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Chibwe K, Sundararaju S, Zhang L, Tsui C, Tang P, Ling F. Intra-hospital microbiome variability is driven by accessibility and clinical activities. Microbiol Spectr 2024; 12:e0029624. [PMID: 38940596 PMCID: PMC11302010 DOI: 10.1128/spectrum.00296-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024] Open
Abstract
The hospital environmental microbiome, which can affect patients' and healthcare workers' health, is highly variable and the drivers of this variability are not well understood. In this study, we collected 37 surface samples from the neonatal intensive care unit (NICU) in an inpatient hospital before and after the operation began. Additionally, healthcare workers collected 160 surface samples from five additional areas of the hospital. All samples were analyzed using 16S rRNA gene amplicon sequencing, and the samples collected by healthcare workers were cultured. The NICU samples exhibited similar alpha and beta diversities before and after opening, which indicated that the microbiome there was stable over time. Conversely, the diversities of samples taken after opening varied widely by area. Principal coordinate analysis (PCoA) showed the samples clustered into two distinct groups: high alpha diversity [the pediatric intensive care unit (PICU), pathology lab, and microbiology lab] and low alpha diversity [the NICU, pediatric surgery ward, and infection prevention and control (IPAC) office]. Least absolute shrinkage and selection operator (LASSO) classification models identified 156 informative amplicon sequence variants (ASVs) for predicting the sample's area of origin. The testing accuracy ranged from 86.37% to 100%, which outperformed linear and radial support vector machine (SVM) and random forest models. ASVs of genera that contain emerging pathogens were identified in these models. Culture experiments had identified viable species among the samples, including potential antibiotic-resistant bacteria. Though area type differences were not noted in the culture data, the prevalences and relative abundances of genera detected positively correlated with 16S sequencing data. This study brings to light the microbial community temporal and spatial variation within the hospital and the importance of pathogenic and commensal bacteria to understanding dispersal patterns for infection control. IMPORTANCE We sampled surface samples from a newly built inpatient hospital in multiple areas, including areas accessed by only healthcare workers. Our analysis of the neonatal intensive care unit (NICU) showed that the microbiome was stable before and after the operation began, possibly due to access restrictions. Of the high-touch samples taken after opening, areas with high diversity had more potential external seeds (long-term patients and clinical samples), and areas with low diversity and had fewer (short-term or newborn patients). Classification models performed at high accuracy and identified biomarkers that could be used for more targeted surveillance and infection control. Though culturing data yielded viability and antibiotic-resistance information, it disproportionately detected the presence of genera relative to 16S data. This difference reinforces the utility of 16S sequencing in profiling hospital microbiomes. By examining the microbiome over time and in multiple areas, we identified potential drivers of the microbial variation within a hospital.
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Affiliation(s)
- Kaseba Chibwe
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Lin Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Clement Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Singapore
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Fangqiong Ling
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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de Bastiani DC, Silva CV, Christoff AP, Cruz GNF, Tavares LD, de Araújo LSR, Tomazini BM, Arns B, Piastrelli FT, Cavalcanti AB, de Oliveira LFV, Pereira AJ. 16S rRNA amplicon sequencing and antimicrobial resistance profile of intensive care units environment in 41 Brazilian hospitals. Front Public Health 2024; 12:1378413. [PMID: 39076419 PMCID: PMC11284946 DOI: 10.3389/fpubh.2024.1378413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Introduction Infections acquired during healthcare setting stay pose significant public health threats. These infections are known as Healthcare-Associated Infections (HAI), mostly caused by pathogenic bacteria, which exhibit a wide range of antimicrobial resistance. Currently, there is no knowledge about the global cleaning process of hospitals and the bacterial diversity found in ICUs of Brazilian hospitals contributing to HAI. Objective Characterize the microbiome and common antimicrobial resistance genes present in high-touch Intensive Care Unit (ICU) surfaces, and to identify the potential contamination of the sanitizers/processes used to clean hospital surfaces. Methods In this national, multicenter, observational, and prospective cohort, bacterial profiles and several antimicrobial resistance genes from 41 hospitals across 16 Brazilian states were evaluated. Using high-throughput 16S rRNA amplicon sequencing and real-time PCR, the bacterial abundance and resistance genes presence were analyzed in both ICU environments and cleaning products. Results We identified a wide diversity of microbial populations with a recurring presence of HAI-related bacteria among most of the hospitals. The median bacterial positivity rate in surface samples was high (88.24%), varying from 21.62 to 100% in different hospitals. Hospitals with the highest bacterial load in samples were also the ones with highest HAI-related abundances. Streptococcus spp., Corynebacterium spp., Staphylococcus spp., Bacillus spp., Acinetobacter spp., and bacteria from the Flavobacteriaceae family were the microorganisms most found across all hospitals. Despite each hospital particularities in bacterial composition, clustering profiles were found for surfaces and locations in the ICU. Antimicrobial resistance genes mecA, bla KPC-like, bla NDM-like, and bla OXA-23-like were the most frequently detected in surface samples. A wide variety of sanitizers were collected, with 19 different active principles in-use, and 21% of the solutions collected showed viable bacterial growth with antimicrobial resistance genes detected. Conclusion This study demonstrated a diverse and spread pattern of bacteria and antimicrobial resistance genes covering a large part of the national territory in ICU surface samples and in sanitizers solutions. This data should contribute to the adoption of surveillance programs to improve HAI control strategies and demonstrate that large-scale epidemiology studies must be performed to further understand the implications of bacterial contamination in hospital surfaces and sanitizer solutions.
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Affiliation(s)
| | | | | | | | | | | | - Bruno Martins Tomazini
- Hospital Sírio Libanês, São Paulo, SP, Brazil
- Hcor Research Institute, Paraíso, SP, Brazil
| | - Beatriz Arns
- Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
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Fijan S, Kürti P, Rozman U, Šostar Turk S. A critical assessment of microbial-based antimicrobial sanitizing of inanimate surfaces in healthcare settings. Front Microbiol 2024; 15:1412269. [PMID: 38933019 PMCID: PMC11199901 DOI: 10.3389/fmicb.2024.1412269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The global rise in antimicrobial resistance (AMR) poses a significant public health threat, especially in healthcare settings, where controlling the spread of antimicrobial genes is crucial. While person-to-person transmission remains the primary route for healthcare-associated infections (HAIs), hospital surfaces serve as key reservoirs for antimicrobial-resistant microorganisms. Regular cleaning and disinfection of these surfaces are essential. Microbial-based products for sanitizing hospital surfaces have emerged as promising tools to combat HAIs and AMR. However, a review of 32 publications found inconsistencies and potential risks. A total of 15 publications included hospital-based trials, while the rest were either in vitro or in situ assays, reviews, book chapters, or commentaries. In most of the hospital-based studies, specific strains of applied microorganisms were not identified, and the term "probiotic" was inaccurately used. These products mainly featured spores from Bacillus and Priestia genera, which was mainly hypothesized to work through competitive exclusion. Most hospital-based studies have shown that the application of microbial-based products resulted in a significant reduction in pathogens on surfaces, thereby contributing to a decrease in the incidence of healthcare-associated infections (HAIs). Further research is however needed to understand the effectiveness, mechanisms of action, and safety of microbial-based sanitizing agents. Strain-level identification is crucial for safety assessments, yet many reviewed products lacked this information. Consequently, there is a need for rigorous safety evaluations within existing regulatory frameworks to ensure the efficacy and safety of microbial-based cleaning products in healthcare settings.
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Affiliation(s)
- Sabina Fijan
- Faculty of Health Sciences, University of Maribor, Maribor, Slovenia
| | | | - Urška Rozman
- Faculty of Health Sciences, University of Maribor, Maribor, Slovenia
| | - Sonja Šostar Turk
- Faculty of Health Sciences, University of Maribor, Maribor, Slovenia
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Liu J, Zhang X, Zhao Q, Mu X, Yang C, Ning Y, Xiong X, Qin X, Chen L. Effects of oropharyngeal administration of own mother's milk on oral microbial colonization in very low birth weight infants fed by gastric tube: A randomized controlled trial. Immun Inflamm Dis 2024; 12:e1247. [PMID: 38629781 PMCID: PMC11022609 DOI: 10.1002/iid3.1247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/10/2024] [Accepted: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
AIMS The aim of the present study was to explore the effect of oropharyngeal mother's milk administration on oral microbial colonization in infants fed by gastric tube at different time points. METHODS Infants (n = 116) with birth weight <1500 g were randomly allocated into two groups which both received breast milk for enteral nutrition. The control group (n = 51) accepted oropharyngeal normal saline administration. The experimental group (n = 53) accepted oropharyngeal mother's milk administration before fed by gastric tube once every 3 h over 21 days after birth. We analyzed the oral microbiota at initiation and 7 and 14 and 21 days later using 16S DNA amplicon sequencing. RESULTS There were no difference in oral microbial diversity between the two groups at any time point, but diversity decreased significantly over time in both groups. On the first day of life, the oral microbiota of the infant in the experimental and control groups consisted mainly of Firmicutes (7.75%, 6.18%) and Proteobacteria (68.65%, 68.69%), respectively. As time increases to 21 days after birth, Firmicutes (77.67%, 77.66%) had replaced Proteobacteria (68.65%, 68.69%) as the predominant phylum. DISCUSSION From birth to 21 days after birth, oropharyngeal mother's milk administration did not change the diversity and structural composition of the oral microbiota. The oral microbial diversity of infants declined significantly over time. Firmicutes had replaced Proteobacteria as the predominant phylum.
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Affiliation(s)
- Jie Liu
- Department of Traditional Chinese Medicine Gynecology, Pediatric Neurorehabilitation Department, Department of NeonatologyShenzhen Maternity and Child Healthcare HospitalShenzhenChina
| | - Xiyang Zhang
- Department of Traditional Chinese Medicine Gynecology, Pediatric Neurorehabilitation Department, Department of NeonatologyShenzhen Maternity and Child Healthcare HospitalShenzhenChina
| | - Qian Zhao
- School of NursingShanxi University of Chinese MedicineTaiyuanShanxiChina
| | - Xiaohe Mu
- Department of Critical care medicineShaanxi Province Kangfu HospitalXi'anChina
| | - Chuanzhong Yang
- Department of Traditional Chinese Medicine Gynecology, Pediatric Neurorehabilitation Department, Department of NeonatologyShenzhen Maternity and Child Healthcare HospitalShenzhenChina
| | - Yan Ning
- Department of Traditional Chinese Medicine Gynecology, Pediatric Neurorehabilitation Department, Department of NeonatologyShenzhen Maternity and Child Healthcare HospitalShenzhenChina
| | - Xiaoyun Xiong
- Department of Traditional Chinese Medicine Gynecology, Pediatric Neurorehabilitation Department, Department of NeonatologyShenzhen Maternity and Child Healthcare HospitalShenzhenChina
| | - Xiaoling Qin
- Department of Traditional Chinese Medicine Gynecology, Pediatric Neurorehabilitation Department, Department of NeonatologyShenzhen Maternity and Child Healthcare HospitalShenzhenChina
| | - Lilian Chen
- Department of Traditional Chinese Medicine Gynecology, Pediatric Neurorehabilitation Department, Department of NeonatologyShenzhen Maternity and Child Healthcare HospitalShenzhenChina
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Spagnolo AM. Bacterial Infections: Surveillance, Prevention and Control. Pathogens 2024; 13:181. [PMID: 38392919 PMCID: PMC10892593 DOI: 10.3390/pathogens13020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Bacteria play a vital role in maintaining human health, but they may also be responsible for many different serious infections and diseases [...].
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Affiliation(s)
- Anna Maria Spagnolo
- Department of Health Sciences, University of Genova, Via Pastore 1, 16132 Genova, Italy
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Nyantakyi E, Caci L, Castro M, Schlaeppi C, Cook A, Albers B, Walder J, Metsvaht T, Bielicki J, Dramowski A, Schultes MT, Clack L. Implementation of infection prevention and control for hospitalized neonates: A narrative review. Clin Microbiol Infect 2024; 30:44-50. [PMID: 36414203 DOI: 10.1016/j.cmi.2022.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/04/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND The most prevalent infections encountered in neonatal care are healthcare-associated infections. The majority of healthcare-associated infections are considered preventable with evidence-based infection prevention and control (IPC) practices. However, substantial knowledge gaps exist in IPC implementation in neonatal care. Furthermore, the knowledge of factors which facilitate or challenge the uptake and sustainment of IPC programmes in neonatal units is limited. The integration of implementation science approaches in IPC programmes in neonatal care aims to address these problems. OBJECTIVES The aim of this narrative review was to identify determinants which have been reported to influence the implementation of IPC programmes and best practices in inpatient neonatal care settings. SOURCES A literature search was conducted in PubMed, MEDLINE (Medical Literature Analysis and Retrieval System Online) and CINAHL (Cumulative Index to Nursing and Allied Health Literature) in May 2022. Primary study reports published in English, French, German, Spanish, Portuguese, Italian, Danish, Swedish or Norwegian since 2000 were eligible for inclusion. Included studies focused on IPC practices in inpatient neonatal care settings and reported determinants which influenced implementation processes. CONTENT The Consolidated Framework for Implementation Research was used to identify and cluster reported determinants to the implementation of IPC practices and programmes in neonatal care. Most studies reported challenges and facilitators at the organizational level as particularly relevant to implementation processes. The commonly reported determinants included staffing levels, work- and caseloads, as well as aspects of organizational culture such as communication and leadership. IMPLICATIONS The presented knowledge about factors influencing neonatal IPC can support the design, implementation, and evaluation of IPC practices.
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Affiliation(s)
- Emanuela Nyantakyi
- Institute for Implementation Science in Health Care, Medical Faculty, University of Zurich, Zurich, Switzerland.
| | - Laura Caci
- Institute for Implementation Science in Health Care, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Marta Castro
- Neonatal Intensive Care Unit, University Children's Hospital, Basel, Switzerland
| | - Chloé Schlaeppi
- Paediatric Infectious Diseases and Vaccinology, University Children's Hospital, Basel, Switzerland
| | - Aislinn Cook
- Centre for Neonatal and Paediatric Infection, St. George's, University of London, London, United Kingdom
| | - Bianca Albers
- Institute for Implementation Science in Health Care, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Joel Walder
- Institute for Implementation Science in Health Care, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Tuuli Metsvaht
- Department of Paediatrics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Julia Bielicki
- Paediatric Infectious Diseases and Vaccinology, University Children's Hospital, Basel, Switzerland; Centre for Neonatal and Paediatric Infection, St. George's, University of London, London, United Kingdom
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marie-Therese Schultes
- Institute for Implementation Science in Health Care, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Lauren Clack
- Institute for Implementation Science in Health Care, Medical Faculty, University of Zurich, Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
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7
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Kelly SA, O'Connell NH, Thompson TP, Dillon L, Wu J, Creevey C, Kiely P, Slevin B, Powell J, Gilmore BF, Dunne CP. Large-scale characterization of hospital wastewater system microbiomes and clinical isolates from infected patients: profiling of multi-drug-resistant microbial species. J Hosp Infect 2023; 141:152-166. [PMID: 37696473 DOI: 10.1016/j.jhin.2023.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND Hospital-acquired infections (HAIs) and infectious agents exhibiting antimicrobial resistance (AMR) are challenges globally. Environmental patient-facing wastewater apparatus including handwashing sinks, showers and toilets are increasingly identified as sources of infectious agents and AMR genes. AIM To provide large-scale metagenomics analysis of wastewater systems in a large teaching hospital in the Republic of Ireland experiencing multi-drug-resistant HAI outbreaks. METHODS Wastewater pipe sections (N=20) were removed immediately prior to refurbishment of a medical ward where HAIs had been endemic. These comprised toilet U-bends, and sink and shower drains. Following DNA extraction, each pipe section underwent metagenomic analysis. FINDINGS Diverse taxonomic and resistome profiles were observed, with members of phyla Proteobacteria and Actinobacteria dominating (38.23 ± 5.68% and 15.78 ± 3.53%, respectively). Genomes of five clinical isolates were analysed. These AMR bacterial isolates were from patients >48 h post-admission to the ward. Genomic analysis determined that the isolates bore a high number of antimicrobial resistance genes (ARGs). CONCLUSION Comparison of resistome profiles of isolates and wastewater metagenomes revealed high degrees of similarity, with many identical ARGs shared, suggesting probable acquisition post-admission. The highest numbers of ARGs observed were those encoding resistance to clinically significant and commonly used antibiotic classes. Average nucleotide identity analysis confirmed the presence of highly similar or identical genomes in clinical isolates and wastewater pipes. These unique large-scale analyses reinforce the need for regular cleaning and decontamination of patient-facing hospital wastewater pipes and effective infection control policies to prevent transmission of nosocomial infection and emergence of AMR within potential wastewater reservoirs.
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Affiliation(s)
- S A Kelly
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - N H O'Connell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland; School of Medicine and Centre for Interventions in Infection, Inflammation and Immunity (4i), University of Limerick, Limerick, Ireland
| | - T P Thompson
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - L Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - J Wu
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - C Creevey
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - P Kiely
- School of Medicine and Centre for Interventions in Infection, Inflammation and Immunity (4i), University of Limerick, Limerick, Ireland
| | - B Slevin
- Department of Infection Prevention and Control, University Hospital Limerick, Limerick, Ireland
| | - J Powell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland; School of Medicine and Centre for Interventions in Infection, Inflammation and Immunity (4i), University of Limerick, Limerick, Ireland
| | - B F Gilmore
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - C P Dunne
- School of Medicine and Centre for Interventions in Infection, Inflammation and Immunity (4i), University of Limerick, Limerick, Ireland.
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8
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Yang J, Li L, Zhu X, He C, Li T, Qin J, Wang Y. Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS. Infect Drug Resist 2023; 16:5121-5134. [PMID: 37576519 PMCID: PMC10422961 DOI: 10.2147/idr.s421702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023] Open
Abstract
Background Surface pathogens in the ICU pose a global public health threat, especially to elderly patients who are immunocompromised. To detect these pathogens, unbiased methods such as metagenomic next-generation sequencing (mNGS) are increasingly utilized for environmental microbiological surveillance. Methods In a six-month study from January to July 2022, we investigated microbial communities in Chinese geriatric ICUs by regularly monitoring multiple surfaces at three-month intervals. Using mNGS sequencing, we analyzed microorganisms present at eight specific locations within the ICU. Additionally, we compared pathogen profiles and drug resistance genes between patient cultures and environmental samples collected during the same period. Results The microbial composition remained relatively stable over time, but significant differences in alpha diversities were observed among various surfaces such as floors, hands, pumps, trolleys, and ventilator inlets/outlets. Surfaces with high contact frequency for healthcare workers, including workstations, ventilator panels, trolleys, pumps, and beds, harbored pathogenic microorganisms such as Acinetobacter baumannii, Cutibacterium acnes, Staphylococcus haemolyticus, Pseudomonas aeruginosa, and Enterococcus faecium. Acinetobacter baumannii, particularly the carbapenem-resistant strain (CRAB), was the most frequently identified pathogen in geriatric ICU patients regardless of testing method used. The mNGS approach enabled detection of viruses, fungi, and parasites that are challenging to culture. Additionally, an abundance of drug resistance genes was found in almost all environmental samples. Conclusion The microbial composition and abundance in the ICU remained relatively constant over time. The floor exhibited the highest microbial diversity and abundance in the ICU environment. Drug-resistant genes in the ICU environment may migrate between patients. Overall, mNGS is an emerging and powerful tool for microbiological monitoring of the hospital environment.
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Affiliation(s)
- Jilin Yang
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Lingyi Li
- Department of Medical, Hangzhou Matridx Biotechnology Company, Hangzhou, People’s Republic of China
| | - Xiaolin Zhu
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Chen He
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Ting Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Jiahong Qin
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Yijie Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
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9
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Hu J, Shuai W, Sumner JT, Moghadam AA, Hartmann EM. Clinically relevant pathogens on surfaces display differences in survival and transcriptomic response in relation to probiotic and traditional cleaning strategies. NPJ Biofilms Microbiomes 2022; 8:72. [PMID: 36123373 PMCID: PMC9485146 DOI: 10.1038/s41522-022-00335-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/02/2022] [Indexed: 02/05/2023] Open
Abstract
Indoor surfaces are paradoxically presumed to be both colonized by pathogens, necessitating disinfection, and "microbial wastelands." In these resource-poor, dry environments, competition and decay are thought to be important drivers of microbial community composition. However, the relative contributions of these two processes have not been specifically evaluated. To bridge this knowledge gap, we used microcosms to evaluate whether interspecies interactions occur on surfaces. We combined transcriptomics and traditional microbiology techniques to investigate whether competition occurred between two clinically important pathogens, Acinetobacter baumannii and Klebsiella pneumoniae, and a probiotic cleaner containing a consortium of Bacillus species. Probiotic cleaning seeks to take advantage of ecological principles such as competitive exclusion, thus using benign microorganisms to inhibit viable pathogens, but there is limited evidence that competitive exclusion in fact occurs in environments of interest (i.e., indoor surfaces). Our results indicate that competition in this setting has a negligible impact on community composition but may influence the functions expressed by active organisms. Although Bacillus spp. remained viable on surfaces for an extended period of time after application, viable colony forming units (CFUs) of A. baumannii recovered following exposure to a chemical-based detergent with and without Bacillus spp. showed no statistical difference. Similarly, for K. pneumoniae, there were small statistical differences in CFUs between cleaning scenarios with or without Bacillus spp. in the chemical-based detergent. The transcriptome of A. baumannii with and without Bacillus spp. exposure shared a high degree of similarity in overall gene expression, but the transcriptome of K. pneumoniae differed in overall gene expression, including reduced response in genes related to antimicrobial resistance. Together, these results highlight the need to fully understand the underlying biological and ecological mechanisms for community assembly and function on indoor surfaces, as well as having practical implications for cleaning and disinfection strategies for infection prevention.
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Affiliation(s)
- Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Weitao Shuai
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jack T Sumner
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Anahid A Moghadam
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
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Kaushik S, Thomas J, Panwar V, Murugesan P, Chopra V, Salaria N, Singh R, Roy HS, Kumar R, Gautam V, Ghosh D. A drug-free strategy to combat bacterial infections with magnetic nanoparticles biosynthesized in bacterial pathogens. NANOSCALE 2022; 14:1713-1722. [PMID: 35072191 DOI: 10.1039/d1nr07435k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The extensive and indiscriminate use of antibiotics in the ongoing COVID-19 pandemic might significantly contribute to the growing number of multiple drug resistant (MDR) bacteria. With the dwindling pipeline of new and effective antibiotics, we might soon end up in a post-antibiotic era, in which even common bacterial infections would be a challenge to control. To prevent this, an antibiotic-free strategy would be highly desirable. Magnetic nanoparticle (MNP)-mediated hyperthermia-induced antimicrobial therapy is an attractive option as it is considered safe for human use. Given that iron and zinc are critical for bacterial virulence, we evaluated the response of multiple pathogenic bacteria to these elements. Treatment with 1 mM iron and zinc precursors resulted in the intracellular biosynthesis of MNPs in multiple Gram-positive and Gram-negative disease-causing bacteria. The superparamagnetic nanoparticles in the treated bacteria/biofilms, generated heat upon exposure to an alternating magnetic field (AMF), which resulted in an increase in the temperature (5-6 °C) of the milieu with a subsequent decrease in bacterial viability. Furthermore, we observed for the first time that virulent bacteria derived from infected samples harbour MNPs, suggesting that the bacteria had biosynthesised the MNPs using the metal ions acquired from the host. AMF treatment of the bacterial isolates from the infected specimens resulted in a strong reduction in viability (3-4 logs) as compared to vancomycin/ciprofloxacin treatment. The therapeutic efficacy of the MNPs to induce bacterial death with AMF alone was confirmed ex vivo using infected tissues. Our proposed antibiotic-free approach for killing bacteria using intracellular MNPs is likely to evolve as a promising strategy to combat a wide range of bacterial infections.
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Affiliation(s)
- Swati Kaushik
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Jijo Thomas
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Vineeta Panwar
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Preethi Murugesan
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Vianni Chopra
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Navita Salaria
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Rupali Singh
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Himadri Shekar Roy
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Rajesh Kumar
- Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Vikas Gautam
- Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Deepa Ghosh
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
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Yen NTP, Nhung NT, Phu DH, Dung NTT, Van NTB, Kiet BT, Hien VB, Larsson M, Olson L, Campbell J, Quynh NPN, Duy PT, Carrique-Mas J. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac038. [PMID: 35449721 PMCID: PMC9018397 DOI: 10.1093/jacamr/dlac038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/13/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Nguyen Thi Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Doan Hoang Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
| | | | | | - Bach Tuan Kiet
- Sub-Department of Animal Health and Production, Dong Thap, Vietnam
| | - Vo Be Hien
- Sub-Department of Animal Health and Production, Dong Thap, Vietnam
| | - Mattias Larsson
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - Linus Olson
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - James Campbell
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, UK
| | | | - Pham Thanh Duy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, UK
- Corresponding author. E-mail:
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Sereia AFR, Christoff AP, Cruz GNF, da Cunha PA, da Cruz GCK, Tartari DC, Zamparette CP, Klein TCR, Masukawa II, Silva CI, E Vieira MLV, Scheffer MC, de Oliveira LFV, Sincero TCM, Grisard EC. Healthcare-Associated Infections-Related Bacteriome and Antimicrobial Resistance Profiling: Assessing Contamination Hotspots in a Developing Country Public Hospital. Front Microbiol 2021; 12:711471. [PMID: 34484149 PMCID: PMC8415557 DOI: 10.3389/fmicb.2021.711471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
Hospital-built environment colonization by healthcare-associated infections-related bacteria (HAIrB) and the interaction with their occupants have been studied to support more effective tools for HAI control. To investigate HAIrB dynamics and antimicrobial resistance (AMR) profile we carried out a 6-month surveillance program in a developing country public hospital, targeting patients, hospital environment, and healthcare workers, using culture-dependent and culture-independent 16S rRNA gene sequencing methods. The bacterial abundance in both approaches shows that the HAIrB group has important representativeness, with the taxa Enterobacteriaceae, Pseudomonas, Staphylococcus, E. coli, and A. baumannii widely dispersed and abundant over the time at the five different hospital units included in the survey. We observed a high abundance of HAIrB in the patient rectum, hands, and nasal sites. In the healthcare workers, the HAIrB distribution was similar for the hands, protective clothing, and mobile phones. In the hospital environment, the healthcare workers resting areas, bathrooms, and bed equipment presented a wide distribution of HAIrB and AMR, being classified as contamination hotspots. AMR is highest in patients, followed by the environment and healthcare workers. The most frequently detected beta-lactamases genes were, blaSHV–like, blaOXA–23–like, blaOXA–51–like, blaKPC–like, blaCTX–M–1, blaCTX–M–8, and blaCTX–M–9 groups. Our results demonstrate that there is a wide spread of antimicrobial resistance due to HAIrB in the hospital environment, circulating among patients and healthcare workers. The contamination hotspots identified proved to be constant over time. In the fight for patient safety, these findings can reorient practices and help to set up new guidelines for HAI control.
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Affiliation(s)
- Aline Fernanda Rodrigues Sereia
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil.,BiomeHub, Florianópolis, Brazil
| | | | | | - Patrícia Amorim da Cunha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | | | - Caetana Paes Zamparette
- Department of Clinical Analysis, Federal University of Santa Catarina, Florianopólis, Brazil
| | - Taise Costa Ribeiro Klein
- Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Ivete Ioshiko Masukawa
- Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Clarice Iomara Silva
- Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Maria Luiza Vieira E Vieira
- Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Mara Cristina Scheffer
- Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | | | - Edmundo Carlos Grisard
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
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Contamination of antimicrobial-resistant bacteria on toothbrushes used with mechanically ventilated patients: A cross sectional study. Intensive Crit Care Nurs 2021; 68:103120. [PMID: 34391630 DOI: 10.1016/j.iccn.2021.103120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/20/2022]
Abstract
OBJECTIVE The purpose of this study was to determine pathogenic and antimicrobial-resistant bacteria on used toothbrushes of mechanically ventilated patients. RESEARCH METHODOLOGY A cross-sectional study was conducted by collecting toothbrushes used with mechanically ventilated patients. The total bacterial count on each toothbrush was assessed by culturing on Trypticase soy agar (TSA). Gram stain and biochemical testing were used to identify bacterial species. Antibiotic susceptibility of pathogenic bacteria was assessed by the Kirby-Bauer disk diffusion method. RESULTS Thirty-five toothbrushes (97%) had bacterial contamination, 27 toothbrushes had at least two bacterial species, and 13 toothbrushes harboured antimicrobial-resistant bacteria. The most commonly isolated bacteria were Klebsiella spp. (21%), followed by Acinetobacter baumannii (18%). Five isolates of A. baumannii, six isolates of K. pneumoniae, and two isolates of Enterobacter cloacae were multidrug-resistant (MDR) strains. Four isolates of K. pneumoniae were identified as extended-spectrum beta-lactamase (ESBL) producing strains, and two isolates of P. aeruginosa were extensively drug-resistant (XDR). The average total bacterial count was 104-105 CFU/toothbrush head. CONCLUSIONS Antimicrobial-resistant bacteria were detected on toothbrushes. Therefore, practice of toothbrush care should be reconsidered in associated to maintaining the oral hygiene of mechanically ventilated patients to prevent ventilator-associated pneumonia (VAP).
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Ventilation-Associated Particulate Matter Is a Potential Reservoir of Multidrug-Resistant Organisms in Health Facilities. Life (Basel) 2021; 11:life11070639. [PMID: 34209235 PMCID: PMC8307074 DOI: 10.3390/life11070639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/14/2021] [Accepted: 06/29/2021] [Indexed: 02/03/2023] Open
Abstract
Most healthcare-associated infections (HCAIs) develop due to the colonisation of patients and healthcare workers by multidrug-resistant organisms (MDRO). Here, we investigated whether the particulate matter from the ventilation systems (Vent-PM) of health facilities can harbour MDRO and other microbes, thereby acting as a potential reservoir of HCAIs. Dust samples collected in the ventilation grilles and adjacent air ducts underwent a detailed analysis of physicochemical properties and biodiversity. All Vent-PM samples included ultrafine PM capable of reaching the alveoli. Strikingly, >70% of Vent-PM samples were contaminated, mostly by viruses (>15%) or multidrug-resistant and biofilm-producing bacterial strains (60% and 48% of all bacteria-contaminated specimens, respectively). Total viable count at 1 m from the ventilation grilles was significantly increased after opening doors and windows, indicating an association between air flow and bacterial contamination. Both chemical and microbial compositions of Vent-PM considerably differed across surgical vs. non-surgical and intensive vs. elective care units and between health facilities located in coal and chemical districts. Reduced diversity among MDRO and increased prevalence ratio in multidrug-resistant to the total Enterococcus spp. in Vent-PM testified to the evolving antibiotic resistance. In conclusion, we suggest Vent-PM as a previously underestimated reservoir of HCAI-causing pathogens in the hospital environment.
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Ndu I, Asinobi I, Ekwochi U, Edelu B, Iheji C, Onu N. Bacterial isolates of surfaces in the neonatal intensive care unit of Enugu State university teaching hospital, Parklane, Enugu, and their antibiotic susceptibility patterns. NIGERIAN JOURNAL OF MEDICINE 2021. [DOI: 10.4103/njm.njm_157_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Draft Genome Sequences of Lactobacillales Isolated from the International Space Station. Microbiol Resour Announc 2020; 9:9/39/e00942-20. [PMID: 32972947 PMCID: PMC7516158 DOI: 10.1128/mra.00942-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nineteen strains from the order Lactobacillales were isolated from the International Space Station and commercial resupply vehicle, and whole-genome sequences (WGS) were generated. WGS would permit the characterization of these potentially pathogenic bacteria that have been adapting to the extreme conditions of the space environment. Nineteen strains from the order Lactobacillales were isolated from the International Space Station and commercial resupply vehicle, and whole-genome sequences (WGS) were generated. WGS would permit the characterization of these potentially pathogenic bacteria that have been adapting to the extreme conditions of the space environment.
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Draft Genome Sequences of Enterobacteriales Strains Isolated from the International Space Station. Microbiol Resour Announc 2020; 9:9/37/e00817-20. [PMID: 32912916 PMCID: PMC7484075 DOI: 10.1128/mra.00817-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The whole-genome sequences of 26 strains isolated from the International Space Station were generated, and the strains were identified as being members of the order Enterobacteriales. Characterization of these whole-genome sequences might enable the identification of potential pathogenic bacteria that have been adapting to the space environment.
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