A polyphasic approach for the differentiation of environmental Vibrio isolates from temperate waters

Genome-wide expanding of genetic evolution and potential pathogenicity in Vibrio alginolyticus

Vibrio alginolyticus, an emergent species of Vibrio genus, exists in aquatic and marine environments. It has undergone genetic diversification, but its detailed genomic diversity is still unclear. Here, we performed a multi-dimensional comparative genomic analysis to explore the population phylogeny, virulence-related genes and potential drug resistance genes of 184 V. alginolyticus isolates. Although genetic diversity is complex, we analysed the population structure using three sub-datasets, including the subdivision for three lineages into sublineages and the distribution of strains in the marine ecological niche. Accessory genes, most of which reclassified V. alginolyticus genomes as different but with relatively close affinities, were nonuniformly distributed among these isolates. We demonstrated that the spread of some post-evolutionary isolates (mainly L3 strains isolated from Chinese territorial seas) was likely to be closely related to human activities, whereas other more ancestral strains (strains in the L1 and L2) tended to be locally endemic and formed clonal complex groups. In terms of pathogenicity, the potential virulence factors were mainly associated with toxin, adherence, motility, chemotaxis, and the type III secretion system (T3SS). We also found five types of antibacterial drug resistance genes. The prevalence of β-lactam resistance genes was 100%, which indicated that there may be a potential risk of natural resistance to β-lactam drugs. Our study reveals insights into genomic characteristics, evolution and potential virulence-associated gene profiles of V. alginolyticus.

Distribution and antibiotic resistance of vibrio population in an urbanized tropical lake-the Vembanad-in the southwest coast of India

Among the diverse Vibrio spp. autochthonous to coastal ecosystems, V. cholerae, V. fluvialis, V. vulnificus and V. parahaemolyticus are pathogenic to humans. Increasing sea-surface temperature, sea-level rise and water-related disasters associated with climate change have been shown to influence the proliferation of these bacteria and change their geographic distribution. We investigated the spatio-temporal distribution of Vibrio spp. in a tropical lake for 1 year at a 20-day interval. The abundance of Vibrio spp. was much higher during the south-west monsoon in 2018, when the lake experienced a once-in-a-century flood. The distribution of Vibrio spp. was influenced by salinity (r = 0.3, p < 0.001), phosphate (r = 0.18, p < 0.01) and nitrite (r = 0.16, p < 0.02) in the water. We isolated 470 colonies of Vibrio-like organisms and 341 could be revived further and identified using 16S rRNA gene sequencing. Functional annotations showed that all the 16 Vibrio spp. found in the lake could grow in association with animals. More than 60% of the isolates had multiple antibiotic resistance (MAR) index greater than 0.5. All isolates were resistant to erythromycin and cefepime. The proliferation of multiple antibiotic-resistant Vibrio spp. is a threat to human health. Our observations suggest that the presence of a diverse range of Vibrio spp. is favoured by the low-saline conditions brought about by heavy precipitation. Furthermore, infections caused by contact with Vibrio-contaminated waters may be difficult to cure due to their multiple antibiotic resistances. Therefore, continuous monitoring of bacterial pollution in the lakes is essential, as is the generation of risk maps of vibrio-infested waters to avoid public contact with contaminated waters and associated disease outbreaks.

Genomic characterization of filamentous phage vB_VpaI_VP-3218, an inducible prophage of Vibrio parahaemolyticus

The seawater temperature rise can promote the growth of potentially pathogenic Vibrio species. In the North Sea, V. parahaemolyticus strains have been isolated and characterized. These strains contain prophages that may contribute to the emergence of pathogenic strains in the marine environment. Here, we present the genome structure and possible biological functions of the inducible phage vB_VpaI_VP-3218, a novel filamentous phage carried by the V. parahaemolyticus strain VN-3218. Prophages of the strain VN-3218 were induced with mitomycin C and the DNA from the phage induction was sequenced. Two incomplete prophages were identified, only one complete phage genome with length of 11,082 bp was characterized. The phage vB_VpaI_VP-3218 belongs to the Inoviridae family and shows close homology to the Saetivirus genus. This phage can integrate into the chromosomal host genome and carries host-related regions absent in similar phage genomes, suggesting that this phage might integrate in other Vibrio host genomes from the environment. Furthermore, this phage might have a role in pathogenicity due to potential zonula occludens toxin genes. Based on its genomic similarity, the genome of vB_VpaI_VP-3218 phage probably integrates into the lysogen's chromosome and replicates as episome. This study complements prophage induction and bioinformatic studies applied to non-model species of potentially pathogenic Vibrio species. The characterization of this phage provides new insights with respect to the presence of filamentous phages in environmental V. parahaemolyticus strains, which might have a role in the emergence of new pathogenic strains in the North Sea.

Looking for the hidden: Characterization of lysogenic phages in potential pathogenic Vibrio species from the North Sea

The incidence of potentially pathogenic Vibrio species in the marine environment around Europe, is correlated with the increase of surface seawater temperature. Despite their importance, little is known about the trigger factors of potential outbreak-causing strains in this region. As prophages may compose a major reservoir of virulence traits in marine ecosystems, this study aims to identify and characterize the genomes of lysogenic Vibrio phages exemplarily from the North Sea. Therefore, 31 isolates from potentially pathogenic Vibrio species from the North Sea were screened for inducible prophages with mitomycin C. From them, one V. cholerae isolate and 40% V. parahaemolyticus isolates carried inducible prophages. Three lysogenic phages were selected for genomic characterization. The phage vB_VpaM_VP-3212 (unclassified Myoviridae) has a genome with a length of 36.81 Kbp and 55 CDS were identified. This lysogenic phage of V. parahaemolyticus contains genes related to replicative transposition mechanism, such as transposase and mobile elements similar to Mu-like viruses. The phage vB_VpaP_VP-3220 (Podoviridae, unclassified Nona33virus) has a genome length of 58,14 Kbp and contains 63 CDS. This V. parahaemolyticus phage probably uses a headful (pac) packaging replication mechanism. The phage vB_VchM_VP-3213 (unclassified Myoviridae) has a genome with a length of 41 Kbp and 63 CDS were identified, including integrase and Xer system for lysogenic recombination. This lysogenic phage of V. cholerae has similar genomic features as lambdoid phages. Although no pathogenicity genes were identified, their similarity among other phage genomes indicates that these phages can affect the development of pathogenic Vibrio strains in marine environments.

Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water

MALDI-TOF Mass Spectrometry in association with the MALDI BioTyper 3.1 software has been evaluated for the identification and classification of 45 Arctic bacteria isolated from Kandalaksha Bay (White Sea, Russia). The high reliability of this method has been already demonstrated, in clinical microbiology, by a number of studies showing high attribution concordance with other credited analyses. Recently, it has been employed also in other branches of microbiology with controversial performance. The phyloproteomic results reported in this study were validated with those obtained by the "gold standard" 16S rDNA analysis. Concordance between the two methods was 100% at the genus level, while at the species level it was 48%. These percentages appeared to be quite high compared with other studies regarding environmental bacteria. However, the performance of MALDI BioTyper changed in relation to the taxonomical group analyzed, reflecting known identification problems related to certain genera. In our case, attribution concordance for Pseudomonas species was rather low (29%), confirming the problematic taxonomy of this genus, whereas that of strains from other genera was quite high (> 60%). Among the isolates tested in this study, two strains (Exiguobacterium oxidotolerans and Pseudomonas costantinii) were misidentified by MALDI BioTyper due to absence of reference spectra in the database. Accordingly, missing spectra were acquired for the database implementation.

Complicated sea urchin-induced wound infection caused by Vibrioalginolyticus and Staphylococcus lugdunensis in a 14-year-old boy

INTRODUCTION

Wound infections with Vibrio alginolyticus, a Gram-negative bacterium found in all temperate oceans, are rarely reported. However, a rising incidence of wound infections caused by V. alginolyticus requires better knowledge about this infectious agent.

CASE PRESENTATION

We report the case of a 14-year-old boy suffering from a wound infection caused by V. alginolyticus and Staphylococcus lugdunensis after stepping on a sea urchin. Despite wound debridement and antibiotic therapy with cefaclor, the lesion did not heal over several weeks. After identification of the pathogens and antibiotic-susceptibility testing, antibiotic therapy was switched to ciprofloxacin, followed by trimethoprim/sulfamethoxazole. Two months after the accident the wound was re-epithelialized. Follow up after 6 months revealed a painful scar.

CONCLUSION

Non-cholera vibrios like V. alginolyticus should be considered as possible causative agents in seawater-contaminated wounds. S. lugdunensis is a relevant pathogen in mixed wound infections. Early microbiological diagnosis and antibiotic-susceptibility testing is crucial to prevent therapeutic failure.

Dangerous hitchhikers? Evidence for potentially pathogenic Vibrio spp. on microplastic particles

The taxonomic composition of biofilms on marine microplastics is widely unknown. Recent sequencing results indicate that potentially pathogenic Vibrio spp. might be present on floating microplastics. Hence, these particles might function as vectors for the dispersal of pathogens. Microplastics and water samples collected in the North and Baltic Sea were subjected to selective enrichment for pathogenic Vibrio species. Bacterial colonies were isolated from CHROMagar™Vibrio and assigned to Vibrio spp. on the species level by MALDI-TOF MS (Matrix Assisted Laser Desorption/Ionisation - Time of Flight Mass Spectrometry). Respective polymers were identified by ATR FT-IR (Attenuated Total Reflectance Fourier Transform - Infrared Spectroscopy). We discovered potentially pathogenic Vibrio parahaemolyticus on a number of microplastic particles, e.g. polyethylene, polypropylene and polystyrene from North/Baltic Sea. This study confirms the indicated occurrence of potentially pathogenic bacteria on marine microplastics and highlights the urgent need for detailed biogeographical analyses of marine microplastics.

MALDI-TOF Mass Spectrometry Discriminates Known Species and Marine Environmental Isolates of Pseudoalteromonas

The genus Pseudoalteromonas constitutes an ecologically significant group of marine Gammaproteobacteria with potential biotechnological value as producers of bioactive compounds and of enzymes. Understanding their roles in the environment and bioprospecting for novel products depend on efficient ways of identifying environmental isolates. Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) biotyping has promise as a rapid and reliable method of identifying and distinguishing between different types of bacteria, but has had relatively limited application to marine bacteria and has not been applied systematically to Pseudoalteromonas. Therefore, we constructed a MALDI-TOF MS database of 31 known Pseudoalteromonas species, to which new isolates can be compared by MALDI-TOF biotyping. The ability of MALDI-TOF MS to distinguish between species was scrutinized by comparison with 16S rRNA gene sequencing. The patterns of similarity given by the two approaches were broadly but not completely consistent. In general, the resolution of MALDI-TOF MS was greater than that of 16S rRNA gene sequencing. The database was tested with 13 environmental Pseudoalteromonas isolates from UK waters. All of the test strains could be identified to genus level by MALDI-TOF MS biotyping, but most could not be definitely identified to species level. We conclude that several of these isolates, and possibly most, represent new species. Thus, further taxonomic investigation of Pseudoalteromonas is needed before MALDI-TOF MS biotyping can be used reliably for species identification. It is, however, a powerful tool for characterizing and distinguishing among environmental isolates and can make an important contribution to taxonomic studies.

Environmental parameters influence on the dynamics of total and pathogenic Vibrio parahaemolyticus densities in Crassostrea virginica harvested from Mexico's Gulf coast

The influence of environmental parameters on the total and pathogenic Vibrio parahaemolyticus seasonal densities in American oysters (Crassostrea virginica) was evaluated for 1 year. Harvesting site A yielded the highest mean densities of V. parahaemolyticus tlh+, tdh+/trh-, tdh-/trh+ and tdh+/trh+ during spring season at 2.57, 1.74, 0.36, and -0.40 log10 MPN/g, respectively, and tdh+/orf8+ during winter season (0.90 log10 MPN/g). V. parahaemolyticus tlh+ densities were associated to salinity (R(2)=0.372, P<0.022), tdh+/trh+ to turbidity (R(2)=0.597, P<0.035), and orf8+ to temperature, salinity, and pH (R(2)=0.964, P<0.001). The exposure to salinity and temperature conditions during winter and spring seasons regulated the dynamics of V. parahaemolyticus harboring potentially pathogenic genotypes within the oyster. The adaptive response of V. parahaemolyticus to seasonal environmental changes may lead to an increase in survival and virulence, threatening the seafood safety and increasing the risk of illness.

VibrioBase: A MALDI-TOF MS database for fast identification of Vibrio spp. that are potentially pathogenic in humans

Mesophilic marine bacteria of the family Vibrionaceae, specifically V. cholerae, V. parahaemolyticus and V. vulnificus, are considered to cause severe illness in humans. Due to climate-change-driven temperature increases, higher Vibrio abundances and infections are predicted for Northern Europe, which in turn necessitates environmental surveillance programs to evaluate this risk. We propose that whole-cell matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling is a promising tool for the fast and reliable species classification of environmental isolates. Because the reference database does not contain sufficient Vibrio spectra we generated the VibrioBase database in this study. Mass spectrometric data were generated from 997 largely environmental strains and filed in this new database. MALDI-TOF MS clusters were assigned based on the species classification obtained by analysis of partial rpoB (RNA polymerase beta-subunit) sequences. The affiliation of strains to species-specific clusters was consistent in 97% of all cases using both approaches, and the extended VibrioBase generated more specific species identifications with higher matching scores compared to the commercially available database. Therefore, we have made the VibrioBase database freely accessible, which paves the way for detailed risk assessment studies of potentially pathogenic Vibrio spp. from marine environments.

Surface immuno-functionalisation for the capture and detection of Vibrio species in the marine environment: a new management tool for industrial facilities

Bacteria from the genus Vibrio are a common and environmentally important group of bacteria within coastal environments and include species pathogenic to aquaculture organisms. Their distribution and abundance are linked to specific environmental parameters, including temperature, salinity and nutrient enrichment. Accurate and efficient detection of Vibrios in environmental samples provides a potential important indicator of overall ecosystem health while also allowing rapid management responses for species pathogenic to humans or species implicated in disease of economically important aquacultured fish and invertebrates. In this study, we developed a surface immuno-functionalisation protocol, based on an avidin-biotin type covalent binding strategy, allowing specific sandwich-type detection of bacteria from the Vibrio genus. The assay was optimized on 12 diverse Vibrio strains, including species that have implications for aquaculture industries, reaching detection limits between 7×10³ to 3×10⁴ cells mL⁻¹. Current techniques for the detection of total Vibrios rely on laborious or inefficient analyses resulting in delayed management decisions. This work represents a novel approach for a rapid, accurate, sensitive and robust tool for quantifying Vibrios directly in industrial systems and in the environment, thereby facilitating rapid management responses.

Evaluation of molecular methods to discriminate the closely related species Vibrio fluvialis and Vibrio furnissii

Vibrio furnissii and Vibrio fluvialis are two closely related species which are regarded as emerging human pathogens. Human infections have been mainly associated with consumption of seafood or drinking of contaminated water. V. furnissii strains can be distinguished from V. fluvialis by their ability to produce gas from fermentation of carbohydrates. In this study, we compare two phenotypic (biochemical testing and matrix-assisted laser desorption/ionisation time of flight mass spectrometry, MALDI-TOF MS) and three genotypic techniques (rpoB sequencing, conventional PCR and real-time PCR) for determination of the two species. The methods were evaluated on a collection of 42 V. furnissii and 32 V. fluvialis strains, which were isolated from marine environments and from animals intended for food production. Four of the applied methods allowed the unambiguous discrimination of the two species, while the biochemical testing was the least reliable technique, due to a high variation in the phenotype of gas production from carbohydrates. In view of the One Health concept reliable diagnostic techniques are a prerequisite for preventive public health measurements, as pathogens isolated from animals can cross species borders and methods for detection of sources, reservoirs and ways of transmission of pathogenic bacteria are indispensable for the prevention of infectious diseases in humans and animals.

Temporal and spatial distribution patterns of potentially pathogenic Vibrio spp. at recreational beaches of the German north sea

The number of reported Vibrio-related wound infections associated with recreational bathing in Northern Europe has increased within the last decades. In order to study the health risk from potentially pathogenic Vibrio spp. in the central Wadden Sea, the seasonal and spatial distribution of Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio cholerae were investigated at ten recreational beaches in this area over a 2-year period. V. alginolyticus and V. parahaemolyticus were found to be omnipresent all year round in the study area, while V. vulnificus occurrence was restricted to summer months in the estuaries of the rivers Ems and Weser. Multiple linear regression models revealed that water temperature is the most important determinant of Vibrio spp. occurrence in the area. Differentiated regression models showed a species-specific response to water temperature and revealed a particularly strong effect of even minor temperature increases on the probability of detecting V. vulnificus in summer. In sediments, Vibrio spp. concentrations were up to three orders of magnitude higher than in water. Also, V. alginolyticus and V. parahaemolyticus were found to be less susceptible towards winter temperatures in the benthic environment than in the water, indicating an important role of sediments for Vibrio ecology. While only a very small percentage of tested V. parahaemolyticus proved to be potentially pathogenic, the presence of V. vulnificus during the summer months should be regarded with care.

Rapid identification of Vibrio parahaemolyticus isolated from shellfish, sea water and sediments of the Khnifiss lagoon, Morocco, by MALDI-TOF mass spectrometry

We establish the presence of Vibrio parahaemolyticus and deepen the comparison of isolates using MALDI-TOF MS for the typing of isolates originating from the Khnifiss lagoon (Morocco). Amongst 48 samples from sea water, sediment and shellfish isolated from different sites of Khnifiss lagoon, Morocco, we obtained 22 isolates of V. parahaemolyticus identified by Vitek 2™ System (bioMérieux) and MALDI Biotyper™ (Bruker Daltonics). All isolates were highly resistant to ampicillin and ticarcillin, moderately resistant to cefalotin, but sensitive to 16 other antimicrobials tested. MALDI-TOF MS was used to discriminate between closely related environmental strains of V. parahaemolyticus. A clustering and distribution based on MALDI-TOF spectra were generated using the BioTyper 1.1™ software. Despite low diversity in regard to the biochemical characteristics and antimicrobial resistance, the isolates evoke a larger biodiversity when analysed through mass spectra of abundant proteins. Different evaluations of a cut-off value showed that, when placed at a 10% threshold of the whole diversity, isolates differed by at least three mass peaks.

Characterization of bacteria in ballast water using MALDI-TOF mass spectrometry

To evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Since International Maritime Organization (IMO) regulations are concerned with the unintended transportation of pathogenic bacteria through ballast water, emphasis was placed on detecting species of Vibrio, enterococci and coliforms. Seawater samples collected from the North Sea were incubated in steel ballast tanks and the presence of potentially harmful species of Pseudomonas was also investigated. At the genus-level, the identification of thirty six isolates using MALDI-TOF MS produced similar results to those obtained by 16S rRNA gene sequencing. No pathogenic species were detected either by 16S rRNA gene analysis or by MALDI-TOF MS except for the opportunistically pathogenic bacterium Pseudomonas aeruginosa. In addition, in house software that calculated the correlation coefficient values (CCV) of the mass spectral raw data and their variation was developed and used to allow the rapid and efficient identification of marine bacteria in ballast water for the first time.

Occurrence of Vibrio parahaemolyticus and Vibrio alginolyticus in the German Bight over a seasonal cycle

Bacteria of the genus Vibrio are an important component of marine ecosystems worldwide. The genus harbors several human pathogens, for instance the species Vibrio parahaemolyticus, a main cause for foodborne gastroenteritis in Asia and the USA. Pathogenic V. parahaemolyticus strains emerged also in Europe, but little is known about the abundance, pathogenicity and ecology of V. parahaemolyticus especially in Northern European waters. This study focuses on V. parahaemolyticus and its close relative Vibrio alginolyticus in the North Sea (Helgoland Roads, Germany). Free-living, plankton-attached and shellfish-associated Vibrio spp. were quantified between May 2008 and January 2010. CFUs up to 4.3 × 10(3) N l(-1) and MPNs up to 240 N g(-1) were determined. Phylogenetic classification based on rpoB gene sequencing revealed V. alginolyticus as the dominant Vibrio species at Helgoland Roads, followed by V. parahaemolyticus. We investigated the intraspecific diversity of V. parahaemolyticus and V. alginolyticus using ERIC-PCR. The fingerprinting disclosed three distinct groups at Helgoland Roads, representing V. parahaemolyticus, V. alginolyticus and one group in between. The species V. parahaemolyticus occurred mainly in summer months. None of the strains carried the virulence-associated genes tdh or trh. We further analyzed the influence of nutrients, secchi depth, temperature, salinity, chlorophyll a and phytoplankton on the abundance of Vibrio spp. and the population structure of V. parahaemolyticus. Spearman Rank analysis revealed that particularly temperature correlated significantly with Vibrio spp. numbers. Based on multivariate statistical analyses we report that the V. parahaemolyticus population was structured by a complex combination of environmental parameters. To further investigate these influences is the key to understanding the dynamics of Vibrio spp. in temperate European waters, where this microbial group and especially the pathogenic species, are likely to gain in importance.