Making waves: Wastewater-based epidemiology for COVID-19 - approaches and challenges for surveillance and prediction

The presence of SARS-CoV-2 in the feces of infected patients and wastewater has drawn attention, not only to the possibility of fecal-oral transmission but also to the use of wastewater as an epidemiological tool. The COVID-19 pandemic has highlighted problems in evaluating the epidemiological scope of the disease using classical surveillance approaches, due to a lack of diagnostic capacity, and their application to only a small proportion of the population. As in previous pandemics, statistics, particularly the proportion of the population infected, are believed to be widely underestimated. Furthermore, analysis of only clinical samples cannot predict outbreaks in a timely manner or easily capture asymptomatic carriers. Threfore, community-scale surveillance, including wastewater-based epidemiology, can bridge the broader community and the clinic, becoming a valuable indirect epidemiological prediction tool for SARS-CoV-2 and other pandemic viruses. This article summarizes current knowledge and discusses the critical factors for implementing wastewater-based epidemiology of COVID-19.

Aliarcobacter vitoriensis sp. nov., isolated from carrot and urban wastewater

Two isolates, one recovered from a carrot and another one from urban wastewater, were characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates clustered together, and were most closely related to Aliarcobacter lanthieri. Multilocus phylogenetic analysis (MLPA) using the concatenated sequences of five housekeeping genes (atpA, gyrA, gyrB, hsp60 and rpoB) suggested that these isolates formed a distinct phylogenetic lineage among the genera derived from the former genus Arcobacter. Whole-genome sequence, in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) value between the genome of strain F199^T and those of related species confirmed that these isolates represent a novel species. These strains can be differentiated from its phylogenetically closest species A. lanthieri by its inability to growth on 1% glycine and by their enzyme activity of esterase lipase (C8) and acid phosphatase. Our results, by the application of a polyphasic analysis, confirmed that these two isolates represent a novel species of the genus Aliarcobacter, for which the name Aliarcobacter vitoriensis sp. nov. is proposed. The type strain is F199^T (=CECT 9230^T=LMG 30050^T).

A Comprehensive Review on Human Aichi Virus

Although norovirus, rotavirus, adenovirus and Astrovirus are considered the most important viral agents transmitted by food and water, in recent years other viruses, such as Aichi virus (AiV), have emerged as responsible for gastroenteritis outbreaks associated with different foods. AiV belongs to the genus Kobuvirus of the family Picornaviridae. It is a virus with icosahedral morphology that presents a single stranded RNA genome with positive sense (8280 nucleotides) and a poly (A) chain. AiV was first detected from clinical samples and in recent years has been involved in acute gastroenteritis outbreaks from different world regions. Furthermore, several studies conducted in Japan, Germany, France, Tunisia and Spain showed a high prevalence of AiV antibodies in adults (between 80% and 99%), which is indicative of a large exposure to this virus. The aim of this review is to bring together all the discovered information about the emerging pathogen human Aichi virus (AiV), discussing the possibles routes of transmission, new detection techniques and future research. Although AiV is responsible for a low percentage of gastroenteritis outbreaks, the high seroprevalence shown by human populations indicates an evident role as an enteric agent. The low percentage of AiV detection could be explained by the fact that the pathogen is more associated to subclinical infections. Further studies will be needed to clarify the real impact of AiV in human health and its importance as a causative gastroenteritis agent worldwide.

Detection of Hepatitis E Virus in Shellfish Harvesting Areas from Galicia (Northwestern Spain)

The hepatitis E virus (HEV) affects almost 20 million individuals annually, causing approximately 3.3 million acute liver injuries, 56,600 deaths, and huge healthcare-associated economic losses. Shellfish produced close to urban and livestock areas can bioaccumulate this virus and transmit it to the human population. The aim of this study was to evaluate the presence of HEV in molluscan shellfish, in order to deepen the knowledge about HEV prevalence in Galicia (northwestern Spain), and to investigate this as a possible route of HEV transmission to humans. A total of 168 shellfish samples was obtained from two different Galician rías (Ría de Ares-Betanzos and Ría de Vigo). The samples were analyzed by reverse transcription-quantitative PCR (RT-qPCR). RT-nested PCR and sequencing were used for further genotyping and phylogenetic analysis of positive samples. HEV was detected in 41 (24.4%) samples, at quantification levels ranging from non-quantifiable (<102 copies of the RNA genome (RNAc)/g tissue) to 1.1 × 105 RNAc/g tissue. Phylogenetic analysis based on the open reading frame (ORF)2 region showed that all sequenced isolates belonged to genotype 3, and were closely related to strains of sub-genotype e, which is of swine origin. The obtained results demonstrate a significant prevalence of HEV in bivalve molluscs from Galician rías, reinforcing the hypothesis that shellfish may be a potential route for HEV transmission to humans.

#EUROmicroMOOC: using Twitter to share trends in Microbiology worldwide

Twitter is one of the most popular social media networks that, in recent years, has been increasingly used by researchers as a platform to share science and discuss ongoing work. Despite its popularity, Twitter is not commonly used as a medium to teach science. Here, we summarize the results of #EUROmicroMOOC: the first worldwide Microbiology Massive Open Online Course taught in English using Twitter. Content analytics indicated that more than 3 million users saw posts with the hashtag #EUROmicroMOOC, which resulted in over 42 million Twitter impressions worldwide. These analyses demonstrate that free Microbiology MOOCs shared on Twitter are valuable educational tools that reach broad audiences throughout the world. We also describe our experience teaching an entire Microbiology course using Twitter and provide recommendations when using social media to communicate science to a broad audience.

Development of a novel digital RT-PCR method for detection of human sapovirus in different matrices

A new nanofluidic digital RT-PCR method was developed for sapovirus (SaV) using control material obtained according to standards for enteric viruses. Primers employed amplify a fragment of 112 bp of the polymerase capsid junction, allowing the detection of human genogroups I, II and IV. Analytical validation was performed in clinical, shellfish and environmental water samples. This novel protocol rendered great effectiveness and repetitiveness, as well as higher sensitivity than real time RT-PCR assay, with differences in quantification ranging from 0.1 to 2.6 log-units. The method described here can constitute a promising tool for standardizing SaV quantification.

Characterization of the microbiota associated to Pecten maximus gonads using 454-pyrosequencing

A next-generation sequencing (NGS) approach was used to study the microbiota associated to Pecten maximus broodstock, applying pyrosequencing of PCR-amplified V1-V4 16S rRNA gene regions. We analysed the resident bacterial communities in female and male scallop gonads before and after spawning. DNA samples were amplified and quality-filtered reads were assigned to family and genus taxonomic levels using the Ribosomal Database Project classifier. A total of 18,520 sequences were detected, belonging to 13 phyla, including Proteobacteria (55%), Bacteroidetes (11,7%), Firmicutes (3%), Actinobacteria (2%) and Spirochaetes (1,2%), and 110 genera. The major fraction of the sequences detected corresponded to Proteobacteria, Beta- and Gammaprotebacteria being the most abundant classes. The microbiota of P. maximus gonad harbour a wide diversity, however differences on male and female samples were observed, where female gonad samples show a larger number of genera and families. The dominant bacterial genera appeared to be Delftia, Acinetobacter, Hydrotalea, Aquabacterium, Bacillus, Sediminibacterium, Sphingomonas, and Pseudomonas that were present among the four analysed samples. This next generation sequencing technique, applied for the first time in P. maximus (great scallop) gonads was useful for the study of the bacterial communities in this mollusc, unravelling the great bacterial diversity in its microbiota. [Int Microbiol 19(2): 93-99(2016)].

Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos

Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.

Hepatitis A Virus Disinfection in Water by Solar Photo-Fenton Systems

This study evaluates and compares the effectiveness of solar photo-Fenton systems for the inactivation of hepatitis A virus (HAV) in water. The effect of solar irradiance, dark- Fenton reaction and three different reactant concentrations (2.5/5, 5/10 and 10/20 mg/L of Fe²⁺/H₂O₂) on the photo-Fenton process were tested in glass bottle reactors (200 mL) during 6 h under natural sunlight. Disinfection kinetics were determined both by RT-qPCR and infectivity assays. Mean water temperatures ranged from 25 to 27.3 °C, with a maximum local noon UV irradiances of 22.36 W/m². Photo-Fenton systems yielded increased viral reduction rates in comparison with the isolated effect under the Fenton reaction in darkness (negligible viral reduction) or the solar radiation (0.25 Log of RNA reduction). With the highest concentration employed (10-20 mg/L Fe²⁺-H₂O₂), an average RNA reduction rate of ~ 1.8 Log (initial concentration of 10⁵ pfu/mL) and a reduction of 80% in the infectivity capacity were reached. Results showed a strong synergistic effect between Fe²⁺/H₂O₂ and sunlight, demonstrating that significant disinfection rates of HAV under photo-Fenton systems may occur with relatively higher efficiency at middle environmental temperatures and without the need for an energy-intensive light source.

Population genetic and evolution analysis of controversial genus Edwardsiella by multilocus sequence typing

At present, the genus Edwardsiella compiles five species: E. tarda, E. hoshinae, E. ictaluri, E. piscicida and E. anguillarum. Some species of this genus such us E. ictaluri and E. piscicida are important pathogens of numerous fish species. With the description of the two latter species, the phylogeny of Edwardsiella became more complicated. With the aim to clarify the relationships among all species in the genus, a multilocus sequence typing (MLST) approach was developed and applied to characterize 56 isolates and 6 reference strains belonging to the five Edwardsiella species. Moreover, several analyses based on the MLST scheme were performed to investigate the evolution within the genus, as well as the influence of recombination and mutation in the speciation. Edwardsiella isolates presented a high genetic variability reflected in the fourteen sequence types (ST) represented by a single isolates out of eighteen total ST. Mutation events were considerably more frequent than recombination, although both approximately equal influenced the genetic diversification. However, the speciation among species occurred mostly by recombination. Edwardsiella genus displays a non-clonal population structure with some degree of geographical isolation followed by a population expansion of E. piscicida. A database from this study was created and hosted on pubmlst.org (http://pubmlst.org/edwardsiella/).

First isolation of Vibrio tapetis and an atypical strain of Aeromonas salmonicida from skin ulcerations in common dab (Limanda limanda) in the North Sea

Skin ulcerations rank amongst the most prevalent lesions affecting wild common dab (Limanda limanda) with an increase in prevalence of up to 3.5% in the Belgian part of the North Sea. A complex aetiology of these ulcerations is suspected, and many questions remain on the exact factors contributing to these lesions. To construct the aetiological spectrum of skin ulcerations in flatfish, a one-day monitoring campaign was undertaken in the North Sea. Fifteen fish presented with one or more ulcerations on the pigmented and/or non-pigmented side. Pathological features revealed various stages of ulcerations with loss of epidermal and dermal tissue, inflammatory infiltrates and degeneration of the myofibers bordering the ulceration, albeit in varying degrees. Upon bacteriological examination, pure cultures of Vibrio tapetis were retrieved in high numbers from five fish and of Aeromonas salmonicida in one fish. The V. tapetis isolates showed cross-reactivity with the sera against the representative strain of serotype O2 originating form a carpet-shell clam (Ruditapes descussatus). Moreover, the A. salmonicida isolates displayed a previously undescribed vapA gene sequence (A-layer type) with possible specificity towards common dab. Further research is necessary to pinpoint the exact role of these agents in the development of skin ulcerations in common dab.

An overview of 20 years of studies on the prevalence of human enteric viruses in shellfish from Galicia, Spain

Galicia (NW Spain) has 1490 km of coastline, and its particular topography, characterized by the presence of fiord-like inlets, called rías, with an important primary production, makes this region very favourable for shellfish growth and culture. In fact, Galicia is one of the most important mussel producers in the world. Due to its proximity to cities and villages and the anthropogenic activities in these estuaries, and despite the routine official controls on the bivalve harvesting areas, contamination with material of faecal origin is sometimes possible but, current regulation based on Escherichia coli as an indicator micro-organism has been revealed as useful for bacterial contaminants, this is not the case for enteric viruses. The aim of this review is to offer a picture on the situation of different harvesting areas in Galicia, from a virological standpoint. A recompilation of results obtained in the last 20 years is presented, including not only the data for the well-known agents norovirus (NoV) and hepatitis A virus (HAV) but also data on emerging viral hazards, including sapovirus (SaV), hepatitis E virus (HEV) and aichivirus (AiV). Epidemiological differences related to diverse characteristics of the harvesting areas, viral genotype distribution or epidemiological links between environmental and clinical strains will also be presented and discussed. The presentation of these historical data all together could be useful for future decisions by competent authorities for a better management of shellfish growing areas.

Genetic studies to re-affiliate Edwardsiella tarda fish isolates to Edwardsiella piscicida and Edwardsiella anguillarum species

Until 2012, the genus Edwardsiella was composed by three species Edwardsiella tarda, Edwardsiella hoshinae and Edwardsiella ictaluri. In 2013, Edwardsiella piscicida, compiling fish pathogenic strains previously identified as E. tarda was described, and more recently a new species isolated from diseased eel was reported, namely Edwardsiella anguillarum. The incorporation of these species into the genus makes necessary a revision of the taxonomic position of the isolates previously identified as E. tarda. Using AFLP technique, MLSA studies and in silico DNA-DNA hybridization, 46 of 49 E. tarda isolates were re-assigned as E. piscicida and 2 as E. anguillarum, whereas it was confirmed previous classification of the Edwardsiella types and reference strains used. The study of the taxonomic resolution of the genes 16S rRNA, adk, atpD, dnaJ, glnA, hsp60, tuf as well as the possible combinations among housekeeping genes, showed that the gene dnaJ was the more resolutive. In conclusion, the use of molecular techniques is necessary to accurately identify Edwardsiella isolates, especially when differentiating new species from E. tarda.

Complete characterization of new isolates of Neptunomonas phycophila leads to emend its description and opens possibilities of biotechnological applications

Five strains were isolated from gonad of Great scallop (Pecten maximus) broodstock in a Norwegian hatchery. The study of 16S rRNA gene sequences showed that these isolates belong to Neptunomonas phycophila, a bacterium originally isolated from a symbiont of the anemone Aiptasia tagetes from Puerto Rico. The gyrB and rpoB genes sequences confirmed the affiliation of the scallop isolates to this species. Phenotypic characterization was performed and some differences between the Norwegian isolates and the type strain of N. phycophila were detected, such as ranges of temperature, pH, and tolerance to salinity or the use of several substrates as sole carbon source which lead to an emended description of the species. The strain 3CM2.5 showed phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The whole genomes of the scallop strain 3CM2.5 and type strain of the species CECT 8716^T were obtained and the annotation of these genomes revealed the presence of genes involved in degradation of aromatic compounds in both strains. Results obtained not only widen the geographical and host ranges of N. phycophila, but also point out possible biotechnological applications for this bacterial species.

Vibrio tapetis from wrasse used for ectoparasite bio-control in salmon farming: phylogenetic analysis and serotyping

So-called 'cleaner fish', including various wrasse (Labridae) species, have become increasingly popular in Norwegian salmon farming in recent years for biocontrol of the salmon louse Lepeophtheirus salmonis. Cleaner fish mortalities in salmon farms are, however, often high. Various bacterial agents are frequently associated with episodes of increased cleaner fish mortality, and Vibrio tapetis is regularly cultured from diseased wrasse. In the present study, we investigated the genetic relationships among 54 V. tapetis isolates (34 from wrasse species) by multilocus sequence analysis (MLSA; rpoD, ftsZ, pyrH, rpoA and atpA). In the resulting phylogenetic tree, all wrasse isolates belonged to sub-clusters within V. tapetis subsp. tapetis. Slide agglutination testing further confirmed the complete dominance amongst these isolates of 4 O-antigen serotypes, designated here as V. tapetis subsp. tapetis serotypes O1, O3, O4 and O5, respectively. A pilot challenge trial using serotypes O3, O4 and O5 did not indicate high pathogenicity towards ballan wrasse Labrus bergylta, thus questioning the role of V. tapetis as a primary pathogen of this fish species.

Arcobacter lekithochrous sp. nov., isolated from a molluscan hatchery

Four bacterial strains, LFT 1.7T, LT2C 2.5, LT4C 2.8 and TM 4.6, were isolated from great scallop (Pecten maximus) larvae and tank seawater in a Norwegian hatchery and characterized by a polyphasic approach including determination of phenotypic, chemotaxonomic and genomic traits. All were Gram-stain-negative, motile rods, oxidase- and catalase-positive and required sea salts for growth. Major fatty acids present were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 8 (C18 : 1ω7c or C18 : 1ω6c), C16 : 0, C14 : 0, summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I), C12 : 0 3-OH and C12 : 0. Strain LFT 1.7T contained menaquinone MK-6 as the sole respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that all strains formed a distinct lineage within the genus Arcobacter with a low similarity to known species (94.77-95.32 %). The DNA G+C content was 28.7 mol%. Results of in silico DNA-DNA hybridization and average nucleotide identity confirmed that the isolates constitute a novel species of Arcobacter, for which the name Arcobacter lekithochrous sp. nov. is proposed. The type strain is LFT 1.7T (=CECT 8942T=DSM 100870T).

New Insights into Pathogenic Vibrios Affecting Bivalves in Hatcheries: Present and Future Prospects

Hatcheries constitute nowadays the only viable solution to support the husbandry of bivalve molluscs due to the depletion and/or overexploitation of their natural beds. Hatchery activities include the broodstock conditioning and spawning, rearing larvae and spat, and the production of microalgae to feed all stages of the production cycle. However, outbreaks of disease continue to be the main bottleneck for successful larval and spat production, most of them caused by different representatives of the genus Vibrio. Therefore, attention must be paid on preventive and management measures that allow the control of such undesirable bacterial populations. The present review provides an updated picture of the recently characterized Vibrio species associated with disease of bivalve molluscs during early stages of development, including the controversial taxonomic affiliation of some of them and relevant advances in the knowledge of their virulence determinants. The problematic use of antibiotics, as well as its eco-friendly alternatives are also critically discussed.

Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation

To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9), and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858.

Comparative Genomic Analysis of Two Vibrio toranzoniae Strains with Different Virulence Capacity Reveals Clues on Its Pathogenicity for Fish

Vibrio toranzoniae is a Gram-negative bacterium of the Splendidus clade within the Vibrio genus. V. toranzoniae was first isolated from healthy clams in Galicia (Spain) but recently was also identified associated to disease outbreaks of red conger eel in Chile. Experimental challenges showed that the Chilean isolates were able to produce fish mortalities but not the strains isolated from clams. The aim of the present study was to determine the differences at the genomic level between the type strain of the species (CECT 7225^T) and the strain R17, isolated from red conger eel in Chile, which could explain their different virulent capacity. The genome-based comparison showed high homology between both strains but differences were observed in certain gene clusters that include some virulence factors. Among these, we found that iron acquisition systems and capsule synthesis genes were the main differential features between both genomes that could explain the differences in the pathogenicity of the strains. Besides, the studied genomes presented genomic islands and toxins, and the R17 strain presented CRISPR sequences that are absent on the type strain. Taken together, this analysis provided important insights into virulence factors of V. toranzoniae that will lead to a better understanding of the pathogenic process.