Genomic-wide analysis approach revealed genomic similarity for environmental Mexican S. Oranienburg genomes.

As the human population grows, an increase in food trade is needed. This elevates the risk of epidemiological outbreaks. One of the prevalent pathogens associated with food production in Mexico has been Salmonella Oranienburg. Effective surveillance systems require microbial genetic knowledge. The objective of this work is to describe the genetic composition of Mexican S. Oranienburg genomes. For that, 53 strains from different environmental sources were isolated and sequenced. Additionally, 109 S. Oranienburg genomes were downloaded. Bioinformatic analyses were used to explore the clonal complex and genomic relatedness. A major clonal group formed by ST23 was identified comprising four STs. 202 SNPs were found the maximum difference among isolates. Virulence genes for host invasion and colonization as rpoS, fimbria type 1, and, T3SS were found common for all isolates. This study suggests that Mexican S. Oranienburg strains are potential pathogens circulating continuously in the region between host and non-host environments.

Genomic signatures of adaptation to natural settings in non-typhoidal Salmonella enterica Serovars Saintpaul, Thompson and Weltevreden.

Salmonella enterica is a pathogenic bacterium responsible for intestinal illness and systemic diseases such as typhoid and paratyphoid fevers. Among clinical manifestation classification, non-typhoidal Salmonella is mainly known as foodborne pathogen associated with the consumption of fecal contaminated food and water. Even though Salmonella hosts include humans and warm-blooded animals, it has been found in non-host environments as river water where the bacteria use different strategies to fitness the environment persisting and establishment. Now with the availability of WGS and bioinformatics tools, we can explore bacterial genomes with higher resolution to increase our understanding of specific genetic signatures among environmental and clinical isolates, being the goal of this work. Pangenome construction allowed the detection of specific environmental and clinical gene clusters related to metabolism and secretion systems as the main signature respectively. Specifically, D-galactonate degradation pathway was observed mainly in environmental genomes while T3SS and flagellum genes were detected for all clinical but not for all environmental isolates. Gene duplication and pseudogenes accumulation were detected as the main adaptation strategy for environmental isolates; thus, isolation source may play an important role in genome plasticity, conferring a selective advantage to survive and persist for environmental Salmonella isolates. Intact prophage sequences with cargo genes were observable for both isolation sources playing an important role in virulence contribution.

Molecular characterizations of Vibrio parahaemolyticus in seafood from the Black Sea, Turkey.

UNLABELLED: Vibrio parahaemolyticus is a marine bacterium that is considered as one of the major causes of bacterial food-borne outbreaks at a global scale. A total of 114 samples including mussel (n = 42), seawater (n = 22) and fish (n = 50) samples were collected and subjected to investigation. Vibrio parahaemolyticus was detected in 45 (39%) of 114 samples with an occurrence in mussel, seawater and fish samples of 76, 40·9 and 8% respectively. A total of 96 isolates were positive for the species-specific genes toxR and tlh and confirmed as V. parahaemolyticus. Presence of the virulence marker gene tdh was not identified in any of the strains investigated; however, four of strains were positive for the trh gene. Serological analysis of eight randomly selected trh-negative isolates identified three different serotypes: O4:K untypeable (KUT), O2:KUT, O3:KUT. Conversely, all four trh-positive strains belonged to a single serotype (O1:K1) and share an undistinguishable genetic profile by PFGE analysis, suggesting the existence of a dominant clone for the trh-positive strains in the region. SIGNIFICANCE AND IMPACT OF THE STUDY: Vibrio parahaemolyticus is the most prevalent food-poisoning bacterium associated with seafood consumption. The number of infections is increasing worldwide and is being reported in areas with no previous incidence. This study provides the first instance of the occurrence of V. parahaemolyticus strains with virulence traits in the Black Sea, contributing to gain a better understanding about potential risk associated with this pathogen in the region.

Multidisciplinary investigation of a multicountry outbreak of Salmonella Stanley infections associated with turkey meat in the European Union, August 2011 to January 2013.

Between August 2011 and January 2013, an outbreak of Salmonella enterica serovar Stanley (S. Stanley) infections affected 10 European Union (EU) countries, with a total of 710 cases recorded. Following an urgent inquiry in the Epidemic Intelligence Information System for food- and waterborne diseases (EPIS-FWD) on 29 June 2012, an international investigation was initiated including EU and national agencies for public health, veterinary health and food safety. Two of three local outbreak investigations undertaken by affected countries in 2012 identified turkey meat as a vehicle of infection. Furthermore, routine EU monitoring of animal sources showed that over 95% (n=298) of the 311 S. Stanley isolates reported from animal sampling in 2011 originated from the turkey food production chain. In 2004­10, none had this origin. Pulsed-field gel electrophoresis (PFGE) profile analysis of outbreak isolates and historical S. Stanley human isolates revealed that the outbreak isolates had a novel PFGE profile that emerged in Europe in 2011. An indistinguishable PFGE profile was identified in 346 of 464 human, food, feed, environmental and animal isolates from 16 EU countries: 102 of 112 non-human isolates tested were from the turkey production chain. On the basis of epidemiological and microbiological evidence, turkey meat was considered the primary source of human infection, following contamination early in the animal production chain.

Complete Genome Sequence of Vibrio parahaemolyticus Environmental Strain UCM-V493.

Vibrio parahaemolyticus is the leading bacterial cause of seafood-related gastroenteritis in the world. Here, we report the complete genome sequence and annotation of an environmental strain of V. parahaemolyticus, UCM-V493, with the aim of understanding the differences between the clinical and environmental isolates of the bacteria. We also make some preliminary sequence comparisons with the clinical strain RIMD2210633.

Molecular analysis and antimicrobial resistance of Salmonella isolates recovered from raw meat marketed in the area of "Grand Tunis", Tunisia.

A total of 315 samples of chicken (60), beef (144), minced meat (56), lamb meat (33), merguez (10) and fish (12) were collected from various local outlet stores in the area of "Grand Tunis", Tunisia between 2006 and 2008. Salmonella was recovered from 80 samples with the highest occurrence in chicken (48.3%) followed by beef (29.8%), minced meat (10.7%) and lamb (6.0%). No Salmonella were isolated from 12 fish and 10 merguez samples (typical Tunisian sausages). Nine serovars were identified among the isolates with the predominance of Salmonella Typhimurium (n=25) followed by Salmonella Kentucky (n=14), Salmonella Suberu (n=12) and Salmonella Zanzibar (n=11). Isolated Salmonella were characterized by serotyping, pulsed-field gel electrophoresis (PFGE) analysis, plasmid content and antimicrobial resistance profiling. Sixteen (20.0%) Salmonella isolates displayed resistance to ampicillin (13 isolates), streptomycin (five isolates), cefoperazone (two isolates), furazolodine (two isolates), with seven of these isolates displaying multiple resistance to at least two of these antimicriobal agents. PFGE analysis showed homogenous restriction patterns in each serovar. Compiled serotyping, PFGE analysis, plasmid profiling and antimicrobial resistance data provided additional discrimination.

Antimicrobial resistance and molecular analysis of non-typhoidal Salmonella isolates from human in Tunisia.

During the period from 2006 to 2007, a total of 32 clinical isolates of Salmonella enterica were isolated from diarrheagenic stool samples and further examined for their susceptibility to various antibiotics. Sixteen of the human isolates were from the capital Tunis, 11 were from Sousse, four were from Nabeul and one was from Mahdia, Tunisia. The isolates were serotyped and identified at the National Centre of Enteropathogenic Bacteria, Pasteur Institute, Tunis (Centre National de Salmonella, Shigella et Vibrio - Institut pasteur de Tunis); nine distinct serovars were identified: Enteritidis (n=20), Typhimurium (n=4), Zanzibar (n=2), Manhattan (n=1), Bovismorbificans (n=1), Amsterdam (n=1), Saint Paul (n=1), Kentucky (n=1) and Muenster (n=1). Our results showed that 25 Salmonella isolates (78.1 %) were resistant to antibiotics with 20 isolates (62.5 %) displayed resistance to ampicillin. Isolates sharing invA gene, as shown by PCR amplification, were further characterized by the techniques of pulsed-field gel electrophoresis (PFGE) using the restriction enzyme XbaI and plasmid analysis to determine possible genetic relationships among Salmonella enterica clinical isolates and to assess genetic diversity. Plasmid profiling identified seven plasmid profiles (with 1-5 plasmids) among the isolates; four isolates (Salmonella Kentucky, Salmonella Muenster, Salmonella Bovismorbificans and Salmonella Zanzibar) did not carry any plasmid. The isolates were differentiated into 10 distinct XbaI-pulsotypes. Our findings show genetic diversity among the different serovars and cluster analysis of compiled serotyping, PFGE, plasmid profiling and antibiotic resistance data provided additional discrimination.

Evaluation of different procedures for the optimized detection of Vibrio parahaemolyticus in mussels and environmental samples.

Vibrio parahaemolyticus is a marine bacterium with a worldwide distribution and is frequently associated with human outbreaks of infection. Detection and isolation of V. parahaemolyticus from natural sources is often problematical because of limitations in the analytical procedures. We evaluated a combination of conventional and molecular protocols previously described for the investigation of V. parahaemolyticus, with the aim of identifying the best procedures for improved detection of this organism in environmental matrixes. A total of 259 samples of zooplankton (103), mussels (48) and seawater (108) were investigated by an Absence-Presence method (A/P), whereas 118 samples of zooplankton (70) and mussels (48) were analyzed by the Most Probable Number (MPN) method. All samples were processed by a two-step enrichment procedure, firstly with APW broth and then with SPB as selective secondary broth. Detection of V. parahaemolyticus was by direct-PCR and by plate culture on TCBS and CHROMagar Vibrio, after sample enrichment in APW and SPB. With the A/P method, V. parahaemolyticus was detected in 23.6% samples by direct-PCR, whereas only 11.2% samples were positive with the plate culture method. With the MPN method, V. parahaemolyticus was detected in 54.2% and 27.1% of the samples by direct-PCR and plate culture respectively; this indicated the existence of 31% false negative results with the A/P method. No significant differences between the use of a single (APW) or two-step enrichment (APW+SPB) were observed by direct-PCR with A/P or MPN, although a significant higher presence of V. parahaemolyticus was detected by plate culture in both protocols with the two-step enrichment procedure. In conclusion, direct-PCR after sample enrichment in APW broth was the most successful method for detection of V. parahaemolyticus with the A/P procedure and enumeration by MPN. Better detection was obtained with MPN than with the A/P protocol. Conversely, the plate culture procedure showed better results with the two-step enrichment protocol in which CHROMagar Vibrio was used as the selective agar.

Contamination of bivalve molluscs by Cryptosporidium oocysts: the need for new quality control standards.

A yearlong study was carried out to investigate the presence and viability of Cryptosporidium oocysts in 203 samples of cultured shellfish from Galicia (NW Spain) and 38 samples imported from other European Union (EU) countries. Shellfish samples included mussels, oysters, clams and cockles. Cryptosporidium oocysts were detected, using a direct immunofluorescence antibody test (IFAT), in 34.4% of the samples analyzed; use of the fluorogenic dye propidium iodide (PI) revealed viable potentially infective oocysts in 53.0% of these samples. There was no relation between the presence of Cryptosporidium oocysts and the microbiological contamination detected in the samples expressed as Most-Probable-Number (MPN) of fecal coliforms, the different species of mollusc, or the month of sampling. One important finding was that the depuration process was ineffective in totally removing oocyst contamination. Furthermore, the existence of viable oocysts in samples with microbiological contamination levels lower than 300 fecal coliforms/100 g, which in accordance with current legislation are considered suitable for human consumption, suggests the need to include parasitological analyses in the quality control for these molluscs.