Lessons learned with molecular methods targeting the BCSP-31 membrane protein for diagnosis of human brucellosis

DNA Sensor for the Detection of Brucella spp. Based on Magnetic Nanoparticle Markers

Due to the limitations of conventional Brucella detection methods, including safety concerns, long incubation times, and limited specificity, the development of a rapid, selective, and accurate technique for the early detection of Brucella in livestock animals is crucial to prevent the spread of the associated disease. In the present study, we introduce a magnetic nanoparticle marker-based biosensor using frequency mixing magnetic detection for point-of-care testing and quantification of Brucella DNA. Superparamagnetic nanoparticles were used as magnetically measured markers to selectively detect the target DNA hybridized with its complementary capture probes immobilized on a porous polyethylene filter. Experimental conditions like density and length of the probes, hybridization time and temperature, and magnetic binding specificity, sensitivity, and detection limit were investigated and optimized. Our sensor demonstrated a relatively fast detection time of approximately 10 min, with a detection limit of 55 copies (0.09 fM) when tested using DNA amplified from Brucella genetic material. In addition, the detection specificity was examined using gDNA from Brucella and other zoonotic bacteria that may coexist in the same niche, confirming the method's selectivity for Brucella DNA. Our proposed biosensor has the potential to be used for the early detection of Brucella bacteria in the field and can contribute to disease control measures.

Increased serum piwi-interacting RNAs as a novel potential diagnostic tool for brucellosis

Background

Piwi-interacting RNAs (piRNAs) have emerged as potential novel indicators for various diseases; however, their diagnostic value for brucellosis remains unclear. This study aimed to evaluate the diagnostic potential of altered serum piRNAs in patients with brucellosis.

Methods

Illumina sequencing via synthesis (SBS) technology was used to screen the serum piRNA profile in brucellosis patients, and markedly dysregulated piRNAs were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) assay in two sets from a cohort of 73 brucellosis patients and 65 controls.

Results

Illumina SBS technology results showed that seven piRNAs were markedly elevated in brucellosis patients compared to normal controls. The seven upregulated piRNAs were further validated individually by qRT-PCR, of which three piRNAs (piR-000753, piR-001312, and piR-016742) were confirmed to be significantly and steadily increased in the patients (> 2-fold, P < 0.01). The area under the receiver operating characteristic (ROC) curve (AUCs) for the three piRNAs ranged from 0.698 to 0.783. The AUC for the three piRNAs combination was 0.772, with a specificity of 86% and a positive predictive value of 90%, respectively.

Conclusions

The three-piRNA panel identified in this study has potential as a novel blood-based auxiliary tool for brucellosis detection.

Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion

Rhomboids are intramembrane serine proteases highly conserved in the three domains of life. Their key roles in eukaryotes are well understood but their contribution to bacterial physiology is still poorly characterized. Here we demonstrate that Brucella abortus, the etiological agent of the zoonosis called brucellosis, encodes an active rhomboid protease capable of cleaving model heterologous substrates like Drosophila melanogaster Gurken and Providencia stuartii TatA. To address the impact of rhomboid deletion on B. abortus physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. About 50% of the B. abortus predicted proteome was identified by quantitative proteomics under two experimental conditions and 108 differentially represented proteins were detected. Membrane associated proteins that showed variations in concentration in the mutant were considered as potential rhomboid targets. This class included nitric oxide reductase subunit C NorC (Q2YJT6) and periplasmic protein LptC involved in LPS transport to the outer membrane (Q2YP16). Differences in secretory proteins were also addressed. Differentially represented proteins included a putative lytic murein transglycosylase (Q2YIT4), nitrous-oxide reductase NosZ (Q2YJW2) and high oxygen affinity Cbb3-type cytochrome c oxidase subunit (Q2YM85). Deletion of rhomboid had no obvious effect in B. abortus virulence. However, rhomboid overexpression had a negative impact on growth under static conditions, suggesting an effect on denitrification enzymes and/or high oxygen affinity cytochrome c oxidase required for growth in low oxygen tension conditions.

Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping

BACKGROUND

The detection and identification of single nucleotide polymorphism (SNP) is essential for determining patient disease susceptibility and the delivery of medicines targeted to the individual. At present, SNP genotyping technology includes Sanger sequencing, TaqMan-probe quantitative polymerase chain reaction (qPCR), amplification-refractory mutation system (ARMS)-PCR, and Kompetitive Allele-Specific PCR (KASP). However, these technologies have some disadvantages: the high cost of development and detection, long and time consuming protocols, and high false positive rates. Focusing on these limitations, we proposed a new SNP detection method named universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR). In this method, only two types of fluorescence-labeled probes were used for SNP genotyping, thus greatly reducing the cost of development and detection for SNP genotyping.

RESULTS

In the amplification process of UPIP-qPCR, unlabeled intermediate primers with template-specific recognition functions could trigger probe hydrolysis and specific signal release. UPIP-qPCR can be used successfully and widely for SNP genotyping. The sensitivity of UPIP-qPCR in SNP genotyping was 0.01 ng, the call rate was more than 99.1%, and the accuracy was more than 99.9%. High-throughput DNA microarrays based on intermediate primers can be used for SNP genotyping.

CONCLUSION

This novel approach is both cost effective and highly accurate; it is a reliable SNP genotyping method that would serve the needs of the clinician in the provision of targeted medicine.

Spatial prediction of human brucellosis (HB) using a GIS-based adaptive neuro-fuzzy inference system (ANFIS)

OBJECTIVE

This study pursues three main objectives: 1) exploring the spatial distribution patterns of human brucellosis (HB); 2) identifying parameters affecting the disease spread; and 3) modeling and predicting the spatial distribution of HB cases in 2012-2016 and 2017-2018, respectively, in rural districts of Mazandaran province, Iran.

METHODS

We collected data on the disease incidence, demography, ecology, climate, topography, and vegetation. Using the Global Moran's I statistic, we measured spatial autocorrelation between log (number of HB cases). We applied the Getis-Ord G_i^* statistic to identify areas with high and low risk of the disease. To investigate the relationships between the factors affecting the incidence of HB as input variables together and the factors with the log (number of HB cases) as an output variable, we used the statistical linear regression model and the Pearson correlation coefficient. Then, we implemented a GIS-based adaptive neuro-fuzzy inference system (ANFIS) with two subtractive clustering and fuzzy c-means (FCM) clustering methods to model and predict the spatial distribution of HB.

RESULTS

Global Moran's I spatial autocorrelation analysis indicated that the type of HB distribution is clustered in all years except 2014 and 2017, which are random. According to the Getis-Ord G_i^* analysis, the location of the hot spots varied during 2012-2018. In 2012 and 2013, most of the hot spots were seen in the west of the province. While in 2018, they were mostly concentrated in the eastern regions of the province. The linear regression model indicated that the parameters affecting the incidence of HB are independent of each other and can explain only 25.3% of the total changes in the log (number of HB cases). The results of the Pearson correlation coefficient showed that there were positive relationships between vegetation, log (population), and the number of sheep and cattle (p-value < 0.05). The above-mentioned factors had the strongest positive correlation with the log (number of HB cases) (p-value < 0.01). These results may be due to the fact that vegetation regions are suitable for livestock grazing, attracting large crowds of people. Therefore, this will increase HB cases. We compared the results of subtractive clustering and FCM clustering methods by evaluation criteria (e.g., linear correlation coefficient (LCC) and mean absolute error (MAE)) in two phases of development and assessment of the ANFIS model. In the assessment phase, we predicted the spatial distribution of log (number of HB cases) in 2017 and 2018 by subtractive clustering (R² = 0.699, LCC or R = 0.692, MAE = 0.509, MSE = 0.455) and by FCM clustering (R² = 0.704, LCC or R = 0.697, MAE = 0.512, MSE = 0.448) that showed FCM clustering outperformed the subtractive clustering.

CONCLUSION

The findings may have important implications for public health. The emergence of the hot spots in the east of the province can be a warning to the health system. Health authorities can use the findings of this study to predict the spread of HB and perform HB prevention programs. They can also investigate the factors affecting the prevalence of the disease, identify high-risk areas, and ultimately allocate resources to high-risk regions.

Comparative study of IS711 and bcsp31-based polymerase chain reaction (PCR) for the diagnosis of human brucellosis in whole blood and serum samples

BACKGROUND

Clinical diagnosis of human brucellosis (HB) is often difficult due to non-specific symptoms. Immunological tests have been the most common method used in HB diagnosis, but molecular methods based on quantitative polymerase chain reaction (qPCR) have largely replaced these diagnostic methods. The aim of this study was to validate a HB diagnostic qPCR method; assessing different target Brucella genes, and the influence of biological matrices (serum vs. whole blood) on analytical parameters.

MATERIAL AND METHODS

Two target genes, IS711 and bcsp31, for HB molecular diagnosis were evaluated, together with biological matrix type (whole blood and serum) using samples spiked with Brucella abortus. In addition, diagnostic parameters of this qPCR method were evaluated in paired whole blood and serum samples from patients with suspected HB.

RESULTS

Both genes could be potential diagnostic targets, but IS711 showed a lower limit of detection. In spiked matrix experiments, whole blood showed a lower limit of detection than serum after probit regression (224 vs. 3681 CFU/mL) and ANOVA analysis showed a significant (p < 0.001) difference between the Cq of whole blood at all dilutions and that of serum. In 12 paired clinical samples, no serum samples and only one whole blood sample tested positive for Brucella using this qPCR detection method.

CONCLUSIONS

This standardized qPCR-based Brucella detection method could improve diagnosis of HB, serving as a rapid, highly sensitive, and specific test. Whole blood is better suited to qPCR-based HB diagnosis due to the presence of higher target DNA loads in this matrix, compared to serum.

Combined nucleic acid assays for diagnosis of A19 vaccine-caused human brucellosis

Brucellosis is a common zoonotic disease caused by Brucella and is an epidemic worldwide. Currently, the most effective way to prevent and control the disease in animals is to use live, attenuated vaccines A19 strain. In China, the live attenuated Brucella abortus vaccine is widely used in animal immunization. To detect and confirm which vaccine strain caused the infection, we developed a new method to distinguish A19 strain from non-A19 strains. By comparing the genomic sequences of A19 and wild strain 2,308, we identified signature sequences that are unique to A19. A PCR assay for specific A19 identification was developed based on the genetic marker ABC transporter permease gene. Samples from the outbreak patients were then analysed using the universal quantitative PCR and A19-specific PCR assay, and the A19 strain was successfully identified in them, providing pathogenic evidence of the vaccine-derived infection outbreak. This combined A19-specific differential diagnosis method can provide a means to distinguish between animal vaccine immunization, natural infection and human infection by the vaccine strain. This strategy also has applications in diagnosis, epidemiology and surveillance of A19-related immunizations or infections.

A novel recombinant multiepitope protein candidate for the diagnosis of brucellosis: A pilot study

Brucellosis is a zoonotic disease transmitted to humans from infected animals. As a systemic disease, it can harm any organ or system of the host body. Human brucellosis presents with various clinical symptoms, which makes diagnosis challenging. Serological diagnosis of brucellosis is based on ELISA or agglutination tests, which use colorimetry to detect antibodies generated against lipopolysaccharide (LPS) or extracts from whole-cell bacteria. To construct a protein that can specifically recognize Brucella, we analyzed hydrophilicity, accessibility, flexibility, antigenicity, and β-turns using a protein network server. Then, we chose the most abundant immunodominant epitopes of the outer membrane proteins omp31, BP26, omp2b and omp16. Based on the sequences of these major epitopes, fifteen major immunodominant epitopes were selected to construct a synthetic Brucella recombinant multiepitope outer membrane protein (rOmp) gene. This recombinant gene was expressed in E. coli, and the produced protein was purified by Ni-NTA affinity purification. The purified protein was tested in an indirect ELISA assay, demonstrating a high level of sensitivity and specificity. This technique is creating a unique antigen that, coupled with overexpression and low-cost purification, offers a promising diagnosis of both human and animal brucellosis, with the potential to avoid the disadvantages of whole brucellosis-antigen-based assays.

Laboratory Diagnosis of Human Brucellosis

The clinical presentation of brucellosis in humans is variable and unspecific, and thus, laboratory corroboration of the diagnosis is essential for the patient's proper treatment. The diagnosis of brucellar infections can be made by culture, serological tests, and nucleic acid amplification assays. Modern automated blood culture systems enable detection of acute cases of brucellosis within the routine 5- to 7-day incubation protocol employed in clinical microbiology laboratories, although a longer incubation and performance of blind subcultures may be needed for protracted cases. Serological tests, though they lack specificity and provide results that may be difficult to interpret in individuals repeatedly exposed to Brucella organisms, nevertheless remain a diagnostic cornerstone in resource-poor countries. Nucleic acid amplification assays combine exquisite sensitivity, specificity, and safety and enable rapid diagnosis of the disease. However, long-term persistence of positive molecular test results in patients that have apparently fully recovered is common and has unclear clinical significance and therapeutic implications. Therefore, as long as there are no sufficiently validated commercial tests or studies that demonstrate an adequate interlaboratory reproducibility of the different homemade PCR assays, cultures and serological methods will remain the primary tools for the diagnosis and posttherapeutic follow-up of human brucellosis.

Prediction of Human Brucellosis in China Based on Temperature and NDVI

Brucellosis occurs periodically and causes great economic and health burdens. Brucellosis prediction plays an important role in its prevention and treatment. This paper establishes relationships between human brucellosis (HB) and land surface temperature (LST), and the normalized difference vegetation index (NDVI). A seasonal autoregressive integrated moving average with exogenous variables (SARIMAX) model is constructed to predict trends in brucellosis rates. The fitted results (Akaike Information Criterion (AIC) = 807.58, Schwarz Bayes Criterion (SBC) = 819.28) showed obvious periodicity and a rate of increase of 138.68% from January 2011 to May 2016. We found a significant effect between HB and NDVI. At the same time, the prediction part showed that the highest monthly incidence per year has a decreasing trend after 2015. This may be because of the brucellosis prevention and control measures taken by the Chinese Government. The proposed model allows the early detection of brucellosis outbreaks, allowing more effective prevention and control.

Optimization and validation of a real-time polymerase chain reaction protocol for the diagnosis of human brucellosis

Due to limitations in commercial diagnostic methods, this study aimed to develop a reliable real-time polymerase chain reaction (Rt-PCR) assay for early diagnosis of brucellosis. Optimization of the Rt-PCR method was performed on serum samples spiked by Brucella melitensis with different densities ranging from 10¹ to 10⁸ colony-forming units (cfu)/mL; each density was prepared in ten samples. The limit of detection was investigated by using Thermo DNA extraction kit with Maxima SYBR Green Rt-PCR and two TaqMan probe-based Rt-PCR protocols performed by QuantiTect and TEMPase multiplex PCR master mixes in two thermal cyclers, which were Rotor-Gene and Bio-Rad. The validation of the optimized protocol was carried on 20 brucellosis-negative samples and 20 samples spiked with B. melitensis by using a combination of Thermo DNA extraction kit with TEMPase PCR master mix. SYBR Green Rt-PCR yielded positive results on all samples having ≥ 10⁴ cfu/mL of B. melitensis in both thermal cyclers. Its limit of detection was 112 DNA copies per reaction. The positivity of both probe-based Rt-PCR protocols was 100% and 80% on the samples having 10³ cfu/mL and 10² cfu/mL of B. melitensis, respectively. The limit of detection of probe-based protocols was defined as 4 DNA copies per reaction. The optimized Rt-PCR protocol showed high-level accuracy, precision, specificity, and sensitivity, each having a rate of 100%. The current study indicated that the TaqMan probe-based Rt-PCR protocol optimized and validated with serum samples can be reliably used for early diagnosis of brucellosis.

Comparisons of brucellosis between human and veterinary medicine

Brucellosis is the world's most widespread zoonosis, but also ranks as one of the seven most neglected diseases, according to the World Health Organization. Additionally, it is recognized as the world's most common laboratory-acquired infection. There are a reported 500,000 incident cases of human brucellosis per year. However, true incidence is estimated to be 5,000,000 to 12,500,000 cases annually. Once diagnosed, focus is directed at treating individual patients with antibiotic regimes, yet overall neglecting the animal reservoir of disease. Countries with the highest incidence of human brucellosis are Syria (1,603.4 cases per 1,000,000 individuals), Mongolia (391.0), and Tajikistan (211.9). Surveillance on animal populations is lacking in many developed and developing countries. According to the World Animal Health Information Database, Mexico had the largest number of reported outbreaks, 5,514 in 2014. Mexico is followed by China (2,138), Greece (1,268), and Brazil (1,142). The majority of these outbreaks is Brucella abortus, the etiologic agent of bovine brucellosis. Brucellosis is an ancient disease that still plagues the world. There are still knowledge gaps and a need for better diagnostics and vaccines to make inroads towards control and eradication.

Comprehensive evaluation of blood-brain barrier-forming micro-vasculatures: Reference and marker genes with cellular composition

Primary brain microvessels (BrMV) maintain the cellular characters and molecular signatures as displayed in vivo, and serve as a vital tool for biomedical research of the blood-brain barrier (BBB) and the development/optimization of brain drug delivery. The variations of relative purities or cellular composition among different BrMV samples may have significant consequences in data interpretation and research outcome, especially for experiments with high-throughput genomics and proteomics technologies. In this study, we aimed to identify suitable reference gene (RG) for accurate normalization of real-time RT-qPCR analysis, and determine the proper marker genes (MG) for relative purity assessment in BrMV samples. Out of five housekeeping genes, β-actin was selected as the most suitable RG that was validated by quantifying mRNA levels of alpha-L-iduronidase in BrMV isolated from mice with one or two expressing alleles. Four marker genes highly/selectively expressed in BBB-forming capillary endothelial cells were evaluated by RT-qPCR for purity assessment, resulting in Cldn5 and Pecam1 as most suitable MGs that were further confirmed by immunofluorescent analysis of cellular components. Plvap proved to be an indicator gene for the presence of fenestrated vessels in BrMV samples. This study may contribute to the building blocks toward overarching research needs on the blood-brain barrier.