wgs-guided
s.pyogenes outbreak control 853
due to patients’ underlying medical conditions and behaviors. In June 2016, S. pyogenes was isolated from 4 patients
(1 bacteremia and 3 wound infections) from a male residential ward (ward A) in a mental health facility in Singapore. Because this was a surge in the baseline incidence of S. pyogenes (1–2 cases over the previous 6 months), an institution-wide out- break investigation was initiated following the identification of these index cases. This facility is a 2,000-bed tertiary-care psychiatric hospital providing acute-care and chronic mental health services. It is situated on a large open-plan campus that includes 50 inpatient wards, 7 specialist outpatient clinics, and long-term residential care units, including assisted living quarters for patients with chronic mental health issues. An outbreak control team was convened to determine the
extent and epidemiology of the outbreak, to identify potential breaches in infection control practice, and to provide recom- mendations to prevent further transmission of infection. Because classicalMprotein gene (emm) typing for S. pyogenes was not available in Singapore, the outbreak control team decided to use whole-genome sequencing (WGS) as the pri- mary typing method to assist traditional epidemiology during this investigation. Here, we report the utility of WGS in guiding the outbreak management, and we present a com- parison if its performance with that of emm typing.
methods Definitions
The study included patients and staff with S. pyogenes infection and/or asymptomatic throat or skin carriage between June 1, 2016, and December 31, 2016. Invasive disease was defined as the isolation of S. pyogenes from normally sterile sites. Com- munity isolates were those with no known epidemiological link to the institution where the outbreak occurred. These isolates were collected from a different healthcare institution between November 2015 and April 2016.
Case Finding
To identify individuals with S. pyogenes infection, we collected oropharyngeal swabs from residents and staff members on the affected wards and swabs from residents with visible wounds on skin. Staff members were questioned regarding signs and symptoms of S. pyogenes infection in the month prior to the identification of the index cases. Medical records were reviewed to track the movements of patients and staff across the hospital to identify possible transmission routes.
Laboratory Investigation of Isolates
Samples taken from patients and staff members at the out- break institution were processed remotely at the Department of Laboratory Medicine in Tan Tock Seng Hospital.
The samples were cultured to detect S. pyogenes using standard methods (see Supplementary Methods). Cultured organisms were identified using matrix-assisted laser desorption/ioniza- tion time-of-flight mass spectroscopy (MALDI-TOF MS; Bruker, Bremen, Germany). Antimicrobial susceptibility test- ing was performed using the disc diffusion method according to the protocol established by the Clinical and Laboratory Standards Institute (M100-S25).13 Thereafter, emm typing was retrospectively performed using polymerase chain reaction (PCR) and Sanger sequencing as described by the Centers for Disease Control and Prevention (CDC;
http://www.cdc.gov /ncidod/biotech/strep/
protocols.html). The emm types were assigned using the CDC database (
http://www2a.cdc.gov/nci- dod/biotech/
strepblast.asp).
Whole-Genome Sequencing of S. pyogenes Isolates
TheWGS of isolates took place on 3 occasions between June 17, 2016, and November 11, 2016, at the Genome Institute of Sin- gapore. Genomic DNA was extracted from 43 isolates from patients and staff from the affected institution and from 24 ran- domly selected community-derived S. pyogenes isolates. The 24 community isolates (GAS001-024) provided background genetic information on S. pyogenes circulating locally. We performed single-nucleotide polymorphism (SNP)–based genome phylo- geny14,15 using genomic regions filtered for mobile genetic ele- ments (see Supplementary Methods section 1.2 for details) in silico emm typing16,17 and in silico multilocus sequence typing (MLST)18 on the S. pyogenes WGS data (see Supplementary Methods). Clusters of closely related strains were identified by manual inspection of the phylogenetic tree; these are referred to
as “genomic clusters” in the rest of the manuscript. Sequencing files (FASTQ) were submitted to the GenBank Sequence Read Archive (SRA; study accession no. SRP111309). The outbreak control team determined the presence of person-to-person transmissions of S. pyogenes (directly or indir- ectly) based on integrating data from epidemiological investiga- tions combined with pairwise SNP differences (fromWGS) and emm types. We compared WGS and emm typing in their ability to support the correct identification of person-to-person trans- missions and to guide the management of the outbreak.
results
As part of the outbreak investigation, 204 patients (11.4% of inpatients) and 152 staff members (6.9% of clinical staff members) were tested for S. pyogenes infection or colonization between June 1 and December 31, 2016. Streptococcus pyogenes was isolated from 35 patients (17% of all patients screened) in 8 wards (A–H) and 2 (1.3%) staff members. Of these 204 patients, 30 patients (14.7%) had dermal colonization and 1 patient (0.5%) had throat colonization. Also, 4 patients had soft-tissue infections requiring hospitalization in an acute-care facility. Of these 4 patients, 2 had bacteremia. One of the bacteremic patients had necrotizing fasciitis and required
Page 1 |
Page 2 |
Page 3 |
Page 4 |
Page 5 |
Page 6 |
Page 7 |
Page 8 |
Page 9 |
Page 10 |
Page 11 |
Page 12 |
Page 13 |
Page 14 |
Page 15 |
Page 16 |
Page 17 |
Page 18 |
Page 19 |
Page 20 |
Page 21 |
Page 22 |
Page 23 |
Page 24 |
Page 25 |
Page 26 |
Page 27 |
Page 28 |
Page 29 |
Page 30 |
Page 31 |
Page 32 |
Page 33 |
Page 34 |
Page 35 |
Page 36 |
Page 37 |
Page 38 |
Page 39 |
Page 40 |
Page 41 |
Page 42 |
Page 43 |
Page 44 |
Page 45 |
Page 46 |
Page 47 |
Page 48 |
Page 49 |
Page 50 |
Page 51 |
Page 52 |
Page 53 |
Page 54 |
Page 55 |
Page 56 |
Page 57 |
Page 58 |
Page 59 |
Page 60 |
Page 61 |
Page 62 |
Page 63 |
Page 64 |
Page 65 |
Page 66 |
Page 67 |
Page 68 |
Page 69 |
Page 70 |
Page 71 |
Page 72 |
Page 73 |
Page 74 |
Page 75 |
Page 76 |
Page 77 |
Page 78 |
Page 79 |
Page 80 |
Page 81 |
Page 82 |
Page 83 |
Page 84 |
Page 85 |
Page 86 |
Page 87 |
Page 88 |
Page 89 |
Page 90 |
Page 91 |
Page 92 |
Page 93 |
Page 94 |
Page 95 |
Page 96 |
Page 97 |
Page 98 |
Page 99 |
Page 100 |
Page 101 |
Page 102 |
Page 103 |
Page 104 |
Page 105 |
Page 106 |
Page 107 |
Page 108 |
Page 109 |
Page 110 |
Page 111 |
Page 112 |
Page 113 |
Page 114 |
Page 115 |
Page 116 |
Page 117 |
Page 118 |
Page 119 |
Page 120 |
Page 121 |
Page 122 |
Page 123 |
Page 124 |
Page 125 |
Page 126 |
Page 127 |
Page 128 |
Page 129 |
Page 130 |
Page 131 |
Page 132 |
Page 133 |
Page 134 |
Page 135 |
Page 136 |
Page 137 |
Page 138 |
Page 139 |
Page 140 |
Page 141 |
Page 142 |
Page 143 |
Page 144
