Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study

Intrahospital dissemination of multidrug-resistant Acinetobacter baumannii at a teaching hospital in Northeast of Mexico

Background

Acinetobacter baumannii is an opportunistic drug-resistant Gram-negative coccobacillus associated with nosocomial infections, representing a worldwide public health problem.

Aim

The aim of this study was to analyse the dissemination of A. baumannii in two hospital buildings in Mexico through phenotypic and genotypic characterization of clinical isolates obtained for three years.

Methods

Clinical strains were collected from two buildings in a tertiary-care hospital in Monterrey, Mexico. After species identification by MALDI-TOF MS and PCR, antimicrobial susceptibility was determined by disk diffusion and microdilution methods, carbapenemase-encoding genes (OXA-23, -24, -51, and -58) were searched, and clonal diversity was analysed by PFGE and MLST.

Findings

Among 204 specimens, 87.3% and 50.5% of the isolates were classified as multidrug-resistant (MDR) and difficult-to-treat-resistant (DTR), respectively. The OXA-24 gene was detected in 95% of the isolates. Most isolates (n=181) were grouped into 15 clones, four which predominated and disseminated after five months. Among ST detected (ST1694, ST758, ST124, and ST490), ST124, which belongs to the high-risk CC636 clonal complex, is reported for the first time in Mexico.

Conclusions

Long-term persistence and dissemination of A. baumannii clones were observed in specific hospital wards from two buildings in a tertiary-care hospital in Mexico. High antimicrobial resistance, such as MDR and DTR, were observed in this hospital. DTR surveillance and early recognition of MDR A. baumannii clones should be performed routinely to prevent their dissemination.

The indoors microbiome and human health

Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.

Department-specific patterns of bacterial communities and antibiotic resistance in hospital indoor environments

The hospital indoor environment has a crucial impact on the microbial exposures that humans encounter. Resistance to antibiotics is a mechanism used by bacteria to develop resilience in indoor environments, and the widespread use of antibiotics has led to changes in the ecological function of resistance genes and their acquisition by pathogens. By integrating the 16S rRNA Illumina sequencing and high-throughput-quantitative PCR approaches with water and air dust samples across seven departments in Peking University Shenzhen Hospital, China, this study yields intriguing findings regarding the department-specific variations, correlations and source tracing of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) within the hospital indoor environment. A notable observation was the pivotal role played by seasonal variations in shaping the bacterial composition across the entire hospital indoor environment. Another department-specific finding was the correlation between ARGs and MGEs abundance, which was evident in the overall hospital indoor environment, but not found in the blood test room, ophthalmology, and gynecology departments. Notably, as an important source of bacteria and ARGs/MGEs for the blood test room, the gynecology department also presented a close link between bacterial communities and the presence of ARGs/MGEs. Additionally, the results reiterate the importance of surveillance and monitoring of antibiotic resistance, specifically in Legionella spp. in man-made water systems, and highlight the significance of understanding genetic elements like Tp614 involved in gene transfer and recombination, and their impact on antimicrobial treatment efficacy. KEY POINTS: • The department-specific variations, correlations and source tracing of bacteria, ARGs, and MGEs were uncovered in the hospital's indoor environment. • Although each department exhibited consistent seasonal impacts on bacterial compositions, the co-occurrence between the presence of ARGs and MGEs was exclusively evident in the emergency, surgery, pneumology and otolaryngology departments. • The gynecology department emerged as a crucial source of bacteria, ARGs and MGEs within the hospital. Additionally, it was found to exhibit a significant correlation between bacterial communities and the presence of ARGs and MGEs.

Healthcare as a driver, reservoir and amplifier of antimicrobial resistance: opportunities for interventions

Antimicrobial resistance (AMR) is a global health challenge that threatens humans, animals and the environment. Evidence is emerging for a role of healthcare infrastructure, environments and patient pathways in promoting and maintaining AMR via direct and indirect mechanisms. Advances in vaccination and monoclonal antibody therapies together with integrated surveillance, rapid diagnostics, targeted antimicrobial therapy and infection control measures offer opportunities to address healthcare-associated AMR risks more effectively. Additionally, innovations in artificial intelligence, data linkage and intelligent systems can be used to better predict and reduce AMR and improve healthcare resilience. In this Review, we examine the mechanisms by which healthcare functions as a driver, reservoir and amplifier of AMR, contextualized within a One Health framework. We also explore the opportunities and innovative solutions that can be used to combat AMR throughout the patient journey. We provide a perspective on the current evidence for the effectiveness of interventions designed to mitigate healthcare-associated AMR and promote healthcare resilience within high-income and resource-limited settings, as well as the challenges associated with their implementation.

Aerosol-Mediated Spread of Antibiotic Resistance Genes: Biomonitoring Indoor and Outdoor Environments

Antimicrobial resistance (AMR) has emerged as a conspicuous global public health threat. The World Health Organization (WHO) has launched the "One-Health" approach, which encourages the assessment of antibiotic resistance genes (ARGs) within an environment to constrain and alleviate the development of AMR. The prolonged use and overuse of antibiotics in treating human and veterinary illnesses, and the inability of wastewater treatment plants to remove them have resulted in elevated concentrations of these metabolites in the surroundings. Microbes residing within these settings acquire resistance under selective pressure and circulate between the air-land interface. Initial evidence on the indoor environments of wastewater treatment plants, hospitals, and livestock-rearing facilities as channels of AMR has been documented. Long- and short-range transport in a downwind direction disseminate aerosols within urban communities. Inhalation of such aerosols poses a considerable occupational and public health risk. The horizontal gene transfer (HGT) is another plausible route of AMR spread. The characterization of ARGs in the atmosphere therefore calls for cutting-edge research. In the present review, we provide a succinct summary of the studies that demonstrated aerosols as a media of AMR transport in the atmosphere, strengthening the need to biomonitor these pernicious pollutants. This review will be a useful resource for environmental researchers, healthcare practitioners, and policymakers to issue related health advisories.

Bacterial response to the combined pollution of benzo[a]pyrene and decabromodiphenyl ether in soil under flooding anaerobic condition

This study investigated the interaction between the co-pollutants of Benzo[a]pyrene (BaP) and decabromodiphenyl ether (BDE-209) and the bacterial community in soil under flooding anaerobic condition. Three levels of combined pollution (at nominal concentrations of 1, 5, and 25 mg/kg, respectively, for each pollutant), their corresponding sterilized controls, and a blank control (CK) were set up. During the incubation time of 270 days, BaP attenuated more easily than BDE-209. The second-order rate constant of BaP attenuation was negatively correlated with the Ln value of initial BaP concentration. Maximal difference in bacterial community occurred between the CK soil and the highly polluted soil. Desulfomonilaceae, Parcubacteria and Rhodanobacter were probably involved in BaP and BDE-209 degradation, while Nitrosomonadaceae, Phenylobacterium and Mitochondria were significantly suppressed by BaP and BDE-209 or their degrading products. Genes narI, bcrC, fadJ, had, dmpC, narG and CfrA were involved in the degradation of BaP and BDE-209. Impacts of BaP and BDE-209 on metabolisms of carbon, nitrogen and sulfur were not significant. The results provide guidance for the management and remediation of the contaminated soil.

Cross-contamination of carbapenem-resistant Gram-negative bacteria between patients and the hospital environment in the first year of a newly built surgical ward

BACKGROUND

Transmission and outbreaks of carbapenem-resistant Gram-negative bacteria (CRGN) in hospitals are often associated with contamination of the wastewater environment. We performed a prospective observational study to investigate the colonization of the hospital wastewater environment during the first year of occupancy of the surgical intermediate and intensive care units of a newly constructed building at the University Hospital of Heidelberg, Germany.

METHODS

We performed monthly screening of the wastewater system (toilets and sinks) for 12 months, starting 1 month before opening (1st October 2020 to 30th October 2021). Admission and weekly rectal screening of patients for CRGN were also performed in parallel. Bacterial isolates were characterized by whole-genome sequencing.

RESULTS

Twenty-seven of 1978 (1.4%) admitted patients were colonized/infected with CRGN. A total of 29 CRGN isolates from 24 patients and 52 isolates were available for sequencing. Within the first month of occupancy, we identified seven patients colonized/infected with CRGN, while none were found in the environmental reservoirs. The first detection of CRGN isolates in the sewage system started five months after the first occupancy. Two previously non-colonized patients were colonized/infected with Pseudomonas aeruginosa strains colonizing the sewage system. The significant identity of plasmids carrying the carbapenemase gene suggests that long-term colonization of the sewage system facilitates the emergence of new carbapenem-resistant clones.

CONCLUSION

Cross-contamination between patients and the hospital environment is bidirectional. Our study demonstrated that contamination of the hospital wastewater environment may lead to persistent colonization and may serve as a reservoir for nosocomial acquisition of CRGN.

Biocontrol in built environments to reduce pathogen exposure and infection risk

The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.

Environmental cleaning to prevent hospital-acquired infections on non-intensive care units: a pragmatic, single-centre, cluster randomized controlled, crossover trial comparing soap-based, disinfection and probiotic cleaning

Background

The impact of environmental hygiene on the occurrence of hospital-acquired infections (HAIs) remains a subject of debate. We determined the effect of three different surface-cleaning strategies on the incidence of HAIs.

Methods

Between June 2017 and August 2018 we conducted a pragmatic, cluster-randomized controlled crossover trial at 18 non-ICU wards in the university hospital of Berlin, Germany. Surfaces in patient rooms on the study wards were routinely cleaned using one of three agents: Soap-based (reference), disinfectant and probiotic. Each strategy was used on each ward for four consecutive months (4m-4m-4m). There was a one-month wash-in period at the beginning of the study and after each change in strategy. The order of strategies used was randomized for each ward. Primary outcome was the incidence of HAIs. The trial was registered with the German Clinical Trials Register, DRKS00012675.

Findings

13,896 admitted patients met the inclusion criteria, including 4708 in the soap-based (reference) arm, 4535 in the disinfectant arm and 4653 in the probiotic arm. In the reference group, the incidence density of HAIs was 2.31 per 1000 exposure days. The incidence density was similar in the disinfectant arm 2.21 cases per 1000 exposure days (IRR 0.95; 95% CI 0.69-1.31; p = 0.953) and the probiotic arm 2.21 cases per 1000 exposure days (IRR 0.96; 95% CI 0.69-1.32; p = 0.955).

Interpretation

In non-ICU wards, routine surface disinfection proved not superior to soap-based or probiotic cleaning in terms of HAI prevention. Thus, probiotic cleaning could be an interesting alternative, especially in terms of environmental protection.

Funding

Federal Ministry of Education and Research of Germany (03Z0818C). Bill and Melinda Gates Foundation (INV-004308).

Environmental contamination with highly resistant microorganisms after relocating to a new hospital building with 100% single-occupancy rooms: A prospective observational before-and-after study with a three-year follow-up

INTRODUCTION

Inanimate surfaces within hospitals can be a source of transmission for highly resistant microorganisms (HRMO). While many hospitals are transitioning to single-occupancy rooms, the effect of single-occupancy rooms on environmental contamination is still unknown. We aimed to determine differences in environmental contamination with HRMO between an old hospital building with mainly multiple-occupancy rooms and a new hospital building with 100% single-occupancy rooms, and the environmental contamination in the new hospital building during three years after relocating.

METHODS

Environmental samples were taken twice in the old hospital, and fifteen times over a three-year period in the new hospital. Replicate Organism Direct Agar Contact-plates (RODACs) were used to determine colony forming units (CFU). Cotton swabs premoistened with PBS were used to determine presence of methicillin-resistant Staphylococcus aureus, carbapenemase-producing Pseudomonas aeruginosa, highly resistant Enterobacterales, carbapenem-resistant Acinetobacter baumannii, and vancomycin-resistant Enterococcus faecium. All identified isolates were subjected to whole genome sequencing (WGS) using Illumina technology.

RESULTS

In total, 4993 hospital sites were sampled, 724 in the old and 4269 in the new hospital. CFU counts fluctuated during the follow-up period in the new hospital building, with lower CFU counts observed two- and three years after relocating, which was during the COVID-19 pandemic. The CFU counts in the new building were equal to or surpassed the CFU counts in the old hospital building. In the old hospital building, 24 (3.3%) sample sites were positive for 49 HRMO isolates, compared to five (0.1%) sample sites for seven HRMO isolates in the new building (P < 0.001). In the old hospital, 89.8% of HRMO were identified from the sink plug. In the new hospital, 71.4% of HRMO were identified from the shower drain, and no HRMO were found in sinks.

DISCUSSION

Our results indicate that relocating to a new hospital building with 100% single-occupancy rooms significantly decreases HRMO in the environment. Given that environmental contamination is an important source for healthcare associated infections, this finding should be taken into account when considering hospital designs for renovations or the construction of hospitals.

Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study aimed to profile the complete microbial community and correlate it with the antibiotic compounds identified in microwave pre-treated healthcare wastes collected from three different waste operators in Peninsular Malaysia. The bacterial and fungal compositions were determined via amplicon sequencing by targeting the full-length 16S rRNA gene and partial 18S with full-length ITS1-ITS2 regions, respectively. The antibiotic compounds were characterized using high-throughput spectrometry. There was significant variation in bacterial and fungal composition in three groups of samples, with alpha- (p-value = 0.04) and beta-diversity (p-values <0.006 and < 0.002), respectively. FC samples were found to acquire more pathogenic microorganisms than FA and FV samples. Paenibacillus and unclassified Bacilli genera were shared among three groups of samples, meanwhile, antibiotic-resistant bacteria Proteus mirabilis, Enterococcus faecium, and Enterococcus faecalis were found in modest quantities. A total of 19 antibiotic compounds were discovered and linked with the microbial abundance detected in the healthcare waste samples. The principal component analysis demonstrated a positive antibiotic-bacteria correlation for genera Pseudomonas, Aerococcus, Comamonas, and Vagococcus, while the other bacteria were negatively linked with antibiotics. Nevertheless, deep bioinformatic analysis confirmed the presence of blaTEM-1 and penP which are associated with the production of class A beta-lactamase and beta-lactam resistance pathways. Microorganisms and contaminants, which serve as putative indicators in healthcare waste treatment evaluation revealed the ineffectiveness of microbial inactivation using the microwave sterilization method. Our findings suggested that the occurrence of clinically relevant microorganisms, antibiotic contaminants, and associated antibiotic resistance genes (ARGs) represent environmental and human health hazards when released into landfills via ARGs transmission.

New frontiers in healthcare environmental hygiene: thoughts from the 2022 healthcare cleaning forum

Healthcare environmental hygiene (HEH) has become recognized as being increasingly important for patient safety and the prevention of healthcare-associated infections. At the 2022 Healthcare Cleaning Forum at Interclean in Amsterdam, the academic lectures focused on a series of main areas of interest. These areas are indicative of some of the main trends and avenues for research in the coming years. Both industry and academia need to take steps to continue the momentum of HEH as we transition out of the acute phase of the Covid-19 pandemic. There is a need for new ways to facilitate collaboration between the academic and private sectors. The Clean Hospitals® network was presented in the context of the need for both cross-disciplinarity and evidence-based interventions in HEH. Governmental bodies have also become more involved in the field, and both the German DIN 13603 standard and the UK NHS Cleaning Standards were analyzed and compared. The challenge of environmental pathogens was explored through the example of how P. aeruginosa persists in the healthcare environment. New innovations in HEH were presented, from digitalization to tracking, and automated disinfection to antimicrobial surfaces. The need for sustainability in HEH was also explored, focusing on the burden of waste, the need for a circular economy, and trends towards increasingly local provision of goods and services. The continued focus on and expansion of these areas of HEH will result in safer patient care and contribute to better health systems.

Bisphenol S degradation in soil and the dynamics of microbial community associated with degradation

Bisphenol S (BPS) has been widely applied as a replacement for BPA in industrial application, leading to the frequent detection in the environment. However, its impact on soil microbial communities has not been well reported. Here, effects of BPS exposure on soil microbial communities in the presence of polystyrene (PS) microplastics were revealed. Rapid degradation of BPS occurred with a degradation rate of up to 98.9 ± 0.001 % at 32 d. The presence of BPS reduced the diversity of soil microbial communities, and changed community structures. After BPS treatment, Proteobacteria, and its members Methylobacillus, Rhodobacteraceae and Mesorhizobium became dominant, and were considered as potential biomarkers indicating BPS contamination. Co-occurrence network analysis revealed the increased relationships of certain groups of microbes after BPS treatment. The resultant low stability and resilience towards environment disturbance of microbial community networks implied the biotoxicity of BPS towards soil ecosystems. The degradation and biotoxicity of BPS (p > 0.05) in soil was not affected by the presence of PS. Our findings showed that exposure to BPS could reshape soil microbial communities and impair the robustness of microbial co-occurrence networks.

A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases

Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a "reservoir" of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.

Comparative analysis of surface sanitization protocols on the bacterial community structures in the hospital environment

OBJECTIVES

In hospital hygiene it remains unclear to which extent surface contamination might represent a potential reservoir for nosocomial pathogens. This study investigates the effects of different sanitization strategies on the microbial structures and the ecological balance of the environmental microbiome in the clinical setting.

METHODS

Three cleaning regimes (disinfectants, detergents and probiotics) were applied subsequently in 9 independent patient rooms at a neurological ward (Charité, Berlin). Weekly sampling procedures included 3 different environmental sites: floor, doorhandle and sink. Characterization of the environmental microbiota and detection of antibiotic resistance genes (ARGs) were performed by 16S rRNA sequencing and multiplex Taq-Man qPCR assays, respectively.

RESULTS

Our results showed a displacement of the intrinsic environmental microbiota after probiotic sanitization, which reached statistical significance in the sink samples (Median 16S-rRNA copies = 138.3; IQR: 24.38-379.5) when compared to traditional disinfection measures (Median 16S-rRNA copies = 1343; IQR: 330.9-9479; p<0.05). This effect was concomitant with a significant increase of the alpha-diversity metrics in both the floor (p<0.001) and the sink samples (p<0.01) during the probiotic strategy. We did not observe a sanitization-dependent change of relative pathogen abundance at any tested site, but a significant reduction of the total ARGs counts in the sink samples during probiotic cleaning (mean ARGs/sample: 0.095 ± 0.067) when compared to the disinfection strategy (mean ARGs/sample: 0.386 ± 0.116; p<0.01).

CONCLUSIONS

The data presented in this study suggest the probiotic sanitization as interesting strategy in hospital hygiene management to be further analyzed and validated in randomized clinical studies.