Detection and identification of enterohemorrhagic Escherichia coli O157:H7 and Vibrio cholerae O139 using oligonucleotide microarray

Probiotics inspired from natural ecosystem to inhibit the growth of Vibrio spp. causing white gut syndrome in Litopenaeus vannamei

Probiotics inspired by host-microbe interactions in the natural ecosystem are propitious in controlling bacterial infections in aquaculture and veterinary systems. Here we report the isolation and characterization of pathogenic Vibrio spp. and lactic acid bacteria from an intensive culture system of Litopenaeus vannamei and natural ecosystem, respectively. The pathogen isolated from the gut of L. vannamei showing the symptoms of white gut disease were identified as V. parahaemolyticus and V. campbelli. Both the pathogens expressed the virulence genes, rtxA, and tcpA and were showing multiple antibiotic resistance (MAR) index of more than 0.5. The lactic acid bacteria isolated from the sediment and gut of benthic organisms (shrimp and polychaetes) collected from a tropical estuary were classified as member of 9 OTUs such as Pediococcus stilessi, Lactobacillus fermentum, L. rhamnosus, Weissella cibaria, Enterococcus durans, E. fecalis, Streptococcus gallolyticus and L. garvieae. Majority of these isolates were facultative in nature and were able to tolerate gastric juice and bile salt. Out of 83 bacteria isolated from sediment and gut, 36 showed abilities to reduce the pH of culture medium to less than five. Many of these isolates (34 Nos.) showed production of hydrolytic enzymes and secondary metabolites with antagonistic activity against both the pathogens (1 No.) or separately toward V. parahaemolyticus (9 Nos.) and V. campbelli (11 Nos.). Overall, the current study proposes a natural ecosystem as a potential source of lactic acid bacteria with probiotic potentials to prevent the vibriosis disease outbreaks in shrimp aquaculture systems. Further studies are required to understand the abilities of lactic acid bacteria to colonize shrimp intestine, stimulate immune system and manipulate microbiome.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02618-2.

Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTube^TM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTube^TM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis.

Rapid Detection Device for Salmonella typhi in Milk, Juice, Water and Calf Serum

A limit of detection of 200 CFU/mL of Salmonella typhi spiked in various sample matrices were achieved in 30 min. The sample matrices were raw/unprocessed milk, commercially available milk, juice from packed bottles, fresh juice from carts, potable water, turbid water and calf serum. The complete protocol comprised of three steps: (a) cell lysis (b) nucleic acid amplification and (c) an in situ optical detection. The cell lysis was carried out using a simple heating based protocol, while the loop-mediated isothermal amplification of DNA was carried out by an in-house designed and fabricated system. The developed system consists of an aluminum block fitted with two cartridge heaters along with a thermocouple. The system was coupled to a light source and spectrometer for a simultaneous in situ detection. Primers specific for STY2879 gene were used to amplify the nucleic acid sequence, isolated from S. typhi cells. The protocol involves 15 min of cell lysis and DNA isolation followed by 15 min for isothermal amplification and simultaneous detection. No cross-reactivity of the primers were observed at 10⁶ CFU/mL of Escherichia coli, Vibrio cholerae, Salmonella typhimurium, Salmonella paratyphi A, Pseudomonas aeruginosa, Bacillus cereus, Lysteria monocytogenes, Clostridium botulinum, Staphylococcus aureus and Salmonella havana. In addition, the system was able to detect S. typhi of 200 CFU/mL in a concoction of 10⁶ CFU/mL of E. coli, 10⁶ CFU/mL of V. cholerae, and 10⁶ CFU/mL of hepatocyte-derived cellular carcinoma HUH7 cells. The proposed rapid diagnostic system shows a promising future in the field of food and medical diagnostics.

Detection and identification of Vibrio parahaemolyticus by multiplex PCR and DNA-DNA hybridization on a microarray

In this paper, we developed a rapid and accurate method for the detection of Vibrio parahaemolyticus strains, using multiplex PCR and DNA-DNA hybridization. Multiplex PCR was used to simultaneously amplify three diagnostic genes (tlh, tdh and fla) that serve as molecular markers of V. parahaemolyticus. Biotinylated PCR products were hybridized to primers immobilized on a microarray, and detected by chemiluminesce with avidin-conjugated alkaline phosphatase. With this method, forty-five samples were tested. Eight known virulent strains (tlh(+)/tdh(+)/fla(+)) and four known avirulent strains (tlh(+)/tdh(-)/fla(+)) of the V. parahaemolyticus were successfully detected, and no non-specific hybridization and cross-hybridization reaction were found from fifteen closely-related strains (tlh(-)/tdh(-)/fla(+)) of the Vibrio spp. In addition, all the other eighteen strains of non-Vibrio bacteria (tlh(-)/tdh(-)/fla(-)) gave negative results. The DNA microarray successfully distinguished V. parahaemolyticus from other Vibrio spp. The results demonstrated that this was an efficient and robust method for identifying virulent strains of V. parahaemolyticus.

A DNA array based assay for the characterization of microbial community in raw milk

An oligonucleotide array based on PCR method containing a combination of probes for taxonomic markers and species-specific virulence genes was developed for the simultaneous identification of 14 Lactic Acid Bacteria (LAB) and food-borne pathogenic bacteria in raw milk. The hypervariable regions V3 and V6 of 16S, together with a variable region of 23S rRNA genes and several genes specific for virulence factors were selected. Universal primers and multiplex PCR were used for the rapid differentiation of bacterial species and low concentration of specific pathogenic and spoilage bacteria were detected in milk. The dominant species such as Streptococcus thermophilus, Enterococcus faecalis, Lactococcus lactis, andLeuconostoc lactis were identified by indirect-labelling reactions based upon incorporation of amino-allyl dUTPs. The results regarding food-borne pathogens detection showed highly specific hybridisation patterns with the genomic DNA from Campylobacter jejuni, Escherichia coli, Salmonella thyphimurium, Listeria monocytogenes and Yersinia enterocolitica. A clear differentiation of dominant species present in a complex microbial community such as raw milk was achieved by the application of short oligonucleotide probes which discriminate sequences differing by few nucleotides.