Genomic sequencing of a national emm66 group A streptococci (GAS) outbreak among people who inject drugs and the homeless community in England and Wales, January 2016-May 2017

Laura Bubba; Nick Bundle; Georgia Kapatai; Roger Daniel; Sooria Balasegaram; Charlotte Anderson; Vicki Chalker; Theresa Lamagni; Colin Brown; Derren Ready; Androulla Efstratiou; Juliana Coelho

doi:10.1016/j.jinf.2019.08.009

Genomic sequencing of a national emm66 group A streptococci (GAS) outbreak among people who inject drugs and the homeless community in England and Wales, January 2016-May 2017

J Infect. 2019 Nov;79(5):435-443. doi: 10.1016/j.jinf.2019.08.009. Epub 2019 Aug 13.

Authors

Affiliations

¹ Bacteriology Reference Department, Public Health England, 61 Colindale Avenue, NW9 5EQ London, UK; European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Gustav III:s boulevard 40, 169 73 Solna, Stockholm, Sweden. Electronic address: [email protected].
² United Kingdom Field Epidemiology Training Programme, Public Health England, 61 Colindale Avenue, NW9 5EQ London, UK; Field Epidemiology Services, National Infection Service, Public Health England, Wellington, Waterloo Rd, Lambeth, London SE1 8UG, London, UK.
³ Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, NW9 5EQ London, UK.
⁴ United Kingdom Field Epidemiology Training Programme, Public Health England, 61 Colindale Avenue, NW9 5EQ London, UK.
⁵ Healthcare-Associated Infection & Antimicrobial Resistance Department, National Infection Service, Public Health England, 61 Colindale Avenue, NW9 5EQ London, UK.
⁶ Bacteriology Reference Department, Public Health England, 61 Colindale Avenue, NW9 5EQ London, UK.

PMID: 31419474
DOI: 10.1016/j.jinf.2019.08.009

Abstract

An outbreak of an uncommon emm type (emm66.0) of group A streptococcus (GAS) occurred in England and Wales between January 2016 and May 2017, involving 52 individuals who were homeless or injecting drugs users. In order to investigate the outbreak, epidemiological and network analysis were performed; moreover 55 isolates (32 outbreak, 5 non-outbreak and 13 historical - 2005-2015) were tested with whole genome sequencing (WGS), antimicrobial resistance determination, Bayesian evolutionary analysis (BEAST). Forty one isolates (including 32 outbreak strains) belonged to a single emm66.0 clade (average SNP difference 6.6; range 0-16 SNPs) separate from the other isolates and two strains previously considered part of the outbreak (SNP average: 5876; range 93-8417 SNPs). Antibiotic resistance was not detected in the outbreak clone. No common source of infection was identified. WGS confirmed expansion of an emm66.0 clone in a hard-to-reach population and enabled refinement of the initial case definition.

Keywords: England; Group A streptococcus; Homeless; Outbreak; People reporting problematic alcohol use; People who inject drugs; Streptococcus pyogenes; Wales; Whole genome sequencing; emm66.

MeSH terms

Adult
Aged
Aged, 80 and over
Antigens, Bacterial / genetics*
Bacterial Outer Membrane Proteins / genetics*
Carrier Proteins / genetics*
Community-Acquired Infections / epidemiology*
Community-Acquired Infections / microbiology
Disease Outbreaks*
Drug Resistance, Bacterial
England / epidemiology
Epidemiologic Methods
Female
Humans
Ill-Housed Persons*
Male
Middle Aged
Molecular Epidemiology
Streptococcal Infections / epidemiology*
Streptococcal Infections / microbiology
Streptococcus pyogenes / classification*
Streptococcus pyogenes / drug effects
Streptococcus pyogenes / genetics
Streptococcus pyogenes / isolation & purification
Substance Abuse, Intravenous / complications*
Wales / epidemiology
Whole Genome Sequencing

Substances

Antigens, Bacterial
Bacterial Outer Membrane Proteins
Carrier Proteins
streptococcal M protein