Development and validation of a modified TaqMan based real-time PCR assay targeting the lipl32 gene for detection of pathogenic Leptospira in canine urine samples

Developing diagnostic tools for canine periodontitis: combining molecular techniques and machine learning models

BACKGROUND

Dental plaque microbes play a key role in the development of periodontal disease. Numerous high-throughput sequencing studies have generated understanding of the bacterial species associated with both canine periodontal health and disease. Opportunities therefore exist to utilise these bacterial biomarkers to improve disease diagnosis in conscious-based veterinary oral health checks. Here, we demonstrate that molecular techniques, specifically quantitative polymerase chain reaction (qPCR) can be utilised for the detection of microbial biomarkers associated with canine periodontal health and disease.

RESULTS

Over 40 qPCR assays targeting single microbial species associated with canine periodontal health, gingivitis and early periodontitis were developed and validated. These were used to quantify levels of the respective taxa in canine subgingival plaque samples collected across periodontal health (PD0), gingivitis (PD1) and early periodontitis (PD2). When qPCR outputs were compared to the corresponding high-throughput sequencing data there were strong correlations, including a periodontal health associated taxa, Capnocytophaga sp. COT-339 (rs =0.805), and two periodontal disease associated taxa, Peptostreptococcaceae XI [G-4] sp. COT-019 (rs=0.902) and Clostridiales sp. COT-028 (rs=0.802). The best performing models, from five machine learning approaches applied to the qPCR data for these taxa, estimated 85.7% sensitivity and 27.5% specificity for Capnocytophaga sp. COT-339, 74.3% sensitivity and 67.5% specificity for Peptostreptococcaceae XI [G-4] sp. COT-019, and 60.0% sensitivity and 80.0% specificity for Clostridiales sp. COT-028.

CONCLUSIONS

A qPCR-based approach is an accurate, sensitive, and cost-effective method for detection of microbial biomarkers associated with periodontal health and disease. Taken together, the correlation between qPCR and high-throughput sequencing outputs, and early accuracy insights, indicate the strategy offers a prospective route to the development of diagnostic tools for canine periodontal disease.

TaqMan real-time PCR for detection of pathogenic Leptospira spp. in canine clinical samples

Introduction

Canine leptospirosis has always been a differential diagnosis in dogs presenting with clinical signs and blood profiles associated with kidney and/or liver disease. The conventional polymerase chain reaction (PCR) provides diagnoses, but real-time PCR-based tests provide earlier confirmation and determine the severity of infection, especially in the acute stage, allowing early detection for immediate treatment decisions. To our knowledge, real-time PCR has not been routinely adopted for clinical investigation in Malaysia. This study evaluated TaqMan real-time PCR (qPCR) assays diagnosing leptospirosis and compared their applicability to clinical samples from dogs with kidney and/or liver disease against a conventional PCR reference.

Material and Methods

The qPCR assays were validated using existing leptospiral isolates. Whole blood and urine samples were analysed using a conventional PCR, LipL32(1) and LipL32(2) qPCRs and a microscopic agglutination test. The sensitivity and specificity of the qPCRs were determined.

Results

The LipL32(1) qPCR assay had more diagnostic value than the LipL32(2) qPCR assay. Further evaluation of this assay revealed that it could detect as low as five DNA copies per reaction with high specificity for the tested leptospiral strains. No cross-amplification was observed with other organisms. Analysing the clinical samples, the LipL32(1) qPCR assay had 100.0% sensitivity and >75.0% specificity.

Conclusion

The LipL32(1) qPCR assay is sensitive, specific and has the potential to be applied in future studies.

Diagnostic accuracy of an immunomagnetic separation-PCR assay to detect pathogenic Leptospira spp. in urine from dairy cattle, using a Bayesian latent class model

Leptospirosis is a zoonotic disease that has spread worldwide and causes significant economic losses in the dairy industry. The causal agents of this infectious disease are members of the genus Leptospira, known as pathogenic Leptospira spp. Specific clinical signs of the infection are difficult to detect. Therefore, the disease is normally under-diagnosed, mostly due to the lack of a cost-effective technique for diagnosing animals with a low bacterial load in their urine. The aim of this study was to assess the diagnostic accuracy of a qPCR coupled with a previous Immunomagnetic separation (IMS) step (IMS-qPCR) against a qPCR without using IMS, using a Bayesian latent class model (2 tests, 3 populations) to determine the leptospirosis infectious status in naturally infected dairy cattle. The results revealed that IMS qPCR had a sensitivity (Se) of 95.7% (95% Probability Interval (PI) = 85.0; 99.4%) and a specificity (Sp) of 98% (95% PI = 96.1; 99.4%), indicating that it is more sensitive than conventional qPCR (Se = 69.7% (95% PI = 59.2; 79.0%); median difference = 25.2% (Monte Carlo Error = 10.2%); and the Sp = 98.8% (95% PI = 97.6; 99.5%), median difference = 0.8% (Monte Carlo Error = 2.1%). Therefore, results shows that IMS-qPCR is a more useful diagnostic tool in terms of accuracy for detecting infectious animals with pathogenic Leptospira in their urine.

Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods

Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.

Comparison of Two Leptospira Type Strains of Serovar Grippotyphosa in Microscopic Agglutination Test (MAT) Diagnostics for the Detection of Infections with Leptospires in Horses, Dogs and Pigs

Simple Summary

Leptospires are bacteria of major health concern as they can cause severe systemic diseases in humans and animals alike. In routine diagnostics, the detection of a leptospirosis heavily relies on the analysis of specific antibodies that were generated by the immune system of an infected species. The most widely used test for the detection of such antibodies is the microscopic agglutination test which itself depends on defined types of laboratory grown Leptospires, so-called serovars. A good judgment of the behaviour of these serovars is vital for interpreting test results and clearly defining what type of Leptospires the patient is infected with as this may have implications for therapy and prognosis. In the following, a study on the reaction pattern of a certain type of serovars named ‘Grippotyphosa’ that itself can be divided into two differently reacting subtypes was conducted. It turned out that, depending on the animal species sampled, a differing reaction patterns to the two Grippotyphosa subtypes in the diagnostic test reflected different distribution of these subtypes in the respective populations. In the future, these insights will further improve test performance and assessment or results.

Abstract

The MAT test is of great importance in the diagnosis of leptospiral infections. Based on various differences, the serovar Grippotyphosa has been divided into two types, Moskva V and Duyster. Differences or similarities of the two type strains in the context of leptospiral diagnostics have not yet been elucidated in more detail; therefore both strains were analysed in MAT diagnostics for the detection of leptospiral infections in pigs, dogs and horses. Serum samples from 2996 pigs, 55 dogs and 35 horses, as well as vitreous and/or aqueous fluid samples from these and 13 additional horses were analysed by MAT; available supplementary samples were tested for leptospires by PCR. In pigs, 92.6% of the samples with both strains received an identical titre result in the MAT test, whereas in dogs and horses only 53.0% and 43.6% had concordant results. Since infections with the serovar Grippotyphosa occur more frequently in dogs and horses overall, more differences were observed here. In the case of discrepant serological results, supplementary samples and PCR examinations were not able to add information on the true status. Further analyses of follow-up studies or at least serum pairs from dogs and horses infected with the serovar Grippotyphosa are necessary.

Insight into the Structure, Functions, and Dynamics of the Leptospira Outer Membrane Proteins with the Pathogenicity

Leptospirosis is a widespread zoonosis that frequently occurs in tropical and subtropical countries. Leptospira enters the host through wounds or mucous membranes and spreads to the whole body through the blood, causing systemic infection. Kidneys are the preferential site where Leptospira accumulates, especially in the renal interstitium and renal tubule epithelial cells. Clinical symptoms in humans include high fever, jaundice, renal failure, and severe multiple-organ failure (Weil’s syndrome). Surface-exposed antigens are located at the outermost layer of Leptospira and these potential virulence factors are likely involved in primary host-pathogen interactions, adhesion, and/or invasion. Using the knockout/knockdown techniques to the evaluation of pathogenicity in the virulence factor are the most direct and effective methods and many virulence factors are evaluated including lipopolysaccharides (LPS), Leptospira lipoprotein 32 (LipL32), Leptospira ompA domain protein 22 (Loa22), LipL41, LipL71, Leptospira immunoglobulin-like repeat A (LigA), LigB, and LipL21. In this review, we will discuss the structure, functions, and dynamics of these virulence factors and the roles of these virulence factors in Leptospira pathogenicity. In addition, a protein family with special Leucine-rich repeat (LRR) will also be discussed for their vital role in Leptospira pathogenicity. Finally, these surface-exposed antigens are discussed in the application of the diagnosis target for leptospirosis and compared with the serum microscope agglutination test (MAT), the gold standard for leptospirosis.

Detection and characterization of Leptospira spp. in dogs diagnosed with kidney and/or liver disease in Selangor, Malaysia

Leptospirosis is a serious bacterial disease that affects both humans and animals. A wide range of symptoms have been described in humans; the disease in dogs is commonly associated with kidney and/or liver disease. In Malaysia, information about the common serovars infecting dogs is limited. Therefore, we investigated the occurrences of leptospirosis in 124 pet dogs diagnosed with kidney and/or liver disease. Blood, urine, abdominal effusion, and/or kidney and liver were collected from the dogs. Based on microscopic agglutination testing, 53 of 124 (42.7%) dogs were seropositive for leptospiral exposure. Sera were frequently positive to serovars Bataviae (n = 12), Javanica (n = 10), and Icterohaemorrhagiae (n = 10). Direct detection using PCR showed that 42 of 124 (33.9%) of the whole blood and 36 of 113 (31.9%) urine samples were positive for pathogenic Leptospira spp. By PCR, 2 of 23 (9.1%) kidney and 2 of 23 (9.1%) liver were positive for pathogenic Leptospira spp. Abdominal effusion from 4 dogs were PCR-positive for pathogenic Leptospira spp. The species detected were L. interrogans, L. borgpetersenii, L. kirschneri, and L. kmetyi by partial 16S rRNA sequencing. We further identified and characterized 11 Leptospira spp. isolates from 8 dogs as serovars Bataviae, Javanica, and Australis. The mortality rate of the Leptospira-infected dogs was high (18 of 53; 34%).

Influence of Selective Agents (EMJH-STAFF), Sample Filtration and pH on Leptospira interrogans Serovar Icterohaemorrhagiae Cultivation and Isolation from Swine Urine

Leptospira spp. cause the zoonotic disease leptospirosis, which occurs in numerous mammalians worldwide. Isolation is still important for serotyping and genotyping of Leptospira, which in turn is essential for epidemiological surveillance of leptospirosis and the development of diagnostic tests and vaccines. However, isolation of Leptospira from clinical specimens is inherently insensitive. This study was conducted to examine the influence of selective agents, sample filtration, sample pH and the use of phosphate buffered saline (PBS) buffer for sample storage to improve the success of cultivation and isolation of Leptospira interrogans serovar Icterohaemorrhagiae from swine urine. EMJH (Ellinghausen McCullough, Johnson and Harris) medium including the selective agents sulfamethoxazole, trimethoprim, amphotericin, fosfomycin and 5-fluorouracil (STAFF) increased the success of Leptospira isolation from spiked swine urine samples. Sample filtration yielded only negative results. Isolation in EMJH-STAFF was successful from swine urine with a density as low as 10⁴ Leptospira/mL, and urine with pH ≤ 7 impaired the cultivation rate. Cultivation and isolation were not improved by the addition of PBS to spiked urine samples prior to storage for 24 h at 4 °C. The results of the study demonstrate that cultivation and isolation of leptospires from swine urine can be improved by enhanced methods.

An overview on the molecular diagnosis of animal leptospirosis

The most common presentation of animal leptospirosis is the subclinical and silent chronic form, that can lead to important reproductive disorders. The diagnosis of this chronic form remains a challenge. The aim of the present study is to gather and critically analyse the current information about molecular tools applied to animal leptospirosis diagnosis, particularly the silent chronic presentation of the infection. Regarding clinical specimens, samples from urinary tract were the most used (69/102, 67·7%), while few studies (12/102, 11·8%) investigated samples from reproductive tract. Concerning the molecular methods applied, the most used is still the conventional polymerase chain reaction (PCR) (46/102, 45%), followed by real-time PCR (38/102, 37·2%). The lipL32 gene is currently the most common target used for Leptospira detection, with 48% of studies applying this genetic marker. From all the studies, only few (21/102, 20·5%) performed gene sequencing. According to the majority of authors, current evidence suggests that lipL32-PCR is useful for an initial screening for Leptospira DNA detection in animal clinical samples. Posteriorly, if DNA sequencing could be performed on positive lipL32-PCR samples, we encourage the use of secY gene as a genetic marker. The molecular methods appear as the most important tools for the diagnosis of the chronic silent leptospirosis on domestic animals, reinforcing its evident impact not only on animal reproduction but also on a One Health context.

Development of monoclonal antibodies against recombinant LipL21 protein of pathogenic Leptospira through phage display technology

Leptospirosis is a potentially fatal zoonosis that is caused by spirochete Leptospira. The signs and symptoms of leptospirosis are usually varied, allowing it to be mistaken for other causes of acute febrile syndromes. Thus, early diagnosis and identification of a specific agent in clinical samples is crucial for effective treatment. This study was aimed to develop specific monoclonal antibodies against LipL21 antigen for future use in leptospirosis rapid and accurate immunoassay. A recombinant LipL21 (rLipL21) antigen was optimized for expression and evaluated for immunogenicity. Then, a naïve phage antibody library was utilized to identify single chain fragment variable (scFv) clones against the rLipL21 antigen. A total of 47 clones were analysed through monoclonal phage ELISA. However, after taking into consideration the background OD₄₀₅ values, only 4 clones were sent for sequencing to determine human germline sequences. The sequence analysis showed that all 4 clones are identical. The in silico analysis of scFv-lip-1 complex indicated that the charged residues of scFv CDRs are responsible for the recognition with rLipL21 epitopes. The generated monoclonal antibody against rLipL21 will be evaluated as a detection reagent for the diagnosis of human leptospirosis in a future study.

Detection of Leptospira in urine of apparently healthy dogs by quantitative polymerase chain reaction in Haryana, India

Background and Aim:

Leptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira. The organism can spread through the urine of infected animals, which can get into water or soil and can survive there for weeks to months. The study was undertaken to detect the pathogenic Leptospira in healthy dogs’ urinary shedding by real-time polymerase chain reaction (qPCR).

Materials and Methods:

Leptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira. To detect the pathogenic Leptospira organisms in dogs’ urinary shedding, 239 urine samples were collected from healthy dogs from April 2018 to March 2019 from different areas of Haryana. All the urine samples were processed for DNA extraction and qPCR technique was used to detect the presence of Leptospira.

Results:

Out of 239 urine samples of dogs, none of the samples resulted in the detection of DNA of pathogenic Leptospira organisms.

Conclusion:

The present study indicated low risk of transmission of Leptospira organisms from dogs’ urine to human beings in Haryana.

Prevalence of leptospirosis in vaccinated working dogs and humans with occupational risk

Introducción.

Los perros de trabajo pueden infectarse con diversas serovariedades de Leptospira que se mantienen en sus túbulos renales e intersticios por mucho tiempo, por lo que se convierten en portadores y fuentes de infección para otros huéspedes.

Objetivo.

Establecer la prevalencia de Leptospira spp. en perros de trabajo vacunados y en población humana con riesgo ocupacional de seis unidades policiales en Colombia.

Materiales y métodos.

Mediante tres instrumentos estructurados, se evaluaron 92 perros de trabajo con inmunización previa contra Leptospira spp. (65 machos y 27 hembras) y 69 personas de seis unidades policiales de los municipios de Manizales, Pereira, Armenia, Ibagué, Tuluá y Cali. Se obtuvieron muestras sanguíneas de las personas y de los perros, las cuales se evaluaron mediante la prueba de microaglutinación (Microscopic Agglutination Test, MAT) en 24 serogrupos. Se hizo un examen clínico de los perros y se obtuvieron muestras de orina para urocultivo.

Resultados.

La seroprevalencia de leptospirosis en las personas fue de 2,9 % (n=2) y en los perros de 57,61 % (n=53). Los serogrupos más prevalentes en los perros fueron Leptospira canicola y L. panama. El urocultivo fue positivo en 58,7 % (54/92) de las muestras y se encontró asociación estadísticamente significativa entre la edad de los perros (≥10 años; p=0,043) y la ubicación de la unidad policial (p=0,016).

Conclusión.

Las características epidemiológicas de la leptospirosis en los perros sugieren una presentación endémica de la infección. Se requieren algoritmos diagnósticos sensibles y específicos para investigar la leptospirosis canina y diferenciar los anticuerpos vacunales de la infección natural.

A Validated Multiplex Real-Time PCR Assay for the Diagnosis of Infectious Leptospira spp.: A Novel Assay for the Detection and Differentiation of Strains From Both Pathogenic Groups I and II

Leptospirosis is recognized as the most globally widespread reemerging zoonosis and represents a serious threat for both human and animal health. Indeed, leptospirosis is linked to more than 60,000 human deaths per year and to incalculable economic burden as consequence of medical treatment costs and livestock loss. The increasing number of reports from species of pathogenic Leptospira spp. group II causing disease in both humans and animals constitutes an additional concern to the complex epidemiology of this zoonotic agent. Diagnostic methods based on qPCR have improved the diagnosis of Leptospira spp. in terms of cost, time, and reliability, but most of the validated assays fail to detect species from the pathogenic group II. Hence, the current study was aimed to develop and validate a novel multiplex qPCR to enable the specific and selective detection of the whole group of infectious Leptospira spp., including both pathogenic groups I and II and moreover, selectively discriminate between them. To fit the "fitness of purpose" for the specific detection of infectious Leptospira spp. and further discrimination between both pathogenic groups three target regions on the 16S RNA gene were selected. These targets facilitated a broad and selective spectrum for the detection of all infectious Leptospira spp. with the exclusion of all saprophytic groups and the novel clade of environmental Leptospira spp. The analytical sensitivity (ASe) showed by the new assay also enables a wide window of detection for the agent at different stages of infection since the assay was able to efficiently detect at 95% of confidence ∼5 leptospires/reaction. From the evaluation of the analytical specificity (ASp) by in silico and in vitro approaches, it was congruently revealed that the primers and probes selected only recognized the specific targets for which the assay was intended. Bayesian latent class analysis of performance of the new assay on 684 clinical samples showed values of diagnostic sensitivity of 99.8% and diagnostic specificity of 100%. Thus, from the evaluation of the analytical and diagnostic parameters, the new multiplex qPCR assay is a reliable method for the diagnosis of Leptospira spp.

Leptospira spp., rotavirus, norovirus, and hepatitis E virus surveillance in a wild invasive golden-headed lion tamarin (Leontopithecus chrysomelas; Kuhl, 1820) population from an urban park in Niterói, Rio de Janeiro, Brazil

The world currently faces severe biodiversity losses caused by anthropogenic activities such as deforestation, pollution, the introduction of exotic species, habitat fragmentation, and climate changes. Disease ecology in altered environments is still poorly understood. The golden-headed lion tamarin (GHLT, Leontopithecus chrysomelas) is an endangered species that became invasive in an urban park in Niterói, Rio de Janeiro, Brazil. The initially few invasive GHLT individuals became hundreds, adapted to living in proximity to humans and domestic animals. These GHLTs were captured as part of a conservation project; some animals were translocated to Bahia and some were kept in captivity. This study tested 593 GHLT for Leptospira serology; 100 and 95 GHLT for polymerase chain reaction (PCR) toLeptospira and hepatitis E virus genotype 3 (HEV-3), respectively, and 101 familiar groups for PCR to viruses (rotavirus A, norovirus GI and GII, and HEV-3). One animal had antibodies for Leptospira serovar Shermani and another for serovar Hebdomadis. One saprophyticLeptospira was found by the 16S PCR and sequencing. Viruses were not detected in samples tested. Findings suggest that the epidemiological importance of such pathogens in this GHLT population is either low or nonexistent. These data are important to understand the local disease ecology, as well as monitoring a translocation project, and to contribute data for species conservation.

Prospective study of canine leptospirosis in shelter and stray dog populations: Identification of chronic carriers and different Leptospira species infecting dogs

Dogs are highly susceptible to the leptospiral infection, notably stray and sheltered dogs. Unsanitary conditions often observed in dog shelters may predispose the introduction and spread of leptospires among sheltered populations, potentially increasing the chances for the inadvertent adoption of asymptomatically infected animals. The present work describes a longitudinal study using a multidisciplinary approach for the identification of chronically infected dogs and the characterization of potentially pathogenic strains circulating among stray and sheltered dog populations in São Paulo, Brazil. A total of 123 dogs from three populations were included. The initial evaluation consisted of blood and urine quantitative PCR testing (qPCR), the detection of specific antibodies by microscopic agglutination test (MAT), physical examination and hematological and serum biochemistry analyses. The qPCR-positive dogs were prospectively examined, and reevaluations also included culture from urine samples. Positive qPCR samples were subjected to 16S rRNA and secY gene phylogenetic analysis. The recovered strains were characterized by Multilocus Sequence Typing, polyclonal serogroup identification and virulence determination. Leptospiruria was detected in all populations studied (13/123), and phylogenetic analysis revealed that 10 dogs had L. interrogans infection. Three dogs (3/13) had L. santarosai infection. The secY phylogenetic analysis revealed that the L. santarosai sequences clustered separately from those obtained from other hosts. Ten leptospiruric dogs were reevaluated, and three dogs presented persistent leptospiruria, allowing culturing from two dogs. The strains were characterized as L. interrogans serogroup Canicola (virulent) and L. santarosai serogroup Sejroe (not virulent). Serum samples were retested by MAT using the DU92 and DU114 strains as antigens, and no increased seroreactivity was detected. Asymptomatic L. santarosai infection was observed in all populations studied, suggesting a possible role of dogs in the chain of transmission of this leptospiral species. The results suggest a genetic distinction between lineages of Brazilian L. santarosai maintained by dogs and other animal hosts. Our findings revealed that dogs could act as maintenance hosts for distinct pathogenic Leptospira, highlighting also that asymptomatically infected dogs can be inadvertently admitted and adopted in dog shelters, potentially increasing the risks of zoonotic transmission.