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Tuo J, Shen Y, Jia S, Liu S, Zhang Q, Wang D, He X, Liu P, Zhang XX. HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment. WATER RESEARCH 2024; 260:121927. [PMID: 38941866 DOI: 10.1016/j.watres.2024.121927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/30/2024]
Abstract
Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.
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Affiliation(s)
- Jinhua Tuo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengnan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qifeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Abu-Halaweh M, Al-Bsoul E. Quadruplex qPCR for detection and discrimination of C. Coli,C. fetus, and C. Jejuni from other Campylobacter species in chicken and sheep meat. Braz J Microbiol 2024:10.1007/s42770-024-01437-4. [PMID: 38977544 DOI: 10.1007/s42770-024-01437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
Campylobacter is gram-negative bacteria considered the predominant genera isolated from poultry samples and associated with gastroenteritis. Due to the problems in conventional cultural methods of time-consuming and technically demanding requirements, a rapid and feasible method for their identification and discrimination of the closely related spp. Including Campylobacter coli, Campylobacter fetus, and Campylobacter jejuni is needed. This study analyzes the chicken and sheep meats samples (n = 125) using culture and pre-enrichment-based Quadraplex real-time PCR by targeting OrfA, CstA, HipO, and 16 S rRNA genes of C. coli, C. fetus, C. jejuni and Campylobacter spp. Respectively. The analysis of 125 chicken and sheep meat samples by culture and real-time PCR showed high concordance between the results of the two methods. The present study show high prevalence of Campylobacter species (35% and 32% from chicken and meat respectively) of which C. jejuni were the most abundant. Reaction efficiencies were between 90 and 110%, and detect as low as 8.9 fg in C. jejuni. The need for quick detection and discrimination methods in sheep and chicken meat can be met using the described Quadraplex real-time PCR methodology.
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Affiliation(s)
- Marwan Abu-Halaweh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan.
| | - Eman Al-Bsoul
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
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Asif A, Chen JS, Hussain B, Hsu GJ, Rathod J, Huang SW, Wu CC, Hsu BM. The escalating threat of human-associated infectious bacteria in surface aquatic resources: Insights into prevalence, antibiotic resistance, survival mechanisms, detection, and prevention strategies. JOURNAL OF CONTAMINANT HYDROLOGY 2024; 265:104371. [PMID: 38851127 DOI: 10.1016/j.jconhyd.2024.104371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Anthropogenic activities and climate change profoundly impact water quality, leading to a concerning increase in the prevalence and abundance of bacterial pathogens across diverse aquatic environments. This rise has resulted in a growing challenge concerning the safety of water sources, particularly surface waters and marine environments. This comprehensive review delves into the multifaceted challenges presented by bacterial pathogens, emphasizing threads to human health within ground and surface waters, including marine ecosystems. The exploration encompasses the intricate survival mechanisms employed by bacterial pathogens and the proliferation of antimicrobial resistance, largely driven by human-generated antibiotic contamination in aquatic systems. The review further addresses prevalent pathogenic bacteria, elucidating associated risk factors, exploring their eco-physiology, and discussing the production of potent toxins. The spectrum of detection techniques, ranging from conventional to cutting-edge molecular approaches, is thoroughly examined to underscore their significance in identifying and understanding waterborne bacterial pathogens. A critical aspect highlighted in this review is the imperative for real-time monitoring of biomarkers associated with waterborne bacterial pathogens. This monitoring serves as an early warning system, facilitating the swift implementation of action plans to preserve and protect global water resources. In conclusion, this comprehensive review provides fresh insights and perspectives, emphasizing the paramount importance of preserving the quality of aquatic resources to safeguard human health on a global scale.
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Affiliation(s)
- Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment, and Mathematics, National Chung Cheng University, Chiayi County, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Disease and Department of Internal Medicine, Chiayi Christian Hospital, Chiayi, Taiwan
| | - Jagat Rathod
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance and Tec (GIFT)-City, Gandhinagar 382355, Gujarat, India
| | - Shih-Wei Huang
- Institute of Environmental Toxin and Emerging Contaminant, Cheng Shiu University, Kaohsiung, Taiwan; Center for Environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan
| | - Chin-Chia Wu
- Division of Colorectal Surgery, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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Martins WF, Severo DDS, Longhi DA, de Aragão GMF. Comparison of SYBR® Green qPCR assay and plate count method to describe growth of Weissella viridescens and Leuconostoc mesenteroides in pure and mixed cultivation. Food Microbiol 2024; 119:104452. [PMID: 38225053 DOI: 10.1016/j.fm.2023.104452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/28/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024]
Abstract
The current study was conducted to statistically compare the SYBR® Green quantitative polymerase chain reaction (qPCR) assay and the conventional plate counting (PC) method to construct growth curves of a cocktail of Weissella viridescens in pure culture under different isothermal storage conditions (4, 8, 14, and 30 °C) and in mixed culture with Leuconostoc mesenteroides at 8 °C. The efficiency and specificity of the qPCR standard curves were confirmed, and both methods were adequate to quantify the growth kinetics of W. viridescens at all isothermal temperatures, demonstrating a good correlation and agreement. The efficiencies of the standard curves varied between 98% and 102%. The SYBR® Green qPCR assay was also able to differentiate the growth curves of W. viridescens and L. mesenteroides in the mixed culture at 8 °C. Additionally, the SYBR® Green qPCR method was considered a faster and more sensitive alternative to construct growth curves under different isothermal conditions and differentiate morphologically similar lactic acid bacteria. Overall, the results suggest that the SYBR® Green qPCR method is a reliable and efficient tool to study microbial growth kinetics in pure and mixed cultures.
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Affiliation(s)
- Wiaslan Figueiredo Martins
- Department of Food Technology, Goiano Federal Institute of Education, Science, and Technology, IF Goiano/Morrinhos Campus, Zip Code 75650-000, Morrinhos, GO, Brazil; Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil.
| | - Danielle de Sousa Severo
- Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil
| | - Daniel Angelo Longhi
- LaBeM - Laboratory of Bioactives and Microbiology, School of Food Engineering, Federal University of Paraná, UFPR/Jandaia do Sul Campus, Zip Code 86900-000, Jandaia do Sul, PR, Brazil
| | - Gláucia Maria Falcão de Aragão
- Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil
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Turanoglu B, Omeroglu MA, Baltaci MO, Adiguzel G, Adiguzel A. Determination of foodborne pathogens in minced beef by real-time PCR without culture enrichment. J Microbiol Methods 2024; 219:106896. [PMID: 38341180 DOI: 10.1016/j.mimet.2024.106896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 12/27/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Meat provides the necessary environment for the growth of foodborne pathogens due to its features such as being rich in protein and having sufficient water activity. Listeria monocytogenes, Salmonella enterica, and Escherichia coli O157:H7, which can be transmitted through many foods, including water, and cause serious diseases, are among the significant pathogens. In the current study. Detection of Listeria monocytogenes, Escherichia coli and Salmonella enterica in 100 minced beef samples collected from different butchers and markets situated in the central districts of Erzurum province was performed by Real-Time PCR without pre-enrichment and DNA isolation. Linear regression equations of Ct values of standard pathogenic bacteria were created. Ct values of minced beef samples obtained as a result of Real-Time PCR analysis were substituted in the equations, and the amounts of pathogenic bacteria in the samples were determined. Listeria monocytogenes, Escherichia coli, and Salmonella enterica were detected in 45, 30, and 29 of 100 minced beef samples, respectively. It is known that the Real-Time PCR method, which is used to detect pathogenic bacteria, is more specific, fast, and reliable than conventional methods. According to the results obtained, it has been clearly observed that with our new approach, pathogenic bacteria growing on foods can be detected sensitively with less cost, shorter amount of time, and minimized workload without pre-enrichment and DNA isolation.
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Affiliation(s)
- Busra Turanoglu
- Department of Molecular Biology and Genetics, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Mehmet Akif Omeroglu
- Department of Molecular Biology and Genetics, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Mustafa Ozkan Baltaci
- Department of Molecular Biology and Genetics, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Gulsah Adiguzel
- Department of Food Science and Technology, Faculty of Veterinary Science, Ataturk University, Erzurum, Turkey
| | - Ahmet Adiguzel
- Department of Molecular Biology and Genetics, Faculty of Science, Ataturk University, Erzurum, Turkey.
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Gottel NR, Hill MS, Neal MJ, Allard SM, Zengler K, Gilbert JA. Biocontrol in built environments to reduce pathogen exposure and infection risk. THE ISME JOURNAL 2024; 18:wrad024. [PMID: 38365248 PMCID: PMC10848226 DOI: 10.1093/ismejo/wrad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.
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Affiliation(s)
- Neil R Gottel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
| | - Megan S Hill
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Maxwell J Neal
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
| | - Sarah M Allard
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Karsten Zengler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
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Jeong J, Song H, Kim WH, Chae M, Lee JY, Kwon YK, Cho S. Tracking the contamination sources of microbial population and characterizing Listeria monocytogenes in a chicken slaughterhouse by using culture-dependent and -independent methods. Front Microbiol 2023; 14:1282961. [PMID: 38098672 PMCID: PMC10720907 DOI: 10.3389/fmicb.2023.1282961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
Listeria monocytogenes is the etiologic agent of listeriosis, a foodborne disease that poses a threat to public health globally. Chicken meat exhibits heightened susceptibility to L. monocytogenes contamination during butchery. The persistence of this pathogen in the slaughterhouse environment enables recurring contamination of meat products. This study aimed at identifying the sources and transmission routes of L. monocytogenes contamination within an abattoir where it was consistently detected for three consecutive years (2019-2021). Furthermore, the environmental factors aiding contamination along chicken processing lines were determined by surveying the microbiome within the facility. Samples collected in 2019 to 2021 were subjected to culture-dependent analysis to assess the prevalence, serotypes, and multi-locus sequence typing (MLST) of L. monocytogenes. Additionally, the specimens collected in 2021 underwent culture-independent analysis via real-time quantitative polymerase chain reaction (qPCR) and 16S rRNA gene amplicon sequencing to identify the contamination sources and characterize the entire microbial community within the slaughterhouse. L. monocytogenes was isolated only from the clean zone, where the final slaughtering stage occurs. Most strains isolated from the final carcasses showed the same genetic cluster as the isolate in the chilling water and were assigned to MLST profile ST3. Culture-independent qPCR confirmed L. monocytogenes contamination in all samples, excluding post-scalding carcasses, prewashed post-evisceration carcasses, and the bleeding areas. Consequently, qPCR enabled more comprehensive identification of L. monocytogenes contamination points than culture-dependent approaches. Moreover, 16S rRNA gene amplicon sequencing demonstrated that psychro-tolerant and spoilage-related bacteria with L. monocytogenes-like attributes exhibited enhanced viability in the clean zone and immersion-chilling water. Metagenomics-based source tracking analysis further revealed that the shackles and chilling waters represent predominant sources of cross-contamination between different slaughterhouse zones, whereas the grading and packaging workstations and chilling water in the clean zone were deemed crucial sources affecting final carcass contamination. Collectively, these findings demonstrate through culture-dependent and -independent methods that L. monocytogenes spreads along the slaughter line, contaminating the slaughterhouse. Moreover, by investigating changes in microbial community and bacterial flow along the slaughter line within the facility, the sources influencing carcass contamination can be effectively traced.
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Affiliation(s)
- Jiyeon Jeong
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Hyokeun Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Woo-Hyun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Myeongju Chae
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Ji-Youn Lee
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Yong-Kuk Kwon
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
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Chen J, Zhong J, Lei H, Ai Y. Label-free multidimensional bacterial characterization with an ultrawide detectable concentration range by microfluidic impedance cytometry. LAB ON A CHIP 2023; 23:5029-5038. [PMID: 37909182 DOI: 10.1039/d3lc00799e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Rapid and accurate identification of bacteria is of great importance to public health in various fields, including medical diagnostics, food safety, and environmental monitoring. However, most existing bacterial detection methods have very narrow detectable concentration ranges and limited detection information, which easily leads to wrong diagnosis and treatment. This work presents a novel high-throughput microfluidic electrical impedance-based multidimensional single-bacterium profiling system for ultrawide concentration range detection and accurate differentiation of viability and Gram types of bacteria. The electrical impedance-based microfluidic cytometry is capable of multi-frequency impedance quantification, which allows profiling of the bacteria size, concentration, and membrane impedance as an indicator of bacterial viability and Gram properties in a single flow-through interrogation. It has been demonstrated that this novel impedance cytometry has an ultrawide bacterial counting range (102-108 cells per mL), and exhibits a rapid and accurate discrimination of viability and Gram types of bacteria in a label-free manner. Escherichia coli (E. coli) has been used as an analog species for the accuracy assessment of the electrical impedance-based bacterial detection system in an authentic complex beverage matrix within 24 hours. The impedance-based quantifications of viable bacteria are consistent with those obtained by the classical bacterial colony counting method (R2 = 0.996). This work could pave the way for providing a novel microfluidic cytometry system for rapid and multidimensional bacterial detection in diverse areas.
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Affiliation(s)
- Jiahong Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety/National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore.
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore.
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Barua S, Bailey M, Zhong K, Iduu N, Dormitorio T, Macklin K, Bourassa D, Price S, Hauck R, Krehling J, Kitchens S, Kyriakis C, Buhr RJ, Wang C. Research Note: Role of darkling beetles (Alphitobius diaperinus) and litter in spreading and maintaining Salmonella Enteritidis and Campylobacter jejuni in chicken flocks. Poult Sci 2023; 102:103061. [PMID: 37717478 PMCID: PMC10514072 DOI: 10.1016/j.psj.2023.103061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/19/2023] [Indexed: 09/19/2023] Open
Abstract
Salmonella and Campylobacter are common foodborne pathogens in chickens, but their persistence mechanisms within flocks are not fully understood. In this study, 4 groups of SPF Leghorn chickens (n = 50) were orally inoculated with 108Salmonella Enteritidis and 108Campylobacter jejuni, housed in BSL-2 rooms inside containers with autoclaved bedding and beetles (n = 200). Phase I (wk 1-3): the infected chickens remained in the containers and were then euthanized while beetles and litter remained in the container (group A), beetles were removed and litter remained in the container (group B), beetles remained and litter was removed (group C), and beetles and litter were removed (group D). Phase II (wk 5-7): autoclaved bedding was added to containers in groups C and D, and new SPF chickens (n = 50) were introduced and kept. Phase III (wk 8-20): all chickens were euthanized, and the litter and/or beetles remained in the containers for 17 wk. The prevalence of Salmonella Enteritidis and Campylobacter was significantly higher when detected by PCR compared to culture. In phase II, when infected chickens were removed and new chickens were introduced, 1 fecal sample in group B and 3 litter samples in groups B and C were found positive for Salmonella Enteritidis, and Campylobacter was still detected in groups A, B, and C litter samples, but not in beetles. In phase III, when all chickens were removed, Salmonella Enteritidis was identified in beetle samples from group A and the litter samples of all tested groups A, B, and C, and C. jejuni was positive in litter samples from groups A and B but not in the beetle. Sixty-nine days after removing infected chickens, culturable Salmonella was still found in beetles. Salmonella and Campylobacter were detectable in litter up to 127 d after removing infected chickens. This study highlights the transmission of Salmonella and Campylobacter via beetles and litter to new flocks in successive rearing cycles. Intensive control programs should target insect exclusion and implement strict poultry litter management or litter changes between flocks.
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Affiliation(s)
- Subarna Barua
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Matthew Bailey
- Department of Poultry Science, Auburn University, Auburn, AL, USA
| | - Kevin Zhong
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Nneka Iduu
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | | | - Kenneth Macklin
- Department of Poultry Science, Mississippi State University, Starkville, AL, USA
| | - Dianna Bourassa
- Department of Poultry Science, Auburn University, Auburn, AL, USA
| | - Stuart Price
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Ruediger Hauck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA; Department of Poultry Science, Auburn University, Auburn, AL, USA
| | - James Krehling
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Steven Kitchens
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Constantinos Kyriakis
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | | | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.
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Sajeer Paramabth M, Varma M. Demystifying PCR tests, challenges, alternatives, and future: A quick review focusing on COVID and fungal infections. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:719-728. [PMID: 37485773 DOI: 10.1002/bmb.21771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The polymerase chain reaction (PCR) technique is one of the most potent tools in molecular biology. It is extensively used for various applications ranging from medical diagnostics to forensic science and food quality testing. This technique has facilitated to survive COVID-19 pandemic by identifying the virus-infected individuals effortlessly and effectively. This review explores the principles, recent advancements, challenges, and alternatives of PCR technique in the context of COVID-19 and fungal infections. The introduction of PCR technique for anyone new to this field is the primary aim of this review and thereby equips them to understand the science of COVID-19 and related fungal infections in a simplistic manner.
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Affiliation(s)
| | - Manoj Varma
- Center for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India
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Saengsawang N, Ruang-Areerate P, Kaeothaisong N, Leelayoova S, Mungthin M, Juntanawiwat P, Hanyanunt P, Potisuwan P, Kesakomol P, Butsararattanagomen P, Wichaiwong P, Dungchai W, Ruang-Areerate T. Validation of quantitative loop-mediated isothermal amplification assay using a fluorescent distance-based paper device for detection of Escherichia coli in urine. Sci Rep 2023; 13:18781. [PMID: 37907677 PMCID: PMC10618465 DOI: 10.1038/s41598-023-46001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) causes up to 90% of urinary tract infections (UTI) which is more prevalent among females than males. In urine, patients with symptomatic UTI usually have a high concentration of bacterial infection, ≥ 105 colony-forming units (CFU) per mL, in which the culture method is regularly the gold standard diagnosis. In this study, a simple and inexpensive distance-based paper device (dPAD) combined with the fluorescent closed tube LAMP assay was validated for simultaneously screening and semi-quantifying the infection level of E. coli in 440 urine samples of patients with UTI. The dPAD could measure the LAMP amplicons and semi-quantify the levels of E. coli infection in heavy (≥ 104 CFU/mL), light (≤ 103 CFU/mL) and no infection. The sensitivity and specificity had reliable performances, achieving as high as 100 and 92.7%, respectively. The one step LAMP assay could be performed within 3 h, which was 7.5 times faster than the culture method. To empower early UTI diagnosis and fast treatment, this inexpensive dPAD tool combined with the fluorescent closed tube LAMP assay is simple, reliably fast and practically portable for point-of-care settings, particularly in resource-limited areas, which can be set up in all levels of healthcare facilities.
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Affiliation(s)
- Natkrittaya Saengsawang
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Panthita Ruang-Areerate
- BIOTEC, National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Nuanlaong Kaeothaisong
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Piraporn Juntanawiwat
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Patomroek Hanyanunt
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Patsanun Potisuwan
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Piyanate Kesakomol
- Department of Microbiology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Pornphan Butsararattanagomen
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Pattarawadee Wichaiwong
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Wijitar Dungchai
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.
| | - Toon Ruang-Areerate
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
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12
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Cui J, Zhang Y, Lun K, Wu B, He L, Wang M, Fang S, Zhang Z, Zhou L. Sensitive detection of Escherichia coli in diverse foodstuffs by electrochemical aptasensor based on 2D porphyrin-based COF. Mikrochim Acta 2023; 190:421. [PMID: 37773421 DOI: 10.1007/s00604-023-05978-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/31/2023] [Indexed: 10/01/2023]
Abstract
The two-dimensional porphyrin-based covalent organic framework (denoted by Tph-TDC-COF) was used as the sensitive layerto build an aptamer-based electrochemical sensor for the detection of Escherichia coli (E.coli). Tph-TDC-COF produced with 5,10,15,20-tetrakis(4-aminophenyl)-21H, 23H-porphine (Tph) and [2,2'-bithiophene]-2,5'-dicarbaldehyde (TDC) as building blocks exhibited a highly conjugated structure, outstanding conductivity, large specific surface area, and strong bioaffinity towards aptamers. The adoption of Tph-TDC-COF-modified electrode resulted in improved sensing performance and increased anchoring affinity toward the E.coli-targeted aptamer. Under optimal conditions, the Tph-TDC-COF-based electrochemical aptasensor demonstrated an extremely low detection limit of 0.17 CFU mL-1 for E.coli detection within a linear range of 10 to 1 × 108 CFU mL-1, accompanied by good stability, excellent reproducibility and regeneration ability, and wide practical applications. The current electrochemical aptasensing technique has the potential to be extended to detect different foodborne bacteria using specific aptamer, therefore widening the application of COFs in biosensing and food safety fields.
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Affiliation(s)
- Jing Cui
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Yu Zhang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Kan Lun
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Baiwei Wu
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Linghao He
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Minghua Wang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Shaoming Fang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China.
| | - Zhihong Zhang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China.
| | - Liming Zhou
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China.
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13
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Mamun AA, McGarrity M, Kim JH, Zhao F. Silicon Carbide-Based DNA Sensing Technologies. MICROMACHINES 2023; 14:1557. [PMID: 37630093 PMCID: PMC10456662 DOI: 10.3390/mi14081557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023]
Abstract
DNA sensing is critical in various applications such as the early diagnosis of diseases and the investigation of forensic evidence, food processing, agriculture, environmental protection, etc. As a wide-bandgap semiconductor with excellent chemical, physical, electrical, and biocompatible properties, silicon carbide (SiC) is a promising material for DNA sensors. In recent years, a variety of SiC-based DNA-sensing technologies have been reported, such as nanoparticles and quantum dots, nanowires, nanopillars, and nanowire-based field-effect-transistors, etc. This article aims to provide a review of SiC-based DNA sensing technologies, their functions, and testing results.
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Affiliation(s)
| | | | | | - Feng Zhao
- School of Engineering and Computer Science, Washington State University, Vancouver, WA 98686, USA
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14
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Park DG, Kwon JG, Ha ES, Kang B, Choi I, Kwak JE, Choi J, Lee W, Kim SH, Kim SH, Park J, Lee JH. Novel next generation sequencing panel method for the multiple detection and identification of foodborne pathogens in agricultural wastewater. Front Microbiol 2023; 14:1179934. [PMID: 37520347 PMCID: PMC10374199 DOI: 10.3389/fmicb.2023.1179934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 06/19/2023] [Indexed: 08/01/2023] Open
Abstract
Detecting and identifying the origins of foodborne pathogen outbreaks is a challenging. The Next-Generation Sequencing (NGS) panel method offers a potential solution by enabling efficient screening and identification of various bacteria in one reaction. In this study, new NGS panel primer sets that target 18 specific virulence factor genes from six target pathogens (Bacillus cereus, Yersinia enterocolitica, Staphylococcus aureus, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus) were developed and optimized. The primer sets were validated for specificity and selectivity through singleplex PCR, confirming the expected amplicon size. Crosscheck and multiplex PCR showed no interference in the primer set or pathogenic DNA mixture. The NGS panel analysis of spiked water samples detected all 18 target genes in a single reaction, with pathogen concentrations ranging from 108 to 105 colony-forming units (CFUs) per target pathogen. Notably, the total sequence read counts from the virulence factor genes showed a positive association with the CFUs per target pathogen. However, the method exhibited relatively low sensitivity and occasional false positive results at low pathogen concentrations of 105 CFUs. To validate the detection and identification results, two sets of quantitative real-time PCR (qPCR) analyses were independently performed on the same spiked water samples, yielding almost the same efficiency and specificity compared to the NGS panel analysis. Comparative statistical analysis and Spearman correlation analysis further supported the similarity of the results by showing a negative association between the NGS panel sequence read counts and qPCR cycle threshold (Ct) values. To enhance NGS panel analysis for better detection, optimization of primer sets and real-time NGS sequencing technology are essential. Nonetheless, this study provides valuable insights into applying NGS panel analysis for multiple foodborne pathogen detection, emphasizing its potential in ensuring food safety.
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Affiliation(s)
- Dong-Geun Park
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Joon-Gi Kwon
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Eun-Su Ha
- Research and Development Center, Sanigen Co., Ltd, Anyang, Republic of Korea
| | - Byungcheol Kang
- Research and Development Center, Sanigen Co., Ltd, Anyang, Republic of Korea
| | - Iseul Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang, Republic of Korea
| | - Jeong-Eun Kwak
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Jinho Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang, Republic of Korea
| | - Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Jeongwoong Park
- Research and Development Center, Sanigen Co., Ltd, Anyang, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
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15
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Flores-Ramírez A, Ortega-Cuenca J, Cuetero-Martínez Y, de Los Cobos D, Noyola A. Viability and removal assessment of Escherichia coli and Salmonella spp. by real-time PCR with propidium monoazide in the hygienization of sewage sludge using three anaerobic processes. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 161:254-262. [PMID: 36907017 DOI: 10.1016/j.wasman.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Sewage sludge should be stabilized for its beneficial use and pathogens, among other factors, should comply with environmental regulations. Three sludge stabilization process were compared to assess their suitability for producing Class A biosolids: MAD-AT (mesophilic (37 °C) anaerobic digestion (MAD) followed by an alkaline treatment (AT)); TAD (thermophilic (55 °C) anaerobic digester); and TP-TAD (mild thermal (80 °C, 1 h) pretreatment (TP) followed by a TAD). E. coli and Salmonella spp. were determined, differentiating three possible states: total cells (qPCR), viable cells using the propidium monoazide method (PMA-qPCR), and culturable cells (MPN). Culture techniques followed by the confirmative biochemical tests identified the presence of Salmonella spp. in PS and MAD samples, while the molecular methods (qPCR and PMA-qPCR) showed negative results in all samples. The TP + TAD arrangement reduced the concentration of total and viable E. coli cells in a greater extent than the TAD process. However, an increase of culturable E. coli was observed in the corresponding TAD step, indicating that the mild thermal pretreatment induced the viable but non-culturable state in E. coli. In addition, the PMA technique did not discriminate viable from non-viable bacteria in complex matrices. The three processes produced Class A biosolids (fecal coliforms < 1000 MPN/gTS and Salmonella spp, < 3 MPN/gTS) maintaining compliance after a 72 h storage period. It appears that the TP step favors the viable but not culturable state in E. coli cells, a finding that should be considered when adopting mild thermal treatment in sludge stabilization process arrangements.
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Affiliation(s)
- A Flores-Ramírez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - J Ortega-Cuenca
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - Y Cuetero-Martínez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - D de Los Cobos
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - A Noyola
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México.
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16
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Shao L, Sun Y, Zou B, Zhao Y, Li X, Dai R. Sublethally injured microorganisms in food processing and preservation: Quantification, formation, detection, resuscitation and adaption. Food Res Int 2023; 165:112536. [PMID: 36869540 DOI: 10.1016/j.foodres.2023.112536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/14/2023] [Accepted: 01/21/2023] [Indexed: 01/29/2023]
Abstract
Sublethally injured state has been recognized as a survival strategy for microorganisms suffering from stressful environments. Injured cells fail to grow on selective media but can normally grow on nonselective media. Numerous microorganism species can form sublethal injury in various food matrices during processing and preservation with different techniques. Injury rate was commonly used to evaluate sublethal injury, but mathematical models for the quantification and interpretation of sublethally injured microbial cells still require further study. Injured cells can repair themselves and regain viability on selective media under favorable conditions when stress is removed. Conventional culture methods might underestimate microbial counts or present a false negative result due to the presence of injured cells. Although the structural and functional components may be affected, the injured cells pose a great threat to food safety. This work comprehensively reviewed the quantification, formation, detection, resuscitation and adaption of sublethally injured microbial cells. Food processing techniques, microbial species, strains and food matrix all significantly affect the formation of sublethally injured cells. Culture-based methods, molecular biological methods, fluorescent staining and infrared spectroscopy have been developed to detect the injured cells. Cell membrane is often repaired first during resuscitation of injured cells, meanwhile, temperature, pH, media and additives remarkably influence the resuscitation. The adaption of injured cells negatively affects the microbial inactivation during food processing.
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Affiliation(s)
- Lele Shao
- Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Yingying Sun
- Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Bo Zou
- Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Yijie Zhao
- Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Xingmin Li
- Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China
| | - Ruitong Dai
- Beijing Higher Institution Engineering Research Center of Animal Product, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China.
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17
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Dong J, Liu L, Chen L, Xiang Y, Wang Y, Zhao Y. The Coexistence of Bacterial Species Restructures Biofilm Architecture and Increases Tolerance to Antimicrobial Agents. Microbiol Spectr 2023; 11:e0358122. [PMID: 36847543 PMCID: PMC10100793 DOI: 10.1128/spectrum.03581-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Chronic infections caused by polymicrobial biofilms are often difficult to treat effectively, partially due to the elevated tolerance of polymicrobial biofilms to antimicrobial treatments. It is known that interspecific interactions influence polymicrobial biofilm formation. However, the underlying role of the coexistence of bacterial species in polymicrobial biofilm formation is not fully understood. Here, we investigated the effect of the coexistence of Enterococcus faecalis, Escherichia coli O157:H7, and Salmonella enteritidis on triple-species biofilm formation. Our results demonstrated that the coexistence of these three species enhanced the biofilm biomass and led to restructuring of the biofilm into a tower-like architecture. Furthermore, the proportions of polysaccharides, proteins, and eDNAs in the extracellular matrix (ECM) composition of the triple-species biofilm were significantly changed compared to those in the E. faecalis mono-species biofilm. Finally, we analyzed the transcriptomic profile of E. faecalis in response to coexistence with E. coli and S. enteritidis in the triple-species biofilm. The results suggested that E. faecalis established dominance and restructured the triple-species biofilm by enhancing nutrient transport and biosynthesis of amino acids, upregulating central carbon metabolism, manipulating the microenvironment through "biological weapons," and activating versatile stress response regulators. Together, the results of this pilot study reveal the nature of E. faecalis-harboring triple-species biofilms with a static biofilm model and provide novel insights for further understanding interspecies interactions and the clinical treatment of polymicrobial biofilms. IMPORTANCE Bacterial biofilms possess distinct community properties that affect various aspects of our daily lives. In particular, biofilms exhibit increased tolerance to chemical disinfectants, antimicrobial agents, and host immune responses. Multispecies biofilms are undoubtedly the dominant form of biofilms in nature. Thus, there is a pressing need for more research directed at delineating the nature of multispecies biofilms and the effects of the properties on the development and survival of the biofilm community. Here, we address the effects of the coexistence of Enterococcus faecalis, Escherichia coli, and Salmonella enteritidis on triple-species biofilm formation with a static model. In combination with transcriptomic analyses, this pilot study explores the potential underlying mechanisms that lead to the dominance of E. faecalis in triple-species biofilms. Our findings provide novel insights into the nature of triple-species biofilms and indicate that the composition of multispecies biofilms should be a key consideration when determining antimicrobial treatments.
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Affiliation(s)
- Jiajun Dong
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Luhan Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Liying Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Yuqiang Xiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Yabin Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
| | - Youbao Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, Henan, China
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18
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Janik-Karpinska E, Ceremuga M, Niemcewicz M, Podogrocki M, Stela M, Cichon N, Bijak M. Immunosensors-The Future of Pathogen Real-Time Detection. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22249757. [PMID: 36560126 PMCID: PMC9785510 DOI: 10.3390/s22249757] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 05/26/2023]
Abstract
Pathogens and their toxins can cause various diseases of different severity. Some of them may be fatal, and therefore early diagnosis and suitable treatment is essential. There are numerous available methods used for their rapid screening. Conventional laboratory-based techniques such as culturing, enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are dominant. However, culturing still remains the "gold standard" for their identification. These methods have many advantages, including high sensitivity and selectivity, but also numerous limitations, such as long experiment-time, costly instrumentation, and the need for well-qualified personnel to operate the equipment. All these existing limitations are the reasons for the continuous search for a new solutions in the field of bacteria identification. For years, research has been focusing on the use of immunosensors in various types of toxin- and pathogen-detection. Compared to the conventional methods, immunosensors do not require well-trained personnel. What is more, immunosensors are quick, highly selective and sensitive, and possess the potential to significantly improve the pathogen and toxin diagnostic-processes. There is a very important potential use for them in various transport systems, where the risk of contamination by bioagents is very high. In this paper, the advances in the field of immunosensor usage in pathogenic microorganism- and toxin-detection, are described.
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Affiliation(s)
- Edyta Janik-Karpinska
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Michal Ceremuga
- Military Institute of Armored and Automotive Technology, Okuniewska 1, 05-070 Sulejowek, Poland
| | - Marcin Niemcewicz
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Marcin Podogrocki
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Maksymilian Stela
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Natalia Cichon
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Michal Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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19
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Khan JA, Rathore RS, Ahmad I, Gill R, Husain FM, Arshad M, Alam P, Albalawi T, Al-Kheraif A, Akhtar J, Albarakaty FM, Neyaz LA, Elbanna K, Abulreesh HH. Assessment of Foodborne Bacterial Pathogens in Buffalo Raw Milk Using Polymerase Chain Reaction Based Assay. Foodborne Pathog Dis 2022; 19:750-757. [PMID: 36301255 DOI: 10.1089/fpd.2022.0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Milk is a putrescible commodity that is extremely prone to microbial contamination. Primarily, milk and dairy products are believed to be easily contaminated by pathogenic microorganisms, including Listeria monocytogenes, Salmonella spp., and Staphylococcus aureus. The microbiological quality of raw milk and dairy products regarding foodborne pathogens is of paramount importance due to concern of human health. In this study 400 buffalo raw milk samples were screened for assessing the prevalence of L. monocytogenes, Salmonella spp., and S. aureus. This study implemented uniplex-polymerase chain reaction (u-PCR) and multiplex-polymerase chain reaction (m-PCR) assays for the fast simultaneous detection of these pathogens comparing to the conventional culturing methods. Raw milk samples were found contaminated with the prevalence of 2.2%, 4.0%, and 14.2% for L. monocytogenes, Salmonella spp., and S. aureus, respectively. These pathogens were detected with the optimized polymerase chain reaction assays after 6 h of enrichment. u-PCR and m-PCR demonstrated the limit of detection as 104, 102, and 10 cells/mL after 6, 12, 18, and 24 h for each culture of the pathogens. A high sensitivity (10 colony-forming unit [CFU]/mL) of the m-PCR protocol was noted. The developed protocol is a cost-effective and rapid method for the simultaneous detection of pathogens associated with raw milk and dairy industries.
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Affiliation(s)
- Javed Ahamad Khan
- Department of Natural Resource Management, Bedele Campus of Agriculture and Forestry, Mettu University, Bedele, Ethiopia
| | - Ram Swaroop Rathore
- Division of Veterinary Public Health, Indian Veterinary Research Institute, Bareilly, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Rubina Gill
- Department of Agronomy, School of Agriculture, Lovely Professional University, Phagwara, India
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Arshad
- Dental Biomaterials Research Chair, Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Thamer Albalawi
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Abdulaziz Al-Kheraif
- Dental Biomaterials Research Chair, Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Javeed Akhtar
- Department of Chemical Engineering, Adigrat University, Adigrat, Ethiopia
| | - Fawziah M Albarakaty
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Leena A Neyaz
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Khaled Elbanna
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Agricultural Microbiology, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Hussein H Abulreesh
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
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20
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Kawser AR, Foysal MJ, Chua EG, Ali MH, Mannan A, Siddik MA, Paul SI, Rahman MM, Tay A. Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh. Lett Appl Microbiol 2022; 75:813-823. [PMID: 35575585 PMCID: PMC9796611 DOI: 10.1111/lam.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/17/2022] [Accepted: 05/03/2022] [Indexed: 01/01/2023]
Abstract
The present study aimed to characterize and compare the skin and gut microbial communities of rohu at various post-harvest stages of consumption using quantitative real-time polymerase chain reaction and 16S rRNA-based amplicon sequencing. Real-time PCR amplification detected higher copy numbers for coliform bacteria-Escherichia coli, Salmonella enterica and Shigella spp. in the marketed fish-compared to fresh and frozen samples. The 16S rRNA data revealed higher alpha diversity measurements in the skin of fish from different retail markets of Dhaka city. Beta ordination revealed distinct clustering of bacterial OTUs for the skin and gut samples from three different groups. At the phylum level, Proteobacteria was most abundant in all groups except the Fusobacteria in the control fish gut. Although Aeromonas was found ubiquitous in all types of samples, diverse bacterial genera were identified in the marketed fish samples. Nonetheless, low species richness was observed for the frozen fish. Most of the differentially abundant bacteria in the skin samples of marketed fish are opportunistic human pathogens enriched at different stages of postharvest handling and processing. Therefore, considering the microbial contamination in the aquatic environment in Bangladesh, post-harvest handling should be performed with proper methods and care to minimize bacterial transmission into fish.
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Affiliation(s)
- A.Q.M. Robiul Kawser
- Department of AquacultureBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh,School of Veterinary Medicine and ScienceUniversity of NottinghamNottinghamUK
| | - Md Javed Foysal
- Department of Genetic Engineering and BiotechnologyShahjalal University of Science and TechnologySylhetBangladesh,School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Eng Guan Chua
- School of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Md Hazrat Ali
- Department of Genetic Engineering and BiotechnologyShahjalal University of Science and TechnologySylhetBangladesh
| | - Adnan Mannan
- Department of Genetic Engineering and BiotechnologyFaculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
| | - Muhammad A.B. Siddik
- Department of Fisheries Biology and GeneticsPatuakhali Science and Technology UniversityPatuakhaliBangladesh
| | - Sulav Indra Paul
- Institute of Biotechnology and Genetic EngineeringBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Md Mahbubur Rahman
- Institute of Biotechnology and Genetic EngineeringBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Alfred Tay
- School of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
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21
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Detection of Campylobacter jejuni Based on a Real-Time Fluorescence Loop-Mediated Isothermal Amplification Method. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3613757. [PMID: 36093400 PMCID: PMC9453007 DOI: 10.1155/2022/3613757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 06/24/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022]
Abstract
Campylobacter jejuni (C. jejuni), a foodborne pathogenic bacterium, is among the most prevalent causes of human gastroenteritis globally. We developed and evaluated a loop-mediated isothermal amplification (LAMP) method to detect C. jejuni. Outer primers and inner primers were designed based on the hipO gene. The ratio between the concentrations of the inner and outer primers and the reaction temperature were then optimized to achieve optimal assay conditions. The analytical specificity tests showed that, among 12 genera of 74 pure bacterial culture strains, only four C. jejuni isolates could be detected, whereas no amplification was observed in C. coli, C. lari, and the other 11 genera of foodborne pathogens (n = 70). Moreover, the LAMP assay showed a higher analytical sensitivity (34.2 fg μL−1) than the conventional PCR method (342 fg μL−1). The limit of detection of C. jejuni based on the LAMP assay was 103 CFU g−1 in the artificially spiked samples of chicken meat. In conclusion, the developed LAMP assay will be a powerful and practical tool for the fast, specific, and sensitive detection of C. jejuni.
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22
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Chutimanukul P, Mosaleeyanon K, Janta S, Toojinda T, Darwell CT, Wanichananan P. Physiological responses, yield and medicinal substance (andrographolide, AP1) accumulation of Andrographis paniculata (Burm. f) in response to plant density under controlled environmental conditions. PLoS One 2022; 17:e0272520. [PMID: 35925998 PMCID: PMC9352076 DOI: 10.1371/journal.pone.0272520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Agricultural practice in adjusting planting density and harvest date are important factors for plant development and crop improvement, reaching maximum yields and enhancing the production of secondary metabolites. However, it is unclear as to the optimal planting densities during mass production that encourage consistent, high yield secondary metabolite content. For this, controlled environment, crop production facilities such as plant factories with artificial lighting (PFAL) offer opportunity to enhance quality and stabilize production of herbal plants. This study assessed the effect of plant density and harvest date on physiological responses, yield and andrographolide (AP1) content in Andrographis paniculata (Andrographis) using hydroponic conditions in a PFAL system. Andrographis, harvested at vegetative stage (30 days after transplanting; 30 DAT) and initial stage of flowering (60 DAT) exhibited no significant differences in growth parameters or andrographolide accumulation according to planting densities. Harvest time at flowering stage (90 DAT) showed the highest photosynthetic rates at a planting density of 15 plants m-2. Highest yield, number of leaves, and Andrographolide (AP1) content (mg per gram of DW in m2) were achieved at a more moderate planting density (30 plants m-2). Finally, five out of seventeen indices of leaf reflectance reveal high correlation (r = 0.8 to 1.0 and r = -0.8 to -1.0, P<0.01) with AP1 content. These results suggest that a planting density of 30 plants m-2 and harvest time of 90 DAT provide optimal growing condition under the hydroponic PFAL system.
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Affiliation(s)
- Panita Chutimanukul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kriengkrai Mosaleeyanon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supattana Janta
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Clive Terence Darwell
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Praderm Wanichananan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
- * E-mail:
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23
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Zhi S, Shen J, Li X, Jiang Y, Xue J, Fang T, Xu J, Wang X, Cao Y, Yang D, Yao Z, Yu D. Development of Recombinase-Aided Amplification (RAA)-Exo-Probe and RAA-CRISPR/Cas12a Assays for Rapid Detection of Campylobacter jejuni in Food Samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9557-9566. [PMID: 35857318 DOI: 10.1021/acs.jafc.2c02581] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Campylobacter jejuni is the major cause of campylobacteriosis, one of the most common foodborne illnesses worldwide. Here, we report the development of RAA-exo-probe and RAA-CRIPSR/Cas12a assays for the detection of C. jejuni in food samples. The two assays were found to be highly specific to C. jejuni and highly sensitive, as they were one log more sensitive compared to the traditional culture method, with detection thresholds of 9 and 5 copies per reaction, respectively. These assays successfully detected C. jejuni in spiked chicken samples and natural meat samples (chicken, beef, mutton, etc.) and were overall less dependent on expensive equipment, only requiring a fluorescent reader. Their ease of use compared to other nucleic acid amplification-based methods indicates that these assays could be adapted for the rapid, routine surveillance of C. jejuni contamination in food samples, particularly for work done in the field or poorly equipped labs.
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Affiliation(s)
- Shuai Zhi
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315211, China
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Jinling Shen
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Xingang Li
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yuan Jiang
- Nanjing Customs District People's Republic of China, Nanjing 210001, China
| | - Junxin Xue
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Taisong Fang
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Jin Xu
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Xuan Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yuhao Cao
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Danting Yang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China
| | - Daniel Yu
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 1C9, Canada
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24
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Kim E, Kim DS, Yang SM, Kim HY. The accurate identification and quantification of six Enterococcus species using quantitative polymerase chain reaction based novel DNA markers. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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25
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Jiang W, Chen L, Wang J, Shao X, Jiang M, Chen Z, Wang J, Huang Y, Fei P. Open-top light-sheet imaging of CLEAR emulsion for high-throughput loss-free analysis of massive fluorescent droplets. Biomed Phys Eng Express 2022; 8. [PMID: 35767965 DOI: 10.1088/2057-1976/ac7d0f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Digital droplet PCR (ddPCR) is classified as the third-generation PCR technology that enables absolute quantitative detection of nucleic acid molecules and has become an increasingly powerful tool for clinic diagnosis. We previously established a CLEAR-dPCR technique based on the combination of CLEAR droplets generated by micro-centrifuge-based microtubule arrays (MiCA) andinsitu3D readout by light-sheet fluorescence imaging. This CLEAR-dPCR technique attains very high readout speed and dynamic range. Meanwhile, it is free from sample loss and contamination, showing its advantages over commercial d-PCR technologies. However, a conventional orthogonal light-sheet imaging setup in CLEAR d-PCR cannot image multiple centrifuge tubes, thereby limiting its widespread application to large-scale, high-speed dd-PCR assays. Herein, we propose an in-parallel 3D dd-PCR readout technique based on an open-top light-sheet microscopy setup. This approach can continuously scan multiple centrifuge tubes which contain CLEAR emulsions with highly diverse concentrations, and thus further boost the scale and throughput of our 3D dd-PCR technique.
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Affiliation(s)
- Wen Jiang
- School of Optical and Electronic Information , Huazhong University of Science and Technology, E417, Wuhan, Hubei, 430074, CHINA
| | - Longbiao Chen
- School of Optical and Electronic Information , Huazhong University of Science and Technology, E417, Wuhan, Hubei, 430074, CHINA
| | - Jie Wang
- Huazhong University of Science and Technology, E417, School of Optical and Electronic Information, Wuhan, Hubei, 430074, CHINA
| | - Xinyang Shao
- Peking-Tsinghua Center for Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing, Beijing, 100871, CHINA
| | - Mengcheng Jiang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Biomedical Pioneering Innovation Center (BIOPIC), Beijing, Beijing, 100871, CHINA
| | - Zitian Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Biomedical Pioneering Innovation Center (BIOPIC), Beijing, Beijing, 100871, CHINA
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, School of Life Sciences, Beijing, Beijing, 100084, CHINA
| | - Yanyi Huang
- College of Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, College of Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Beijing, 100871, CHINA
| | - Peng Fei
- School of Optical and Electronic Information, Huazhong University of Science and Technology, E417, Wuhan, 430074, CHINA
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26
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Dong M, Feng H. Microbial Community Analysis and Food Safety Practice Survey-Based Hazard Identification and Risk Assessment for Controlled Environment Hydroponic/Aquaponic Farming Systems. Front Microbiol 2022; 13:879260. [PMID: 35663856 PMCID: PMC9161294 DOI: 10.3389/fmicb.2022.879260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
Hydroponic and aquaponic farming is becoming increasingly popular as a solution to address global food security. Plants in hydroponic systems are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, hydroponics and aquaponics might have very different sources of microbial food safety risks that remain under-examined. In this study, we investigated the microbiomes, microbial hazards, and potential bacterial transmission routes inside two commercial hydroponic and aquaponic farming systems using 16S-ITS-23S rRNA sequencing and a hydroponic food safety practice survey. The hydroponic farming system microbiome was analyzed from the fresh produce, nutrient solution, tools, and farmworkers. Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes were the main components of hydroponic/aquaponic farming systems, with Pseudomonas being the most abundant genus in fresh produce samples. We further identified the presence of multiple spoilage bacteria and potential human, plant, and fish pathogens at the subspecies level. Spoilage Pseudomonas spp. and spoilage Clostridium spp. were abundant in the hydroponic microgreen farm and aquaponic lettuce farm, respectively. Moreover, we demonstrated the mapping of Escherichia coli 16s-ITS-23s rRNA sequence reads (∼2,500 bp) to small or large subunit rRNA databases and whole-genome databases to confirm pathogenicity and showed the potential of using 16s-ITS-23s rRNA sequencing for pathogen identification. With the SourceTracker and overlapping amplicon sequence variants, we predicted the bidirectional transmission route between plants and the surrounding environment and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans.
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Affiliation(s)
| | - Hao Feng
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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27
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Choi CH, Kim E, Yang SM, Kim DS, Suh SM, Lee GY, Kim HY. Comparison of Real-Time PCR and Droplet Digital PCR for the Quantitative Detection of Lactiplantibacillus plantarum subsp. plantarum. Foods 2022; 11:foods11091331. [PMID: 35564054 PMCID: PMC9105557 DOI: 10.3390/foods11091331] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 12/04/2022] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is one of the newest and most promising tools providing absolute quantification of target DNA molecules. Despite its emerging applications in microorganisms, few studies reported its use for detecting lactic acid bacteria. This study evaluated the applicability of a ddPCR assay targeting molecular genes obtained from in silico analysis for detecting Lactiplantibacillus plantarum subsp. plantarum, a bacterium mainly used as a starter or responsible for fermentation in food. The performance characteristics of a ddPCR were compared to those of a quantitative real-time PCR (qPCR). To compare the linearity and sensitivity of a qPCR and ddPCR, the calibration curve for a qPCR and the regression curve for a ddPCR were obtained using genomic DNA [102−108 colony-forming units (CFU)/mL] extracted from a pure culture and spiked food sample. Both the qPCR and ddPCR assays exhibited good linearity with a high coefficient of determination in the pure culture and spiked food sample (R2 ≥ 0.996). The ddPCR showed a 10-fold lower limit of detection, suggesting that a ddPCR is more sensitive than a qPCR. However, a ddPCR has limitations in the absolute quantitation of high bacterial concentrations (>106 CFU/mL). In conclusion, a ddPCR can be a reliable method for detecting and quantifying lactic acid bacteria in food.
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Affiliation(s)
| | | | | | | | | | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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28
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Songca SP. Applications of Nanozymology in the Detection and Identification of Viral, Bacterial and Fungal Pathogens. Int J Mol Sci 2022; 23:4638. [PMID: 35563029 PMCID: PMC9100627 DOI: 10.3390/ijms23094638] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/12/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
Nanozymes are synthetic nanoparticulate materials that mimic the biological activities of enzymes by virtue of their surface chemistry. Enzymes catalyze biological reactions with a very high degree of specificity. Examples include the horseradish peroxidase, lactate, glucose, and cholesterol oxidases. For this reason, many industrial uses of enzymes outside their natural environments have been developed. Similar to enzymes, many industrial applications of nanozymes have been developed and used. Unlike the enzymes, however, nanozymes are cost-effectively prepared, purified, stored, and reproducibly and repeatedly used for long periods of time. The detection and identification of pathogens is among some of the reported applications of nanozymes. Three of the methodologic milestones in the evolution of pathogen detection and identification include the incubation and growth, immunoassays and the polymerase chain reaction (PCR) strategies. Although advances in the history of pathogen detection and identification have given rise to novel methods and devices, these are still short of the response speed, accuracy and cost required for point-of-care use. Debuting recently, nanozymology offers significant improvements in the six methodological indicators that are proposed as being key in this review, including simplicity, sensitivity, speed of response, cost, reliability, and durability of the immunoassays and PCR strategies. This review will focus on the applications of nanozymes in the detection and identification of pathogens in samples obtained from foods, natural, and clinical sources. It will highlight the impact of nanozymes in the enzyme-linked immunosorbent and PCR strategies by discussing the mechanistic improvements and the role of the design and architecture of the nanozyme nanoconjugates. Because of their contribution to world health burden, the three most important pathogens that will be considered include viruses, bacteria and fungi. Although not quite seen as pathogens, the review will also consider the detection of cancer cells and helminth parasites. The review leaves very little doubt that nanozymology has introduced remarkable advances in enzyme-linked immunosorbent assays and PCR strategies for detecting these five classes of pathogens. However, a gap still exists in the application of nanozymes to detect and identify fungal pathogens directly, although indirect strategies in which nanozymes are used have been reported. From a mechanistic point of view, the nanozyme technology transfer to laboratory research methods in PCR and enzyme-linked immunosorbent assay studies, and the point-of-care devices such as electronic biosensors and lateral flow detection strips, that is currently taking place, is most likely to give rise to no small revolution in each of the six methodological indicators for pathogen detection and identification. While the evidence of widespread research reports, clinical trials and point-of-care device patents support this view, the gaps that still exist point to a need for more basic research studies to be conducted on the applications of nanozymology in pathogen detection and identification. The multidisciplinary nature of the research on the application of nanozymes in the detection and identification of pathogens requires chemists and physicists for the design, fabrication, and characterization of nanozymes; microbiologists for the design, testing and analysis of the methodologies, and clinicians or clinical researchers for the evaluation of the methodologies and devices in the clinic. Many reports have also implicated required skills in mathematical modelling, and electronic engineering. While the review will conclude with a synopsis of the impact of nanozymology on the detection and identification of viruses, bacteria, fungi, cancer cells, and helminths, it will also point out opportunities that exist in basic research as well as opportunities for innovation aimed at novel laboratory methodologies and devices. In this regard there is no doubt that there are numerous unexplored research areas in the application of nanozymes for the detection of pathogens. For example, most research on the applications of nanozymes for the detection and identification of fungi is so far limited only to the detection of mycotoxins and other chemical compounds associated with fungal infection. Therefore, there is scope for exploration of the application of nanozymes in the direct detection of fungi in foods, especially in the agricultural production thereof. Many fungal species found in seeds severely compromise their use by inactivating the germination thereof. Fungi also produce mycotoxins that can severely compromise the health of humans if consumed.
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Affiliation(s)
- Sandile Phinda Songca
- School of Chemistry and Physics, College of Agriculture Engineering and Science, University of KwaZulu-Natal, Durban 4041, South Africa
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29
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M A, Sebastian D. Evaluation of Sensitivity and Cost-Effectiveness of Molecular Methods for the Co-detection of Waterborne Pathogens in India. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:955-963. [PMID: 34714447 DOI: 10.1007/s10126-021-10078-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Waterborne microbial diseases are regarded as a major public health concern, particularly in nations with poor sanitation, a lack of social awareness, and problems linked with low socioeconomic status. Waterborne pathogen identification using traditional culture methods is time-consuming and labor-intensive. As a result, there is a growing demand for quick pathogen detection technologies. High sensitivity, specificity, and rapidity are all advantages of using molecular techniques like polymerase chain reaction (PCR) in such instances. In this study, we designed multiplex PCR and quantitative real-time PCR (qPCR) assays for the co-detection and enumeration of waterborne pathogens such as Aeromonas hydrophila, Pseudomonas aeruginosa, Salmonella enterica, Yersinia enterocolitica, Escherichia coli, Vibrio cholerae, and Shigella spp. Specific primers were selected against the virulence and species-specific genes of the seven target pathogens. For all seven target organisms, the detection limits for conventional culture methods were in the range of 103-104 cells/ml. While employing multiplex PCR method in this study, Pseudomonas aeruginosa and Shigella spp. have a detection sensitivity of 101 cells/ml, Vibrio cholerae and Aeromonas hydrophila have a detection sensitivity of 102 cells/ml, whereas Salmonella enterica, E. coli, and Yersinia enterocolitica have a detection sensitivity of only 103 cells/ml. According to our cost-benefit analysis, these molecular technologies are less expensive, with unit analysis costs of ₹52 and ₹173 for qPCR and multiplex PCR, respectively. Furthermore, all of the target genes had a detection limit of 1 cell/ml in qPCR. Because of their speed, sensitivity, specificity, and cost-effectiveness, these multiplex and qPCR assays could be employed for successful co-detection of aquatic pathogens.
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Affiliation(s)
- Ambili M
- Department of Life Sciences, University of Calicut, Malappuram, Kerala-673635, India
| | - Denoj Sebastian
- Department of Life Sciences, University of Calicut, Malappuram, Kerala-673635, India.
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30
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Sun A, Stanton JAL, Bergquist PL, Sunna A. Universal Enzyme-Based Field Workflow for Rapid and Sensitive Quantification of Water Pathogens. Microorganisms 2021; 9:2367. [PMID: 34835492 PMCID: PMC8618791 DOI: 10.3390/microorganisms9112367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022] Open
Abstract
A universal filtration and enzyme-based workflow has been established to allow for the rapid and sensitive quantification of leading pathogens Cryptosporidium parvum, Giardia gamblia, Campylobacter jejuni, and Escherichia coli from tap water samples with volumes up to 100 mL, and the potential to scale up to larger volumes. qPCR limits of quantification as low as four oocysts for Cryptosporidium, twelve cysts for Giardia, two cells for C. jejuni, and nineteen cells for E. coli per reaction were achieved. A polycarbonate filter-based sampling method coupled with the prepGEM enzyme-based DNA extraction system created a single-step transfer workflow that required as little as 20 min of incubation time and a 100 µL reaction mix. The quantification via qPCR was performed directly on the prepGEM extract, bypassing time-consuming, labour-intensive conventional culture-based methods. The tap water samples were shown to contain insoluble particles that inhibited detection by reducing the quantification efficiency of a representative pathogen (C. jejuni) to 30-60%. This sample inhibition was effectively removed by an on-filter treatment of 20% (v/v) phosphoric acid wash. Overall, the established workflow was able to achieve quantification efficiencies of 92% and higher for all four leading water pathogens, forming the basis of a rapid, portable, and low-cost solution to water monitoring.
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Affiliation(s)
- Angela Sun
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
| | - Jo-Ann L. Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Peter L. Bergquist
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
- Department of Molecular Medicine & Pathology, University of Auckland, Auckland 1142, New Zealand
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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31
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Barr KL, Sturdivant RX, Williams DN, Harris D. Bacteria Associated with Healthcare-Associated Infections on Environmental Samples Obtained from Two Fire Departments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182211885. [PMID: 34831638 PMCID: PMC8621870 DOI: 10.3390/ijerph182211885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022]
Abstract
(1) Background: Firefighters spend about 64% of their time responding to medical emergencies and providing medical care without a patient history, which can render them vulnerable to healthcare-associated infections (HAI). Infection prevention, control, and surveillance systems have been instituted at hospitals. However, the prevalence of firefighters’ exposure to HAI is unknown. The objective of this study was to document evidence of HAI on surfaces in fire stations and engines to inform disinfection procedures and identify which pathogens might contribute to occupational exposures. (2) Methods: High-touch or high-use surfaces of two fire departments were sampled during five separate occasions. One fire station from one fire department was sampled over a 4-week period, whereas four fire stations were sampled from a different fire department only once. Sampled surfaces included: entryway floor, washing machine, medical bag, back seat of engine, keyboard of reporting computer, engine console, and uniform pants. (3) Results: Multiple statistical models determined that bacterial contamination was similar between the two fire departments and their stations. Keyboards were the most contaminated surface for all fire stations and departments, E. coli was the most common bacteria detected, and C. difficile was the least detected bacteria. Adjustments for rates of contamination found that contamination rates varied between fire stations. (4) Conclusions: Comprehensive environmental sampling and clinical studies are needed to better understand occupational exposures of firefighters to HAI.
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Affiliation(s)
- Kelli L. Barr
- Center for Global Health Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL 10921, USA;
| | | | - Denise N. Williams
- Department of Human Sciences and Design, College of Health and Human Science, Baylor University, Waco, TX 76798, USA;
| | - Debra Harris
- Department of Human Sciences and Design, College of Health and Human Science, Baylor University, Waco, TX 76798, USA;
- Correspondence: ; Tel.: +1-254-710-7255
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Papatheodorou SA, Halvatsiotis P, Houhoula D. A comparison of different DNA extraction methods and molecular techniques for the detection and identification of foodborne pathogens. AIMS Microbiol 2021; 7:304-319. [PMID: 34708174 PMCID: PMC8500797 DOI: 10.3934/microbiol.2021019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022] Open
Abstract
Foodborne infections continue to plague Europe. Food safety monitoring is in crisis as the existing techniques for detecting pathogens do not keep up with the global rising of food production and consumption. Thus, the development of innovative techniques for detecting and identifying pathogenic bacteria has become critical. The aim of the present study was firstly to develop an innovative simple and low cost method of extracting bacterial DNA from contaminated food and water samples with Salmonella enteric(a) subsp. enteric(a) serovar Typhimurium and Listeria monocytogenes and its comparison with two commercial DNA extraction kits (Qiagen, Macherey-Nagel). Finally, pathogens' detection using two molecular techniques (PCR-electrophoresis, LAMP), in order to evaluate the best combination of DNA extraction and identification based on their sensitivity, cost, rapidity and simplicity. Considering the above criteria, among them, best was proved an in-house bacterial DNA extraction method, based on the chloroform-isoamyl alcohol protocol, with certain modifications. This technique showed statistically similar results in terms of sensitivity, compared to the commercial kits, while at the same time maintained high rapidity and much lower cost. Lastly, between the molecular techniques, LAMP was found more promising considering its simplicity, high rapidity and sensitivity. Conclusively, the in-house DNA extraction method along with the LAMP technique, was proven to be the best among the presented combinations.
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Affiliation(s)
| | - Panagiotis Halvatsiotis
- 2nd Propaedeutic Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, "ATTIKON" University Hospital, Chaidari Greece
| | - Dimitra Houhoula
- Department of Food Science & Technology, School of Food Sciences, University of West Attica
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Xin S, Zhu H, Tao C, Zhang B, Yao L, Zhang Y, Afayibo DJA, Li T, Tian M, Qi J, Ding C, Yu S, Wang S. Rapid Detection and Differentiating of the Predominant Salmonella Serovars in Chicken Farm by TaqMan Multiplex Real-Time PCR Assay. Front Cell Infect Microbiol 2021; 11:759965. [PMID: 34660351 PMCID: PMC8512842 DOI: 10.3389/fcimb.2021.759965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/10/2021] [Indexed: 01/27/2023] Open
Abstract
Salmonella has been known as an important zoonotic pathogen that can cause a variety of diseases in both animals and humans. Poultry are the main reservoir for the Salmonella serovars Salmonella Pullorum (S. Pullorum), Salmonella Gallinarum (S. Gallinarum), Salmonella Enteritidis (S. Enteritidis), and Salmonella Typhimurium (S. Typhimurium). The conventional serotyping methods for differentiating Salmonella serovars are complicated, time-consuming, laborious, and expensive; therefore, rapid and accurate molecular diagnostic methods are needed for effective detection and prevention of contamination. This study developed and evaluated a TaqMan multiplex real-time PCR assay for simultaneous detection and differentiation of the S. Pullorum, S. Gallinarum, S. Enteritidis, and S. Typhimurium. In results, the optimized multiplex real-time PCR assay was highly specific and reliable for all four target genes. The analytical sensitivity corresponded to three colony-forming units (CFUs) for these four Salmonella serovars, respectively. The detection limit for the multiplex real-time PCR assay in artificially contaminated samples was 500 CFU/g without enrichment, while 10 CFU/g after pre-enrichment. Moreover, the multiplex real-time PCR was applied to the poultry clinical samples, which achieved comparable results to the traditional bacteriological examination. Taken together, these results indicated that the optimized TaqMan multiplex real-time PCR assay will be a promising tool for clinical diagnostics and epidemiologic study of Salmonella in chicken farm and poultry products.
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Affiliation(s)
- Suhua Xin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hong Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chenglin Tao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Beibei Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lan Yao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yaodong Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | | | - Tao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Mingxing Tian
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jingjing Qi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Shengqing Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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Nesakumar N, Lakshmanakumar M, Srinivasan S, Jayalatha JBB A, Balaguru Rayappan JB. Principles and Recent Advances in Biosensors for Pathogens Detection. ChemistrySelect 2021. [DOI: 10.1002/slct.202101062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Noel Nesakumar
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Chemical and Biotechnology SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Muthaiyan Lakshmanakumar
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Soorya Srinivasan
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Arockia Jayalatha JBB
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - John Bosco Balaguru Rayappan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
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Azimirad M, Nadalian B, Alavifard H, Negahdar Panirani S, Mahdigholi Vand Bonab S, Azimirad F, Gholami F, Jabbari P, Yadegar A, Busani L, Asadzadeh Aghdaei H, Zali MR. Microbiological survey and occurrence of bacterial foodborne pathogens in raw and ready-to-eat green leafy vegetables marketed in Tehran, Iran. Int J Hyg Environ Health 2021; 237:113824. [PMID: 34365294 DOI: 10.1016/j.ijheh.2021.113824] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/19/2021] [Accepted: 08/01/2021] [Indexed: 01/28/2023]
Abstract
Fresh leafy (FL) and ready-to-eat (RTE) vegetables are recognized as an important source of foodborne disease outbreaks worldwide. Currently, there are no data available for the prevalnce of bacterial foodborne pathogens (FBPs) in raw vegetables consumed in Iran. Here, we evalated the presence of common bacterial FBPs among 366 samples of raw vegetables including 274 FL and 92 RTE collected from 21 districts of Tehran. The presence of FBPs were screened using conventional microbiological culture methods and real-time PCR assays. Overall, a higher rate of bacterial contamination was detected in FL compared to RTE samples using both detection methods. The results obtained by microbiological methods showed that Staphylococcus aureus (134/366, 36.6%), followed by Escherichia coli (85/366, 23.2%) and Clostridium perfringens (66/366, 18%) were detetcted as the most prevalent pathogens in this study. Vibrio cholerae was not detected in any of the samples either by microbiological methods or by the real-time PCR assays. There was a noticeable reduction in the proportion of Campylobacter positive samples using conventional microbiological methods (3.5%) compared to the real-time PCR assay (20.7%). The proportion of FL and RTE positive samples obtained by conventional microbiological methods was significantly different (P < 0.05) for C. perfringens, Campylobacter spp. and S. aureus. The proportion of positive samples in FL and RTE vegetables obtained by the real-time PCR assays was significantly different (P < 0.05) for C. perfringens, S. aureus, Helicobacter pylori and STEC/EHEC, the last one was found more frequently in RTE than in FL samples. Our findings indicated a contamination of FL and RTE vegetables in Iran with a range of well-known and emerging FBPs. Positivity and the distribution of bacterial species from the current data indicated different contamination sources, and overall a lack of effective decontamination steps during the production chain. Moreover, further information about the quality of the water, the hygiene measures implemented during the processing, storage and marketing are required to better identify the critical points and define the proper measures.
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Affiliation(s)
- Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Banafsheh Nadalian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Helia Alavifard
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaho Negahdar Panirani
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Solmaz Mahdigholi Vand Bonab
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fahimeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Gholami
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parnia Jabbari
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Luca Busani
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Abstract
PURPOSE OF REVIEW Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize diarrheagenic Escherichia coli (DEC) pathotype definitions and discuss existing and emerging molecular, genomic, and gut microbiome methods to detect, define, and study DEC pathotypes. RECENT FINDINGS DEC pathotypes are currently diagnosed by molecular detection of unique virulence genes. However, some pathotypes have defied coherent molecular definitions because of imperfect gene targets, and pathotype categories are complicated by hybrid strains and isolation of pathotypes from asymptomatic individuals. Recent progress toward more efficient, sensitive, and multiplex DEC pathotype detection has been made using emerging PCR-based technologies. Genomics and gut microbiome detection methods continue to advance rapidly and are contributing to a better understanding of DEC pathotype diversity and functional potential. SUMMARY DEC pathotype categorizations and detection methods are useful but imperfect. The implementation of molecular and sequence-based methods and well designed epidemiological studies will continue to advance understanding of DEC pathotypes. Additional emphasis is needed on sequencing DEC genomes from regions of the world where they cause the most disease and from the pathotypes that cause the greatest burden of disease globally.
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Artavia G, Cortés-Herrera C, Granados-Chinchilla F. Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis. Foods 2021; 10:1081. [PMID: 34068197 PMCID: PMC8152966 DOI: 10.3390/foods10051081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/13/2021] [Accepted: 03/19/2021] [Indexed: 12/28/2022] Open
Abstract
This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.
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Affiliation(s)
- Graciela Artavia
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
| | - Carolina Cortés-Herrera
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
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Wang Y, Qi W, Wang L, Lin J, Liu Y. Magnetic Bead Chain-Based Continuous-Flow DNA Extraction for Microfluidic PCR Detection of Salmonella. MICROMACHINES 2021; 12:mi12040384. [PMID: 33916235 PMCID: PMC8066728 DOI: 10.3390/mi12040384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 01/04/2023]
Abstract
Nucleic acid extraction is crucial for PCR detection of pathogenic bacteria to ensure food safety. In this study, a new magnetic extraction method was developed using 3D printing and magnetic silica beads (MSBs) to extract the target DNA from a large volume of bacterial sample and combined with microfluidic PCR to determine the bacteria. After proteinase K was added into a bacterial sample to lyse the bacteria and release the DNA, it was continuous-flow injected into the serpentine channel of the extraction chip, where magnetic silica bead chains had been formed in advance using a homogeneous magnetic field generated by two concentric semicircle magnets to capture the MSBs. Then, the flowing DNA was captured by the MSB chains, washed with alcohol, dried with gas, and eluted with deionized water to obtain the purified and concentrated DNA. Finally, the extracted DNA templates were injected into a microfluidic PCR chip with lyophilized amplification reagents and determined using a commercial qPCR device. The experimental results showed that the DNA extraction efficiency was more than 90%, and the lower detection limit of Salmonella was 102 CFU/mL. This new Salmonella detection method is promising to provide the rapid, sensitive, and simultaneous detection of multiple foodborne pathogens.
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Rajagopal R, Barnes CA, David JM, Goseland J, Goseland J. Evaluation of a commercial loop-mediated isothermal amplification assay, 3M TM Molecular Detection Assay 2 - Campylobacter, for the detection of Campylobacter from poultry matrices. Br Poult Sci 2021; 62:404-413. [PMID: 33517711 DOI: 10.1080/00071668.2021.1879992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. The objective of this study was to evaluate performance of a commercial loop-mediated isothermal amplification (LAMP) method as an alternative method for the detection of Campylobacter spp. in primary production samples, poultry rinses and raw poultry products, as compared to the US Department of Agriculture Food Inspection Service Microbiology Laboratory Guide Book PCR reference method, MLG 41A.2. The Campylobacter spp. LAMP was used in conjunction with a ready-to-use enrichment broth that does not require microaerophilic incubation. After enrichment, boot swabs from poultry farms, carcase rinses and raw poultry products were tested by the LAMP method and the MLG 41A PCR method.3. The ready-to-use enrichment broth enabled the growth of Campylobacter spp. within 22 to 28 hours under aerobic incubation conditions. The LAMP method enabled Campylobacter detection in the enriched samples of various poultry matrices and had equivalent sensitivity and specificity to the MLG 41A PCR method.4. No significant difference (95% confidence interval) was found between the alternative and the MLG 41A PCR method, as determined by probability of detection analysis, except for neutralising buffered peptone water post-chill rinsates. For the post-chill neutralising buffered peptone water rinsates, the LAMP method had significantly higher confirmed portions.
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Affiliation(s)
| | | | | | - J Goseland
- WBA Analytical Laboratories, Inc., Springdale, AR, USA
| | - J Goseland
- WBA Analytical Laboratories, Inc., Springdale, AR, USA
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On SLW, Zhang Y, Gehring A, Patsekin V, Chelikani V, Flint S, Wang H, Billington C, Fletcher GC, Lindsay J, Robinson JP. Elastic Light Scatter Pattern Analysis for the Expedited Detection of Yersinia Species in Pork Mince: Proof of Concept. Front Microbiol 2021; 12:641801. [PMID: 33679677 PMCID: PMC7928378 DOI: 10.3389/fmicb.2021.641801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/29/2021] [Indexed: 11/23/2022] Open
Abstract
Isolation of the pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis from foods typically rely on slow (10–21 day) “cold enrichment” protocols before confirmed results are obtained. We describe an approach that yields results in 39 h that combines an alternative enrichment method with culture on a non-selective medium, and subsequent identification of suspect colonies using elastic light scatter (ELS) analysis. A prototype database of ELS profiles from five Yersinia species and six other bacterial genera found in pork mince was established, and used to compare similar profiles of colonies obtained from enrichment cultures from pork mince samples seeded with representative strains of Y. enterocolitica and Y. pseudotuberculosis. The presumptive identification by ELS using computerised or visual analyses of 83/90 colonies in these experiments as the target species was confirmed by partial 16S rDNA sequencing. In addition to seeded cultures, our method recovered two naturally occurring Yersinia strains. Our results indicate that modified enrichment combined with ELS is a promising new approach for expedited detection of foodborne pathogenic yersiniae.
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Affiliation(s)
- Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Yuwei Zhang
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Andrew Gehring
- Eastern Regional Research Center, Agricultural Research Service, USDA, Wyndmoor, PA, United States
| | - Valery Patsekin
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, United States
| | - Venkata Chelikani
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Haoran Wang
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Craig Billington
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Graham C Fletcher
- New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - James Lindsay
- Agricultural Research Service, Office of National Programs, USDA, Washington, DC, United States
| | - J Paul Robinson
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States
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Galieni A, D'Ascenzo N, Stagnari F, Pagnani G, Xie Q, Pisante M. Past and Future of Plant Stress Detection: An Overview From Remote Sensing to Positron Emission Tomography. FRONTIERS IN PLANT SCIENCE 2021; 11:609155. [PMID: 33584752 PMCID: PMC7873487 DOI: 10.3389/fpls.2020.609155] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/18/2020] [Indexed: 05/24/2023]
Abstract
Plant stress detection is considered one of the most critical areas for the improvement of crop yield in the compelling worldwide scenario, dictated by both the climate change and the geopolitical consequences of the Covid-19 epidemics. A complicated interconnection of biotic and abiotic stressors affect plant growth, including water, salt, temperature, light exposure, nutrients availability, agrochemicals, air and soil pollutants, pests and diseases. In facing this extended panorama, the technology choice is manifold. On the one hand, quantitative methods, such as metabolomics, provide very sensitive indicators of most of the stressors, with the drawback of a disruptive approach, which prevents follow up and dynamical studies. On the other hand qualitative methods, such as fluorescence, thermography and VIS/NIR reflectance, provide a non-disruptive view of the action of the stressors in plants, even across large fields, with the drawback of a poor accuracy. When looking at the spatial scale, the effect of stress may imply modifications from DNA level (nanometers) up to cell (micrometers), full plant (millimeters to meters), and entire field (kilometers). While quantitative techniques are sensitive to the smallest scales, only qualitative approaches can be used for the larger ones. Emerging technologies from nuclear and medical physics, such as computed tomography, magnetic resonance imaging and positron emission tomography, are expected to bridge the gap of quantitative non-disruptive morphologic and functional measurements at larger scale. In this review we analyze the landscape of the different technologies nowadays available, showing the benefits of each approach in plant stress detection, with a particular focus on the gaps, which will be filled in the nearby future by the emerging nuclear physics approaches to agriculture.
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Affiliation(s)
- Angelica Galieni
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics, Monsampolo del Tronto, Italy
| | - Nicola D'Ascenzo
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Department of Medical Physics and Engineering, Istituto Neurologico Mediterraneo, I.R.C.C.S, Pozzilli, Italy
| | - Fabio Stagnari
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Giancarlo Pagnani
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Qingguo Xie
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Department of Medical Physics and Engineering, Istituto Neurologico Mediterraneo, I.R.C.C.S, Pozzilli, Italy
| | - Michele Pisante
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
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Mohammad Z, Beck S, King M, Griffin D, Castillo A. Comparison between the Real-Time PCR and Crystal Diagnostic Xpress Immunoassay Methods for Detecting Salmonella and Shiga Toxin-Producing Escherichia coli in the Air of Beef Slaughter Establishments. J Food Prot 2021; 84:31-38. [PMID: 32818256 DOI: 10.4315/jfp-19-616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 08/10/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT The aim of this study was to compare the effectiveness of a quantitative real-time PCR (qPCR) molecular method and the Crystal Diagnostic Xpress (CDx) immunoassay for detecting Salmonella and Shiga toxin-producing Escherichia coli (STEC) in air samples collected from abattoirs in Texas. The 70 air samples were collected from two small and two large meat processing plants in the spring and summer with a wetted wall cyclone air sampler. The samples were divided equally into two parts: one part was used for the qPCR assay, and the other part was enriched for 18 and 36 h and evaluated with the CDx immunoassay. All samples for which positive results were obtained were confirmed by plating and by biochemical and serological tests as recommended by AOAC International to verify results of rapid methods. With the qPCR and CDx assays and 36 h of enrichment, 37.5 and 57.1% of the samples, respectively, were positive for Salmonella (P < 0.05) and 65.0 and 60.7%, respectively, were positive for STEC (P > 0.05). Air samples required longer enrichment for the CDx immunoassay than recommended by the manufacturer for food samples. Recovery of Salmonella and STEC increased 16 and 47%, respectively, when enrichment was extended from 18 to 36 h. The prevalence of Salmonella and STEC obtained with both methods was affected by the size of the processing plant and the processing stage. Detection rates for samples from larger plants were higher for both pathogens. Significantly higher prevalence was obtained for samples from the stunning and dehiding areas than for those from the fabrication rooms and chillers. Salmonella detection was higher with the CDx assay than with the qPCR assay, but no differences were found for the detection of STEC by the qPCR and CDx assays. These results highlight the importance of method adjustments when testing matrices other than foods. More research is needed to understand the dynamics of pathogen dispersal in aerosols and how this affects the effectiveness of current rapid detection methods. HIGHLIGHTS
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Affiliation(s)
- Zahra Mohammad
- Department of Nutrition and Food Science, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843 (ORCID: https://orcid.org/0000-0002-9373-1923 [Z.M.])
| | - Samuel Beck
- Department of Mechanical Engineering, College of Engineering, Texas A&M University, College Station, Texas 77840, USA
| | - Maria King
- Department of Biological & Agricultural Engineering, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843
| | - Davey Griffin
- Department of Animal Science, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843
| | - Alejandro Castillo
- Department of Animal Science, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843
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Noviyanti F, Hosotani Y, Inatsu Y, Kawasaki S. A comparison of Listeria monocytogenes growth monitoring in ground pork samples by real-time polymerase chain reaction to conventional agar and most probable number methods. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2021. [DOI: 10.3136/fstr.27.647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Fia Noviyanti
- National Food Research Institute, Food Hygiene Laboratory
| | - Yukie Hosotani
- National Food Research Institute, Food Hygiene Laboratory
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Application of Nucleic Acid Reference Material for Rapid Detection of Cronobacter sakazakii (Cronobacter spp.) in Flammulina velutipes. J FOOD QUALITY 2020. [DOI: 10.1155/2020/8821330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cronobacter sakazakii (C. sakazakii) widely exists in the environment and is a common foodborne pathogenic microorganism. It can cause meningitis, bacteremia, and necrotizing enterocolitis in infants and elderly people with low immunity. Therefore, the development of the rapid detection method for foodborne pathogen C. sakazakii is very important for food safety control. This study has developed a kind of genomic nucleic acid reference material as a positive reference for the rapid detection of C. sakazakii in the edible fungus Flammulina velutipes. First, the genomic nucleic acids were extracted from the standard strain of C. sakazakii, and the nucleic acids were lyophilized. The uniformity test result of the lyophilized powder showed that there were no significant differences between samples. In short-term stability tests at 4°C and 37°C for 14 days, the properties of the nucleic acid reference material were good, and in long-term stability tests at 4°C and −20°C for 8 months, the samples are still stable. To verify the application of this nucleic acid reference material, it was used as a positive control template for PCR detection and applied to the rapid detection of C. sakazakii in F. velutipes. It was found that 13 of the 15 F. velutipes samples were positive for C. sakazakii. As far as we know, this is the first attempt to detect C. sakazakii in F. velutipes using the PCR method with nucleic acid reference material as the positive reference. This study is helpful in promoting the extensive and in-depth application of nucleic acid reference materials in foodborne pathogens detection.
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Lapa SA, Klochikhina ES, Miftakhov RA, Zolotov AM, Zasedatelev AS, Chudinov AV. Multiplex PCR for Identification of Bacterial Pathogens of Infectious Pneumonia. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020; 46:859-861. [PMID: 33132678 PMCID: PMC7583683 DOI: 10.1134/s1068162020050131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 11/23/2022]
Abstract
A multiplex PCR system has been developed and optimized for rapid detection of the five main pathogens of bacterial pneumonia. The system can be expanded to analyze viral pathogens of pneumonia (DNA- and RNA-containing viruses), as well as those of a fungal nature.
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Affiliation(s)
- S A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E S Klochikhina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A M Zolotov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Begić M, Josić D. Biofilm formation and extracellular microvesicles-The way of foodborne pathogens toward resistance. Electrophoresis 2020; 41:1718-1739. [PMID: 32901923 DOI: 10.1002/elps.202000106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/08/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022]
Abstract
Almost all known foodborne pathogens are able to form biofilms as one of the strategies for survival under harsh living conditions, to ward off the inhibition and the disinfection during food production, transport and storage, as well as during cleaning and sanitation of corresponding facilities. Biofilms are communities where microbial cells live under constant intracellular interaction and communication. Members of the biofilm community are embedded into extracellular matrix that contains polysaccharides, DNA, lipids, proteins, and small molecules that protect microorganisms and enable their intercellular communication under stress conditions. Membrane vesicles (MVs) are produced by both Gram positive and Gram negative bacteria. These lipid membrane-enveloped nanoparticles play an important role in biofilm genesis and in communication between different biofilm members. Furthermore, MVs are involved in other important steps of bacterial life like cell wall modeling, cellular division, and intercellular communication. They also carry toxins and virulence factors, as well as nucleic acids and different metabolites, and play a key role in host infections. After entering host cells, MVs can start many pathologic processes and cause serious harm and cell death. Prevention and inhibition of both biofilm formation and shedding of MVs by foodborne pathogens has a very important role in food production, storage, and food safety in general. Better knowledge of biofilm formation and maintaining, as well as the role of microbial vesicles in this process and in the process of host cells' infection is essential for food safety and prevention of both food spoilage and host infection.
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Affiliation(s)
- Marija Begić
- Faculty of Medicine, Juraj Dobrila University, Pula, Croatia
| | - Djuro Josić
- Faculty of Medicine, Juraj Dobrila University, Pula, Croatia.,Warren Alpert Medical School, Brown University, Providence, RI, USA
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Yang R, Xu G, Wang X, Qing Z, Fu L. Establishment and Application of a Dual TaqMan Real-Time PCR Method for Proteus Mirabilis and Proteus Vulgaris. Pol J Microbiol 2020; 69:293-300. [PMID: 33574858 PMCID: PMC7810114 DOI: 10.33073/pjm-2020-032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 11/05/2022] Open
Abstract
Proteus species are common opportunistic bacteria and foodborne pathogens. The proper detection of Proteus can effectively reduce the occurrence of food-borne public health events. Proteus mirabilis and Proteus vulgaris are the two most important pathogens in the Proteus genus. In this study, a dual TaqMan Real-Time PCR method was established to simultaneously detect and distinguish P. mirabilis and P. vulgaris in samples. The method exhibited good specificity, stability, and sensitivity. Specifically, the minimum detection concentrations of P. mirabilis and P. vulgaris in pure bacterial cultures were 6.08 × 102 colony forming units (CFU)/ml and 4.46 × 102 CFU/ml, respectively. Additionally, the minimum detectable number of P. mirabilis and P. vulgaris in meat and milk was 103 CFU/g. In addition, the method can be used to distinguish between strains of P. mirabilis and P. vulgaris within two hours. Overall, it is a sensitive, easy-to-use, and practical test for the identification and classification of Proteus in food.
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Affiliation(s)
- Rui Yang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Guoyang Xu
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xiaoyou Wang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Zhichu Qing
- Chongqing Nanchuan Animal Disease Prevention And Control Center, Chongqing, China
| | - Lizhi Fu
- Chongqing Academy of Animal Science, Chongqing, China
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Soheili V, Taghdisi SM, Abnous K, Ebrahimi M. Point-of-care detection of Escherichia coli O157:H7 in water using AuNPs-based aptasensor. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2020; 23:901-908. [PMID: 32774812 PMCID: PMC7395186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
OBJECTIVES Access to safe drinking and irrigation water has always been one of the major human concerns worldwide. Thus, rapid, sensitive, and inexpensive approaches for pathogenic bacteria detection, such as Escherichia coli O157:H7 (EHEC) that can induce important infectious diseases, are highly on demand. MATERIALS AND METHODS In this study, a sensitive aptamer-based AuNPs bioassay was developed that demonstrated its potential to detect EHEC. In the presence of the target bacterium, the specific adsorbed aptamer, leaves AuNPs surface and interacts with EHEC. The bare nanoparticles aggregate in the presence of NaCl and the color shifts from red to purple and blue depending on the bacterial concentration. RESULTS The proposed aptasensor exhibited a good linear response over a wide concentration range of 876 to 107 CFU/ml and was closely correlated with the line equation of "y=0.0094x+0.0006" (R2= 0.9861). It also showed a low detection limit (LOD) of 263 CFU/ml (Signal/Noise=3). No response was recorded in the presence of other tested bacterial strains including Listeria monocytogenes and Salmonella typhi, indicating the high selectivity of the aptasensor. CONCLUSION This biosensor may be used as a smart device to screen water reservoirs and prevents the outbreak of EHEC-related life-threatening contagious diseases.
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Affiliation(s)
- Vahid Soheili
- Department of Pharmacology and Toxicology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Ebrahimi
- Department of Pharmacology and Toxicology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran,Corresponding author: Mohsen Ebrahimi. Department of Pharmacology and Toxicology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran. Tel: +98-21-39954958; Fax: +98-51-38823251;
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Yao W, Shi J, Ling J, Guo Y, Ding C, Ding Y. SiC-functionalized fluorescent aptasensor for determination of Proteus mirabilis. Mikrochim Acta 2020; 187:406. [PMID: 32594319 DOI: 10.1007/s00604-020-04378-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/07/2020] [Indexed: 01/04/2023]
Abstract
Aptamer-modified SiC quantum dots (DNA-SiC QDs) as fluorescent aptasensor are described for the determination of Proteus mirabilis. The SiC QDs were synthesized through one-pot hydrothermal method with particle sizes of about 14 nm. The amino-modified aptamers against P. mirabilis were conjugated to the surfaces of SiC QDs for bacteria recognition. The aptamer with an affinity for target protein can bound to P. mirabilis and this causes a decrease in the fluorescence intensity of DNA-SiC QDs. P. mirabilis levels were tested by the aptasensor within 35 min with fluorescence excitation/emission maxima at 320/420 nm. The linear range is from 103 to 108 CFU mL-1 and the limit of detection is 526 CFU mL-1 (S/N = 3). The aptasensor was used for determination of P. mirabilis in pure milk samples and obtained good accuracy (87.6-104.5%) and recovery rates (85-110.2%) were obtained. The detection in simulated forensic identification samples (pure milk, milk powder, blood, and urine) obtained gave satisfactory coincidence rates with the method of bacterial isolation and identification as standard. These results demonstrate that the fluorescent aptasensor is a potential tool for identification of P. mirabilis in forensic food poisoning cases. Graphical abstract Determination of P. mirabilis is based on SiC QDs fluorescence aptasensor. The SiC QDs with plentiful carboxyl groups on the surface can be synthesized via one-pot hydrothermal route. After activated by EDC/NHS, the SiC QDs can bind to aptamer to form fluorescence aptasensors. When the target P. mirabilis exists, the fluorescence of aptasensor will be quenched and the determination of the P. mirabilis based on the fluorescence change can be analyzed.
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Affiliation(s)
- Wenyan Yao
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Jian Shi
- The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Jiang Ling
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Chensen Ding
- Institute of Computational Engineering, University of Luxembourg, Maison du Nombre, 6 Avenue de la Fonte, 4364, Esch-sur-Alzette, Luxembourg.
| | - Yanjun Ding
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, China.
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50
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Mohsina K, Kaur M, Bowman JP, Powell S, Tamplin ML. qPCR quantification of Carnobacterium maltaromaticum, Brochothrix thermosphacta, and Serratia liquefaciens growth kinetics in mixed culture. J Microbiol Methods 2020; 175:105961. [PMID: 32479869 DOI: 10.1016/j.mimet.2020.105961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 10/24/2022]
Abstract
Quantifying growth kinetics of specific spoilage microorganisms in mixed culture is required to describe the evolution of food microbiomes. A qPCR method was developed to selectively amplify individual meat spoilage bacteria, Carnobacterium maltaromaticum, Brochothrix thermosphacta and Serratia liquefaciens, within a broth medium designed to simulate the composition of beef. An optimized method of DNA extraction was produced for standard curve construction. Method specificity was determined by individual single peaks in melt curves. Reaction efficiency for standard curves of C. maltaromaticum, B. thermosphacta and S. liquefaciens was high (R2 = 0.98-0.99), and linear quantification was achieved over a 5 log CFU/ml range. Coefficient of variation was calculated considering both threshold cycle (Ct) and bacterial concentration; the value did not exceed 14% for inter- or intra-runs for either method. Comparison of growth kinetic parameters derived from plate count and qPCR showed no significant variation (P > .05) for growth rate (GR) and maximum population density (MPD); lag phase duration (LPD) was not included in this comparison due to high innate variability. Log quantification of each isolate was validated in a mixed-culture experiment for all three species with qPCR and plate count differing less than 0.3 log CFU/ml (average 0.10 log CFU/ml, R2 = 0.98).
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Affiliation(s)
- Kaniz Mohsina
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - Mandeep Kaur
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - Shane Powell
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - Mark L Tamplin
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
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