High Resolution Melt Assays to Detect and Identify Vibrio parahaemolyticus, Bacillus cereus, Escherichia coli, and Clostridioides difficile Bacteria

High-Resolution Melting PCR as a Fast and Simple Molecular Biology-Based Method for the Identification of Hypervirulent Clostridioides difficile Strains Directly in Stool Samples

Clostridioides difficile became one of the main causes of nosocomial infections in all clinical settings worldwide, especially among patients undergoing antibiotic therapy. The incidence and severity of C. difficile infections, from mild diarrhea to life-threatening pseudomembranous colitis, correlate with the spread of the hypervirulent binary toxin (CDT)-producing strains. The use of the real-time HRM-PCR method enables the identification of hypervirulent C. difficile strains directly in the diarrheal stool samples of patients suspected of being infected with this bacterium. For this purpose, the cdtA and cdtB genes encoding CDT subunits, as well as the species-specific gluD gene, were detected to identify the presence of this bacterium in the tested samples. The sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) of the established method were also assessed. The obtained results were compared with the results of eazyplex® C. difficile complete test (AmplexDiagnostics GmbH) based on the LAMP method, used in standard microbiological diagnostics. The values of the assessed diagnostic parameters for the detected genes ranged from 58.82% to 98.85%. The lowest value (58.82%) was obtained for the PPV of cdtB and the highest (98.85%) for the NPV of this gene. The real-time HRM-PCR method enables fast and simple detection of the investigated genes of hypervirulent C. difficile strains and, after careful optimization, may demonstrate high potential for usefulness in routine microbiological diagnostics.

Synergistic action of bacteriophage and metabolites of Pseudomonas fluorescens JB3B and Streptomyces thermocarboxydus 18PM against Enterotoxigenic Escherichia coli and Bacillus cereus and their biofilm

BACKGROUND

Foodborne disease and food spoilage are the prime public health issue and food security round the globe. Significant disease outbreaks mostly linked to the existence of pathogenic bacteria that extremely challenging due to the persistence of biofilm-forming. Proteins and bacterial metabolites have been shown to have good antibacterial activity and effectively removal bacterial biofilm. Recently, bacteriophage and their encoded lytic proteins such as lysin have attracted attention as potential alternative agent to control undesirable pathogens in human body infection, increasing food safety as advance preservations and medical treatment such as phage therapy. For these reasons, the efficacy of bacteriophage and their potential in combination with bacterial metabolites from Phyllosphere and Actinomycetes bacteria (Pseudomonas fluorescens JB3B and Streptomyces thermocarboxydus 18PM crude extracts) was the aim of this present study.

RESULTS

In this study, bacteriophage BC-VP (1.28 ± 0.29 × 1011 PFU/ml) and ETEC-phage-TG (8.9 ± 2.19 × 108 PFU/ml) isolated from artificial lake water from previous study showed potential activity to control Bacillus cereus (BC) and Enterotoxigenic Escherichia coli (ETEC) population. The combination of BC-VP with metabolite (P. fluorescens JB3B and S. thermocarboxydus 18PM) which were known from previous study had antibiofilm activities were able to inhibit (86.1%; 83.3%) and destruct (41%; 45.5%) biofilm formation of B. cereus respectively. Likewise, the synergy of bacteriophage ETEC-phage-TG with the same crude extract also showed promising activity against biofilm of ETEC with percentage of inhibition (81.9%; 76.4%) and percentage of destruction (54.1%; 44.4%). Application in various food, combination of BC-VP and bacterial metabolite extract (P. fluorescens JB3B; S. thermocarboxydus 18PM) were able to reduce Bacillus cereus population in mashed potato (99.6%; 99.4%) at cold temperature (4 °C) and (68.9%; 56.6%) at room temperature (28 °C), boiled pasta (99.5%; 99.4%) and (84.7%; 75.7%), also soymilk (96.9%; 96.7%) and (42.4%; 39.4%) respectively. Likewise, combination of ETEC-phage-TG and bacterial metabolite (P. fluorescens JB3B; S. thermocarboxydus 18PM) potentially reduced ETEC population after two different temperatures (4 °C and 28 °C) incubation in bean sprouts (TFTC; TFTC) and (47.5%; 49.1%), chicken meat (TFTC; TFTC) and (58.1%; 54%), also minced beef (99.5%; 99.4%) and (41.1%; 28%). GC-MS determination performed, oxalic acid, phenol, phenylethyl alcohol, N-hexadecanoic acid, and pyrolol[1,2-a]pyrazine-1,4-dione, hexadro-3-92-methylpropyl was the most active compound in P. fluorescens JB3B. 2,4-Di-tert-butylphenol, phenyl acetic acid, N-Hexadecanoic acid, pyrolol[1,2-a]pyrazine-1,4-dione, hexadro-3-92-methylpropyl, and Bis(2-ethylhexyl) phthalate was most active compound in the S. thermocarboxydus 18PM isolates.

CONCLUSIONS

The combination of isolated bacteriophages and bacterial metabolite showed promising results to be used as biocontrol candidate to overcome biofilm formed by foodborne and food spoilage bacteria using their ability to produce antibiofilm compounds and lytic activity. In addition, this combination also potentially reduces the use or replace the drawbacks of common application such as antibiotic treatment.

Quadruplex qPCR for detection and discrimination of C. Coli,C. fetus, and C. Jejuni from other Campylobacter species in chicken and sheep meat

Campylobacter is gram-negative bacteria considered the predominant genera isolated from poultry samples and associated with gastroenteritis. Due to the problems in conventional cultural methods of time-consuming and technically demanding requirements, a rapid and feasible method for their identification and discrimination of the closely related spp. Including Campylobacter coli, Campylobacter fetus, and Campylobacter jejuni is needed. This study analyzes the chicken and sheep meats samples (n = 125) using culture and pre-enrichment-based Quadraplex real-time PCR by targeting OrfA, CstA, HipO, and 16 S rRNA genes of C. coli, C. fetus, C. jejuni and Campylobacter spp. Respectively. The analysis of 125 chicken and sheep meat samples by culture and real-time PCR showed high concordance between the results of the two methods. The present study show high prevalence of Campylobacter species (35% and 32% from chicken and meat respectively) of which C. jejuni were the most abundant. Reaction efficiencies were between 90 and 110%, and detect as low as 8.9 fg in C. jejuni. The need for quick detection and discrimination methods in sheep and chicken meat can be met using the described Quadraplex real-time PCR methodology.

Development of Polymerase Chain Reaction-High-Resolution Melt Assay for Waterborne Pathogens Legionella pneumophila, Vibrio parahaemolyticus, and Camplobacter jejuni

Legionella pneumophila is the waterborne pathogen primarily responsible for causing both Pontiac Fever and Legionnaire's Disease in humans. L. pneumophila is transmitted via aerosolized water droplets. The purpose of this study was to design and test primers to allow for rapid polymerase chain reaction (PCR) melt detection and identification of this infectious agent in cases of clinical or emergency response detection. New PCR primers were designed for this species of bacteria; the primer set was purchased from IDT and the target bacterial DNA was purchased from ATCC. The L. pneumophila primers targeted the macrophage infectivity potentiator gene (mip), which inhibits macrophage phagocytosis. The primers were tested for specificity, repeatability, and sensitivity using PCR-high-resolution melt (HRM) assays. The primer set was found to be specific to the designated bacteria and did not amplify the other twenty-one species from the panel. The L. pneumophila assay was able to be multiplexed. The duplex assay consists of primers for L. pneumophila and Vibrio parahaemolyticus, which are both waterborne pathogens. The triplex assay consists of primers for L. pneumophila, V. parahaemolyticus, and Campylobacter jejuni. The unique melting temperature for the L. pneumophila primer assay is 82.84 ± 0.19 °C, the C. jejuni assay is 78.10 ± 0.58 °C, and the V. parahaemolyticus assay is 86.74 ± 0.65 °C.

Improving bacteria identification from digital melt assay via oligonucleotide-based temperature calibration

BACKGROUND

Bacterial infections, especially polymicrobial infections, remain a threat to global health and require advances in diagnostic technologies for timely and accurate identification of all causative species. Digital melt - microfluidic chip-based digital PCR combined with high resolution melt (HRM) - is an emerging method for identification and quantification of polymicrobial bacterial infections. Despite advances in recent years, existing digital melt instrumentation often delivers nonuniform temperatures across digital chips, resulting in nonuniform digital melt curves for individual bacterial species. This nonuniformity can lead to inaccurate species identification and reduce the capacity for differentiating bacterial species with similar digital melt curves.

RESULTS

We introduce herein a new temperature calibration method for digital melt by incorporating an unamplified, synthetic DNA fragment with a known melting temperature as a calibrator. When added at a tuned concentration to an established digital melt assay amplifying the commonly targeted 16S V1 - V6 region, this calibrator produced visible low temperature calibrator melt curves across-chip along with the target bacterial melt curves. This enables alignment of the bacterial melt curves and correction of heating-induced nonuniformities. Using this calibration method, we were able to improve the uniformity of digital melt curves from three causative species of bacteria. Additionally, we assessed calibration's effects on identification accuracy by performing machine learning identification of three polymicrobial mixtures comprised of two bacteria with similar digital melt curves in different ratios. Calibration greatly improved mixture composition prediction.

SIGNIFICANCE

To the best of our knowledge, this work represents the first DNA calibrator-supplemented assay and calibration method for nanoarray digital melt. Our results suggest that this calibration method can be flexibly used to improve identification accuracy and reduce melt curve variabilities across a variety of pathogens and assays. Therefore, this calibration method has the potential to elevate the diagnostic capabilities of digital melt toward polymicrobial bacterial infections and other infectious diseases.

Cheilitis in an atopic dermatitis patient associated with co-infection of Staphylococcus pseudintermedius and Staphylococcus aureus

BACKGROUND

Atopic dermatitis (AD) is an inflammatory skin condition distinguished by an activated Th2 immune response. The local skin microbial dysbiosis is a contributing factor to the development of AD. The pathogenic coagulase-positive Staphylococcus aureus is the primary species responsible for the progression of AD. Even though Staphylococcus pseudintermedius is an animal-origin pathogen, it is increasingly becoming a source of concern in human diseases. As another coagulase-positive Staphylococci, it is crucial to pay more attention to S. pseudintermedius isolated from the lesion site.

RESULTS

In our investigation, we presented a case of cheilitis in a patient with atopic dermatitis (AD). We utilized culture and next-generation genomic sequencing (NGS) to identify the bacteria present on the skin swabs taken from the lip sites both prior to and following treatment. Our findings indicated that the predominant bacteria colonizing the lesion site of AD were S. pseudintermedius and S. aureus, both of which were eradicated after treatment. The Multi-locus sequence typing (MLST) of S. pseudintermedius and S. aureus demonstrated coordinated antibiotic susceptibility, with ST2384 and ST22 being the respective types. Although the skin abscess area resulting from S. pseudintermedius infection was significantly smaller than that caused by S. aureus in mice, the expression of cytokines interleukin-4 (IL-4) and interleukin-5 (IL-5) were significantly higher in the S. pseudintermedius-infected mice.

CONCLUSIONS

The S. pseudintermedius strain isolated from the lesion site of the AD patient exhibited a higher expression of IL-4 and IL-5 when colonized on mouse skin, as compared to S. aureus. This observation confirms that S. pseudintermedius can effectively induce the Th2 response in vivo. Our findings suggest that animal-origin S. pseudintermedius may play a role in the development of AD when colonized on the skin, emphasizing the importance of taking preventive measures when in contact with animals.

Multiplex high-resolution melting assay for simultaneous detection of five key bacterial pathogens in urinary tract infections: A pilot study

The diagnosis of urinary tract infections (UTIs) is usually based on the results of urine culture, but it is time-consuming, labor-intensive and has a low sensitivity. The aim of this study was to develop multiplex high-resolution melting assay (MHRM) for the simultaneous detection of five common bacterial pathogens (Escherichia coli, Klebsiella pneumoniae, Staphylococcus saprophyticus, Enterococcus faecalis, and group B streptococci (GBS)) directly from urine samples. A total of 287 urine specimens were evaluated by HRM assay and the results were compared with the conventional culture method. Five different melt curves generated and differentiated five bacterial pathogens. The detection limit of the MHRM assay was 1.5 × 10³ CFU/ml for E. coli and K. pneumoniae and 1.5 × 10² CFU/ml for S. saprophyticus, E. faecalis and GBS. Compared to culture, the specificity of the MHRM assay ranged from 99.3 to 100%, and sensitivity 100% for all test pathogens. The MHRM assay developed in the current study might be functional tool for the diagnosis of UTIs and has the potential for direct detection of the organism in the clinical samples. Additionally, it creates results in less than 5 h, helping clinicians to start treatment with appropriate antimicrobial agents. This method could be a useful supplement to urine culture.

Simultaneous Detection of Foodborne Pathogens Using a Real-Time PCR Triplex High-Resolution Melt Assay

Foodborne pathogens pose risks to populations all over the world. Pathogens can be used as bioterrorism agents, causing an outbreak that affects many individuals through the consumption of a commonly affected food or beverage. A PCR assay can be used to identify pathogens through their unique melting points using a high-resolution melt assay. Assays can be used to detect the bacteria individually or from a mixture using species-specific primers. An assay was developed to detect and identify three pathogens that routinely cause multistate foodborne outbreaks, as documented by the U.S. Centers for Disease Control and Prevention, Campylobacter jejuni (C. jejuni), Escherichia coli (E. coli), and Salmonella enterica (S. enterica), in single bacterium assays and a multiplex. The primers were targeted to specific and unique gene sequences of each pathogen, including cadF, yedN, and hilA, respectively. Each pathogen was identified by its unique melting temperature in single assays: 78.10 ± 0.58 °C for C. jejuni, 81.96 ± 0.42 °C for E. coli, and 87.55 ± 0.37 °C for S. enterica. The multiplex successfully detected and identified all three of the pathogens with the distinctly separated melt peaks. The PCR high-resolution melt assay also proved to be specific, reproducible, fast, and sensitive in experiments.

Special Issue: Microbiota-Gut-Brain Axis

There is emerging evidence that human health and disease are modulated by the microbiota and their various metabolites, formed through intestinal and gut bacterial metabolism [...].

Development of high-resolution melting (HRM) assay to differentiate the species of Shigella isolates from stool and food samples

Shigella species, a group of intracellular foodborne pathogens, are the main causes of bacillary dysentery and shigellosis in humans worldwide. It is essential to determine the species of Shigella in outbreaks and food safety surveillance systems. The available immunological and molecular methods for identifying Shigella species are relatively complicated, expensive and time-consuming. High resolution melting (HRM) assay is a rapid, cost-effective, and easy to perform PCR-based method that has recently been used for the differentiation of bacterial species. In this study, we designed and developed a PCR-HRM assay targeting rrsA gene to distinguish four species of 49 Shigella isolates from clinical and food samples and evaluated the sensitivity and specificity of the assay. The assay demonstrated a good analytical sensitivity with 0.01–0.1 ng of input DNA template and an analytical specificity of 100% to differentiate the Shigella species. The PCR-HRM assay also was able to identify the species of all 49 Shigella isolates from clinical and food samples correctly. Consequently, this rapid and user-friendly method demonstrated good sensitivity and specificity to differentiate species of the Shigella isolates from naturally contaminated samples and has the potential to be implemented in public health and food safety surveillance systems.

Development of a high resolution melting method based on a novel molecular target for discrimination between Bacillus cereus and Bacillus thuringiensis

Delimitation within the Bacillus cereus group is confusing due to the highly similar genetic background of its constituent bacteria. This study aimed to develop a rapid and efficient method for the identification of Bacillus cereus and Bacillus thuringiensis, two closely related species within the B. cereus group. Using average nucleotide identity analysis (ANI) and ribosomal multilocus sequence typing (rMLST), the authenticity of the genomes of B. cereus and B. thuringiensis was determined. Emetic B. cereus and Bacillus bombysepticus were also included to provide novel genomic insights into the boundaries within the B. cereus group. Using pan-genome analysis, ispD, a novel core and single-copy molecular target, was identified for the differentiation between B. cereus and B. thuringiensis. Based on the single nucleotide polymorphism within ispD, a high resolution melting (HRM) method for the determination of B. cereus and B. thuringiensis was developed. This method can not only distinguish B. cereus and B. thuringiensis, but can also separate B. cereus from other foodborne pathogenic bacteria. The detection limit of this method could reach 1 pg of pure genomic DNA and 3.7 × 10² cfu/mL of pure culture. Moreover, this new method could effectively differentiate B. cereus and B. thuringiensis in spiked, mixed, and real food samples. Collectively, the established HRM method can provide a new reference paradigm for the sensitive and specific nucleic acid detection of pathogens with identical genomes.

Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms

Routinely used typing methods including MLST, rep-PCR and whole genome sequencing (WGS) are time-consuming, costly, and often low throughput. Here, we describe a novel mini-MLST scheme for Eschericha coli as an alternative method for rapid genotyping. Using the proposed mini-MLST scheme, 10,946 existing STs were converted into 1,038 Melting Types (MelTs). To validate the new mini-MLST scheme, in silico analysis was performed on 73,704 strains retrieved from EnteroBase resulting in discriminatory power D = 0.9465 (CI 95% 0.9726-0.9736) for mini-MLST and D = 0.9731 (CI 95% 0.9726-0.9736) for MLST. Moreover, validation on clinical isolates was conducted with a significant concordance between MLST, rep-PCR and WGS. To conclude, the great portability, efficient processing, cost-effectiveness, and high throughput of mini-MLST represents immense benefits, even when accompanied with a slightly lower discriminatory power than other typing methods. This study proved mini-MLST is an ideal method to screen and subgroup large sets of isolates and/or quick strain typing during outbreaks. In addition, our results clearly showed its suitability for prospective surveillance monitoring of emergent and high-risk E. coli clones'.