Available visualisations and tables

Sam Abbott

2019-07-11

Required Packages

library(tbinenglanddataclean)

## Registered S3 methods overwritten by 'ggplot2':
##   method         from 
##   [.quosures     rlang
##   c.quosures     rlang
##   print.quosures rlang

library(kableExtra)
library(rlang)
library(ggplot2)

TB Interventions

A timeline of interventions against TB. Antibiotics used to treat TB are commonly given together, with those with the fewest side effects given first. Second line antibiotics are then used if the initial treatment fails or tests show the strain is multiply drug resistant. BCG - Bacillus Calmette–Guérin; TB – Tuberculosis; MRSA - Methicillin-resistant Staphylococcus aureus; DOTS - Directly Observed Treatment Short-course

Year	Intervention	Type	Line	Detail
1921	BCG	Vaccination		The first use of the Bacillus Calmette–Guerin (BCG) vaccine in humans, it remains the only vaccine against Tuberculosis (TB). Efficacy has been shown to vary depending on latitude and there is only strong evidence of protection for 10-15 years after vaccination.
1944	Streptomycin	Antibiotic	Second	The first antibiotic and the first bacterial agent against TB.
1944	4-Aminosalicylic acid	Antibiotic	Second	The second antiobiotic to be developed. Due to lower potency than other antibiotics it is not considered a first line treatment.
1952	Isoniazid	Antibiotic	First	Used against both active and latent TB, it may also be given as a prophylatic therapy.
1952	Cycloserine	Antibiotic	Second	An antibiotic with severe side effects such as kidney failure and neurological conditions, which is therefore restricted for use against multiple drug resistant TB.
1952	Pyrazinamide	Antibiotic	First	Discovered in 1936, it was first used against TB in 1952. Although showing no effect in-vitro it was shown to be effective in treating TB in mice. Used only for treating TB and never on its own.
1953	School age BCG	Vaccination		After a successful trial which showed high effectiveness for the vaccine, BCG was introduced in the UK for those at school leaving age as peak incidence was then in young, working adults.
1962	Ethambutol	Antibiotic	First	Believed to work by interfering with TB bacteria’s metabolism. There are some concerns that it may not be safe to give during pregancy, as it may lead to vision loss in the baby.
1971	Rifampicin	Antibiotic	First	Taken daily for at least a period of 6 months, if given alone resistance develops quickly. It may also be used in the treatment of MRSA amongst other diseases.
1995	DOTS	Strategy		Directly Observed Treatment, Short-Course (DOTS) is introdued by the World Health Organization as a control strategy for TB. The intermittent, supervised system aims to eliminate drug default.
2005	Neonatal high risk BCG	Vaccination		Due to a continued decline in TB incidence rates in the indigenous UK population, the BCG programme was refocused as risk-based. This meant vaccinating high risk neonates rather than those most likely to transmit TB.
2012	Bedaquiline	Antibiotic	Second	The first new antiobiotic for use against TB in 40 years, reserved for use against multiple drug resistant TB. Approved via a fast track process, higher mortality in those that recieve the antibiotic has caused significant concern.

TB Notifications

TB notifications in England and Wales from 1913 to 2017, stratified initially by respiratory/non-respiratory status and from 1982 by pulmonary/non-pulmonary TB. Interventions are highlighted with vertical lines, with linetype denoting the type of intervention, more information on each intervention is available in the corresponding table. Figure produced using tbinenglanddataclean (https://www.samabbott.co.uk/tbinenglanddataclean/)

Pulmonary Vs. Extra-Pulmonary TB

From 1913 until 1981 the figure shows the proportion respiratory vs. non-respiratory cases and from 1982 it shows the proportion of pulmonary vs. non-pulmonary TB. Figure produced using tbinenglanddataclean (https://www.samabbott.co.uk/tbinenglanddataclean/)