Polymicrobial interactions: impact on pathogenesis and human disease

Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity

Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.

In vitro analysis of interactions between Pseudomonas aeruginosa and Candida albicans treated with silver sulfadiazine in wound infections

Background

Microorganisms tend to rely on close relationships with other species to survive. Consequently, biofilms formed by interactions of different species have been shown to delay the wound healing process. Studies suggest these mixed-population infections contribute to the development of drug resistance and inhibition of host immune response. Silver sulfadiazine (SSD) has been shown to effectively decrease the risk of infection in an open wound. Typically, these are bacterial wound infections; however, the role of fungal species needs further attention.

Objectives

The purpose of this in vitro study was to determine the effect of SSD on interactions between Pseudomonas aeruginosa 09-009 (PA1) or P. aeruginosa 09-010 (PA2) and Candida albicans ATTC 64550 (CA).

Methods

A mixture of 4 mL of tryptic soy broth (TSB) and 100 µL of CA and/or PA1 or PA2 (∼106 log cfu/mL) inoculums were deposited into either wells or vials. The wells or vials were then sonicated (50 W for 10 s) to separate microorganisms attached to the walls. After incubation, cell counts were performed at 24 and 48 h for each microorganism using specific media.

Results

Our results show that without SSD treatment, P. aeruginosa exhibits an inhibitory effect on C. albicans. Treatment with SSD demonstrated significant reduction of P. aeruginosa; however, C. albicans persisted. This experiment demonstrates that SSD was effective in reducing the bioburden of both P. aeruginosa strains after 24 and 48 h; however, it was not as effective in reducing C. albicans.

Conclusions

The data suggest that for polymicrobial mixed infections containing Pseudomonas spp. and C. albicans, treatment with SSD may be beneficial but does not provide adequate microorganism eradication. As such, added treatments that provide coverage for Candida infection are necessary. Additional in vivo studies are needed to obtain a better understanding of the complex interactions between these organisms.

Anaerobes in diabetic foot infections: pathophysiology, epidemiology, virulence, and management

SUMMARYDiabetic foot infections (DFI) are a public health problem worldwide. DFI are polymicrobial, biofilm-associated infections involving complex bacterial communities organized in functional equivalent pathogroups, all including anaerobes. Indeed, multiple pathophysiological factors favor the growth of anaerobes in this context. However, the prevalence, role, and contribution of anaerobes in wound evolution remain poorly characterized due to their challenging detection. Studies based on culture reviewed herein showed a weighted average of 17% of patients with anaerobes. Comparatively, the weighted average of patients with anaerobes identified by 16S rRNA gene sequencing was 83.8%. Culture largely underestimated not only the presence but also the diversity of anaerobes compared with cultivation-independent approaches but both methods showed that anaerobic Gram-negative bacilli and Gram-positive cocci were the most commonly identified in DFI. Anaerobes were more present in deeper lesions, and their detection was associated with fever, malodorous lesions, and ulcer depth and duration. More specifically, initial abundance of Peptoniphilus spp. was associated with ulcer-impaired healing, Fusobacterium spp. detection was significantly correlated with the duration of DFI, and the presence of Bacteroides spp. was significantly associated with amputation. Antimicrobial resistance of anaerobes in DFI remains slightly studied and warrants more consideration in the context of increasing resistance of the most frequently identified anaerobes in DFI. The high rate of patients with DFI-involving anaerobes, the increased knowledge on the species identified, their virulence factors, and their potential role in wound evolution support recommendations combining debridement and antibiotic therapy effective on anaerobes in moderate and severe DFI.

Development of a risk prediction model for subsequent infection after colonization with carbapenem-resistant Enterobacterales: a retrospective cohort study

BACKGROUND

Colonization of carbapenem-resistant Enterobacterale (CRE) is considered as one of vital preconditions for infection, with corresponding high morbidity and mortality. It is important to construct a reliable prediction model for those CRE carriers with high risk of infection.

METHODS

A retrospective cohort study was conducted in two Chinese tertiary hospitals for patients with CRE colonization from 2011 to 2021. Univariable analysis and the Fine-Gray sub-distribution hazard model were utilized to identify potential predictors for CRE-colonized infection, while death was the competing event. A nomogram was established to predict 30-day and 60-day risk of CRE-colonized infection.

RESULTS

879 eligible patients were enrolled in our study and divided into training (n = 761) and validation (n = 118) group, respectively. There were 196 (25.8%) patients suffered from subsequent CRE infection. The median duration of subsequent infection after identification of CRE colonization was 20 (interquartile range [IQR], 14-32) days. Multisite colonization, polymicrobial colonization, catheterization and receiving albumin after colonization, concomitant respiratory diseases, receiving carbapenems and antimicrobial combination therapy before CRE colonization within 90 days were included in final model. Model discrimination and calibration were acceptable for predicting the probability of 60-day CRE-colonized infection in both training (area under the curve [AUC], 74.7) and validation dataset (AUC, 81.1). Decision-curve analysis revealed a significantly better net benefit in current model. Our prediction model is freely available online at https://ken-zheng.shinyapps.io/PredictingModelofCREcolonizedInfection/ .

CONCLUSIONS

Our nomogram has a good predictive performance and could contribute to early identification of CRE carriers with a high-risk of subsequent infection, although external validation would be required.

Interactions among microorganisms open up a new world for anti-infectious therapy

The human microbiome, containing bacteria, fungi, and viruses, is a community that coexists peacefully with humans most of the time, but with the potential to cause disease under certain conditions. When the environment changes or certain stimuli are received, microbes may interact with each other, causing or increasing the severity of disease in a host. With the appropriate methods, we can make these microbiota work for us, creating new applications for human health. This review discusses the wide range of interactions between microorganisms that result in an increase in susceptibility to, severity of, and mortality of diseases, and also briefly introduces how microorganisms interact with each other directly or indirectly. The study of microbial interactions and their mechanisms has revealed a new world of treatments for infectious disease. The regulation of the balance between intestinal flora, the correct application of probiotics, and the development of effective drugs by symbiosis all demonstrate the great contributions of the microbiota to human health and its powerful potential value. Consequently, the study of interactions between microorganisms plays an essential role in identifying the causes of diseases and the development of treatments.

Triple threat: how diabetes results in worsened bacterial infections

Diabetes mellitus, characterized by impaired insulin signaling, is associated with increased incidence and severity of infections. Various diabetes-related complications contribute to exacerbated bacterial infections, including hyperglycemia, innate immune cell dysfunction, and infection with antibiotic-resistant bacterial strains. One defining symptom of diabetes is hyperglycemia, resulting in elevated blood and tissue glucose concentrations. Glucose is the preferred carbon source of several bacterial pathogens, and hyperglycemia escalates bacterial growth and virulence. Hyperglycemia promotes specific mechanisms of bacterial virulence known to contribute to infection chronicity, including tissue adherence and biofilm formation. Foot infections are a significant source of morbidity in individuals with diabetes and consist of biofilm-associated polymicrobial communities. Bacteria perform complex interspecies behaviors conducive to their growth and virulence within biofilms, including metabolic cross-feeding and altered phenotypes more tolerant to antibiotic therapeutics. Moreover, the metabolic dysfunction caused by diabetes compromises immune cell function, resulting in immune suppression. Impaired insulin signaling induces aberrations in phagocytic cells, which are crucial mediators for controlling and resolving bacterial infections. These aberrancies encompass altered cytokine profiles, the migratory and chemotactic mechanisms of neutrophils, and the metabolic reprogramming required for the oxidative burst and subsequent generation of bactericidal free radicals. Furthermore, the immune suppression caused by diabetes and the polymicrobial nature of the diabetic infection microenvironment may promote the emergence of novel strains of multidrug-resistant bacterial pathogens. This review focuses on the "triple threat" linked to worsened bacterial infections in individuals with diabetes: (i) altered nutritional availability in diabetic tissues, (ii) diabetes-associated immune suppression, and (iii) antibiotic treatment failure.

Aptamer-based therapy for fighting biofilm-associated infections

Biofilms are key players in the pathogenesis of most of chronic infections associated with host tissue or fluids and indwelling medical devices. These chronic infections are hard to be treated due to the increased biofilms tolerance towards antibiotics in comparison to planktonic (or free living) cells. Despite the advanced understanding of their formation and physiology, biofilms continue to be a challenge and there is no standardized therapeutic approach in clinical practice to eradicate them. Aptamers offer distinctive properties, including excellent affinity, selectivity, stability, making them valuable tools for therapeutic purposes. This review explores the flexibility and designability of aptamers as antibiofilm drugs but, importantly, as targeting tools for diverse drug and delivery systems. It highlights specific examples of application of aptamers in biofilms of diverse species according to different modes of action including inhibition of motility and adhesion, blocking of quorum sensing molecules, and dispersal of biofilm-cells to planktonic state. Moreover, it discusses the limitations and challenges that impaired an increased success of the use of aptamers on biofilm management, as well as the opportunities related to aptamers modifications that can significantly expand their applicability on the biofilm field.

Shift in risk factors for mortality by period of the bloodstream infection timeline

BACKGROUND

This study was designed to determine changes in risk factors on the prognosis of patients during each period of the bloodstream infection (BSI) timeline.

METHODS

Through an integrated study of multivariable regressions with machine learning techniques, the risk factors for mortality during each period of BSI were analyzed.

RESULTS

A total of 302,303 inpatients who underwent blood cultures during 2011-2021 were enrolled. More than 8 % of BSI cases progressed to subsequent BSI, and risk factors were identified as gut colonization with vancomycin-resistant enterococci (aOR 1.82; 95 % CI 1.47-2.24), intensive care unit admission (aOR 3.37; 95 % CI 3.35-4.28), and current cancer chemotherapy (aOR 1.54; 95 % CI 1.36-1.74). The mean SOFA score of the deceased patients during the first 7 days was 10.6 (SD 4.3), which was significantly higher than those on days 8-30 (7.0 ± 4.2) and after Day 30 (4.0 ± 3.5). BSIs caused by Acinetobacter baumannii and Candida albicans were more likely to result in deaths of patients for all time periods (all, P < 0.001). BSIs caused by Enterococcus faecalis and Enterococcus faecium were associated with a poor outcome in the period after Day 30 (both, P < 0.001). Nonsusceptible phenotypes to β-lactam/β-lactamase inhibitors of Escherichia coli and Klebsiella pneumoniae influenced the prognoses of patients with BSI in terms of high mortality rates during both days 8-30 and after Day 30.

CONCLUSION

Influence of microbiological factors on mortality, including BSI-causative microorganisms and their major antimicrobial resistance, was emphasized in both periods of days 8-30 and after Day 30.

Advances in bacteriophage-mediated strategies for combating polymicrobial biofilms

Bacteria and fungi tend to coexist within biofilms instead of in planktonic states. Usually, such communities include cross-kingdom microorganisms, which make them harder to remove from abiotic surfaces or infection sites. Additionally, the produced biofilm matrix protects embedded microorganisms from antibiotics, disinfectants, or the host immune system. Therefore, classic therapies based on antibiotics might be ineffective, especially when multidrug-resistant bacteria are causative factors. The complexities surrounding the eradication of biofilms from diverse surfaces and the human body have spurred the exploration of alternative therapeutic modalities. Among these options, bacteriophages and their enzymatic counterparts have emerged as promising candidates, either employed independently or in synergy with antibiotics and other agents. Phages are natural bacteria killers because of mechanisms of action that differ from antibiotics, phages might answer worldwide problems with bacterial infections. In this review, we report the attempts to use bacteriophages in combating polymicrobial biofilms in in vitro studies, using different models, including the therapeutical use of phages. In addition, we sum up the advantages, disadvantages, and perspectives of phage therapy.

Bacterial synergies and antagonisms affecting Pseudomonas aeruginosa virulence in the human lung, skin and intestine

Pseudomonas aeruginosa requires a significant breach in the host defense to cause an infection. While its virulence factors are well studied, its tropism cannot be explained only by studying its interaction with the host. Why are P. aeruginosa infections so rare in the intestine compared with the lung and skin? There is not enough evidence to claim specificity in virulence factors deployed by P. aeruginosa in each anatomical site, and host physiology differences between the lung and the intestine cannot easily explain the observed differences in virulence. This perspective highlights a relatively overlooked parameter in P. aeruginosa virulence, namely, potential synergies with bacteria found in the human skin and lung, as well as antagonisms with bacteria of the human intestine.

Defining microbial community functions in chronic human infection with metatranscriptomics

IMPORTANCE

The microbial diversity in polymicrobial infections (PMIs) allows for community members to establish interactions with one another, which can result in enhanced disease outcomes such as increased antibiotic tolerance and chronicity. Chronic PMIs result in large burdens on health systems, as they affect a significant proportion of the population and are expensive and difficult to treat. However, investigations into physiology of microbial communities in actual human infection sites are lacking. Here, we highlight that the predominant functions in chronic PMIs differ, and anaerobes, often described as bystanders, may be significant in the progression of chronic infections. Determining the community structure and functions in PMIs is a critical step toward understanding the molecular mechanisms that increase the virulence potential of the microbial community in these environments.

Drosophila melanogaster as a model to study polymicrobial synergy and dysbiosis

The fruit fly Drosophila melanogaster has emerged as a valuable model for investigating human biology, including the role of the microbiome in health and disease. Historically, studies involving the infection of D. melanogaster with single microbial species have yielded critical insights into bacterial colonization and host innate immunity. However, recent evidence has underscored that multiple microbial species can interact in complex ways through physical connections, metabolic cross-feeding, or signaling exchanges, with significant implications for healthy homeostasis and the initiation, progression, and outcomes of disease. As a result, researchers have shifted their focus toward developing more robust and representative in vivo models of co-infection to probe the intricacies of polymicrobial synergy and dysbiosis. This review provides a comprehensive overview of the pioneering work and recent advances in the field, highlighting the utility of Drosophila as an alternative model for studying the multifaceted microbial interactions that occur within the oral cavity and other body sites. We will discuss the factors and mechanisms that drive microbial community dynamics, as well as their impacts on host physiology and immune responses. Furthermore, this review will delve into the emerging evidence that connects oral microbes to systemic conditions in both health and disease. As our understanding of the microbiome continues to evolve, Drosophila offers a powerful and tractable model for unraveling the complex interplay between host and microbes including oral microbes, which has far-reaching implications for human health and the development of targeted therapeutic interventions.

Small molecular adjuvants repurpose antibiotics towards Gram-negative bacterial infections and multispecies bacterial biofilms

Gram-negative bacterial infections pose a significant challenge due to two major resistance elements, including the impermeability of the outer membrane and the overexpression of efflux pumps, which contribute to antibiotic resistance. Additionally, the coexistence of multispecies superbugs in mixed species biofilms further complicates treatment, as these infections are refractory to most antibiotics. To address this issue, combining obsolete antibiotics with non-antibiotic adjuvants that target bacterial membranes has shown promise in combating antibacterial resistance. However, the clinical translation of this cocktail therapy has been hindered by the toxicity associated with these membrane active adjuvants, mainly due to a limited understanding of their structure and mechanism of action. Towards this goal, herein, we have designed a small molecular adjuvant by tuning different structural parameters, such as the balance between hydrophilic and hydrophobic groups, spatial positioning of hydrophobicity and hydrogen bonding interactions, causing moderate membrane perturbation in bacterial cells without any toxicity to mammalian cells. Moderate membrane perturbation not only enhances the internalization of antibiotics, but also increases the intracellular concentration of drugs by hampering the efflux machinery. This revitalises the efficacy of various classes of antibiotics by 32-512 fold, without inducing toxicity. The leading combination not only exhibits potent bactericidal activity against A. baumannii biofilms but also effectively disrupts mature multispecies biofilms composed of A. baumannii and methicillin-resistant Staphylococcus aureus (MRSA), which is typically resistant to most antibiotics. Importantly, the combination therapy demonstrates good biocompatibility and excellent in vivo antibacterial efficacy (>99% reduction) in a skin infection model of A. baumannii. Interestingly, A. baumannii shows reduced susceptibility to develop resistance against the leading combination, underscoring its potential for treating multi-drug resistant infections.

Bacteriophage endolysin Ply113 as a potent antibacterial agent against polymicrobial biofilms formed by enterococci and Staphylococcus aureus

Antibiotic resistance in Enterococcus faecium, Enterococcus faecalis, and Staphylococcus aureus remains a major public health concern worldwide. Furthermore, these microbes frequently co-exist in biofilm-associated infections, largely nullifying antibiotic-based therapy. Therefore, it is imperative to develop an efficient therapeutic strategy for combating infections caused by polymicrobial biofilms. In this study, we investigated the antibacterial and antibiofilm activity of the bacteriophage endolysin Ply113 in vitro. Ply113 exhibited high and rapid lytic activity against E. faecium, E. faecalis, and S. aureus, including vancomycin-resistant Enterococcus and methicillin-resistant S. aureus isolates. Transmission electron microscopy revealed that Ply113 treatment led to the detachment of bacterial cell walls and considerable cell lysis. Ply113 maintained stable lytic activity over a temperature range of 4-45°C, over a pH range of 5.0-8.0, and in the presence of 0-400 mM NaCl. Ply113 treatment effectively eliminated the mono-species biofilms formed by E. faecium, E. faecalis, and S. aureus in a dose-dependent manner. Ply113 was also able to eliminate the dual-species biofilms of E. faecium-S. aureus and E. faecalis-S. aureus. Additionally, Ply113 exerted potent antibacterial efficacy in vivo, distinctly decreasing the bacterial loads in a murine peritoneal septicemia model. Our findings suggest that the bacteriophage endolysin Ply113 is a promising antimicrobial agent for the treatment of polymicrobial infections.

Expanded Multiplexing on Sensor-Constrained Microfluidic Partitioning Systems

Microfluidics can split samples into thousands or millions of partitions, such as droplets or nanowells. Partitions capture analytes according to a Poisson distribution, and in diagnostics, the analyte concentration is commonly inferred with a closed-form solution via maximum likelihood estimation (MLE). Here, we present a new scalable approach to multiplexing analytes. We generalize MLE with microfluidic partitioning and extend our previously developed Sparse Poisson Recovery (SPoRe) inference algorithm. We also present the first in vitro demonstration of SPoRe with droplet digital PCR (ddPCR) toward infection diagnostics. Digital PCR is intrinsically highly sensitive, and SPoRe helps expand its multiplexing capacity by circumventing its channel limitations. We broadly amplify bacteria with 16S ddPCR and assign barcodes to nine pathogen genera by using five nonspecific probes. Given our two-channel ddPCR system, we measured two probes at a time in multiple groups of droplets. Although individual droplets are ambiguous in their bacterial contents, we recover the concentrations of bacteria in the sample from the pooled data. We achieve stable quantification down to approximately 200 total copies of the 16S gene per sample, enabling a suite of clinical applications given a robust upstream microbial DNA extraction procedure. We develop a new theory that generalizes the application of this framework to many realistic sensing modalities, and we prove scaling rules for system design to achieve further expanded multiplexing. The core principles demonstrated here could impact many biosensing applications with microfluidic partitioning.

Extracellular vesicles in bacterial and fungal diseases - Pathogenesis to diagnostic biomarkers

Intercellular communication among microbes plays an important role in disease exacerbation. Recent advances have described small vesicles, termed as "extracellular vesicles" (EVs), previously disregarded as "cellular dust" to be vital in the intracellular and intercellular communication in host-microbe interactions. These signals have been known to initiate host damage and transfer of a variety of cargo including proteins, lipid particles, DNA, mRNA, and miRNAs. Microbial EVs, referred to generally as "membrane vesicles" (MVs), play a key role in disease exacerbation suggesting their importance in pathogenicity. Host EVs help coordinate antimicrobial responses and prime the immune cells for pathogen attack. Hence EVs with their central role in microbe-host communication, may serve as important diagnostic biomarkers of microbial pathogenesis. In this review, we summarize current research regarding the roles of EVs as markers of microbial pathogenesis with specific focus on their interaction with host immune defence and their potential as diagnostic biomarkers in disease conditions.

Treatment of Staphylococcus aureus and Candida albicans polymicrobial biofilms by phloroglucinol-gold nanoparticles

The co-isolation of Staphylococcus aureus and Candida albicans from host tissues and organs and their in vitro and in vivo interaction studies suggest a synergistic relationship in forming polymicrobial biofilms. In particular, during polymicrobial biofilm formation, S. aureus becomes coated in the extracellular matrix secreted by C. albicans, leading to enhanced resistance to antibiotics. Accordingly, understanding the interactions between S. aureus and C. albicans in polymicrobial biofilms is of utmost importance in establishing treatment strategies for polymicrobial infections. As an alternate technique, nanoparticles were used in this investigation to suppress polymicrobial biofilm. The current study aims to manufacture gold nanoparticles (AuNPs) using phloroglucinol (PG), a natural chemical, and test their inhibitory capabilities against S. aureus and C. albicans biofilms in standard and host-mimicking media (like saliva and sputum). PG-AuNPs have a spherical form with an average size of 46.71 ± 6.40 nm. The minimum inhibitory concentration (MIC) values differed when PG-AuNPs were evaluated in the standard and host-mimicking artificial media. The MIC of PG-AuNPs against S. aureus and C. albicans was 2048 μg/mL in both the standard and artificial sputum media. However, the MIC in saliva was only 128 μg/mL. The initial stage polymicrobial biofilm of S. aureus and C. albicans was dramatically decreased at the sub-MIC of PG-AuNPs in both standard and host-mimicking media. S. aureus and C. albicans mature polymicrobial biofilms were more effectively eliminated by MIC and sub-MIC of PG-AuNPs. This study indicates that PG-AuNPs have the ability to limit the formation of polymicrobial biofilms caused by bacterial and fungal diseases.

The Great Imitator: Cervicofacial Actinomycosis Masquerading as Cancer Recurrence

Cervicofacial actinomycosis being one of the unusual infections is of high relevance to a head and neck onco-surgeon. As the diagnosis may be made difficult by its nature to mimic malignancy and egregiously low culture sensitivity, the differential diagnosis for a lesion appearing to be malignant after irradiation does not usually include actinomycotic infection. Treatment usually requires a long-term antibiotic course after confirmation with histopathology, albeit surgical debridement is required in selective cases. Here we report two cases that were clinico-radiologically diagnosed as osteoradionecrosis and histopathological analysis done to rule out cancer recurrence. Unanticipated, they turned out to be cervicofacial actinomycosis, subsequently treated with long-term antibiotics following which the infection subsided.

Copper reduces the virulence of bacterial communities at environmentally relevant concentrations

Increasing environmental concentrations of metals as a result of anthropogenic pollution are significantly changing many microbial communities. While there is evidence metal pollution can result in increased antibiotic resistance, the effects of metal pollution on the virulence of bacterial communities remains largely undetermined. Here, we experimentally test whether metal stress alters the virulence of bacterial communities. We do this by incubating three wastewater influent communities under different environmentally relevant copper concentrations for three days. We then quantify the virulence of the community phenotypically using the Galleria mellonella infection model, and test if differences are due to changes in the rate of biomass accumulation (productivity), copper resistance, or community composition (quantified using 16S amplicon sequencing). The virulence of the communities was found to be reduced by the highest copper concentration, but not to be affected by the lower concentration. As well as reduced virulence, communities exposed to the highest copper concentration were less diverse and had lower productivity. This work highlights that metal pollution may decrease virulence in bacterial communities, but at a cost to diversity and productivity.

Impact of Biofilms on Chronic Infections and Medical Challenges

Biofilms which are intricate colonies of bacteria encapsulated in a self-produced matrix are becoming more widely recognized for their importance in persistent infections. Biofilm-related infections provide distinct diagnostic and therapy issues needing novel approaches. Biofilms are common in clinical settings and contribute to the persistence of diseases related to medical devices, dental health, respiratory disorders, and chronic infection. Overcoming these problems requires a thorough understanding of the elements that influence biofilm development and their complex interactions within the microbial community. Emerging diagnostic techniques and therapy approaches that target biofilm-related disorders at different levels give hope for improved patient outcomes. This review looks at how biofilm formation affects chronic infections in a variety of ways, including increased drug resistance, immune system evasion, and delayed diagnosis.

Antimicrobial susceptibility and clinical characteristics of multidrug-resistant polymicrobial infections in Pakistan, a retrospective study 2019-2021

Background: We determined the prevalence of antimicrobial resistance (AMR) in polymicrobial pathogens in Pakistan. Methods: A total of 70,518 clinical samples were collected aseptically and confirmation of isolates and antibiogram were performed by the VITEK 2 system. Results: Of 70,518 samples, 441 (0.62%) were polymicrobial samples, with 882 (1.2%) polymicrobial pathogens with 689 (78.1%) Gram-negative rods (GNRs), 166 (18.8%) Gram-positive cocci and 27 (3.1%) Candida albicans. Among GNRs, 28.8% were Escherichia coli and 25.9% were Klebsiella pneumoniae. Majority, 15.1% of Pseudomonas aeruginosa and K. pneumoniae were found in combination. 30.1% of isolates were ESBL producers, 9.7% carbapenem-resistant organisms, 35.5% MRSA and 6.0% VRE. 100% of E. coli were resistant to ampicillin and 98% of K. pneumoniae were resistant to piperacillin. Conclusion: A high prevalence of AMR in polymicrobial pathogens was observed.

Interspecies interactions of non-O1/O139 Vibrio cholerae and Salmonella typhimurium: a rare coinfection case report

Infectious diseases are commonly demonstrated to be caused by polymicrobial infections, which correlate with increased infection severity and poorer clinical outcomes. In this study, we report a rare intestinal coinfection case of non-O1/O139 Vibrio cholerae and Salmonella typhimurium, along with V. cholerae septicemia. The data of quantitative real-time PCR and competition assay showed that V. cholerae may present enhanced virulence in the presence of S. typhimurium, and exerted an inhibitory growth effect over S. typhimurium in vitro.

Rapid and strain-specific resistance evolution of Staphylococcus aureus against inhibitory molecules secreted by Pseudomonas aeruginosa

IMPORTANCE

Polymicrobial infections are common. In chronic infections, the different pathogens may repeatedly interact, which could spur evolutionary dynamics with pathogens adapting to one another. Here, we explore the potential of Staphylococcus aureus to adapt to its competitor Pseudomonas aeruginosa. These two pathogens frequently co-occur, and P. aeruginosa is seen as the dominant species being able to displace S. aureus. We studied three different S. aureus strains and found that all became quickly resistant to inhibitory compounds secreted by P. aeruginosa. Our experimental evolution revealed strains-specific adaptations with three main factors contributing to resistance evolution: (i) overproduction of staphyloxanthin, a molecule protecting from oxidative stress; (ii) the formation of small colony variants also protecting from oxidative stress; and (iii) alterations of membrane transporters possibly reducing toxin uptake. Our results show that species interactions can change over time potentially favoring species co-existence, which in turn could affect disease progression and treatment options.

Protection against lethal sepsis following immunization with Candida species varies by isolate and inversely correlates with bone marrow tissue damage

Protection against lethal Candida albicans (Ca)/Staphylococcus aureus (Sa) intra-abdominal infection (IAI)-mediated sepsis can be achieved by a novel form of trained innate immunity (TII) involving Gr-1+ myeloid-derived suppressor cells (MDSCs) that are induced by inoculation (immunization) with low virulence Candida species [i.e., Candida dubliniensis (Cd)] that infiltrate the bone marrow (BM). In contrast, more virulent Candida species (i.e., C. albicans), even at sub-lethal inocula, fail to induce similar levels of protection. The purpose of the present study was to test the hypothesis that the level of TII-mediated protection induced by Ca strains inversely correlates with damage in the BM as a reflection of virulence. Mice were immunized by intraperitoneal inoculation with several parental and mutant strains of C. albicans deficient in virulence factors (hyphal formation and candidalysin production), followed by an intraperitoneal Ca/Sa challenge 14 d later and monitored for sepsis and mortality. Whole femur bones were collected 24 h and 13 d after immunization and assessed for BM tissue/cellular damage via ferroptosis and histology. While immunization with standard but not sub-lethal inocula of most wild-type C. albicans strains resulted in considerable mortality, protection against lethal Ca/Sa IAI challenge varied by strain was usually less than that for C. dubliniensis, with no differences observed between parental and corresponding mutants. Finally, levels of protection afforded by the Ca strains were inversely correlated with BM tissue damage (R 2 = -0.773). TII-mediated protection against lethal Ca/Sa sepsis induced by Candida strain immunization inversely correlates with BM tissue/cellular damage as a reflection of localized virulence.

The Complicated Relationship of Short-Chain Fatty Acids and Oral Microbiome: A Narrative Review

The human oral microbiome has emerged as a focal point of research due to its profound implications for human health. The involvement of short-chain fatty acids in oral microbiome composition, oral health, and chronic inflammation is gaining increasing attention. In this narrative review, the results of early in vitro, in vivo, and pilot clinical studies and research projects are presented in order to define the boundaries of this new complicated issue. According to the results, the current research data are disputable and ambiguous. When investigating the role of SCFAs in human health and disease, it is crucial to distinguish between their local GI effects and the systemic influences. Locally, SCFAs are a part of normal oral microbiota metabolism, but the increased formation of SCFAs usually attribute to dysbiosis; excess SCFAs participate in the development of local oral diseases and in oral biota gut colonization and dysbiosis. On the other hand, a number of studies have established the positive impact of SCFAs on human health as a whole, including the reduction of chronic systemic inflammation, improvement of metabolic processes, and decrease of some types of cancer incidence. Thus, a complex and sophisticated approach with consideration of origin and localization for SCFA function assessment is demanded. Therefore, more research, especially clinical research, is needed to investigate the complicated relationship of SCFAs with health and disease and their potential role in prevention and treatment.

Molecular studies of phages-Klebsiella pneumoniae in mucoid environment: innovative use of mucolytic agents prior to the administration of lytic phages

Mucins are important glycoproteins that form a protective layer throughout the gastrointestinal and respiratory tracts. There is scientific evidence of increase in phage-resistance in the presence of mucin for some bacterial pathogens. Manipulation in mucin composition may ultimately influence the effectiveness of phage therapy. In this work, two clinical strains of K. pneumoniae (K3574 and K3325), were exposed to the lytic bacteriophage vB_KpnS-VAC35 in the presence and absence of mucin on a long-term co-evolution assay, in an attempt to mimic in vitro the exposure to mucins that bacteria and their phages face in vivo. Enumerations of the bacterial and phage counts at regular time intervals were conducted, and extraction of the genomic DNA of co-evolved bacteria to the phage, the mucin and both was performed. We determined the frequency of phage-resistant mutants in the presence and absence of mucin and including a mucolytic agent (N-acetyl L-cysteine, NAC), and sequenced them using Nanopore. We phenotypically demonstrated that the presence of mucin induces the emergence of bacterial resistance against lytic phages, effectively decreased in the presence of NAC. In addition, the genomic analysis revealed some of the genes relevant to the development of phage resistance in long-term co-evolution, with a special focus on the mucoid environment. Genes involved in the metabolism of carbohydrates were mutated in the presence of mucin. In conclusion, the use of mucolytic agents prior to the administration of lytic phages could be an interesting therapeutic option when addressing K. pneumoniae infections in environments where mucin is overproduced.

Dynamic interactions between Candida albicans and different streptococcal species in a multispecies oral biofilm

The oral cavity is colonized by a plethora of bacteria, fungi, and archaea, including streptococci of the mitis group (MSG) and the yeast Candida albicans. This study aims to investigate the role of streptococcal species in the development of oral biofilm and the cross-kingdom interactions between some of the members of the commensal MSG and the pathogen yeast C. albicans using a multispecies supragingival biofilm model. A total of nine different in vitro biofilms were grown, quantified with culture analyses, and visually examined with confocal laser scanning microscopy (CLSM). A four-species biofilm without any streptococcal species was used as a basic biofilm. In each subsequent inoculum, one species of MSG was added and afterward combined with Streptococcus mutans. The eight-species biofilm contained all eight strains used in this study. Culture analyses showed that the presence of S. mutans in a four-species biofilm with Streptococcus oralis or S. oralis subsp. tigurinus did not differ significantly in C. albicans colony-forming unit (CFU) counts compared to biofilms without S. mutans. However, compared to other mitis species, Streptococcus gordonii combined with S. mutans resulted in the lowest CFUs of C. albicans. Visual observation by CLSM showed that biofilms containing both S. mutans and one species of MSG seemed to induce the formation of filamentous form of C. albicans. However, when several species of MSG were combined with S. mutans, C. albicans was again found in its yeast form.

Transcriptional profiling and genetic analysis of a cystic fibrosis airway-relevant model shows asymmetric responses to growth in a polymicrobial community

Bacterial infections in the lungs of persons with cystic fibrosis are typically composed of multispecies biofilm-like communities, which modulate clinically relevant phenotypes that cannot be explained in the context of a single species culture. Most analyses to date provide a picture of the transcriptional responses of individual pathogens; however, there is relatively little data describing the transcriptional landscape of clinically relevant multispecies communities. Harnessing a previously described cystic fibrosis-relevant, polymicrobial community model consisting of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica, we performed an RNA-Seq analysis on the biofilm population to elucidate the transcriptional profiles of the community grown in artificial sputum medium (ASM) as compared to growth in monoculture, without mucin, and in fresh medium supplemented with tobramycin. We provide evidence that, although the transcriptional profile of P. aeruginosa is community agnostic, the transcriptomes of S. aureus and S. sanguinis are community aware. Furthermore, P. aeruginosa and P. melaninogenica are transcriptionally sensitive to the presence of mucin in ASM, whereas S. aureus and S. sanguinis largely do not alter their transcriptional profiles in the presence of mucin when grown in a community. Only P. aeruginosa shows a robust response to tobramycin. Genetic studies of mutants altered in community-specific growth provide complementary data regarding how these microbes adapt to a community context. IMPORTANCE Polymicrobial infections constitute the majority of infections in the cystic fibrosis (CF) airway, but their study has largely been neglected in a laboratory setting. Our lab previously reported a polymicrobial community that can help explain clinical outcomes in the lungs of persons with CF. Here, we obtained transcriptional profiles of the community versus monocultures to provide transcriptional information about how this model community responds to CF-related growth conditions and perturbations. Genetic studies provide complementary functional outputs to assess how the microbes adapt to life in a community.

Evaluation of the Antifungal Effect of Rhus verniciflua Stokes Extract for Oral Application Potential

Background and Objectives: This study confirms the possibility of using Rhus verniciflua Stokes (RVS) extract as a natural treatment for oral candidiasis. Materials and Methods: RVS was extracted with 70% ethanol to examine the antioxidant activity through polyphenol, flavonoid content, and DPPH (1,1-diphenyl-2-picrylhydrazyl). To evaluate the antifungal effect against Candida albicans (C. albicans; KCTC 7965/ATCC 10231) and evaluate the stability of RVS, a water-soluble tetrazolium salt (WST-1) assay was performed in human keratinocytes (HaCaT). Results: The findings revealed that RVS extract has fairly high antioxidant activity. The clear zones of the RVS extract against C. albicans increased in diameter due to the inhibition of fungal growth at higher concentrations. Treatment with the 1.25 mg/mL RVS extract had a more than 99% antifungal effect against C. albicans, and the 20 mg/mL RVS extract had a 100% antifungal effect. The WST-1 assay showed that the RVS extract induced low cell viability in the HaCaT cells, which inhibited their proliferation, and the RVS extract is also toxic to normal cells. Conclusions: Although the RVS extract with high antioxidant activity showed clear antifungal activity against C. albicans, it exhibited a low survival rate. Therefore, the development of a safe natural antibiotic is necessary.

A Dual-Pathogen Mitral Valve Endocarditis Caused by Coxiella burnetii and Streptococcus gordonii-Which Came First?

Infective endocarditis (IE) is still a life-threatening disease with high morbidity and mortality. While usually caused by a single bacterium, poly-microbial infective endocarditis (IE) is rare. Here, we report a (blood-culture-negative) dual pathogen mitral valve IE caused by Coxiella burnetii and Streptococcus gordonii: A 53-year-old woman was presented to an internal medicine department with abdominal pain for further evaluation. Within the diagnostic work up, transthoracic echocardiography (TTE) revealed an irregularly shaped echogenic mass (5 × 13 mm) adherent to the edge of the posterior mitral valve leaflet and protruding into the left atrium. As infected endocarditis was suspected, blood cultures were initially obtained, but they remained negative. Chronic Q fever infection was diagnosed using serologic testing. After the occurrence of cerebral thromboembolic events, the patient was admitted for mitral valve surgery. Intraoperatively, a massively destructed mitral valve with adhering vegetations was noted. Examination of the mitral valve by broad-range bacterial polymerase chain reaction (PCR) and amplicon sequencing confirmed Coxiella burnetii infection and yielded Streptococcus gordonii as the second pathogen. Based on the detailed diagnosis, appropriate antibiotic therapy of both pathogens was initiated, and the patient could be discharged uneventfully on the 11th postoperative day after a successful minimal-invasive mitral valve replacement.

Computationally Designed AMPs with Antibacterial and Antibiofilm Activity against MDR Acinetobacter baumannii

The discovery of new antimicrobials is necessary to combat multidrug-resistant (MDR) bacteria, especially those that infect wounds and form prodigious biofilms, such as Acinetobacter baumannii. Antimicrobial peptides (AMPs) are a promising class of new therapeutics against drug-resistant bacteria, including gram-negatives. Here, we utilized a computational AMP design strategy combining database filtering technology plus positional analysis to design a series of novel peptides, named HRZN, designed to be active against A. baumannii. All of the HRZN peptides we synthesized exhibited antimicrobial activity against three MDR A. baumannii strains with HRZN-15 being the most active (MIC 4 µg/mL). This peptide also inhibited and eradicated biofilm of A. baumannii strain AB5075 at 8 and 16 µg/mL, which is highly effective. HRZN-15 permeabilized and depolarized the membrane of AB5075 rapidly, as demonstrated by the killing kinetics. HRZN 13 and 14 peptides had little to no hemolysis activity against human red blood cells, whereas HRZN-15, -16, and -17 peptides demonstrated more significant hemolytic activity. HRZN-15 also demonstrated toxicity to waxworms. Further modification of HRZN-15 could result in a new peptide with an improved toxicity profile. Overall, we successfully designed a set of new AMPs that demonstrated activity against MDR A. baumannii using a computational approach.

Epidemic Trends and Biofilm Formation Mechanisms of Haemophilus influenzae: Insights into Clinical Implications and Prevention Strategies

Haemophilus influenzae (H. influenzae) is a significant pathogen responsible for causing respiratory tract infections and invasive diseases, leading to a considerable disease burden. The Haemophilus influenzae type b (Hib) conjugate vaccine has notably decreased the incidence of severe infections caused by Hib strains, and other non-typable H. influenzae (NTHi) serotypes have emerged as epidemic strains worldwide. As a result, the global epidemic trends and antibiotic resistance characteristics of H. influenzae have been altered. Researches on the virulence factors of H. influenzae, particularly the mechanisms underlying biofilm formation, and the development of anti-biofilm strategies hold significant clinical value. This article provides a summary of the epidemic trends, typing methods, virulence factors, biofilm formation mechanisms, and prevention strategies of H. influenzae. The increasing prevalence of NTHi strains and antibiotic resistance among H. influenzae, especially the high β-lactamase positivity and the emergence of BLNAR strains have increased clinical difficulties. Understanding its virulence factors, especially the formation mechanism of biofilm, and formulating effective anti-biofilm strategies may help to reduce the clinical impact. Therefore, future research efforts should focus on developing new approaches to prevent and control H. influenzae infections.

P. aeruginosa interactions with other microbes in biofilms during co-infection

This review addresses the topic of biofilms, including their development and the interaction between different counterparts. There is evidence that various diseases, such as cystic fibrosis, otitis media, diabetic foot wound infections, and certain cancers, are promoted and aggravated by the presence of polymicrobial biofilms. Biofilms are composed by heterogeneous communities of microorganisms protected by a matrix of polysaccharides. The different types of interactions between microorganisms gives rise to an increased resistance to antimicrobials and to the host's defense mechanisms, with the consequent worsening of disease symptoms. Therefore, infections caused by polymicrobial biofilms affecting different human organs and systems will be discussed, as well as the role of the interactions between the gram-negative bacteria Pseudomonas aeruginosa, which is at the base of major polymicrobial infections, and other bacteria, fungi, and viruses in the establishment of human infections and diseases. Considering that polymicrobial biofilms are key to bacterial pathogenicity, it is fundamental to evaluate which microbes are involved in a certain disease to convey an appropriate and efficacious antimicrobial therapy.

Osteosynthesis-associated infection in maxillofacial surgery by bacterial biofilms: a retrospective cohort study of 11 years

OBJECTIVES

The aim of this retrospective cohort study was to determine risk factors for osteosynthesis-associated infections (OAI) with subsequent necessity of implant removal in oral and maxillofacial surgery.

MATERIALS AND METHODS

A total of 3937 records of patients who received either orthognathic, trauma, or reconstructive jaw surgery from 2009 to 2021 were screened for osteosynthetic material removal due to infection. Treatment-intervals, volume of applied osteosynthetic material, and respective surgical procedures were also assessed. Moreover, intraoperatively harvested microbial flora was cultured and subsequently identified by MALDI TOF. Bacteria were then screened for antibiotic resistance via VITEK system or, if necessary, via agar diffusion or epsilometer test. Data was analyzed utilizing SPSS statistical software. For statistical analysis of categorical variables, chi-square tests or Fisher exact tests were used. Continuous variables were compared via non-parametric tests. The level of significance for p-values was set at < 0.05. Descriptive analysis was also performed.

RESULTS

The lower jaw was more prone to OAI than the mid face region. Larger volumes of osteosynthetic material led to significantly more OAI, resulting in reconstruction plates bearing the highest risk for OAI especially when compared to small-volume mini-plates frequently applied in trauma surgery. Among OAI associated with implant volumes smaller than 1500 mm3, the detection of Streptococcus spp., Prevotella spp., Staphylococcus spp., and Veillonella spp. was significantly elevated, whereas implant volumes larger than 1500 mm3 showed a significant increase of Enterococcus faecalis, Proteus mirabilis and Pseudomonas aeruginosa. High susceptibility rates (87.7-95.7%) were documented for 2nd- and 3rd-generation cephalosporines and piperacillin/tazobactam.

CONCLUSION

High material load and lower jaw reconstruction bear the greatest risks for OAI. When working with large volume osteosynthetic implants, gram-negative pathogens must be considered when choosing an appropriate antibiotic regime. Suitable antibiotics include, e.g., piperacillin/tazobactam and 3rd-generation cephalosporines.

CLINICAL RELEVANCE

Osteosynthetic material utilized in reconstructive procedures of the lower jaw may be colonized with drug-resistant biofilms.

Staphylococcus aureus in Polymicrobial Skinand Soft Tissue Infections: Impact of Inter-Species Interactionsin Disease Outcome

Polymicrobial biofilms provide a complex environment where co-infecting microorganisms can behave antagonistically, additively, or synergistically to alter the disease outcome compared to monomicrobial infections. Staphylococcus aureus skin and soft tissue infections (Sa-SSTIs) are frequently reported in healthcare and community settings, and they can also involve other bacterial and fungal microorganisms. This polymicrobial aetiology is usually found in chronic wounds, such as diabetic foot ulcers, pressure ulcers, and burn wounds, where the establishment of multi-species biofilms in chronic wounds has been extensively described. This review article explores the recent updates on the microorganisms commonly found together with S. aureus in SSTIs, such as Pseudomonas aeruginosa, Escherichia coli, Enterococcus spp., Acinetobacter baumannii, and Candida albicans, among others. The molecular mechanisms behind these polymicrobial interactions in the context of infected wounds and their impact on pathogenesis and antimicrobial susceptibility are also revised.

Clinical Features and Outcomes of VAP Due to Multidrug-Resistant Klebsiella spp.: A Retrospective Study Comparing Monobacterial and Polybacterial Episodes

VAP due to multidrug-resistant (MDR) bacteria is a frequent infection among patients in ICUs. Patient characteristics and mortality in mono- and polybacterial cases of VAP may differ. A single-centre, retrospective 3-year study was conducted in the four ICUs of a Lithuanian referral university hospital, aiming to compare both the clinical features and the 60-day ICU all-cause mortality of monobacterial and polybacterial MDR Klebsiella spp. VAP episodes. Of the 86 MDR Klebsiella spp. VAP episodes analyzed, 50 (58.1%) were polybacterial. The 60-day mortality was higher (p < 0.05) in polybacterial episodes: overall (50.0 vs. 27.8%), in the sub-group with less-severe disease (SOFA < 8) at VAP onset (45.5 vs. 15.0%), even with appropriate treatment (41.7 vs. 12.5%), and the sub-group of extended drug-resistant (XDR) Klebsiella spp. (46.4 vs. 17.6%). The ICU mortality (44.0 vs. 22.5%) was also higher in the polybacterial episodes. The monobacterial MDR Klebsiella spp. VAP was associated (p < 0.05) with prior hospitalization (61.1 vs. 40.0%), diabetes mellitus (30.6 vs. 5.8%), obesity (30.6 vs. 4.7%), prior antibiotic therapy (77.8 vs. 52.0%), prior treatment with cephalosporins (66.7 vs. 36.0%), and SOFA cardiovascular ≥ 3 (44.4 vs. 10.0%) at VAP onset. Patients with polybacterial VAP were more likely (p < 0.05) to be comatose (22.2 vs. 52.0%) and had a higher SAPS II score (median [IQR] 45.0 [35.25-51.1] vs. 50.0 [40.5-60.75]) at VAP onset. Polybacterial MDR Klebsiella spp. VAP had distinct demographic and clinical characteristics compared to monobacterial, and was associated with poorer outcomes.

Defining Microbial Community Functions in Chronic Human Infection with Metatranscriptomics

Chronic polymicrobial infections (cPMIs) harbor complex bacterial communities with diverse metabolic capacities, leading to competitive and cooperative interactions. Although the microbes present in cPMIs have been established through culture-dependent and-independent methods, the key functions that drive different cPMIs and the metabolic activities of these complex communities remain unknown. To address this knowledge gap, we analyzed 102 published metatranscriptomes collected from cystic fibrosis sputum (CF) and chronic wound infections (CW) to identify key bacterial members and functions in cPMIs. Community composition analysis identified a high prevalence of pathogens, particularly Staphylococcus and Pseudomonas, and anaerobic members of the microbiota, including Porphyromonas, Anaerococcus, and Prevotella. Functional profiling with HUMANn3 and SAMSA2 revealed that while functions involved in bacterial competition, oxidative stress response, and virulence were conserved across both chronic infection types, >40% of the functions were differentially expressed (padj < 0.05, fold-change >2). Higher expression of antibiotic resistance and biofilm functions were observed in CF, while tissue destructive enzymes and oxidative stress response functions were highly expressed in CW samples. Of note, strict anaerobes had negative correlations with traditional pathogens in both CW (P = -0.43) and CF (P = -0.27) samples and they significantly contributed to the expression of these functions. Additionally, we show microbial communities have unique expression patterns and distinct organisms fulfill the expression of key functions in each site, indicating the infection environment strongly influences bacterial physiology and that community structure influences function. Collectively, our findings indicate that community composition and function should guide treatment strategies for cPMIs.

Intestinal bacteria-a powerful weapon for fungal infections treatment

The morbidity and mortality of invasive fungal infections are rising gradually. In recent years, fungi have quietly evolved stronger defense capabilities and increased resistance to antibiotics, posing huge challenges to maintaining physical health. Therefore, developing new drugs and strategies to combat these invasive fungi is crucial. There are a large number of microorganisms in the intestinal tract of mammals, collectively referred to as intestinal microbiota. At the same time, these native microorganisms co-evolve with their hosts in symbiotic relationship. Recent researches have shown that some probiotics and intestinal symbiotic bacteria can inhibit the invasion and colonization of fungi. In this paper, we review the mechanism of some intestinal bacteria affecting the growth and invasion of fungi by targeting the virulence factors, quorum sensing system, secreting active metabolites or regulating the host anti-fungal immune response, so as to provide new strategies for resisting invasive fungal infection.

Oral Myco- and Bacteriobiota and Yeast Infections in Mechanically Ventilated COVID-19 Patients

Critically ill COVID-19 patients requiring mechanical ventilation in the intensive care unit are at risk of developing invasive candidiasis. In this study we aimed to (1) characterize oral cultivable mycobiota of mechanically ventilated adult COVID-19 patients in an ICU setting by sampling four distinct oral niches in two fixed time points with regards to oral health status, (2) investigate Candida spp. infections in this population, and (3) compare oral mycobiota with selected bacteriobiota strains during the observation in the ICU. We recruited 56 adult COVID-19 patients who qualified for mechanical ventilation. Patients received either standard or extended oral care procedures with tooth brushing. Oral samples were taken first within 36 h and after 7 days of intubation. Yeast-like fungi were identified by MALDI/TOF mass spectrometry. Yeast infection cases were retrospectively analyzed. Candida spp. in oral sampling was identified in 80.4% and 75.7%, C. albicans in 57.1% and 61.1%, and non-albicans Candida species in 48.2% and 47.2% patients at baseline and follow-up, respectively. There were no differences in the overall CFU counts of Candida spp. species and individual Candida species in oral samples, both at baseline and follow-up. At baseline, a higher prevalence of Candida spp. was associated with a higher identification rate of Lactobacillus spp. (64.4% vs. 27.3%, p = 0.041). At follow-up, there was a borderline lower prevalence of Candida spp. in patients with Lactobacillus spp. identified (57.1% vs. 87.0%, p = 0.057). The incidence rate of candidiasis was 5.4% and the incidence density was 3.1/1000 pds. In conclusion, non-albicans Candida species in oral samples were identified in nearly half of patients. Oral health was moderately impaired. A high incidence of yeast infections, including invasive cases, in patients hospitalized in the ICU due to COVID-19 and requiring mechanical ventilation was noted. Severe COVID-19 and disease-specific interventions within the ICU possibly played a major role promoting Candida spp. infections.

Mechanistic Assessment of Metabolic Interaction between Single Oral Commensal Cells by Scanning Electrochemical Microscopy

The human oral microbiome heavily influences the status of oral and systemic diseases through different microbial compositions and complex signaling between microbes. Recent evidence suggests that investigation of interactions between oral microbes can be utilized to understand how stable communities are maintained and how they may preserve health. Herein, we investigate two highly abundant species in the human supragingival plaque, Streptococcus mitis and Corynebacterium matruchotii, to elucidate their real-time chemical communication in commensal harmony. Specifically, we apply nanoscale scanning electrochemical microscopy (SECM) using a submicropipet-supported interface between two immiscible electrolyte solutions as an SECM probe not only to image the permeability of S. mitis and C. matruchotii membranes to tetraethylammonium (TEA⁺) probe ions but also to real-time visualize the metabolic interaction between two microbes via lactate production/consumption at a single-cell level. The metabolic relationship between two strains is quantitatively assessed by determining (1) the passive permeability of both bacterial membranes of 2.4 × 10^-4 cm/s to the free diffusion of TEA⁺, (2) 0.5 mM of the lactate concentration produced by a single S. mitis strain at a rate of 2.7 × 10^-4 cm/s, and (3) a lactate oxidation rate ≥5.0 × 10⁶ s^-1 by an individual C. matruchotii strain. Significantly, this study, for the first time, describes a mechanism of in situ metabolic interaction between oral commensals at the single-cell level through quantitative analysis, which supports the observed in vivo spatial arrangements of these microbes.

Transcriptional Profiling and Genetic Analysis of a Cystic Fibrosis Airway-Relevant Model Shows Asymmetric Responses to Growth in a Polymicrobial Community

Bacterial infections in the lungs of persons with cystic fibrosis are typically composed of multispecies biofilm-like communities, which modulate clinically relevant phenotypes that cannot be explained in the context of a single species culture. Most analyses to-date provide a picture of the transcriptional responses of individual pathogens, however, there is relatively little data describing the transcriptional landscape of clinically-relevant multispecies communities. Harnessing a previously described cystic fibrosis-relevant, polymicrobial community model consisting of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis and Prevotella melaninogenica , we performed an RNA-Seq analysis to elucidate the transcriptional profiles of the community grown in artificial sputum medium (ASM) as compared to growth in monoculture, without mucin, and in fresh medium supplemented with tobramycin. We provide evidence that, although the transcriptional profile of P. aeruginosa is community agnostic, the transcriptomes of S. aureus and S. sanguinis are community aware. Furthermore, P. aeruginosa and P. melaninogenica are transcriptionally sensitive to the presence of mucin in ASM, whereas S. aureus and S. sanguinis largely do not alter their transcriptional profiles in the presence of mucin when grown in a community. Only P. aeruginosa shows a robust response to tobramycin. Genetic studies of mutants altered in community-specific growth provide complementary data regarding how these microbes adapt to a community context.

Importance

Polymicrobial infections constitute the majority of infections in the cystic fibrosis (CF) airway, but their study has largely been neglected in a laboratory setting. Our lab previously reported a polymicrobial community that can explain clinical outcomes in the lungs of persons with CF. Here we obtain transcriptional profiles of the community versus monocultures to provide transcriptional information about how this model community responds to CF-related growth conditions and perturbations. Genetic studies provide complementary functional outputs to assess how the microbes adapt to life in a community.

Dual Burst and Sustained Release of p-Coumaric Acid from Shape Memory Polymer Foams for Polymicrobial Infection Prevention in Trauma-Related Hemorrhagic Wounds

Hemorrhage is the primary cause of trauma-related death. Of patients that survive, polymicrobial infection occurs in 39% of traumatic wounds within a week of injury. Moreover, traumatic wounds are susceptible to hospital-acquired and drug-resistant bacterial infections. Thus, hemostatic dressings with antimicrobial properties could reduce morbidity and mortality to enhance traumatic wound healing. To that end, p-coumaric acid (PCA) was incorporated into hemostatic shape memory polymer foams by two mechanisms (chemical and physical) to produce dual PCA (DPCA) foams. DPCA foams demonstrated excellent antimicrobial and antibiofilm properties against native Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis; co-cultures of E. coli and S. aureus; and drug-resistant S. aureus and S. epidermidis at short (1 h) and long (7 days) time points. Resistance against biofilm formation on the sample surfaces was also observed. In ex vivo experiments in a porcine skin wound model, DPCA foams exhibited similarly high antimicrobial properties as those observed in vitro, indicating that PCA was released from the DPCA foam to successfully inhibit bacterial growth. DPCA foams consistently showed improved antimicrobial properties relative to those of clinical control foams containing silver nanoparticles (AgNPs) against single and mixed species bacteria, single and mixed species biofilms, and bacteria in the ex vivo wound model. This system could allow for physically incorporated PCA to first be released into traumatic wounds directly after application for instant wound disinfection. Then, more tightly tethered PCA can be continuously released into the wound for up to 7 days to kill additional bacteria and protect against biofilms.

Inhibition of Mixed Biofilms of Candida albicans and Staphylococcus aureus by β-Caryophyllene-Gold Nanoparticles

Polymicrobial biofilms, consisting of fungal and bacterial pathogens, often contribute to the failure of antimicrobial treatment. The growing resistance of pathogenic polymicrobial biofilms to antibiotics has led to the development of alternative strategies to combat polymicrobial diseases. To this end, nanoparticles synthesized using natural molecules have received significant attention for disease treatment. Here, gold nanoparticles (AuNPs) were synthesized using β-caryophyllene, a bioactive compound isolated from various plant species. The shape, size, and zeta potential of the synthesized β-c-AuNPs were found to be non-spherical, 17.6 ± 1.2 nm, and -31.76 ± 0.73 mV, respectively. A mixed biofilm of Candida albicans and Staphylococcus aureus was used to test the efficacy of the synthesized β-c-AuNPs. The results revealed a concentration-dependent inhibition of the initial stages of formation of single-species as well as mixed biofilms. Furthermore, β-c-AuNPs also eliminated mature biofilms. Therefore, using β-c-AuNPs to inhibit biofilm and eradicate bacterial-fungal mixed biofilms represents a promising therapeutic approach for controlling polymicrobial infections.

Microbial mat compositions and localization patterns explain the virulence of black band disease in corals

Black band disease (BBD) in corals is characterized by a distinctive, band-like microbial mat, which spreads across the tissues and often kills infected colonies. The microbial mat is dominated by cyanobacteria but also commonly contains sulfide-oxidizing bacteria (SOB), sulfate-reducing bacteria (SRB), and other microbes. The migration rate in BBD varies across different environmental conditions, including temperature, light, and pH. However, whether variations in the migration rates reflect differences in the microbial consortium within the BBD mat remains unknown. Here, we show that the micro-scale surface structure, bacterial composition, and spatial distribution differed across BBD lesions with different migration rates. The migration rate was positively correlated with the relative abundance of potential SOBs belonging to Arcobacteraceae localized in the middle layer within the mat and negatively correlated with the relative abundance of other potential SOBs belonging to Rhodobacteraceae. Our study highlights the microbial composition in BBD as an important determinant of virulence.

Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms

Extracellular polymeric substances (EPS) are core biofilm components, yet how they mediate interactions within and contribute to the structuring of biofilms is largely unknown, particularly for non-culturable microbial communities that predominate in environmental habitats. To address this knowledge gap, we explored the role of EPS in an anaerobic ammonium oxidation (anammox) biofilm. An extracellular glycoprotein, BROSI_A1236, from an anammox bacterium, formed envelopes around the anammox cells, supporting its identification as a surface (S-) layer protein. However, the S-layer protein also appeared at the edge of the biofilm, in close proximity to the polysaccharide-coated filamentous Chloroflexi bacteria but distal to the anammox bacterial cells. The Chloroflexi bacteria assembled into a cross-linked network at the edge of the granules and surrounding anammox cell clusters, with the S-layer protein occupying the space around the Chloroflexi. The anammox S-layer protein was also abundant at junctions between Chloroflexi cells. Thus, the S-layer protein is likely transported through the matrix as an EPS and also acts as an adhesive to facilitate the assembly of filamentous Chloroflexi into a three-dimensional biofilm lattice. The spatial distribution of the S-layer protein within the mixed species biofilm suggests that it is a "public-good" EPS, which facilitates the assembly of other bacteria into a framework for the benefit of the biofilm community, and enables key syntrophic relationships, including anammox.

The Virtuous Galleria mellonella Model for Scientific Experimentation

The first research on the insect Galleria mellonella was published 85 years ago, and the larva is now widely used as a model to study infections caused by bacterial and fungal pathogens, for screening new antimicrobials, to study the adjacent immune response in co-infections or in host-pathogen interaction, as well as in a toxicity model. The immune system of the G. mellonella model shows remarkable similarities with mammals. Furthermore, results from G. mellonella correlate positively with mammalian models and with other invertebrate models. Unlike other invertebrate models, G. mellonella can withstand temperatures of 37 °C, and its handling and experimental procedures are simpler. Despite having some disadvantages, G. mellonella is a virtuous in vivo model to be used in preclinical studies, as an intermediate model between in vitro and mammalian in vivo studies, and is a great example on how to apply the bioethics principle of the 3Rs (Replacement, Reduction, and Refinement) in animal experimentation. This review aims to discuss the progress of the G. mellonella model, highlighting the key aspects of its use, including experimental design considerations and the necessity to standardize them. A different score in the “cocoon” category included in the G. mellonella Health Index Scoring System is also proposed.

Structural modification of the Pseudomonas aeruginosa alkylquinoline cell-cell communication signal, HHQ, leads to benzofuranoquinolines with anti-virulence behaviour in ESKAPE pathogens

Microbial populations have evolved intricate networks of negotiation and communication through which they can coexist in natural and host ecosystems. The nature of these systems can be complex and they are, for the most part, poorly understood at the polymicrobial level. The Pseudomonas Quinolone Signal (PQS) and its precursor 4-hydroxy-2-heptylquinoline (HHQ) are signal molecules produced by the important nosocomial pathogen Pseudomonas aeruginosa . They are known to modulate the behaviour of co-colonizing bacterial and fungal pathogens such as Bacillus atropheaus, Candida albicans and Aspergillus fumigatus. While the structural basis for alkyl-quinolone signalling within P. aeruginosa has been studied extensively, less is known about how structural derivatives of these molecules can influence multicellular behaviour and population-level decision-making in other co-colonizing organisms. In this study, we investigated a suite of small molecules derived initially from the HHQ framework, for anti-virulence activity against ESKAPE pathogens, at the species and strain levels. Somewhat surprisingly, with appropriate substitution, loss of the alkyl chain (present in HHQ and PQS) did not result in a loss of activity, presenting a more easily accessible synthetic framework for investigation. Virulence profiling uncovered significant levels of inter-strain variation among the responses of clinical and environmental isolates to small-molecule challenge. While several lead compounds were identified in this study, further work is needed to appreciate the extent of strain-level tolerance to small-molecule anti-infectives among pathogenic organisms.

2-Octylcyclopentanone Inhibits Beta Lactam Resistant Diabetic Wound Pathogens

Microbial infection is a frequent complication of diabetic foot ulcers, with up to 82% of ulcers being infected at the initial stage of diabetes. Furthermore, the emergence of beta lactam resistant pathogens managed to eliminate the use of beta lactam antibiotics as a chemotherapeutic alternative. This further increases the amputation and mortality rate. Hence, the aim of this study is to evaluate antimicrobial efficacy of a ketone derivative 2-octylcyclopentanone against diabetic wound pathogens. The inhibitory activity of the compound was determined using disc diffusion and broth microdilution assay. Generally, 2-octylcyclopentanone showed broad-spectrum antimicrobial activity, particularly against beta lactam resistant pathogens. The compound showed comparably better antimicrobial activity than all reference antibiotics, including chloramphenicol, streptomycin, ampicillin and penicillin. In addition, the same compound also inhibits a clinically isolated Pseudonomas aeruginosa that was resistant to all reference antibiotics. The activity was microbicidal based on the low minimal lethality concentration recorded, particularly on MRSA, P. aeruginosa and Candida utilis. The killing efficiency of the compound was concentration dependent. During kill curve analysis, the inhibitory activity of 2-octylcyclopentanone was concentration and time-dependent. 99.9% of reduction of bacterial growth was observed. MRSA and P. aeruginosa, two significant diabetic wound infections, are totally inhibited by the molecule at a concentration of minimum lethality concentration. In short, 2-octylcyclopentanone exhibited significant inhibitory towards wide range of diabetic wound pathogens. Which is considered crucial since it will provide a safe and effective alternative treatment for diabetic ulcer infection.

Escherichia coli, but Not Staphylococcus aureus, Functions as a Chelating Agent That Exhibits Antifungal Activity against the Pathogenic Yeast Candida albicans

Humans are colonized by diverse populations of microbes. Infections by Candida albicans, an opportunistic fungal pathogen, are a result of imbalances in the gut microbial ecosystem and are due to the suppressed immunity of the host. Here, we explored the potential effects of the polymicrobial interactions of C. albicans with Staphylococcus aureus, a Gram-positive bacterium, and Escherichia coli, a Gram-negative bacterium, in dual and triple in vitro culture systems on their respective growth, morphology, and biofilms. We found that S. aureus promoted the fungal growth and hyphal transition of C. albicans through cell-to-cell contacts; contrarily, both the cell and cell-free culture filtrate of E. coli inhibited fungal growth. A yet to be identified secretory metabolite of E. coli functionally mimicked EDTA and EGTA to exhibit antifungal activity. These findings suggested that E. coli, but not S. aureus, functions as a chelating agent and that E. coli plays a dominant role in regulating excessive growth and, potentially, the commensalism of C. albicans. Using animal models of systemic candidiasis, we found that the E. coli cell-free filtrate suppressed the virulence of C. albicans. In general, this study unraveled a significant antimicrobial activity and a potential role in the nutritional immunity of E. coli, and further determining the underlying processes behind the E. coli–C. albicans interaction could provide critical information in understanding the pathogenicity of C. albicans.

Clinical Evaluation of Metagenomic Next-Generation Sequencing Method for the Diagnosis of Suspected Ascitic Infection in Patients with Liver Cirrhosis in a Clinical Laboratory

Metagenomic next-generation sequencing (mNGS), mostly carried out in independent clinical laboratories, has been increasingly applied in clinical pathogen diagnosis. We aimed to explore the feasibility of mNGS in clinical laboratories and analyze its potential in the diagnosis of infectious ascites. Two reference panels composed of 12 strains commonly appearing in peritonitis were constructed to evaluate the performance metrics based on in-house mNGS protocols. The mNGS clinical detection value was analyzed in 211 ascitic samples and compared with culture and composite standards. Finally, eight patients with cirrhosis were prospectively enrolled to verify the clinical value of mNGS in peritoneal infection diagnosis. The mNGS analytical performance showed that the assay had great linearity, specificity, stability, interference, and limits of detection of 33 to 828 CFU/mL. The sensitivity and specificity of mNGS for bacterial or fungal detection using culture standards were 84.2% and 82.0%, respectively. After adjustment using digital PCR and clinical judgment, the sensitivity and specificity increased to 87.2% and 90.1%, respectively. Compared with culture, mNGS detected a broad range of pathogens and more polymicrobial infections (49% versus 9%, P < 0.05). The pathogen results were obtained within 24 h using mNGS in eight prospective cases, which effectively guided antibiotics therapy. mNGS testing in clinical laboratories affiliated with a hospital has certain advantages. It has unique superiority in pathogens detection, particularly in patients with polymicrobial infections. However, considering spectrum characteristics and test cost, pertinent pathogen panels should be developed in clinical practice. IMPORTANCE This study established and evaluated a complete metagenomics next-generation sequencing assay to improve the diagnosis of suspected ascitic infection in a clinical laboratory affiliated with a hospital. The assay is superior to traditional culture testing and will aid in the early and accurate identification of pathogens, particularly in patients with polymicrobial infections. This assay is also essential for precision therapy and can reduce the incidence of drug resistance stemming from irrational use of antibiotics.