Diversity changes of microbial communities into hospital surface environments

Antibiotic Resistance as a Functional Characteristic of Urban Dust Particles' Microbial Communities

Urban dust samples were collected in Moscow (Russia) in June 2021. The samples were collected in three functional zones of Moscow (traffic, residential, and recreational) and included air microparticles, leaf dust, and paved dust. Data on the taxonomic composition of bacterial communities were obtained for dust samples, and their functional characteristics were predicted using PICRUSt2 2.5.0 and FAPROTAX 1.8.0 software. The culturable part of the bacterial community was examined for the presence of antibiotic-resistant strains with respect to β-lactams, tetracyclines, amphenicols, and aminoglycosides. The presence of bacteria resistant to ceftazidime, cefepime, and tetracycline was detected in all dust samples. The presence of bacteria resistant to meropenem and amikacin was only observed in the dust collected from leaves in the residential and traffic zones. The overall abundance of cultured antibiotic-resistant bacteria from the total heterotrophs ranged from 0.03% to 1.88%, with the highest percentage observed in dust from the residential zone. Notably, strains resistant to all antibiotics tested were observed in the leaf dust bacterial community.

Evaluation of a peracetic-acid-based sink drain disinfectant on the intensive care unit of a tertiary care centre in Belgium

BACKGROUND

Sink drains in hospitals are notorious reservoirs of bacteria, hosting both planktonic micro-organisms and biofilms within the siphon. Disinfectants based on peracetic acid are both non-corrosive and effective in eliminating biofilm and planktonic micro-organisms, presenting a potential solution for decontaminating sink drains.

AIM

To examine the effectiveness of Clinell Drain Disinfectant, a peracetic-acid-based disinfectant, in the intensive care unit (ICU) of UZ Brussel.

METHODS

All 10 sinks in one of the ICU subunits known to be heavily contaminated were treated with Clinell Drain Disinfectant for one month. Throughout the treatment period, bacterial growth in the P-traps was systematically monitored qualitatively (using eSwab) and quantitatively (employing a sterile catheter and syringe) on various selective agar plates, processed and incubated in the WASPLab system. Matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy was used to identify all morphologically distinct colonies.

FINDINGS

At baseline, most of the sink drains were colonized by high concentrations of multidrug-resistant micro-organisms, primarily VIM-producing P. aeruginosa. The cultures taken immediately after decontamination yielded negative results, with only a very few exceptions. Nonetheless, it was observed that the biofilm in the upper section of the drain system remained unaffected, and within two days it was capable of recolonizing the liquid in the P-traps at a concentration >100,000 cfu/mL. After one month, this disinfecting protocol did not result in a lasting decontamination of the sink drains.

CONCLUSION

This study demonstrated the disinfectant's efficacy in decontaminating the P-trap liquid.

Investigating the changing taxonomy and antimicrobial resistance of bacteria isolated from door handles in a new infectious disease ward pre- and post-patient admittance

Healthcare-associated infections (HAIs) are a significant burden to health systems, with antimicrobial resistance (AMR) further compounding the issue. The hospital environment plays a significant role in the development of HAIs, with microbial surveillance providing the foundation for interventions. We sampled 40 door handles at a newly built hospital prior to patients being admitted and then 6 and 12 months after this date. We utilized 16S rDNA sequencing to identify unique colonies, disc diffusion assays to assess the antibiotic resistance of Staphylococcus spp., and whole-genome sequenced (WGS) multidrug-resistant (MDR) isolates. Before patient admission, 43% of sites harbored Staphylococcus spp., increasing to 55% and 65% at six and 12 months, respectively, while Bacillus spp. saw a large increase from 3% to 68% and 85%, respectively. No ESKAPE pathogens were identified. Staphylococcus spp. showed relatively low resistance to all antibiotics except cefoxitin (56%) before patient admittance. Resistance was highest after 6 months of ward use, with an increase in isolates susceptible to all antibiotics after 12 months (11% and 54% susceptibility, respectively). However, MDR remained high. WGS revealed blaZ (25/26), and mecA (22/26) and aac6-aph2 (20/26) were the most abundant resistance genes. Two Staphylococcus hominis isolates identified at the first two time points, respectively, and three Staphylococcus epidermidis isolates identified at all three time points, respectively, were believed to be clonal. This study highlighted the prevalence of a resistant reservoir of bacteria recoverable on high-touch surfaces and the long-term persistence of Staphylococcus spp. first introduced prior to patient admission.

IMPORTANCE

Healthcare-associated infections (HAIs) are a significant burden to health systems, conferring increased morbidity, mortality, and financial costs to hospital admission. Antimicrobial resistance (AMR) further compounds the issue as viable treatment options are constrained. Previous studies have shown that environmental cleaning interventions reduced HAIs. To ensure the effectiveness of these, it is important to analyze the hospital environment at a microbial level, particularly high-touch surfaces which see frequent human interaction. In addition to identifying infectious microorganisms, it is also beneficial to assess typically non-infectious organisms, as traits including AMR can be transferred between the two. Our study identified that there were high levels of antibiotic resistance in typically non-infectious organisms found on high touch surfaces on a hospital ward. However, the organisms identified suggested that the cleaning protocols in place were sufficient, with their presence being due to repeated recolonization events through human interaction after cleaning had taken place.

In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes

Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/plasmid reconstruction, we demonstrate that microbial composition differs in a stable way between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps and were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were more present on plasmids. This could be of particular importance for patient-related areas (CL2), as the potential spread of antibiotic resistances could be a major concern in this area. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Since restrictive confinement selects for resistant microorganisms, strategies are required to deepen our understanding of dynamic processes of microbiome and resistome within hospital environments.

IMPORTANCE

Effective measures to combat antibiotic resistances and healthcare-associated infections are urgently needed, including optimization of microbial control. However, previous studies have indicated that stringent control can lead to an increase in the resistance capacities of microbiomes on surfaces. This study adds to previous knowledge by focusing on the conditions in a single hospital, resolving the microbiomes and their resistomes in three different confinement levels (CL): operating room, patient-related areas, and non-patient-related areas. We were able to identify stable key taxa; profiled the capacities of taxa, functions, and antimicrobial resistances (AMR); and reconstruct genomes and plasmids in each CL. Our results show that the most restrictive CL indeed had the highest functional diversity, but that resistances were mostly encoded on chromosomes, indicating a lower possibility of resistance spread. However, clever strategies are still required to strike a balance between microbial control and selective pressures in environments where patients need protection.

Biofilms, mobile genetic elements and the persistence of pathogens on environmental surfaces in healthcare and food processing environments

Biofilms are the natural state for bacterial and fungal species. To achieve surface hygiene in commercial facilities, the presence of biofilms must be adequately considered. However, standard disinfectant and sanitizer efficacy tests required by the US-EPA and the European Committee for Standardization (CEN) do not currently consider the role of environmental biofilms. This selective review will discuss what biofilms are and why they are important. We will also cover where they are commonly found in healthcare and food processing facilities and explore how current antimicrobial test methods required for product registration do not test for the presence of biofilms. Additionally, we will explore how a lack of efficacy against biofilms may play a role in the development of antimicrobial resistance in healthcare facilities due to the exchange of mobile genetic elements that occur readily in a biofilm matrix.

Trends in viable microbial bioburden on surfaces within a paediatric bone marrow transplant unit

BACKGROUND

Despite their role being historically overlooked, environmental surfaces have been shown to play a key role in the transmission of pathogens causative of healthcare-associated infection. To guide infection prevention and control (IPC) interventions and inform clinical risk assessments, more needs to be known about microbial surface bioburdens.

AIM

To identify the trends in culturable bacterial contamination across communal touch sites over time in a hospital setting.

METHODS

Swab samples were collected over nine weeks from 22 communal touch sites in a paediatric bone marrow transplant unit. Samples were cultured on Columbia blood agar and aerobic colony counts (ACC) per 100 cm2 were established for each site. Individual colony morphologies were grouped and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or 16s rDNA sequencing.

FINDINGS

Highest mean counts were observed for sites associated with ward management activity and computer devices (3.29 and 2.97 ACC/100 cm2 respectively). A nurses' station keyboard had high mean ACC/100 cm2 counts (10.67) and diversity, while laundry controls had high mean ACC/100 cm2 counts (4.70) and low diversity. Micrococcus luteus was identified in all sampling groups. Clinical staff usage sites were contaminated with similar proportions of skin and environmental flora (52.19-46.59% respectively), but sites associated with parental activities were predominantly contaminated by environmental microflora (86.53%).

CONCLUSION

The trends observed suggest patterns in microbial loading based on site activities, surface types and user groups. Improved understanding of environmental surface contamination could help support results interpretation and IPC interventions, improving patient safety.

Evaluating the antibacterial efficacy of a silver nanocomposite surface coating against nosocomial pathogens as an antibiofilm strategy to prevent hospital infections

Antimicrobial nanocoatings may be a means of preventing nosocomial infections, which account for significant morbidity and mortality. The role of hospital sink traps in these infections is also increasingly appreciated. We describe the preparation, material characterization and antibacterial activity of a pipe cement-based silver nanocoating applied to unplasticized polyvinyl chloride, a material widely used in wastewater plumbing. Three-dimensional surface topography imaging and scanning electron microscopy showed increased roughness in all surface finishes versus control, with grinding producing the roughest surfaces. Silver stability within nanocoatings was >99.89% in deionized water and bacteriological media seeded with bacteria. The nanocoating exhibited potent antibiofilm (99.82-100% inhibition) and antiplanktonic (99.59-99.99% killing) activity against three representative bacterial species and a microbial community recovered from hospital sink traps. Hospital sink trap microbiota were characterized by sequencing the 16S rRNA gene, revealing the presence of opportunistic pathogens from genera including Pseudomonas, Enterobacter and Clostridioides. In a benchtop model sink trap system, nanocoating antibiofilm activity against this community remained significant after 11 days but waned following 25 days. Silver nanocoated disks in real-world sink traps in two university buildings had a limited antibiofilm effect, even though in vitro experiments using microbial communities recovered from the same traps demonstrated that the nanocoating was effective, reducing biofilm formation by >99.6% and killing >98% of planktonic bacteria. We propose that conditioning films forming in the complex conditions of real-world sink traps negatively impact nanocoating performance, which may have wider relevance to development of antimicrobial nanocoatings that are not tested in the real-world.

Human pathogenic bacteria on high-touch dry surfaces can be controlled by warming to human-skin temperature under moderate humidity

Healthcare-associated infections have become a major health issue worldwide. One route of transmission of pathogenic bacteria is through contact with "high-touch" dry surfaces, such as handrails. Regular cleaning of surfaces with disinfectant chemicals is insufficient against pathogenic bacteria and alternative control methods are therefore required. We previously showed that warming to human-skin temperature affected the survival of pathogenic bacteria on dry surfaces, but humidity was not considered in that study. Here, we investigated environmental factors that affect the number of live bacteria on dry surfaces in hospitals by principal component analysis of previously-collected data (n = 576, for CFU counts), and experimentally verified the effect of warming to human-skin temperature on the survival of pathogenic bacteria on dry surfaces under humidity control. The results revealed that PCA divided hospital dry surfaces into four groups (Group 1~4) and hospital dry surfaces at low temperature and low humidity (Group 3) had much higher bacterial counts as compared to the others (Group 1 and 4) (p<0.05). Experimentally, warming to human-skin temperature (37°C with 90% humidity) for 18~72h significantly suppressed the survival of pathogenic bacteria on dry surfaces, such as plastic surfaces [p<0.05 vs. 15°C (Escherichia coli DH5α, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and blaNDM-5 E. coli)] or handrails [p<0.05 vs. 15~25°C (E. coli DH5α, S. aureus, P. aeruginosa, A. baumannii)], under moderate 55% humidity. Furthermore, intermittent heating to human-skin temperature reduced the survival of spore-forming bacteria (Bacillus subtilis) (p<0.01 vs. continuous heating to human-skin temperature). NhaA, an Na+/H+ antiporter, was found to regulate the survival of bacteria on dry surfaces, and the inhibitor 2-aminoperimidine enhanced the effect of warming at human-skin temperature on the survival of pathogenic bacteria (E. coli DH5α, S. aureus, A. baumannii) on dry surfaces. Thus, warming to human-skin temperature under moderate humidity is a useful method for impairing live pathogenic bacteria on high-touch surfaces, thereby helping to prevent the spread of healthcare-associated infections.

Novel Designed Surgical Drapes Reducing Fluid Permeability in the Surgical Critical Area of a Sterile Operation Interface: A Randomized Controlled Trial

Aim

To compare the impact and cost effects of medical long fiber polyester drapes and cotton fabric drapes on operative sterile operation interfaces.

Background

The comparison of the properties of the commonly used surgical drapes materials in terms of leakage, device slip, and prevention of intraoperative adverse events is not clear.

Method

A prospective randomized controlled study was conducted in the operating room of a tertiary hospital in Chengdu, China. A total of 400 patients who underwent urology surgery were enrolled and randomly divided into two groups by computer, the study group (200 cases) selected the new long-fiber polyester cloth, while the control group (200 cases) selected conventional cotton fabric surgical drapes during the operation to maintain a sterile operating interface. The impermeability and water absorption of surgical drapes, the rate of device slip and skin scald in surgical patients, and the cost effect of the two kinds of surgical drapes were compared.

Results

The long fiber polyester surgical drapes were superior to conventional cotton cloth in water absorption (g/m2) (835 ± 15.8 VS 225 ± 21.0, t = 328.261, P < 0.001), preventing surgical site infections (2.5% VS 8.0%, χ 2 = 6.081, P=0.014), device slip (7.5% VS 17.0%, χ 2 = 8.396, P=0.004), patients from burning (0 VS 1, Fisher P=1.0), and total cost per use ($) (0.83 VS 0.96-1.09).

Conclusion

Long fiber polyester fabric has a stronger antipenetration ability of fluid and microorganisms thus forming an effective protective barrier. It also has strong hygroscopicity, and its special design can prevent the occurrence of sliding of surface instruments and skin scald in patients. In addition, its cost effect is superior. Implications for Nursing Management. Operating room nursing managers can introduce long fiber polyester drapes into the selection of medical textiles to construct aseptic surgical barriers and prevent surgical site infection.

How Does Hospital Microbiota Contribute to Healthcare-Associated Infections?

Healthcare-associated infections (HAIs) are still a global public health concern, associated with high mortality and increased by the phenomenon of antimicrobial resistance. Causative agents of HAIs are commonly found in the hospital environment and are monitored in epidemiological surveillance programs; however, the hospital environment is a potential reservoir for pathogenic microbial strains where microorganisms may persist on medical equipment surfaces, on the environment surrounding patients, and on corporal surfaces of patients and healthcare workers (HCWs). The characterization of hospital microbiota may provide knowledge regarding the relatedness between commensal and pathogenic microorganisms, their role in HAIs development, and the environmental conditions that favor its proliferation. This information may contribute to the effective control of the dissemination of pathogens and to improve infection control programs. In this review, we describe evidence of the contribution of hospital microbiota to HAI development and the role of environmental factors, antimicrobial resistance, and virulence factors of the microbial community in persistence on hospital surfaces.

Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates

Background

Healthcare-associated infections due to antibiotic-resistant organisms pose an acute and rising threat to critically ill and immunocompromised patients. To evaluate reservoirs of antibiotic-resistant organisms as a source of transmission to patients, we interrogated isolates from environmental surfaces, patient feces, and patient blood infections from an established and a newly built intensive care unit.

Methods

We used selective culture to recover 829 antibiotic-resistant organisms from 1594 environmental and 72 patient fecal samples, in addition to 81 isolates from blood cultures. We conducted antibiotic susceptibility testing and short- and long-read whole genome sequencing on recovered isolates.

Results

Antibiotic-resistant organism burden is highest in sink drains compared to other surfaces. Pseudomonas aeruginosa is the most frequently cultured organism from surfaces in both intensive care units. From whole genome sequencing, different lineages of P. aeruginosa dominate in each unit; one P. aeruginosa lineage of ST1894 is found in multiple sink drains in the new intensive care unit and 3.7% of blood isolates analyzed, suggesting movement of this clone between the environment and patients.

Conclusions

These results highlight antibiotic-resistant organism reservoirs in hospital built environments as an important target for infection prevention in hospitalized patients.

Temporal variation in bacterial community profile on patients' bedsheets in a primary healthcare unit

Fabrics serve as fomites in spreading nosocomial infections. As a patient is in close contact with bedsheets, it is important to assess the seasonal variation in bacterial diversity on these in healthcare units. The study was conducted to characterise the bacterial diversity on patients' bedsheets across 7 months in a primary healthcare unit. Polyester-cotton blend fabric was stitched on bedsheets, and temporal dynamics of bacterial communities was assessed from May to November 2019. qPCR and amplicon sequencing of 16S rRNA gene was performed for profiling of bacterial community. Results revealed the dominance of Bacillota followed by Pseudomonadota, and Actinomycetota. A seasonal variation was observed in the bacterial load, with maximum values in June. This indicates the impact of environmental conditions on bacterial abundance and composition on fabrics in healthcare unit. The presence of priority pathogens on the patient bedsheets is a human health concern reiterating the need for season-specific laundering protocol.

Mobilizable antibiotic resistance genes are present in dust microbial communities

The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.

Effect of thermal control of dry fomites on regulating the survival of human pathogenic bacteria responsible for nosocomial infections

We monitored the survival of human pathogenic bacteria [Escherichia coli (ATCC), extended-spectrum β-lactamase-producing E. coli (Clinical isolate), New Delhi metallo-β-lactamase-producing E. coli (clinical isolate), Staphylococcus aureus (ATCC)] on dry materials (vinyl chloride, aluminum, plastic, stainless steel) at distinct temperatures (room temperature or 15°C–37°C). These bacteria favored a lower temperature for their prolonged survival on the dry fomites, regardless of the material type. Interestingly, when mixed with S. aureus, E. coli survived for a longer time at a lower temperature. Cardiolipin, which can promote the survival of S. aureus in harsh environments, had no effect on maintaining the survival of E. coli. Although the trends remained unchanged, adjusting the humidity from 40% to 60% affected the survival of bacteria on dry surfaces. Scanning electron microscopic analysis revealed no morphological differences in these bacteria immediately before or after one day of dry conditions. In addition, ATP assessment, a method used to visualize high-touch surfaces in hospitals, was not effective at monitoring bacterial dynamics. A specialized handrail device fitted with a heater, which was maintained at normal human body core temperature, successfully prohibited the prolonged survival of bacteria [Enterococcus faecalis (ATCC), E. coli (ATCC), Pseudomonas aeruginosa (ATCC), S. aureus (ATCC), Acinetobacter baumannii (clinical isolate), and Serratia marcescens (clinical isolate)], with the exception of spore-forming Bacillus subtilis (from our laboratory collection) and the yeast-like fungus Candida albicans (from our laboratory collection)] on dry surfaces. Taken together, we concluded that the tested bacteria favor lower temperatures for their survival in dry environments. Therefore, the thermal control of dry fomites has the potential to control bacterial survival on high-touch surfaces in hospitals.

Diversity of nasal microbiota and its interaction with surface microbiota among residents in healthcare institutes

Nasal microbial communities may have crucial implications for human health, including for residents of healthcare institutes (HCIs). Factors that determine the diversity of nasal microbiota in HCIs remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationship between nasal and surface microbiota in three HCIs. Participants were classified into a hospitalised or nonhospitalised group based on their most recent date of hospitalisation. A total of 88 nasal samples and 83 surface samples were analysed. Dysgonomonas and Corynebacterium were the most abundant taxa in the surface and nasal samples, respectively. Significant differences were discovered in microbiota diversity among HCIs when comparing the surface and nasal samples. Fifteen taxa were identified as present in all the surface and nasal samples. SourceTracker analysis revealed that the ventilation conditions of environment might be associated with the proportion of shared microbial communities between nasal and surface. Additionally, as compared with the nonhospitalised group, the hospitalised group had a higher proportion of surface microbiota in their nasal samples, which might lead to a higher risk of human-related microorganisms or pathogens colonising the nasal cavity. The data suggest that nasal bacterial diversity could be influenced by both health status and living environment. Our results therefore highlight the importance of the indoor environment for HCI residents.

Impact of bacterial traces belonging to the Enterobacteriaceae on the prevalence of Chlamydia trachomatis in women visiting a community hospital in Japan

We explored the bacteria present in the vaginal microbiota facilitating the prevalence of Chlamydia trachomatis in women visiting a community hospital in Sapporo, Japan, by amplicon sequencing. A total of 273 cervical swab samples were collected, and bacterial vaginosis was evaluated in all specimens by assessment of the Nugent score. In 16 of the samples, bacterial 16S rDNA could not be detected and they were therefore omitted from subsequent experiments (n = 257). A significant negative correlation was observed between the Nugent scores and the amount of Lactobacillus 16S rDNA. Among the 257 samples, chlamydial plasmid was detected in 20 samples and was used for amplicon sequencing. No significant association between the Nugent score and the prevalence of C. trachomatis was detected. Based on the results of chlamydial plasmid detection and the Nugent score, chlamydia-negative samples (n = 27) were randomly selected. Finally, the number of operational taxonomic units (OTUs) obtained from amplicon sequencing was compared between chlamydia-positive (n = 20) and -negative samples (n = 27), revealing that a significant difference was only detected for the OTU numbers of Enterobacteriaceae between the C. trachomatis-positive and -negative groups. However, almost all of the samples utilized for amplicon sequencing failed to grow on MacConkey agar plates and produce indole. Taken together, we concluded that traces of bacteria, not live bacteria, belonging to the Enterobacteriaceae indicated the flow of bacteria through the anogenital route along with gut indole, and the resulting impact on the prevalence of C. trachomatis in the cervicogenital tract of women in Japan.