Identification of Brucella spp. isolates and discrimination from the vaccine strain Rev.1 by MALDI-TOF mass spectrometry

Diagnosis and control of brucellosis through food: The contribution of omics sciences

More than 60 percent of emerging infectious diseases in humans are zoonoses, and about 70 percent of these come from wildlife. In this context, infectious diseases in animals are no longer a problem confined to the livestock and animal health sector but have important repercussions in public health-related risk assessment and management. One of the most relevant risks in the transmission of zoonoses is certainly the consumption of food contaminated with pathogens, especially because of the potential epidemiological relevance of foodborne outbreaks. Brucellosis represents one of the most prevalent zoonoses worldwide and one of the most important foodborne zoonoses, particularly in the Mediterranean and developing countries; The European Union has funded numerous eradication and control programs in at-risk herds. This review aims to analyze current diagnostic methods used in the detection of Brucella in food matrices. It will highlight issues related to the timing and specificity of classical diagnostic methods while also analyzing new diagnostic methods in the current literature. The focus of this work is on emphasizing the potential that integrated omics sciences have in developing early and highly sensitive diagnostic tools. It analyzes strengths and weaknesses and underscores, through a review of recent scientific articles in the "PubMed" and "Google Scholar" databases, the importance of current and future research, especially those based on an omics approach, in providing fundamental biological data and knowledge. This, in turn, could play a crucial role in designing innovative diagnostic tests to complement those currently in use.

Brucella melitensis periprosthetic joint infection

Brucellosis, caused by a facultative intracellular gram-negative coccobacillus, is one of the most common zoonotic infections worldwide. Very rarely, brucellosis can cause periprosthetic joint infections (PJI). In this case-based literature review, we summarize the current medical literature regarding Brucella PJI, with the aim to raise awareness among clinicians, particularly in non-endemic areas. We report a case of a woman with a 3 weeks history of increasing hip pain, who was eventually diagnosed with Brucella PJI. We searched multiple databases to identify all case reports on Brucella PJI in humans published from February, 1983 to December, 2023. A total of 42 cases from 38 published articles were retrieved and summarized, along with our case. Mean age was 65.5 years, with sex ratio nearly one. Almost all patients presented with local symptoms and 56% with systemic symptoms. Only knee (n=30) and hip (n=13) prosthetic joint were involved. If performed, culture showed positive results on synovial fluid (74%), intra- operative tissue (79%), and/or blood (38%). Serological confirmation was obtained in 97%. Antimicrobial treatment consisted of a combination of doxycycline and rifampin in most cases, with in nearly half of the cases the addition of an aminoglycoside. The majority of patients (n=24) were surgically treated with a two stage exchange arthroplasty; although other options were successful as well. Brucella PJI is a rare but potentially severe manifestation of brucellosis. Brucella PJI must be considered in patients from endemic areas, especially when another causative agent has not been isolated. If culture results remain negative, PCR or serology should be performed. To date, there is no uniform recommendation for the duration of antimicrobial therapy nor the preferred surgical procedure. Relapse is possible even with adequate therapy.

Brucellae as resilient intracellular pathogens: epidemiology, host-pathogen interaction, recent genomics and proteomics approaches, and future perspectives

Brucellosis is considered one of the most hazardous zoonotic diseases all over the world. It causes formidable economic losses in developed and developing countries. Despite the significant attempts to get rid of Brucella pathogens in many parts of the world, the disease continues to spread widely. Recently, many attempts proved to be effective for the prevention and control of highly contagious bovine brucellosis, which could be followed by others to achieve a prosperous future without rampant Brucella pathogens. In this study, the updated view for worldwide Brucella distribution, possible predisposing factors for emerging Brucella pathogens, immune response and different types of Brucella vaccines, genomics and proteomics approaches incorporated recently in the field of brucellosis, and future perspectives for prevention and control of bovine brucellosis have been discussed comprehensively. So, the current study will be used as a guide for researchers in planning their future work, which will pave the way for a new world without these highly contagious pathogens that have been infecting and threatening the health of humans and terrestrial animals.

Effect of Tryptic Digestion on Sensitivity and Specificity in MALDI-TOF-Based Molecular Diagnostics through Machine Learning

The digestion of protein into peptide fragments reduces the size and complexity of protein molecules. Peptide fragments can be analyzed with higher sensitivity (often > 102 fold) and resolution using MALDI-TOF mass spectrometers, leading to improved pattern recognition by common machine learning algorithms. In turn, enhanced sensitivity and specificity for bacterial sorting and/or disease diagnosis may be obtained. To test this hypothesis, four exemplar case studies have been pursued in which samples are sorted into dichotomous groups by machine learning (ML) software based on MALDI-TOF spectra. Samples were analyzed in 'intact' mode in which the proteins present in the sample were not digested with protease prior to MALDI-TOF analysis and separately after the standard overnight tryptic digestion of the same samples. For each case, sensitivity (sens), specificity (spc), and the Youdin index (J) were used to assess the ML model performance. The proteolytic digestion of samples prior to MALDI-TOF analysis substantially enhanced the sensitivity and specificity of dichotomous sorting. Two exceptions were when substantial differences in chemical composition between the samples were present and, in such cases, both 'intact' and 'digested' protocols performed similarly. The results suggest proteolytic digestion prior to analysis can improve sorting in MALDI/ML-based workflows and may enable improved biomarker discovery. However, when samples are easily distinguishable protein digestion is not necessary to obtain useful diagnostic results.

A Combination of MALDI-TOF MS Proteomics and Species-Unique Biomarkers' Discovery for Rapid Screening of Brucellosis

Brucellosis is considered to be a zoonotic infection with a predominant incidence in most parts of Iran that may even simply involve diagnostic laboratory personnel. In the present study, we apply matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for rapid and reliable discrimination of Brucella abortus and Brucella melitensis, based on proteomic mass patterns from chemically treated whole-cell analyses. Biomarkers of the low molecular weight proteome in the MALDI-TOF MS spectra were assigned to conserved ribosomal and structural protein families that were found in genome assemblies of B. abortus and B. melitensis in the NCBI database. Significant protein mass signals successfully mapped to ribosomal proteins and structural proteins, such as integration host factor subunit alpha, cold-shock proteins, HU family DNA-binding protein, ATP synthase subunit C, and GNAT family N-acetyltransferase, with specific biomarker peaks that have been identified for each virulent and vaccine strain. Web-accessible bioinformatics algorithms, with a robust data analysis workflow, followed by ribosomal and structural protein mapping, significantly enhanced the reliable assignment of key proteins and accurate identification of Brucella species. Furthermore, clinical samples were analyzed to confirm the most dominant protein biomarker candidates and their relevance for the identifications of B. melitensis and B. abortus. With proper optimization, we envision that the presented MALDI-TOF MS proteomics analyses, coupled with special usage of bioinformatics, could be used as a cost-efficient strategy for the diagnostics of brucellosis and introduce a reliable identification protocol for species of dangerous bacteria.

Molecular characterization and antimicrobial susceptibility testing of clinical and non-clinical Brucella melitensis and Brucella abortus isolates from Egypt

Brucellosis is a highly contagious and incapacitating disease of humans, livestock and wildlife species globally. Treatment of brucellosis in animals is not recommended, and in humans, combinations of antibiotics recommended by the World Health Organization are used. However, sporadic antimicrobial-resistant (AMR) isolates and relapse cases have been reported from different endemic regions. In the current study, molecular characterization and antibiotic susceptibility testing using the microdilution method for 35 B. abortus and B. melitensis strains isolated from humans, milk and animal were carried out. Additionally, Next-Generation-Sequencing (NGS) technology was applied to confirm Brucella at the species level and investigate AMR and pathogenicity-associated determinants. MALDI-TOF seemed to be a rapid and reliable tool for routine identification of brucellae to the genus level; however, DNA-based identification is indispensable for accurate species identification. Brucella abortus strains were isolated from two human cases and a sheep. Such infections are uncommon in Egypt. Egyptian Brucella strains are still in-vitro susceptible to doxycycline, tetracyclines, gentamicin, ciprofloxacin, levofloxacin, chloramphenicol, streptomycin, trimethoprim/sulfamethoxazole and tigecycline. Probable (no CLSI/EUCAST breakpoints have been defined yet) in-vitro resistance to rifampicin and azithromycin was observed. WGS failed to determine classical AMR genes, and no difference in the distribution of virulence-associated genes in all isolates was found. Isolates of human and non-human origins were still susceptible to the majority of antibiotics used for treatment in humans. The absence of classical AMR genes in genomes of "resistant" Brucella strains may reflect a lack of information in databases, or resistance might not be encoded by single resistance genes. The One Health approach is necessary for tackling brucellosis. Continuous susceptibility testing, updating of breakpoints, assessing mutations that lead to resistance are needed.

Protein Biomarker Identification for the Discrimination of Brucella melitensis Field Isolates From the Brucella melitensis Rev.1 Vaccine Strain by MALDI-TOF MS

Brucella melitensis Rev.1 is a live attenuated vaccine strain that is widely used to control brucellosis in small ruminants. For successful surveillance and control programs, rapid identification and characterization of Brucella isolates and reliable differentiation of vaccinated and naturally infected animals are essential prerequisites. Although MALDI-TOF MS is increasingly applied in clinical microbiology laboratories for the diagnosis of brucellosis, species or even strain differentiation by this method remains a challenge. To detect biomarkers, which enable to distinguish the B. melitensis Rev.1 vaccine strain from B. melitensis field isolates, we initially searched for unique marker proteins by in silico comparison of the B. melitensis Rev.1 and 16M proteomes. We found 113 protein sequences of B. melitensis 16M that revealed a homologous sequence in the B. melitensis Rev.1 annotation and 17 of these sequences yielded potential biomarker pairs. MALDI-TOF MS spectra of 18 B. melitensis Rev.1 vaccine and 183 Israeli B. melitensis field isolates were subsequently analyzed to validate the identified marker candidates. This approach detected two genus-wide unique biomarkers with properties most similar to the ribosomal proteins L24 and S12. These two proteins clearly discriminated B. melitensis Rev.1 from the closely related B. melitensis 16M and the Israeli B. melitensis field isolates. In addition, we verified their discriminatory power using a set of B. melitensis strains from various origins and of different MLVA types. Based on our results, we propose MALDI-TOF MS profiling as a rapid, cost-effective alternative to the traditional, time-consuming approach to differentiate certain B. melitensis isolates on strain level.