Occurrences of Buruli ulcer infections in humans and Mycobacterium ulcerans in animal and environmental samples - Codebook

Permanent Identifier:

https://doi.org/10.17037/DATA.00001909

Data Description

Records of human cases of Buruli ulcer collated through literature review and from surveillance programmes by national control programmes. For details on the review methodology, see Simpson et al 2019: Mapping the global distribution of Buruli ulcer: a systematic review with evidence consensus.

Data capture description

The surveillance datasets were compiled through routine surveillance for Buruli ulcer in Cameroon, Ghana, Nigeria and Togo.

Peer-reviewed literature was identified from searches of PubMed and Web of Science databases, updated on 06/08/2018. Additional publications were identified from reference lists of identified papers. We used the search terms (OR): “Buruli ulcer*”, (“Mycob* AND ulcer*”), “Bairnsdale ulcer”. There were no limits on publication date, study type, or location. We included English, French, and Spanish language publications. Publications were eligible for inclusion if they reported geographical locations with evidence of M. ulcerans infection in humans or animals, or detection of M. ulcerans in animal and environmental samples. There were no limits on publication date, participant population, study type or location. Articles that did not report original data were excluded. Studies that recruited patients from health facilities or used strains of M. ulcerans isolated from clinical samples were included in the evidence consensus framework only if patients’ home addresses were provided. Cases with recorded travel history to several endemic regions were excluded. If a dataset was duplicated in numerous papers, the most comprehensive was included.

For full details on literature review methodology, please see Simpson et al. 2019: Mapping the global distribution of Buruli ulcer: a systematic review with evidence consensus. Data contributed by the programme for National Yaws, Leishmaniasis, Leprosy and Buruli ulcer Control Programme in Cameroon are under the ownership of the Ministry of Health in Cameroon and their use is subject to the approval of the Ministry of Health.

Version control

This data collection is an update to https://doi.org/10.17037/DATA.00001143.

Environmental Results codebook (Environmental_results-LIT)

Occurrences of Mycobacterium ulcerans in animals and environmental samples

Field name Description
Occurrence_ID Unique identifier assigned to record in data extratction 
source_type Source of record: LIT = literature review, NPR = national programme surveillance data
ADM0_NAME Country name
ISO_code3 Country ISO code
ADM1_NAME First-order administrative divisions name according to GADM  https://gadm.org
GADM1_ID First-order administrative divisions ID according to GADM  https://gadm.org
ADM2_NAME Second-order administrative divisions name according to GADM  https://gadm.org
GADM2_ID Second-order administrative divisions ID according to GADM  https://gadm.org
Location_name Name of location given in source
lat latitude of location 
long longitude of location 
Geo_reliability Reliability of georeferenced location:
  1. 1= given in paper/ by authors;
  2. 2=estimated from map presented in paper;
  3. 3= Remotely georeferenced, highly reliable (validated in 2 sources);
  4. 4= Remotely georeferenced, moderately reliable (e.g. opencage, not verified);
  5. 5= Remotely georeferenced, not reliable (e.g. no settlement visible in google maps)  OR approximate location given in paper 6: geonames only 7:polygon area but shapefile not available 
max_year Year of sample as given in source (maximum if range given)
N_positive Number of positive results for location as given in source (maximum if range given)
higher_taxon higher taxon for animal samples
lower_taxon most specific taxonomic level given
Sample_type type of sample:
aquatic animal;
aquatic non-animal;
terrestrial vertebrate- clinical;
terrestrial invertebrate;
terrestrial vertebrate- faeces;
terrestrial vertebrate- clinical;
terrestrial non-animal;
PCR_Test PCR target reported
ER_result reported result of PCR targeting endoreticulase gene
KR_result reported result of PCR targeting ketoreductase gene
IS2404_result reported result of PCR targeting insertion sequence 2404
16SrRNAresults reported result of PCR targeting 16S RNA sequence
16S_23S ITS reported result of PCR targeting 16s-23s internal transcribed spacer region
IS2606_result reported result of PCR targeting insertion sequence 2606
VNTR_MIRU_result_MU reported results of variable nucleotide tandem repeat typing for M. ulcerans
VNTR_result_MPM reported results of variable nucleotide tandem repeat typing for mycolactone producing mycobacteria
qPCR_confirmed reported results of quantitative PCR to confirm M. ulcerans
other tests other tests reported
other results reported results of other tests
MU_confirmed DNA or organism confirmed as M. ulcerans (yes or no)

Human occurrences dataset codebook (Human_occurrences-LIT)

Occurrences of Buruli ulcer infections in humans.

Field name Description
Occurrence_ID Unique ID for the location record. Point for point locations and Pol for polygon areas
source_type Source type (literature for open access records; author or national programme for restricted access records)
reference Author, year and journal for literature records, data owner for programme records
ADM0_NAME Country name
ISO_code3 Country ISO code
ADM1_NAME Name of upper administrative level from Global Administrative Areas Database
GADM1_ID Upper administrative level ID from Global Administrative Areas Database
ADM2_NAME Name of second administrative level from Global Administrative Areas Database
GADM2_ID Second administrative level ID from Global Administrative Areas Database
Location_name Location name reported in the source
lat Latitude of location (point locations only)
long Longitude of location (point locations only)
Geo_reliability reliability of coordinates: 1 = reported in source; 2 = georeferenced from map provided in source; 3 = remotely georerefenced, exact location identified; 4 = remotely georeferenced, exact location not identified; 5 = nearby location georeferenced
max_year Year of diganosis if reported; most recent year if data spans a range; publication year if year of diagnosis is not reported
number Number of cases reported. 1 if number not reported/ ambiguous
Clinical_dxo Clinical diagnosis reported
Ziehl_Neelsen_stain Ziehl Neelsen test reported
ZN_result Result of Ziehl Neelsen test
ZN_n_tested Number of cases tested by ZN if reported
ZN_n_positive Number of cases positive by ZN if reported
ZN_pr_positive Percentage of cases positive by ZN if reported
Culture Use of culture reported
Culture_result culture result 
Culture_n_tested Number of cases tested by culture if reported
Culture_n_positive Number of cases positive by culture if reported
Culture_pr_positive Percentage of cases positive by culture if reported
Histo Use of histopathological analysis reported
histo_result histopathology result
histo_n_tested Number of cases tested by histopathology if reported
histo_n_positive Number of cases positive by histopathology if reported
histo_pr_positive Percentage of cases positive by histopathology if reported
PCR_Test PCR test reported
PCR_result Result of PCR test
PCR_n_tested Number of cases tested by PCR if reported
PCR_n_positive Number of cases positive by PCR if reported
PCR_pr_positive Percentage of cases positive by PCR if reported
diagnostic_score Score for accuracy of diagnosis: PCR or histopathological confirmation = 1; culture and/or ZN confirmation without other confirmatory tests = 0.95; clinical diagnosis alone = 0.5
diagnostic_notes Notes to assist interpretation of diagnostic score

Human_occurrences-NPR

Data contributed by the programme for National Yaws, Leishmaniasis, Leprosy and Buruli ulcer Control Programme in Cameroon (contained within 'human_occurrences-NPR') are under the ownership of the Ministry of Health in Cameroon and their use is subject to the approval of the Ministry of Health.

The dataset contains the following values (see above for description)