Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
6.4
4.5
Journals
Microorganisms
Special Issues
Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants
share announcement

Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants

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

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 15865

Special Issue Editors

Dr. Seong-Jae Kim

E-Mail Website
Guest Editor
Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
Interests: detection of microbial contamination; tattoo ink microbiology; food microbiology; evaluation of microbial contaminants; mycobacteria; bacterial biodegradation; industrial microbiology
Dr. Ohgew Kweon

E-Mail Website
Guest Editor
Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
Interests: detection of microbial contaminants; multi-omics approach to identify an antimicrobial resistance marker; comparative study to evaluate molecular assays; next generation sequencing (NGS); food microbiology; virulence factors; bioinformatics methods
Dr. Sunghyun Yoon

E-Mail Website
Guest Editor
National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, USA
Interests: antimicrobial resistance; whole genome sequencing; virulence factors; Staphylococcus aureus; Salmonella; veterinary microbiology
Dr. Sandeep Kondakala

E-Mail Website
Guest Editor
National Center for Toxicological Research, U.S. FDA, Jefferson, AR 72079, USA
Interests: pesticide exposure; obesity; endocannabinoids; microbial genetics; gut microbe; toxicology bioremediation
Special Issues, Collections and Topics in MDPI journals
Dr. Minjae Kim

E-Mail Website
Guest Editor
Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, USA
Interests: environmental microbiology; human microbiome; cross resistance between disinfectants and antibiotics

Special Issue Information

Dear Colleagues,

Microbiological contamination, the unintended or accidental introduction of microorganisms such as bacteria, yeast, mold, fungi, virus, prions, protozoa, or their toxins and byproducts, is a worldwide public health concern. Most countries have documented significant increases in the incidence of diseases caused by microbial contaminants over the past few decades. Microbiological contamination can happen through various means in food, pharmaceutical drugs, cosmetics, medical devices, etc. A great deal of progress is currently being made in the detection of pathogenic microorganisms and in understanding their fate in the environment, essential for practical risk assessments for all stakeholders, including end users. This Special Issue seeks to gather papers on various aspects of microbial contamination, including microbiological surveys of emerging pathogens and studies on the relationship between microbial contamination and health effects. We especially encourage the submission of interdisciplinary work and manuscripts related to 1) new detection methods for microbiological surveys, such as the use of next-generation sequencing (NGS), 2) genotypic and phenotypic characterization of pathogenic contaminants, and 3) antimicrobial resistance of microbial contaminants. In this Special Issue, there are many possible objects of microbiological contamination, including but not limited to food, pharmaceutical drugs, cosmetics, tattoo inks, medical devices, and the environment of clinical hospitals. We welcome original research papers as well as reviews

Dr. Seong-Jae Kim
Dr. Ohgew Kweon
Dr. Sunghyun Yoon
Dr. Sandeep Kondakala
Dr. Minjae Kim
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

  • microbiological survey
  • microbial contamination
  • detection method
  • pathogenic contaminant
  • risk assessment
  • genotype
  • phenotype
  • food microbiology
  • antimicrobial susceptibility
  • antimicrobial resistance
  • virulence factors
  • endotoxin
  • mutation
  • food animal
  • next-generation sequencing (NGS)

Published Papers (7 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Editorial

Jump to: Research

5 pages, 200 KiB  
Editorial
Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants
by Sunghyun Yoon, Sandeep Kondakala, Minjae Kim, Steven L. Foley, Ohgew Kweon and Seongjae Kim
Microorganisms 2023, 11(5), 1350; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11051350 - 22 May 2023
Viewed by 1404
Abstract
Microbial contamination is the inadvertent presence of microbes or their byproducts in materials or environments [...] Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)

Research

Jump to: Editorial

11 pages, 1498 KiB  
Article
Distribution and Characterization of Antimicrobial Resistant Pathogens in a Pig Farm, Slaughterhouse, Meat Processing Plant, and in Retail Stores
by Dongryeoul Bae, Donah Mary Macoy, Waqas Ahmad, Son Peseth, Binn Kim, Jung-Whan Chon, Gyeong Ryul Ryu, Ga-Hee Ban, Sun Ae Kim, Hye Jeong Kang, Jin San Moon and Min Gab Kim
Microorganisms 2022, 10(11), 2252; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112252 - 14 Nov 2022
Cited by 2 | Viewed by 2696
Abstract
The emergence of antibiotic resistance in foodborne pathogens isolated from meat pro-ducts and their producing environment has been an increasing and leading threat to public health. The aim of the study was to identify pathogens and their antimicrobial resistance isolated from pig production [...] Read more.
The emergence of antibiotic resistance in foodborne pathogens isolated from meat pro-ducts and their producing environment has been an increasing and leading threat to public health. The aim of the study was to identify pathogens and their antimicrobial resistance isolated from pig production to pork meat distribution phases. Through this study, food spoilage and foodborne or clinical pathogenic bacteria were isolated and identified from pork (belly and neck) meat product and its related environmental samples that include pig swabs, diets, feces, liquid manure, workers’ gloves, dust fan swabs, carcass swabs, floor swabs, and drain water in the affiliated farm, slaughterhouse, meat processing plant, and in retail stores. All carcasses at the slaughterhouse and meat products at the meat processing plant were tracked from pigs at a targeted farm. Nine different selective media agars were used to effectively isolate various pathogenic bacteria. A total of 283 presumptive pathogenic bacteria isolated from 126 samples were selected and identified using MALDI-ToF MS. Twenty-three important foodborne pathogens were identified, and some of them, Shiga-toxin-producing E. coli (STEC), Listeria monocytogenes, Staphylococcus aureus, and Yersinia enterocolitica, were further confirmed using PCR. The PFGE patterns of 12 STEC isolates were grouped by sample source or site. All the foodborne pathogens used in the study were not resistant to amoxicillin/clavulanate, ciprofloxacin, and gentamicin, whereas some of the STEC, L. monocytogenes, and S. aureus isolates were resistant to various antibiotics, including ampicillin, erythromycin, tetracycline, and vancomycin. The most common antimicrobial resistance pattern in the pathogenic STEC isolates was AMP-KAN-STR-SXT-TET. Consequently, this study provides valuable information for the distribution of antimicrobial-resistant pathogens along the pork meat production chain and can assist farmers and stakeholders to develop a systematic strategy for reducing the current emergence and spread of antimicrobial resistance in the different phases of pig production and distribution. Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)
►▼ Show Figures

Figure 1

11 pages, 2467 KiB  
Article
Inactivation of Airborne Avian Pathogenic E. coli (APEC) via Application of a Novel High-Pressure Spraying System
by Dongryeoul Bae, Kwang-Young Song, Donah Mary Macoy, Min Gab Kim, Chul-Kyu Lee and Yu-Seong Kim
Microorganisms 2022, 10(11), 2201; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112201 - 07 Nov 2022
Cited by 2 | Viewed by 1774
Abstract
Infectious diseases of livestock caused by novel pathogenic viruses and bacteria are a major threat to global animal health and welfare and their effective control is crucial for agronomic health and for securing global food supply. It has been widely recognized that the [...] Read more.
Infectious diseases of livestock caused by novel pathogenic viruses and bacteria are a major threat to global animal health and welfare and their effective control is crucial for agronomic health and for securing global food supply. It has been widely recognized that the transmission of infectious agents can occur between people and/or animals in indoor spaces. Therefore, infection control practices are critical to reduce the transmission of the airborne pathogens. ViKiller®-high-pressure sprayer and Deger®-disinfectant are newly developed spraying systems that can produce an optimal size of disinfectants to reduce airborne microbes. The system was evaluated to reduce the infection caused by avian pathogenic Escherichia coli (APEC), an airborne bacterium which survives in indoor spaces. pH-neutral electrolyzed water (NEW) containing 100 ppm of free chlorine, laboratory-scale chambers, a recently developed sprayer, and a conventional sprayer were used in the study. A total of 123 day-of-hatch male layer chicks (Hy-Line W-36) were randomly classified into five groups (negative control (NC): no treatment; treatment 1 (Trt 1): spraying only NEW without APEC; treatment 2 (Trt 2): spraying NEW + APEC using a high-pressure sprayer; treatment 3 (Trt 3): spraying NEW + APEC using a conventional sprayer; positive control (PC): spraying only APEC). Experimental chicks in the chambers were daily exposed to 50 mL of NEW and/or APEC (1.0 × 106 cfu/mL) until the end of the experiment (day 35). APEC strains were sprayed by ViKiller®. At least four chicks in each group were evaluated weekly to monitor APEC infection and determine the lesion. Data showed that our spraying system significantly reduced airborne APEC concentrations, mortality rate, respiratory infection, and APEC lesions in birds in the chamber space (p < 0.05). The results demonstrate that the antibacterial effect of the novel spraying sprayer with NEW on APEC was far superior compared to the conventional sprayer. This study provides a new insight for preventive measures against airborne microorganisms in indoor spaces. Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)
►▼ Show Figures

Figure 1

14 pages, 3633 KiB  
Article
Specific Detection and Enumeration of Burkholderia cepacia Complex by Flow Cytometry Using a Fluorescence-Labeled Oligonucleotide Probe
by Soumana Daddy Gaoh, Anna Williams, David Le, Ohgew Kweon, Pierre Alusta, Dan A. Buzatu and Youngbeom Ahn
Microorganisms 2022, 10(6), 1170; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061170 - 07 Jun 2022
Cited by 3 | Viewed by 2072
Abstract
Burkholderia cepacia complex (BCC) contamination has resulted in recalls of non-sterile pharmaceutical products. The fast, sensitive, and specific detection of BCC is critical for ensuring the quality and safety of pharmaceutical products. In this study, a rapid flow cytometry-based detection method was developed [...] Read more.
Burkholderia cepacia complex (BCC) contamination has resulted in recalls of non-sterile pharmaceutical products. The fast, sensitive, and specific detection of BCC is critical for ensuring the quality and safety of pharmaceutical products. In this study, a rapid flow cytometry-based detection method was developed using a fluorescence-labeled oligonucleotide Kef probe that specifically binds a KefB/KefC membrane protein sequence within BCC. Optimal conditions of a 1 nM Kef probe concentration at a 60 °C hybridization temperature for 30 min were determined and applied for the flow cytometry assay. The true-positive rate (sensitivity) and true-negative rate (specificity) of the Kef probe assay were 90% (18 positive out of 20 BCC species) and 88.9% (16 negative out of 18 non-BCC), respectively. The detection limit for B. cenocepacia AU1054 with the Kef probe flow cytometry assay in nuclease-free water was 1 CFU/mL. The average cell counts using the Kef probe assay from a concentration of 10 μg/mL chlorhexidine gluconate and 50 μg/mL benzalkonium chloride were similar to those of the RAPID-B total plate count (TPC). We demonstrate the potential of Kef probe flow cytometry as a more sensitive alternative to culture-based methods for detecting BCC in non-sterilized pharmaceutical raw materials and products with regards to water-based environments. Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)
►▼ Show Figures

Figure 1

13 pages, 1265 KiB  
Article
A Propidium Monoazide (PMAxx)-Droplet Digital PCR (ddPCR) for the Detection of Viable Burkholderia cepacia Complex in Nuclease-Free Water and Antiseptics
by Soumana Daddy Gaoh, Ohgew Kweon, Yong-Jin Lee, David Hussong, Bernard Marasa and Youngbeom Ahn
Microorganisms 2022, 10(5), 943; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050943 - 30 Apr 2022
Cited by 11 | Viewed by 2484
Abstract
Pharmaceutical products contaminated with Burkholderia cepacia complex (BCC) strains constitute a serious health issue for susceptible individuals. New detection methods to distinguish DNA from viable cells are required to ensure pharmaceutical product quality and safety. In this study, we have assessed a droplet [...] Read more.
Pharmaceutical products contaminated with Burkholderia cepacia complex (BCC) strains constitute a serious health issue for susceptible individuals. New detection methods to distinguish DNA from viable cells are required to ensure pharmaceutical product quality and safety. In this study, we have assessed a droplet digital PCR (ddPCR) with a variant propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in autoclaved nuclease-free water after 365 days, in 0.001% chlorhexidine gluconate (CHX), and in 0.005% benzalkonium chloride (BZK) solutions after 184 days. Using 10 μM PMAxx and 5 min light exposure, a proportion of dead BCC was quantified by ddPCR. The detection limit of culture-based method was 104 CFU/mL, equivalent to 9.7 pg/μL for B. cenocepacia J2315, while that of ddPCR was 9.7 fg/μL. The true positive rate from nuclease-free water and CHX using PMAxx-ddPCR assay was 60.0% and 38.3%, respectively, compared to 85.0% and 74.6% without PMAxx (p < 0.05), respectively. However, in BZK-treated cells, no difference in the detection rate was observed between the ddPCR assay on samples treated with PMAxx (67.1%) and without PMAxx (63.3%). This study shows that the PMAxx-ddPCR assay provides a better tool for selective detection of live BCC cells in non-sterile pharmaceutical products. Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)
►▼ Show Figures

Figure 1

9 pages, 963 KiB  
Article
Microbiological Survey of 47 Permanent Makeup Inks Available in the United States
by Sunghyun Yoon, Sandeep Kondakala, Seong Won Nho, Mi Sun Moon, Mei Chiung J. Huang, Goran Periz, Ohgew Kweon and Seongjae Kim
Microorganisms 2022, 10(4), 820; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10040820 - 15 Apr 2022
Cited by 3 | Viewed by 2266
Abstract
In two previous surveys, the U.S. Food and Drug Administration (FDA) identified microbial contamination in 53 of 112 (47%) unopened tattoo inks and tattoo-ink-related products (e.g., diluents) from 15 manufacturers in the U.S. In this study, we primarily focused our microbiological survey on [...] Read more.
In two previous surveys, the U.S. Food and Drug Administration (FDA) identified microbial contamination in 53 of 112 (47%) unopened tattoo inks and tattoo-ink-related products (e.g., diluents) from 15 manufacturers in the U.S. In this study, we primarily focused our microbiological survey on permanent makeup (PMU) inks. We conducted a survey of 47 unopened PMU inks from nine manufacturers and a comparative species-centric co-occurrence network (SCN) analysis using the survey results. Aerobic plate count and enrichment culture methods using the FDA’s Bacteriological Analytical Manual (BAM) Chapter 23 revealed that 9 (19%) inks out of 47, from five manufacturers, were contaminated with microorganisms. The level of microbial contamination was less than 250 CFU/g in eight inks and 980 CFU/g in one ink. We identified 26 bacteria that belong to nine genera and 21 species, including some clinically relevant species, such as Alloiococcus otitis, Dermacoccus nishinomiyaensis, Kocuria rosea, and Pasteurella canis. Among the identified microorganisms, the SCN analysis revealed dominance and a strong co-occurrence relation of spore-forming extreme environment survivors, Bacillus spp., with close phylogenetic/phenotypic relationships. These results provide practical insights into the possible microbial contamination factors and positive selection pressure of PMU inks. Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)
►▼ Show Figures

Figure 1

10 pages, 1152 KiB  
Article
Molecular Typing, Antibiotic Resistance and Enterotoxin Gene Profiles of Staphylococcus aureus Isolated from Humans in South Korea
by Sunghyun Yoon, Yon Kyoung Park, Tae Sung Jung and Seong Bin Park
Microorganisms 2022, 10(3), 642; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030642 - 17 Mar 2022
Cited by 2 | Viewed by 1953
Abstract
The emergence of antimicrobial-resistant Staphylococcus aureus has become a grave concern worldwide. In this study, 95 strains of S. aureus isolated from stool samples were collected from Busan, South Korea to characterize their antimicrobial susceptibility, enterotoxin genes, and molecular typing using matrix-assisted laser [...] Read more.
The emergence of antimicrobial-resistant Staphylococcus aureus has become a grave concern worldwide. In this study, 95 strains of S. aureus isolated from stool samples were collected from Busan, South Korea to characterize their antimicrobial susceptibility, enterotoxin genes, and molecular typing using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and random amplification of polymorphic DNA (RAPD) assay. Only two strains showed no drug resistance, whereas resistance to three or more antibiotics was observed in 87.4% of strains. Ampicillin resistance was the most common at 90% and all strains were susceptible to vancomycin. The distribution of enterotoxin genes encoded in isolates was sea (32.6%), sec (11.6%), seg (19%), sea & sec (2.1%), and sec & seg (34.7%). Molecular typing using both MALDI-TOF MS and RAPD indicated that S. aureus exhibited diverse clonal lineages and no correlations were observed among the profiling of enterotoxin, MALDI-TOF MS, and RAPD. This investigation provides useful information on foodborne pathogenic S. aureus that has a significant public health impact in South Korea. Full article
(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-7
Back to TopTop