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Environmental Microbiology: Perspectives for Medicine and Public Health

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A special issue of International Journal of Environmental Research and Public Health (ISSN 1660-4601).

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 17453

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Special Issue Editor

Dr. João Brandão

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Guest Editor

Department of Environmental Health, National Institute of Health Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal
Interests: sand microbiology; beach; water quality indicators; climate change mitigation; environmental exposure; medical mycology

Special Issue Information

Dear Colleagues,

The analysis of microorganisms is crucial in several research fields, and especially in medicine and public health. In these two fields, an accurate microbiological analysis is part of a wider process aimed at the definition of the interactions between human beings and environment.

In the medicine field, such as legal, occupational, and preventive medicine, microbiological identification and evaluation are crucial for effective risk management and the definition of safety procedures. The achievement of these objectives requires the comprehension of microbial biodiversity, not only the identification of few biomarkers. In the public health field, microbiological analysis is required to detect diseases, analyze the etiology, and identify the right treatment.

Our Special Issue titled “Environmental Microbiology: Perspectives for Medicine and Public Health” offers a venue for researchers and practitioners to share their experience on the evaluation and identification of environmental microorganisms and their applications in medicine and public health. Original research articles and review papers are welcomed.

Dr. João Brandão
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Environmental Research and Public Health is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2500 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

environmental microbiology
microbiology in public health
clinical microbiology
medical microbiology
medical mycology

Published Papers (9 papers)

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Research

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11 pages, 2157 KiB

Open AccessArticle

Seasonal Variation in Fungi in Beach Sand in Summertime: Stintino (Italy)

by Massimo Deligios, Vittorio Mazzarello, Maura Fiamma, Aleksandra Barac, Lorenzo Diana, Marco Ferrari, Manuela Murgia, Bianca Paglietti and Salvatore Rubino

Int. J. Environ. Res. Public Health 2023, 20(23), 7134; https://doi.org/10.3390/ijerph20237134 - 1 Dec 2023

Viewed by 1216

Abstract

Background: The goal of this study was to monitor the microbial biodiversity in beach sand that is heavily visited by tourists during the summer, and to determinate whether the high presence of bathers (around 5000 per day) can modify sand microbial composition. Methods: Between 2016 and 2020, 150 sand samples were collected from nine different points at La Pelosa beach in Sardinia, Italy. Non-culturing methods were used; DNA extraction and meta-barcode sequencing were performed. All samples were analyzed with sequencing methods for 16S and ITS sequences. Results: Fungal genera differ on the three beaches and in the winter/summer zones. The ITS sequence showed the most common presence of Candida during summer and Paradendryphiella in the winter. The greatest diversity was found in the dune during winter, while in other parts of the beach, there are differences between bacteria and fungi, particularly in the wash zone during the winter, with high diversity for 16S sequences but low diversity for ITS sequences. Conclusions: It appears reasonable that the sands, even on non-urban beaches, should be included in health monitoring programs in addition to the waters, and that access to them should be regulated by limiting the number of bathers with the aim of reducing the presence of pathogenic fungal species. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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13 pages, 2575 KiB

Open AccessArticle

Occurrence of Vibrio spp. in Selected Recreational Water Bodies in Belgium during 2021 Bathing Season

by Rosalie Sacheli, Camille Philippe, Cécile Meex, Samy Mzougui, Pierrette Melin and Marie-Pierre Hayette

Int. J. Environ. Res. Public Health 2023, 20(20), 6932; https://doi.org/10.3390/ijerph20206932 - 17 Oct 2023

Viewed by 1411

Abstract

In recent years, a global increase in the number of reports of human vibriosis involving V. cholerae non-O1/O139 (NOVC) and other Vibrio spp. has been observed. In this context, the Belgian National Reference Center for Vibrio conducted an assessment of the presence of Vibrio spp. in recreational waters. Water sampling was performed monthly in different lakes in Wallonia and Flanders, including the North Sea. The collected water was then filtrated and cultured, and Vibrio spp. was quantified according to the Most Probable Number (MPN). Presumptive colonies were confirmed via MALDI-TOF, and PCR for virulence genes was applied if justified. No Vibrio spp. was found in the analyzed water bodies in Wallonia. However, NOVC was isolated from three different lakes in Flanders and from coastal water. In addition, V. alginolyticus and V. parahaemolyticus were also detected in coastal water. No clear impact of the pH and temperature was observed on Vibrio spp. occurrence. Our study demonstrates the presence of Vibrio spp. in different bathing water bodies, mostly in the north of Belgium, and supports the recommendation to include Vibrio spp. as a water quality indicator for bathing water quality assessment to ensure the safety of water recreational users in Belgium. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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17 pages, 3234 KiB

Open AccessArticle

Serratia marcescens Outbreak at a Correctional Facility: Environmental Sampling, Laboratory Analyses and Genomic Characterization to Assess Sources and Persistence

by Donna Ferguson, Rahil Ryder, Rawni Lunsford, Arie Dash, Amanda Kamali, Akiko Kimura, John Crandall, Rituparna Mukhopadhyay, Heather Dowless, Nancy Ortiz and Nathaniel K. Jue

Int. J. Environ. Res. Public Health 2023, 20(17), 6709; https://doi.org/10.3390/ijerph20176709 - 4 Sep 2023

Viewed by 1674

Abstract

Serratia marcescens is an environmental bacterium and clinical pathogen that can cause an array of infections. We describe an environmental sampling and comparative genomics approach used to investigate a multi-year outbreak of S. marcescens at a correctional facility. Whole genome sequencing analysis revealed a predominant cluster of clonally related S. marcescens from nine patient cases and items associated with illicit drug use. Closely related strains found among items associated with case-patient cells and diluted Cell Block 64 (CB64), a quaternary ammonium disinfectant, and Break Out (BO), a multipurpose cleaner, highlighted their role as environmental reservoirs for S. marcescens in this outbreak. Comparative genomic analysis suggested outbreak strains were both persistent (identical strains found over long periods and in multiple locations of the correctional facility) and diverse (strains clustered with multiple global samples from NCBI database). No correlation was found between antimicrobial resistance (AMR) genes of outbreak strains; NCBI strains have more AMR genes. Principal component analysis (PCA) of virulence factors associated with persistence and infectivity indicated variation based on phylogroups, including the predominant cluster; identifiable variations among environmental versus clinical strains were not observed. Identification of multiple distinct genetic groups highlights the importance of putting epidemiological genomic studies in a proper genetic context. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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12 pages, 2131 KiB

Open AccessArticle

Stability of SARS-CoV-2 on Commercial Aircraft Interior Surfaces with Implications for Effective Control Measures

by Kenrie P. Y. Hui, Alex W. H. Chin, John Ehret, Ka-Chun Ng, Malik Peiris, Leo L. M. Poon, Karen H. M. Wong, Michael C. W. Chan, Ian Hosegood and John M. Nicholls

Int. J. Environ. Res. Public Health 2023, 20(16), 6598; https://doi.org/10.3390/ijerph20166598 - 18 Aug 2023

Viewed by 1406

Abstract

Background: The COVID-19 pandemic from 2019 to 2022 devastated many aspects of life and the economy, with the commercial aviation industry being no exception. One of the major concerns during the pandemic was the degree to which the internal aircraft environment contributed to virus transmission between humans and, in particular, the stability of SARS-CoV-2 on contact surfaces in the aircraft cabin interior. Method: In this study, the stability of various major strains of SARS-CoV-2 on interior aircraft surfaces was evaluated using the TCID₅₀ assessment. Results: In contrast to terrestrial materials, SARS-CoV-2 was naturally less stable on common contact points in the aircraft interior, and, over a 4 h time period, there was a 90% reduction in culturable virus. Antiviral and surface coatings were extremely effective at mitigating the persistence of the virus on surfaces; however, their benefit was diminished by regular cleaning and were ineffective after 56 days of regular use and cleaning. Finally, successive strains of SARS-CoV-2 have not evolved to be more resilient to survival on aircraft surfaces. Conclusions: We conclude that the mitigation strategies for SARS-CoV-2 on interior aircraft surfaces are more than sufficient, and epidemiological evidence over the past three years has not found that surface spread is a major route of transmission. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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7 pages, 7681 KiB

Open AccessCommunication

Scanning Electron Microscope Examination as an Alternative to Classical Microbiology in the Diagnostics of Catheter-Related Sepsis?

by Anna Kluzik, Hanna Tomczak, Marek Nowicki, Małgorzata Grześkowiak and Krzysztof Kusza

Int. J. Environ. Res. Public Health 2023, 20(6), 5028; https://doi.org/10.3390/ijerph20065028 - 13 Mar 2023

Viewed by 1427

Abstract

Central venous catheters are essential elements enabling the treatment of intensive care unit patients. However, these catheters are sometimes colonised by both bacteria and fungi, and thus, they may become a potential source of systemic infections—catheter-related bloodstream infections (CRBSI). The identification of the pathogen responsible for CRBSI is a time-consuming process. At the same time, the relationship between the quick identification of the pathogen and the implementation of targeted antibiotic therapy is of key importance for controlling the clinical symptoms of sepsis and septic shock in the patient. Quick diagnosis is of key importance to reduce morbidity and mortality in this group of patients. In our study, we attempted to create a catalogue of images of the most commonly cultured pathogens responsible for CRBSI. An FEI Quanta 250 FEG Scanning Electron Microscope (SEM) was used for measurements. SEM images obtained during the analysis were included in this study. Images of SEM are three-dimensional and comparable to the images seen with the human eye and are a tool used for research and measurement whenever it is necessary to analyse the state of the surface and assess its morphology. The method described in our study will not replace the current procedures recognised as the gold standard, i.e., pathogen culturing, determination of the count of microorganisms (CFU –colony forming units), and assessment of drug sensitivity. However, in some cases, the solution proposed in our study may aid the diagnosis of patients with suspected catheter-related bloodstream infections leading to sepsis and septic shock. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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11 pages, 366 KiB

Open AccessArticle

Environmental Dissemination of SARS-CoV-2 in a University Hospital during the COVID-19 5th Wave Delta Variant Peak in Castile-León, Spain

by Priscilla Gomes da Silva, José Gonçalves, Andrés Torres Franco, Elisa Rodriguez, Israel Diaz, Antonio Orduña Domingo, Sonsoles Garcinuño Pérez, Gabriel Alberto March Roselló, Carlos Jesús Dueñas Gutiérrez, Maria São José Nascimento, Sofia I.V. Sousa, Pedro Garcia Encina and João R. Mesquita

Int. J. Environ. Res. Public Health 2023, 20(2), 1574; https://doi.org/10.3390/ijerph20021574 - 15 Jan 2023

Cited by 2 | Viewed by 1575

Abstract

The dominant SARS-CoV-2 Delta variant (B.1.617.2) became the main circulating variant among countries by mid 2021. Attention was raised to the increased risk of airborne transmission, leading to nosocomial outbreaks even among vaccinated individuals. Considering the increased number of COVID-19 hospital admissions fueled by the spread of the variant, with Spain showing the highest COVID-19 rates in mainland Europe by July 2021, the aim of this study was to assess SARS-CoV-2 environmental contamination in different areas of a University Hospital in the region of Castile-León, Spain, during the peak of the 5th wave of COVID-19 in the country (July 2021). Air samples were collected from sixteen different areas of the Hospital using a Coriolis^® μ air sampler. Surface samples were collected in these same areas using sterile flocked plastic swabs. RNA extraction followed by a one-step RT-qPCR were performed for detection of SARS-CoV-2 RNA. Of the 21 air samples, only one was positive for SARS-CoV-2 RNA, from the emergency waiting room. Of the 40 surface samples, 2 were positive for SARS-CoV-2 RNA, both from the microbiology laboratory. These results may be relevant for risk assessment of nosocomial infection within healthcare facilities, thus helping prevent and minimize healthcare staff’s exposure to SARS-CoV-2, reinforcing the importance of always wearing appropriate and well-fit masks at all times and proper PPE when in contact with infected patients. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

15 pages, 1938 KiB

Open AccessArticle

High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico

by Ana K. Tapia-Arreola, Daniel A. Ruiz-Garcia, Hectorina Rodulfo, Ashutosh Sharma and Marcos De Donato

Int. J. Environ. Res. Public Health 2022, 19(21), 13988; https://doi.org/10.3390/ijerph192113988 - 27 Oct 2022

Cited by 4 | Viewed by 2262

Abstract

The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the bla_CTX,qnrB, qnrS y, and aac(6′)lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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17 pages, 1511 KiB

Open AccessArticle

Microbial Source Tracking as a Method of Determination of Beach Sand Contamination

by Elisabete Valério, Maria Leonor Santos, Pedro Teixeira, Ricardo Matias, João Mendonça, Warish Ahmed and João Brandão

Int. J. Environ. Res. Public Health 2022, 19(13), 7934; https://doi.org/10.3390/ijerph19137934 - 28 Jun 2022

Cited by 13 | Viewed by 2429

Abstract

Beach sand may act as a reservoir for numerous microorganisms, including enteric pathogens. Several of these pathogens originate in human or animal feces, which may pose a public health risk. In August 2019, high levels of fecal indicator bacteria (FIB) were detected in the sand of the Azorean beach Prainha, Terceira Island, Portugal. Remediation measures were promptly implemented, including sand removal and the spraying of chlorine to restore the sand quality. To determine the source of the fecal contamination, during the first campaign, supratidal sand samples were collected from several sites along the beach, followed by microbial source tracking (MST) analyses of Bacteroides marker genes for five animal species, including humans. Some of the sampling sites revealed the presence of marker genes from dogs, seagulls, and ruminants. Making use of the information on biological sources originating partially from dogs, the municipality enforced restrictive measures for dog-walking at the beach. Subsequent sampling campaigns detected low FIB contamination due to the mitigation and remediation measures that were undertaken. This is the first case study where the MST approach was used to determine the contamination sources in the supratidal sand of a coastal beach. Our results show that MST can be an essential tool to determine sources of fecal contamination in the sand. This study shows the importance of holistic management of beaches that should go beyond water quality monitoring for FIB, putting forth evidence for beach sand monitoring. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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Other

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14 pages, 869 KiB

Open AccessStudy Protocol

Impacts of Antibiotic Residues in the Environment on Bacterial Resistance and Human Health in Eastern China: An Interdisciplinary Mixed-Methods Study Protocol

by Shenghan Cai, Na Wang, Like Xu, Fei Yan, Qingwu Jiang, Xinping Zhao, Wei Wang, Hexing Wang, Lufang Jiang, Wenjuan Cong, Samuel K. Sheppard, Jason Weeks, Barbara Kasprzyk-Hordern, Chaowei Fu and Helen Lambert

Int. J. Environ. Res. Public Health 2022, 19(13), 8145; https://doi.org/10.3390/ijerph19138145 - 2 Jul 2022

Cited by 7 | Viewed by 2489

Abstract

Antibiotic resistance is a global health challenge that threatens human and animal lives, especially among low-income and vulnerable populations in less-developed countries. Its multi-factorial nature requires integrated studies on antibiotics and resistant bacteria in humans, animals, and the environment. To achieve a comprehensive understanding of the situation and management of antibiotic use and environmental transmission, this paper describes a study protocol to document human exposure to antibiotics from major direct and indirect sources, and its potential health outcomes. Our mixed-methods approach addresses both microbiological and pathogen genomics, and epidemiological, geospatial, anthropological, and sociological aspects. Implemented in two rural residential areas in two provinces in Eastern China, linked sub-studies assess antibiotic exposure in population cohorts through household surveys, medicine diaries, and biological sampling; identify the types and frequencies of antibiotic resistance genes in humans and food-stock animals; quantify the presence of antibiotic residues and antibiotic resistance genes in the aquatic environment, including wastewater; investigate the drivers and behaviours associated with human and livestock antibiotic use; and analyse the national and local policy context, to propose strategies and systematic measurements for optimising and monitoring antibiotic use. As a multidisciplinary collaboration between institutions in the UK and China, this study will provide an in-depth understanding of the influencing factors and allow comprehensive awareness of the complexity of AMR and antibiotic use in rural Eastern China. Full article

(This article belongs to the Special Issue Environmental Microbiology: Perspectives for Medicine and Public Health)

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