammonium compound (QAC) efflux genes increase the minimum inhibitory concentration of Listeria monocytogenes (Lm) to benzalkonium chloride sanitizer, but the contribution of these genes to persistence in food processing environments is unclear. The goal of this study was to leverage genomic data and associated metadata for 4969 Lm isolates collected between 1999 and 2019 to: (1) evaluate the prevalence of QAC efflux genes among Lm isolates from diverse US food processors, (2) use comparative genomic analyses to assess confounding factors, such as clonal complex identity and stress tolerance genotypes, and (3) identify patterns in QAC efflux gene gain and loss among persistent clones within specific facilities over time.

Results

The QAC efflux gene cassette bcrABC was present in nearly half (46%) of all isolates. QAC efflux gene prevalence among isolates was associated with clonal complex (𝛘² < 0.001) and clonal complex was associated with the facility type (𝛘² < 0.001). Consequently, changes in the prevalence of QAC efflux genes within individual facilities were generally attributable to changes in the prevalence of specific clonal complexes. Additionally, a GWAS and targeted BLAST search revealed that clonal complexes with a high prevalence of QAC efflux genes commonly possessed other stress tolerance genes. For example, a high prevalence of bcrABC in a clonal complex was significantly associated with the presence of the SSI-1 gene cluster (p < 0.05). QAC efflux gene gain and loss were both observed among persistent populations of Lm in individual facilities, suggesting a limited direct role for QAC efflux genes as predictors of persistence.

Conclusion

This study suggests that although there is evidence that QAC efflux genes are part of a suite of adaptations common among Lm isolated from some food production environments, these genes may be neither sufficient nor necessary to enhance persistence. This is a crucial distinction for decision making in the food industry. For example, changes to sanitizer regimen targeting QAC tolerance would not address other contributing genetic or non-genetic factors, such as equipment hygienic design which physically mediates sanitizer exposure.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08695-2.

FepR as a Central Genetic Target in the Adaptation to Quaternary Ammonium Compounds and Cross-Resistance to Ciprofloxacin in Listeria monocytogenes

The foodborne pathogen, Listeria monocytogenes, (Lm), frequently undergoes selection pressure associated with the extensive use of disinfectants, such as quaternary ammonium compounds, which are widely used in food processing plants. The repeated exposure to sub-inhibitory biocide concentrations can induce increased tolerance to these compounds, but can also trigger the development of antibiotic resistance, and both increase the risk of food contamination and persistence in food production environments. Although the acquisition of genes can explain biocide tolerance, the genetic mechanisms underlying the adaptive cross-resistance to antibiotics remain unclear. We previously showed that repeated exposure to benzalkonium chloride (BC) and didecyldimethyl ammonium chloride (DDAC) led to reduced susceptibility to ciprofloxacin in Lm strains from diverse sources. Here, we compared the genomes of 16 biocide-adapted and 10 parental strains to identify the molecular mechanisms of fluoroquinolone cross-resistance. A core genome SNP analysis identified various mutations in the transcriptional regulator fepR (lmo2088) for 94% of the adapted strains and mutations in other effectors at a lower frequency. FepR is a local repressor of the MATE fluoroquinolone efflux pump FepA. The impact of the mutations on the structure and function of the protein was assessed by performing in silico prediction and protein homology modeling. Our results show that 75% of the missense mutations observed in fepR are located in the HTH domain of the protein, within the DNA interaction site. These mutations are predicted to reduce the activity of the regulator, leading to the overexpression of the efflux pump responsible for the ciprofloxacin-enhanced resistance.

Biocides as Biomedicines against Foodborne Pathogenic Bacteria

Biocides are currently considered the first line of defense against foodborne pathogens in hospitals or food processing facilities due to the versatility and efficiency of their chemical active ingredients. Understanding the biological mechanisms responsible for their increased efficiency, especially when used against foodborne pathogens on contaminated surfaces and materials, represents an essential first step in the implementation of efficient strategies for disinfection as choosing an unsuitable product can lead to antibiocide resistance or antibiotic–biocide cross-resistance. This review describes these biological mechanisms for the most common foodborne pathogens and focuses mainly on the antipathogen effect, highlighting the latest developments based on in vitro and in vivo studies. We focus on biocides with inhibitory effects against foodborne bacteria (e.g., Escherichia spp., Klebsiella spp., Staphylococcus spp., Listeria spp., Campylobacter spp.), aiming to understand their biological mechanisms of action by looking at the most recent scientific evidence in the field.

Assessing the risk of resistance to cationic biocides incorporating realism-based and biophysical approaches

The control of microorganisms is a key objective in disease prevention and in medical, industrial, domestic, and food-production environments. Whilst the effectiveness of biocides in these contexts is well-evidenced, debate continues about the resistance risks associated with their use. This has driven an increased regulatory burden, which in turn could result in a reduction of both the deployment of current biocides and the development of new compounds and formulas. Efforts to balance risk and benefit are therefore of critical importance and should be underpinned by realistic methods and a multi-disciplinary approach, and through objective and critical analyses of the literature. The current literature on this topic can be difficult to navigate. Much of the evidence for potential issues of resistance generation by biocides is based on either correlation analysis of isolated bacteria, where reports of treatment failure are generally uncommon, or laboratory studies that do not necessarily represent real biocide applications. This is complicated by inconsistencies in the definition of the term resistance. Similar uncertainties also apply to cross-resistance between biocides and antibiotics. Risk assessment studies that can better inform practice are required. The resulting knowledge can be utilised by multiple stakeholders including those tasked with new product development, regulatory authorities, clinical practitioners, and the public. This review considers current evidence for resistance and cross-resistance and outlines efforts to increase realism in risk assessment. This is done in the background of the discussion of the mode of application of biocides and the demonstrable benefits as well as the potential risks.

Landscape of Stress Response and Virulence Genes Among Listeria monocytogenes Strains

The pathogenic microorganism Listeria monocytogenes is ubiquitous and responsible for listeriosis, a disease with a high mortality rate in susceptible people. It can persist in different habitats, including the farm environment, the food production environments, and in foods. This pathogen can grow under challenging conditions, such as low pH, low temperatures, and high salt concentrations. However, L. monocytogenes has a high degree of strain divergence regarding virulence potential, environmental adaption, and stress response. This review seeks to provide the reader with an up-to-date overview of clonal and serotype-specific differences among L. monocytogenes strains. Emphasis on the genes and genomic islands responsible for virulence and resistance to environmental stresses is given to explain the complex adaptation among L. monocytogenes strains. Moreover, we highlight the use of advanced diagnostic technologies, such as whole-genome sequencing, to fine-tune quantitative microbiological risk assessment for better control of listeriosis.

The Use of Ozone as an Eco-Friendly Strategy against Microbial Biofilm in Dairy Manufacturing Plants: A Review

Managing spoilage and pathogenic bacteria contaminations represents a major challenge for the food industry, especially for the dairy sector. Biofilms formed by these microorganisms in food processing environment continue to pose concerns to food manufacturers as they may impact both the safety and quality of processed foods. Bacteria inside biofilm can survive in harsh environmental conditions and represent a source of repeated food contamination in dairy manufacturing plants. Among the novel approaches proposed to control biofilm in food processing plants, the ozone treatment, in aqueous or gaseous form, may represent one of the most promising techniques due to its antimicrobial action and low environmental impact. The antimicrobial effectiveness of ozone has been well documented on a wide variety of microorganisms in planktonic forms, whereas little data on the efficacy of ozone treatment against microbial biofilms are available. In addition, ozone is recognized as an eco-friendly technology since it does not leave harmful residuals in food products or on contact surfaces. Thus, this review intends to present an overview of the current state of knowledge on the possible use of ozone as an antimicrobial agent against the most common spoilage and pathogenic microorganisms, usually organized in biofilm, in dairy manufacturing plants.

Effect of Gaseous Ozone on Listeria monocytogenes Planktonic Cells and Biofilm: An In Vitro Study

Among food-borne pathogens, Listeria monocytogenes continues to pose concerns to food business operators due to its capacity to form biofilm in processing environments. Ozone may be an eco-friendly technology to control microbial contaminations, but data concerning its effect on Listeria monocytogenes biofilm are still limited. In this study, the effect of gaseous ozone at 50 ppm on planktonic cells and biofilm of reference and food-related Listeria monocytogenes strains was evaluated. Ozone caused a reduction in microbial loads of 3.7 ± 0.4 and 3.9 ± 0.4 Log10 CFU/mL after 10 and 30 min, respectively. A complete inactivation of planktonic cells after 6 h of treatment was observed. Biofilm inhibition and eradication treatments (50 ppm, 6 h) resulted in a significant decrease of the biofilm biomass for 59% of the strains tested, whilst a slight dampening of live cell loads in the biofilm state was observed. In conclusion, gaseous ozone is not sufficient to completely counteract Listeria monocytogenes biofilm, but it may be useful as an additional tool to contrast Listeria monocytogenes free-living cells and to improve the existing sanitization procedures in food processing environments.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Low-Level Tolerance to Fluoroquinolone Antibiotic Ciprofloxacin in QAC-Adapted Subpopulations of Listeria monocytogenes

There was a development of low-level tolerance to fluoroquinolone antibiotic ciprofloxacin in Listeria monocytogenes after sublethal adaptation to quaternary ammonium compound (QAC). Using eight L. monocytogenes strains, we determined the changes in short-range MIC, growth rate, and survival for heterologous stress response to ciprofloxacin, after sublethal exposure to daily cycles of fixed or gradually increasing concentration of QAC. Three main findings were observed. (1) MIC increase—QAC-adapted subpopulations exhibited a significant increase in short-range MIC of ciprofloxacin, by 1.5 to 2.9 fold, as compared to non-adapted control for 4/8 strains (p < 0.05). (2) Growth rate increase—QAC-adapted subpopulations exhibited significant 2.1- to 6.8- fold increase in growth rate (OD₆₀₀ at 10 h) in ciprofloxacin-containing broth, as compared to non-adapted control for 5/8 strains (p < 0.05). (3) Survival increase—QAC-adapted subpopulations of L. monocytogenes yielded significantly higher survival in ciprofloxacin-containing agar by 2.2 to 4.3 log CFU/mL for 4/8 strains, as compared to non-adapted control (p ˂ 0.05). However, for other 4/8 strains of L. monocytogenes, there was no increase in survival of QAC-adapted subpopulations, as compared to non-adapted control in ciprofloxacin. These findings suggest the potential formation of low-level ciprofloxacin-tolerant subpopulations in some L. monocytogenes strains when exposed to residual QAC concentrations (where QAC might be used widely) and such cells if not inactivated might create food safety risk.

Selection of a Gentamicin-Resistant Variant Following Polyhexamethylene Biguanide (PHMB) Exposure in Escherichia coli Biofilms

Antibiotic resistance is one of the most important issues facing modern medicine. Some biocides have demonstrated the potential of selecting resistance to antibiotics in bacteria, but data are still very scarce and it is important to better identify the molecules concerned and the underlying mechanisms. This study aimed to assess the potential of polyhexamethylene biguanide (PHMB), a widely used biocide in a variety of sectors, to select antibiotic resistance in Escherichia coli grown in biofilms. Biofilms were grown on inox coupons and then exposed daily to sublethal concentrations of PHMB over 10 days. Antibiotic-resistant variants were then isolated and characterized phenotypically and genotypically to identify the mechanisms of resistance. Repeated exposure to PHMB led to the selection of an E. coli variant (Ec04m1) with stable resistance to gentamycin (8-fold increase in minimum inhibitory concentration (MIC) compared to the parental strain. This was also associated with a significant decrease in the growth rate in the variant. Sequencing and comparison of the parental strain and Ec04m1 whole genomes revealed a nonsense mutation in the aceE gene in the variant. This gene encodes the pyruvate dehydrogenase E1 component of the pyruvate dehydrogenase (PDH) complex, which catalyzes the conversion of pyruvate to acetyl-CoA and CO₂. A growth experiment in the presence of acetate confirmed the role of this mutation in a decreased susceptibility to both PHMB and gentamicin (GEN) in the variant. This work highlights the potential of PHMB to select resistance to antibiotics in bacteria, and that enzymes of central metabolic pathways should be considered as a potential target in adaptation strategies, leading to cross-resistance toward biocides and antibiotics in bacteria.