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Shrestha S, Malla B, Haramoto E. High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater. ENVIRONMENTAL RESEARCH 2024; 255:119156. [PMID: 38759773 DOI: 10.1016/j.envres.2024.119156] [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: 04/12/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.
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Affiliation(s)
- Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
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2
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Zeeshan, Bahrami S, Park S, Cho S. Antibody functionalized capacitance sensor for label-free and real-time detection of bacteria and antibiotic susceptibility. Talanta 2024; 272:125831. [PMID: 38428133 DOI: 10.1016/j.talanta.2024.125831] [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: 08/10/2023] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
The effective management of infectious diseases and the growing concern of antibiotic resistance necessitates accurate and targeted therapies, highlighting the importance of antibiotic susceptibility testing. This study aimed to develop a real-time impedimetric biosensor for identifying and monitoring bacterial growth and antibiotic susceptibility. The biosensor employed a gold 8-channel disk-shaped microelectrode array with specific antibodies as bio-recognition elements. This setup was allowed for the analysis of bacterial samples, including Staphylococcus aureus, Bacillus cereus, and Micrococcus luteus. These microorganisms were successfully cultured and detected within 1 h of incubation even with a minimal bacterial concentration of 10 CFU/ml. Overall, the developed biosensor array exhibits promising capabilities for monitoring S. aureus, B. cereus and M. luteus, showcasing an excellent linear response ranging from 10 to 104 CFU/ml with a detection limit of 0.95, 1.22 and 1.04 CFU/mL respectively. Moreover, real-time monitoring of antibiotic susceptibility was facilitated by changes in capacitance, which dropped when bacteria were exposed to antibiotic doses higher than their minimum inhibitory concentration (MIC), indicating suppressed bacterial growth. The capacitance measurements enabled determination of half-maximal cytotoxic concentrations (CC50) values for each bacteria-antibiotic pair. As a proof-of-concept application, the developed sensor array was employed as a sensing platform for the real time detection of bacteria in milk samples, which ensured the reliability of the sensor for in-field detection of foodborne pathogens and rapid antimicrobial susceptibility tests (ASTs).
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Affiliation(s)
- Zeeshan
- Department of Electronic Engineering, Gachon University, 1342 Seongnamdaero, Seongnam-si, Gyeonggi-do, 13120, South Korea.
| | - Sadra Bahrami
- School of Mechanical Engineering, Sungkyunkwan University (SKKU), Seobu-ro 2066, Jangan-gu, Suwon, 16419, South Korea.
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University (SKKU), Seobu-ro 2066, Jangan-gu, Suwon, 16419, South Korea.
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, 1342 Seongnamdaero, Seongnam-si, Gyeonggi-do, 13120, South Korea; Department of Health Science and Technology, GAIHST, Gachon University, Incheon, 21999, South Korea.
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3
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Su Y, Gao R, Huang F, Liang B, Guo J, Fan L, Wang A, Gao SH. Occurrence, transmission and risks assessment of pathogens in aquatic environments accessible to humans. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120331. [PMID: 38368808 DOI: 10.1016/j.jenvman.2024.120331] [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: 11/06/2023] [Revised: 01/24/2024] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
Pathogens are ubiquitously detected in various natural and engineered water systems, posing potential threats to public health. However, it remains unclear which human-accessible waters are hotspots for pathogens, how pathogens transmit to these waters, and what level of health risk associated with pathogens in these environments. This review collaboratively focuses and summarizes the contamination levels of pathogens on the 5 water systems accessible to humans (natural water, drinking water, recreational water, wastewater, and reclaimed water). Then, we showcase the pathways, influencing factors and simulation models of pathogens transmission and survival. Further, we compare the health risk levels of various pathogens through Quantitative Microbial Risk Assessment (QMRA), and assess the limitations of water-associated QMRA application. Pathogen levels in wastewater are consistently higher than in other water systems, with no significant variation for Cryptosporidium spp. among five water systems. Hydraulic conditions primarily govern the transmission of pathogens into human-accessible waters, while environmental factors such as temperature impact pathogens survival. The median and mean values of computed public health risk levels posed by pathogens consistently surpass safety thresholds, particularly in the context of recreational waters. Despite the highest pathogens levels found in wastewater, the calculated health risk is significantly lower than in other water systems. Except pathogens concentration, variables like the exposure mode, extent, and frequency are also crucial factors influencing the public health risk in water systems. This review shares valuable insights to the more accurate assessment and comprehensive management of public health risk in human-accessible water environments.
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Affiliation(s)
- Yiyi Su
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Rui Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Fang Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China.
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Faherty EAG, Yuce D, Korban C, Bemis K, Kowalski R, Gretsch S, Ramirez E, Poretsky R, Packman A, Leisman KP, Pierce M, Kittner A, Teran R, Pacilli M. Correlation of wastewater surveillance data with traditional influenza surveillance measures in Cook County, Illinois, October 2022-April 2023. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169551. [PMID: 38135071 PMCID: PMC10913165 DOI: 10.1016/j.scitotenv.2023.169551] [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: 09/25/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Influenza is a respiratory illness that can result in serious outcomes, particularly among persons who are immunocompromised, aged <5 years or aged >65 years. Traditional influenza surveillance approaches rely upon syndromic surveillance of emergency departments and public health reporting from clinicians and laboratories. Wastewater surveillance infrastructure developed to monitor SARS-CoV-2 is being used for influenza surveillance in the Chicago area. The goal was to evaluate timeliness and correlations between influenza virus detected through wastewater surveillance and traditional influenza surveillance measures to assess utility of wastewater surveillance for influenza at the county level. Specifically, we measured correlations between influenza virus gene copies in wastewater samples and 1) the number of intensive care unit admissions associated with a diagnosis of influenza, 2) the percentage emergency department (ED) visits for influenza-like-illness, and 3) the percentage of ED visits with influenza diagnosis at discharge2 in Cook County. Influenza concentrations in wastewater were strongly correlated with traditional influenza surveillance measures, particularly for catchment areas serving >100,000 residents. Wastewater indicators lagged traditional influenza surveillance measures by approximately one week when analyzed in cross-correlations. Although wastewater data lagged traditional influenza surveillance measures in this analysis, it can serve as a useful surveillance tool as a complement to syndromic surveillance; it is a form of influenza surveillance that does not rely on healthcare-seeking behavior or reporting by healthcare providers.
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Affiliation(s)
- Emily A G Faherty
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, United States of America; Chicago Department of Public Health, United States of America.
| | - Deniz Yuce
- Chicago Department of Public Health, United States of America
| | - Colin Korban
- Chicago Department of Public Health, United States of America
| | - Kelley Bemis
- Cook County Department of Public Health, United States of America
| | - Rishi Kowalski
- Cook County Department of Public Health, United States of America
| | | | - Enrique Ramirez
- Chicago Department of Public Health, United States of America
| | | | | | | | - Melissa Pierce
- University of Illinois System, Discovery Partners Institute, United States of America
| | - Alyse Kittner
- Chicago Department of Public Health, United States of America
| | - Richard Teran
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, United States of America; Chicago Department of Public Health, United States of America
| | - Massimo Pacilli
- Chicago Department of Public Health, United States of America
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Katayama YA, Hayase S, Iwamoto R, Kuroita T, Okuda T, Kitajima M, Masago Y. Simultaneous extraction and detection of DNA and RNA from viruses, prokaryotes, and eukaryotes in wastewater using a modified COPMAN. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167866. [PMID: 37863234 DOI: 10.1016/j.scitotenv.2023.167866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Wastewater surveillance can offer a comprehensive grasp of infectious disease prevalence and human health because wastewater contains various human-derived microbial pathogens, including viruses, bacteria, and fungi. However, methods capable of simultaneous detection of multiple groups of targets in the automated systems and large-scale surveillance are still under development. Here, we demonstrated the modification, involving the addition of bead-beating, to the existing COPMAN (COagulation and Proteolysis method using MAgnetic beads for detection of Nucleic acids in wastewater) enabled enhanced detection of various microorganisms, including SARS-CoV-2. The modified method, termed bead-beating COPMAN (BB-COPMAN), was evaluated through spike-and-recovery experiments and comparative analysis against three previously reported methods for simultaneous DNA/RNA detection. Our study targeted a range of microorganisms, including enveloped and non-enveloped RNA viruses (SARS-CoV-2, PMMoV), a DNA virus (crAssphage), archaea, gram-negative and gram-positive bacteria (E. coli, Lachnospiraceae), antibiotic resistance gene (ampC), and fungi (Candida albicans). The recovery rates of BB-COPMAN for gram-negative and gram-positive bacteria were 17 and 2.1-fold higher, respectively, compared to the method for DNA/RNA detection. Additionally, BB-COPMAN exhibited the highest extraction efficiency among the tested methods, achieving 1.2-5.7 times more DNA and 1.1-69 times more RNA yield on average. BB-COPMAN allowed the detection of SARS-CoV-2 from all nine samples and PMMoV at concentrations 39-97 times higher than other methods. Moreover, BB-COPMAN detected larger amounts of DNA for four out of six DNA targets than the previously reported DNA/RNA detection method. These results demonstrated that BB-COPMAN enables enhanced detection of multiple targets in a single flow of nucleic acid extraction, making the method well-suited for automated systems. In conclusion, BB-COPMAN is a promising method in wastewater surveillance for assessing the prevalence of wide range of pathogenic microorganisms.
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Affiliation(s)
- Yuka Adachi Katayama
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shin Hayase
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Ryo Iwamoto
- Shionogi & Co., Ltd., Head Office, 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan; AdvanSentinel Inc., 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Tomohiro Kuroita
- Shionogi & Co., Ltd., Head Office, 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan; AdvanSentinel Inc., 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Tomohiko Okuda
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Yusaku Masago
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.
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6
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Zhang S, Shi J, Li X, Tiwari A, Gao S, Zhou X, Sun X, O'Brien JW, Coin L, Hai F, Jiang G. Wastewater-based epidemiology of Campylobacter spp.: A systematic review and meta-analysis of influent, effluent, and removal of wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166410. [PMID: 37597560 DOI: 10.1016/j.scitotenv.2023.166410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Campylobacter spp. is one of the four leading causes of diarrhoeal diseases worldwide, which are generally mild but can be fatal in children, the elderly, and immunosuppressed persons. The existing disease surveillance for Campylobacter infections is usually based on untimely clinical reports. Wastewater surveillance or wastewater-based epidemiology (WBE) has been developed for the early warning of disease outbreaks and the detection of the emerging new variants of human pathogens, especially after the global pandemic of COVID-19. However, the WBE monitoring of Campylobacter infections in communities is rare due to a few large data gaps. This study is a meta-analysis and systematic review of the prevalence of Campylobacter spp. in various wastewater samples, primarily the influent of wastewater treatment plants. The results showed that the overall prevalence of Campylobacter spp. was 53.26 % in influent wastewater and 52.97 % in all types of wastewater samples. The mean concentration in the influent was 3.31 ± 0.39 log10 gene copies or most probable number (MPN) per 100 mL. The detection method combining culture and PCR yielded the highest positive rate of 90.86 %, while RT-qPCR and qPCR were the two most frequently used quantification methods. In addition, the Campylobacter concentration in influent wastewater showed a seasonal fluctuation, with the highest concentration in the autumn at 3.46 ± 0.41 log10 gene copies or MPN per 100 mL. Based on the isolates of all positive samples, Campylobacter jejuni (62.34 %) was identified as the most prevalent species in wastewater, followed by Campylobacter coli (30.85 %) and Campylobacter lari (4.4 %). These findings provided significant data to further develop and optimize the wastewater surveillance of Campylobacter spp. infections. In addition, large data gaps were found in the decay of Campylobacter spp. in wastewater, indicating insufficient research on the persistence of Campylobacter spp. in wastewater.
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Affiliation(s)
- Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Jiahua Shi
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Australia
| | - Xuan Li
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ananda Tiwari
- Department of Health Security, Expert Microbiology Research Unit, Finnish Institute for Health and Welfare, Finland
| | - Shuhong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xu Zhou
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xiaoyan Sun
- School of Civil Engineering, Sun Yat-sen University, 519082 Zhuhai, China
| | - Jake W O'Brien
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Australia
| | - Lachlan Coin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Faisal Hai
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Australia.
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7
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Tsikopoulos K, Drago L, Meroni G, Kitridis D, Chalidis B, Papageorgiou F, Papaioannidou P. In vitro laboratory infection research in orthopaedics: Why, when, and how. World J Orthop 2023; 14:598-603. [PMID: 37662661 PMCID: PMC10473912 DOI: 10.5312/wjo.v14.i8.598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023] Open
Abstract
The musculoskeletal system involves multiple tissues which are constantly exposed to being exposed to various biological and mechanical stimuli. As such, isolating and studying a particular system from a complex human clinical environment is not always a realistic expectation. On top of that, recruitment limitations, in addition to the nature of orthopaedic interventions and their associated cost, sometimes preclude consideration of human trials to answer a clinical question. Therefore, in this mini review, we sought to rationalize the rapid evolution of biomedical research at a basic scientific level and explain why the perception of orthopaedic conditions has fundamentally changed over the last decades. In more detail, we highlight that the number of orthopaedic in vitro publications has soared since 1990. Last but not least, we elaborated on the minimum requirements for conducting a scientifically sound infection-related laboratory experiment to offer valuable information to clinical practitioners. We also explained the rationale behind implementing molecular biology techniques, ex vivo experiments, and artificial intelligence in this type of laboratory research.
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Affiliation(s)
- Konstantinos Tsikopoulos
- 1st Department of Pharmacology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Lorenzo Drago
- Department of Biomedical Sciences for Health, School of Medicine, University of Milan, Milan 20133, Italy
| | - Gabriele Meroni
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan 20133, Italy
| | - Dimitrios Kitridis
- 1st Department of Orthopaedic, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 57010, Greece
| | - Byron Chalidis
- 1st Department of Orthopaedic, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 57010, Greece
| | - Fotios Papageorgiou
- Department of Orthopaedic Surgery, 404 General Army Hospital, Larisa 41222, Greece
| | - Paraskevi Papaioannidou
- 1st Department of Pharmacology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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8
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Tiwari A, Ahmed W, Oikarinen S, Sherchan SP, Heikinheimo A, Jiang G, Simpson SL, Greaves J, Bivins A. Application of digital PCR for public health-related water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155663. [PMID: 35523326 DOI: 10.1016/j.scitotenv.2022.155663] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 05/25/2023]
Abstract
Digital polymerase chain reaction (dPCR) is emerging as a reliable platform for quantifying microorganisms in the field of water microbiology. This paper reviews the fundamental principles of dPCR and its application for health-related water microbiology. The relevant literature indicates increasing adoption of dPCR for measuring fecal indicator bacteria, microbial source tracking marker genes, and pathogens in various aquatic environments. The adoption of dPCR has accelerated recently due to increasing use for wastewater surveillance of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) - the virus that causes Coronavirus Disease 2019 (COVID-19). The collective experience in the scientific literature indicates that well-optimized dPCR assays can quantify genetic material from microorganisms without the need for a calibration curve and often with superior analytical performance (i.e., greater sensitivity, precision, and reproducibility) than quantitative polymerase chain reaction (qPCR). Nonetheless, dPCR should not be viewed as a panacea for the fundamental uncertainties and limitations associated with measuring microorganisms in water microbiology. With dPCR platforms, the sample analysis cost and processing time are typically greater than qPCR. However, if improved analytical performance (i.e., sensitivity and accuracy) is critical, dPCR can be an alternative option for quantifying microorganisms, including pathogens, in aquatic environments.
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Affiliation(s)
- Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, Queensland, Australia
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, USA; Department of Biology, Morgan State University, Baltimore, MD 21251, USA; BioEnvironmental Science Program, Department of Biology, Morgan State University, Baltimore, MD 21251, USA
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Finnish Food Authority, Seinäjoki, Finland
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | | | - Justin Greaves
- School of Environmental Sustainability, Loyola University Chicago, 6364 N. Sheridan Rd, Chicago, IL 60660, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, LA, USA.
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9
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Nnachi RC, Sui N, Ke B, Luo Z, Bhalla N, He D, Yang Z. Biosensors for rapid detection of bacterial pathogens in water, food and environment. ENVIRONMENT INTERNATIONAL 2022; 166:107357. [PMID: 35777116 DOI: 10.1016/j.envint.2022.107357] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Conventional techniques (e.g., culture-based method) for bacterial detection typically require a central laboratory and well-trained technicians, which may take several hours or days. However, recent developments within various disciplines of science and engineering have led to a major paradigm shift in how microorganisms can be detected. The analytical sensors which are widely used for medical applications in the literature are being extended for rapid and on-site monitoring of the bacterial pathogens in food, water and the environment. Especially, within the low-resource settings such as low and middle-income countries, due to the advantages of low cost, rapidness and potential for field-testing, their use is indispensable for sustainable development of the regions. Within this context, this paper discusses analytical methods and biosensors which can be used to ensure food safety, water quality and environmental monitoring. In brief, most of our discussion is focused on various rapid sensors including biosensors and microfluidic chips. The analytical performances such as the sensitivity, specificity and usability of these sensors, as well as a brief comparison with the conventional techniques for bacteria detection, form the core part of the discussion. Furthermore, we provide a holistic viewpoint on how future research should focus on exploring the synergy of different sensing technologies by developing an integrated multiplexed, sensitive and accurate sensors that will enable rapid detection for food safety, water and environmental monitoring.
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Affiliation(s)
- Raphael Chukwuka Nnachi
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Ning Sui
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Bowen Ke
- Laboratory of Anesthesiology & Critical Care Medicine, Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 61004, PR China
| | - Zhenhua Luo
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern Ireland, United Kingdom; Healthcare Technology Hub, Ulster University, Jordanstown Shore Road, BT37 0QB, Northern Ireland, United Kingdom
| | - Daping He
- School of Science, Wuhan University of Technology, Wuhan 430070, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom.
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10
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Chetty K, McCarthy T, Hai F, Zhang S, Song Y, Jiang G. Physiological suitability of sulfate reducing granules for the development of bioconcrete. Biotechnol Bioeng 2022; 119:2743-2756. [PMID: 35841264 DOI: 10.1002/bit.28184] [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: 03/18/2022] [Revised: 06/03/2022] [Accepted: 07/10/2022] [Indexed: 11/06/2022]
Abstract
Regular monitoring and timely repair of concrete cracks are required to minimise further deterioration. Self-healing of cracks has been proposed as an alternative to the crack maintenance procedures. One of the proposed techniques is to use axenic cultures to exploit microbial induced calcite precipitation (MICP). However, such healing agents are not cost-effective for in situ use. As the market for bio-based self-healing concrete necessitates a low-cost bio-agent, non-axenic sulfate reducing bacterial (SRB) granules were investigated in this study through cultivation in an upflow anaerobic sludge blanket (UASB) reactor. The compact granules can protect the bacteria from adverse conditions without encapsulation. This study investigated the microbial activities of SRB granules at different temperatures, pH, and COD concentrations which the microbes would experience during the concrete casting and curing process. The attenuation and recovery of microbial activities were measured before and after the exposure. Moreover, the MICP yield was also tested for a possible use in self-healing bioconcrete. The results consistently showed that SRB granules were able to survive starvation, high temperature (50-60 o C), and high pH (12), together with SEM/EDS/XRD evidence. Microbial staining analysis demonstrated the formation of spores in the granules during their exposure to the harsh conditions. SRB granule was thus demonstrated to be a viable self-healing non-axenic agent for low-cost bioconcrete. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kirthi Chetty
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Timothy McCarthy
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Faisal Hai
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Yarong Song
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Queensland, Australia
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, 2522, Australia
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11
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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