1
|
Fridman Y, Wang Z, Maslov S, Goyal A. Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments. PLoS Comput Biol 2022; 18:e1010244. [PMID: 36574450 PMCID: PMC9829172 DOI: 10.1371/journal.pcbi.1010244] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 01/09/2023] [Accepted: 12/05/2022] [Indexed: 12/28/2022] Open
Abstract
Recent observations have revealed that closely related strains of the same microbial species can stably coexist in natural and laboratory settings subject to boom and bust dynamics and serial dilutions, respectively. However, the possible mechanisms enabling the coexistence of only a handful of strains, but not more, have thus far remained unknown. Here, using a consumer-resource model of microbial ecosystems, we propose that by differentiating along Monod parameters characterizing microbial growth rates in high and low nutrient conditions, strains can coexist in patterns similar to those observed. In our model, boom and bust environments create satellite niches due to resource concentrations varying in time. These satellite niches can be occupied by closely related strains, thereby enabling their coexistence. We demonstrate that this result is valid even in complex environments consisting of multiple resources and species. In these complex communities, each species partitions resources differently and creates separate sets of satellite niches for their own strains. While there is no theoretical limit to the number of coexisting strains, in our simulations, we always find between 1 and 3 strains coexisting, consistent with known experiments and observations.
Collapse
Affiliation(s)
- Yulia Fridman
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Zihan Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Sergei Maslov
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (SM); (AG)
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (SM); (AG)
| |
Collapse
|
2
|
Huang Y, Lyu B, Zhang X, Tian Y, Lin C, Shen L, Yan H, Zhang D, Jia L, Qu M, Wang Q. Vibrio parahaemolyticus O10:K4: An Emergent Serotype with Pandemic Virulence Traits as Predominant Clone Detected by Whole-Genome Sequence Analysis - Beijing Municipality, China, 2021. China CDC Wkly 2022; 4:471-477. [PMID: 35812779 PMCID: PMC9257694 DOI: 10.46234/ccdcw2022.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Vibrio parahaemolyticus (V. parahaemolyticus) is a common foodborne pathogen which causes gastroenteritis in humans, especially the O3:K6 pandemic clone which is still a prominent serotype in Beijing, China. In this study, we observed a novel serotype O10:K4 isolated from clinical diarrhea cases, which became the most prevalent clone in 2021. Methods 73 clinical isolates were collected through sentinel hospitals' surveillance in 2021. Serum agglutination testing and antimicrobial susceptibility testing were conducted. Whole genome sequencing was applied to characterize 73 V. parahaemolyticus strains and complete phylogenetic analysis. Results Seven serotypes were identified among 73 strains. O10:K4 was the most common serotype (83.6%), followed by O2:KUT, O4:KUT, and O1:KUT. Multilocus sequence typing divided the 73 isolates into 10 sequence types (STs) with ST3 as the most prevalent, which covered all O10:K4 strains. Most isolates were sensitive to common antimicrobial agents apart from colistin. All the O10:K4 isolates were positive for the thermostable direct hemolysin gene, toxRS/new, andorf8, and negative for the TDH-related hemolysin gene. The whole genome sequencing-single nucleotide polymorphism phylogenetic analysis revealed O10:K4 strains formed a main genetic lineage, which was genetically distinct from other serotypes. We also demonstrated the presence of two type III secretion system genes (T3SS1 and T3SS2) and β lactamase resistance gene blaCARB-22 in all O10:K4 strains. Conclusions The study confirmed the emergence of V. parahaemolyticus O10:K4 possessing virulence factors similar to the O3:K6 pandemic clone, which may have enabled them to become prevalent in Beijing, China.
Collapse
Affiliation(s)
- Ying Huang
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Bing Lyu
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Xin Zhang
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Yi Tian
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Changying Lin
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Lingyu Shen
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Hanqiu Yan
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Daitao Zhang
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Lei Jia
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Mei Qu
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China,Mei Qu,
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China,Quanyi Wang,
| |
Collapse
|
3
|
Goyal A, Bittleston LS, Leventhal GE, Lu L, Cordero O. Interactions between strains govern the eco-evolutionary dynamics of microbial communities. eLife 2022; 11:74987. [PMID: 35119363 PMCID: PMC8884728 DOI: 10.7554/elife.74987] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic data has revealed that genotypic variants of the same species, that is, strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically equivalent, and at what characteristic genetic distance they might exhibit distinct interactions and dynamics. Here, we address this problem by tracking 10 taxonomically diverse microbial communities from the pitcher plant Sarracenia purpurea in the laboratory for more than 300 generations. Using metagenomic sequencing, we reconstruct their dynamics over time and across scales, from distant phyla to closely related genotypes. We find that most strains are not ecologically equivalent and exhibit distinct dynamical patterns, often being significantly more correlated with strains from another species than their own. Although even a single mutation can affect laboratory strains, on average, natural strains typically decouple in their dynamics beyond a genetic distance of 100 base pairs. Using mathematical consumer-resource models, we show that these taxonomic patterns emerge naturally from ecological interactions between community members, but only if the interactions are coarse-grained at the level of strains, not species. Finally, by analyzing genomic differences between strains, we identify major functional hubs such as transporters, regulators, and carbohydrate-catabolizing enzymes, which might be the basis for strain-specific interactions. Our work suggests that fine-scale genetic differences in natural communities could be created and stabilized via the rapid diversification of ecological interactions between strains.
Collapse
Affiliation(s)
- Akshit Goyal
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Leonora S Bittleston
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Gabriel E Leventhal
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Lu Lu
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Otto Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| |
Collapse
|
4
|
He M, Lei T, Jiang F, Zhang J, Zeng H, Wang J, Chen M, Xue L, Wu S, Ye Q, Pang R, Ding Y, Wu Q. Genetic Diversity and Population Structure of Vibrio parahaemolyticus Isolated From Clinical and Food Sources. Front Microbiol 2021; 12:708795. [PMID: 34385993 PMCID: PMC8353399 DOI: 10.3389/fmicb.2021.708795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/02/2021] [Indexed: 01/22/2023] Open
Abstract
Vibrio parahaemolyticus is a common foodborne pathogen that causes gastroenteritis worldwide. Determining its prevalence and genetic diversity will minimize the risk of infection and the associated economic burden. Multilocus sequence typing (MLST) is an important tool for molecular epidemiology and population genetic studies of bacteria. Here, we analyzed the genetic and evolutionary relationships of 162 V. parahaemolyticus strains isolated in the Guangdong Province, China, using MLST. In the study, 120 strains were isolated from food samples, and 42 strains were isolated from clinical samples. All strains were categorized into 100 sequence types (STs), of which 58 were novel (48 from the food isolates and 10 from the clinical isolates). ST415 was the most prevalent ST among the food isolates, while ST3 was the most prevalent ST among the clinical isolates. Further, 12 clonal complexes, 14 doublets, and 73 singletons were identified in all ST clusters, indicating high genetic diversity of the analyzed strains. At the concatenated sequence level, non-synonymous sites in both, food and clinical isolates, were associated with purifying selection. Of note, the dN/dS ration was greater than 1 for some housekeeping genes in all isolates. This is the first time that some loci under positive selection were identified. These observations confirm frequent recombination events in V. parahaemolyticus. Recombination was much more important than mutation for genetic heterogeneity of the food isolates, but the probabilities of recombination and mutations were almost equal for the clinical isolates. Based on the phylogenetic analysis, the clinical isolates were concentrated in the maximum-likelihood tree, while the food isolates were heterogeneously distributed. In conclusion, the food and clinical isolates of V. parahaemolyticus from the Guangdong Province are similar, but show different evolutionary trends. This may help prevent large-scale spread of highly virulent strains and provides a genetic basis for the discovery of microevolutionary relationships in V. parahaemolyticus populations.
Collapse
Affiliation(s)
- Min He
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Fufeng Jiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haiyan Zeng
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| |
Collapse
|
5
|
Chen H, Dong S, Yan Y, Zhan L, Zhang J, Chen J, Zhang Z, Zhang Y, Mei L. Prevalence and Population Analysis of Vibrio parahaemolyticus Isolated from Freshwater Fish in Zhejiang Province, China. Foodborne Pathog Dis 2021; 18:139-146. [PMID: 33493422 DOI: 10.1089/fpd.2020.2798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Objectives: The previous researches revealed that Vibrio parahaemolyticus has been detected in freshwater fish samples. However, the molecular characteristics of V. parahaemolyticus isolated from freshwater fish, including pathogenic and pandemic strains, are still unknown. This study aims to characterize and identify molecular properties of the bacterium. In addition, it identifies the source of V. parahaemolyticus from freshwater fish samples in Zhejiang Province, China. Methods: Four hundred and twenty-one freshwater fish samples (from fishing farms, retail markets, and restaurants) and 212 seafood samples (from retail markets) were collected in 10 cities of Zhejiang Province. V. parahaemolyticus strains were isolated from these samples and comparatively analyzed by multilocus sequence typing, serotyping, antimicrobial susceptibility test, and polymerase chain reaction, targeting common toxin genes (tdh, trh) and markers for pandemic strains (orf8, toxRS/new). Results: Sixty-eight V. parahaemolyticus strains were isolated from the 421 freshwater fish samples, and 89 V. parahaemolyticus isolates were identified out of 212 seafood samples. The detection rate of V. parahaemolyticus was significantly different (p < 0.05) between the fishing farms, the retail markets, and the restaurants. The isolates from freshwater fish samples were divided into eight O serotypes with three O3:K6 isolates, which contain three pandemic complexes (tdh+, orf8+, toxRS/new+). A total of 53 different sequence types (STs) were identified among the 68 isolates, including 28 novel STs. Antimicrobial susceptibility results indicated that 76.5% of the strains were resistant to ampicillin. A third (3/9) of the isolates from fishing farm sources shared the same STs with their counterparts from retail markets. Compared with the isolates from the seafood samples collected in the same sampling sites, 13.2% (9/68) freshwater fish isolates overlapped with seafood isolates. Conclusions: Our study showed that V. parahaemolyticus population in freshwater fish is genetically diverse. The V. parahaemolyticus contaminates might have come from both fishing farm sources and cross-contamination from seafood in the closed area at the markets. Freshwater fish may work as a reservoir of pathogenic and pandemic V. parahaemolyticus isolates, indicating potential public health and food safety risks associated with the consumption of freshwater fish.
Collapse
Affiliation(s)
- Honghu Chen
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Yu Yan
- Health Science Department, Sargent College, Boston University, Boston, Massachusetts, USA
| | - Li Zhan
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Junyan Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Jiancai Chen
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Zheng Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Yunyi Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Lingling Mei
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, P.R. China
| |
Collapse
|
6
|
Abstract
Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. Vibrio parahaemolyticus is becoming the leading cause of acute bacterial gastroenteritis, but its population dynamics in aquafarms have received limited attention. To address this research gap, we selected three shellfish farms to examine the impacts of ocean currents and the transport of live aquatic animals on the transmission and microevolution of V. parahaemolyticus by using multilocus sequence typing (MLST) and whole-genome sequencing. MLST and genomic analysis revealed that the community structure of V. parahaemolyticus in Dalian and Donggang was relatively stable in the presence of ocean currents; however, horizontal gene transfer of mobile genetic elements (MGEs) between Dalian and Donggang was very common. Further analysis indicated that the transport of live aquatic animals from Dalian to Xiamen not only introduced new V. parahaemolyticus populations but also allowed the exchange of genetic material between the two sites. More interestingly, Dalian-originated strain ST722 was introduced to Xiamen farms, resulting in one MLST allele change and the acquisition of two genomic islands from indigenous isolates in Xiamen within 8 months; such alterations are thought to promote the adaptation of V. parahaemolyticus. These results provide direct observations of how ocean currents and the transport of live aquatic animals contribute to the dissemination and genetic mixture of V. parahaemolyticus, which provides insights into the dynamics and microevolution of V. parahaemolyticus in aquacultural environments. IMPORTANCE Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. This study revealed that the transregional transport of aquatic animals and the movement of ocean currents both contributed to the mixing of V. parahaemolyticus populations. More importantly, this study demonstrated how genetic mixture occurred between introduced and endemic V. parahaemolyticus populations via the transport of aquatic animals, which accelerated bacterial adaptation by transferring ecologically important functions. These results suggest that human activities entail a risk of the emergence of new virulent populations for both aquatic animals and humans by horizontal gene transfer and provide important insights into the microevolution and population mixing of V. parahaemolyticus.
Collapse
|
7
|
Jesser KJ, Valdivia-Granda W, Jones JL, Noble RT. Clustering of Vibrio parahaemolyticus Isolates Using MLST and Whole-Genome Phylogenetics and Protein Motif Fingerprinting. Front Public Health 2019; 7:66. [PMID: 31139608 PMCID: PMC6519141 DOI: 10.3389/fpubh.2019.00066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/06/2019] [Indexed: 01/22/2023] Open
Abstract
Vibrio parahaemolyticus is a ubiquitous and abundant member of native microbial assemblages in coastal waters and shellfish. Though V. parahaemolyticus is predominantly environmental, some strains have infected human hosts and caused outbreaks of seafood-related gastroenteritis. In order to understand differences among clinical and environmental V. parahaemolyticus strains, we used high quality DNA sequencing data to compare the genomes of V. parahaemolyticus isolates (n = 43) from a variety of geographic locations and clinical and environmental sample matrices. We used phylogenetic trees inferred from multilocus sequence typing (MLST) and whole-genome (WG) alignments, as well as a novel classification and genome clustering approach that relies on protein motif fingerprints (MFs), to assess relationships between V. parahaemolyticus strains and identify novel molecular targets associated with virulence. Differences in strain clustering at more than one position were observed between the MLST and WG phylogenetic trees. The WG phylogeny had higher support values and strain resolution since isolates of the same sequence type could be differentiated. The MF analysis revealed groups of protein motifs that were associated with the pathogenic MLST type ST36 and a large group of clinical strains isolated from human stool. A subset of the stool and ST36-associated protein motifs were selected for further analysis and the motif sequences were found in genes with a variety of functions, including transposases, secretion system components and effectors, and hypothetical proteins. DNA sequences associated with these protein motifs are candidate targets for future molecular assays in order to improve surveys of pathogenic V. parahaemolyticus in the environment and seafood.
Collapse
Affiliation(s)
- Kelsey J Jesser
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, United States
| | | | - Jessica L Jones
- Gulf Coast Seafood Laboratory, Division of Seafood Science and Technology, U.S. Food and Drug Administration, Dauphin Island, AL, United States
| | - Rachel T Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, United States
| |
Collapse
|
8
|
Li Y, Yin HQ, Xia J, Luo H, Wang MY. Population structure and genetic diversity of Vibrio parahaemolyticus from a coastal area of China based on a multi-locus sequence typing (MLST) scheme. Antonie van Leeuwenhoek 2019; 112:1199-1211. [DOI: 10.1007/s10482-019-01252-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 02/26/2019] [Indexed: 01/22/2023]
|
9
|
Jiang Y, Chu Y, Xie G, Li F, Wang L, Huang J, Zhai Y, Yao L. Antimicrobial resistance, virulence and genetic relationship of Vibrio parahaemolyticus in seafood from coasts of Bohai Sea and Yellow Sea, China. Int J Food Microbiol 2019; 290:116-124. [DOI: 10.1016/j.ijfoodmicro.2018.10.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/11/2018] [Accepted: 10/05/2018] [Indexed: 12/21/2022]
|
10
|
Zhou M, Chen W, Shi C, Wang H, Shi X. Combination of Multilocus Sequence Typing and GS-PCR Reveals an Association of Pandemic Vibrio parahaemolyticus Clone with Clinical and Seafood Isolates. J Food Sci 2018; 83:2536-2543. [PMID: 30256419 DOI: 10.1111/1750-3841.14335] [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: 01/18/2018] [Revised: 06/15/2018] [Accepted: 08/05/2018] [Indexed: 11/27/2022]
Abstract
Vibrio parahaemolyticus is a global leading cause of seafood-borne bacterial gastroenteritis. Clinical, seafood, and environmental V. parahaemolyticus isolates from the eastern coast of China were analyzed for their virulence, and for phenotypic and molecular traits. The frequency of pandemic isolates was 50.9% among clinical isolates and 42.8% among seafood isolates as confirmed by group-specific polymerase chain reaction (GS-PCR). Serological analysis indicated that O3:K6, O1:K25, O1:KUT, O3:K68, and O4:K68 were the predominant serotypes among these pandemic isolates. It is worth noting that the pandemic serotypes were not exclusively identified from clinical samples. Rather, they were also isolated from seafood samples. It was also shown by multilocus sequence typing (MLST) typing that isolates from clinical (59), seafood (28), and environmental samples (18) were grouped into 17, 23, and 17 sequence types (STs), respectively. We updated 17 STs in the MLST database. ST-3 and ST-189 were the dominant ones among clinical isolates. Interestingly, ST-3 was also the most abundant among seafood isolates, and represented a significant risk to food safety due to the clear association with tdh and the GS-PCR marker. A minimum-evolution (ME) tree generated from the concatenated sequences of the 7 loci of the 54 STs uncovered phylogenetic relationships between seafood and clinical isolates. The MLST results also indicated a high degree of nucleotide diversity in recA that had the greatest influence on the phylogenetic relationships. Our findings provided new insight into the phylogenic relationship among pandemic V. parahaemolyticus isolates from various samples and enhanced the MLST database as well as microbiological risk assessment. PRACTICAL APPLICATION Pandemic V. parahaemolyticus isolates have become a serious public health concern. This study demonstrated the characteristics of clinical and seafood V. parahaemolyticus isolates, and determined the phylogenetic relatedness among them. These results can be used for microbiological risk assessment in China.
Collapse
Affiliation(s)
- Min Zhou
- School of Food Science and Engineering, Wuhan Polytechnic Univ., Wuhan, 430023, China
| | - Wanyi Chen
- Mérieux NutriSciences China, Sino Silliker Testing Services (Shanghai) Co., Ltd., Shanghai, 200231, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| | - Hongxun Wang
- School of Food Science and Engineering, Wuhan Polytechnic Univ., Wuhan, 430023, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong Univ., Shanghai, 200240, China
| |
Collapse
|
11
|
Li P, Xin W, Kang L, Chen Z, Guo C, Gao S, Yang H, Ji B, Yan Y, Wang H, Zhou D, Yang W, Wang J. Genetic and population analyses of Vibrio parahaemolyticus isolates from three major coastal regions in China. Future Microbiol 2018; 13:1261-1269. [PMID: 30238770 PMCID: PMC6190215 DOI: 10.2217/fmb-2018-0060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/21/2018] [Indexed: 11/21/2022] Open
Abstract
AIM This study aims to evaluate the genetic and population structure of Vibrio parahaemolyticus in the major coastal regions of China. MATERIALS & METHODS Multilocus sequence typing was performed. RESULTS Insertion of large sequence into recA happened in nearly 30 strains, which were untypeable by multilocus sequence typing. A collection of 307 V. parahaemolyticus isolates were typed into 160 sequence types, including 117 novel ones. eBURST analysis revealed five clonal complexes, 11 doublets, and 108 singletons. The 160 sequence types formed two main lineages in the phylogenetic analysis. CONCLUSION V. parahaemolyticus along the Chinese coastal regions exhibits high levels of genetic diversity and has undergone significant purifying selection and frequent recombination. A deeper understanding of V. parahaemolyticus genetic diversity could be obtained at the level of genome sequences.
Collapse
Affiliation(s)
- Ping Li
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control & Prevention, Jiaxing 314050, PR China
- Graduate College, Anhui Medical University, Hefei 230032, PR China
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Wenwen Xin
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Lin Kang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control & Prevention, Jiaxing 314050, PR China
| | - Chenyi Guo
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Shan Gao
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Hao Yang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Bin Ji
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control & Prevention, Jiaxing 314050, PR China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control & Prevention, Jiaxing 314050, PR China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Wenhui Yang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Jinglin Wang
- Graduate College, Anhui Medical University, Hefei 230032, PR China
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| |
Collapse
|
12
|
Molecular Typing ofVibrio parahaemolyticusStrains Isolated from Mollusks in the North Adriatic Sea. Foodborne Pathog Dis 2017; 14:454-464. [DOI: 10.1089/fpd.2016.2263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
13
|
Han C, Tang H, Ren C, Zhu X, Han D. Sero-Prevalence and Genetic Diversity of Pandemic V. parahaemolyticus Strains Occurring at a Global Scale. Front Microbiol 2016; 7:567. [PMID: 27148244 PMCID: PMC4840284 DOI: 10.3389/fmicb.2016.00567] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 04/05/2016] [Indexed: 01/22/2023] Open
Abstract
Pandemic Vibrio parahaemolyticus is an emerging public health concern as it has caused numerous gastroenteritis outbreaks worldwide. Currently, the absence of a global overview of the phenotypic and molecular characteristics of pandemic strains restricts our overall understanding of these strains, especially for environmental strains. To generate a global picture of the sero-prevalence and genetic diversity of pandemic V. parahaemolyticus, pandemic isolates from worldwide collections were selected and analyzed in this study. After a thorough analysis, we found that the pandemic isolates represented 49 serotypes, which are widely distributed in 22 countries across four continents (Asia, Europe, America and Africa). All of these serotypes were detected in clinical isolates but only nine in environmental isolates. O3:K6 was the most widely disseminated serotype, followed by O3:KUT, while the others were largely restricted to certain countries. The countries with the most abundant pandemic serotypes were China (26 serotypes), India (24 serotypes), Thailand (15 serotypes) and Vietnam (10 serotypes). Based on MLST analysis, 14 sequence types (STs) were identified among the pandemic strains, nine of which fell within clonal complex (CC) 3. ST3 and ST305 were the only two STs that have been reported in environmental pandemic strains. Pandemic ST3 has caused a wide range of infections in as many as 16 countries. Substantial serotypic diversity was mainly observed among isolates within pandemic ST3, including as many as 12 combinations of O/K serotypes. At the allele level, the dtdS and pntA, two loci that perfectly conserved in CC3, displayed a degree of polymorphism in some pandemic strains. In conclusion, we provide a comprehensive understanding of sero-prevalence and genetic differentiation of clinical and environmental pandemic isolates collected from around the world. Although, further studies are needed to delineate the specific mechanisms by which the pandemic strains evolve and spread, the findings in this study are helpful when seeking countermeasures to reduce the spread of V. parahaemolyticus in endemic areas.
Collapse
Affiliation(s)
- Chongxu Han
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Hui Tang
- Experimental Research Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Chuanli Ren
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Xiaoping Zhu
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Dongsheng Han
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| |
Collapse
|
14
|
ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol 2015; 33:1045-52. [PMID: 26344404 PMCID: PMC4676274 DOI: 10.1038/nbt.3319] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 07/16/2015] [Indexed: 01/21/2023]
Abstract
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.
Collapse
|
15
|
Chen X, Song Y, Xu H, Menghe B, Zhang H, Sun Z. Genetic relationships among Enterococcus faecalis isolates from different sources as revealed by multilocus sequence typing. J Dairy Sci 2015; 98:5183-93. [DOI: 10.3168/jds.2015-9571] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/27/2015] [Indexed: 11/19/2022]
|
16
|
Han D, Tang H, Ren C, Wang G, Zhou L, Han C. Prevalence and genetic diversity of clinical Vibrio parahaemolyticus isolates from China, revealed by multilocus sequence typing scheme. Front Microbiol 2015; 6:291. [PMID: 25914691 PMCID: PMC4391058 DOI: 10.3389/fmicb.2015.00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/24/2015] [Indexed: 01/22/2023] Open
Abstract
The population structure of clinical Vibrio parahaemolyticus isolates spreading in China remains undefined. We brought 218 clinical isolates from the pubMLST database originating from different regions of China collected since the year of 1990, analyzed by multilocus sequence typing (MLST), to elucidate the prevalence and genetic diversity of V. parahaemolyticus circulating in Chinese population. The MLST scheme produced 137 sequence types (STs). These STs were clustered into six clonal complexes (CCs), six doublets, and 91 singletons, exhibiting a high level of genetic diversity. However, less diversity was displayed on the peptide level: only 46 different peptide sequence type (pST) were generated, with pST2 (44.0%, 96/218) and pST1 (15.1%, 33/218) the predominant. Further analysis confirmed all the pSTs belong to a single complex founded by pST1, pST2, pST3, and pST4. recA presented the highest degree of nucleotide diversity (0.026) and the largest number of variable sites (176) on the nucleotide level. pyrC was the most diverse locus on the peptide level, possessing the highest percentage of variable sites (9.2%, 15/163). Significant linkage disequilibrium with the alleles was detected when the Standardized Index of Association (ISA) was calculated both for the entire isolates collection (0.7169, P < 0.01) and for the 137 STs (ISA = 0.2648, P < 0.01). In conclusion, we provide an overview of prevalence and genetic diversity of clinical V. parahaemolyticus spreading in Chinese population using MLST analysis. The results would offer genetic evidences for uncovering the microevolution relationship of V. parahaemolyticus populations.
Collapse
Affiliation(s)
- Dongsheng Han
- Department of Clinical Microbiology, Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Hui Tang
- Department of Biobank, Northern Jiangsu People's Hospital Yangzhou, China
| | - Chuanli Ren
- Department of Clinical Microbiology, Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Guangzhou Wang
- Department of Clinical Microbiology, Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Lin Zhou
- Department of Clinical Microbiology, Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| | - Chongxu Han
- Department of Clinical Microbiology, Clinical Medical Examination Center, Northern Jiangsu People's Hospital Yangzhou, China
| |
Collapse
|