Novel detection of Leishmania RNA virus-1 (LRV-1) in clinical isolates of Leishmania Viannia panamensis

American tegumentary leishmaniasis comprises a discrete set of clinical presentations endemic to Latin America. Leishmania RNA virus-1 (LRV-1) is a double-stranded RNA virus identified in 20–25% of the Leishmania Viannia braziliensis and L. V. guyanensis, however not in L. V. panamensis. This is the first report of LRV-1 in L. V. panamensis and its associations with clinical phenotypes of ATL. Unique surplus discard clinical isolates of L. V. panamensis were identified from the Public Health Ontario Laboratory (PHOL) and the Leishmania Clinic of the Instituto de Medicina Tropical ‘Alexander von Humboldt’ between 2012 and 2019 and screened for LRV-1 by real-time polymerase chain reaction. Patient isolates were stratified according to clinical phenotype. Of 30 patients with L. V. panamensis, 14 (47%) and 16 (53%) patients had severe and non-severe ATL, respectively. Five (36%) of 14 severe cases and 2 (12%) of 16 non-severe cases were positive for LRV-1, respectively. No differences in sex were observed for clinical phenotype and LRV-1 status. Although an association between LRV-1 status and clinical phenotype was not demonstrated, this is the first description of the novel detection of LRV-1 in L. V. panamensis, a species that has been documented predominantly in Central America.

Interventions to enhance testing and linkage to treatment for hepatitis C infection for people who inject drugs: A systematic review and meta-analysis

BACKGROUND

With the advent of direct acting antiviral (DAA) therapies for the treatment of hepatitis C virus (HCV), the World Health Organization recommended a goal to eliminate HCV as a public health threat globally by 2030. With the majority of new and existing infections in high income countries occurring among people who inject drugs, achieving this goal will require the design and implementation of interventions which address the unique barriers to HCV care faced by this population.

METHODS

In this systematic review and meta-analysis, we searched bibliographic databases and conference abstracts to July 21, 2020 for studies assessing interventions to improve the following study outcomes: HCV antibody testing, HCV RNA testing, linkage to care, and treatment initiation. We included both randomised and non-randomised studies which included a comparator arm. We excluded studies which enrolled only paediatric populations (<18 years old) and studies where the intervention was conducted in a different healthcare setting than the control or comparator. This analysis was restricted to studies conducted among people who inject drugs. Data were extracted from the identified records and meta-analysis was used to pool the effect of interventions on study outcomes. This study was registered in PROSPERO (CRD42020178035).

FINDINGS

Of 15,342 unique records, 45 studies described the implementation of an intervention to improve HCV testing, linkage to care and treatment initiation among people who inject drugs. These included 27 randomised trials and 18 non-randomised studies with the risk of bias rated as "critical" for most non-randomised studies. Patient education and patient navigation to address patient-level barriers to HCV care were shown to improve antibody testing uptake and linkage to HCV care respectively although patient education did not improve antibody testing when restricted to randomised studies. Provider care coordination to address provider level barriers to HCV care was effective at improving antibody testing uptake. Three different interventions to address systems-level barriers to HCV care were effective across different stages of HCV care: point-of-care antibody testing (linkage to care); dried blood-spot testing (antibody testing uptake); and integrated care (linkage to care and treatment initiation).

INTERPRETATION

Multiple interventions are available that can address the barriers to HCV care for people who inject drugs at the patient-, provider-, and systems-level. The design of models of care to improve HCV testing and treatment among people who inject drugs must consider the unique barriers to care that this population faces. Further research, including high-quality randomised controlled trials, are needed to robustly assess the impact these interventions can have in varied populations and settings.

Predictors of Chronic Fatigue Syndrome and Mood Disturbance After Acute Infection

Prospective cohort studies following individuals from acute infections have documented a prevalent post-infective fatigue state meeting diagnostic criteria for chronic fatigue syndrome (CFS) – that is, a post-infective fatigue syndrome (PIFS). The Dubbo Infection Outcomes Study (DIOS) was a prospective cohort following individuals from acute infection with Epstein-Barr virus (EBV), Ross River virus (RRV), or Q fever through to assessment of caseness for CFS designated by physician and psychiatrist assessments at 6 months. Previous studies in DIOS have revealed that functional genetic polymorphisms in both immunological (pro- and anti-inflammatory cytokines) and neurological (the purinergic receptor, P2X7) genes are associated with both the severity of the acute infection and subsequent prolonged illness. Principal components analysis was applied to self-report data from DIOS to describe the severity and course of both the overall illness and concurrent mood disturbance. Associations between demographics and acute infection characteristics, with prolonged illness course as well as the PIFS outcome were examined using multivariable statistics. Genetic haplotype-driven functional variations in the neuropeptide Y (NPY) gene previously shown to be associated with brain responses to stress, and to trait anxiety were also examined as predictors. The sample included 484 subjects (51% female, median age 32, IQR 19–44), of whom 90 (19%) met diagnostic criteria for CFS at 6 months. Participants with greater overall illness severity and concurrent mood disturbance in the acute illness had a more prolonged illness severity (HR = 0.39, 95% CI: 0.34–0.46, p &lt; 0.001) and mood disturbance (HR = 0.36, 95% CI: 0.30–0.42, p &lt; 0.001), respectively. Baseline illness severity and RRV infection were associated with delayed recovery. Female gender and mood disturbance in the acute illness were associated with prolonged mood disturbance. Logistic regression showed that the odds of an individual being diagnosed with PIFS increased with greater baseline illness severity (OR = 2.24, 95% CI: 1.71–2.94, p &lt; 0.001). There was no association between the NPY haplotypes with overall illness severity or mood disturbance either during the acute illness phase or with prolonged illness (p &gt; 0.05). Severe acute infective illnesses predicted prolonged illness, prolonged mood disturbance and PIFS. These factors may facilitate early intervention to manage both PIFS and mood disturbances.

Elevated baseline expression of seven virulence factor RNA transcripts in visceralizing species of Leishmania: a preliminary quantitative PCR study

Introduction:

Leishmaniasis is a neglected tropical disease that manifests as three major disease phenotypes: cutaneous, mucocutaneous, and visceral. In this preliminary study, we quantified virulence factor (VF) RNA transcript expression in Leishmania species, stratified by geographic origin and propensity for specific disease phenotypes.

Methods:

Cultured promastigotes of 19 Leishmania clinical and ATCC isolates were extracted for total cellular RNA, cDNA was reverse transcribed, and qPCR assays were performed to quantify VF RNA transcript expression for hsp23, hsp70, hsp83, hsp100, mpi, cpb, and gp63.

Results:

Comparison of visceralizing species (Leishmania donovani, Leishmania chagasi, and Leishmania infantum) versus non-visceralizing species [Leishmania (Viannia) spp., Leishmania tropica, Leishmania major, Leishmania mexicana, and Leishmania amazonensis] revealed a significantly greater pooled transcript expression for visceralizing species (p = 0.0032). Similarly, Old World species demonstrated significantly higher VF RNA transcript expression than New World species (p = 0.0015). On a per-gene basis, species with a propensity to visceralize ubiquitously expressed higher levels of gp63 (p = 0.005), cpb (p = 0.0032), mpi (p = 0.0032), hsp23 (p = 0.0039), hsp70 (p = 0.0032), hsp83 (p = 0.0032), and hsp100 (p = 0.0032).

Conclusion:

Here, we provide quantitative, preliminary evidence of elevated VF RNA transcript expression driven largely by the visceralizing causative species of Leishmania. This work highlights the extensive heterogeneity in pathogenicity mechanisms between Leishmania species, which may partly underpin the fatal progression of visceral leishmaniasis.

Interventions to enhance testing, linkage to care, and treatment initiation for hepatitis C virus infection: a systematic review and meta-analysis

BACKGROUND

Despite the goal set by WHO to eliminate hepatitis C virus (HCV) as a public health threat, uptake of HCV testing and treatment remains low. To achieve this target, evidence-based interventions are needed to address the barriers to care for people with, or at risk of, HCV infection. We aimed to assess the efficacy of interventions to improve HCV antibody testing, HCV RNA testing, linkage to HCV care, and treatment initiation.

METHODS

In this systematic review and meta-analysis, we searched MEDLINE (PubMed), Scopus, Web of Science, the Cochrane Central Register of Controlled Trials, and PsycINFO without language restrictions for reports published between database inception and July 21, 2020, assessing the following primary outcomes: HCV antibody testing; HCV RNA testing; linkage to HCV care; and direct-acting antiviral treatment initiation. We also searched key conference abstracts. We included randomised and non-randomised studies assessing non-pharmaceutical interventions that included a comparator or control group. Studies were excluded if they enrolled only paediatric populations (aged <18 years) or if they conducted the intervention in a different health-care setting to that of the control or comparator. Authors were contacted to clarify study details and to obtain additional population-level data. Data were extracted from the records identified into a pre-piloted and standardised data extraction form and a random-effects meta-analysis was used to pool the effects of the interventions on study outcomes. This study is registered in PROSPERO, CRD42020178035.

FINDINGS

Of 15 342 unique records identified, 142 were included, which reported on 148 unique studies (47 randomised controlled trials and 101 non-randomised studies). Medical chart reminders, provider education, and point-of-care antibody testing significantly improved at least three study outcomes compared with a comparator or control. Interventions that simplified HCV testing, including dried blood spot testing, point-of-care antibody testing, reflex RNA testing, and opt-out screening, significantly improved testing outcomes compared with a comparator or control. Enhanced patient and provider support through patient education, provider care coordination, and provider education also significantly improved testing outcomes compared with a comparator or control. Integrated care and patient navigation or care coordination significantly improved linkage to care and the uptake of direct-acting antiviral treatment compared with a comparator or control.

INTERPRETATION

Several interventions to improve HCV care that address several key barriers to HCV care were identified. New models of HCV care must be designed and implemented to address the barriers faced by the population of interest. Further high-quality research, including rigorously designed randomised studies, is still needed in key populations.

FUNDING

None.

Evaluation of a point-of-care molecular detection device for Leishmania spp. and intercurrent fungal and mycobacterial organisms in Peruvian patients with cutaneous ulcers

PURPOSE

Overlapping clinical features of cutaneous leishmaniasis (CL) with ulcers caused by fungi and mycobacteria necessitate confirmatory diagnostic testing. We evaluated a handheld battery-operated device for detection of CL and common fungal and mycobacterial causes of ulcers.

METHODS

We validated Palm PCR™ for detection of common ulcerative skin pathogens using ATCC^® reference and clinical strains of Leishmania, mycobacteria, and fungi in the lab and field. Amplified products were Sanger sequenced. Performance characteristics were calculated using conventional PCR as a reference standard.

RESULTS

Palm PCR™ detected 100% of ATCC^® strains of Leishmania, fungi, and mycobacteria, with sensitivity and specificity of 90% and 91.7%, respectively. In the field, the sensitivity for detection of Leishmania in patients with suspected CL was 100%. In 61% of CL patients, co-colonization with genera such as Malassezia, Aspergillus, Candida, and Cladosporium was detected. In 50% of CL patients with an inflammatory (secondarily infected) phenotype, detected fungal species had known associations with human cutaneous disease.

CONCLUSIONS

Palm PCR™ performs comparably to conventional PCR for detection of Leishmania, fungi, and mycobacteria. This work has implications for the diagnostic approach to tropical ulcers, and has the potential to improve field detection of ulcerative pathogens in resource constrained areas.

Comparison of Whole Genome Sequencing versus Standard Molecular Diagnostics for Species Identification in the Leishmania Viannia Subgenus

The prognosis and treatment of New World tegumentary leishmaniasis is dependent on the infecting species, yet such species identification in the Leishmania Viannia subgenus poses a diagnostic challenge. Currently, speciation relies on standard molecular techniques such as restriction fragment length polymorphism (RFLP) analysis, and Sanger sequencing (SS). Whole-genome sequencing (WGS) is a robust and increasingly cost-efficient tool that may improve Leishmania species identification. We evaluated WGS versus standard RFLP-SS for species identification in three reference and five clinical strains of Leishmania Viannia spp. Internal transcribed spacer1 (its1), cysteine proteinase b (cpb), and heat shock protein 70 (hsp70) polymerase chain reaction-restriction fragment length polymorphism (RFLP) was performed, followed by SS of the its2, cpb, hsp70, and mannose phosphate isomerase (mpi) loci. After de novo assembly, sequences were mapped, and homology compared with both reference strains and reference genomes on National Center for Biotechnology Information. All American Type Culture Collection strains were confirmed to be single-species of L. V. braziliensis, L. V. guyanensis, or L. V. panamensis by WGS. Conversely, RFLP-SS was able to definitively identify one of three isolates to the species level. Clinical samples were identified as either single-species (N = 3), mixed (N = 1), or hybrid (N = 1) infections by WGS, while standard molecular diagnosis required multi-target composite analysis for identification due to loci-dependent results by RFLP-SS. We have corroborated the utility of WGS as a diagnostic tool to speciate members of the L. Viannia subgenus and to discriminate between mixed and hybrid infections. WGS is a potentially useful complement to multistaged RFLP-SS for species identification in Leishmania infections.

The severity of the pathogen-induced acute sickness response is affected by polymorphisms in genes of the NLRP3 inflammasome pathway

The acute sickness response (ASR) is a stereotyped set of symptoms including fatigue, pain, and disturbed mood, which are present in most acute infections. The immunological mechanisms of the ASR are conserved, with variations in severity determined partly by the pathogen, but also by polymorphisms in host genes. The ASR was characterised in three different serologically-confirmed acute infections in Caucasians (n = 484) across four symptom domains or endophenotypes (termed 'Fatigue', 'Musculoskeletal pain', 'Mood disturbance', and 'Acute sickness'). Correlations were sought with functional single nucleotide polymorphisms in the NLRP3 inflammasone pathway and severity of the endophenotypes. Individuals with severe Fatigue, Musculoskeletal pain, or Mood endophenotypes were more likely to have prior episodes of significant fatigue (11.4 vs. 3.8%, p = 0.07), pain (14.3 vs. 1.2%, p = 0.001), or Mood disturbance (13 vs 1%, p=0.001), suggesting trait characteristics. The high functioning allele of the rs35829419 SNP in NLRP3 was more common in those with severe Fatigue (OR = 13.3, 95% CI: 1.7-104), particularly in a dominant inheritance pattern (OR = 13.4, 95% CI: 1.8-586.3). In a multivariable analysis assuming dominant inheritance, both rs35829419 and the rs4848306 SNP in Interleukin(IL)-1β, were independently associated with severe Fatigue (OR = 29.6, 95% CI: 2.6-330.9 and OR = 13, 95% CI: 2.7-61.8, respectively). The severity of fatigue in acute infection is influenced by genetic polymorphisms in NLRP3 and IL-1β.

Single molecule, near full-length genome sequencing of dengue virus

Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome. This process is laborious, costly and requires at least 10 primers per serotype, thus increasing the likelihood of PCR bias. We introduce an assay to amplify near full-length dengue virus genomes as intact molecules, sequence these amplicons with third generation “nanopore” technology without fragmenting and use the sequence data to differentiate within-host viral variants with a bioinformatics tool (Nano-Q). The new assay successfully generated near full-length amplicons from DENV serotypes 1, 2 and 3 samples which were sequenced with nanopore technology. Consensus DENV sequences generated by nanopore sequencing had over 99.5% pairwise sequence similarity to Illumina generated counterparts provided the coverage was > 100 with both platforms. Maximum likelihood phylogenetic trees generated from nanopore consensus sequences were able to reproduce the exact trees made from Illumina sequencing with a conservative 99% bootstrapping threshold (after 1000 replicates and 10% burn-in). Pairwise genetic distances of within host variants identified from the Nano-Q tool were less than that of between host variants, thus enabling the phylogenetic segregation of variants from the same host.

Leishmania RNA Virus 1 (LRV-1) in Leishmania (Viannia) braziliensis Isolates from Peru: A Description of Demographic and Clinical Correlates

RNA virus 1-1 (LRV-1-1) is a dsRNA virus identified in isolates of Leishmania (Viannia) braziliensis and thought to advance localized cutaneous leishmaniasis (LCL) to mucocutaneous or mucosal leishmaniasis (MCL/ML). We examined the prevalence of LRV-1 and its correlation to phenotypes of American tegumentary leishmaniasis caused by L. (V.) braziliensis from Peru to better understand its epidemiology. Clinical isolates of L. (V.) braziliensis were screened for LRV-1 by real-time polymerase chain reaction (PCR) and stratified according to the phenotype: LCL (< 4 ulcers in number) MCL/ML; inflammatory ulcers (erythematous, purulent, painful ulcers with or without lymphatic involvement) or multifocal ulcers (≥ 4 in ≥ 2 anatomic sites). Proportionate LRV-1 positivity was compared across phenotypes. Of 78 L. (V.) braziliensis isolates, 26 (54.2%) had an inflammatory phenotype, 22 (28%) had the MCL/ML phenotype, whereas 30 (38.5%) had LCL. Mucocutaneous or mucosal leishmaniasis was found exclusively in adult male enrollees. Leishmania RNA virus 1 positivity by phenotype was as follows: 9/22 (41%) with MCL/ML; 5/26 (19%) with an inflammatory/multifocal cutaneous leishmaniasis phenotype; and 7/30 (23%) with LCL (P = 0.19). Leishmania RNA virus 1 positivity was not associated with age (P = 0.55) or gender (P = 0.49). Relative LRV-1 copy number was greater in those with MCL/ML than those with inflammatory/multifocal CL (P = 0.02). A direct association between LRV-1 status and clinical phenotype was not demonstrated; however, relative LRV-1 copy number was highest in those with MCL/ML. Future analyses to understand the relationship between viral burden and pathogenesis are required to determine if LRV-1 is truly a contributor to the MCL/ML phenotype.

Virulence factor RNA transcript expression in the Leishmania Viannia subgenus: influence of species, isolate source, and Leishmania RNA virus-1

BACKGROUND

Leishmania RNA virus-1 (LRV1) is a double-stranded RNA virus identified in 20-25% of Viannia-species endemic to Latin America, and is believed to accelerate cutaneous to mucosal leishmaniasis over time. Our objective was to quantify known virulence factor (VF) RNA transcript expression according to LRV1 status, causative species, and isolate source.

METHODS

Eight cultured isolates of Leishmania were used, four of which were LRV1-positive (Leishmania Viannia braziliensis [n = 1], L. (V.) guyanensis [n = 1], L. (V.) panamensis [n = 2]), and four were LRV1-negative (L. (V.) panamensis [n = 3], L. (V.) braziliensis [n = 1]). Promastigotes were inoculated into macrophage cultures, and harvested at 24 and 48 h. RNA transcript expression of hsp23, hsp70, hsp90, hsp100, mpi, cpb, and gp63 were quantified by qPCR.

RESULTS

RNA transcript expression of hsp100 (p = 0.012), cpb (p = 0.016), and mpi (p = 0.022) showed significant increases from baseline pure culture expression to 24- and 48-h post-macrophage infection, whereas hsp70 (p = 0.004) was significantly decreased. A trend toward increased transcript expression of hsp100 at baseline in isolates of L. (V.) panamensis was noted. Pooled VF RNA transcript expression by L. (V.) panamensis isolates was lower than that of L. (V.) braziliensis and L. (V.) guyananesis at 24 h (p = 0.03). VF RNA transcript expression did not differ by LRV1 status, or source of cultured isolate at baseline, 24, or 48 h; however, a trend toward increased VF RNA transcript expression of 2.71- and 1.93-fold change of mpi (p = 0.11) and hsp90 (p = 0.11), respectively, in LRV1 negative isolates was noted. Similarly, a trend toward lower levels of overall VF RNA transcript expression in clinical isolates (1.15-fold change) compared to ATCC® strains at 24 h was noted (p = 0.07).

CONCLUSIONS

Our findings suggest that known VF RNA transcript expression may be affected by the process of macrophage infection. We were unable to demonstrate definitively that LRV-1 presence affected VF RNA transcript expression in the species and isolates studied. L. (V.) guyanensis and L. (V.) braziliensis demonstrated higher pooled VF RNA transcript expression than L. (V.) panamensis; however, further analyses of protein expression to corroborate this finding are warranted.

Quantification of Leishmania (Viannia) Kinetoplast DNA in Ulcers of Cutaneous Leishmaniasis Reveals Inter-site and Inter-sampling Variability in Parasite Load

Background

Cutaneous leishmaniasis (CL) is a skin disease caused by the protozoan parasite Leishmania. Few studies have assessed the influence of the sample collection site within the ulcer and the sampling method on the sensitivity of parasitological and molecular diagnostic techniques for CL. Sensitivity of the technique can be dependent upon the load and distribution of Leishmania amastigotes in the lesion.

Methodology/Principal Findings

We applied a quantitative real-time PCR (qPCR) assay for Leishmania (Viannia) minicircle kinetoplast DNA (kDNA) detection and parasite load quantification in biopsy and scraping samples obtained from 3 sites within each ulcer (border, base, and center) as well as in cytology brush specimens taken from the ulcer base and center. A total of 248 lesion samples from 31 patients with laboratory confirmed CL of recent onset (≤3 months) were evaluated. The kDNA-qPCR detected Leishmania DNA in 97.6% (242/248) of the examined samples. Median parasite loads were significantly higher in the ulcer base and center than in the border in biopsies (P<0.0001) and scrapings (P = 0.0002). There was no significant difference in parasite load between the ulcer base and center (P = 0.80, 0.43, and 0.07 for biopsy, scraping, and cytology brush specimens, respectively). The parasite load varied significantly by sampling method: in the ulcer base and center, the descending order for the parasite load levels in samples was: cytology brushes, scrapings, and biopsies (P<0.0001); in the ulcer border, scrapings had higher parasite load than biopsies (P<0.0001). There was no difference in parasite load according to L. braziliensis and L. peruviana infections (P = 0.4).

Conclusion/Significance

Our results suggest an uneven distribution of Leishmania amastigotes in acute CL ulcers, with higher parasite loads in the ulcer base and center, which has implications for bedside collection of diagnostic specimens. The use of scrapings and cytology brushes is recommended instead of the more invasive biopsy.

Cutaneous leishmaniasis (CL) is a parasitic disease of the skin caused by obligate intra-macrophage protozoa of the genus Leishmania which usually presents as ulcerative lesions at the site of infection. Traditionally, histopathological and diagnostic studies on CL have employed samples collected from the border of the ulcer since this area is believed to contain the highest amount of parasites. However, no formal demonstration of the distribution of Leishmania parasites in the ulcer has been provided yet. Focusing on human skin lesions of recent onset (≤3 months) caused by L. (Viannia) species, we estimated the parasite loads among different skin lesion sites by means of quantitative real-time PCR targeting the parasite kinetoplast DNA. Paired lesion samples collected by use of different sampling methods were analyzed. We found that the ulcerated zone of the lesion contained a higher parasite load than the ulcer border, and that scraping and cytology brush specimens presented higher parasite loads as compared to the more invasive biopsy. Our results have implications for bedside collection of diagnostic and post-therapeutic follow-up specimens from CL patients.

[Detection of Leishmania spp. based on the gene encoding HSP20]

OBJECTIVES

Explore a new target for molecular diagnosis of Leishmania.

MATERIALS AND METHODS

We evaluated the utility of the gene that encodes the heat shock protein 20-kDa (Hsp20) for detecting Leishmania by polymerase chain reaction (PCR). PCR was normalized and analytical parameters were determined, as well as the validity and diagnostic accuracy, and concordance with the PCR - 18S. PCR-Hsp20 with DNA was obtained from a group of clinical samples from different sources.

RESULTS

The analytical parameters were adequate. The sensitivity obtained was 86% and the specificity was 100%. The concordance with the reference method was good (κ = 0.731), which supports its potential use for diagnosis. The possibility of subsequent identification of the species by sequencing the amplified product gives an additional advantage.

CONCLUSIONS

The usefulness of this gene as a new target for the detection of Leishmania was demonstrated. Because of its potential, it is recommended to improve the sensitivity of the method and to evaluate it in different endemic regions.

Clinical and demographic stratification of test performance: a pooled analysis of five laboratory diagnostic methods for American cutaneous leishmaniasis

We evaluated performance characteristics of five diagnostic methods for cutaneous leishmaniasis. Patients who came to the Leishmania Clinic of Hospital Nacional Cayetano Heredia in Lima, Peru, were enrolled in the study. Lesion smears, culture, microculture, polymerase chain reaction (PCR), and leishmanin skin test (LST) were performed. A total of 145 patients with 202 lesions were enrolled: 114 patients with 161 lesions fulfilled criteria for cutaneous leishmaniasis. Sensitivity and specificity were 57.8% (95% confidence interval [CI] = 50.2-65.4%) and 100.0% for culture, 78.3% (95% CI = 71.9-84.7%) and 100.0% for microculture, 71.4% (95% CI = 64.4-78.4%) and 100.0% for smears, 78.2% (95% CI = 70.6-85.8%) and 77.4% (95% CI = 62.7-92.1%) for LST, and 96.9% (95% CI = 94.2-99.6%) and 65.9% (95% CI = 51.4-80.4%) for PCR. PCR was more sensitive than the other assays (P < 0.001). Sensitivities of culture, smears, and LST varied by lesion duration and appearance. PCR offers performance advantages over other assays, irrespective of patient age, sex, lesion duration, or appearance. That clinical factors influence performance of non-molecular assays offers clinicians a patient-focused approach to diagnostic test selection.