Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms

Eco-Evolutionary Drivers of Vibrio parahaemolyticus Sequence Type 3 Expansion: Retrospective Machine Learning Approach

BACKGROUND

Environmentally sensitive pathogens exhibit ecological and evolutionary responses to climate change that result in the emergence and global expansion of well-adapted variants. It is imperative to understand the mechanisms that facilitate pathogen emergence and expansion, as well as the drivers behind the mechanisms, to understand and prepare for future pandemic expansions.

OBJECTIVE

The unique, rapid, global expansion of a clonal complex of Vibrio parahaemolyticus (a marine bacterium causing gastroenteritis infections) named Vibrio parahaemolyticus sequence type 3 (VpST3) provides an opportunity to explore the eco-evolutionary drivers of pathogen expansion.

METHODS

The global expansion of VpST3 was reconstructed using VpST3 genomes, which were then classified into metrics characterizing the stages of this expansion process, indicative of the stages of emergence and establishment. We used machine learning, specifically a random forest classifier, to test a range of ecological and evolutionary drivers for their potential in predicting VpST3 expansion dynamics.

RESULTS

We identified a range of evolutionary features, including mutations in the core genome and accessory gene presence, associated with expansion dynamics. A range of random forest classifier approaches were tested to predict expansion classification metrics for each genome. The highest predictive accuracies (ranging from 0.722 to 0.967) were achieved for models using a combined eco-evolutionary approach. While population structure and the difference between introduced and established isolates could be predicted to a high accuracy, our model reported multiple false positives when predicting the success of an introduced isolate, suggesting potential limiting factors not represented in our eco-evolutionary features. Regional models produced for 2 countries reporting the most VpST3 genomes had varying success, reflecting the impacts of class imbalance.

CONCLUSIONS

These novel insights into evolutionary features and ecological conditions related to the stages of VpST3 expansion showcase the potential of machine learning models using genomic data and will contribute to the future understanding of the eco-evolutionary pathways of climate-sensitive pathogens.

Antimicrobial resistance, virulence factors and phylogenetic profiles of Vibrio parahaemolyticus in the eastern coast of Shenzhen

Vibrio parahaemolyticus (V. parahaemolyticus) is a major food-borne pathogen which causes human gastroenteritis. Since the characteristics of V. parahaemolyticus remain unknown, 220 isolates selected from clinical and environmental samples in Dapeng of Shenzhen were tested for the presence of two hemolysin-expressing genes tdh and trh. Among 27 clinical isolates, 26 carrired the tdh gene, and the other one carried both tdh and trh genes, however neither genes were detected in environmental isolates. Meanwhile, antimicrobial susceptibility profiles revealed the isolates with high frequency of resistance to ampicillin (77.73%) and colistin (71.82%) and medium to streptomycin (57.27%). Genetically, by whole genome sequencing (WGS), comparative genomics studies was performed on isolates from various districts and GenBank. Data analysis showed that antimicrobial resistance genes (ARGs) blaCARB, tet(34) and tet(35) were harbored in all genomes and other ARGs was absent in the genomes of 27 clinical isolates. Besides, little regional difference was observed. As for virulence factors, MAM7, T3SS1, T3SS1 secret effector, T3SS2, T3SS2 secret effector, and VpadF were carried by most isolates. Two isolates from other districts were tdh gene positive which clustered with clinical isolates from Dapeng in the same clade, indicating close genetic distance. This study revealed the widely distribution of V. parahaemolyticus in Shenzhen and the diverse ARGs and virulence genes it carried. Furthermore, pathways that pathogen disseminated through were discussed.

Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture

Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 106 CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.

Polyamide microplastics can mitigate the effects of pathogenic bacterium on the health of marine mussels

Vibrio parahaemolyticus and microplastics are prevalent in the ocean. Bacteria attach onto plastic particles, forming harmful biofilms that collectively threaten bivalve health. This study investigates the interaction between polyamide microplastics (PA: particle size 38 ± 12 µm) and V. parahaemolyticus, as well as their combined impact on thick-shelled mussels (Mytilus coruscus). We introduced 1011 CFU/L of V. parahaemolyticus into varying PA concentrations (0, 5, 50, and 500 particles/L) to observe growth over 14 h and biofilm formation after 48 h. Our findings indicate that microplastics suppress biofilm formation and virulence gene expression. Four treatments were established to monitor mussel responses: a control group without PA or V. parahaemolyticus; a group with 50 particles/L PA; a group with 1011 CFU/L V. parahaemolyticus; and a co-exposure group with both 50 particles/L PA and 1011 CFU/L V. parahaemolyticus, over a 14-day experiment. However, combined stress from microplastics and Vibrio led to immune dysregulation in mussels, resulting in intestinal damage and microbiome disruption. Notably, V. parahaemolyticus had a more severe impact on mussels than microplastics alone, yet their coexistence reduced some harmful effects. This study is the first to explore the interaction between microplastics and V. parahaemolyticus, providing important insights for ecological risk assessments.

Characterization of a secondary palmitoleoyltransferase of lipid A in Vibrio parahaemolyticus

The detection of pathogenicity and immunogenicity in Vibrio parahaemolyticus poses a significant challenge due to its threat to human health and food safety, which is strongly correlated with lipid A. Lipid A, a critical component found in most Gram-negative bacteria, functions as a hydrophobic anchor for lipopolysaccharide. V. parahaemolyticus synthesizes multiple lipid A species with various secondary acyl chains. In this study, a secondary acyltransferase of lipid A encoded by VP_RS08405 in V. parahaemolyticus was identified. Based on sequence alignment analysis, V. parahaemolyticus VP_RS08405 has high homology to E. coli lpxL, lpxM and lpxP which encode the three secondary acyltransferases of lipid A. Therefore, V. parahaemolyticus VP_RS08405 was cloned into pBAD33, and the resulting pB08405 was introduced in E. coli mutants WHL00 in which lpxL was deleted, WHM00 in which lpxM was deleted, WHP00 in which lpxP was deleted, and WH300 in which lpxL, lpxM and lpxP were deleted. The recombinant strains WHL00/pB08405, WHM00/pB08405, WHP00/pB08405, WH300/pB08405, as well as their vector controls, were grown at normal and low temperatures. Lipid A species were isolated from the above strains and analyzed by using high-performance liquid chromatography-tandem mass spectrometry and thin-layer chromatography. After comparing the secondary acyl alterations of lipid A from different recombinant strains, it is concluded that VP_RS08405 specifically catalyzed the addition of a palmitoleate to the 2'-position of lipid A and its activity is not temperature-sensitive. In addition, to determine the dependence of VP_RS08405 on Kdo, VP_RS08405 was overexpressed in E. coli mutants WH001 in which waaA was deleted, and WH400 in which waaA, lpxL, lpxM and lpxP were deleted. Lipid A species were isolated from WH001/pB08405 and WH400/pB08405, and analyzed. The results show that the function of VP_RS08405 is Kdo-dependent. These findings provide a better understanding of the structural diversity of lipid A in V. parahaemolyticus.

Characterization of a secondary hydroxy-acyltransferase for lipid A in Vibrio parahaemolyticus

Lipid A plays a crucial role in Vibrio parahaemolyticus. Previously we have reported the diversity of secondary acylation of lipid A in V. parahaemolyticus and four V. parahaemolyticus genes VP_RS08405, VP_RS01045, VP_RS12170, and VP_RS00880 exhibiting homology to the secondary acyltransferases in Escherichia coli. In this study, the gene VP_RS12170 was identified as a specific lipid A secondary hydroxy-acyltransferase responsible for transferring a 3-hydroxymyristate to the 2'-position of lipid A. Four E. coli mutant strains WHL00, WHM00, WH300, and WH001 were constructed, and they would synthesize lipid A with different structures due to the absence of genes encoding lipid A secondary acyltransferases or Kdo transferase. Then V. parahaemolyticus VP_RS12170 was overexpressed in W3110, WHL00, WHM00, WH300, and WH001, and lipid A was isolated from these strains and analyzed by using thin-layer chromatography and high-performance liquid chromatography-tandem mass spectrometry. The detailed structural changes of lipid A in these mutant strains with and without VP_RS12170 overexpression were compared and conclude that VP_RS12170 can specifically transfer a 3-hydroxymyristate to the 2'-position of lipid A. This study also demonstrated that the function of VP_RS12170 is Kdo-dependent and its favorite substrate is Kdo-lipid IVA. These findings give us better understanding the biosynthetic pathway and the structural diversity of V. parahaemolyticus lipid A.

Comparative genomic analysis reveals the potential transmission of Vibrio parahaemolyticus from freshwater food to humans

Vibrio parahaemolyticus is an increasingly important foodborne pathogen that cause acute gastroenteritis in humans. However, the prevalence and transmission of this pathogen in freshwater food remains unclear. This study aimed to determine the molecular characteristics and genetic relatedness of V. parahaemolyticus isolates obtained from freshwater food, seafood, environmental, and clinical samples. A total of 138 (46.6%) isolates were detected from 296 food and environmental samples, and 68 clinical isolates from patients. Notably, V. parahaemolyticus was more prevalent in freshwater food (56.7%, 85/150) than in seafood (38.8%, 49/137). Virulence phenotype analyses revealed that the high motility of isolates from freshwater food (40.0%) and clinical isolates (42.0%) was higher than that of isolates from seafood (12.2%), whereas the biofilm-forming capacity of freshwater food isolates (9.4%) was lower than that of seafood (22.4%) and clinical isolates (15.9%). Virulence genes analysis showed that 46.4% of the clinical isolates contained the tdh gene encoding thermostable direct hemolysin (TDH) and only two freshwater food isolates contained the trh gene encoding TDH-related hemolysin (TRH). Multilocus sequence typing (MLST) analysis divided the 206 isolates into 105 sequence types (STs), including 56 (53.3%) novel STs. ST2583, ST469, and ST453 have been isolated from freshwater food and clinical samples. Whole-genome sequence (WGS) analyses revealed that the 206 isolates were divided into five clusters. Cluster II contained isolates from freshwater food and clinical samples, whereas the other clusters contained isolates from seafood, freshwater food, and clinical samples. In addition, we observed that ST2516 had the same virulence pattern, with a close phylogenetic relationship to ST3. The increased prevalence and adaption of V. parahaemolyticus in freshwater food is a potential cause of clinical cases closely related to the consumption of V. parahaemolyticus contaminated freshwater food.

Genome-wide identification and characterization of Toll-like receptors (TLR) genes in Haliotis discus hannai, H. rufescens, and H. laevigata

Toll-like receptors (TLRs) play essential roles in the innate immune system and have been extensively studied in mollusks. In this study, through a genome-wide search, TLR genes were identified as 29 in Haliotis discus hannai, 33 in H. rufescens, and 16 in H. laevigata. Domain analysis indicated that these TLR genes contain leucine-rich repeat (LRR) and Toll/IL-1 receptor (TIR) domains and exons ranging from 1 to 5. Polymorphism analysis showed that the TLRs in abalones did not have high diversities with 143 SNPs and no Indel in H. discus hannai, 92 SNPs and 3 Indels together with 6 missense mutations in H. rufescens, and no SNP or Indel in H. laevigata. The expression of 8 TLR genes in H. discus hannai was confirmed in the hepatopancreas, gill, hemolymph, gonads, intestine, muscle, and mantle. The expression of five TLR genes (out of 8) in gills (p < 0.05), three in hepatopancreas (p < 0.05), and three in hemolymph (p < 0.05) was upregulated separately in response to the infection caused by Vibrio parahaemolyticus. The findings in this study would contribute to a better understanding of the molecular immune mechanism of H. discus hannai against stimulation by V. parahaemolyticus and provide a basis for the study of TLRs in abalones.

Distinct respiratory microbiota associates with lung cancer clinicopathological characteristics

Introduction

Commensal microbiota dysbiosis is associated with the development of lung cancer. The current studies about composition of respiratory microbiota in lung cancer patients yielded inconsistent results. This study aimed to examine the association between airway microbiota and lung cancer clinicopathological characteristics.

Methods

Surgically removed lesion tissues from 75 non-small cell lung cancer patients and 7 patients with benign pulmonary diseases were analyzed by 16S rRNA sequencing. Taxonomy, relative abundance, and diversity of respiratory microbiota were compared among lung cancer of different pathology and TNM stages. The effects of antibiotic and cigarette exposure on respiratory microbiota in lung cancer patients were also evaluated.

Results

Bacterial relative abundance and alpha- and beta-diversity analysis of lung microbiota showed significant differences among lung cancer of different pathology and benign pulmonary diseases. At the genus level, the abundance differences of 13 taxa between lung squamous cell carcinoma and lung adenocarcinoma, 63 taxa between lung squamous cell carcinoma and benign pulmonary diseases, and 4 taxa between lung adenocarcinoma and benign pulmonary diseases reached statistical significance. In contrast, diversity differences were not as significant across lung cancer of different stages. No significant differences were observed in tissue taxonomic abundances and diversity at all taxonomic levels between lung cancer patients with and without antibiotic exposure 3 months prior to surgery. For lung adenocarcinoma, respiratory bacterial abundance and diversity at all taxonomic levels did not show significant differences between smokers and non-smokers.

Conclusions

Our results confirm significantly differential respiratory microbiome taxa, abundance, and diversity in lung cancer of different pathology and some stages. Short-term antibiotic application might play a minor role in molding airway microbiota in lung cancer patients. Composition and diversity of respiratory microbiota in lung adenocarcinoma are not affected by cigarette exposure.

Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment

Very little is known about how microbiome interactions shape the horizontal transfer of antibiotic resistance genes in aquacultural environment. To this end, we first conducted 16S rRNA gene amplicon sequencing to monitor the dynamics of bacterial community compositions in one shrimp farm from 2019 to 2020. Next, co-occurrence analysis was then conducted to reveal the interactions network between Vibrio spp. and other species. Subsequently, 21 V. parahaemolyticus isolates and 15 related bacterial species were selected for whole-genome sequencing (WGS). The 16S rDNA amplicon sequencing results identified a remarkable increase of Vibrio and Providencia in September-2019 and a significant rise of Enterobacter and Shewanella in Septtember-2020. Co-occurrence analysis revealed that Vibrio spp. positively interacted with the above species, leading to the sequencing of their isolates to further understand the sharing of the resistant genomic islands (GIs). Subsequent pan-genomic analysis of V. parahaemolyticus genomes identified 278 horizontally transferred genes in 10 GIs, most of which were associated with antibiotic resistance, virulence, and fitness of metabolism. Most of the GIs have also been identified in Providencia, and Enterobacter, suggesting that exchange of genetic traits might occur in V. parahaemolyticus and other cooperative species in a specific niche. No genetic exchange was found between the species with negative relationships. The knowledge generated from this study would greatly improve our capacity to predict and mitigate the emergence of new resistant population and provide practical guidance on the microbial management during the aquacultural activities.

Distinct dynamics of Vibrio parahaemolyticus populations in two farming models

AIMS

Despite the recent prosperity of shrimp cultivation in China, very little is known about how different shrimp farming models influence the dynamics of Vibrio parahaemolyticus populations and the antibiotic resistance of this bacterium.

METHODS AND RESULTS

To this end, we conducted continuous surveillance of V. parahaemolyticus on four farms over 3 years: two traditional shrimp farms with daily water exchange and two farms operated in the recirculating aquaculture systems (RAS). No antibiotics were used in these farms to exclude the potential impacts of antibiotics on the emergence of antibacterial resistance. Multilocus sequence typing was utilized to characterize the dynamics of V. parahaemolyticus populations. Whole-genome sequencing (WGS) was conducted to determine the representative sequence types (STs) at each farm. Results revealed that the population structure of V. parahaemolyticus remained stable over time in both RAS farms, with only nine and four STs observed at each. In contrast, annual replacement of V. parahaemolyticus populations was observed in traditional farms with 26 and 28 STs identified in rearing water. WGS of 50 isolates divided them into five clusters, of which ST917a isolates harboured a genomic island that disrupted the gene recA. Pair-wised genomic comparison of isolates from the same STs showed that they were genetically related but belonged to different clones associated with geographical distribution.

CONCLUSIONS

These results suggested that RAS presented a specific ecological niche by minimizing the water exchanges with the external environment. In contrast, traditional farming might pose a food safety issue by introducing new V. parahaemolyticus populations with antibiotic resistance genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results expose the potential food safety issue associated with conventional agriculture and should encourage the development of preventive strategies to reduce the emergence of resistant V. parahaemolyticus populations.