Development of a Multiplex Droplet Digital PCR Assay for the Detection of Babesia, Bartonella, and Borrelia Species

Molecular detection of Bartonella spp. DNA in dogs with hemangiosarcoma

INTRODUCTION

The potential role of pathogens, particularly vector-transmitted infectious agents, as a cofactor or cause of neoplasia has not been intensively investigated. We previously reported a potential link between Bartonella spp. bacteremia and splenic hemangiosarcoma (HSA) in dogs living in the United States. The purpose of this study was to: 1/ further determine the prevalence of Bartonella spp. DNA in dogs with splenic HSA from throughout the United States; 2/ assess the impact of sample preservation methods on Bartonella spp. DNA amplification using characterized tissue samples from dogs diagnosed with HSA.

METHODS

In a blinded manner, we determined the presence of Bartonella spp. DNA in scrolls from biorepository formalin-fixed paraffin-embedded (FFPE) spleens from dogs living in three distant locations geographically transecting the United States. DNA extracted from non-lesional spleens (n = 249), nodular lymphoid hyperplasia spleens (n = 248), and splenic HSA (n = 330) were tested by quantitative polymerase chain reaction (qPCR), and droplet digital PCR (ddPCR). Subsequently, Bartonella PCR results from FFPE tissues and formalin-fixed tissues were compared using previously tested fresh frozen tissues from an additional 48 dogs with HSA.

RESULTS

There was no significant difference in the proportion of Bartonella PCR positive FFPE tissues from dogs diagnosed with an alesional spleen, nodular lymphoid hyperplasia, and splenic HSA. Regardless of the histological diagnosis, the most common Bartonella species identified was B. henselae (32/38). Bartonella spp. DNA was detected in a significantly larger proportion of fresh frozen tissues compared to FFPE tissues, when tested by qPCR (22/48 versus 1/48; p <0.0001) or ddPCR (19/48 versus 1/48; p <0.0001). Using ddPCR, Bartonella DNA was more often amplified from formalin-fixed tissues compared to FFPE tissues (15/39 versus 1/39; p <0.0001). The sensitivity of qPCR on FFPE samples and formalin-fixed samples, when comparing to fresh frozen samples as the reference standard, was 4.5% and 11.8%, respectively.

CONCLUSION

Due to decreased DNA amplification efficiency, FFPE scrolls should not be used for the detection of Bartonella infection in spleen samples from dogs with HSA. PCR testing of fresh frozen tissues substantially improves the detection of Bartonella spp. infection. If fresh frozen tissues are not available, formalin-fixed tissues should be tested with digital PCR to enhance Bartonella DNA detection.

Bartonella henselae, Babesia odocoilei and Babesia divergens-like MO-1 infection in the brain of a child with seizures, mycotoxin exposure and suspected Rasmussen's encephalitis

Background

In conjunction with more sensitive culture and molecular diagnostic testing modalities, simultaneous or sequential infection with more than 1 vector borne zoonotic pathogen is being increasingly documented in human patients. On a frequent basis, many people are exposed to apparently healthy, but infected, domestic and wild animals, the arthropod vectors with which these animals have co-evolved, and the bacterial, protozoal and other pathogens for which various animals are reservoirs. Unsuspected zoonotic transmission by scratch, bite, or vector exposures can result in chronic, indolent, or potentially life-threatening infections.

Methods

In December 2016, at 2 years of age, a male child residing in Ontario, Canada received facial scratches from a feral cat. In August 2018, seizures began 8 days after the child developed a focal, suspected insect bite rash. In June 2019, potential mold toxicity in the child's bedroom was assessed by fungal culture and urinary mycotoxin assays. Beginning in January 2022, Bartonella spp. serology (indirect fluorescent antibody assays), polymerase chain reaction (PCR) amplification, DNA sequencing, and enrichment blood and brain cultures were used on a research basis to assess Bartonella spp. bloodstream and central nervous system (brain biopsy) infection. In 2024, using recently developed PCR and DNA sequencing targets, Babesia species infection was retrospectively assessed due to the rash observed in 2018.

Results

Although there was historical cat and suspected tick exposures, serological testing for Bartonella henselae and Borrelia burgdorferi were repeatedly negative. Sequential neurodiagnostic testing partially supported a diagnosis of Rasmussen's encephalitis. Astrogliosis was the only brain biopsy histopathological abnormality. Bartonella henselae DNA was amplified and sequenced from enrichment cultures of brain tissue. Retrospectively, Babesia odocoilei and Babesia divergens-like MO-1 infections were confirmed by amplification and sequencing of DNA extracted from enrichment blood cultures processed in January 2022, from blood and brain tissue cultures in June 2022, and blood in January and June 2023.

Conclusions

Infection with B. henselae, B. odocoilei, and B. divergens-like MO-1, complicated by mycotoxin exposure, created a complex clinical scenario for this child, his parents, and his doctors.

A One Health Zoonotic Vector Borne Infectious Disease Family Outbreak Investigation

This study reinforces the value of a One Health approach to infectious disease outbreak investigations. After the onset of neuropsychiatric symptoms in their son, our investigation focused on a family composed of a mother, father, two daughters, the son, two dogs, and a rabbit, all with exposures to vectors (fleas and ticks), rescued dogs, and other animals. Between 2020 and 2022, all family members experienced illnesses that included neurological symptoms. Prolonged menorrhagia (130d) in the youngest daughter ultimately resolved following antibiotic administration. One dog was diagnosed with a splenic hematoma and months later spinal histiocytic sarcoma. The father, both daughters, and one dog were seroreactive to multiple Bartonella spp. antigens, whereas the mother and son were not seroreactive. Bartonella quintana DNA was amplified from specimens obtained from all family members. Based upon DNA sequencing, infection with B. quintana was confirmed for the mother and both pet dogs. Bartonella henselae DNA was amplified and sequenced from the youngest daughter, the son, and one dog (co-infected with B. quintana), and from Ctenocephalides felis collected from their pet rabbit. All five family members and one dog were infected with Babesia divergens-like MO-1. Both parents were co-infected with Babesia microti. Droplet digital PCR supported potential infection with a Borrelia species in three family members. This study provided additional case-based evidence supporting the role of stealth Babesia, Bartonella, and Borrelia pathogens as a cause or cofactor in neurological and neuropsychiatric symptoms. We conclude that a One Health investigation approach, particularly for stealth vector borne pathogens such as Babesia, Bartonella, and Borrelia spp., will enhance clinical and epidemiological understanding of these organisms for animal and human health. During outbreak investigations it is critical to document travel and vector exposure histories, symptoms, and pathology in pets and human patients, contact with rescued, wild, or feral animals and perform diagnostic testing that includes family members, pets, and vectors.

Development of Multiplex Assays for the Identification of Zoonotic Babesia Species

More than one-hundred Babesia species that affect animals and humans have been described, eight of which have been associated with emerging and underdiagnosed zoonoses. Most diagnostic studies in humans have used serology or molecular assays based on the 18S rRNA gene. Because the 18S rRNA gene is highly conserved, obtaining an accurate diagnosis at the species level is difficult, particularly when the amplified DNA fragment is small. Also, due to its low copy number, sequencing of the product is often unsuccessful. In contrast, because the Babesia internal transcribed regions (ITS), between 18S rRNA and 5.8S rRNA, and between 5.8S rRNA and 28S rRNA, contain highly variable non-coding regions, the sequences in these regions provide a good option for developing molecular assays that facilitate differentiation at the species level. In this study, the complete ITS1 and ITS2 intergenic regions of different Piroplasmida species were sequenced to add to the existing GenBank database. Subsequently, ITS1 and ITS2 sequences were used to develop species-specific PCR assays and specific single-plex and multiplex conventional (c)PCR, quantitative real-time (q)PCR, and digital (d)PCR assays for four zoonotic Babesia species (Babesia divergens, Babesia odocoilei, Babesia duncani, and Babesia microti). The efficacy of the assay protocols was confirmed by testing DNA samples extracted from human blood or enrichment blood cultures. Primers were first designed based on the 18S rRNA-5.8S rRNA and 5.8S rRNA-28S rRNA regions to obtain the ITS1 and ITS2 sequences derived from different Piroplasmida species (B. odocoilei, Babesia vulpes, Babesia canis, Babesia vogeli, Babesia gibsoni, Babesia lengau, Babesia divergens-like, B. duncani, B. microti, Babesia capreoli, Babesia negevi, Babesia conradae, Theileria bicornis, and Cytauxzoon felis). Subsequently, using these sequences, single-plex or multiplex protocols were optimized targeting the ITS1 region of B. divergens, B. microti, and B. odocoilei. Each protocol proved to be sensitive and specific for the four targeted Babesia sp., detecting 10-2 (for B. microti and B. odocoilei) and 10-1 (for B. divergens and B. duncani) DNA copies per microliter. There was no cross-amplification among the Babesia species tested. Using 226 DNA extractions from blood or enrichment blood cultures obtained from 82 humans, B. divergens (seven individuals), B. odocoilei (seven individuals), and B. microti (two individuals) were detected and identified as a single infection, whereas co-infection with more than one Babesia sp. was documented by DNA sequencing in six (7.3%) additional individuals (representing a 26.8% overall prevalence). These newly developed protocols proved to be effective in detecting DNA of four Babesia species and facilitated documentation of co-infection with more than one Babesia sp. in the same individual.

Human Babesia odocoilei and Bartonella spp. co-infections in the Americas

BACKGROUND

In recent years, Babesia and Bartonella species co-infections in patients with chronic, nonspecific illnesses have continued to challenge and change the collective medical understanding of "individual pathogen" vector-borne infectious disease dynamics, pathogenesis and epidemiology. The objective of this case series is to provide additional molecular documentation of Babesia odocoilei infection in humans in the Americas and to emphasize the potential for co-infection with a Bartonella species.

METHODS

The development of improved and more sensitive molecular diagnostic techniques, as confirmatory methods to assess active infection, has provided increasing clarity to the healthcare community.

RESULTS

Using a combination of different molecular diagnostic approaches, infection with Babesia odocoilei was confirmed in seven people suffering chronic non-specific symptoms, of whom six were co-infected with one or more Bartonella species.

CONCLUSIONS

We conclude that infection with Babesia odocoilei is more frequent than previously documented and can occur in association with co-infection with Bartonella spp.

Bartonella species bacteremia in association with adult psychosis

Introduction

The potential role of pathogens, particularly vector-transmitted infectious agents, as a cause of psychosis has not been intensively investigated. We have reported a potential link between Bartonella spp. bacteremia and neuropsychiatric symptoms, including pediatric acute onset neuropsychiatric syndrome and schizophrenia. The purpose of this study was to further assess whether Bartonella spp. exposure or infection are associated with psychosis.

Methods

In a blinded manner, we assessed the presence of anti-Bartonella antibodies by indirect immunofluorescence assays (IFA), and infection by amplification of bacterial DNA from blood by quantitative polymerase chain reaction (qPCR), digital PCR (dPCR), and droplet digital PCR (ddPCR) in 116 participants. Participants were categorized into one of five groups: 1) controls unaffected by psychosis (n = 29); 2) prodromal participants (n = 16); 3) children or adolescents with psychosis (n = 7); 4) adults with psychosis (n = 44); and 5) relatives of a participant with psychosis (n = 20).

Results

There was no significant difference in Bartonella spp. IFA seroreactivity between adults with psychosis and adult controls unaffected by psychosis. There was a higher proportion of adults with psychosis who had Bartonella spp. DNA in the bloodstream (43.2%) compared to adult controls unaffected by psychosis (14.3%, p = 0.021). The Bartonella species was determined for 18 of the 31 bacteremic participants, including infection or co-infection with Bartonella henselae (11/18), Bartonella vinsonii subsp. berkhoffii (6/18), Bartonella quintana (2/18), Bartonella alsatica (1/18), and Bartonella rochalimae (1/18).

Discussion

In conjunction with other recent research, the results of this study provide justification for a large national or international multi-center study to determine if Bartonella spp. bacteremia is more prevalent in adults with psychosis compared to adults unaffected by psychosis. Expanding the investigation to include a range of vector-borne and other microbial infections with potential CNS effects would enhance knowledge on the relationship between psychosis and infection.

Present and Future Applications of Digital PCR in Infectious Diseases Diagnosis

Infectious diseases account for about 3 million deaths per year. The advent of molecular techniques has led to an enormous improvement in their diagnosis, both in terms of sensitivity and specificity and in terms of the speed with which a clinically useful result can be obtained. Digital PCR, or 3rd generation PCR, is based on a series of technical modifications that result in more sensitive techniques, more resistant to the action of inhibitors and capable of direct quantification without the need for standard curves. This review presents the main applications that have been developed for the diagnosis of viral, bacterial, and parasitic infections and the potential prospects for the clinical use of this technology.

An approach for integrating droplet generation and detection in digital polymerase chain reaction applications based on a bifunctional microfluidic cross-structure

Digital polymerase chain reaction (dPCR) is an approach for absolute nucleic acid quantification with high sensitivity. Although several successful commercial dPCR devices have been developed to date, further miniaturizing device dimensions, decreasing cross-contamination, and improving automation level are still research highlights. In this study, we developed a fully contamination-free dPCR detection chip with fluorescence flow cytometry and micro droplet approach. A bifunctional cross-structure (BFCS) was designed to realize monodisperse sample droplet generation in forward flow and droplet detection in backward flow with simple pneumatic control and fixed chip position. In order to improve droplet detection efficiency and accuracy, droplets morphology and sequence pattern during microfluidic droplet generation and backward flow droplet detection at the same cross-structure were observed and analyzed under different pneumatic pressures. In addition, during backward flow droplet detection, an optimized declination angle of the chip was applied to increase droplet reflux rates. For the validation of PCR performance, temperature changing processes during PCR cycles were achieved by heating the monodispersed droplet array with a customized PCR amplification device. The fluorescence signal of each droplet right after passing the cross-structure was excitated and detected. The absolute quantification ability of our integrated dPCR microfluidic chip utilizing flow fluorescence cytometry was tested and verified with Influenza A virus gene (from 7.5 copies/μL to 30000 copies/μL). Thus, our platform provides a novel and integrated approach for ddPCR analysis.

Case report: Substantial improvement of autism spectrum disorder in a child with learning disabilities in conjunction with treatment for poly-microbial vector borne infections

Poly-microbial vector-borne infections may have contributed to neuropsychiatric symptoms in a boy diagnosed with autism spectrum disorder. Targeted antimicrobial treatment resulted in substantial improvement in cognitive (such as learning disabilities, focus, concentration) and neurobehavioral (such as oppositional, defiant, anti-social, disordered mood, immaturity, tics) symptoms.

Lyme borreliosis diagnosis: state of the art of improvements and innovations

With almost 700 000 estimated cases each year in the United States and Europe, Lyme borreliosis (LB), also called Lyme disease, is the most common tick-borne illness in the world. Transmitted by ticks of the genus Ixodes and caused by bacteria Borrelia burgdorferi sensu lato, LB occurs with various symptoms, such as erythema migrans, which is characteristic, whereas others involve blurred clinical features such as fatigue, headaches, arthralgia, and myalgia. The diagnosis of Lyme borreliosis, based on a standard two-tiered serology, is the subject of many debates and controversies, since it relies on an indirect approach which suffers from a low sensitivity depending on the stage of the disease. Above all, early detection of the disease raises some issues. Inappropriate diagnosis of Lyme borreliosis leads to therapeutic wandering, inducing potential chronic infection with a strong antibody response that fails to clear the infection. Early and proper detection of Lyme disease is essential to propose an adequate treatment to patients and avoid the persistence of the pathogen. This review presents the available tests, with an emphasis on the improvements of the current diagnosis, the innovative methods and ideas which, ultimately, will allow more precise detection of LB.

Blood Supplementation Enhances Bartonella henselae Growth and Molecular Detection of Bacterial DNA in Liquid Culture

Bacteria of the genus Bartonella, a member of the Alphaproteobacteria, are fastidious, Gram-negative, aerobic bacilli that comprise numerous species, subspecies, and genotypes. Bartonella henselae, with a worldwide distribution, infects cats, dogs, horses, humans, and other mammals. Diagnostically, direct detection of Bartonella henselae in patient blood specimens by culture or molecular methods is required to confirm infection with this bacterium. Enrichment blood culture combined with quantitative PCR (qPCR) or ddPCR enhances the sensitivity of direct detection. The addition of sheep blood to liquid culture media increased the Bartonella henselae DNA concentration compared to controls, additionally improving PCR direct detection sensitivity. IMPORTANCE This study aims to improve diagnostic detection of Bartonella henselae. Patient samples are combined with enriched bacterial cultures aimed at growing Bartonella henselae for the best possible chance at detection. However, current Bartonella growth methods could be improved. The DNA extraction method used by most laboratories should also be optimized. Sheep blood was added to increase the growth of Bartonella henselae and multiple DNA extraction methods were to be compared to each other.

Multiplex Digital PCR Assay to Detect Multiple KRAS and GNAS Mutations Associated with Pancreatic Carcinogenesis from Minimal Specimen Amounts

Digital PCR (dPCR) allows for highly sensitive quantification of low-frequency mutations and facilitates early detection of cancer. However, low-throughput targeting of single hotspots in dPCR hinders variant specification when multiple probes are used. We developed a dPCR method to simultaneously identify major variants related to pancreatic carcinogenesis. Using a two-dimensional plot of droplet fluorescence under the optimized concentration of two fluorescent probe pools, the absolute quantification of different KRAS and GNAS variants was determined. Successful detection of the multiple driver mutations was verified in 24 surgically resected tumor samples from 19 patients and 22 fine-needle aspiration samples from patients with pancreatic ductal adenocarcinoma. Precise quantification of the variant allele frequency was optimized by using template DNA at a concentration as low as 1 to 10 ng. Furthermore, amplicons targeting multiple hotspots were successfully enriched with fewer false-positive findings using high-fidelity polymerase, allowing for the detection of various KRAS and GNAS mutations with high probability in small amount of cell/tissue specimens. Using this target enrichment, mutations at a rate of 90% in small residual tissues, such as the fine-needle aspiration needle flush and microscopic lesions in resected specimens, were successfully identified. The proposed method allows for low-cost, accurate detection of driver mutations to diagnose cancers, even with minimal tissue collection.

Digital PCR: modern solution to parasite diagnostics and population trait genetics

The use of polymerase chain reaction (PCR)-based diagnostic approaches has steadily increased in the field of parasitology in recent decades. The most recent large-scale technological modification of the PCR formula, also known as third-generation PCR, came in the form of digital PCR (dPCR). Currently, the most common form of dPCR on the market is digital droplet PCR (ddPCR). Unlike quantitative real-time PCR (qPCR), the digital format allows for highly sensitive, absolute quantification of nucleic acid targets and does not require external standards to be included in the developed assays. Dividing each sample into thousands of compartments and using statistical models also eliminates the need for technical replicates. With unprecedented sensitivity and enforcement of binary endpoint reactions, ddPCR not only allows the use of tiny sample volumes (especially important when working with limited amounts of DNA) but also minimises the impact of variations in amplification efficiency and the presence of inhibitors. As ddPCR is characterised by excellent features such as high throughput, sensitivity and robust quantification, it is widely used as a diagnostic tool in clinical microbiology. Due to recent advances, both the theoretical background and the practical, current applications related to the quantification of nucleic acids of eukaryotic parasites need to be updated. In this review, we present the basics of this technology (particularly useful for new users) and consolidate recent advances in the field with a focus on applications to the study of helminths and protozoan parasites.

Detecting the Neuraminidase R294K Mutation in Avian Influenza A (H7N9) Virus Using Reverse Transcription Droplet Digital PCR Method

The R294K mutation in neuraminidase (NA) causes resistance to oseltamivir in the avian influenza virus H7N9. Reverse transcription droplet digital polymerase chain reaction (RT-dd PCR) is a novel technique for detecting single-nucleotide polymorphisms. This study aimed to develop an RT-dd PCR method for detecting the R294K mutation in H7N9. Primers and dual probes were designed using the H7N9 NA gene and the annealing temperature was optimized at 58.0 °C. The sensitivity of our RT-dd PCR method was not significantly different from that of RT-qPCR (p = 0.625), but it could specifically detect R294 and 294K in H7N9. Among 89 clinical samples, 2 showed the R294K mutation. These two strains were evaluated using a neuraminidase inhibition test, which revealed that their sensitivity to oseltamivir was greatly reduced. The sensitivity and specificity of RT-dd PCR were similar to those of RT-qPCR and its accuracy was comparable to that of NGS. The RT-dd PCR method had the advantages of absolute quantitation, eliminating the need for a calibration standard curve, and being simpler in both experimental operation and result interpretation than NGS. Therefore, this RT-dd PCR method can be used to quantitatively detect the R294K mutation in H7N9.

Multiplex ddPCR: A Promising Diagnostic Assay for Early Detection and Drug Monitoring in Bovine Theileriosis

Accurate quantification based on nucleic acid amplification is necessary to avoid the spread of pathogens, making early diagnosis essential. Droplet digital PCR (ddPCR) stands out for absolute parasite quantification because it combines microfluidics with the TaqMan test. This helps deliver maximum accuracy without needing a reference curve. This study assessed the efficacy of ddPCR as a detection tool for the bovine theileriosis (BT) caused by Theileria parasites. We developed and validated a duplex ddPCR method that detects and quantifies the Theileria genus (18S rRNA) and identifies clinically significant Theileria annulata parasites (TaSP) in experimental and clinical samples. ddPCR was shown to be as effective as qPCR throughout a 10-fold sample dilution range. However, ddPCR was more sensitive than qPCR at lower parasite DNA concentrations and reliably assessed up to 8.5 copies/µL of the TaSP gene in the infected DNA (0.01 ng) samples. The ddPCR was very accurate and reproducible, and it could follow therapeutic success in clinical cases of theileriosis. In conclusion, our ddPCR assays were highly sensitive and precise, providing a valuable resource for the study of absolute parasite quantification, drug treatment monitoring, epidemiological research, large-scale screening, and the identification of asymptomatic parasite reservoirs in the pursuit of BT eradication.