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Microorganisms
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Bacterial and Antibiotic Resistance in the Environment
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Bacterial and Antibiotic Resistance in the Environment

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 9450

Special Issue Editors

Dr. Maria King

E-Mail Website
Guest Editor
Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX, USA
Interests: aerobiology; collection and analysis of bioaerosols; computational modeling of bioaerosol transmission; antibiotic resistance; environmental factors
Dr. Xingmao Ma

E-Mail Website
Guest Editor
Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, USA
Interests: environmental nanotechnology; biogeochemistry; advanced materials; emerging contaminants; photocatalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic resistance (AR) is one of the most serious public health threats of our time. Modern life has introduced novel technologies, including widespread antibiotics, ventilation, and plastics, that pose new challenges to bacteria. The misuse of antibiotics has historically resulted in the rise of antimicrobial resistance, leading to the transmission of untreatable illnesses and, in some cases, death. Aerosolization stress in airborne bacteria seems to be involved in the development of the response to environmental factors including temperature, relative humidity, and air exchange rates. Recently, microplastics (MPs) with a diameter of less than 5 mm have displayed a high tendency to enrich antibiotic-resistant bacteria and genes (ARBs and ARGs) in attached biofilms. Hotspots for antibiotic-resistant bacteria include wastewater systems, food and animal production sites, and clinical settings such as hospitals. However, mechanisms for the acquirement of AR by the microbes exposed to these environmental challenges remain largely unknown.

The importance of this field justifies a Special Issue of Microorganisms devoted to the latest progress in the detection, assessment, and modeling of antibiotic resistance in the environment. Accordingly, as Guest Editors, we invite you to submit research articles focusing on environmental factors affecting the behavior and transmission of bacteria, potentially triggering antibiotic resistance.

Dr. Maria King
Dr. Xingmao Ma
Guest Editors

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. Microorganisms 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 2700 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

  • antibiotic-resistant bacteria (ARBs)
  • antibiotic-resistant genes (ARGs)
  • environmental stress
  • bioaerosols
  • biofilms
  • membrane channels
  • microplastics (MPs)
  • transmission
  • modeling
  • wastewater
  • hospitals

Published Papers (7 papers)

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Research

15 pages, 1505 KiB  
Article
Isolation of Thermophilic Bacteria from Extreme Environments in Northern Chile
by Bernardita Valenzuela, Francisco Solís-Cornejo, Rubén Araya and Pedro Zamorano
Microorganisms 2024, 12(3), 473; https://doi.org/10.3390/microorganisms12030473 - 27 Feb 2024
Viewed by 1145
Abstract
The northern region of Chile boasts unique geographical features that support the emergence of geothermal effluents, salt lagoons, and coastal creeks. These extreme climate conditions create polyextreme habitats for microorganisms, particularly adapted to survive these harsh environments. These extremophilic microorganisms hold immense potential [...] Read more.
The northern region of Chile boasts unique geographical features that support the emergence of geothermal effluents, salt lagoons, and coastal creeks. These extreme climate conditions create polyextreme habitats for microorganisms, particularly adapted to survive these harsh environments. These extremophilic microorganisms hold immense potential as a source of hydrolytic enzymes, among other biotechnological applications. In this study, we isolated 15 strains of aerobic thermophilic bacteria (45–70 °C) from sediment samples collected at five different ecological sites, including hot springs, geothermal fields, and lagoons in the Atacama Desert and Andes high planes. Analyses of the 16S rRNA gene sequences of the isolates showed a close genetic similarity (98–100%) with microorganisms of the genera Parageobacillus, Geobacillus, Anoxybacillus, and Aeribacillus. Notably, these thermophiles exhibited significant hydrolytic enzyme activity, particularly amylases, lipases, and proteases. These findings underscore the potential of using these thermophilic bacterial strains as an invaluable source of thermozymes with wide-ranging applications in diverse industries, such as detergent formulations, pharmaceutical processing, and food technology. This research highlights the ecological significance of these extreme environments in the Atacama Desert and Andes high plains, which serve as vital ecological niches housing extremophilic bacteria as a genetic source of relevant thermozymes, promising great potential for innovation in the biotechnology industry. Full article
(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)
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13 pages, 3329 KiB  
Article
The Pangenome of Gram-Negative Environmental Bacteria Hides a Promising Biotechnological Potential
by Cláudia Covas, Gonçalo Figueiredo, Margarida Gomes, Tiago Santos, Sónia Mendo and Tânia S. Caetano
Microorganisms 2023, 11(10), 2445; https://doi.org/10.3390/microorganisms11102445 - 29 Sep 2023
Viewed by 1286
Abstract
Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bacteria lags [...] Read more.
Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bacteria lags behind that of its Gram-positive counterparts. In this regard, Pedobacter spp. have recently gained attention, not only for their role as plant growth promoters but also for their potential in producing antimicrobials. This study focuses on the genomic analysis of Pedobacter spp. to unveil the diversity of the SMs encoded in their genomes. Among the 41 genomes analyzed, a total of 233 biosynthetic gene clusters (BGCs) were identified, revealing the potential for the production of diverse SMs, including RiPPs (27%), terpenes (22%), hybrid SMs (17%), PKs (12%), NRPs (9%) and siderophores (6%). Overall, BGC distribution did not correlate with phylogenetic lineage and most of the BGCs showed no significant hits in the MIBiG database, emphasizing the uniqueness of the compounds that Pedobacter spp. can produce. Of all the species examined, P. cryoconitis and P. lusitanus stood out for having the highest number and diversity of BGCs. Focusing on their applicability and ecological functions, we investigated in greater detail the BGCs responsible for siderophore and terpenoid production in these species and their relatives. Our findings suggest that P. cryoconitis and P. lusitanus have the potential to produce novel mixtures of siderophores, involving bifunctional IucAC/AcD NIS synthetases, as well as carotenoids and squalene. This study highlights the biotechnological potential of Pedobacter spp. in medicine, agriculture and other industries, emphasizing the need for a continued exploration of its SMs and their applications. Full article
(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)
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16 pages, 5322 KiB  
Article
The Effects of Airflow on the Mechanosensitive Channels of Escherichia coli MG1655 and the Impact of Survival Mechanisms Triggered
by Violette I. Ramirez, Robin Wray, Paul Blount and Maria D. King
Microorganisms 2023, 11(9), 2236; https://doi.org/10.3390/microorganisms11092236 - 05 Sep 2023
Cited by 1 | Viewed by 936
Abstract
Understanding how bacteria respond to ventilated environments is a crucial concept, especially when considering accurate airflow modeling and detection limits. To properly design facilities for aseptic conditions, we must minimize the parameters for pathogenic bacteria to thrive. Identifying how pathogenic bacteria continue to [...] Read more.
Understanding how bacteria respond to ventilated environments is a crucial concept, especially when considering accurate airflow modeling and detection limits. To properly design facilities for aseptic conditions, we must minimize the parameters for pathogenic bacteria to thrive. Identifying how pathogenic bacteria continue to survive, particularly due to their multi-drug resistance characteristics, is necessary for designing sterile environments and minimizing pathogen exposure. A conserved characteristic among bacterial organisms is their ability to maintain intracellular homeostasis for survival and growth in hostile environments. Mechanosensitive (MS) channels are one of the characteristics that guide this phenomenon. Interestingly, during extreme stress, bacteria will forgo favorable homeostasis to execute fast-acting survival strategies. Physiological sensors, such as MS channels, that trigger this survival mechanism are not clearly understood, leaving a gap in how bacteria translate physical stress to an intracellular response. In this paper, we study the role of mechanosensitive ion channels that are potentially triggered by aerosolization. We hypothesize that change in antimicrobial uptake is affected by aerosolization stress. Bacteria regulate their defense mechanisms against antimicrobials, which leads to varying susceptibility. Based on this information we hypothesize that aerosolization stress affects the antimicrobial resistance defense mechanisms of Escherichia coli (E. coli). We analyzed the culturability of knockout E. coli strains with different numbers of mechanosensitive channels and compared antibiotic susceptibility under stressed and unstressed airflow conditions. As a result of this study, we can identify how the defensive mechanisms of resistant bacteria are triggered for their survival in built environments. By changing ventilation airflow velocity and observing the change in antibiotic responses, we show how pathogenic bacteria respond to ventilated environments via mechanosensitive ion channels. Full article
(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)
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11 pages, 4258 KiB  
Article
Sampling and Characterization of Bioaerosols in Poultry Houses
by Brooke L. Smith and Maria D. King
Microorganisms 2023, 11(8), 2068; https://doi.org/10.3390/microorganisms11082068 - 11 Aug 2023
Viewed by 926
Abstract
Two poultry Confined Animal Feeding Units (CAFUs), “House A” and “House B”, were selected from the TAMU poultry facility for the study, and samples were collected over a five-day period. Bioaerosol sampling was conducted using a Wetted Wall Cyclone (WWC) bioaerosol collector at [...] Read more.
Two poultry Confined Animal Feeding Units (CAFUs), “House A” and “House B”, were selected from the TAMU poultry facility for the study, and samples were collected over a five-day period. Bioaerosol sampling was conducted using a Wetted Wall Cyclone (WWC) bioaerosol collector at the two CAFU houses, in which House A housed approximately 720 broiler chickens and roosters, while House B remained unoccupied and served as a reference. Both houses consisted of 24 pens arranged on either side of a central walkway. Bacterial content analysis was conducted using microbial plating, real-time Polymerase Chain Reaction (PCR), and Fatty Acid Methyl Ester (FAME) analysis, while ambient temperature and relative humidity were also monitored. The concentrations of microorganisms in House A showed a highly dynamic range, ranging from 4000 to 60,000 colony forming units (CFU) per cubic meter of air. Second, the WWC samples contained approximately ten-fold more bacterial DNA than the filter samples, suggesting higher levels of viable cells captured by the WWC. Third, significant concentrations of pathogens, including Salmonella, Staphylococcus, and Campylobacter, were detected in the poultry facility. Lastly, the WWC system demonstrated effective functionality and continuous operation, even in the challenging sampling environment of the CAFU. The goal of this study was to characterize the resident population of microorganisms (pathogenic and non-pathogenic) present in the CAFUs and to evaluate the WWC’s performance in such an environment characterized by elevated temperature, high dust content, and feathers. This knowledge could then be used to improve understanding microorganism dynamics in CAFUs including the spread of bacterial infections between animals and from animals to humans that work in these facilities, as well as of the WWC performance in this type of environment (elevated temperature, high content of dust and feathers). A more comprehensive understanding can aid in improving the management of bacterial infections in these settings. Full article
(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)
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14 pages, 1258 KiB  
Article
Contribution of Manure-Spreading Operations to Bioaerosols and Antibiotic Resistance Genes’ Emission
by Mahsa Baghdadi, Patrick Brassard, Stéphane Godbout, Valérie Létourneau, Nathalie Turgeon, Florent Rossi, Émie Lachance, Marc Veillette, Marie-Lou Gaucher and Caroline Duchaine
Microorganisms 2023, 11(7), 1797; https://doi.org/10.3390/microorganisms11071797 - 13 Jul 2023
Cited by 1 | Viewed by 1256
Abstract
Manure spreading from farm animals can release antibiotic-resistant bacteria (ARB) carrying antimicrobial resistance genes (ARGs) into the air, posing a potential threat to human and animal health due to the intensive use of antibiotics in the livestock industry. This study analyzed the effect [...] Read more.
Manure spreading from farm animals can release antibiotic-resistant bacteria (ARB) carrying antimicrobial resistance genes (ARGs) into the air, posing a potential threat to human and animal health due to the intensive use of antibiotics in the livestock industry. This study analyzed the effect of different manure types and spreading methods on airborne bacterial emissions and antibiotic resistance genes in a controlled setting. Cow, poultry manure, and pig slurry were spread in a confined environment using two types of spreaders (splash plate and dribble bar), and the resulting emissions were collected before, during, and after spreading using high-volume air samplers coupled to a particle counter. Total bacteria, fecal indicators, and a total of 38 different subtypes of ARGs were further quantified by qPCR. Spreading poultry manure resulted in the highest emission rates of total bacteria (1011 16S gene copies/kg manure spread), Archaea (106 16S gene copies/kg manure), Enterococcus (105 16S gene copies/kg manure), and E. coli (104 16S gene copies/kg manure), followed by cow manure and pig slurry with splash plates and the dribble bar. Manure spreading was associated with the highest rates of airborne aminoglycoside genes for cow and poultry (106 gene copies/kg manure), followed by pig slurry (104 gene copies/kg manure). This study shows that the type of manure and spreading equipment can affect the emission rates of airborne bacteria, and ARGs. Full article
(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)
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14 pages, 19700 KiB  
Article
Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa
by Yayu Xiao, Peiyu Zhang, Huan Zhang, Huan Wang, Guo Min, Hongxia Wang, Yuyu Wang and Jun Xu
Microorganisms 2023, 11(3), 765; https://doi.org/10.3390/microorganisms11030765 - 16 Mar 2023
Viewed by 1317
Abstract
Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of [...] Read more.
Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further. Full article
(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)
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13 pages, 2795 KiB  
Article
Quiescence of Escherichia coli Aerosols to Survive Mechanical Stress during High-Velocity Collection
by Brooke L. Smith and Maria D. King
Microorganisms 2023, 11(3), 647; https://doi.org/10.3390/microorganisms11030647 - 03 Mar 2023
Cited by 1 | Viewed by 1607
Abstract
A low cutpoint wetted wall bioaerosol sampling cyclone (LCP-WWC), with an aerosol sampling flow rate of 300 L/min at 55″ H2O pressure drop and a continuous liquid outflow rate of about 0.2 mL/min, was developed by upgrading an existing system. The [...] Read more.
A low cutpoint wetted wall bioaerosol sampling cyclone (LCP-WWC), with an aerosol sampling flow rate of 300 L/min at 55″ H2O pressure drop and a continuous liquid outflow rate of about 0.2 mL/min, was developed by upgrading an existing system. The laboratory strain Escherichia coli MG1655 was aerosolized using a six-jet Collison Nebulizer and collected at high velocity using the LCP-WWC for 10 min with different collection liquids. Each sample was quantitated during a 15-day archiving period after aerosolization for culturable counts (CFUs) and gene copy numbers (GCNs) using microbial plating and whole-cell quantitative polymerase chain (qPCR) reaction. The samples were analyzed for protein composition and antimicrobial resistance using protein gel electrophoresis and disc diffusion susceptibility testing. Aerosolization and collection were followed by an initial period of quiescence or dormancy. After 2 days of archiving at 4 °C and RT, the bacteria exhibited increased culturability and antibiotic resistance (ABR), especially to cell wall inhibitors (ampicillin and cephalothin). The number of resistant bacteria on Day 2 increased nearly four-times compared to the number of cells at the initial time of collection. The mechanical stress of aerosolization and high-velocity sampling likely stunned the cells triggering a response of dormancy, though with continued synthesis of vital proteins for survival. This study shows that an increase in intensity in environmental conditions surrounding airborne bacteria affects their ability to grow and their potential to develop antimicrobial resistance. Full article
(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)
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