Comparison of Diagnostic Accuracy of PCR Targeting the 47-Kilodalton Protein Membrane Gene of Treponema pallidum and PCR Targeting the DNA Polymerase I Gene: Systematic Review and Meta-analysis

Prevalence and Predictors of Oral Treponema pallidum Detection by Quantitative Polymerase Chain Reaction in Early Syphilis

BACKGROUND

Treponema pallidum prevalence and burden at oral and lesion sites in adults with early syphilis were assessed by quantitative polymerase chain reaction (qPCR). Factors associated with oral shedding were also examined.

METHODS

Pretreatment oral and lesion swabs were collected from adults with early syphilis in a US multicenter syphilis treatment trial. Oral swabs were collected in the presence and absence of oral lesions. Following DNA extraction, qPCR and whole-genome sequencing (WGS) were performed to assess burden and strain variability.

RESULTS

All 32 participants were male, mean age was 35 years, and 90.6% with human immunodeficiency virus (HIV). T. pallidum oral PCR positivity varied by stage: 16.7% primary, 44.4% secondary, and 62.5% in early latent syphilis. Median oral T. pallidum burden was highest in secondary syphilis at 63.2 copies/µL. Lesion PCR positivity was similar in primary (40.0%) and secondary syphilis (38.5%). Age 18-29 years was significantly associated with oral shedding (vs age 40+ years) in adjusted models. WGS identified 2 distinct strains.

CONCLUSIONS

T. pallidum DNA was directly detected at oral and lesion sites in a significant proportion of men with early syphilis. Younger age was associated with oral shedding. Ease of oral specimen collection and increased PCR availability suggest opportunities to improve syphilis diagnostic testing. Clinical Trials Registration. NCT03637660.

Resurgence of syphilis: focusing on emerging clinical strategies and preclinical models

Syphilis, a sexually transmitted disease (STD) caused by Treponema pallidum (T. pallidum), has had a worldwide resurgence in recent years and remains a public health threat. As such, there has been a great deal of research into clinical strategies for the disease, including diagnostic biomarkers and possible strategies for treatment and prevention. Although serological testing remains the predominant laboratory diagnostic method for syphilis, it is worth noting that investigations pertaining to the DNA of T. pallidum, non-coding RNAs (ncRNAs), chemokines, and metabolites in peripheral blood, cerebrospinal fluid, and other bodily fluids have the potential to offer novel perspectives on the diagnosis of syphilis. In addition, the global spread of antibiotic resistance, such as macrolides and tetracyclines, has posed significant challenges for the treatment of syphilis. Fortunately, there is still no evidence of penicillin resistance. Hence, penicillin is the recommended course of treatment for syphilis, whereas doxycycline, tetracycline, ceftriaxone, and amoxicillin are viable alternative options. In recent years, efforts to discover a vaccine for syphilis have been reignited with better knowledge of the repertoire of T. pallidum outer membrane proteins (OMPs), which are the most probable syphilis vaccine candidates. However, research on therapeutic interventions and vaccine development for human subjects is limited due to practical and ethical considerations. Thus, the preclinical model is ideal for conducting research, and it plays an important role in clinical transformation. Different preclinical models have recently emerged, such as in vitro culture and mouse models, which will lay a solid foundation for clinical treatment and prevention of syphilis. This review aims to provide a comprehensive summary of the most recent syphilis tactics, including detection, drug resistance treatments, vaccine development, and preclinical models in clinical practice.

Development and clinical validation of a one-step pentaplex real-time reverse transcription PCR assay for detection of hepatitis virus B, C, E, Treponema pallidum, and a human housekeeping gene

BACKGROUND

With the safety of blood transfusion being a major public health concern, the development of a rapid, sensitive, specific, and cost-effective multiplex PCR assay for simultaneous detection of hepatitis B virus(HBV), hepatitis C virus (HCV), hepatitis E virus (HEV), and Treponema pallidum(T. pallidum) in blood is crucial.

METHODS

Five primer pairs and probes were designed towards conserved regions of target genes and used to establish a one-step pentaplex real-time reverse transcription PCR(qRT-PCR) assay for simultaneous detection of HBV, HCV, HEV, T. pallidum, and RNase P(housekeeping gene), providing sample quality check. The clinical performance of the assay was further determined with 2400 blood samples from blood donors and patients in Zhejiang province, and compared the results with commercial singleplex qPCR and serological assays.

RESULTS

The 95% limit of detection(LOD) of HBV, HCV, HEV, and T. pallidum were 7.11 copies/µL, 7.65 copies/µL, 8.45 copies/µL, and 9.06 copies/µL, respectively. Moreover, the assay has good specificity and precision. Compared to the singleplex qPCR assay, the novel assay for detecting HBV, HCV, HEV, and T. pallidum presented 100% clinical sensitivity, specificity, and consistency. Several discrepant results between serological and pentaplex qRT-PCR assays were found. Of 2400 blood samples, there were 2(0.08%) HBsAg positive samples, 3(0.13%) anti-HCV positive samples, 29(1.21%) IgM anti-HEV positive samples and 6(0.25%) anti-T. pallidum positive samples proven negative in nucleic acid detection. 1(0.04%) HBV DNA positive sample and 1(0.04%) HEV RNA positive sample were detected negative by serological testing.

CONCLUSIONS

The developed pentaplex qRT-PCR is the first assay on simultaneous, sensitive, specific, and reproducible detection of HBV, HCV, HEV, T. pallidum, and RNase P in a single tube. It could detect pathogens in blood during the window period of infection and is a good tool for effectively screening blood donors and early clinical diagnosis.

Syphilis

Syphilis is a curable systemic infectious disease with a clear increase in incidence in recent years. The disease presents with a broad clinical spectrum and challenges clinicians due to the long incubation period and the sometimes complex interpretation of serological test results. Penicillin G remains the treatment of choice in all stages of syphilis.

Specific detection of Treponema pallidum in clinical samples: validation of a qPCR assay combining two genomic targets

OBJECTIVES

We evaluated a real-time quantitative PCR (qPCR) for detection of the Treponema pallidum (TP) genome in clinical samples through simultaneous detection of two genomic targets.

METHODS

We performed qPCR with TaqMan technology using two TP genes, polA and tpp47, as targets, with an internal positive control. The qPCR assay was compared with syphilis diagnosis based on a combination of clinical examination, serological results and inhouse nested PCR (nPCR). Samples were analysed at the National Reference Center for STIs at Cochin Hospital in Paris.

RESULTS

In total, from October 2010 to December 2016, 320 documented clinical samples (mucosal and cutaneous swabs) were collected from patients with or without syphilis attending STI centres in France. The qPCR had an overall sensitivity of 89% (95% CI 85.1% to 92.1%), a specificity of 100%, a positive predictive value of 100% and a negative predictive value of 88% (95% CI 84.3% to 91.5%). The agreement between qPCR and nPCR results was 94% (κ=0.88, 95% CI 0.83 to 0.93). Calibration of the qPCR assay, by cloning both the polA and tpp47 genes, defined the detection threshold as 1 copy/µL of DNA elution.

CONCLUSIONS

We validated a new qPCR for detecting the TP genome in clinical samples with excellent sensitivity and specificity. The cloning of polA and tpp47 genes for calibration would be interesting in the evaluation of bacterial loads in samples.

Multiplex Polymerase Chain Reaction/Pooled Antibiotic Susceptibility Testing Was Not Associated with Increased Antibiotic Resistance in Management of Complicated Urinary Tract Infections

Objective

To compare antibiotic resistance results at different time points in patients with urinary tract infections (UTIs), who were either treated based upon a combined multiplex polymerase chain reaction (M-PCR) and pooled antibiotic susceptibility test (P-AST) or were not treated.

Methods

The M-PCR/P-AST test utilized here detects 30 UTI pathogens or group of pathogens, 32 antibiotic resistance (ABR) genes, and phenotypic susceptibility to 19 antibiotics. We compared the presence or absence of ABR genes and the number of resistant antibiotics, at baseline (Day 0) and 5-28 days (Day 5-28) after clinical management in the antibiotic-treated (n = 52) and untreated groups (n = 12).

Results

Our results demonstrated that higher percentage of patients had a reduction in ABR gene detection in the treated compared to the untreated group (38.5% reduction vs 0%, p = 0.01). Similarly, significantly more patients had reduced numbers of resistant antibiotics, as measured by the phenotypic P-AST component of the test, in the treated than in the untreated group (42.3% reduction vs 8.3%, p = 0.04).

Conclusion

Our results with both resistance gene and phenotypic antibiotic susceptibility results demonstrated that treatment based upon rapid and sensitive M-PCR/P-AST resulted in reduction rather than induction of antibiotic resistance in symptomatic patients with suspected complicated UTI (cUTI) in an urology setting, indicating this type of test is valuable in the management of these types of patients. Further studies of the causes of gene reduction, including elimination of ABR gene-carrying bacteria and loss of ABR gene(s), are warranted.

Multilocus sequence typing of Treponema pallidum pallidum in children with acquired syphilis by nonsexual contact

Background: There are scarce data of Treponema pallidum subsp. pallidum (TPA) characterization in children with syphilis. Nonsexually acquired transmission (NSAT) of TPA is possible in infants through close contact. Methods: A descriptive study in five families with NSAT of syphilis was conducted. Polymerase chain reaction detection of TPA in pediatric index cases (n = 6) and their relatives (n = 44) were conducted followed by multilocus sequence typing (MLST). Results: TPA was detected in swab samples in 16 cases and 12 were characterized by MLST. Nichols lineage was identified in two of five families and SS14-lineage in three of five. In four families, MLST profiles linked index cases to relatives. Conclusion: This is the first report of TPA characterization in children infected by NSAT.

A suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples

The performance of commonly used assays for diagnosis of syphilis varies considerably depending on stage of infection and sample type. In response to the need for improved syphilis diagnostics, we develop assays that pair PCR pre-amplification of the tpp47 gene of Treponema pallidum subsp. pallidum with CRISPR-LwCas13a. The PCR-LwCas13a assay achieves an order of magnitude better analytical sensitivity than real-time PCR with equivalent specificity. When applied to a panel of 216 biological specimens, including 135 clinically confirmed primary and secondary syphilis samples, the PCR-LwCas13a assay demonstrates 93.3% clinical sensitivity and 100% specificity, outperforming tpp47 real-time PCR and rabbit-infectivity testing. We further adapt this approach to distinguish Treponema pallidum subsp. pallidum lineages and identify genetic markers of macrolide resistance. Our study demonstrates the potential of CRISPR-based approaches to improve diagnosis and epidemiological surveillance of syphilis.

Performance of Molecular Tests in the Diagnosis of Syphilis From 2009 to 2019: A Systematic Review and Meta-Analysis

BACKGROUND

Syphilis continues to be a public health problem, and its diagnosis still has limitations. Molecular diagnosis provides an alternative for rapid and effective management. The objective is to determine the accuracy of tests in the molecular diagnosis of syphilis.

METHODS

We searched PubMed and Web of Sciences for articles related to molecular detection of syphilis from January 1, 2009, to December 31, 2019. The bivariate Reitsma model and the hierarchical receiver operating characteristic curve model were used to evaluate the diagnostic performance of molecular tests at a 95% confidence interval. A subgroup meta-analysis was performed to explore sources of heterogeneity.

RESULTS

Forty-seven articles were identified for qualitative synthesis, of which 23 met the inclusion criteria for meta-analysis. The pooled sensitivities in conventional polymerase chain reaction (PCR) and real-time PCR were 77.52 (59.50-89.01) and 68.43 (54.96-79.39), respectively. The pooled specificities were 98.00 (90.73-99.59) and 98.84 (97.55-99.46), respectively. Ulcer samples had a better performance (sensitivity of 79.88 [69.00-87.62] and specificity of 98.58 [97.25-99.27]), and the major target genes were the polymerase A gene and tpp47 gene.

CONCLUSIONS

Our work showed that conventional PCR was more widely used than real-time PCR in the diagnosis of syphilis, and ulcers were the best specimens. Sample types and target genes are factors that may influence the quality of the different tests. These results could provide evidence for further work in the direction of providing a more efficient diagnostic test.

[Syphilis infection in the ENT area]

The number of reported cases of syphilis has been increasing for years. The sexually transmitted disease is caused by the spirochete Treponema pallidum subspecies pallidum and progresses in different stages. Symptoms in the ENT area can occur in all stages. This means that a syphilis infection should always be considered by the ENT doctor as a differential diagnosis if the symptoms are suitable. Thus, with increasing oral sexual intercourse, the primary effect/hard chancre is more often observed in the oral cavity. In addition, symptoms can occur not only in the oral cavity, but also in the ear, nose, larynx, cervical and facial regions. The diagnosis is confirmed by direct pathogen detection or by serological detection. The spirochete cannot be cultivated. The therapeutic gold standard is the administration of benzathine penicillin G or procaine penicillin G. Doxycycline, macrolides or ceftriaxone are available as alternatives. In case of inner ear or cranial nerve involvement, the additional administration of a glucocorticoid is recommended. Before antibiotic therapy is administered, the patient must be informed about the possibility of a Jarisch-Herxheimer reaction. In cases of a syphilis infection, a collegial cooperation with the venereologists is always recommended so that an effective and comprehensive diagnosis and therapy can be carried out.

Detection A2058G and A2059G on the 23S rRNA Gene by Multiplex Nested PCR to Identify Treponema pallidum Resistance to Azithromycin in Indonesia

Azithromycin is one of the antibiotics used to treat syphilis, especially in the context of penicillin allergy. Resistance to azithromycin is widely reported associated with one and/or two point mutations on the 23S rRNA gene but has yet to be described in Indonesia. Specimens were collected from 220 patients diagnosed with secondary syphilis. A multiplex nested PCR testing system using the 23S rRNA target gene of Treponema pallidum was designed using three pairs of primers. The first step used PCR pairs of primers to detect T. pallidum. In the second step of PCR using 2 pairs of primers were achieved to identify azithromycin resistant T. pallidum based on A2058G and A2059G point mutations. There was no T.pallidum identified resistant to azithromycin in Jakarta and Bandung. T. pallidum resistance to azithromycin were found in Makassar, Medan, and Bali. The majority of azithromycin resistance was found among heterosexual males and in patients living with HIV. This study has demonstrated T. pallidum resistance to azithromycin in Indonesia appears to be a novel variant of resistance, containing both the A2058G and A2059G mutations that was found in Medan and Makassar.

A New Gold Rush: A Review of Current and Developing Diagnostic Tools for Urinary Tract Infections

Urinary tract infections (UTIs) are one of the most common infections in the United States and consequently are responsible for significant healthcare expenditure. The standard urine culture is the current gold standard for diagnosing urinary tract infections, however there are limitations of the test that directly contribute to increased healthcare costs. As a result, new and innovative techniques have been developed to address the inefficiencies of the current standard-it remains to be seen whether these tests should be performed adjunctly to, or perhaps even replace the urine culture. This review aims to analyze the advantages and disadvantages of the newer and emerging diagnostic techniques such as PCR, expanded quantitative urine culture (EQUC), and next generation sequencing (NGS).

Laboratory Diagnostic Tools for Syphilis: Current Status and Future Prospects

With the increasing number of patients infected with syphilis in the past 20 years, early diagnosis and early treatment are essential to decline syphilis prevalence. Owing to its diverse manifestations, which may occur in other infections, the disease often makes clinicians confused. Therefore, a sensitive method for detecting T. pallidum is fundamental for the prompt diagnosis of syphilis. Morphological observation, immunohistochemical assay, rabbit infectivity test, serologic tests, and nucleic acid amplification assays have been applied to the diagnosis of syphilis. Morphological observation, including dark-field microscopy, silver-staining, and direct fluorescent antibody staining for T. pallidum, can be used as a direct detection method for chancre specimens in primary syphilis. Immunohistochemistry is a highly sensitive and specific assay, especially in the lesion biopsies from secondary syphilis. Rabbit infectivity test is considered as a sensitive and reliable method for detecting T. pallidum in clinical samples and used as a historical standard for the diagnosis of syphilis. Serologic tests for syphilis are widely adopted using non-treponemal or treponemal tests by either the traditional or reverse algorithm and remain the gold standard in the diagnosis of syphilis patients. In addition, nucleic acid amplification assay is capable of detecting T. pallidum DNA in the samples from patients with syphilis. Notably, PCR is probably a promising method but remains to be further improved. All of the methods mentioned above play important roles in various stages of syphilis. This review aims to provide a summary of the performance characteristics of detection methods for syphilis.

The challenging diagnosis of overlapping oral primary/secondary syphilis with nonreactive serology

The prevalence of oral syphilis, known as "the great imitator" because of its diagnostic complexity and varied clinical manifestations, is increasing worldwide, particularly in people living with HIV (PLWH), who could present false-negative serological results. Although some studies have described the variable presentation of oral syphilis in the context of HIV infection, the difficulty in distinguishing between the primary and secondary stages, clinically and histopathologically, underscores the need to describe atypical cases. We report the case of a 28-year-old HIV-positive man presenting with a 3-month history of painless white/red ulcerated lesion on the soft palate. Physical examination revealed an ulcerated lesion with local signs of inflammation. Initial biopsy revealed a nonspecific inflammatory process and immunohistochemistry (IHC) using anti-Treponema pallidum antibodies showed negative results. The results of serological tests for syphilis (Venereal Disease Research Laboratory and fluorescent treponemal antibody-absorption test) were negative on repeated occasions. Nonetheless, polymerase chain reaction (PCR) assay and subsequent IHC for T. pallidum showed positive results, confirming the diagnosis of oral syphilis. This case illustrates that the diagnosis of oral syphilis is challenging in the absence of serological evidence, and specific tests such as PCR and IHC are useful complementary diagnostic tools.

Bacterial sexually transmitted infections

Worldwide, the incidence of bacterial sexually transmitted infections (STIs) has shown a significant increase in recent years. In Germany, this circumstance is reflected by a rise in the number of reported syphilis cases. There has also been an uptick in the incidence of non-notifiable STIs such as gonorrhea and infections caused by Chlamydia trachomatis and Mycoplasma genitalium. A key factor in the spread of these infections is their varied clinical presentation, which includes urogenital, pharyngeal and rectal involvement as well as a large number of asymptomatic cases. New real-time multiplex PCR methods allow for rapid and targeted detection of STI pathogens. The most common bacterial STI is urogenital chlamydial infection caused by serovars D-K, which affects young adults in particular. Lymphogranuloma venereum (LGV) caused by L serovars often presents as chlamydial proctitis. In recent years, Neisseria (N.) gonorrhoeae has shown a significant development of resistance, with high-level monoresistance and multiresistance to antibiotics commonly used for treatment. It is therefore imperative that sensitivity testing of N. gonorrhoeae be performed in addition to nucleic acid amplification tests (NAATs). Increased drug resistance has also been observed for Mycoplasma genitalium, a fact that complicates treatment.

Multiplex PCR Based Urinary Tract Infection (UTI) Analysis Compared to Traditional Urine Culture in Identifying Significant Pathogens in Symptomatic Patients

OBJECTIVE

To evaluate whether multiplex PCR-based molecular testing is noninferior to urine culture for detection of bacterial infections in symptomatic patients.

METHODS

Retrospective record review of 582 consecutive elderly patients presenting with symptoms of lower urinary tract infection (UTI) was conducted. All patients had traditional urine cultures and PCR molecular testing run in parallel.

RESULTS

A total of 582 patients (mean age 77; range 60-95) with symptoms of lower UTI had both urine cultures and diagnostic PCR between March and July 2018. PCR detected uropathogens in 326 patients (56%, 326/582), while urine culture detected pathogens in 217 patients (37%, 217/582). PCR and culture agreed in 74% of cases (431/582): both were positive in 34% of cases (196/582) and both were negative in 40% of cases (235/582). However, PCR and culture disagreed in 26% of cases (151/582): PCR was positive while culture was negative in 22% of cases (130/582), and culture was positive while PCR was negative in 4% of cases (21/582). Polymicrobial infections were reported in 175 patients (30%, 175/582), with PCR reporting 166 and culture reporting 39. Further, polymicrobial infections were identified in 67 patients (12%, 67/582) in which culture results were negative. Agreement between PCR and urine culture for positive cultures was 90%, exceeding the noninferiority threshold of 85% (95% conflict of interest 85.7%-93.6%).

CONCLUSION

Multiplex PCR is noninferior to urine culture for detection and identification of bacteria. Further investigation may show that the accuracy and speed of PCR to diagnose UTI can significantly improve patient outcomes.

Accuracy of PCR and serological testing for the diagnosis of primary syphilis: Both tests are necessary

Syphilis, caused by the spirochete Treponema pallidum subspecies pallidum, is a rising global public health concern and laboratory diagnostics remain challenging. Especially during early disease, rapid and accurate diagnosis is crucial to ensure patients and their contacts receive timely treatment to eradicate infection and prevent further transmission. In this prospective observational study, we evaluated the performance of polymerase chain reaction (PCR) and serological testing for the diagnosis of primary syphilis by evaluating anogenital swabs and sera from 178 Cuban patients presenting with ulcers. Three different PCR assays were evaluated targeting polA, tpp47 and 16S rDNA loci. Sera were evaluated with venereal disease research laboratory (VDRL) and T. pallidum hemagglutination (TPHA) assays. Assuming both methods were confirmatory, our data showed that PCR and serology did not correlate well (agreement = 52.3%, kappa 0.0512, 95% CI −0.0928–0.1951, p = 0.496). The sensitivities, specificities, positive and negative predictive values of the PCR assays were 76.1%, 100%, 100% and 57.9%, respectively, while the values for serology were 62.5%, 100%, 100% and 45.2%, respectively. The combination of PCR and serology can offer valuable information for the diagnosis of syphilis in patients presenting with anogenital ulceration avoiding further clinical complications and disease transmission.

PCR detection for syphilis diagnosis: Status and prospects

Syphilis, a re‐emerging public health problem worldwide caused by Treponema pallidum subsp pallidum (T. pallidum), usually induces systemic and chronic inflammation in hosts who do not receive timely therapy after exposing to high‐risk factors such as leprous sexual contact. Before the treatment, rapid and accurate detection of syphilis is essential. However, the existing detection methods, which focus on the treponemal or non‐treponemal antibody test, both have inherent limitations. For instance, both of them cannot distinguish the stage and severity of syphilis. Non‐treponemal test such as RPR, which is generally deemed to be used for assessing treatment response, is influenced by biological false positives. Therefore, it is imperative to seek out a new and effective diagnostic test. With recent advancements in molecular biology and whole‐genome sequencing, the molecular diagnosis has increased in popularity, especially the use of polymerase chain reaction (PCR). Here, we firstly present a mini‐review on the research of PCR detection methods used for syphilis diagnosis over the past decade, and we then compare these methodologies to assess their potential and the challenges faced. This information can provide a fresh perspective to help researchers address the current challenges.

Bakterielle sexuell übertragbare Infektionen

Bakterielle sexuell übertragbare Infektionen (STI) zeigen seit Jahren weltweit eine deutliche Zunahme. In Deutschland wird diese Tatsache durch steigende Meldezahlen für Syphilis bestätigt. Auch für die nicht meldepflichtigen STI Gonorrhoe, Chlamydia-trachomatis- und Mycoplasma-genitalium-Infektionen wird eine zunehmende Inzidenz beobachtet. Entscheidend für die Weiterverbreitung ist, dass das breite klinische Spektrum, welches neben Urogenitalsitus auch Pharynx und Rektum einbezieht, durch eine hohe Zahl asymptomatischer Verläufe ergänzt wird. Neue Real-Time-Multiplex-Diagnostikverfahren ermöglichen einen schnellen und gezielten Nachweis von STI-Erregern. Die häufigste bakterielle STI ist die urogenitale Chlamydieninfektion mit den Serovaren D-K, die besonders bei jungen Erwachsenen auftritt. Einer Chlamydien-Proktitis kann eine Infektion mit L-Serovaren und damit eine Lymphogranuloma-venereum (LGV)-Infektion zugrunde liegen. Neisseria (N.) gonorrhoeae zeigte in den letzten Jahren eine starke Resistenzentwicklung mit Ausbildung von Einzel- und Multiresistenzen gegenüber bisher gängigen Antibiotika. Daher ist für N. gonorrhoeae zusätzlich zum nucleic acid amplification test (NAAT) eine kulturelle Empfindlichkeitstestung durchzuführen. Auch für Mycoplasma genitalium sind Resistenzentwicklungen bekannt, die eine Therapie erschweren können.

Functional Annotation of Proteins Encoded by the Minimal Bacterial Genome Based on Secondary Structure Element Alignment

In synthetic biology, one of the key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0, which only encoded 438 essential proteins. However, among them functions of 149 proteins remain unknown because of the lack of effective annotation method. Here, we report a secondary structure element alignment method called SSEalign based on an effective training data set extracting from various bacterial genomes. The experimentally validated homologous genes in different species were selected as training positives, while unrelated genes in different species were selected as training negatives. Moreover, SSEalign used a set of well-defined basic alignment elements with the backtracking line search algorithm to derive the best parameters for accurate prediction. Experimental results showed that SSEalign achieved 88.2% test accuracy, which is better than the existing prediction methods. SSEalign was subsequently applied to identify the functions of those unannotated proteins in the latest published minimal bacteria genome JCVI-syn3.0. Results indicated that at least 136 proteins out of 149 unannotated proteins in the JCVI-syn3.0 genome could be annotated by SSEalign. Our method is effective for the identification of protein homology in JCVI-syn3.0 and can be used to annotate those hypothetical proteins in other bacterial genomes.

Sensitive detection of Treponema pallidum DNA from the whole blood of patients with syphilis by the nested PCR assay

The aim of this work was to investigate the application of the nested PCR assay for the detection of Treponema pallidum (TP) DNA from the blood of patients with different stages of syphilis. In this study, a nested PCR method targeting the Tpp47 and polA genes (Tpp47-Tp-PCR and polA-Tp-PCR) was developed to detect TP-DNA in whole blood samples collected from 262 patients with different stages of syphilis (84 primary syphilis, 97 secondary syphilis, and 81 latent syphilis patients). The PCR assay detected T. pallidum DNA in 53.6% and 62.9% of the patients with primary and secondary syphilis, respectively, which was much higher than the detection levels in patients with latent syphilis (7.4%) (both p < 0.001). For primary syphilis, a low RPR (0–16) was correlated with a higher detection rate of TP-DNA, whereas for secondary syphilis, the higher detection rate of blood TP-DNA was correlated with higher blood RPR titers (at or beyond 32). For latent syphilis, TP-DNA was only detectable by PCR in the early phase of the latent infection. Thus, blood RPR titers were correlated with the blood T. pallidum burden, but the correlations varied with primary and secondary syphilis. The results indicate that nested PCR is a sensitive method for detecting blood TP-DNA and is especially useful for detecting early syphilis including primary syphilis and secondary syphilis. The findings also suggest that the PCR assay may be used to complement other methods to enhance the diagnosis of syphilis.

Detección de Treponema pallidum subespecie pallidum para el diagnóstico de sífilis congénita mediante reacción en cadena de la polimerasa anidada

Introducción. La sífilis es una enfermedad producida por Treponema pallidum subespecie pallidum cuya incidencia mundial es de 12 millones de casos por año, aproximadamente; de estos, más de dos millones se presentan en mujeres gestantes, siendo la sífilis congénita la complicación más grave de esta infección en el embarazo.Objetivo. Detectar la presencia de T. pallidum subespecie pallidum en muestras clínicas para el diagnóstico de sífilis congénita mediante reacción en cadena de la polimerasa (PCR) anidada y determinar su concordancia con las pruebas serológicas.Materiales y métodos. Mediante PCR convencional y anidada, se amplificaron tres genes diana (polA, 16S ADNr y TpN47) y se confirmaron los productos de amplificación de los genes TpN47 y polA por secuenciación. Las pruebas serológicas empleadas fueron la VDRL (Venereal Disease Research Laboratory), la de reagina plasmática rápida (Rapid Plasma Reagin, RPR) y la de aglutinación de partículas para Treponema pallidum (Treponema pallidum Particle Agglutination Assay, TPPA).Resultados. La sensibilidad para la PCR convencional fue de 52 pg y, para la PCR anidada, de 0,52 pg. La especificidad con los iniciadores TpN47 y polA fue de 100 %; los resultados de la secuenciación mostraron una identidad de 97 % con T. pallidum. En 70 % de las muestras, los resultados de las pruebas serológicas y la PCR anidada concordaron.Conclusión. El gen TpN47 resultó ser el mejor blanco molecular para la identificación de T. pallidum. La PCR anidada se presenta como una alternativa de diagnóstico molecular promisoria para el diagnóstico de sífilis congénita.

Cross-sectional study of Treponema pallidum PCR in diagnosis of primary and secondary syphilis

BACKGROUND

Syphilis remains a major challenge and a complex diagnosis. We aim to evaluate the role of polymerase chain reaction (PCR) in Treponema pallidum (Tp) detection in various types of biological samples in the diagnosis of early syphilis.

METHODS

We conducted a cross-sectional study including all attendees of the STI clinic with clinical suspicion of early syphilis. One or more specimens for the detection of Tp by PCR testing were collected.

RESULTS

The overall sensitivity of Tp PCR test was 82.61% (95% CI: 68.6-92.2%). Tp PCR test had sensitivity of 84.6% (95% CI: 54.6-98.1%) in primary syphilis cases and 81.8% (95% CI: 64.5-93%) in secondary syphilis cases. PCR test performance was independent of HIV status.

CONCLUSION

Tp PCR test is a fast and reliable method for the detection of Tp in skin lesions of early syphilis, and it is a powerful tool in clinical settings.

Return of the Great Pox

Syphilis is on the increase globally. While recognized more frequently in patients with, HIV/AIDS, it is not unusual among immune competent individuals sometimes presenting with unusual manifestations and/or behaviour. This paper reviews the history and clinical features of syphilis and draws attention to the oral manifestations. CPD/Clinical Relevance: Syphilis should be in the differential diagnosis of oral ulcers or unusual oral lesions.