The Microbial Diversity of Non-Korean Kimchi as Revealed by Viable Counting and Metataxonomic Sequencing.

Kimchi is recognized worldwide as the flagship food of Korea. To date, most of the currently available microbiological studies on kimchi deal with Korean manufactures. Moreover, there is a lack of knowledge on the occurrence of eumycetes in kimchi. Given these premises, the present study was aimed at investigating the bacterial and fungal dynamics occurring during the natural fermentation of an artisan non-Korean kimchi manufacture. Lactic acid bacteria were dominant, while Enterobacteriaceae, Pseudomonadaceae, and yeasts progressively decreased during fermentation. Erwinia spp., Pseudomonasveronii, Pseudomonasviridiflava, Rahnellaaquatilis, and Sphingomonas spp. were detected during the first 15 days of fermentation, whereas the last fermentation phase was dominated by Leuconostoc kimchi, together with Weissellasoli. For the mycobiota at the beginning of the fermentation process, Rhizoplaca and Pichia orientalis were the dominant Operational Taxonomic Units (OTUs) in batch 1, whereas in batch 2 Protomyces inundatus prevailed. In the last stage of fermentation, Saccharomyces cerevisiae, Candida sake,Penicillium, and Malassezia were the most abundant taxa in both analyzed batches. The knowledge gained in the present study represents a step forward in the description of the microbial dynamics of kimchi produced outside the region of origin using local ingredients. It will also serve as a starting point for further isolation of kimchi-adapted microorganisms to be assayed as potential starters for the manufacturing of novel vegetable preserves with high quality and functional traits.

Molecular characterization and drug susceptibility of non-O1/O139 V. cholerae strains of seafood, environmental and clinical origin, Italy.

Toxigenic and antimicrobial susceptibility patterns and genetic relatedness of 42 non-O1/O139 V. cholerae strains, the majority of them isolated from seafood and marine water of the Adriatic sea, Italy, and 9 clinical strains, two of which with seawater of the Adriatic as the source of infection, were studied. All strains had hlyA El Tor gene but lacked ctxA gene. Four and two isolates, respectively, also had stn/sto and tcpA Class genes. More than 90% of strains showed susceptibility to cefotaxime, ciprofloxacin, cloramphenicol, tetracycline, trimethoprim + sulfamethoxazole and intermediate or full resistance to tetracycline and erythromycin. Six strains of seafood and clinical source were multi-drug resistant. PFGE analysis allowed to type all the strains with 50 banding patterns. Twenty-one strains, 11 and 8 from seafood and seawater, respectively, and 2 of clinical origin, were grouped into 9 different clusters. We report the presence of toxigenic and multidrug resistant non-O1/O139 V. cholerae strains in Adriatic, some of which genetically related, and support that they represent a potential reservoir of toxin and antibiotic resistance genes.

Occurrence of Arcobacter spp. and correlation with the bacterial indicator of faecal contamination Escherichia coli in bivalve molluscs from the Central Adriatic, Italy.

A total of 162 samples of bivalve molluscs (45 mussels and 117 clams) collected between December 2012 and 2014 from harvesting areas of the Central Adriatic were analysed by a culturing method for the presence of Arcobacter spp. Species identification was performed by PCR and sequencing analysis of a fragment of the rpoB gene. Overall, Arcobacter species were detected in 30% of samples, specifically 33% clams and 22% mussels. A. butzleri was the most common species (20% of the samples), followed by A. cryaerophilus (9%) and A. skirrowii (1%). A seasonal association of A. butzleri contamination was detected. A. butzleri was significantly more commonly recovered from samples collected during the winter-spring period (29%) than from those of the summer-autumn (8%). A. cryaerophilus was cultured from 6% to 11% of the samples collected in summer-autumn and winter-spring, respectively, but these differences were not statistically significant. A. skirrowii was recovered from a sample of mussels harvested in May 2014. To identify associations between the occurrence of Arcobacter spp. and E. coli levels, samples were divided into groups generating results with E. coli at >230MPN/100g and E. coli at ≤230MPN/100g, the latter corresponding to EU microbiological criteria allowed for live bivalve molluscs at retail level. A. butzleri was significantly more commonly detected in samples with higher E. coli levels (48%) than in those with lower levels of E. coli (10%), providing evidence for considering E. coli as an index organism for A. butzleri contamination in bivalve molluscs.

Trh (tdh-/trh+) gene analysis of clinical, environmental and food isolates of Vibrio parahaemolyticus as a tool for investigating pathogenicity.

Sequencing analysis of the trh gene encoding the TDH-related haemolysin of tdh-/trh+ Vibrio parahaemolyticus isolated in Italy between 2002 and 2011 from clinical, environmental, and food samples revealed the presence of the trh2 variant in all isolates. The trh2 of the clinical isolate was 100% identical to other clinical tdh-/trh2 V. parahaemolyticus from Europe. Nucleotide and amino acid differences in the trh2 sequences of clinical isolates from Italy and other countries allowed a differentiation of the clinical strains from the majority of environmental or food strains isolated in Italy. Aspartic acid and isoleucine at positions 113 and 115, encoded by nucleotide triplets GAT and ATT at positions 337-339 and 343-345 of the complete trh gene sequence, were present in clinical strains from Europe (Italy, Norway and Germany), Asia and the United States. Only 35.5% of the tdh-/trh2 V. parahaemolyticus of environmental or food origin from Italy shared the same triplets/amino acid detected in clinical isolates, while 64.5% of isolates from the marine environment were different from those of clinical origins, demonstrating that differences occur amongst the trh2 sequences of strains from the environment and these polymorphisms may differentiate potentially pathogenic from less or non-pathogenic cultures found in the environment and seafood. In addition the distribution of T3SS2 genes was investigated in this group of tdh-/trh+ V. parahaemolyticus from different sources and in three clinical tdh+/trh- V. parahaemolyticus isolates. All tdh-/trh+ V. parahaemolyticus of environmental or food source, independent of year of isolation or geographical origin, amplified all the screened T3SS2ß genes and tested negative to PCR assays for all five T3SS2α genes, as the tdh-/trh+ clinical V. parahaemolyticus isolate. The vopC genes, encoding for one of the effector proteins of T3SS2, were partially sequenced and compared to clinical tdh-/trh+ and tdh+/trh+ V. parahaemolyticus isolates from other countries. Analysis of T3SS2ß vopC sequences revealed variation in tdh-/trh2 isolates from Italy, which were separated from a group of vopC sequences derived from trh2 V. parahaemolyticus from the USA.

Nontoxigenic Vibrio parahaemolyticus strains causing acute gastroenteritis.

We investigated the virulence properties of four Vibrio parahaemolyticus strains causing acute gastroenteritis following consumption of indigenous mussels in Italy. The isolated strains were cytotoxic and adhesive but, surprisingly, lacked tdh, trh, and type three secretion system 2 (T3SS2) genes. We emphasize that nontoxigenic V. parahaemolyticus can induce acute gastroenteritis, highlighting the need for more investigation of the pathogenicity of this microorganism.