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Risk Assessment of Water Resources and Food: Microbial Contaminants, Antibiotics...
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Risk Assessment of Water Resources and Food: Microbial Contaminants, Antibiotics and Antibiotic Resistance Genes

A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Water and One Health".

Deadline for manuscript submissions: closed (15 May 2022) | Viewed by 18908

Special Issue Editors

Dr. Abasiofiok Mark Ibekwe

E-Mail Website
Guest Editor
U.S. Salinity Laboratory, USDA-ARS, 450 West Big Springs Road, Riverside, CA 92507, USA
Interests: antibiotic-resistant bacteria (ARB); antibiotics resistance genes (ARGs); microbial community; pathogen; constructed wetlands; metagenomics; microbial ecology; fate and transport
Special Issues, Collections and Topics in MDPI journals
Dr. Adelumola Oladeinde

E-Mail Website
Co-Guest Editor
Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center USDA Agricultural Research Service, 950 College Station Rd, Athens, GA 30605
Interests: microbial ecology of food-borne pathogens; antimicrobial resistance in poultry production settings

Special Issue Information

Dear Colleagues,

Antibiotic resistance is a global health threat, and to reduce the spread of resistance, we must consider the possible sources and understand the pathway and mechanisms by which resistance are disseminated. To combat this problem many international organizations have developed Risk Assessment protocols and action plans for combating antibiotic resistant bacteria that emphasizes monitoring antimicrobial susceptibilities of selected bacteria, modelling patterns/impacts of antibiotic use in food/food-producing animals and developing mitigation procedures to reduce the dissemination of antimicrobial resistance (AMR) to production environments. The dissemination of antibiotic resistance can be attributed to the transfer of bacterial mobile antibiotic resistance gene (ARGs) across different environmental niches. Therefore, in this special issue, we plan to present papers that identify the transfer network of the mobile resistome and the selection forces driving acquisition of AMR in many ecosystems. Papers dealing with the root sources and causes of AMR and the role of environmental processes in AMR dissemination will be of higher priority. As it is true of many other grand challenges, AMR is a complex problem that requires a holistic approach that advocate for a “One Health” perspective that simultaneously addresses the impacts of AMR on humans, animals, and the environment. Review papers and others dealing with AMR holistically will be highly welcome.

Dr. Abasiofiok Mark Ibekwe
Dr. Adelumola Oladeinde
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. Water is an international peer-reviewed open access semimonthly 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 2600 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

  • Food safety
  • Wastewater quality
  • Indicator bacteria, pathogens, and virulence factors
  • Microbiological, chemical, and ecotoxicological assessments
  • Antibiotic resistance genes/bacteria in surface water and irrigation water
  • Horizontal gene transfer (HGT) (Mobile genetic transfer-conjugation, transformation, and transduction)
  • Antibiotic pollution
  • Emergence and potential spread of antibiotic resistance
  • Emerging pollutants
  • Effluent discharges

Published Papers (5 papers)

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Research

11 pages, 431 KiB  
Article
Prevalence of Antibiotic Resistance Genes in Pharmaceutical Wastewaters
by Amarachukwu Obayiuwana, Adeniyi Ogunjobi and Abasiofiok Ibekwe
Water 2021, 13(13), 1731; https://doi.org/10.3390/w13131731 - 23 Jun 2021
Cited by 5 | Viewed by 2697
Abstract
Pharmaceutical wastewaters are recognized as reservoirs of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), and also as hotspots for their horizontal gene transfer (HGT) using mobile genetic elements. Our study employed the use of PCR analysis of metagenomic DNA samples obtained [...] Read more.
Pharmaceutical wastewaters are recognized as reservoirs of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), and also as hotspots for their horizontal gene transfer (HGT) using mobile genetic elements. Our study employed the use of PCR analysis of metagenomic DNA samples obtained from four pharmaceutical wastewaters using known primers to study the prevalence of thirty-six ARGs and four MGEs active against the commonly used antibiotics in Nigeria. The ARGs most frequently detected from the metagenomic DNA samples in each of the antibiotic classes under study include tetracycline [tet(G)], aminoglycoside [aadA, strA and strB], chloramphenicol [catA1], sulphonamides [sulI and sulII], and β-lactams and penicillins [blaOXA]. The ARGs showed a 100% prevalence in their various environmental sources. The pharmaceutical facility PFIV showed the highest concentration of ARGs in this study. The highest concentration for MGEs was shown by pharmaceutical facility PFIII, positive for intl1, intl2, and IFS genes. This study highlights the wide distribution of ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens. Full article
(This article belongs to the Special Issue Risk Assessment of Water Resources and Food: Microbial Contaminants, Antibiotics and Antibiotic Resistance Genes)
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22 pages, 4138 KiB  
Article
The Effect of the Effluent from a Small-Scale Conventional Wastewater Treatment Plant Treating Municipal Wastewater on the Composition and Abundance of the Microbial Community, Antibiotic Resistome, and Pathogens in the Sediment and Water of a Receiving Stream
by Kertu Tiirik, Hiie Nõlvak, Marika Truu, Angela Peeb, Margit Kõiv-Vainik and Jaak Truu
Water 2021, 13(6), 865; https://doi.org/10.3390/w13060865 - 23 Mar 2021
Cited by 7 | Viewed by 3923
Abstract
The effluents of wastewater treatment plants (WWTPs) are major contributors of nutrients, microbes—including those carrying antibiotic resistance genes (ARGs)—and pathogens to receiving waterbodies. The effect of the effluent of a small-scale activated sludge WWTP treating municipal wastewater on the composition and abundance of [...] Read more.
The effluents of wastewater treatment plants (WWTPs) are major contributors of nutrients, microbes—including those carrying antibiotic resistance genes (ARGs)—and pathogens to receiving waterbodies. The effect of the effluent of a small-scale activated sludge WWTP treating municipal wastewater on the composition and abundance of the microbial community as well as the antibiotic resistome and pathogens in the sediment and water of the receiving stream and river was studied using metagenome sequencing and a quantitative approach. Elevated Bacteroidetes proportions in the prokaryotic community, heightened sulfonamide and aminoglycoside resistance determinants proportions, and an increase of up to three orders of magnitude of sul1–sul2–aadA–blaOXA2 gene cluster abundances were recorded in stream water and sediments 0.3 km downstream of a WWTP discharge point. Further downstream, a gradual recovery of affected microbial communities along a distance gradient from WWTP was recorded, culminating in the mostly comparable state of river water and sediment parameters 3.7 km downstream of WWTP and stream water and sediments upstream of the WWTP discharge point. Archaea, especially Methanosarcina, Methanothrix, and Methanoregula, formed a substantial proportion of the microbial community of WWTP effluent as well as receiving stream water and sediment, and were linked to the spread of ARGs. Opportunistic environmental-origin pathogens were predominant in WWTP effluent and receiving stream bacterial communities, with Citrobacter freundii proportion being especially elevated in the close vicinity downstream of the WWTP discharge point. Full article
(This article belongs to the Special Issue Risk Assessment of Water Resources and Food: Microbial Contaminants, Antibiotics and Antibiotic Resistance Genes)
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15 pages, 7070 KiB  
Article
Comparative Use of Quantitative PCR (qPCR), Droplet Digital PCR (ddPCR), and Recombinase Polymerase Amplification (RPA) in the Detection of Shiga Toxin-Producing E. coli (STEC) in Environmental Samples
by Mark A. Ibekwe, Shelton E. Murinda, Stanley Park, Amarachukwu Obayiuwana, Marcia A. Murry, Gregory Schwartz and Trygve Lundquist
Water 2020, 12(12), 3507; https://doi.org/10.3390/w12123507 - 13 Dec 2020
Cited by 8 | Viewed by 4221
Abstract
E. coli O157:H7 is a foodborne pathogen that constitutes a global threat to human health. However, the quantification of this pathogen in food and environmental samples may be problematic at the low cell numbers commonly encountered in environmental samples. In this study, we [...] Read more.
E. coli O157:H7 is a foodborne pathogen that constitutes a global threat to human health. However, the quantification of this pathogen in food and environmental samples may be problematic at the low cell numbers commonly encountered in environmental samples. In this study, we used recombinase polymerase amplification (RPA) for the detection of E. coli O157:H7, real-time quantitative PCR (qPCR) for quantification, and droplet digital PCR (ddPCR) for absolute and accurate quantification of E. coli O157:H7 from spiked and environmental samples. Primer and probe sets were used for the detection of stx1 and stx2 using RPA. Genes encoding for stx1, stx2, eae, and rfbE were used to quantify E. coli O157:H7 in the water samples. Furthermore, duplex ddPCR assays were used to quantify the pathogens in these samples. Duplex assay set 1 used stx1 and rfbE genes, while assay set 2 used stx2 and eae genes. Droplet digital PCR was used for the absolute quantification of E. coli O15:H7 in comparison with qPCR for the spiked and environmental samples. The RPA results were compared to those from qPCR and ddPCR in order to assess the efficiency of the RPA compared with the PCR methods. The assays were further applied to the dairy lagoon effluent (DLE) and the high rate algae pond (HRAP) effluent, which were fed with diluted DLE. The RPA detected was <10 CFU/mL, while ddPCR showed quantification from 1 to 104 CFU/mL with a high reproducibility. In addition, quantification by qPCR was from 103 to 107 CFU/mL of the wastewater samples. Therefore, the RPA assay has potential as a point of care tool for the detection of E. coli O157:H7 from different environmental sources, followed by quantification of the target concentrations. Full article
(This article belongs to the Special Issue Risk Assessment of Water Resources and Food: Microbial Contaminants, Antibiotics and Antibiotic Resistance Genes)
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19 pages, 2496 KiB  
Article
Occurrence of Extended Spectrum Beta-Lactamase Gram-Negative Bacteria from Non-Clinical Sources in Dubai, United Arab Emirates
by Munawwar A. Khan, Nicola E. Thurgood, Sultan M. Faheem, Naushad Rais, Mohammad Z. Ansari, Sultan M. Kaleem and Shams T. Khan
Water 2020, 12(9), 2562; https://doi.org/10.3390/w12092562 - 14 Sep 2020
Cited by 6 | Viewed by 3231
Abstract
Extended-spectrum beta-lactamase (ESBL) producing bacteria of the Enterobacteriaceae family are a significant threat to public health, posing a challenge for health authorities worldwide. In the UAE, very little information is available about ESBL producing bacteria from non-clinical sources. In this study, 206 pure [...] Read more.
Extended-spectrum beta-lactamase (ESBL) producing bacteria of the Enterobacteriaceae family are a significant threat to public health, posing a challenge for health authorities worldwide. In the UAE, very little information is available about ESBL producing bacteria from non-clinical sources. In this study, 206 pure cultures belonging to the Enterobacteriaceae family were isolated from food and wastewater sources in Dubai, UAE. All the isolates were tested against third-generation cephalosporin antibiotics by the disc diffusion method and screened on ESBL chromogenic agar. Among all isolates (n = 86), 41.7% were potential ESBL producers belonging to E. coli, Klebsiella, Enterobacter, Shigella, and Citrobacter (KESC group), and Proteus. Of all the potential ESBL producing isolates, 19 (22%) were confirmed as ESBL producers by a double-disc diffusion test with the fourth generation cephalosporin–Cefpirome. The multiplex polymerase chain reaction was used for the detection of ESBL bla genes in the screened isolates. Out of a total of 86 isolates, 52.3% possessed only the blaTEM gene; 39.5% contained both blaTEM and blaSHV genes, while only 3.5% contained the blaCTX-M gene. The carbapenemase resistance test showed eight isolates resistant to imipenem, and only one isolate with metallo-beta-lactamase activity. This study highlights the occurrence of ESBL bla genes among non-clinical isolates from food and wastewater sources in the UAE and emphasizes the importance of food and wastewater surveillance programs in controlling the spread of antibiotic resistance. Full article
(This article belongs to the Special Issue Risk Assessment of Water Resources and Food: Microbial Contaminants, Antibiotics and Antibiotic Resistance Genes)
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11 pages, 499 KiB  
Article
Antibiotic Resistance Genes Occurrence in Wastewaters from Selected Pharmaceutical Facilities in Nigeria
by Amarachukwu Obayiuwana and Abasiofiok M. Ibekwe
Water 2020, 12(7), 1897; https://doi.org/10.3390/w12071897 - 03 Jul 2020
Cited by 22 | Viewed by 4135
Abstract
The proliferation of antibiotic-resistant bacteria (ARB) and the prevalence of antibiotic resistance genes (ARGs) in wastewaters are well-established factors that contribute to the reduced potency of antibiotics used in healthcare worldwide. The human health risk associated with the proliferation of ARB and ARGs [...] Read more.
The proliferation of antibiotic-resistant bacteria (ARB) and the prevalence of antibiotic resistance genes (ARGs) in wastewaters are well-established factors that contribute to the reduced potency of antibiotics used in healthcare worldwide. The human health risk associated with the proliferation of ARB and ARGs need to be understood in order to design mitigation measures to combat their dissemination. Using the PCR analysis of genomic DNA, the prevalence of 41 ARGs active against the commonly used six classes of antibiotics was evaluated in 60 bacterial isolates obtained from pharmaceutical wastewaters in Nigeria. The ARGs most frequently detected from the bacterial isolates in each of the antibiotic classes under study include catA1 (58.3%); sulI (31.7%); tet(E) (30%); aac(3)-IV (28.3%); ermC (20%); blaTEM, blaCTX-M, blaNDM-1 at 18.3% each; which encode for resistance to chloramphenicol, sulfonamides, tetracycline, aminoglycoside, macrolide-lincosamide-streptogramin and β-lactams and penicillins, respectively. Acinetobacter spp., accession number MH396735 expressed the highest number of ARGs of all the bacterial isolates, having at least one gene that encodes for resistance to all the classes of antibiotics in the study. This study highlights wide distribution of ARB and ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens. Full article
(This article belongs to the Special Issue Risk Assessment of Water Resources and Food: Microbial Contaminants, Antibiotics and Antibiotic Resistance Genes)
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