Genotyping of Mycobacterium leprae for understanding the distribution and transmission of leprosy in endemic provinces of China

Molecular epidemiological characteristics of Mycobacterium leprae in highly endemic areas of China during the COVID-19 epidemic

Objectives

The present study analyzed the impact of the COVID-19 pandemic on the prevalence and incidence of new leprosy cases, as well as the diversity, distribution, and temporal transmission of Mycobacterium leprae strains at the county level in leprae-endemic provinces in Southwest China.

Methods

A total of 219 new leprosy cases during two periods, 2018-2019 and 2020-2021, were compared. We genetically characterized 83 clinical isolates of M. leprae in Guizhou using variable number tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). The obtained genetic profiles and cluster consequences of M. leprae were compared between the two periods.

Results

There was an 18.97% decrease in the number of counties and districts reporting cases. Considering the initial months (January-March) of virus emergence, the number of new cases in 2021 increased by 167% compared to 2020. The number of patients with a delay of >12 months before COVID-19 (63.56%) was significantly higher than that during COVID-19 (48.51%). Eighty-one clinical isolates (97.60%) were positive for all 17 VNTR types, whereas two (2.40%) clinical isolates were positive for 16 VNTR types. The (GTA)9, (TA)18, (TTC)21 and (TA)10 loci showed higher polymorphism than the other loci. The VNTR profile of these clinical isolates generated five clusters, among which the counties where the patients were located were adjacent or relatively close to each other. SNP typing revealed that all clinical isolates possessed the single SNP3K.

Conclusion

COVID-19 may have a negative/imbalanced impact on the prevention and control measures of leprosy, which could be a considerable fact for official health departments. Isolates formed clusters among counties in Guizhou, indicating that the transmission chain remained during the epidemic and was less influenced by COVID-19 preventative policies.

Multiplex PCR-based RFLP assay for early identification of prevalent Mycobacterium leprae genotypes

Mycobacterium leprae is classified into four SNP genotypes and 16 subtypes (from 1A to 4P) that exhibit phylogeographical association reported from around the world. Among them, genotypes 1D and 3I represent more than 60% of M. leprae strains. Here, we report a new method for M. leprae genotyping which identifies the genotypes 1D and 3I by combining multiplex PCR amplification and restriction fragment length polymorphism (RFLP) of a M. leprae DNA amplicons using AgeI restriction enzyme. Agarose gel electrophoresis showed a deletion of 11 bp only among 3I genotypes by electrophoresis. When this multiplex PCR reaction is subjected to AgeI digestion, successful restriction digestion shows three bands for all the genotypes except 1D where only two bands were observed due to loss of restriction site. This method gives us the advantage of 1-step identification of the two most prevalent strains of M. leprae without using specialized equipments such as the Sanger sequencing system or quantitative PCR.

Leprosy among new child cases in China: Epidemiological and clinical analysis from 2011 to 2020

BACKGROUND

Leprosy, caused by Mycobacterium leprae infection, mainly affects skin and peripheral nerves and may further lead to disability and deformity if not treated timely. The new case detection rate of leprosy in children reflects the active transmission of leprosy infection. This study aims to present the epidemiology and clinical characteristics of new leprosy cases in children in China from 2011 to 2020.

METHODOLOGY/PRINCIPAL FINDINGS

All data from leprosy patients younger than 15 years old were extracted from the Leprosy Management Information System in China (LEPMIS). Statistical Package for the Social Sciences (SPSS) version 12.0 was used for descriptive and analytical statistics of the epidemiological and clinical indicators by the Mann-Whitney test, Kruskal-Wallis test, and Fisher's exact test. And geographical distribution was analyzed by ArcGIS 10.5. A total of 152 pediatric new cases of leprosy were found over the last decade. The new case detection rate of pediatric leprosy cases decreased from 0.13 to 0.02 per 1,000,000 population over the last ten years. New pediatric cases had a higher new case detection rate in Guizhou, Sichuan, and Yunnan Provinces. All but 7 provinces in China achieved zero new child case for consecutive five years. The onset of leprosy peaked between 10 and 14 years of age, and the male to female ratio was 1.71:1. Pediatric patients were predominantly infected from symptomatic household adult contacts HHCs. Multibacillary leprosy (MB) was the most common. However, a low proportion of patients developed leprosy reaction and grade 2 disability.

CONCLUSIONS/SIGNIFICANCE

The new case detection rate of pediatric leprosy cases has decreased over the past ten years in China. Spatial analysis indicated clusters in high-endemic areas. Leprosy transmission has stopped in the majority of provinces in China. However, sporadic cases may continue to exist for a long time. Active surveillance especially contact tracing should be focused on in future plan for management of leprosy, and interventions in leprosy clusters should be prioritized.

Leprosy Epidemiology According to Leprosy Type in 13 Teaching Hospitals in Indonesia between 2018 and 2020

BACKGROUND: Leprosy or Hansen’s disease is an infectious disease caused by Mycobacterium leprae (M. leprae) bacilli which results in chronic infections in humans that affect the peripheral nerves, skin, and other organs such as the eyes, mucous membranes, bones, and testicles. Leprosy has a variety of clinical presentations, depending on the cell-mediated immunity of the host. Leprosy is classified by the World Health Organization (WHO) as paucibacillary type (PB) and multibacillary type (MB) depending on the number of lesions. This multicenter study aims to provide representation of leprosy types and its epidemiology in Indonesia. AIM: The purpose of this study is to find out the epidemiology according to the leprosy type in 13 teaching hospitals in Indonesia between 2018 and 2020. METHODS: This is a descriptive study with cross-sectional design. All patients with the diagnosis of PB or MB type of leprosy who underwent Multidrug Therapy (MDT) treatment between 2018 and 2020 were included in this study. Data collection was carried out by tracing medical records data in 13 teaching hospitals in Indonesia. RESULTS: A total of 2129 leprosy patients were included in this study. There were 232 cases (10.8%) of PB leprosy and 1897 cases (89.1%) of MB leprosy. The average age of the patients is 38.7 years (SD ± 16.2 years). Males are more affected by leprosy (n = 1,441; 67.7%) compared to female (n = 688; 32.3%). CONCLUSION: Leprosy remains as a national health problem. The increasing cases of MB leprosy in Indonesia are caused by several factors including the lack of knowledge about leprosy, the delay in diagnosis of leprosy, and the stigma of leprosy within the community; therefore, it becomes a challenge to eliminate leprosy in Indonesia.

Utility of Multi-target Nested PCR and ELISPOT Assays for the Detection of Paucibacillary Leprosy: A Possible Conclusion of Clinical Laboratory Misdiagnosis

The diagnosis of paucibacillary (PB) leprosy often possesses a diagnostic challenge, especially for pure neuritic and lesser skin lesions with the zero bacillary load, requiring a sensitive and accurate diagnostic tool. We have included 300 clinically diagnosed new leprosy cases (comprising 98 PB cases) and analyzed the sensitivity and specificity of PB leprosy cases by nested PCR with folP, gyrA, rpoB, RLEP, and 16SrRNA and Enzyme-linked Immunospot Assay test (ELISPOT) with MMPII, NDO-BSA, and LID-1 antigens by detecting interferon gamma (IFN-γ) release. The overall positivity rates of genes tested in 300 clinical specimens were identified as 55% of 16SrRNA, 59% of RLEP, 59.3% of folP, 57.3% of rpoB, 61% of gyrA while 90% of nested folP, 92.6% of nested rpoB, and 95% of nested gyrA, and 285 (95%) of at least one gene positive cases. For PB specimens, 95% PCR positivity was achieved by three tested genes in nested PCR. The data obtained from ELISPOT for three antigens were analyzed for IFN-γ expression with 600 subjects. Among 98 PB leprosy cases, the sensitivity of MMP II, LID-1, and NDO-BSA was 90%, 87%, and 83%, respectively, and the specificity was 90%, 91%, and 86%, respectively. The total number of cases positive for at least one antigen was 90 (91.8%) in PB, which is significantly higher than that in multibacillary (MB) leprosy (56.7%). The combination of multi-targets nested PCR and ELISPOT assay provides a specific tool to early clinical laboratory diagnosis of PB leprosy cases. The two assays are complementary to each other and beneficial for screening PB patients.

Single-Nucleotide Polymorphisms Related to Leprosy Risk and Clinical Phenotypes Among Chinese Population

Background

Genome-wide association studies (GWASs) have identified some immune-related single-nucleotide polymorphisms (SNPs) to be associated with leprosy.

Methods

This study investigated the association of 17 SNPs based on previously published GWAS studies with susceptibility to leprosy, different polar forms and immune states of leprosy in a case–control study from southwestern China, including 1344 leprosy patients and 2732 household contacts (HHCs) (1908 relatives and 824 genetically unrelated contact individuals). The differences of allele distributions were analyzed using chi-squared analysis and logistic regression.

Results

After adjusting covariate factors, rs780668 and rs3764147 polymorphisms influenced susceptibilities to genetically related or unrelated leprosy contact individuals. rs142179458 was associated with onset early cases, rs73058713 A allele and rs3764147 A allele increased the risk of reversal reaction, while rs3764147 G allele had higher risk to present lepromatous leprosy and erythema nodosum leprosum.

Conclusion

Our results demonstrated that genetic variants in the LACC1, HIF1A, SLC29A3 and CDH18 genes were positively correlated with the occurrence of leprosy and leprosy clinical phenotypes, providing new insights into the immunogenetics of the disease.

Predictive nomogram for leprosy using genetic and epidemiological risk factors in Southwestern China: Case-control and prospective analyses

Background

There is a high incidence of leprosy among house-contacts compared with the general population. We aimed to establish a predictive model using these genetic factors along with epidemiological factors to predict leprosy risk of leprosy household contacts (HHCs).

Methods

Weighted genetic risk score (wGRS) encompassing genome wide association studies (GWAS) variants and five non-genetic factors were examined in a case–control design associated with leprosy risk including 589 cases and 647 controls from leprosy HHCs. We constructed a risk prediction nomogram and evaluated its performance by concordance index (C-index) and calibration curve. The results were validated using bootstrap resampling with 1000 resamples and a prospective design including 1100 HHCs of leprosy patients.

Finding

The C-index for the risk model was 0·792 (95% confidence interval [CI] 0·768-0·817), and was confirmed to be 0·780 through bootstrapping validation. The calibration curve for the probability of leprosy showed good agreement between the prediction of the nomogram and actual observation. HHCs were then divided into the low-risk group (nomogram score ≤ 81) and the high-risk group (nomogram score > 81). In prospective analysis, 12 of 1100 participants had leprosy during 63 months’ follow-up. We generated the nomogram for leprosy in the validation cohort (C-index 0·773 [95%CI 0·658-0·888], sensitivity75·0%, specificity 66·8%). Interpretation The nomogram achieved an effective prediction of leprosy in HHCs. Using the model, the risk of an individual contact developing leprosy can be determined, which can lead to a rational preventive choice for tracing higher-risk leprosy contacts.

Funding

The ministry of health of China, ministry of science and technology of China, Chinese academy of medical sciences, Jiangsu provincial department of science and technology, Nanjing municipal science and technology bureau.