Evidence map›Paper›PMID 32736602›Full record

ArticleBMC infectious diseases2020

Machine learning reveals that Mycobacterium tuberculosis genotypes and anatomic disease site impacts drug resistance and disease transmission among patients with proven extra-pulmonary tuberculosis.

Doctor B Sibandze, Beki T Magazi, Lesibana A Malinga, Nontuthuko E Maningi, Bong-Akee Shey, Jotam G Pasipanodya, Nontombi N Mbelle

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC infectious diseases, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
0.1field-weighted citation impact, top 42% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 17 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Cutaneous Manifestations ofPathogens (Basel, Switzerland) · 2023
    Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 5 institutions in 4 countries.

Doctor B SibandzeDepartment of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
Beki T MagaziDepartment of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
Lesibana A MalingaDepartment of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
Nontuthuko E ManingiDepartment of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
Bong-Akee SheyDepartment of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
Jotam G PasipanodyaCenter For Infectious Diseases Research and Experimental Therapeutics, Texas Tech University Health Sciences Center, 5920 Forest Park Road, Dallas, TX, 75235, USA. jpasipanodya@hotmail.com.ORCID http://orcid.org/0000-0002-8984-8379
Nontombi N MbelleDepartment of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
National Health Laboratory Service · ZAUniversity of Pretoria · ZAMinistry of Health · MNSouth African Medical Research Council · ZATexas Tech University · US

Funding

National Health Laboratory Service Research Trust Grant 004_94389
6 · The paper itself

Abstract

backgroundThere is a general dearth of information on extrapulmonary tuberculosis (EPTB). Here, we investigated Mycobacterium tuberculosis (Mtb) drug resistance and transmission patterns in EPTB patients treated in the Tshwane metropolitan area, in South Africa.

methodsConsecutive Mtb culture-positive non-pulmonary samples from unique EPTB patients underwent mycobacterial genotyping and were assigned to phylogenetic lineages and transmission clusters based on spoligotypes. MTBDRplus assay was used to search mutations for isoniazid and rifampin resistance. Machine learning algorithms were used to identify clinically meaningful patterns in data. We computed odds ratio (OR), attributable risk (AR) and corresponding 95% confidence intervals (CI).

resultsOf the 70 isolates examined, the largest cluster comprised 25 (36%) Mtb strains that belonged to the East Asian lineage. East Asian lineage was significantly more likely to occur within chains of transmission when compared to the Euro-American and East-African Indian lineages: OR = 10.11 (95% CI: 1.56-116). Lymphadenitis, meningitis and cutaneous TB, were significantly more likely to be associated with drug resistance: OR = 12.69 (95% CI: 1.82-141.60) and AR = 0.25 (95% CI: 0.06-0.43) when compared with other EPTB sites, which suggests that poor rifampin penetration might be a contributing factor.

conclusionsThe majority of Mtb strains circulating in the Tshwane metropolis belongs to East Asian, Euro-American and East-African Indian lineages. Each of these are likely to be clustered, suggesting on-going EPTB transmission. Since 25% of the drug resistance was attributable to sanctuary EPTB sites notorious for poor rifampin penetration, we hypothesize that poor anti-tuberculosis drug dosing might have a role in the development of resistance.

Indexed as

AdolescentAdultAgedAged, 80 and overChildChild, PreschoolDrug Resistance, BacterialFemaleGenotypeHumansInfantIsoniazidMachine LearningMaleMiddle AgedMutationIsoniazidRifampinAcquired drug resistanceAttributable riskNumber needed to screenPharmacokinetic variabilitySpoligotypesStochastic gradient boosting

Identifiers

PMID32736602
PMCPMC7393820
OpenAlexW3046487465

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.