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Nkemngong C, Teska P. Biofilms, mobile genetic elements and the persistence of pathogens on environmental surfaces in healthcare and food processing environments. Front Microbiol 2024; 15:1405428. [PMID: 38894974 PMCID: PMC11183103 DOI: 10.3389/fmicb.2024.1405428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
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.
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Affiliation(s)
| | - Peter Teska
- Diversey-A Solenis Company, Fort Mill, SC, United States
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2
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Emelyanenko AM, Omran FS, Teplonogova MA, Chernukha MY, Avetisyan LR, Tselikina EG, Putsman GA, Zyryanov SK, Butranova OI, Emelyanenko KA, Boinovich LB. An Antimicrobial Copper-Plastic Composite Coating: Characterization and In Situ Study in a Hospital Environment. Int J Mol Sci 2024; 25:4471. [PMID: 38674057 PMCID: PMC11050275 DOI: 10.3390/ijms25084471] [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: 03/25/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
A method has been proposed for creating an operationally durable copper coating with antimicrobial properties for the buttons of electrical switches based on the gas dynamic spray deposition of copper on acrylonitrile butadiene styrene (ABS) plastic. It is shown that during the coating process, a polymer film is formed on top of the copper layer. Comparative in situ studies of microbial contamination have shown that the copper-coated buttons have a significant antimicrobial effect compared to standard buttons. Analysis of swabs over a 22-week study in a hospital environment showed that the frequency of contamination for a copper-coated button with various microorganisms was 2.7 times lower than that of a control button. The presented results allow us to consider the developed copper coating for plastic switches an effective alternative method in the fight against healthcare-associated infections.
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Affiliation(s)
- Alexandre M. Emelyanenko
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
| | - Fadi S. Omran
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
| | - Maria A. Teplonogova
- N. S. Kurnakov Institute of General and Inorganic Chemistry, Leninsky Prospect 31, 119071 Moscow, Russia;
| | - Marina Y. Chernukha
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
- Department of Medical Microbiology, Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 18 Gamaleya St., 123098 Moscow, Russia;
| | - Lusine R. Avetisyan
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
- Department of Medical Microbiology, Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 18 Gamaleya St., 123098 Moscow, Russia;
| | - Eugenia G. Tselikina
- Department of Medical Microbiology, Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 18 Gamaleya St., 123098 Moscow, Russia;
| | - Gleb A. Putsman
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
- City Clinical Hospital No. 24, Moscow City Health Department, 10 Pistsovaya St., 127015 Moscow, Russia
| | - Sergey K. Zyryanov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
- Department of General and Clinical Pharmacology, Institute of Medicine, Peoples’ Friendship University of Russia named after Patrice Lumumba, 6 Miklukho-Maklaya St. 117198 Moscow, Russia
| | - Olga I. Butranova
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
- Department of General and Clinical Pharmacology, Institute of Medicine, Peoples’ Friendship University of Russia named after Patrice Lumumba, 6 Miklukho-Maklaya St. 117198 Moscow, Russia
| | - Kirill A. Emelyanenko
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
| | - Ludmila B. Boinovich
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospect 31, 119071 Moscow, Russia; (F.S.O.); (M.Y.C.); (L.R.A.); (G.A.P.); (S.K.Z.); (O.I.B.); (K.A.E.)
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Marcondes MA, Pessôa R, José da Silva Duarte A, Clissa PB, Sanabani SS. Temporal patterns of bacterial communities in the Billings Reservoir system. Sci Rep 2024; 14:2062. [PMID: 38267511 PMCID: PMC10808195 DOI: 10.1038/s41598-024-52432-6] [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: 08/29/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO4-2), phosphate (P), ammonia (NH3), and nitrate (NO3-) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH3 are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.
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Affiliation(s)
- Marta Angela Marcondes
- Post-Graduation Program in Translational Medicine, Department of Medicine, Federal University of São Paulo, São Paulo, 04021-001, Brazil
| | - Rodrigo Pessôa
- Post-Graduation Program in Translational Medicine, Department of Medicine, Federal University of São Paulo, São Paulo, 04021-001, Brazil
| | - Alberto José da Silva Duarte
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology LIM 56, Faculty of Medicine, University of São Paulo, São Paulo, 05403-000, Brazil
| | | | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation 03 (LIM03), Clinics Hospital, Faculty of Medicine, University of São Paulo, São Paulo, 05403-000, Brazil.
- Laboratory of Dermatology and Immunodeficiency, LIM56/03, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3º Andar, São Paulo, 05403 000, Brazil.
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4
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Sah GP, Kovalick G, Chopyk J, Kuo P, Huang L, Ghatbale P, Das P, Realegeno S, Knight R, Gilbert JA, Pride DT. Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic. Microbiol Spectr 2023; 11:e0450922. [PMID: 36916973 PMCID: PMC10100919 DOI: 10.1128/spectrum.04509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/11/2023] [Indexed: 03/15/2023] Open
Abstract
The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.
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Affiliation(s)
- Govind Prasad Sah
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Grace Kovalick
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Jessica Chopyk
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Lina Huang
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Promi Das
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
| | - Susan Realegeno
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Scripps Institution of Oceanography and Department of Pediatrics, University of California San Diego, San Diego, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, San Diego, California, USA
- Department of Medicine, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
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Li H, Zhou SYD, Neilson R, An XL, Su JQ. Skin microbiota interact with microbes on office surfaces. ENVIRONMENT INTERNATIONAL 2022; 168:107493. [PMID: 36063613 DOI: 10.1016/j.envint.2022.107493] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized the bacterial and fungal communities from various sources typical of a working office environment including dust, fingers, and computer keyboards and mice. The composition of the dust bacterial community was significantly different from the other tested surfaces (P < 0.05), whereas the dust fungal community was only significantly different from fingers (P < 0.05). Bacterial and fungal communities were both shaped by deterministic processes, and bacterial communities had a higher migration rate. Results of a network analysis showed that the microbial community interactions of keyboards and mice were mainly competitive. Fast expectation-maximization microbial source tracking (FEAST) identified the sources of > 70 % of the keyboard and mouse microbial communities. Biomarkers for each sample types were identified by LDA Effect Size (LEfSE) analysis, some of which were soil-derived and potential anthropogenic pathogens, indicating the potential for exchange of microbes among outdoor, human and indoor surfaces. The current study shows that the source of microorganisms at the office interface is highly traceable and that their migration is linked to human activity. The migration of potentially pathogenic microbes were identified, emphasising the importance of personal hygiene.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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Characterization of Bacterial Communities from the Surface and Adjacent Bottom Layers of Water in the Billings Reservoir. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081280. [PMID: 36013459 PMCID: PMC9409723 DOI: 10.3390/life12081280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]
Abstract
Here, we describe the bacterial diversity and physicochemical properties in freshwater samples from the surface and bottom layers of the Billings Reservoir, the largest open-air storage ecosystem in the São Paulo (Brazil) metropolitan area. Forty-four samples (22 from the surface and 22 from the bottom layers) were characterized based on 16S rRNA gene analysis using Illumina MiSeq. Taxonomical composition revealed an abundance of the Cyanobacteria phylum, followed by Proteobacteria, which were grouped into 1903 and 2689 different genera in the surface and the deep-water layers, respectively. Chroobacteria, Actinobacteria, Betaproteobacteria, and Alphaproteobacteria were the most dominant classes. The Shannon diversity index was in the range of 2.3–5.39 and 4.04–6.86 in the surface and bottom layers, respectively. Flavobacterium was the most predominant pathogenic genus. Temperature and phosphorus concentrations were among the most influential factors in shaping the microbial communities of both layers. Predictive functional analysis suggests that the reservoir is enriched in motility genes involved in flagellar assembly. The overall results provide new information on the diversity composition, ecological function, and health risks of the bacterial community detected in the Billings freshwater reservoir. The broad bacterial diversity indicates that the bacterioplankton communities in the reservoir were involved in multiple essential environmental processes.
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Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia. Pharmaceuticals (Basel) 2022; 15:ph15050611. [PMID: 35631436 PMCID: PMC9145440 DOI: 10.3390/ph15050611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
The escalating transmission of hospital-acquired infections, especially those due to antimicrobial-resistant bacteria, is a major health challenge worldwide. In this study, a culturomic analysis of bacterial community in a tertiary care hospital in the western region of Saudi Arabia is performed using environmental samples. The genome sequencing of four Acinetobacter baumannii was performed on isolates recovered from an intensive care unit (ICU) environment and clinical samples. A total of 361 bacterial isolates from surface and air samples were identified by MALDI-TOF technique or 16S rRNA gene sequencing. The isolates were classified into 70 distinct species, including ESKAPE pathogens. Resistance in Gram-positive isolates was mainly found to be against benzylpenicillin, azithromycin, ampicillin, and trimethoprim/sulfamethoxazole. Carbapenem- and multidrug-resistant isolates of A. baumannii and Klebsiella pneumonia were found on the ICU surfaces. Genome sequencing revealed that the carbapenem-resistant A. baumannii isolate from ICU environment was linked with those of clinical origin. The isolate Ab133-HEnv was classified as a novel sequence type (ST2528) based on a new allele of Oxf_gdhB-286. Three beta-lactam-antibiotic-resistance genes, blaADC-25, blaOXA-23, and blaOXA-66, were found in most of the analyzed genomes. Collectively, the results of this study highlight the spread of antimicrobial-resistant nosocomial pathogens in a health care facility in Saudi Arabia.
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A new class of antimicrobial molecules derived from kefir, effective against Pseudomonas aeruginosa and methicillin resistant Staphylococcus aureus (MRSA) strains. Sci Rep 2020; 10:17434. [PMID: 33060654 PMCID: PMC7566650 DOI: 10.1038/s41598-020-73651-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/18/2020] [Indexed: 11/10/2022] Open
Abstract
Many studies have linked the antimicrobial properties of kefir with the presence of bacteriocins and organic acids. In the present work, results obtained from bacteriostatic and bactericidal studies, and from RP-HPLC, Mass Spectrometry and proton NMR analysis, show that a sample of milk kefir grains is able to produce an antimicrobial fraction, denoted FK-1000, composed of sugars and amino acids, predominantly polymers of alanine, doublets of tyrosine and phenylalanine. Since this fraction is a lyophilized product whose molecular profile is different from bacteriocins and simple carboxylic acids, its antimicrobial effect cannot be attributed to these molecules, or to alcohols or hydrogen peroxide. The fraction is bactericidal against weak-acid-resistant MRSA and weak-acid resistant P. aeruginosa at pH 5, and is bacteriostatic against both pathogens at pH 7. In combination formulation, the FK-1000 fraction is able to increase fivefold the effect of streptomycin against P. aeruginosa and it is not toxic to human epithelial cells at antimicrobial concentrations. 16 S rRNA microbiota analysis of antimicrobial-producing and non-producing kefir grains demonstrated that they are distinct. In summary, the results indicate that milk kefir grains can produce different classes of molecules with potent antibiotic activity against resistant bacteria.
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Bacterial community composition and potential pathogens along the Pinheiros River in the southeast of Brazil. Sci Rep 2020; 10:9331. [PMID: 32518363 PMCID: PMC7283273 DOI: 10.1038/s41598-020-66386-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 05/07/2020] [Indexed: 11/08/2022] Open
Abstract
The Pinheiros River in São Paulo, Brazil, crosses through the capital city and has its confluence with the River Tiete, which comprises several reservoirs along its course. Although Pinheiros River is considered one of the heaviest polluted rivers in Brazil, little is known about its bacterial composition, their metabolic functions or how these communities are affected by the physicochemical parameters of the river. In this study, we used the 16S rRNA gene Illumina MiSeq sequencing to profile the bacterial community from the water surface at 11 points along the course of the River. Taxonomical composition revealed an abundance of Proteobacteria phyla, followed by Firmicutes and Bacteroidetes, with a total of 233 classified bacterial families and 558 known bacterial genera. Among the 35 potentially pathogenic bacteria identified, Arcobacter was the most predominant genus. The disrupted physicochemical parameters detected in this study may possibly contribute to the composition and distribution of the bacterial community in the Pinheiros River. Predictive functional analysis suggests the River is abundant in motility genes, including bacterial chemotaxis and flagellar assembly. These results provide novel and detailed insights into the bacterial communities and putative function of the surface water in the Pinheiros River.
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Hansen S, Pessôa R, Nascimento A, El-Tholoth M, Abd El Wahed A, Sanabani SS. Dataset of the microbiome composition in skin lesions caused by lumpy skin disease virus via 16s rRNA massive parallel sequencing. Data Brief 2019; 27:104764. [PMID: 31763412 PMCID: PMC6864129 DOI: 10.1016/j.dib.2019.104764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/22/2019] [Accepted: 10/30/2019] [Indexed: 12/04/2022] Open
Abstract
Lumpy Skin Disease (LSD) is a highly contagious viral disease affecting cattle mainly and induced by the Lumpy Skin Virus within the Capripoxvirus genus of the family Poxviridae. LSD infected animals exhibit pyrexia and sudden appearance of localized or generalized skin nodules that may slough leaving ulcers. The disease has negative economic impacts as a result of hide damage, mastitis, infertility and losses in milk production. Secondary bacterial infection in the affected skin lesions can increase the severity and prolong the course of the disease. Little is known about the microbiome in the ulcerated skin sites. Therefore, the present study was directed to identify the prevalent bacterial communities in affected lesion via the 16s rRNA gene sequencing. Up to 98 species were found in the samples, most of them belonging to the phyla of Proteobacteria, followed by Firmicutes, Actinobacteria, and Bacteroidetes. All found bacterial species are known as opportunistic pathogens, but can withstand the inflammatory reaction.
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Affiliation(s)
- Sören Hansen
- Division of Microbiology and Animal Hygiene, University of Goettingen, Burckhardtweg 2, D-37077, Göttingen, Germany
| | - Rodrigo Pessôa
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, Av. Dr. Enéas Carvalho de Aguiar, 470 - Jardim America, São Paulo, SP, 05403-000, Brazil
| | - Andrezza Nascimento
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, Av. Dr. Enéas Carvalho de Aguiar, 470 - Jardim America, São Paulo, SP, 05403-000, Brazil
| | - Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, 35516, Mansoura, Egypt
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, University of Goettingen, Burckhardtweg 2, D-37077, Göttingen, Germany
- Corresponding author.
| | - Sabri S. Sanabani
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, Av. Dr. Enéas Carvalho de Aguiar, 470 - Jardim America, São Paulo, SP, 05403-000, Brazil
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11
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Gupta M, Lee S, Bisesi M, Lee J. Indoor Microbiome and Antibiotic Resistance on Floor Surfaces: An Exploratory Study in Three Different Building Types. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16214160. [PMID: 31661921 PMCID: PMC6862025 DOI: 10.3390/ijerph16214160] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/17/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022]
Abstract
Floor materials in indoor environments are known to be reservoirs of microbes. We focused on examining bacterial community composition, antibiotic resistance (AR) and microbial source tracking (MST) of fecal bacteria on the floor surfaces. Swab samples were collected from carpet and vinyl floors in three different buildings (medical, veterinary, and office buildings) from high and low traffic areas. Bacterial communities were determined with 16S rRNA sequencing, and AR (tetracycline (tetQ), sulfonamide, and carbapenem (KPC)) and MST (human-, canine-, avian-, and ruminant-specific fecal bacteria) were examined with quantitative polymerase chain reaction (PCR). The results show that Proteobacteria and Actinobacteria were the most abundant phyla. Traffic level significantly affected the number of operational taxonomic units. Traffic level was a key factor for distinctive bacterial community in the medical center. Targeted ARGs were detected from all buildings and tetQ concentration was related with traffic level, and KPC was only detected from the medical center. Most of the floor surfaces showed the presence of dog-specific fecal bacteria (83%) followed by bird-specific fecal bacteria (75%). The results suggest that traffic levels affected the bacterial levels and fecal contamination is prevalent on the floor surfaces. This is the first study that reports KPC presence on the floor surfaces.
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Affiliation(s)
- Mridula Gupta
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Seungjun Lee
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Michael Bisesi
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Jiyoung Lee
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA.
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12
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Rampelotto PH, Sereia AF, de Oliveira LFV, Margis R. Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling. Int J Mol Sci 2019; 20:ijms20123099. [PMID: 31242612 PMCID: PMC6696720 DOI: 10.3390/ijms20123099] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
The aim of this work was to analyze and compare the bacterial communities of 663 samples from a Brazilian hospital by using high-throughput sequencing of the 16S rRNA gene. To increase taxonomic profiling and specificity of 16S-based identification, a strict sequence quality filtering process was applied for the accurate identification of clinically relevant bacterial taxa. Our results indicate that the hospital environment is predominantly inhabited by closely related species. A massive dominance of a few taxa in all taxonomic levels down to the genera was observed, where the ten most abundant genera in each facility represented 64.4% of all observed taxa, with a major predominance of Acinetobacter and Pseudomonas. The presence of several nosocomial pathogens was revealed. Co-occurrence analysis indicated that the present hospital microbial network had low connectedness, forming a clustered topology, but not structured among groups of nodes (i.e., modules). Furthermore, we were able to detect ecologically relevant relationships between specific microbial taxa, in particular, potential competition between pathogens and non-pathogens. Overall, these results provide new insight into different aspects of a hospital microbiome and indicate that 16S rRNA sequencing may serve as a robust one-step tool for microbiological identification and characterization of a wide range of clinically relevant bacterial taxa in hospital settings with a high resolution.
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Affiliation(s)
- Pabulo H. Rampelotto
- PPGBCM, Center of Biotechnology, Federal University of Rio Grande do Sul, 9500, Porto Alegre, RS 91501-970, Brazil;
- Laboratory of Experimental Hepatology and Gastroenterology, Hospital de Clínicas de Porto Alegre (HCPA), 2350, Porto Alegre, RS 90035-903, Brazil
| | - Aline F.R. Sereia
- Neoprospecta Microbiome Technologies, 1302, Florianópolis, SC 88057-260, Brazil; (A.F.R.S.); (L.F.d.V.O.)
| | - Luiz Felipe V. de Oliveira
- Neoprospecta Microbiome Technologies, 1302, Florianópolis, SC 88057-260, Brazil; (A.F.R.S.); (L.F.d.V.O.)
| | - Rogério Margis
- PPGBCM, Center of Biotechnology, Federal University of Rio Grande do Sul, 9500, Porto Alegre, RS 91501-970, Brazil;
- Correspondence:
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13
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Querido MM, Aguiar L, Neves P, Pereira CC, Teixeira JP. Self-disinfecting surfaces and infection control. Colloids Surf B Biointerfaces 2019; 178:8-21. [PMID: 30822681 PMCID: PMC7127218 DOI: 10.1016/j.colsurfb.2019.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/27/2022]
Abstract
According to World Health Organization, every year in the European Union, 4 million patients acquire a healthcare associated infection. Even though some microorganisms represent no threat to healthy people, hospitals harbor different levels of immunocompetent individuals, namely patients receiving immunosuppressors, with previous infections, or those with extremes of age (young children and elderly), requiring the implementation of effective control measures. Public spaces have also been found an important source of infectious disease outbreaks due to poor or none infection control measures applied. In both places, surfaces play a major role on microorganisms' propagation, yet they are very often neglected, with very few guidelines about efficient cleaning measures and microbiological assessment available. To overcome surface contamination problems, new strategies are being designed to limit the microorganisms' ability to survive over surfaces and materials. Surface modification and/or functionalization to prevent contamination is a hot-topic of research and several different approaches have been developed lately. Surfaces with anti-adhesive properties, with incorporated antimicrobial substances or modified with biological active metals are some of the strategies recently proposed. This review intends to summarize the problems associated with contaminated surfaces and their importance on infection spreading, and to present some of the strategies developed to prevent this public health problem, namely some already being commercialized.
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Affiliation(s)
- Micaela Machado Querido
- National Institute of Health, Environmental Health Department, Porto, Portugal; EPIUnit - Institute of Public Health, University of Porto, Porto, Portugal
| | - Lívia Aguiar
- National Institute of Health, Environmental Health Department, Porto, Portugal
| | - Paula Neves
- National Institute of Health, Environmental Health Department, Porto, Portugal
| | - Cristiana Costa Pereira
- National Institute of Health, Environmental Health Department, Porto, Portugal; EPIUnit - Institute of Public Health, University of Porto, Porto, Portugal.
| | - João Paulo Teixeira
- National Institute of Health, Environmental Health Department, Porto, Portugal; EPIUnit - Institute of Public Health, University of Porto, Porto, Portugal
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Torkar KG, Ivić S. Surveillance of bacterial colonisation on contact surfaces in different medical wards. Arh Hig Rada Toksikol 2018; 68:116-126. [PMID: 28665797 DOI: 10.1515/aiht-2017-68-2892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 05/01/2017] [Indexed: 11/15/2022] Open
Abstract
This study was conducted to determine the bacterial colonization of some bacterial groups, including extended-spectrum β-lactamase (ESBLs) producers and methicillin-resistant Staphylococcus aureus (MRSA), on surfaces of the equipment and instruments in patient rooms and other workspaces in three different medical wards. The number of microorganisms on swabs was determined with the colony count method on selective microbiological mediums. The aerobic mesophylic microorganisms were found in 73.5 % out of 102 samples, with the average and maximum values of 2.6 × 102 and 4.6 × 103 colony forming units (CFU) 100 cm-2, respectively. Members of the family Enterobacteriaceae, coagulase positive staphylococci, coagulase-negative staphylococci, and enterococci were detected in 23.4, 31.4, 53.2, and 2.9 % of samples, respectively. The differences in bacterial counts on the surfaces of the psychiatric, oncology, and paediatric wards were statistically significant (P<0.001). About 40 % out of 19 isolates from the family Enterobacteriaceae showed multiple resistance to three or more different groups of tested antibiotics, while ESBL was confirmed for only one strain. Staphylococci isolates were mostly resistant to penicillin. MRSA was confirmed in 5.2 % of the tested S. aureus isolates. Greater attention should be paid to cleaning and the appropriate choice of disinfectants, especially in the psychiatric ward. Employees should be informed about the prevention of the spreading of nosocomial infections. Routine application of rapid methods for hygiene control of surfaces is highly recommended.
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Pereira da Fonseca TA, Pessôa R, Sanabani SS. Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine. Data Brief 2016; 8:399-403. [PMID: 27331120 PMCID: PMC4908281 DOI: 10.1016/j.dib.2016.05.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 11/25/2022] Open
Abstract
This article contains data on the bacterial population of two frequently used surfaces in the São Paulo Institute of Tropical Medicine (ITM) using the Illumina sequencing for massive parallel investigation of the bacterial 16S ribosomal RNA gene. Surface samples were obtained from restroom surfaces and the fingerprint door clock system. Mothur package and Shannon-ace-table.pl software programs (Chunlab Inc.: Seoul, Korea) were used to compute the diversity indices of bacterial community. The sequencing data from both surfaces have been uploaded to Zenodo: http://dx.doi.org/10.5281/zenodo.47709
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Affiliation(s)
- Tairacan Augusto Pereira da Fonseca
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | - Rodrigo Pessôa
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
| | - Sabri Saeed Sanabani
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo 05403 000, Brazil
- São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo 05403 000, Brazil
- Correspondence to: Universidade de São Paulo, Faculdade de Medicina Instituto de Medicina, Tropical de São Paulo, LIM 56-Av. Dr. Enéas Carvalho de Aguiar, 470-2° andar-Cerqueira Cesar, 05403-000 Sao Paulo, SP-Brasil. Tel.: +55 11 3061 8699; fax: +55 11 3061 7020.Universidade de São PauloFaculdade de Medicina Instituto de MedicinaTropical de São PauloLIM 56-Av. Dr. Enéas Carvalho de Aguiar470-2° andar-Cerqueira CesarSao Paulo05403-000SP-Brasil
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Pereira da Fonseca TA, Pessôa R, Felix AC, Sanabani SS. Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:152. [PMID: 26805866 PMCID: PMC4772172 DOI: 10.3390/ijerph13020152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/28/2022]
Abstract
Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients.
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Affiliation(s)
- Tairacan Augusto Pereira da Fonseca
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo 05403 000, Brazil.
| | - Rodrigo Pessôa
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo 05403 000, Brazil.
| | - Alvina Clara Felix
- São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo 05403 000, Brazil.
| | - Sabri Saeed Sanabani
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo 05403 000, Brazil.
- São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo 05403 000, Brazil.
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