Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/616789

Smear positive tuberculosis and genetic diversity of M. tuberculosis isolates in individuals visiting health facilities in South Gondar Zone, northwest Ethiopia

Alelign, A.·Petros, B.·Ameni, G.
View original source ↗Export metadata ↓

Abstract

BackgroundTuberculosis (TB), a bacterial infectious disease, persisted to be a public health concern in many developing countries. However, lack of enough data concerning the public health burden and potential risk factors for the disease hampered control programs in target areas. Therefore, the present study aimed in determining the prevalence of TB and genetic diversity of M. tuberculosis isolates in South Gondar Zone, northwest Ethiopia.\n\nMethodsA cross-sectonal study was conducte between March 2015 and April 2017. Bacteriological examination, region of difference (RD) 9 based polymerase chain reaction (PCR) and spoligotyping were used to undertake the study.\n\nResultsThe overall prevalence of smear positive all forms TB was 6.3% (186/2953). Extra pulmonary TB (EPTB) was clinically characterized on about 62.4% (116/186) TB-positive cases. Some of the patients demographic characteristics such as [patients origin (chi-square ({chi}2) value; 62.8, p<0.001) were found to be significantly associated risk factors for the occurrence of TB in the study area. All the mycobacterial isolates were found to be M. tuberculosis. Among the 35 different spoligotype patterns identified, 22 patterns were shared types. The three dominantly identified families were T, CAS and Manu, each consisting of 46.9%, 24.0% and 10.4% of the isolates, respectively\n\nConclusionThe presented study revealed that TB continued to be a public health problem in South Gondar Zone which suggests a need of implementing effective disease control strategies.

Source connections

Explore related subjects

epidemiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Alelign, A., Petros, B., Ameni, G.. 2019-04-23. Smear positive tuberculosis and genetic diversity of M. tuberculosis isolates in individuals visiting health facilities in South Gondar Zone, northwest Ethiopia. https://doi.org/10.1101/616789

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2019

One-year descriptive analysis of patients treated at an anti-rabies clinic - a retrospective study from Kashmir

BackgroundDog bites in humans are a major public health problem in India in general and Kashmir in particular. Canine rabies is almost non-existent in developed countries and exists mainly in the poorer, low socioeconomic strata of society in the developing world. The objective of this study was to determine the characteristics, pattern, and burden of dog bite injuries in the Kashmir valley.\n\nMethodology and principal findingsData from Anti-Rabies Clinic of a tertiary care hospital in Srinagar, the summer capital of the state of Jammu & Kashmir, was collated and analyzed. Analysis of records of all the patients who had reported between April 2016 and March 2017 was done. A total of 6172 patients had reported to the Anti-Rabies Clinic for management of animal bites from 1st April 2016 to 31st March 2017. Most of the patients were young males. Almost half (47.7%) of the patients were bitten in the afternoon. Lower limbs were the most common site of bite (71.7%). Most of the bites were of Category III (57.6%) followed by Category II (42.3%); only one case of Category I was recorded. Almost all (98.0%) cases reported being bitten by dogs.\n\nConclusionsCategory III dog bites on lower limbs are the most common type of animal bites. Children have more chances of a bite on head and neck region. Serious and workable efforts have to be made to reduce the incidence and consequences of animal bites.\n\nAuthor summaryIn Kashmir, dog bite is an important public health problem. Thousands of people become victims of an animal bite, especially dog bite, and some of them develop rabies. Rabies is an invariably fatal viral disease resulting in approximately 59 000 human deaths per year globally, with 95% of cases occurring in Africa and Asia. The only way to prevent a rabies death is vaccination of an animal bite victim. In Kashmir, the burden and characteristics of dog bites are not routinely captured by the health system in place. We, therefore, attempted to find out the burden and characteristics of animal bite victims by analyzing one-year data from an Anti-Rabies Clinic at a tertiary care hospital in Kashmir. We found that 98% of the patients registered at the clinic during the period were victims of a dog bite. The victims were mostly young males but females and children were not shown any mercy either. Lower limbs were the most favorite site of the bite. Our analysis of the data also revealed that children under 15 years were more prone to a bite in the head and neck region. We concluded that the burden of animal bites, especially dog bites, is huge in Kashmir and recommended that serious efforts directed towards immunizing and decreasing the stray dog population need to be put into practice to decrease the number of animal bite victims and prevent any rabies deaths.

epidemiology↗
bioRxiv2019

Starting antiretroviral therapy within seven days of a positive HIV test increased the risk of loss to follow up in a primary healthcare clinic: a retrospective cohort study in Masaka, Uganda.

BackgroundRetention of patients initiated on antiretroviral therapy (ART) and good adherence remain cornerstones to long-term viral suppression. In this era of test and treat (T&T), ensuring that patients initiated on ART remain connected to HIV clinics will be key to the achievement of the UNAIDS 90-90-90 targets. Currently, limited studies have evaluated the effect instant ART initiation has on loss to follow up in a typical service healthcare setting. We studied the cumulative incidence, incidence rate of loss to follow up (LTFU), and factors associated with loss to follow up (LTFU) in a primary healthcare clinic that has practiced test and treat since 2012.\n\nMethodsWe retrospectively drew routine program data of patients initiated on ART from January 2012 to December 2016. We defined LTFU as failure of a patient to return to the HIV clinic for at least 90 days from the date of their last appointment. We calculated cumulative incidence, incidence rate and fitted a multivariable Cox proportion hazards regression model to determine factors associated with LTFU.\n\nResultsOf the 8,136 patients included in our sample, 3,606 (44.3%) started ART within seven days of HIV diagnosis. Females were 62.3%, median (interquartile range) age at start of ART was 30 (25, 37) years, 50.1% had access to a mobile phone, 54.0% had a baseline CD4 cell count of <350 cells/ml, 14.8% were in either WHO stage 3 or 4 at baseline and 75.9% had a normal body mass index (BMI). There were 1,207 cases of LTFU observed over 15953.0 person years at risk. The overall incidence rate (IR) of LTFU was 7.6 (95% CI=7.2-8.0) per 100 person years of observation (pyo). Cumulative incidence of LTFU increased with duration of follow up from 8.8% (95% CI=8.2-9.4%) and 12.0% (95% CI=11.2-12.7%) at 6 and 12 months, to 17.9% (95% CI=16.9-18.9%) and 20.1% (95% CI=18.9-21.3%) at 36, and 48 months respectively. Predictors of elevated risk of LTFU were; starting ART within 7 days of a positive diagnosis ((aHR) =1.39, 95% CI, 1.13-1.71), lack of access to a telephone set (aHR=1.60, 95% CI, 1.29-1.99) and baseline WHO clinical stage 3 or 4 (aHR =1.53, 95% CI, 1.11-2.11). Factors associated with a reduced risk of LTFU were; baseline age [&ge;]25years, and having a BMI [&ge;] 30 (aHR =0.28, 95% CI, 0.15-0.51).\n\nConclusionInitiation of ART within 7 days of an HIV diagnosis was associated with an elevated risk of loss to follow up. Steep ART initiation needs to be backed by enhanced adherence and retention counseling to reach the 2020 UNAIDS goals and beyond.

epidemiology↗
bioRxiv2019

Evolution and expansion of multidrug resistant malaria in Southeast Asia: a genomic epidemiology study

BackgroundA multidrug resistant co-lineage of Plasmodium falciparum malaria, named KEL1/PLA1, spread across Cambodia c.2008-2013, causing high treatment failure rates to the frontline combination therapy dihydroartemisinin-piperaquine. Here, we report on the evolution and spread of KEL1/PLA1 in subsequent years.\n\nMethodsWe analysed whole genome sequencing data from 1,673 P. falciparum clinical samples collected in 2008-2018 from northeast Thailand, Laos, Cambodia and Vietnam. By investigating genome-wide relatedness between parasites, we inferred patterns of shared ancestry in the KEL1/PLA1 population.\n\nFindingsKEL1/PLA1 spread rapidly from 2015 into all of the surveyed countries and now exceeds 80% of the P. falciparum population in several regions. These parasites maintained a high level of genetic relatedness reflecting their common origin. However, several genetic subgroups have recently emerged within this co-lineage with diverse geographical distributions. Some of these emerging KEL1/PLA1 subgroups carry recent mutations in the chloroquine resistance transporter (crt) gene, which arise on a specific genetic background comprising multiple genomic regions.\n\nInterpretationAfter emerging and circulating for several years within Cambodia, the P. falciparum KEL1/PLA1 co-lineage diversified into multiple subgroups and acquired new genetic features including novel crt mutations. These subgroups have rapidly spread into neighbouring countries, suggesting enhanced fitness. These findings highlight the urgent need for elimination of this increasingly drug-resistant parasite co-lineage, and the importance of genetic surveillance in accelerating elimination efforts.\n\nFundingWellcome Trust, Bill & Melinda Gates Foundation, UK Medical Research Council, UK Department for International Development.\n\nResearch in context O_TEXTBOXEvidence before this studyThis study updates our previous work describing the emergence and spread of a multidrug resistant P. falciparum co-lineage (KEL1/PLA1) within Cambodia up to 2013. Since then, a regional genetic surveillance project, GenRe-Mekong, has reported that markers of dihydroartemisinin-piperaquine (DHA-PPQ) resistance have increased in frequency in neighbouring countries. A PubMed search (terms: \"artemisinin\", \"piperaquine\", \"resistance\", \"southeast asia\") for articles listed since our previous study (from 30/10/2017 to 05/01/2019) yielded 28 results, including reports of a recent sharp decline in DHA-PPQ clinical efficacy in Vietnam; the spread of genetic markers of DHA-PPQ resistance into neighbouring countries by Imwong and colleagues; and multiple reports associating mutations in the crt gene with piperaquine resistance, including newly emerging crt variants in Southeast Asia.\n\nAdded value of this studyWe analysed P. falciparum whole genomes collected up to early 2018 from Eastern Southeast Asia (Cambodia and surrounding regions), describing the fine-scale epidemiology of multiple KEL1/PLA1 genetic subgroups that have spread out from Cambodia since 2015 and taken over indigenous parasite populations in northeastern Thailand, southern and central Vietnam and parts of southern Laos. Several newly emerging crt mutations accompanied the spread and expansion of KEL1/PLA1 subgroups, suggesting an active proliferation of biologically fit, multidrug resistant parasites.\n\nImplications of all the available evidenceThe problem of P. falciparum multidrug resistance has dramatically worsened in Eastern Southeast Asia since previous reports. KEL1/PLA1 has diversified and spread widely across Eastern Southeast Asia since 2015, becoming the predominant parasite group in several regions. This may have been fuelled by continued parasite exposure to DHA-PPQ, resulting in sustained selection after KEL1/PLA1 became established. Continued drug pressure enabled the acquisition of further mutations, resulting in higher levels of resistance. These data demonstrate the value of pathogen genetic surveillance and the urgent need to eliminate these dangerous parasites.\n\nC_TEXTBOX

epidemiology↗