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Antimicrobial and Antimicrobial Resistance in the Environment

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A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 22984

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Special Issue Editor

Dr. Manuela Oliveira

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Guest Editor

Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, Universidade de Lisboa, Lisbon, Portugal
Interests: antimicrobial resistance; bacterial virulence; biofilms; genomics; infections pathogenesis; food safety
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global dissemination of multidrug-resistant bacterial species to last-resource antibiotics and associated human and animal infections is a major concern, and expected to rise in the future. However, the role of natural environments in antimicrobials accumulation and resistance development and dissemination has been overlooked until recently. Monitoring environmental resistance is extremely relevant for the safeguarding of One Health, especially in settings which are highly subjected to anthropogenic contamination, as resistance dispersion in the environment may allow for the inference of the extent of selective pressure due to the use of antimicrobials in humans and animals. In fact, antimicrobial compounds residues and resistant strains originating from agriculture, animal and human wastes, or even from wild animals, can disseminate through the environment, especially through groundwaters, entering habitats in which no antimicrobials are directly administered to animals or humans. Besides being associated with the selective pressure posed by antimicrobial residues, resistance dissemination in the environment can also be triggered by the increase in environmental temperature, which is one of the major consequences of climate change. In fact, most bacteria may easily adapt to an environmental temperature rise, promoting the dissemination of resistant determinants between humans, animals and the environment.

Characterizing environmental-resistant strains represents a potential aid for surveillance and management programs aiming to unveil AMR evolution mechanisms and dissemination routes in natural environments, as well as assessing possible consequences for human and animal health. This Special Issue aims to publish manuscripts that contribute to our understanding of the impact of antimicrobials and bacterial antimicrobial resistance in environmental health.

Dr. Manuela Oliveira
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. Antibiotics 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 2900 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

agriculture
animal production
antimicrobial resistance
aquatic environment
environmental resistance
epidemiology
genomics
infections pathogenesis
One Health
wildlife

Published Papers (7 papers)

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Research

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15 pages, 2409 KiB

Open AccessArticle

Evaluation of the Correspondence between the Concentration of Antimicrobials Entering Sewage Treatment Plant Influent and the Predicted Concentration of Antimicrobials Using Annual Sales, Shipping, and Prescriptions Data

by Takashi Azuma, Takashi Nakano, Ryuji Koizumi, Nobuaki Matsunaga, Norio Ohmagari and Tetsuya Hayashi

Antibiotics 2022, 11(4), 472; https://doi.org/10.3390/antibiotics11040472 - 01 Apr 2022

Cited by 2 | Viewed by 3368

Abstract

The accuracy and correspondence between the measured concentrations from the survey and predicted concentrations on the basis of the three types of statistical antimicrobial use in Japan was evaluated. A monitoring survey of ten representative antimicrobials: ampicillin (APL), cefdinir (CDN), cefpodoxime proxetil (CPXP), ciprofloxacin (CFX), clarithromycin (CTM), doxycycline (DCL), levofloxacin (LFX), minocycline (MCL), tetracycline (TCL), and vancomycin (VMC), in the influent of sewage treatment plant (STP) located in urban areas of Japan, was conducted. Then, the measured values were verified in comparison with the predicted values estimated from the shipping volumes, sales volumes, and prescription volumes based on the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB). The results indicate that the correspondence ratios between the predicted concentrations calculated on the basis of shipping and NDB volumes and the measured concentrations (predicted concentration/measured concentration) generally agreed for the detected concentration of antimicrobials in the STP influent. The correspondence ratio on the basis of shipping volume was, for CFX, 0.1; CTM, 2.9; LFX, 0.5; MCL, 1.9; and VMC, 1.7, and on the basis of NDB volume the measured concentration was CFX, 0.1; CTM, 3.7; DCL, 0.4; LFX, 0.7; MCL, 1.9; TCL, 0.6; and VMC, 1.6. To our knowledge, this is the first report to evaluate the accuracy of predicted concentrations based on sales, shipping, NDB statistics and measured concentrations for antimicrobials in the STP influent. Full article

(This article belongs to the Special Issue Antimicrobial and Antimicrobial Resistance in the Environment)

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14 pages, 531 KiB

Open AccessArticle

Nocturnal Birds of Prey as Carriers of Staphylococcus aureus and Other Staphylococci: Diversity, Antimicrobial Resistance and Clonal Lineages

by Vanessa Silva, Ana Filipa Lopes, Vanessa Soeiro, Manuela Caniça, Vera Manageiro, José Eduardo Pereira, Luís Maltez, José Luis Capelo, Gilberto Igrejas and Patrícia Poeta

Antibiotics 2022, 11(2), 240; https://doi.org/10.3390/antibiotics11020240 - 12 Feb 2022

Cited by 16 | Viewed by 3064

Abstract

Owls are nocturnal predators that inhabit urbanized and farmlands. They are in direct contact with other animals, both livestock and small wild rodents that they mostly feed on. Staphylococci can be both commensal and pathogenic bacteria that are widespread across the various ecological niches. We aimed to isolate staphylococci from owls and to characterize their antimicrobial resistance, virulence factors and genetic lineages. Swab samples were collected from the throat and cloaca of 114 owls admitted to two rehabilitation centers in Portugal. The identification of staphylococci species was performed by MALDI-TOF. Staphylococci antimicrobial resistance and virulence genes were investigated by means of the disk diffusion method and PCR. Staphylococcus aureus isolates were characterized by MLST, agr and spa-typing. Of the tested animals, 66 isolates were recovered, including 10 different species of staphylococci, of which 25 were coagulase-positive (CoPS) and 41 were coagulase-negative (CoNS). Twenty-three S. aureus were isolated, of which one mecC-MRSA was identified. The isolates were mainly resistant to penicillin, aminoglycosides, clindamycin and tetracycline. mecC-MRSA belonged to ST1245 and spa-type t843 and the remaining S. aureus were ascribed to 12 STs and 15 spa types. A high diversity of clonal lineages was identified among the S. aureus isolated from wild owls. Owls feed mainly on small rodents often exposed to waste and anthropogenic sources, which may explain the moderate prevalence of S. aureus in these animals. Full article

(This article belongs to the Special Issue Antimicrobial and Antimicrobial Resistance in the Environment)

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11 pages, 707 KiB

Open AccessArticle

Evidence of Linezolid Resistance and Virulence Factors in Enterococcus spp. Isolates from Wild and Domestic Ruminants, Italy

by Camilla Smoglica, Alberto Vergara, Simone Angelucci, Anna Rita Festino, Antonio Antonucci, Fulvio Marsilio and Cristina Esmeralda Di Francesco

Antibiotics 2022, 11(2), 223; https://doi.org/10.3390/antibiotics11020223 - 10 Feb 2022

Cited by 14 | Viewed by 1834

Abstract

The aim of this study was to evaluate the resistance patterns against selected critically and highly important antibiotics (quinupristin/dalfopristin, vancomycin, and linezolid) in 48 Enterococcus isolates obtained from wild (red deer and Apennine chamois) and domestic (cattle, sheep, and goats) ruminants living with varying degrees of sympatry in the protected area of Maiella National Park (central Italy). According to CLSI breakpoints, 9 out of 48 isolates (18.8%) showed resistance to at least one antibiotic. One Apennine chamois isolate was resistant to all tested antibiotics. The PCR screening of related resistance genes highlighted the occurrence of msrC or cfrD in seven Enterococcus resistant isolates. In addition, msrC and vanC genes were amplified in susceptible isolates. Specific sequences of virulence genes (gelE, ace, efa, asa1, and esp) related to pathogenic enterococci in humans were amplified in 21/48 isolates (43.75%), belonging mostly to wild animals (15/21; 71.42%). This is the first report of linezolid-resistant enterococci harboring virulence genes in Italian wildlife with special regard to the red deer and Apennine chamois species. The results allow us to evaluate the potential role of wild animals as indicators of antibiotic resistance in environments with different levels of anthropic pressure. Full article

(This article belongs to the Special Issue Antimicrobial and Antimicrobial Resistance in the Environment)

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15 pages, 916 KiB

Open AccessArticle

Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany

by Timo Homeier-Bachmann, Anne K. Schütz, Sylvia Dreyer, Julien Glanz, Katharina Schaufler and Franz J. Conraths

Antibiotics 2022, 11(2), 123; https://doi.org/10.3390/antibiotics11020123 - 18 Jan 2022

Cited by 16 | Viewed by 2624

Abstract

Antimicrobial resistance (AMR) is a serious global health threat and extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales are a major contributor. This study aimed to gain a deeper insight into the AMR burden of wild animals. In total, 1595 fecal samples were collected by two systematic searches in Mecklenburg-Western Pomerania, north-east Germany. Samples were screened for ESBL-carrying Escherichia (E.) coli and isolates found were further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. We found an estimated prevalence of 1.2% ESBL-producing E. coli in wild boar and 1.1% in wild ruminants. CTX-M-1 was the most abundant CTX-M type. We also examined fecal samples from wild boar and wild ruminants using shotgun metagenomics to gain insight into the resistome in wild animals. The latter revealed significantly lower normalized counts for AMR genes in wildlife samples compared to farm animals. The AMR gene levels were lower in wild ruminants than in wild boar. In conclusion, our study revealed a low prevalence of ESBL-producing E. coli and a low overall AMR gene burden in wild boar and wild ruminants, probably due to the secluded location of the search area. Full article

(This article belongs to the Special Issue Antimicrobial and Antimicrobial Resistance in the Environment)

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12 pages, 843 KiB

Open AccessArticle

Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria Isolated from Loggerhead Sea Turtles (Caretta caretta) of the Island of Maio, Cape Verde

by Matilde Fernandes, Miguel L. Grilo, Carla Carneiro, Eva Cunha, Luís Tavares, Juan Patino-Martinez and Manuela Oliveira

Antibiotics 2021, 10(7), 771; https://doi.org/10.3390/antibiotics10070771 - 24 Jun 2021

Cited by 11 | Viewed by 2886

Abstract

Previous studies revealed high levels of antimicrobial resistance (AMR) in loggerhead sea turtles (Caretta caretta), describing this species as prime reservoir of antimicrobial-resistant bacteria. This study aimed to characterise, for the first time, the AMR and virulence profiles of Gram-negative bacteria isolated from 33 nesting loggerhead turtles of the island of Maio, Cape Verde. Cloacal, oral, and egg content swab samples (n = 99) were collected and analysed using conventional bacteriological techniques. Shewanella putrefaciens, Morganella morganii, and Vibrio alginolyticus were isolated from the samples under study. The isolates obtained from this loggerhead subpopulation (North-East Atlantic) revealed lower levels of AMR, compared with the results of studies performed in other subpopulations (e.g., Mediterranean). However, the detection of resistance to carbapenems and multiple antimicrobial resistance indices higher than 0.20, raises concern about the potential association of these animals to points of high antimicrobial exposure. Furthermore, virulence phenotypic characterisation revealed that the isolates presented complex virulence profiles, including the ability to produce biofilms. Finally, due to their pathogenic potential, and considering the evidence of illegal consumption of turtle-related products on the island of Maio, the identified bacteria may represent a significant threat to public health. Full article

(This article belongs to the Special Issue Antimicrobial and Antimicrobial Resistance in the Environment)

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26 pages, 2083 KiB

Open AccessArticle

Molecular Epidemiology, Virulence Traits and Antimicrobial Resistance Signatures of Aeromonas spp. in the Critically Endangered Iberochondrostoma lusitanicum Follow Geographical and Seasonal Patterns

by Miguel L. Grilo, Sara Isidoro, Lélia Chambel, Carolina S. Marques, Tiago A. Marques, Carla Sousa-Santos, Joana I. Robalo and Manuela Oliveira

Antibiotics 2021, 10(7), 759; https://doi.org/10.3390/antibiotics10070759 - 22 Jun 2021

Cited by 4 | Viewed by 2985

Abstract

Despite the fact that freshwater fish populations are experiencing severe declines worldwide, our knowledge on the interaction between endangered populations and pathogenic agents remains scarce. In this study, we investigated the prevalence and structure of Aeromonas communities isolated from the critically endangered Iberochondrostoma lusitanicum, a model species for threatened Iberian leuciscids, as well as health parameters in this species. Additionally, we evaluated the virulence profiles, antimicrobial resistance signatures and genomic relationships of the Aeromonas isolates. Lesion prevalence, extension and body condition were deeply affected by location and seasonality, with poorer performances in the dry season. Aeromonas composition shifted among seasons and was also different across river streams. The pathogenic potential of the isolates significantly increased during the dry season. Additionally, isolates displaying clinically relevant antimicrobial resistance phenotypes (carbapenem and fluroquinolone resistance) were detected. As it inhabits intermittent rivers, often reduced to disconnected pools during the summer, the dry season is a critical period for I. lusitanicum, with lower general health status and a higher potential of infection by Aeromonas spp. Habitat quality seems a determining factor on the sustainable development of this fish species. Also, these individuals act as reservoirs of important antimicrobial resistant bacteria with potential implications for public health. Full article

(This article belongs to the Special Issue Antimicrobial and Antimicrobial Resistance in the Environment)

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Review

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22 pages, 951 KiB

Open AccessReview

Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications

by Joseph Kusi, Catherine Oluwalopeye Ojewole, Akinloye Emmanuel Ojewole and Isaac Nwi-Mozu

Antibiotics 2022, 11(6), 821; https://doi.org/10.3390/antibiotics11060821 - 18 Jun 2022

Cited by 11 | Viewed by 4897

Abstract

Human health is threatened by antibiotic-resistant bacteria and their related infections, which cause thousands of human deaths every year worldwide. Surface waters are vulnerable to human activities and natural processes that facilitate the emergence and spread of antibiotic-resistant bacteria in the environment. This study evaluated the pathways and drivers of antimicrobial resistance (AR) in surface waters. We analyzed antibiotic resistance healthcare-associated infection (HAI) data reported to the CDC’s National Healthcare Safety Network to determine the number of antimicrobial-resistant pathogens and their isolates detected in healthcare facilities. Ten pathogens and their isolates associated with HAIs tested resistant to the selected antibiotics, indicating the role of healthcare facilities in antimicrobial resistance in the environment. The analyzed data and literature research revealed that healthcare facilities, wastewater, agricultural settings, food, and wildlife populations serve as the major vehicles for AR in surface waters. Antibiotic residues, heavy metals, natural processes, and climate change were identified as the drivers of antimicrobial resistance in the aquatic environment. Food and animal handlers have a higher risk of exposure to resistant pathogens through ingestion and direct contact compared with the general population. The AR threat to public health may grow as pathogens in aquatic systems adjust to antibiotic residues, contaminants, and climate change effects. The unnecessary use of antibiotics increases the risk of AR, and the public should be encouraged to practice antibiotic stewardship to decrease the risk. Full article

(This article belongs to the Special Issue Antimicrobial and Antimicrobial Resistance in the Environment)

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