Detection and Identification of Salmonella enterica, Escherichia coli, and Shigella spp. via PCR-electrospray ionization mass spectrometry: isolate testing and analysis of food samples

A novel biochemistry approach combined with MALDI-TOF MS to discriminate Escherichia coli and Shigella species

Escherichia coli and Shigella spp. are closely related, making it crucial to accurately identify them for disease control and prevention. In this study, we utilized MALDI-TOF MS to identify characteristic peaks of decarboxylation products of lysine and ornithine to distinguish between E. coli and Shigella spp. Our findings indicate that the peak at m/z 103.12 ± 0.1 of the product cadaverine from lysine decarboxylase is unique to E. coli, while all Shigella species lack the m/z 103.12 ± 0.1 peak. However, S. sonnei and S. boydii serotype C13 exhibit a specific peak at m/z 89.10 ± 0.1, which is the product of putrescine from ornithine decarboxylase. We were able to correctly identify 97.06% (132 of 136) of E. coli and Shigella isolates and 100% (8 of 8) of S. sonnei isolates using this biochemical-based MALDI-TOF MS detection system. This technology is advantageous for its high-throughput, high quality, and ease of operation, and is of significant value for the diagnosis of E. coli and Shigella-related diseases.

A multiplex PCR assay with a common primer for the detection of eleven foodborne pathogens

Salmonella enterica, Listeria monocytogenes, Shigella flexneri, Escherichia coli O157:H7, Vibrio parahaemolyticus, Staphylococcus aureus, Vibrio cholerae, Clostridium botulinum type A, Bacillus cereus, Clostridium perfringens Alpha toxin, and Yersinia enterocolitica are 11 common foodborne pathogens. Traditional bacterial culture methods for detecting pathogens are time-consuming and labor-intensive. Multiplex PCR technology, which can detect multiple targets in a single tube, has been increasingly applied to microbial detection due to its high specificity, sensitivity, and fast response. This paper is to establish a multiplex PCR technology mediated by a common primer for the detection of these 11 common foodborne pathogens in order to achieve the goal of nondirectional screening for these 11 common foodborne pathogens. The specificity of the established CP-MPCR detection system was first verified by 100 clinical isolates. The sensitivity of the CP-MPCR detection system was then detected by using cultured bacteria preparations and has been confirmed with a high sensitivity of 10³ to 10⁴ CFU/mL, among them, the sensitivity of the CP-MPCR for Vibrio cholerae and S. flexneri can even achieve 10² CFU/mL. Sixty anal swab samples collected from Suzhou CDC and 16 enrichment cultured solutions of food samples collected from the Suzhou Food Inspection and Testing Center were tested using the CP-MPCR system. A total of 32 positive results were detected. PRACTICAL APPLICATION: Food poisoning incidents occur frequently around the world, mainly because of the contamination of food by pathogenic bacteria and serious harm to human health. The method provided in this study can detect 11 foodborne pathogens in food, which can effectively prevent the spread of pathogenic microorganisms. At the same time, for the food poisoning incident that has already occurred, this method can be used for diagnosis to find out the cause.

A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections

With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.

Progress of electrospray ionization and rapid evaporative ionization mass spectrometric techniques for the broad-range identification of microorganisms

Electrospray ionization and rapid evaporative ionization mass spectrometric techniques have attracted much attention in the identification of microorganisms, and in the diagnosis of bacterial infections from clinical samples.

Detecting and Discriminating Shigella sonnei Using an Aptamer-Based Fluorescent Biosensor Platform

In this paper, a Whole-Bacteria SELEX (WB-SELEX) strategy was adopted to isolate specific aptamers against Shigella sonnei. Real-time PCR amplification and post-SELEX experiment revealed that the selected aptmers possessed a high binding affinity and specificity for S. sonnei. Of the 21 aptamers tested, the C(t) values of the SS-3 and SS-4 aptamers (Ct = 13.89 and Ct = 12.23, respectively) had the lowest value compared to other aptamer candidates. The SS-3 and SS-4 aptamers also displayed a binding affinity (K_D) of 39.32 ± 5.02 nM and 15.89 ± 1.77 nM, respectively. An aptamer-based fluorescent biosensor assay was designed to detect and discriminate S. sonnei cells using a sandwich complex pair of SS-3 and SS-4. The detection of S. sonnei by the aptamer based fluorescent biosensor platform consisted of three elements: (1) 5’amine-SS-4 modification in a 96-well type microtiter plate surface (N-oxysuccinimide, NOS) as capture probes; (2) the incubation with S. sonnei and test microbes in functionalized 96 assay wells in parallel; (3) the readout of fluorescent activity using a Cy5-labeled SS-3 aptamer as the detector. Our platform showed a significant ability to detect and discriminate S. sonnei from other enteric species such as E. coli, Salmonella typhimurium and other Shigella species (S. flexneri, S. boydii). In this study, we demonstrated the feasibility of an aptamer sensor platform to detect S. sonnei in a variety of foods and pave the way for its use in diagnosing shigellosis through multiple, portable designs.

Emerging technologies for the clinical microbiology laboratory

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.

Salmonella, Shigella, and yersinia

Salmonella, Shigella, and Yersinia cause a well-characterized spectrum of disease in humans, ranging from asymptomatic carriage to hemorrhagic colitis and fatal typhoidal fever. These pathogens are responsible for millions of cases of food-borne illness in the United States each year, with substantial costs measured in hospitalizations and lost productivity. In the developing world, illness caused by these pathogens is not only more prevalent but also associated with a greater case-fatality rate. Classic methods for identification rely on selective media and serology, but newer methods based on mass spectrometry and polymerase chain reaction show great promise for routine clinical testing.

Portable evanescent wave fiber biosensor for highly sensitive detection of Shigella

A portable evanescent wave fiber biosensor was developed to achieve the rapid and highly sensitive detection of Shigella. In this study, a DNA probe was covalently immobilized onto fiber-optic biosensors that can hybridize with a fluorescently labeled complementary DNA. The sensitivity of detection for synthesized oligonucleotides can reach 10(-10) M. The surface of the sensor can be regenerated with 0.5% sodium dodecyl sulfate solution (pH 1.9) for over 30 times without significant deterioration of performance. The total analysis time for a single sample, including the time for measurement and surface regeneration, was less than 6 min. We employed real-time polymerase chain reaction (PCR) and compared the results of both methods to investigate the actual Shigella DNA detection capability of the fiber-optic biosensor. The fiber-optic biosensor could detect as low as 10(2) colony-forming unit/mL Shigella. This finding was comparable with that by real-time PCR, which suggests that this method is a potential alternative to existing detection methods.

Profile of Volatile Components of Hydrodistilled and Extracted Leaves of Jacaranda acutifolia and their Antimicrobial Activity Against Foodborne Pathogens

Volatile constituents of the essential oil and n-hexane extract of Jacaranda acutifolia Humb. and Bonpl. (Bignoniaceae) leaves were determined, and their antimicrobial activities were investigated using an agar diffusion method. The minimum inhibitory concentrations (MIC) were determined and compared with those of standard antibiotics (penicillin, gentamicin and nystatin). The chemical composition of the oils was analyzed by capillary gas chromatography (GLC-FID) and gas chromatography–mass spectrometry (GLC-MS). Thirty-four components, comprising almost 93.8% of the total peak area, were identified in the leaf essential oil. The main components were methyl linolenate (26.7%), 1-octen-3-ol (10.8%), methyl phenyl acetate (9.9%), β-linalool (5.5%) and palmitic acid (4.7%). The n-hexane extract revealed similar oil constituents, but also p-benzoquinone, phenyl acetic acid, resorcinol and homogentisic acid. The oil showed some activity against Staphylococcus aureus and Escherichia coli with MIC values of 2.2 and 2.9 mg/mL, respectively, and moderate activity against Candida albicans, Salmonella typhimurium and Shigella flexneri. The n-hexane extract showed moderate activities against all tested microorganisms, with MIC values ranging from 3.5 to 10.2 mg/mL. The antimicrobial activities of the hydrodistilled and extracted leaves make their local traditional uses rational.

Rapid detection and differentiation of human noroviruses using RT-PCR coupled to electrospray ionization mass spectrometry

The goal of this study was to develop an assay for the detection and differentiation of noroviruses using RT-PCR followed by electrospray ionization mass spectrometry (ESI-MS). Detection of hepatitis A virus was also considered. Thirteen primer pairs were designed for use in this assay and a reference database was created using GenBank sequences and reference norovirus samples. The assay was tested for inclusivity and exclusivity using 160 clinical norovirus samples, 3 samples of hepatitis A virus and 3 other closely related viral strains. Results showed that the assay was able to detect norovirus with a sensitivity of 92% and a specificity of 100%. Norovirus identification at the genogroup level was correct for 98% of samples detected by the assay and for 75% of a subset of samples (n = 32) compared at the genotype level. Identification of norovirus genotypes is expected to improve as more reference samples are added to the database. The assay was also capable of detecting and genotyping hepatitis A virus in all 3 samples tested. Overall, the assay developed here allows for detection and differentiation of noroviruses within one working day and may be used as a tool in surveillance efforts or outbreak investigations.

Assessment criteria and approaches for rapid detection methods to be used in the food industry

The number of commercially available kits and methods for rapid detection of foodborne pathogens continues to increase at a considerable pace, and the diversity of methods and assay formats is reaching a point where it is very difficult even for experts to weigh the advantages and disadvantages of different methods and to decide which methods to choose for a certain testing need. Although a number of documents outline quantitative criteria that can be used to evaluate different detection methods (e.g., exclusivity and inclusivity), a diversity of criteria is typically used by industry to select specific methods that are used for pathogen detection. This article is intended to provide an overall outline of criteria that the food industry can use to evaluate new rapid detection methods, with a specific focus on nucleic acid-based detection methods.

Current trends in detecting non-O157 Shiga toxin-producing Escherichia coli in food

Non-O157 Shiga toxin-producing Escherichia coli (non-O157 STEC) strains are increasingly recognized as important foodborne pathogens worldwide. Together with E. coli O157:H7, six additional STEC serogroups (O26, O45, O103, O111, O121, and O145) are now regulated as adulterants in certain raw beef products in the United States. However, effective detection and isolation of non-O157 STEC strains from food matrices remain challenging. In the past decade, great attention has been paid to developing rapid and reliable detection methods for STEC in general (targeting common virulence factors) and specific STEC serogroups in particular (targeting serogroup-specific traits). This review summarizes current trends in detecting non-O157 STEC in food, including culture, immunological, and molecular methods, as well as several novel technologies.