Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections

Abstract

Background Bloodstream infections due to Staphylococcus aureus cause significant patient morbidity and mortality worldwide. Of major concern is the emergence and spread of methicillin-resistant S. aureus (MRSA) in bloodstream infections, which are associated with therapeutic failure and increased mortality. Methods We generated high quality draft genomes from 323 S. aureus blood culture isolates from patients diagnosed with bloodstream infection at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA in 2010–2018. Results In silico detection of antimicrobial resistance genes revealed that 133/323 isolates (41.18%) carry horizontally acquired genes conferring resistance to at least three antimicrobial classes, with resistance determinants for aminoglycosides, beta-lactams and macrolides being the most prevalent. The most common resistance genes were blaZ and mecA, which were found in 262/323 (81.11%) and 104/323 (32.20%) isolates, respectively. Majority of the MRSA (102/105 isolates or 97.14%) identified using in vitro screening were related to two clonal complexes (CC) 5 and 8. The two CCs emerged in the New Hampshire population at separate times. We estimated that the time to the most recent common ancestor of CC5 was 1973 (95% highest posterior density (HPD) intervals: 1966–1979) and 1946 for CC8 (95% HPD intervals: 1924–1959). The effective population size of CC8 increased until the late 1960s when it started to level off until late 2000s. The levelling off of CC8 in 1968 coincided with the acquisition of SCCmec Type IV in majority of the strains. The plateau in CC8 also coincided with the acceleration in the population growth of CC5 carrying SCCmec Type II in the early 1970s, which eventually leveled off in the early 1990s. Lastly, we found evidence for frequent recombination in the two clones during their recent clonal expansion, which has likely contributed to their success in the population. Conclusions We conclude that the S. aureus population was shaped mainly by the clonal expansion, recombination and co-dominance of two major MRSA clones in the last five decades in New Hampshire, USA. These results have important implications on the development of effective and robust strategies for intervention, control and treatment of life-threatening bloodstream infections.

Genome Evolution of Invasive Methicillin-Resistant Staphylococcus aureus in the Americas

“…S1; Table S1). These came from three states in the United States: Minnesota ( n = 48 genomes) ( 13 ), New Hampshire ( n = 102) ( 14 ), and New York ( n = 131) ( 15 ), as well as nine countries from Central and South America ( n = 105) ( 16 ). The latter group included Argentina ( n = 8), Brazil ( n = 13), Chile ( n = 16), Colombia ( n = 16), Ecuador ( n = 12), Guatemala ( n = 18), Mexico ( n = 5), Peru ( n = 8), and Venezuela ( n = 9).…”

“…We also only included data sets with time (month, year) of isolation from patients. Genome sequences were derived from isolates sampled in Minnesota, USA ( n = 48 genomes, BioProject: PRJNA384623 ) ( 13 ), New Hampshire, USA ( n = 102, BioProject: PRJNA673382 ) ( 14 ), New York, USA ( n = 131, BioProject: PRJNA470993 ) ( 15 ), and nine countries from Central and South America ( n = 105, BioProject: PRJNA291213 ) ( 16 ). The latter group included Argentina, Brazil, Chile, Colombia, Ecuador, Guatemala, Mexico, Peru, and Venezuela.…”

Pandemic clone USA300 in a Brazilian hospital: detection of an emergent lineage among methicillin-resistant Staphylococcus aureus isolates from bloodstream infections

“…Molecular studies have helped the epidemiological surveillance of S. aureus BSI, highlighting the constant clonal change that has been taking place in health institutions and the dissemination of MRSA clones that can lead to higher rates of morbidity and mortality [ 14 ]. Moreover, constant monitoring of S. aureus BSI can also help surveillance programs in containing the spread of their resistance and virulence.…”

Pandemic clone USA300 in a Brazilian hospital: detection of an emergent lineage among methicillin-resistant Staphylococcus aureus from bloodstream infections

“…Molecular studies have helped the epidemiological surveillance of S. aureus BSI, highlighting the constant clonal change that has been taking place in health institutions and the dissemination of MRSA clones that can lead to higher rates of morbidity and mortality [14]. Besides, the constantly monitoring of S. aureus BSI could help surveillance programs in containing the spread of their resistance and virulence.…”

“…However, they could carry the Panton-Valentine leukocidin (PVL) and are considered as hypervirulent. Thus, once present in the environment, they can spread, leading to infections with high mortality rates [13].Molecular studies have helped the epidemiological surveillance of S. aureus BSI, highlighting the constant clonal change that has been taking place in health institutions and the dissemination of MRSA clones that can lead to higher rates of morbidity and mortality [14]. Besides, the constantly monitoring of S. aureus BSI could help surveillance programs in containing the spread of their resistance and virulence.…”