Real-time fluorescence loop-mediated isothermal amplification assay for rapid and sensitive detection of Streptococcus gallolyticus subsp. gallolyticus associated with colorectal cancer

Sample preparation and detection methods in point-of-care devices towards future at-home testing

Timely and accurate diagnosis is critical for effective healthcare, yet nearly half the global population lacks access to basic diagnostics. Point-of-care (POC) testing offers partial solutions by enabling low-cost, rapid diagnosis at the patient's location. At-home POC devices have the potential to advance preventive care and early disease detection. Nevertheless, effective sample preparation and detection methods are essential for accurate results. This review surveys recent advances in sample preparation and detection methods at POC. The goal is to provide an in-depth understanding of how these technologies can enhance at-home POC devices. Lateral flow assays, nucleic acid tests, and virus detection methods are at the forefront of POC diagnostic technology, offering rapid and sensitive tools for identifying and measuring pathogens, biomarkers, and viral infections. By illuminating cutting-edge research on assay development for POC diagnostics, this review aims to accelerate progress towards widely available, user-friendly, at-home health monitoring tools that empower individuals in personalized healthcare in the future.

Mayaro virus detection by integrating sample preparation with isothermal amplification in portable devices

Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed a portable device that integrates sample preparation with real-time, reverse-transcription, loop-mediated isothermal amplification (rRT-LAMP). First, we designed a rRT-LAMP assay targeting MAYV's non-structural protein (NS1) gene and determined the limit of detection of at least 10 viral genome equivalents per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. The rRT-LAMP assay was integrated with a sample preparation device (SPD) wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting, while subsequent real-time amplification device (RAD) enables virus detection at the point of care (POC). The functions of our platform were demonstrated using purified MAYV RNA or blood samples containing viable viruses. We have used the devices for detection of MAYV in as short as 13 min, with limit of detection to as low as 10 GEs/reaction.

Loop-mediated isothermal amplification assay for fluorescence analysis and lateral flow detection of male DNA

Male DNA screening is important in forensic investigations, such as sexual assault cases. Although quantitative real-time PCR is a robust method for detection of male DNA, it is time-consuming and labor-intensive. We herein report the development of a male DNA-targeted loop-mediated isothermal amplification (LAMP) assay that can be used for both laboratory-based fluorescence analysis and on-site lateral flow detection. The two detection systems are independent, but we streamlined the reaction before the detection by introducing a fluorescence probe and biotin-labeled primer into a single reaction. This allowed the evaluation of fluorescence signal followed by lateral flow detection. Both the fluorescence and lateral flow analyses detected as low as 10 pg of male DNA. We also integrated an alkaline lysis method with our LAMP assay. The direct assay successfully detected male DNA from forensic samples without purification. The workflow requires only <40 min for fluorescence analysis and <45 min for lateral flow detection. Furthermore, when combined with a lateral flow strip, this workflow does not require any sophisticated instruments. These findings suggest that our assay is a promising strategy for on-site male DNA screening as well as laboratory-based testing.

Identification of Streptococcus gallolyticus in tumor samples of Iranian patients diagnosed with colorectal cancer

Objective

Clinical outcomes of infection by S. gallolyticus have not been investigated extensively. We aimed to determine the prevalence of S. gallolyticus in tumor specimens obtained from Iranian patients diagnosed with colorectal cancer. Polymerase chain reaction was used to confirm the presence of S. gallolyticus in patients’ tissue samples.

Results

Of 176 patients, 65 were diagnosed with colorectal cancer whereas 111 did not have any colon disease. No correlation was found between age, colonization with S. gallolyticus, gender, or risk factors. Overall, 72 (40%) patients carried S. gallolyticus; only 29% of the patients without colorectal cancer were positive for S. gallolyticus. Diagnosis of colorectal cancer and presence of S. gallolyticus significantly correlated (P = 0.006; odds ratio = 1.46; 95% CI = 1.21–3.87). Among the patients with colorectal cancer, 39 (60%) were positive with S. gallolyticus (P = 0.006) whereas 33 of 111 (29.7%) control subjects were positive for S. gallolyticus (P > 0.05); thus, 70.3% of the control subjects were not infected with S. gallolyticus. We found a high prevalence of S. gallolyticus among an Iranian cohort of patients with colorectal cancer. Despite previous reports, we report a positive correlation between colorectal cancer and S. gallolyticus colonization.

Analysis and validation of silica-immobilised BST polymerase in loop-mediated isothermal amplification (LAMP) for malaria diagnosis

Bacillus stearothermophilus large fragment (BST_LF) DNA polymerase is reported, isolated on silica via a fused R5 silica-affinity peptide and used in nucleic acid diagnostics. mCherry (mCh), included in the fusion construct, was shown as an efficient fluorescent label to follow the workflow from gene to diagnostic. The R5 immobilisation on silica from cell lysate was consistent with cooperative R5-specific binding of R5₂-mCh-FL-BST_LF or R5₂-mCh-H10-BST_LF fusion proteins followed by non-specific protein binding (including E. coli native proteins). Higher R5-binding could be achieved in the presence of phosphate, but phosphate residue reduced loop-mediated isothermal amplification (LAMP) performance, possibly blocking sites on the BST_LF for binding of β- and γ-phosphates of the dNTPs. Quantitative assessment showed that cations (Mg²⁺ and Mn²⁺) that complex the PPi product optimised enzyme activity. In malaria testing, the limit of detection depended on Plasmodium species and primer set. For example, 1000 copies of P. knowlesi 18S rRNA could be detected with the P.KNO-LAU primer set with Si-R5₂-mCh-FL-BST_LF , but 10 copies of P. ovale 18S rRNA could be detected with the P.OVA-HAN primer set using the same enzyme. The Si-immobilised BST_LF outperformed the commercial enzyme for four of the nine Plasmodium LAMP primer sets tested. Si-R5₂-mCh-FL-BST_LF production was transferred from Cambridge to Accra and set up de novo for a trial with clinical samples. Different detection limits were found, targeting the mitochondrial DNA or the 18S rRNA gene for P. falciparum. The results are discussed in comparison with qPCR and sampling protocol and show that the Si-BST_LF polymerase can be optimised to meet the WHO recommended guidelines.

Development of multiplex HRM-based loop-mediated isothermal amplification method for specific and sensitive detection of Treponema pallidum

Syphilis is a sexually transmitted disease caused by the spirochaete bacterium Treponema pallidum. This study has developed a multiplex High-Resolution Melt-curve Loop-mediated isothermal amplification (multiplex HRM-LAMP) assay targeting the marker genes polA and tprL to detect T. pallidum. The multiplex HRM-LAMP assay conditions were optimized at 65 °C for 45 min. Real-time melt-curve analysis of multiplex HRM-LAMP shows two melt-curve peaks corresponding to polA and tprL with a Tm value of 80 ± 0.5 °C and 87 ± 0.5 °C, respectively. The detection limit of multiplex HRM-LAMP was found to be 6.4 × 10^-4 ng/μL (3.79 copies/μL) of T. pallidum. The specificity was evaluated using seven different bacterial species, and the developed method was 100% specific in detecting T. pallidum. A total of 64 blood samples of T. pallidum suspected cases were used to validate the assay method. The clinical validation showed that the assay was 96.43% sensitive and 100% specific in detecting syphilis. Thus, the developed method was more rapid and sensitive than other available methods and provides a multigene-based diagnostic approach to detect T. pallidum.

Pathogenicity and drug resistance of animal streptococci responsible for human infections

Bacteria of the genus Streptococcus, earlier considered typically animal, currently have also been causing infections in humans. It is necessary to make clinicians aware of the emergence of new species that may cause the development of human diseases. There is an increasing frequency of isolation of streptococci such as S. suis, S. dysgalactiae, S. iniae and S. equi from people. Isolation of Streptococcus bovis/Streptococcus equinus complex bacteria has also been reported. The streptococcal species described in this review are gaining new properties and virulence factors by which they can thrive in new environments. It shows the potential of these bacteria to changes in the genome and the settlement of new hosts. Information is presented on clinical cases that concern streptococcus species belonging to the groups Bovis, Pyogenic and Suis. We also present the antibiotic resistance profiles of these bacteria. The emerging resistance to β-lactams has been reported. In this review, the classification, clinical characteristics and antibiotic resistance of groups and species of streptococci considered as animal pathogens are summarized.

Detection of Streptococcus gallolyticus in colorectal cancer and inflammatory bowel disease patients compared to control group in southwest of Iran

There are several pieces of evidence regarding the role of bacteria, such as Streptococcus bovis/gallolyticus in the etiology of gastrointestinal diseases such as colorectal cancer (CRC) and inflammatory bowel disease (IBD). Therefore, the aim of this study was to detect S. gallolyticus subsp. gallolyticus (Sgg) in fecal samples of CRC and IBD patients by culture and molecular methods, in Ahvaz, southwest of Iran. A total of 106 fecal samples were collected from 22 CRC patients, 44 IBD patients, and 40 healthy individuals. The prevalence of Sgg was investigated by culture and polymerase chain reaction (PCR) with specific primers for sodA gene. The results of the stool culture showed that the overall prevalence of Sgg was 9 (13.6%) out of 66 patients. Meanwhile, the number of Sgg isolated from IBD and CRC patients was 7 (15.9%) and 2 (9%), respectively. The bacteria were not isolated from any of the control groups. On the basis of PCR, S. gallolyticus was detected in 24 (36.4%) out of 66 patients. Meanwhile, the number of IBD patients with positive sodA gene was 15 (34.1%) out of 44 cases. In CRC patients, the sodA gene was detected in 9 (40.9%) of 22 cases. Two (5%) of the specimens in the control group had the sodA gene. According to our results, S. gallolyticus subsp. gallolyticus might be involved in CRC and IBD pathogenesis. More investigation with different samples in the various areas might be shaded light on these results.