Impact of Delftia tsuruhatensis and Achromobacter xylosoxidans on Escherichia coli dual-species biofilms treated with antibiotic agents

Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce

Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.

Imaging biofilms using fluorescence in situ hybridization: seeing is believing

Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.

Interactions of microorganisms within a urinary catheter polymicrobial biofilm model

Biofilms are often polymicrobial in nature, which can impact their behavior and overall structure, often resulting in an increase in biomass and enhanced antimicrobial resistance. Using plate counts and locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH), we studied the interactions of four species commonly associated with catheter-associated urinary tract infections (CAUTI): Enterococcus faecalis, Escherichia coli, Candida albicans, and Proteus mirabilis. Eleven combinations of biofilms were grown on silicone coupons placed in 24-well plates for 24 h, 37°C, in artificial urine medium (AUM). Results showed that P. mirabilis was the dominant species and was able to inhibit both E. coli and C. albicans growth. In the absence of P. mirabilis, an antagonistic relationship between E. coli and C. albicans was observed, with the former being dominant. E. faecalis growth was not affected in any combination, showing a more mutualistic relationship with the other species. Imaging results correlated with the plate count data and provided visual verification of species undetected using the viable plate count. Moreover, the three bacterial species showed overall good repeatability SD (S_r ) values (0.1-0.54) in all combinations tested, whereas C. albicans had higher repeatability S_r values (0.36-1.18). The study showed the complexity of early-stage interactions in polymicrobial biofilms. These interactions could serve as a starting point when considering targets for preventing or treating CAUTI biofilms containing these species.

Impact of N-Acetylcysteine and Antibiotics Against Single and Dual Species Biofilms of Pseudomonas aeruginosa and Achromobacter xylosoxidans

Lungs of cystic fibrosis patients are often colonized or infected with organisms, such as Pseudomonas aeruginosa and other emerging pathogenic bacteria such as Achromobacter xylosoxidans. Further, it is well established that infections of the cystic fibrosis lung airways are caused by polymicrobial infections, although its composition and diversity may change throughout the patient's life. In the present study, we investigated the effects of N-acetylcysteine (NAC) and amikacin, aztreonam, ciprofloxacin, and tobramycin alone and in combination against single- and dual-species biofilms of P. aeruginosa and A. xylosoxidans, in vitro and in the Caenorhabditis elegans infection model. Results showed that tobramycin and ciprofloxacin were the most effective antibiotics, while aztreonam was the least effective antibiotic against both single- and dual-species biofilms of P. aeruginosa and A. xylosoxidans. However, NAC showed little effect on both single- and dual-species, even with a combination of antibiotics. Increased survival was observed in C. elegans when treated with NAC in combination with tobramycin or ciprofloxacin, compared to no treatment or NAC alone. Tobramycin and ciprofloxacin were found effective in biofilms, but more research is needed to better understand the effects of NAC and antibiotics against single- and dual-species biofilms.

Biofilms vs. cities and humans vs. aliens - a tale of reproducibility in biofilms

Biofilms are complex and dynamic structures that include many more components than just viable cells. Therefore, the apparently simple goal of growing reproducible biofilms is often elusive. One of the challenges in defining reproducibility for biofilm research is that different research fields use a spectrum of parameters to define reproducibility for their particular application. For instance, is the researcher interested in achieving a similar population density, height of biofilm structures, or function of the biofilm in a certain ecosystem/industrial context? Within this article we categorize reproducibility into four different levels: level 1, no reproducibility; level 2, standard reproducibility; level 3, potential standard reproducibility; and level 4, total reproducibility. To better understand the need for these different levels of reproducibility, we expand on the 'cities of microbes' analogy for biofilms by imagining that a new civilization has reached the Earth's outskirts and starts studying the Earth's cities. This will provide a better sense of scale and illustrate how small details can impact profoundly on the growth and behavior of a biofilm and our understanding of reproducibility.

Increased Intraspecies Diversity in Escherichia coli Biofilms Promotes Cellular Growth at the Expense of Matrix Production

Intraspecies diversity in biofilm communities is associated with enhanced survival and growth of the individual biofilm populations. Studies on the subject are scarce, namely, when more than three strains are present. Hence, in this study, the influence of intraspecies diversity in biofilm populations composed of up to six different Escherichia coli strains isolated from urine was evaluated in conditions mimicking the ones observed in urinary tract infections and catheter-associated urinary tract infections. In general, with the increasing number of strains in a biofilm, an increase in cell cultivability and a decrease in matrix production were observed. For instance, single-strain biofilms produced an average of 73.1 µg·cm⁻² of extracellular polymeric substances (EPS), while six strains biofilms produced 19.9 µg·cm⁻². Hence, it appears that increased genotypic diversity in a biofilm leads E. coli to direct energy towards the production of its offspring, in detriment of the production of public goods (i.e., matrix components). Apart from ecological implications, these results can be explored as another strategy to reduce the biofilm burden, as a decrease in EPS matrix production may render these intraspecies biofilms more sensitive to antimicrobial agents.

A fast and effective alternative to a high-ethanol disinfectant: Low concentrations of fermented ethanol, caprylic acid, and citric acid synergistically eradicate biofilm-embedded methicillin-resistant Staphylococcus aureus

BACKGROUND

There is a growing need to develop a powerful bactericidal method with low ethanol concentrations due to the frequent ineffectiveness of traditional antibiotics against biofilms and the side effect of a high ethanol concentration.

OBJECTIVES

This study aims to develop a novel synergistic technique replacing a high-ethanol disinfectant.

METHODS

Low concentrations of fermented ethanol (FE, 10-20%) with naturally derived antimicrobials, citric acid (CTA, 0.5-1.0%) and caprylic acid (CAP, 0.05-0.15%), were examined against a methicillin-resistant S. aureus (MRSA) biofilm formed on silicone coupons (catheter materials).

RESULTS

CTA and CAP were identified as effective antimicrobials that exhibited a synergistic interaction with FE. Complete eradication of MRSA biofilms (>7 log reduction) was obtained within 5 min after treatment with 20% FE plus 1.0% CTA and 0.15% CAP at both 22 and 37 °C, while individual treatments with each material showed negligible bactericidal effects (<1 log reduction except 0.15% CAP treatment at 37 °C). No bacteria were recovered from the surface after the combined treatment (five enrichment tests). The developed compounds were able to disinfect surfaces with more than 5 log-reduction within only 1 min at 22 °C. Confocal microscopy images showed that the combination of all three materials resulted in remarkable membrane damage and cell detachment from the silicone surface.

DISCUSSON

Application of FE plus CTA and CAP, therefore, can be a valuable decontamination technique for medical devices or can work as a surface disinfectant, reducing the concerns regarding undesirable high ethanol concentrations in disinfectants.

Synergistic cranberry juice combinations with natural-borne antimicrobials for the eradication of uropathogenic Escherichia coli biofilm within a short time

Urinary tract infections (UTI), one of the most common diseases in humans, are caused primarily by uropathogenic Escherichia coli (UPEC). Cranberry juice (CB) is a widely known prophylaxis for UTI, but the treatment of CB alone could not effectively eradicate preformed UPEC biofilms. The aim of this study was to develop enforced CB composites within a short time by adding a small quantity of natural borne antimicrobials. UPEC biofilms (initial: 6·0 log CFU per cm² ), formed on silicone coupons in artificial urine medium, were exposed to CB (4-8%), caprylic acid (CAR; 0·025-0·05%) and thymol (TM; 0·025-0·05%) at 37°C for 1 min. Individual treatment of each compound did not show the significant antibacterial effect on UPEC biofilms (P > 0·05). Otherwise, the survivor counts of biofilms were synergistically reduced with CB containing any of the antimicrobials. For example combined treatment with CB (8%) + CAR (0·05%) + TM (0·05%) resulted in a 6 log reduction in UPEC populations in the biofilm (no detectable bacteria remained) with 4·6 log of synergistic bactericidal effect. The confocal laser scanning microscope images indicated that any composites including TM might result in biofilm detachment from the surface. The present method is cost-effective and more acceptable to consumers as it is based on the synergistic interaction of natural borne antimicrobials. The results of this study could be widely applicable in the functional food, medical and healthcare field. SIGNIFICANCE AND IMPACT OF THE STUDY: Anti-biofilm effect of cranberry juice (CB) has been focused mainly on inhibiting biofilm formation of uropathogenic Escherichia coli (UPEC); however, combined treatment with natural borne antimicrobials derived from coconut oil (caprylic acid) and oregano essential oil (thymol) could synergistically enhance its eradicating activity against biofilms. This study developed novel CB composites showing marked anti-biofilm effects (complete eradication of UPEC biofilms within just 1 min).

Response surface modeling of reductions in uropathogenic Escherichia coli biofilms on silicone by cranberry extract, caprylic acid, and thymol

A response surface methodology was used to build a model to predict reductions in uropathogenic Escherichia coli biofilms in response to three compounds: cranberry extract [CB] at 3.0-9.0%, and caprylic acid [CAR] and thymol [TM] at 0.01%-0.05%. The predictive model for microbial reduction had a high regression coefficient (R² = 0.9988), and the accuracy of the model was verified (R² = 0.9527). Values of CAR, TM, and the quadratic term CAR² were the most significant (P < 0.0001) for bacterial reduction. Interactions between CB and CAR, and TM and CB, also affected bacterial reduction. The optimum conditions (a 5.8 log₁₀ reduction) determined by ridge analysis were 8.3% CB +0.04% CAR +0.04% TM at 37 °C for 1 min. The model could be used to predict the most cost-efficient amounts of antimicrobial agents for anti-urinary tract infection products such as catheter lock solution and antimicrobial coatings for catheters.

Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress

Cystic fibrosis (CF) infections are invariably biofilm-mediated and polymicrobial, being safe to assume that a myriad of factors affects the sociomicrobiology within the CF infection site and modulate the CF community dynamics, by shaping their social activities, overall functions, virulence, ultimately affecting disease outcome. This work aimed to assess changes in the dynamics (particularly on the microbial composition) of dual-/three-species biofilms involving CF-classical (Pseudomonas aeruginosa) and unusual species (Inquilinus limosus and Dolosigranulum pigrum), according to variable oxygen conditions and antibiotic exposure. Low fluctuations in biofilm compositions were observed across distinct oxygen environments, with dual-species biofilms exhibiting similar relative proportions and P. aeruginosa and/or D. pigrum populations dominating three-species consortia. Once exposed to antibiotics, biofilms displayed high resistance profiles, and microbial compositions, distributions, and microbial interactions significantly challenged. The antibiotic/oxygen environment supported such fluctuations, which enhanced for three-species communities. In conclusion, antibiotic therapy hugely disturbed CF communities' dynamics, inducing significant compositional changes on multispecies consortia. Clearly, multiple perturbations may disturb this dynamic, giving rise to various microbiological scenarios in vivo, and affecting disease phenotype. Therefore, an appreciation of the ecological/evolutionary nature within CF communities will be useful for the optimal use of current therapies and for newer breakthroughs on CF antibiotherapy.

Impact of polymicrobial biofilms in catheter-associated urinary tract infections

Recent reports have demonstrated that most biofilms involved in catheter-associated urinary tract infections are polymicrobial communities, with pathogenic microorganisms (e.g. Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and uncommon microorganisms (e.g. Delftia tsuruhatensis, Achromobacter xylosoxidans) frequently co-inhabiting the same urinary catheter. However, little is known about the interactions that occur between different microorganisms and how they impact biofilm formation and infection outcome. This lack of knowledge affects CAUTIs management as uncommon bacteria action can, for instance, influence the rate at which pathogens adhere and grow, as well as affect the overall biofilm resistance to antibiotics. Another relevant aspect is the understanding of factors that drive a single pathogenic bacterium to become prevalent in a polymicrobial community and subsequently cause infection. In this review, a general overview about the IMDs-associated biofilm infections is provided, with an emphasis on the pathophysiology and the microbiome composition of CAUTIs. Based on the available literature, it is clear that more research about the microbiome interaction, mechanisms of biofilm formation and of antimicrobial tolerance of the polymicrobial consortium are required to better understand and treat these infections.