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Feng S, Karanth S, Almuhaideb E, Parveen S, Pradhan AK. Machine learning to predict the relationship between Vibrio spp. concentrations in seawater and oysters and prevalent environmental conditions. Food Res Int 2024; 188:114464. [PMID: 38823834 DOI: 10.1016/j.foodres.2024.114464] [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: 02/26/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/03/2024]
Abstract
Vibrio parahaemolyticus and Vibrio vulnificus are bacteria with a significant public health impact. Identifying factors impacting their presence and concentrations in food sources could enable the identification of significant risk factors and prevent incidences of foodborne illness. In recent years, machine learning has shown promise in modeling microbial presence based on prevalent external and internal variables, such as environmental variables and gene presence/absence, respectively, particularly with the generation and availability of large amounts and diverse sources of data. Such analyses can prove useful in predicting microbial behavior in food systems, particularly under the influence of the constant changes in environmental variables. In this study, we tested the efficacy of six machine learning regression models (random forest, support vector machine, elastic net, neural network, k-nearest neighbors, and extreme gradient boosting) in predicting the relationship between environmental variables and total and pathogenic V. parahaemolyticus and V. vulnificus concentrations in seawater and oysters. In general, environmental variables were found to be reliable predictors of total and pathogenic V. parahaemolyticus and V. vulnificus concentrations in seawater, and pathogenic V. parahaemolyticus in oysters (Acceptable Prediction Zone >70 %) when analyzed using our machine learning models. SHapley Additive exPlanations, which was used to identify variables influencing Vibrio concentrations, identified chlorophyll a content, seawater salinity, seawater temperature, and turbidity as influential variables. It is important to note that different strains were differentially impacted by the same environmental variable, indicating the need for further research to study the causes and potential mechanisms of these variations. In conclusion, environmental variables could be important predictors of Vibrio growth and behavior in seafood. Moreover, the models developed in this study could prove invaluable in assessing and managing the risks associated with V. parahaemolyticus and V. vulnificus, particularly in the face of a changing environment.
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Affiliation(s)
- Shuyi Feng
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
| | - Shraddha Karanth
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
| | - Esam Almuhaideb
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Salina Parveen
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Abani K Pradhan
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA.
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Zhu Y, Ma S, Wen Y, Zhao W, Jiang Y, Li M, Zou K. Deciphering assembly processes, network complexity and stability of potential pathogenic communities in two anthropogenic coastal regions of a highly urbanized estuary. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124444. [PMID: 38936795 DOI: 10.1016/j.envpol.2024.124444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/01/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
The existence of potential pathogens may lead to severe water pollution, disease transmission, and the risk of infectious diseases, posing threats to the stability of aquatic ecosystems and human health. In-depth research on the dynamic of potential pathogenic communities is of significant importance, it can provide crucial support for assessing the health status of aquatic ecosystems, maintaining ecological balance, promoting sustainable economic development, and safeguarding human health. Nevertheless, the current understanding of the distribution and geographic patterns of potential pathogens in coastal ecosystems remains rather limited. Here, we investigated the diversity, assembly, and co-occurrence network of potential pathogenic communities in two anthropogenic coastal regions, i.e., the eight mouths (EPR) and nearshore region (NSE), of the Pearl River Estuary (PRE) and a total of 11 potential pathogenic types were detected. The composition and diversity of potential pathogenic communities exhibited noteworthy distinctions between the EPR and NSE, with 6 shared potential pathogenic families. Additionally, in the NSE, a significant pattern of geographic decay was observed, whereas in the EPR, the pattern of geographic decay was not significant. Based on the Stegen null model, it was noted that undominant processes (53.36%/69.24%) and heterogeneous selection (27.35%/25.19%) dominated the assembly of potential pathogenic communities in EPR and NSE. Co-occurrence network analysis showed higher number of nodes, a lower average path length and graph diameter, as well as higher level of negative co-occurrences and modularity in EPR than those in NSE, indicating more complex and stable correlations between potential pathogens in EPR. These findings lay the groundwork for the effective management of potential pathogens, offering essential information for ecosystem conservation and public health considerations in the anthropogenic coastal regions.
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Affiliation(s)
- Yiyi Zhu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Shanshan Ma
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yongjing Wen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Wencheng Zhao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yun Jiang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Min Li
- Key Laboratory for Sustainable Utilization of Open-sea Fishery, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Keshu Zou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China.
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Padovan AC, Turnbull AR, Nowland SJ, Osborne MWJ, Kaestli M, Seymour JR, Gibb KS. Growth of V. parahaemolyticus in Tropical Blacklip Rock Oysters. Pathogens 2023; 12:834. [PMID: 37375524 DOI: 10.3390/pathogens12060834] [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: 02/23/2023] [Revised: 03/14/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The opportunistic pathogen Vibrio parahaemolyticus poses a significant food safety risk worldwide, and understanding its growth in commercially cultivated oysters, especially at temperatures likely to be encountered post-harvest, provides essential information to provide the safe supply of oysters. The Blacklip Rock Oyster (BRO) is an emerging commercial species in tropical northern Australia and as a warm water species, it is potentially exposed to Vibrio spp. In order to determine the growth characteristics of Vibrio parahaemolyticus in BRO post-harvest, four V. parahaemolyticus strains isolated from oysters were injected into BROs and the level of V. parahaemolyticus was measured at different time points in oysters stored at four temperatures. Estimated growth rates were -0.001, 0.003, 0.032, and 0.047 log10 CFU/h at 4 °C, 13 °C, 18 °C, and 25 °C, respectively. The highest maximum population density of 5.31 log10 CFU/g was achieved at 18 °C after 116 h. There was no growth of V. parahaemolyticus at 4 °C, slow growth at 13 °C, but notably, growth occurred at 18 °C and 25 °C. Vibrio parahaemolyticus growth at 18 °C and 25 °C was not significantly different from each other but were significantly higher than at 13 °C (polynomial GLM model, interaction terms between time and temperature groups p < 0.05). Results support the safe storage of BROs at both 4 °C and 13 °C. This V. parahaemolyticus growth data will inform regulators and assist the Australian oyster industry to develop guidelines for BRO storage and transport to maximise product quality and safety.
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Affiliation(s)
- Anna C Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0810, Australia
| | - Alison R Turnbull
- Institute of Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia
| | - Samantha J Nowland
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0810, Australia
- Aquaculture Unit, Department of Industry, Tourism and Trade, Northern Territory Government, Darwin, NT 0801, Australia
| | - Matthew W J Osborne
- Aquaculture Unit, Department of Industry, Tourism and Trade, Northern Territory Government, Darwin, NT 0801, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0810, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Karen S Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0810, Australia
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Hassan M, Mohd Ali MR, Zamri HF, Nor Amdan NA, Azmai MNA, Maniam S, Mohamed Alipiah N, Hashim R. Distribution, Prevalence, and Antibiotic Susceptibility Profiles of Infectious Noncholera Vibrio Species in Malaysia. J Trop Med 2023; 2023:2716789. [PMID: 37274080 PMCID: PMC10238136 DOI: 10.1155/2023/2716789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/05/2023] [Accepted: 05/06/2023] [Indexed: 06/06/2023] Open
Abstract
Background The noncholera Vibrio spp. which cause vibriosis are abundantly found in our water ecosystem. These bacteria could negatively affect both humans and animals. To date, there is a paucity of information available on the existence and pathogenicity of this particular noncholera Vibrio spp. in Malaysia in comparison to their counterpart, Vibrio cholera. Methods In this study, we extracted retrospective data from Malaysian surveillance database. Analysis was carried out using WHONET software focusing noncholera Vibrio spp. including Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio fluvialis, Vibrio alginolyticus, Vibrio hollisae (Grimontia hollisae), Vibrio mimicus, Vibrio metschnikovii, and Vibrio furnissii. Results Here, we report the first distribution and prevalence of these species isolated in Malaysia together with the antibiotic sensitivity profile based on the species. We found that V. parahaemolyticus is the predominant species isolated in Malaysia. Noticeably, across the study period, V. fluvialis is becoming more prevalent, as compared to V. parahaemolyticus. In addition, this study also reports the first isolation of pathogenic V. furnissii from stool in Malaysia. Conclusion These data represent an important step toward understanding the potential emergence of noncholera Vibrio spp. outbreaks.
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Affiliation(s)
- Murnihayati Hassan
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Mohammad Ridhuan Mohd Ali
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Hana Farizah Zamri
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Nur Asyura Nor Amdan
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Mohammad Noor Amal Azmai
- Aquatic Animal Health & Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Saraswathiy Maniam
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Norfarrah Mohamed Alipiah
- Aquatic Animal Health & Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Rohaidah Hashim
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
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Gao Q, Ma X, Wang Z, Chen H, Luo Y, Wu B, Qi S, Lin M, Tian J, Qiao Y, Grossart HP, Xu W, Huang L. Seasonal variation, virulence gene and antibiotic resistance of Vibrio in a semi-enclosed bay with mariculture (Dongshan Bay, Southern China). MARINE POLLUTION BULLETIN 2022; 184:114112. [PMID: 36113173 DOI: 10.1016/j.marpolbul.2022.114112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 08/09/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
In this study, the virulence genes, antibiotic resistance of culturable Vibrio and the environmental factors affecting Vibrio abundance were analyzed in four seasons in DongShan Bay with different intensity of aquaculture practice. A total of 253 bacteria isolates were obtained, of which 177 Vibrio strains belonged to 26 species. Annual Vibrio abundance in this region ranged from 20 to 11,600 CFU mL-1 and the most significant positive correlation occurred with temperature. Detection of 9 different Vibrio virulence genes revealed that most isolates contained atypical virulence genes in addition to the typical ones. In particular, virulence genes of hemolysin such as tdh, trh, and hlyA (6.32 %, 15.52 %, and 11.30 %) showed different degrees of horizontal gene transfer (HGT). In our antibiotic resistance test, the multiple antibiotic resistance (MAR) index of the isolates ranged from 0.01 to 0.03 in different seasons, and three MAR Vibrio strains were detected. Overall, our study sheds new light on the spatial distribution patterns and the occurrence of virulence genes and antibiotics resistance Vibrio isolated from a subtropical bay with intensive aquaculture. Our study provides a suitable microbial quality surveillance in a mariculture impacted coastal environment. It will help to establish effective disease prevention measures in this area and provide useful guidance and support for formulating local antibiotics use policies.
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Affiliation(s)
- Qiancheng Gao
- Fisheries College, Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen, Fujian, China
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, China
| | - Zhichao Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Haisheng Chen
- Fishery Technology Promotion Station of Dongshan, Zhangzhou 363400, China
| | - Yu Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Bi Wu
- Fisheries College, Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen, Fujian, China
| | - Shanni Qi
- Fisheries College, Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen, Fujian, China
| | - Miaozhen Lin
- Fisheries College, Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen, Fujian, China
| | - Jing Tian
- Fisheries College, Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen, Fujian, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, China
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin 16775, Germany; Institute of Biochemistry and Biology, Potsdam University, Potsdam 14469, Germany
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, China.
| | - Lixing Huang
- Fisheries College, Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen, Fujian, China.
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