Phylogenetic analysis of streptococcal isolates from outbreaks

NAISS 2023/22-322


NAISS Small Compute

Principal Investigator:

Erik Senneby


Lunds universitet

Start Date:


End Date:


Primary Classification:

30109: Microbiology in the medical area




Some bacterial species, called beta-hemolytic streptococci, are known to cause severe infections in women after childbirth, called puerperal infections (in Swedish barnsängsfeber). Most often the pregnant woman is colonized before childbirth. However, it is also possible to get infected during childbirth at hospital. This is called a nosocomial infection and have historically been a major problem in hospital settings with poor hygiene. Streptococci can be spread from the hands of a colonized health care workers to a woman’s genital area during childbirth, or through objects in the environment, such as a contaminated shower head. Women with puerperal infections are cultured from vagina or cervix. When there is growth of a beta-hemolytic streptococci (S. pyogenes or S. dysgalactiae) the bacterial isolate is routinely typed through sequencing of the emm gene. More than 250 emm types have been identified. When there are two or more cases with the same emm type at a hospital, an outbreak investigation should be initiated. It is however known from previous studies that two strains with the same emm type is not always closely related to each other (due to horizontal transfer of genes between different clones). To decide the genetic relatedness between two streptococcal strains the whole genomes need to be sequenced and compared. We have 84 whole genome sequences of beta-hemolytic streptococci from suspected outbreaks from the last decade. Our aim is to investigate the relatedness between the strains in the different outbreaks through constructing phylogenetic trees based on SNPs, and compared this with the result from the emm typing. We are also intersted at looking for various virulence genes in the outbreak casuing isolates.