INTRODUCTION
Cystic fibrosis (CF) is among the most common recessive genetic disorders globally and affects South Africans at varying frequencies depending on race.1,2 This disorder occurs at incidences of 1:3 000, 1:10 300 and 1:14 000 in white, mixed-race and black South African population groups, respectively.3Pseudomonas aeruginosa (P. aeruginosa ) is recognised as one of the most significant CF lung pathogens in South Africa and worldwide.4Persistent lung colonisation of CF patients with P. aeruginosahas been associated with poorer patient outcomes such as accelerated decline in lung function and higher rates of mortality.4-6
Cystic fibrosis patients are typically infected or colonised with a unique strain ofP. aeruginosa . 7However, CF clinics globally have reported multiple instances where CF patients that have shared environments such as CF clinics, or even shared geographical locations carried identical shared P. aeruginosastrains. 5,8These shared P. aeruginosa strains, which have also been referred to as epidemic or transmissible strains have been reported in some settings to be more virulent, multidrug resistant (MDR) and associated with increased mortality rates.9,10 In 1996, the first epidemic P. aeruginosa strain was identified in CF patients from Liverpool, England and was termed the Liverpool Epidemic Strain (LES).11 Since then, epidemic strains of P. aeruginosa have been reported in CF patients from Australia, North America and multiple European countries.12
Australia is among the countries with the highest number of reported epidemic P. aeruginosa strains in CF patients.12,13 The P. aeruginosa Australian Epidemic Strains (AES) now renamed AUST have been described in CF patients from Tasmania and Australia.12,14Pseudomonas aeruginosa AUST-01 (ST649), AUST-02 (ST775) and AUST-03 (ST242) are among the most common epidemic strains in these regions.5,12 The P. aeruginosa AUST-03 (also known as AES-III) epidemic strain was first described in CF patients from Tasmania in 2003 and has caused outbreaks in Tasmania and Australia.12,15
The frequent genomic surveillance of CF pathogens in high income countries has enabled the detection of epidemic strains infecting CF patients. However, in low to middle income countries (LMICs) such as South Africa and other African countries where resources are limited, surveillance of CF pathogens is performed infrequently or not at all. The identification of CF lung pathogens that are of increased virulence and are epidemic in nature is of paramount importance for the prevention of outbreaks. To our knowledge, highly transmissible or epidemic strains of P. aeruginosa have not been reported in CF patients from South Africa. Here we report the presence of the Australian/Tasmanian epidemic strain AUST-03 (ST 242) discovered in two CF patients at a public academic hospital in Gauteng, South Africa. The aim of this study was to describe the genomic resistance characteristics of the P. aeruginosa ST 242 (AUST-03) strains discovered at this hospital during a previous study and to make phylogenetic comparisons with P. aeruginosa AUST-03 strains reported in other geographic settings.