Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species

Prevalence, Characterization, and Epidemiological Relationships between ESBL and Carbapenemase-Producing Escherichia coli, Klebsiella pneumoniae, and Acinetobacter spp. Isolated from Humans and the Kitchen Environment of Two Greek Hospitals

BACKGROUND

Extended-spectrum-β-lactamase (ESBL) and carbapenemase-producing Enterobacterales and Acinetobacter spp. pose significant challenges as nosocomial pathogens, demonstrating resistance against various antimicrobials. Their presence in food suggests that hospital kitchens could serve as antibiotic resistance reservoirs leading to patients' infection.

OBJECTIVES

The aim of this study was to assess the prevalence and characteristics of β-lactam-resistant strains of Escherichia coli, Klebsiella pneumoniae, and Acinetobacter spp. isolated from the kitchen environment and from the staff of two Greek hospitals.

METHODS

Strains were recovered after selective isolation with β-lactams and were identified with MALDI-TOF MS. Antimicrobial susceptibility and presence of common β-lactamase genes were evaluated. Protein profiles were examined to analyze potential relationships of the strain with those from hospital patients. E. coli strains were further categorized into phylogenetic groups.

RESULTS

The overall prevalence in the kitchen environment was 4.5%, 1.5%, and 15.0% for E. coli, K. pneumoniae, and Acinetobacter spp., respectively, whereas the prevalence of Acinetobacter spp. in human skin was 4.0%. Almost all strains were multidrug-resistant. All E. coli strains were ESBL producers and belonged to phylogroups A and B1. All K. pneumoniae and seven Acinetobacter strains were carbapenemase-producers. A protein profile analysis showed relatedness between chicken and kitchen environment strains, as well as between kitchen environment and patient strains originated either from the same or from different hospitals.

CONCLUSIONS

The results suggest that hospital kitchens may act as important pathogen hotspots contributing to the circulation of resistant strains in the hospital environment.

Viability discrimination of bacterial microbiomes in home kitchen dish sponges using propidium monoazide treatment

Dish sponges are known to support the proliferation of human bacterial pathogens, yet they are commonly used by consumers. Exposure to foodborne pathogens via sponge use may lead to illness, a serious concern among susceptible populations. The extent of exposure risks from sponge use has been limited by constraints associated with culture-independent or dependent methods for bacterial community characterization. Therefore, five used dish sponges were characterized to evaluate the presence of viable bacterial foodborne pathogens using the novel application of propidium monoazide (PMA) treatment and targeted 16S rRNA gene amplicon sequencing. Select pathogen viability was confirmed using targeted selective enrichment. The taxonomic abundance profiles of total and viable sponge microbiomes did not vary significantly. The numbers of unique bacterial species (p = 0.0465) and foodborne pathogens (p = 0.0102) identified were significantly lower in viable sponge microbiomes. Twenty unique bacterial foodborne pathogens were detected across total and viable sponge microbiomes, and three to six viable foodborne pathogens were identified in each sponge. Escherichia coli and Staphylococcus aureus were identified in each viable sponge microbiome, and viable E. coli were recovered from two sponges via targeted selective enrichment. These findings suggest that sponge-associated bacterial communities are primarily viable and contain multiple viable bacterial foodborne pathogens.

Microbial extracellular polymeric substances in the environment, technology and medicine

Microbial biofilms exhibit a self-produced matrix of extracellular polymeric substances (EPS), including polysaccharides, proteins, extracellular DNA and lipids. EPS promote interactions of the biofilm with other cells and sorption of organics, metals and chemical pollutants, and they facilitate cell adhesion at interfaces and ensure matrix cohesion. EPS have roles in various natural environments, such as soils, sediments and marine habitats. In addition, EPS are relevant in technical environments, such as wastewater and drinking water treatment facilities, and water distribution systems, and they contribute to biofouling and microbially influenced corrosion. In medicine, EPS protect pathogens within the biofilm against the host immune system and antimicrobials, and emerging evidence suggests that EPS can represent potential virulence factors. By contrast, EPS yield a wide range of valuable products that include their role in self-repairing concrete. In this Review, we aim to explore EPS as a functional unit of biofilms in the environment, in technology and in medicine.

Characterizing Biofilm Interactions between Ralstonia insidiosa and Chryseobacterium gleum

Ralstonia insidiosa and Chryseobacterium gleum are bacterial species commonly found in potable water systems, and these two species contribute to the robustness of biofilm formation in a model six-species community from the International Space Station (ISS) potable water system. Here, we set about characterizing the interaction between these two ISS-derived strains and examining the extent to which this interaction extends to other strains and species in these two genera. The enhanced biofilm formation between the ISS strains of R. insidiosa and C. gleum is robust to starting inoculum and temperature and occurs in some but not all tested growth media, and evidence does not support a soluble mediator or coaggregation mechanism. These findings shed light on the ISS R. insidiosa and C. gleum interaction, though such enhancement is not common between these species based on our examination of other R. insidiosa and C. gleum strains, as well as other species of Ralstonia and Chryseobacterium. Thus, while the findings presented here increase our understanding of the ISS potable water model system, not all our findings are broadly extrapolatable to strains found outside of the ISS. IMPORTANCE Biofilms present in drinking water systems and terminal fixtures are important for human health, pipe corrosion, and water taste. Here, we examine the enhanced biofilm of cocultures for two very common bacteria from potable water systems: Ralstonia insidiosa and Chryseobacterium gleum. While strains originally isolated on the International Space Station show enhanced dual-species biofilm formation, terrestrial strains do not show the same interaction properties. This study contributes to our understanding of these two species in both dual-culture and monoculture biofilm formation.

Real time degradation studies on polyurethane household sponges in Danish weather and marine environments

Polyurethane (PUR) ether sponges represent a widely-used cleaning tool with a short service lifetime resulting in the production of high quantities of waste. However, the fate of PUR in natural environments is poorly understood. In this study, sponges were exposed to the natural environments of Danish weather and seawater for two years. Physiochemical changes were monitored using visual, microscopic, spectroscopic and chromatographic techniques. Results from Attenuated Total Reflection-Fourier Transform Infrared spectroscopy and change in mass indicated that photo-oxidation was the primary degradation pathway of polyurethane ether- based sponges with a specific surface degradation rate of 12,500 μm year^-1 in Danish weather. Significantly, analysis by gas chromatography-mass spectrometry showed the release to the environment of toxic substance TDI as a product of photo-oxidation. Although PUR degraded more slowly in seawater than in weather, flame retardant TMCP leached from sponges to water, indicating potential health risks of PUR waste to aquatic life.

Evaluation of the kitchen microbiome and food safety behaviors of predominantly low-income families

Bacterial pathogens in the domestic environment present a risk to residents, particularly among susceptible populations. However, the impact of consumer demographic characteristics and food handling methods on kitchen microbiomes is not fully understood. The domestic kitchen bacterial communities of ten predominantly low-income families in Houston, TX, were assessed in conjunction with a cross-sectional food safety survey to evaluate differences in household and surface-specific microbiomes and bacterial foodborne pathogen presence. Three kitchen surfaces within each household, including the sink drain, the refrigerator handle, and the counter, were environmentally sampled and metataxonomically evaluated via targeted 16S rRNA sequencing. Disposable dish sponges were also acquired and examined. Results indicated that alpha diversity did not vary by the households, sampling locations, or demographic characteristics evaluated. Significant differences in beta diversity were observed among the bacterial communities of five pairs of households and between refrigerator handle and disposable dish sponge microbiomes. A total of 89 unique bacterial foodborne pathogens were identified across surface types. Each household contained at least one contaminated surface, and the most common bacterial foodborne pathogens identified were Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae. All parents reported washing their hands before meal preparation, washing fresh fruits and vegetables, and washing cutting boards with soap after use to prepare raw animal proteins. Gaps in food safety behaviors identified included a lack of serious concern for food contamination with germs and inappropriate handwashing, food handling, and cleaning behaviors. The number of unique bacterial foodborne pathogens identified within households was significantly higher among households whose respondent parent reported that they did not consider food contamination with germs to be a serious food safety problem (median: 41.0 species) compared to households whose respondent parent did consider food contamination to be a serious food safety problem (median: 3.0 species; p value = 0.0218). These results demonstrate that domestic kitchen taxonomic abundance profiles vary according to household and surface type. Data suggest that low-income consumers may be at risk of foodborne pathogen exposure from contaminated home kitchen surfaces, and that food safety attitudes may directly contribute to this hazard.

Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota

Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.

Bacterial levels and diversity in kitchen sponges and dishwashing brushes used by consumers

AIMS

The purpose of the work was to investigate bacterial levels and diversity as well as survival of Salmonella in used dish washing sponges and brushes and identify consumer practices that can potentially explain bacterial status of these items.

METHODS AND RESULTS

Used washing up utensils were collected from consumers. The bacterial numbers (TVC) were very variable with an extremely high median level (10.3 log cfu/item) in Portuguese sponges and lower levels in Norwegian items (7.3 and 7.0 cfu/item for sponges and brushes). No self-reported practices or household composition could explain differences found in TVC levels among the collected sponges. Lower mean TVC levels were found in unworn brushes and brushes regularly cleaned with soap, but the differences were modest (1.5 log or less). A common set of bacteria was found in brushes and sponges, dominated by Acinetobacter, Chryseobacterium, Enhydrobacter, Enterobacteriaceae and Pseudomonas. There was no difference in TVC or bacterial diversity between conventional and antimicrobial sponges containing silver after four weeks of use. For used brushes inoculated with Salmonella and allowed to dry overnight, a significant reduction in Salmonella numbers was observed. No reduction was observed for brushes stored humid (in a plastic bag) or for sponges regardless of storing conditions.

CONCLUSIONS

Overall, lower bacterial levels were observed in used brushes than in sponges, and Salmonella died more rapidly in brushes. A common set of non-pathogenic bacteria dominated in brushes and sponges.

SIGNIFICANCE AND IMPACT OF STUDY

The study demonstrates that the use of brushes may be more hygienic than the use of sponges.

Raman Spectroscopy-A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings

Rapid and accurate identification of pathogens causing infections is one of the biggest challenges in medicine. Timely identification of causative agents and their antimicrobial resistance profile can significantly improve the management of infection, lower costs for healthcare, mitigate ever-growing antimicrobial resistance and in many cases, save lives. Raman spectroscopy was shown to be a useful-quick, non-invasive, and non-destructive -tool for identifying microbes from solid and liquid media. Modifications of Raman spectroscopy and/or pretreatment of samples allow single-cell analyses and identification of microbes from various samples. It was shown that those non-culture-based approaches could also detect antimicrobial resistance. Moreover, recent studies suggest that a combination of Raman spectroscopy with optical tweezers has the potential to identify microbes directly from human body fluids. This review aims to summarize recent advances in non-culture-based approaches of identification of microbes and their virulence factors, including antimicrobial resistance, using methods based on Raman spectroscopy in the context of possible use in the future point-of-care diagnostic process.

Dual Action Gels Containing DsiRNA Loaded Gold Nanoparticles: Augmenting Diabetic Wound Healing by Promoting Angiogenesis and Inhibiting Infection

Hyperglycemia induces the prostaglandin transporter (PGT) gene overexpression, leading to poor vascularization and wound healing. Dicer substrate small interfering RNA (DsiRNA) and gold nanoparticles (AuNPs) co-loaded into PF127 gel was developed to overcome the disturbance and infections. The AuNPs were biosynthesized using cold and hot water extracts of Lignosus rhinocerotis (abbreviated CLRE and HLRE, respectively). The wound healing efficacy of a PF127 gel containing DsiRNA-AuNPs-CLRE and -HLRE (assigned as F2 and F3, respectively) was evaluated in a diabetes-induced Wistar rat model. The F2 (DC) and F3 (DH) treated groups revealed a faster wound closure (92.67 ± 3.4% and 85.1 ± 7.3%, respectively) than the positive control (commercial gel, DTI)(74.9 ± 13.3%). DH and DC groups presented an increased blood vessel density, along with decreased inflammatory cells. In comparison to positive control, higher prostaglandin E₂ (PGE₂) (495 ±79 and 50 ±121 pg/mL, for DC and DH group, respectively), vascular endothelial growth factor (VEGF) (49 ±15 and 38 ±3 pg/mL, for DC and DH group, respectively) and VEGF-A levels were detected in both groups (DC and DH), indicating the effectiveness of DsiRNA in enhancing PGE₂ production and vascularization. On evaluating microbiomes adhered to the wound areas, Gram-positive bacteria Staphylococcus and Corynebacterium, as well as Gram-negative Pseudomonas, Rodentibacter, and Acinetobacter, were found to be sensitive to the gel. Collectively, the gel was confirmed as a promising dressing for diabetic wound therapy, warranting further studies for clinical use.

Controlling bacteriological contamination of environmental surfaces at the biological isolation and containment unit of a veterinary teaching hospital

Background

The Biological Isolation and Containment Unit (BICU) is a subunit of the Teaching Hospital of the Faculty of Veterinary Medicine of the University of Lisbon, Portugal, for the admission of animals with confirmed infectious diseases or under clinical suspicion and waiting for a diagnosis. As a high-risk environment for the transmission of infectious agents, it is extremely important to implement programs for the surveillance of nosocomial microorganisms in these facilities. The purpose of this study was to evaluate the level of bacterial contamination of the BICU environmental surfaces and to implement corrective actions on disinfection protocols. Swab samples were collected from selected environmental surfaces in 3 different areas of the BICU (isolation, work, and preparatory rooms) to evaluate the total aerobic bacterial load and investigate the presence of 4 nosocomial microorganisms: vancomycin-resistant Enterococcus spp., methicillin-resistant Staphylococcus aureus, 3rd-generation cephalosporin-resistant Escherichia coli, and carbapenem-resistant Pseudomonas aeruginosa. Bacterial quantification was performed by using non-selective media, while specific selective media were used for the isolation of the target microorganisms. Isolates were identified based on their macro and microscopic characteristics and their biochemical profile. Subsequently, new disinfection protocols were implemented, and their effectiveness evaluated.

Results

The surfaces with the highest bacterial load in the isolation, preparatory, and worker’s rooms were the cages, hand-held sponge, and telephone, respectively. Regarding the 4 pathogens investigated, Enterococcus spp. were the most frequently isolated (11.3%), followed by E. coli (1.5%) and P. aeruginosa (1.5%). One of the P. aeruginosa isolates obtained was resistant to imipenem. In the end, new disinfection protocols were implemented, which proved to be effective in reducing bacterial counts by 99.99% in cages and the sponge, and by 90 to 99% on the telephone.

Conclusions

This study allows to conclude that the cages and the human contact surfaces were the most contaminated in the isolation rooms. Nevertheless, the new disinfection strategies seemed to be effective in reducing environmental contamination, including by some potentially nosocomial agents, although more samples must be analyzed for definitive conclusions. These results may contribute to highlight the importance of infection prevention and control measures, as fundamental tools to reduce the spread of infectious agents in the hospital environment.

Laundry Hygiene and Odor Control: State of the Science

Laundering of textiles—clothing, linens, and cleaning cloths—functionally removes dirt and bodily fluids, which prevents the transmission of and reexposure to pathogens as well as providing odor control. Thus, proper laundering is key to controlling microbes that cause illness and produce odors. The practice of laundering varies from region to region and is influenced by culture and resources. This review aims to define laundering as a series of steps that influence the exposure of the person processing the laundry to pathogens, with respect to the removal and control of pathogens and odor-causing bacteria, while taking into consideration the types of textiles. Defining laundering in this manner will help better educate the consumer and highlight areas where more research is needed and how to maximize products and resources. The control of microorganisms during laundering involves mechanical (agitation and soaking), chemical (detergent and bleach), and physical (detergent and temperature) processes. Temperature plays the most important role in terms of pathogen control, requiring temperatures exceeding 40°C to 60°C for proper inactivation, while detergents play a role in reducing the microbial load of laundering through the release of microbes attached to fabrics and the inactivation of microbes sensitive to detergents (e.g., enveloped viruses). The use of additives (enzymes) and bleach (chlorine and activated oxygen) becomes essential in washes with temperatures below 20°C, especially for certain enteric viruses and bacteria. A structured approach is needed that identifies all the steps in the laundering process and attempts to identify each step relative to its importance to infection risk and odor production.

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota

BACKGROUND

While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors.

RESULTS

Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features.

CONCLUSIONS

Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.

Living with Legionella and Other Waterborne Pathogens

Legionella spp. and other opportunistic premise plumbing pathogens (OPPPs), including Pseudomonas aeruginosa, Mycobacterium avium, Stenotrophomonas maltophilia, and Acinetobacter baumannii, are normal inhabitants of natural waters, drinking water distribution systems and premise plumbing. Thus, humans are regularly exposed to these pathogens. Unfortunately, Legionella spp. and the other OPPPs share a number of features that allow them to grow and persist in premise plumbing. They form biofilms and are also relatively disinfectant-resistant, able to grow at low organic matter concentrations, and able to grow under stagnant conditions. Infections have been traced to exposure to premise plumbing or aerosols generated in showers. A number of measures can lead to reduction in OPPP numbers in premise plumbing, including elevation of water heater temperatures.

Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding

The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.

Acinetobacter spp. in food and drinking water - A review

Acinetobacter spp. has emerged as a pathogen of major public health concern due to their increased resistance to antibiotics and their association with a wide range of nosocomial infections, community-acquired infections and war and natural disaster-related infections. It is recognized as a ubiquitous organism however, information about the prevalence of different pathogenic species of this genus in food sources and drinking water is scarce. Since the implementation of molecular techniques, the role of foods as a source of several species, including the Acinetobacter baumannii group, has been elucidated. Multidrug resistance was also detected among Acinetobacter spp. isolated from food products. This highlights the importance of foods as potential sources of dissemination of Acinetobacter spp. between the community and clinical environments and reinforces the need for further investigations on the potential health risks of Acinetobacter spp. as foodborne pathogens. The aim of this review was to summarize the published data on the occurrence of Acinetobacter spp. in different food sources and drinking water. This information should be taken into consideration by those responsible for infection control in hospitals and other healthcare facilities.

Dishwashing sponges and brushes: Consumer practices and bacterial growth and survival

Sponges are frequently used in kitchens and have been shown to harbor large numbers of bacteria, occasionally also pathogens. Less is known about kitchen brushes regarding usage and presence of bacteria. In the present study, the use of sponges and brushes was studied in a survey among 9966 European consumers in ten countries, and growth and survival of bacteria in sponges and brushes were examined in laboratory experiments. Sponges were the preferred hand-cleaning utensils for washing-up in the majority of countries, while brushes were most frequently used in Denmark and Norway. Consumers mostly change their sponges at regular times, but also sensory cues (looks dirty, smelly, slimy) and usage occurrences such as wiping up meat juices may trigger replacement. Besides cleaning the dishes, over a quarter of the dish brush users also use it to clean a chopping board after soilage from chicken meat juices. The water uptake and drying rate varied considerably, both between different sponges and between brushes and sponges, where brushes dried fastest. Campylobacter survived one day in all sponges and Salmonella more than seven days in two of three types of sponges. In the type of sponge that dried slowest, Salmonella grew on the first day and was always found in higher levels than in the other sponges. Non-pathogenic bacteria grew in the sponges and reached levels around 9 log CFU/sponge. In brushes all types of bacteria died over time. Campylobacter and Salmonella were reduced by more than 2.5 log to below the detection limit after one and three days, respectively. Bacteriota studies revealed a tendency for a dominance by Gram-negative bacteria and a shift to high relative prevalence of Pseudomonas over time in sponges. Both enumeration by agar plating and bacteriota analysis confirmed that the pathogens were in a minority compared to the other bacteria. Treatments of sponges and brushes with chlorine, boiling or in the dishwasher were effective to reduce Salmonella. We conclude that brushes are more hygienic than sponges and that their use should be encouraged. Contaminated sponges or brushes should be replaced or cleaned when they may have been in contact with pathogenic microorganisms, e.g. used on raw food spills. Cleaning of sponges and brushes with chlorine, boiling or dishwasher may be a safe alternative to replacing them with new ones.

Microbiological quality of kitchens sponges used in university student dormitories

Background

Kitchen sponges are a major source of cross-contamination as they can transfer foodborne pathogens, infectious agents and spoilage causing microorganisms to food contact surfaces. Several studies have revealed that university students adopt poor practices regarding food safety, hygiene, and the handling of kitchen cleaning equipment.

Methods

A total of fifty kitchen sponges were collected along with a questionnaire addressing social demographics and kitchen sponge usage by students living at the University of Sharjah dormitories. The effect of storage (3 and 10 days) on the microbial population of kitchen sponges at room temperature (21 °C) was assessed. Enterobacteriaceae isolated from sponges were identified and their antibiotic resistance determined.

Results

Student responses revealed that kitchen sponges used to clean food contact surfaces were also used to clean the oven (32%), sink (26%), refrigerator (10%), and to clean spills on the floor (4%). Kitchen sponges contained high counts of mesophilic aerobic bacteria (7.9 log₁₀/cm³), coliform (7.2 log₁₀/cm³), Enterobacteriaceae (7.3 log₁₀/cm³) and yeasts and molds (7.0 log₁₀/cm³). After storage of the sponges at room temperature (21 °C) for 3 and 10 days, the number of mesophilic aerobic bacteria, coliform, Enterobacteriaceae and yeasts and molds decreased by 0.4 and 1.3 log₁₀/cm³, 0.7 and 1.4 log₁₀/cm³, 0.4 and 1.1 log₁₀/cm³, and 0.6 and 1.3 log₁₀/cm³, respectively. The most frequently isolated Enterobacteriaceae were Enterobacter cloacae (56%) and Klebsiella oxytoca (16%). All E. cloacae isolates were resistant to amoxicillin, cefalotin, cefoxitin and cefuroxime axetil.

Conclusions

This study showed that students living in dormitories lacked good hygienic practices and were at increased risk of food poisoning. Kitchen sponges were highly contaminated with potentially pathogenic bacteria which could be transferred from the general kitchen environment to food contact surfaces and consequently lead to food contamination.

Microorganisms populating the water-related indoor biome

Modernisation of our households created novel opportunities for microbial growth and thus changed the array of microorganisms we come in contact with. While many studies have investigated microorganisms in the air and dust, tap water, another major input of microbial propagules, has received far less attention. The quality of drinking water in developed world is strictly regulated to prevent immediate danger to human health. However, fungi, algae, protists and bacteria of less immediate concern are usually not screened for. These organisms can thus use water as a vector of transmission into the households, especially if they are resistant to various water treatment procedures. Good tolerance of unfavourable abiotic conditions is also important for survival once microbes enter the household. Limitation of water availability, high or low temperatures, application of antimicrobial chemicals and other measures are taken to prevent indoor microbial overgrowth. These conditions, together with a large number of novel chemicals in our homes, shape the diversity and abundance of indoor microbiota through constant selection of the most resilient species, resulting in a substantial overlap in diversity of indoor and natural extreme environments. At least in fungi, extremotolerance has been linked to human pathogenicity, explaining why many species found in novel indoor habitats (such as dishwasher) are notable opportunistic pathogens. As a result, microorganisms that often enter our households with water and are then enriched in novel indoor habitats might have a hitherto underestimated impact on the well-being of the increasingly indoor-bound human population. KEY POINTS: Domestic environment harbours a large diversity of microorganisms. Microbiota of water-related indoor habitats mainly originates from tap water. Bathrooms, kitchens and household appliances select for polyextremotolerant species. Many household-related microorganisms are human opportunistic pathogens.

Eye-Catching Microbes-Polyphasic Analysis of the Microbiota on Microscope Oculars Verifies Their Role as Fomites

Microscopes are used in virtually every biological and medical laboratory. Previous cultivation-based studies have suggested that direct contact with microscope eyepieces increases the risk of eye infections. To obtain a deeper insight into the microbiota on oculars, we analysed 10 recently used university microscopes. Their left oculars were used for a cultivation-based approach, while the right oculars served for massive gene sequencing. After cleaning with isopropyl alcohol, the oculars were re-sampled and analysed again. All oculars were found to be contaminated with bacteria, with a maximum load of 1.7 × 10³ CFU cm^-2. MALDI Biotyping revealed mainly Cutibacterium (68%), Staphylococcus (14%) and Brevibacterium (10%), with the most abundant species being Cutibacterium acnes (13%) and Staphylococcus capitis (6%). Cleaning reduced the microbial load by up to 2 log scales. Within 10 uncleaned and 5 cleaned samples, 1480 ASVs were assigned to 10 phyla and 262 genera. The dominant genera before cleaning were Cutibacterium (78%), Paracoccus (13%), Pseudomonas (2%) and Acinetobacter (1%). The bacteriota composition on the cleaned oculars was similar; however, it probably largely represented dead bacteria. In summary, used oculars were significantly contaminated with skin and environmental bacteria, including potential pathogens. Regular cleaning is highly recommended to prevent eye and skin infections.

Metagenomic Analysis of Regularly Microwave-Treated and Untreated Domestic Kitchen Sponges

Kitchen sponges massively absorb and spread microorganisms, leading to contamination of kitchen appliances, surfaces, and food. Microwaving as an effective and widespread technique can rapidly reduce the microbial load of kitchen sponges. However, long-term effects of such treatments are largely unknown. Notably, it has been speculated that regularly applied domestic cleaning and disinfection may select for microbial communities with a higher pathogenic potential and/or malodorous properties. In this study, we distributed newly purchased polyurethane kitchen sponges to 20 participants, with the instruction to use them under normal household conditions for four weeks. Ten of the participants sanitized their sponges regularly by a standardized microwaving protocol, while the remaining ten sponges remained untreated. Metagenomic sequence data evaluation indicated that, in addition to bacteria, viruses, eukaryotes, and archaea were also part of the kitchen sponge microbiome. Comparisons of sanitized and untreated kitchen sponges indicated a trend towards a reduced structural microbial diversity while functional diversity increased. Microwave sanitization appeared to alter composition and metabolic properties of the microbial communities. Follow-up studies will have to show whether these changes are more positive or negative in terms of domestic hygiene, human health, and well-being.

Site-specific molecular analysis of the bacteriota on worn spectacles

Regularly touched surfaces are usually contaminated with microorganisms and might be considered as fomites. The same applies for spectacles, but only little is known about their microbial colonization. Previous cultivation-based analyses from our group revealed a bacterial load strongly dominated by staphylococci. To better account for aerotolerant anaerobes, slow growing and yet-uncultivated bacteria, we performed an optimized 16S rRNA gene sequencing approach targeting the V1-V3 region. 30 spectacles were swab-sampled at three sites, each (nosepads, glasses and earclips). We detected 5232 OTUs affiliated with 19 bacterial phyla and 665 genera. Actinobacteria (64%), Proteobacteria (22%), Firmicutes (7%) and Bacteroidetes (5%) were relatively most abundant. At genus level, 13 genera accounted for 84% of the total sequences of all spectacles, having a prevalence of more than 1% relative abundance. Propionibacterium (57%), Corynebacterium (5%), Staphylococcus (4%), Pseudomonas, Sphingomonas and Lawsonella (3%, each) were the dominant genera. Interestingly, bacterial diversity on the glasses was significantly higher compared to nosepads and earclips. Our study represents the first cultivation-independent study of the bacteriota of worn spectacles. Dominated by bacteria of mostly human skin and epithelia origin and clearly including potential pathogens, spectacles may play a role as fomites, especially in clinical environments.

Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines

Modern, mainly sustainability-driven trends, such as low-temperature washing or bleach-free liquid detergents, facilitate microbial survival of the laundry processes. Favourable growth conditions like humidity, warmth and sufficient nutrients also contribute to microbial colonization of washing machines. Such colonization might lead to negatively perceived staining, corrosion of washing machine parts and surfaces, as well as machine and laundry malodour. In this study, we characterized the bacterial community of 13 domestic washing machines at four different sampling sites (detergent drawer, door seal, sump and fibres collected from the washing solution) using 16S rRNA gene pyrosequencing and statistically analysed associations with environmental and user-dependent factors. Across 50 investigated samples, the bacterial community turned out to be significantly site-dependent with the highest alpha diversity found inside the detergent drawer, followed by sump, textile fibres isolated from the washing solution, and door seal. Surprisingly, out of all other investigated factors only the monthly number of wash cycles at temperatures ≥ 60 °C showed a significant influence on the community structure. A higher number of hot wash cycles per month increased microbial diversity, especially inside the detergent drawer. Potential reasons and the hygienic relevance of this finding need to be assessed in future studies.

Evaluation of bacterial and fungal contamination of kitchens of Birjand University of Medical Sciences

Objective

This study aims to evaluate the total bacterial and fungal count of tools, devices and surfaces of kitchens of the centers affiliated to Birjand University of Medical Sciences. In this study, 200 samples from four kitchens of Birjand University of Medical Sciences were obtained. After the preparation of serial dilutions, samples were cultured in plate count agar (PCA) plates and Sabouraud dextrose agar (SDA). After incubation at 37 and 25 °C for 24–48 and 72–96 h respectively, the microbial and fungal colonies were counted.

Results

The mean bacterial and fungal count of kitchens was 7.7 * 10⁷ and 7.6 * 10⁴, respectively. The highest and lowest levels of bacterial contamination were related to tools/devices and cover of tools/work clothes and the highest and lowest levels of fungal count were related to forks and spoons and the tools and devices of the storage site. The rate of contamination in the kitchens of Birjand University of Medical Sciences was relatively high. Thus, serious, continuous and accurate monitoring of the units, training of people working in all stages of cooking and disinfection the tools and devices are essential for control and prevention of disease transmission.

Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present

Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.

Gut bacteria of the cowpea beetle mediate its resistance to dichlorvos and susceptibility to Lippia adoensis essential oil

Bacteria inhabiting the gut of insects provide many benefits to their hosts, such as aiding in food digestion, reproduction, and immunity, tissue homeostasis, adaptation to environment and resistance to pathogen and pesticides. The cowpea beetle, Callosobruchus maculatus, is a serious cosmopolitan pest of pulses. This beetle has lent itself as a guinea pig for several ecological studies. It harbors a consortium of bacterial communities in its gut, but the evidence for their role in its physiology is fragmentary. In this work, we hypothesized that gut microbiota mediates C. maculatus resistance to dichlorvos (DDVP or O,O-dimethyl O-2,2-dichlorovinylphosphate) and represent the target of Lippia adoensis (Gambian Tea Bush) essential oil (EO). Symbiotic and aposymbiotic beetles were exposed to artificial cowpea seeds earlier treated with DDVP or EO. Adult mortality and changes in gut bacterial community composition and abundance were examined at F1 and F5 generations. The susceptibility of experimental beetles to DDVP was significantly affected by their symbiotic status. The adult mortality decreased across generations in DDVP treatments, and remained significantly higher in aposymbiotic groups. In EO treatments, the mortality was consistent irrespective of symbiotic status and experimental generations. When compared to DDVP and the Control, EO treatments had significantly lower bacterial richness and diversity, as well as lower abundance of Proteobacteria, Firmicutes, and Bacteroidetes. These results support our hypothesis and describe the responses of gut microbial communities to pesticide treatments. This could be of interest for developing new management strategies of this pest.

Study on microbial communities in domestic kitchen sponges: Evidence of Cronobacter sakazakii and Extended Spectrum Beta Lactamase (ESBL) producing bacteria

Domestic environment, in particular, kitchen setting is a well-established source of microbial contamination. Kitchen sponges represent an important vehicle of microbial transmission and maintenance of spoilage bacteria and pathogenic strains responsible for food borne diseases. The aim of this study was to evaluate the microbial communities of 100 'in-use' kitchen sponges, improving the knowledge on their role in cross-contamination in domestic environment and transmission of ESBLproducing strains. Sponges were processed for: aerobic mesophilic bacteria (AMB), Enterobacteriaceae (EB), yeasts and molds (YM), coagulase-positive staphylococci (CPS), micrococci (MCC), anaerobic sulfite reducing bacteria (ASR), and for the detection of Listeria monocytogenes, Salmonella spp. and Yersinia enterocolitica. A total of 309 enterobacteria strains were identified and then processed for ESBL (Extended Spectrum Beta Lactamase) phenotypical expression. A high contamination level of kitchen sponges was observed (mean value AMB 8.25±1.1; EB 5.89±1.2; YM 5.57±1.1; MCC 4.82±0.1 log CFU/g). Identified enterobacteria strains revealed several opportunistic and pathogenic agents such as Enterobacter cloacae (28%), Citrobacter freundii (23.3%), Cronobacter sakazakii (14.6%) and other strains in lower percentage. Listeria monocytogenes was found in only one sponge (1%). A total of 69 (22.3%) enterobacteria resulted ESBL+, with the following prevalence: P. rettgeri (50%), L. adenocarboxilata (30%), K. pneumoniae (25%), K. oxytoca (25%), C. sakazakii (20%), E. cloacae (20.7%), C. freundii (20.1%). Results confirm the potential role of kitchen sponges as vehicle for food-borne pathogens such as, C. sakazakii for the first time, infectious agents and spoilage microorganisms. The observed high contamination level and the presence of several ESBLs opportunistic pathogens, stresses the necessity to improve a proper education of the consumers on the effective treatment to reduce their microbial loads.

Honor Thy Lodgers? – Structure and Function of the Human Built Environment Microbiome

The microbiome of the built environment (BE) and its interactions with the human occupants represent a new and highly interdisciplinary research field. The BE is characterized by a great microbial diversity as well as very fluctuating environmental conditions and sharp gradients of physicochemical parameters, which significantly shape the resident microbiomes. A great significance of the BE microbiome for human health is obvious, but far from being fully understood. However, there is a growing body of evidence that antimicrobial and probiotic strategies will have to be balanced in a well-considered manner to successfully manage the BE microbiome in a way that finally is most beneficial for human health.

Critical Assessment of Methods to Quantify Biofilm Growth and Evaluate Antibiofilm Activity of Host Defence Peptides

Biofilms are multicellular communities of bacteria that can adhere to virtually any surface. Bacterial biofilms are clinically relevant, as they are responsible for up to two-thirds of hospital acquired infections and contribute to chronic infections. Troublingly, the bacteria within a biofilm are adaptively resistant to antibiotic treatment and it can take up to 1000 times more antibiotic to kill cells within a biofilm when compared to planktonic bacterial cells. Identifying and optimizing compounds that specifically target bacteria growing in biofilms is required to address this growing concern and the reported antibiofilm activity of natural and synthetic host defence peptides has garnered significant interest. However, a standardized assay to assess the activity of antibiofilm agents has not been established. In the present work, we describe two simple assays that can assess the inhibitory and eradication capacities of peptides towards biofilms that are formed by both Gram-positive and negative bacteria. These assays are suitable for high-throughput workflows in 96-well microplates and they use crystal violet staining to quantify adhered biofilm biomass as well as tetrazolium chloride dye to evaluate the metabolic activity of the biofilms. The effect of media composition on the readouts of these biofilm detection methods was assessed against two strains of Pseudomonas aeruginosa (PAO1 and PA14), as well as a methicillin resistant strain of Staphylococcus aureus. Our results demonstrate that media composition dramatically alters the staining patterns that were obtained with these dye-based methods, highlighting the importance of establishing appropriate biofilm growth conditions for each bacterial species to be evaluated. Confocal microscopy imaging of P. aeruginosa biofilms grown in flow cells revealed that this is likely due to altered biofilm architecture under specific growth conditions. The antibiofilm activity of several antibiotics and synthetic peptides were then evaluated under both inhibition and eradication conditions to illustrate the type of data that can be obtained using this experimental setup.

Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome

The microbiome has been heralded as a gauge of and contributor to both human health and environmental conditions. Current challenges in probing, engineering, and harnessing the microbiome stem from its microscopic and nanoscopic nature, diversity and complexity of interactions among its members and hosts, as well as the spatiotemporal sampling and in situ measurement limitations induced by the restricted capabilities and norm of existing technologies, leaving some of the constituents of the microbiome unknown. To facilitate significant progress in the microbiome field, deeper understanding of the constituents' individual behavior, interactions with others, and biodiversity are needed. Also crucial is the generation of multimodal data from a variety of subjects and environments over time. Mobile imaging and sensing technologies, particularly through smartphone-based platforms, can potentially meet some of these needs in field-portable, cost-effective, and massively scalable manners by circumventing the need for bulky, expensive instrumentation. In this Perspective, we outline how mobile sensing and imaging technologies could lead the way to unprecedented insight into the microbiome, potentially shedding light on various microbiome-related mysteries of today, including the composition and function of human, animal, plant, and environmental microbiomes. Finally, we conclude with a look at the future, propose a computational microbiome engineering and optimization framework, and discuss its potential impact and applications.

Martin-Sanchez, Meyer W, Seung-Yoon Oh, Jose Paulo Sampaio, Seifert KA, Sklenář F, Dirk Stubbe, Suh SO, Summerbell R, Svantesson S, Martin Unterseher, Cobus M. Visagie, Weiss M, Woudenberg JHC, Christian Wurzbacher, den Wyngaert SV, Yilmaz N, Andrey Yurkov, Kõljalg U, Abarenkov K. Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK)

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.