Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit

Abstract

Background: Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-genome sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay.

Methods: Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-genome sequencing to investigate their relatedness at high resolution.

Results: Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-genome sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA).

Conclusions: Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-genome sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-genome sequencing should replace conventional methods for detection of nosocomial S. aureus transmission.

Keywords: Staphylococcus aureus transmission; adult; intensive care unit; spa typing; whole-genome sequencing.

Figure 1.

Sampling of patients involved in the study. Including nasal and extranasal samples and serial samples, Staphylococcus aureus was isolated 329 times as follows: 206 isolates (*), 8 isolates (†), 115 isolates (‡). Includes 1 patient who changed strains twice (§) and 1 patient who experienced 2 strain changes after acquiring S. aureus (¶). Abbreviations: ICU, intensive care unit; MRSA, methicillin-resistant Staphylococcus aureus.

Figure 2.

Sampling histories of 41 patients who acquired Staphylococcus aureus. Patient 33 experienced 3 separate acquisition events, and patient 35 experienced 2 acquisitions. *Routine spa typing assigned this isolate to t012, but whole-genome sequencing (WGS) revealed that it actually belongs to a different lineage. Patient-to-patient transmissions are identified as transmissions identified using WGS (†) and transmissions indicated by conventional criteria (‡; spa typing and overlapping stay). Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus; MSSA, methicillin-sensitive Staphylococcus aureus; WGS, whole-genome sequencing.

Figure 3.

Staphylococcus aureus diversity shown by pairwise genetic distances in single-nucleotide variants: maximum diversity within individual patients over time and between nasal and extranasal sites; minimum diversity between different patients (for isolates cultured within 24 hours of intensive care unit admission); minimum diversity between new acquisitions and isolates cultured within 24 hours of admission. Each dot represents a pair of isolates and is shaded according to whether the pair has concordant () or discordant spa types ().

Figure 4.

A, Intensive care unit stays of all 17 patients from whom methicillin-resistant Staphylococcus aureus (MRSA) t032 was isolated. Patients are labeled A–Q. The numbers 35, 41, 38, and 19 correspond with patients shown in Figure 2. The red box highlights a putative “outbreak” suggested by conventional criteria (same spa type plus overlapping stay). B, Maximum likelihood tree representing the genetic relatedness of MRSA t032 isolates in patients A–Q. The branch length reflects single-nucleotide variants (SNVs) identified between isolates (annotated). Nodes have been colored according to isolate type (red = acquisition isolate, yellow = carriage isolates, black = hypothetical node). Isolates sharing circles are genetically indistinguishable and touching nodes differ by 1 SNV. Twenty-six isolates were available from 17 patients, including 2 genetically distinct isolates from patient I (I1 and I2), 2 isolates from 7 patients (*), and 4 isolates from 1 patient (†). Abbreviation: ICU, intensive care unit.

Figure 4

Continued.