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Diversity and Persistence of MRSA and VRE in Skilled Nursing Facilities: Environmental Screening, Whole Genome Sequencing, Development of a Dispersion Index
Environmental contamination with methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) in skilled nursing facilities (SNFs) may contribute to patient acquisition. We assessed diversity and association of MRSA and VRE isolates in a SNF wing and developed a mathematical index to define each strain’s tendency to persist in rooms and spread horizontally.
Methods
Longitudinal study of MRSA and VRE colonization and contamination among successive patient occupancies in a cluster of nine SNF private rooms during eight months characterized by microbiological testing and whole genome isolate typing. ‘Dispersion index” of a strain is defined as the number of rooms it was found in (including the patient), divided by the average of times it was found consecutively in the same room.
Findings
MRSA (ten strain types) and VRE (seven types) were recovered from room or patient in 16.4% and 35.6% of the occupancies, respectively. MRSA showed moderate horizontal spread and several episodes of same-room persistence (three distinct strain types) (overall dispersion index: 1.08). VRE showed high tendency towards horizontal spread /new introductions (overall dispersion index: 3.25), and only one confirmed persistence episode.
Interpretation
The emerging picture of high diversity among contaminating strains and high likelihood of room persistence despite terminal cleaning (MRSA) and horizontal spread between rooms (VRE) in this setting calls for improved cleaning practices, heightened contact precautions, and most of all to establish individually tailored facility screening programs to enable informed choices based on local, measurable and actionable epidemiologic parameters.
Funding
University of Michigan OAIC REC Scholarship to M.C. National Institutes of Health K24 AG050685 to L.M.
Introduction
Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) is of special concern among frail patients in skilled nursing facilities (SNFs), where they are among the most prevalent pathogens and responsible for unfavorable outcomes.
Interplay Between Patient Colonization and Environmental Contamination with Vancomycin-Resistant Enterococci and Their Association With Patient Health Outcomes in Postacute Care.
Exposure to MRSA and VRE in the environment is associated with patient new acquisition risk, thus increasing colonization pressure and maintaining a vicious cycle of transmission.
Environmental Panels as a Proxy for Nursing Facility Patients with Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus Colonization.
Most SNF patients are admitted directly from a hospital setting, with a high proportion having received antimicrobial therapy during their stay, facilitating introduction of antimicrobial-resistant pathogens.
While the prevention and control of these pathogens require a multi-pronged approach to curb their spread between patients and between healthcare facilities, previous work suggests that environmental contamination with MRSA and VRE may contribute to patient acquisition.
showing that admission screening can reduce prevalence, including across interconnecting hospitals and even when only a proportion of patients is screened.
Very limited evidence is currently available on the usefulness of such approaches for VRE. In this study, we employed high-intensity targeted screening of environmental surfaces, genomic surveillance, and developed a simple mathematical index to characterize the distribution and persistence of MRSA and VRE in a SNF setting, to help determine which strategies will be effective to reduce the burden of these pathogens.
To understand the pattern of MRSA/VRE environmental contamination in this setting, we screened a wing of a SNF longitudinally over an eight-month time span and assessed MRSA and VRE prevalence in patient rooms as well as colonization of the patients themselves when available. We then performed whole genome sequencing on non-redundant isolates and assessed their potential association in time and/or space. In particular, we investigated whether specific strains may persist in patient rooms during changes of occupancy after patient discharge, in addition to examining the diversity and potential source of these isolates. Lastly, we developed a mathematical index to estimate each strain’s balance of ability to persist in rooms, versus their ability to spread to other rooms.
Methods
Study format, sample collection
Longitudinal study of MRSA and VRE colonization and contamination among successive patient occupancies in a cluster of nine SNF private rooms. The SNF hosted a mix of patients with diverse needs ranging from palliative care to rehabilitation. A majority of patients were mobile but typically only left the room for physical therapy or diagnostic sessions. Common areas were seldom used by patients, and all patients had meals in their room. Each room had its own bathroom. Five high-touch surfaces (bed controls, nurse call button and TV remote control accessory, bed railing, bedside table, toilet seat) were swabbed three times a week for 34 weeks (April 1st to November 22th, 2019), using flocked swabs with liquid storage system (Copan, Marietta, GA). Approximately 40 cm2 were swabbed for small objects, and a 1 cm wide area along the borders for larger, flat objects. Newly admitted patients (within 48 hours) were also eligible to enroll and were screened (nares, groin, hands) at the same time as their room if providing informed consent to participate. For patients unable to consent (alert and oriented status score less than three), we contacted their legally authorized representative within 48 hours.
Specimen processing, identification
Samples were transported to the laboratory and processed within 4 hours of collection. After sample agitation, 0.2 ml of each sample were inoculated in Brain Hearth Infusion Broth (DIFCO, Franklin lakes, NJ) overnight at 36°C, and subsequently streaked onto Tryptone Soy Agar with 5% sheep blood (TSA blood), Mannitol Salt Agar (MSA) and Bile-Esculin/Vancomycin 6 mg/L (BEV6) agar for estimation of total bacterial burden and for isolation of S. aureus and VRE. Bacterial growth was identified using a previously published protocol.
Environmental Panels as a Proxy for Nursing Facility Patients with Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus Colonization.
Briefly, all plates were read after 24 to 48 hours incubation at 36°C. Growth suggestive of S. aureus was confirmed using catalase and coagulase test (Staphaurex, Remel, Lenexa, KS), after which disc-diffusion cefoxitin resistance in Mueller-Hinton agar was performed according to the Kirby-Bauer method to identify MRSA strains.
Growth suggestive of VRE on BEV6 was confirmed with pyrrolidonyl arylamidase testing (PYR) (DrySlide, BD, Franklin Lakes, NJ).
Whole genome sequencing (WGS)
Bacterial DNA was extracted using a DNeasy UltraClean Microbial kit and protocol (Qiagen, Germantown, MD). Whole genome sequencing was performed on an Illumina Novaseq instrument in the University of Michigan Advanced Genomic Core, and analysis of genetic relatedness based on single nucleotide variants was performed using Snippy software (Victorian Bioinformatic Consortium, Australia, https://github.com/tseemann/snippy). Variant sites located in putative recombination regions were removed using Gubbins.
Potential persistence episodes were flagged when either MRSA or VRE were recovered in the same room during two consecutive occupancy events (event one: occupancy of the room by one patient, and the patient and/or the room are found to be colonized/contaminated; event two: discharge of the earlier patient and terminal cleaning of the room, after which either the room and/or the newly admitted patient are found to be colonized/contaminated again with the same microorganism). WGS analysis was used to confirm clonal persistence where strains recovered from the two occupancy events showed no or very limited genomic variation. Although setting arbitrary thresholds is not necessarily the optimal solution in all situations,
Opportunities for persistence were defined as any case where a room and/or patient was colonized/contaminated and sampling from a subsequent occupancy event was performed.
A priori probability of isolation in consecutive occupancies
Isolation of the same strain in two consecutive events is suggestive of persistence during the change of room occupancy, but could also be the result of chance (reintroduction of the same strain from another source). The likelihood that a specific strain type would be recovered in two consecutive occupancies just by chance during the duration of the study was calculated for all strain types isolated at least three times during the study, using the following algorithm: probability of isolation in one occupancy, multiplied by the times the strain was found and sampling was performed during the successive occupancy (N. isolations/N. opportunities * following occupancies when sampling was performed). For example, a specific strain found 3 times in three different rooms which collectively had been sampled in 45 different occupancy events (3/45 = 0.067 chance of being recovered at any specific once), would have a 0.067*3 = 0.200 chance of being recovered in two consecutive occupancies just by chance
Dispersion index
A “dispersion index” was calculated for each sequence type strain, to quantify its tendency to be found in different rooms/patients (high dispersion index value) versus its tendency to persist in the same room across consecutive occupancy events (low dispersion index value). Specifically, the numerator of the index corresponds to the number of different rooms (including the patient) in which the strain was found, while the denominator equals the average number of times it was found in the same room (limited to consecutive occupancy events). When a strain was absent from the room for two or more occupancy events and then found again at a later time, the second occurrence was considered as a new finding in a new room. For example, a strain found in two rooms over the duration of the study, of which once only in a single occasion and once noted to persist across consecutive occupancy events, would have a numerator of two and a denominator of 1.5 (found once in one room and twice in the other room, 1.5 times average) and thus a dispersion index of 1.33 (2/1.5). We propose that a dispersion index higher than two indicates high tendency for horizontal transmissions (and/or multiple introductions) in the facility, a dispersion index lower than one indicates a high tendency toward persistence, while an index between one and two points to a “balanced” behaviour.
Role of the funding sources
The funding sources had no role in the design and conduct of the study, analysis, interpretation of the data, or preparation, review, or approval of the manuscript.
Results
Facility prevalence observations
One-hundred forty-six distinct occupancy events were captured during the study (16.5 average per room, range 11-22), across 837 study room visits and 4670 total swabs collected, of which 1279 (27%) from patients. Forty-eight patients were recruited (295 of the 837 visits included patient sampling). Overall prevalence of and colonization/contamination rates for MRSA and VRE as described in Table 1. Both pathogens were found frequently, with VRE approximately twice as much as MRSA (35.6% vs. 16.4% of occupancies). New contamination in a room with MRSA or VRE was observed in 45 cases accounting to an average of 2.1 times per room during the study period for MRSA (SD: 0.99), and 3.5 times (SD: 1.06) per room for VRE. Also, 14 patients were colonized with MRSA and/or VRE (Table 1) (50 and 31 total swabs respectively, upon 24 and 23 separate visits). In seven cases, a non-colonized patient occupying a contaminated room became colonized with either MRSA (four cases, including at least two with the same strain type), or VRE (three cases, two with the same strain type), while the opposite was documented in one instance (MRSA).
Table 1Prevalence of MRSA and VRE colonization and contamination in study rooms and patients.
Potential persistence of a strain during occupancy changes, defined as MRSA or VRE isolated in the same room and/or its patients in two consecutive occupancy events was observed in 25 (5 MRSA, 20 VRE) out of 76 (25 MRSA, 51 VRE) opportunities (32.9% overall, 20.0% for MRSA and 39.2% for VRE). Sequencing of 67 unique isolates followed by variant analysis identified at least 17 separate clades belonging to different MLST types and with a SNV range between 50 and >5000, of which at least seven enterococcal clades (defined as “types”) and ten MRSA clades (six USA100 and four USA300), indicating a complex epidemiological scenario with a high degree of strain diversity, and a high likelihood of multiple introductions in the facility during the study period (Figure 1).
Figure 1Pairwise SNV comparison heatmaps and dendrograms for sequenced E. faecalis (A), S. aureus USA100 (B), S. aureus USA300 (C), and E. faecium study isolates (D).
Figure 1Pairwise SNV comparison heatmaps and dendrograms for sequenced E. faecalis (A), S. aureus USA100 (B), S. aureus USA300 (C), and E. faecium study isolates (D).
Specifically, most MRSA strains belonged to the MLST clonal complex 5 (USA100 strains), described in North America since 1989 and first found in New York,
The evolution of methicillin resistance in Staphylococcus aureus: similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones.
One USA100 MRSA strain, isolated in successive occupancies in a room, showed a never previously reported allele pattern, possibly belonging to a novel clonal complex (Figure 1). The diversity found in SNV among a small set of highly prevalent MLST clonal complexes may be compatible with ongoing strain evolution in this geographic area.
Most vancomycin-resistant E. faecalis strains belonged to sequence type 6, described in North America since 1989 and first found in Houston, TX. Less commonly found were sequence types 236, 254, and 636, all of which have been reported in Europe. The majority of vancomycin-resistant E. faecium strains belonged to sequence type 117 (first isolated in North America in Chicago, IL, and Portland, OR in 2001), sequence type 80, which has been first reported in 1997 in Israel and later in Europe and South Korea, sequence type 17, found worldwide and first isolated in London, UK in 1990, and sequence type 132, present in Europe and Africa since at least 2003.
MRSA and VRE strains persistence and dispersion in the study facility rooms
MRSA. MRSA USA100 strain type 1 (MLST CC5) was found in two different rooms (rooms 5 and 9, during just one occupancy event in each case) (dispersion index: 2, see Table 2) with the closest confirmed occurrence being four days apart, pointing to possible horizontal transmission (Figure 2).
Table 2Dispersion Index of typed MRSA and VRE strains.
MRSA
VRE
N. rooms found/
Dispersion
N. rooms found/
Dispersion
avg. times found
index
avg. times found
index
Strain type
1
2/1
2
10/1.3
7.7
2
4/1
4
4/1
4
3
1/2
0.5
3/1
3
4
1/2
0.5
7/1
7
5
1/2
0.5
1/1
1
6
1/1
1
1/1
1
7
1/1
1
1/2
0.5
8
1/1
1
NA
N/A
9
1/1
1
NA
N/A
10
1/1
1
NA
N/A
Overall
14/13
1.08
27/8.3
3.25
MRSA: methicillin-resistant Staphylococcus aureus. VRE: vancomycin-resistant Enterococcus. Avg.: average. N/A: not applicable. Dispersion index definition: number of different rooms in which the strain was found, divided the average number of times it was found in the same room (limited to consecutive occupancy events).
Figure 2Diagram of MRSA types persistence and diversity in the study rooms over the duration of the study. Sequenced and non-sequenced, non-redundant strains. Red boxes indicate episodes of persistence. Blue and green circles indicate episodes of possible horizontal spread in MRSA strain types 1 and 2, respectively.
We detected MRSA USA100-type 2 (also MLST CC5) in four different rooms (rooms 2, 4, 6, 9) during the duration of the study, but limited to a single occupancy in each room (dispersion index: 4). Three of such four isolations occurred withing the span of one month, suggesting possible horizontal transfer. For this strain type the number of expected consecutive contamination events just by chance was 0.307.
MRSA USA100-type 3 (novel MLST clonal complex) was found in only one room (room 6) and showed ability to persist as it was recovered during two consecutive occupancy events (dispersion index: 0.5).
MRSA USA300-type 4 (MLST CC8) was also found in one room (room 9) and noted to persist across consecutive occupancy events (dispersion index: 0.5). Likewise, MRSA USA300-type 5 (also MLST CC8) was found in one room only (room 3) and noted to persist in that room across consecutive occupancy events (dispersion index: 0.5).
MRSA USA100 type 6, 7, 8 (all MLST CC5), and USA300 type 9, and 10 strains (all MLST CC8) were each found in one occupancy event only (dispersion index: 1) (Figure 2). The dispersion index overall for all typed MRSA strains was 1.08.
Overall, in all three cases where possible persistence of a MRSA strain was noted, whole genome sequencing confirmed the persistence of that strain during a change of room occupancy. One such case refers to a MRSA strain persisting in a terminally cleaned room before admission of the next patient, while in the other two cases the samples demonstrating persistence were collected after the admission of the next patient. The three MRSA strain types involved in persistence events were different from each other, and none of them was found in any other room at any time during the study period (Figure 2). Thus, these events are unlikely to be due to reintroductions or horizontal transmission, but rather they suggest strain persistence in the patient room over occupancy changes.
VRE. VR E. faecium type 1 (MLST ST117) was found very often during the duration of the study, amounting to 13 total occupancy events distributed among six different rooms (rooms 1, 2, 4, 5, 7, and 8) (Figure 3). Those included three potential same-room persistence events, plus four additional cases of recovery in non-consecutive occupancy events, but within the timespan of one month or less in each case (dispersion index: 7.7, see Table 2). The putative three cases of persistence during room occupancy changes cannot be confirmed despite their identical sequence, due to the strain’s endemicity (Figure 3). Alternatively, or in addition to true persistence, multiple horizontal transmission events, and possibly also re-introduction events might be at play for this specific strain type. Indeed, it would be expected a priori just by chance to observe, during the duration of the whole study, 1.61 cases of consecutive contamination events for a strain found as often as that specific strain.
Figure 3Diagram of VRE types persistence and diversity in the study rooms over the duration of the study. Sequenced and non-sequenced, non-redundant strains. Green, yellow, and blue circles indicate episodes of possible horizontal spread in VRE strain types 1, 2 and 4, respectively.
VR E. faecium type 7 (closest described MLST type: ST17) was detected in only two events during the study, in the same room (room 7) (dispersion index 0.5). Such events were consecutive occupancies (same room persistence event). For this strain type the number of expected consecutive contamination events just by chance was very low (0.065). We detected VR E. faecium type 2 (MLST ST80) in four different rooms (rooms 1, 2, 7, and 9) with no observed possible persistence events (dispersion index: 4). Two of these findings occurred in adjacent rooms in the span of four days. For this strain type the number of expected consecutive contamination events just by chance was 0.271. VR E. faecium type 5 (MLST ST132) was found only once (room 9) (dispersion index: 1).
VR E. faecalis type 4 (MLST ST6) was found in five different rooms (rooms 1, 2, 4, 6, and 8) over the course of the study, including two repeated isolations at different events in the same room (Figure 3). However, such events were not consecutive, and occurred many weeks apart (dispersion index: 7). For this strain type the number of expected consecutive contamination events just by chance was 0.575. We detected VR E. faecalis type 3 (MLST ST636, plus one closely related strain belonging to ST group 254) in three occupancy events (each one in a different room, specifically rooms 2, 4, and 5) (dispersion index 3), with two of those occurring only one week apart from each other, again suggesting potential horizontal transmission. For this strain type the number of expected consecutive contamination events just by chance was 0.200. VR E. faecalis type 6 (MLST ST236) was only recovered once (room 7) (dispersion index 1). The dispersion index overall for all typed VRE strains was 3.25, compared to 1.08 for MRSA.
Discussion
Among the first to use WGS for epidemiological investigations outside of outbreak scenarios in the post-acute care setting, our study was specifically geared to investigate environmental diversity and burden of MRSA and VRE, an important but understudied determinant of colonization pressure in patients. In particular, our investigation was designed to assess the frequency of MRSA and VRE persistence in rooms during patient turnover and compare it with their ability to spread horizontally between rooms. The emerging picture is one of high diversity among contaminating strains, even when only a relatively small fraction of all the facilities’ patient rooms was considered. Since this diversity may be the result of frequent new introductions by patients, admission screening could be an integral and important part of a tailored program to reduce the burden of MRSA and VRE.
Moreover, we documented several cases of persistence in single rooms despite terminal cleaning using products active against MRSA and VRE, among other organisms, following the patient’s discharge, as well as a high degree of horizontal transmission among the facility’s rooms, especially for VRE. Notwithstanding worrisome high prevalence for both, our data demonstrate important epidemiological differences between these two main pathogens.
In the case of MRSA, at least ten different strains had been present in the facility during the course study. MRSA showed a high propensity towards persistence in patient rooms, with three different strain types (including both USA100 and USA300) isolated during two consecutive occupancies. Based on these observations, it could be postulated that the determinants conferring ability to persist in MRSA are not specific of a few genotypes, but rather a relatively common characteristic of MRSA.
Besides the above-mentioned strains, other MRSA USA100 and USA300 were only isolated on one occasion during the course of the study, pointing to limited horizontal spread, at least compared to new introductions.
VRE, on the other hand, showed endemicity (Figure 3) suggested by high rates of horizontal spread and a likely contribution by re-introductions, presumably from strains endemic in the region’s hospitals.
Persistence seemed to be a less important determinant toward the burden of VRE. Indeed, it was only occasionally observed, despite the many opportunities granted by the very high burden observed in the facility, with only one case confirmed while the other potential episodes involved a strain that was so common that a certain number of repeated isolations would be expected just by chance. It is possible that this difference could be due to better susceptibility of VRE to environmental cleaning, either in general or to the specific practices used in the facility. Some cases of potential horizontal transmission were also evidenced for MRSA, for example for USA100 CC5 strains, and especially for one strain which was not found at any other time during the study (USA100 CC5 type 1, Figure 2). In this case independent multiple introductions cannot be excluded, especially in patients admitted from the same hospital. Since not all patients were enrolled for this study, and since occupancies consisting of empty, terminally cleaned rooms were also assessed, information on hospital of provenience is not consistently available or applicable. Notably, the most common MRSA and VRE sequence types found in our study are also the most common in other SNFs in SE Michigan.
While horizontal transmission was clearly an important determinant of pathogen spread, especially for VRE, more work and specifically designed studies are needed to pinpoint the exact pathways and mechanisms leading to new patient acquisitions in the SNF setting. In our case, while most patients were mobile and spent time outside of their room (mostly in the physical therapy facility, and in some cases diagnostic and therapeutic appointments), it is important to note that healthcare personnel may be an important transmission vector. Thus, sampling of personnel hands will be an important tool to clarify epidemiologic trends in SNFs.
Our findings are a demonstration of the importance of obtaining a true understanding of the epidemiology of important pathogens in post-acute care facilities, since what actions will be or will not be effective in preventing new patient acquisitions and successive infections closely depends on the specific epidemiological characteristics of each target pathogen. Our dispersion index showed a marked difference between MRSA, which at 1.08 falls at the lower limit of the “balanced” category, (between 1 and 2, while <1 defines a tendency towards “persistence”) and VRE, which at 3.25 indicates a tendency towards ”dispersion” (>2)). This index is a new attempt to create a simple tool to understand different pathogens’ transmission patterns in post-acute care, and therefore it is possible that it would benefit from improvements/modifications in order to ensure its usefulness in a broader range of scenarios. Additionally, it requires granular documentation of isolates source, and accurate molecular typing of isolates, unless target pathogen’s prevalence is very low. It would be very interesting to calculate the dispersion index for other facilities in the future to understand whether it is consistent across different facilities, and over time, for each specific pathogen. If it is, this would enable findings from a limited number of facilities to be translated to others. If not, it would underscore the importance of deploying reasonable resources to gain at least a general understanding of the specific epidemiology of key pathogens in each facility. Many factors may affect the use of this or similar indexes, including for example the size and interconnectedness of the healthcare networks in which a specific facility operates, and the specific epidemiological scenarios in each particular geographic area, among others.
The dispersion index, or other similarly developed indexes may be useful as a guide to gauge the pattern/s each pathogen is most likely to follow in this unique patient population as they establish themselves as endemic, and thus helping choose the best fitting prevention strategy. Among these, heightened surveillance and a number of targeted policy improvements to prevent persistence as well as horizontal transfer, from admission screening, to obtaining colonization data from previous healthcare provider, to expanding and improving cleaning procedures to critical surfaces with appropriate antiseptics active against MRSA and VRE (especially during patient transitions), to establishing/enforcing better barrier precautions, including for healthcare workers, to limit horizontal spread of VRE.
The choice of body sampling sites was determined in order to maximize patient sampling consistency and minimize selection bias. Similarly, the choice of environmental sampling was determined to ensure consistency over time and in different rooms, as well as sensitivity for room contamination.
Environmental Panels as a Proxy for Nursing Facility Patients with Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus Colonization.
Additionally, multiple body and environmental sampling can compensate for the potential decrease in sensitivity due to lack of s specific body site (for example, rectal sampling for VRE), through increased recovery of microorganisms shed by the patient.
Our study focused exclusively on single-occupancy (private) rooms, which are becoming more and more common in hospitals but also gradually increasing in post-acute care facilities and expected to eventually become standard assuming appropriate resources will be available. Our choice has the advantage of avoiding bias generated in complex scenarios such as shedding of pathogen from a roommate for which there may be no colonization information due to patient not being enrolled in the study.
On the other hand, eliminating multiple-occupancy rooms which are expected to have a higher burden of MRSA and/or VRE may lead to underestimation of the overall prevalence in the facility as well as missing cases of horizontal transmission. Indeed, single rooms constitute an initial barrier to transmission, especially in the case of MRSA.
Private patient rooms and hospital-acquired methicillin-resistant Staphylococcus aureus: A hospital-level analysis of administrative data from the United States.
The choice of prevention strategy must take the proportion of single versus multiple room in account, or alternatively different protocols may need to be used in single and in multiple room and the patients occupying them.
Although obtained in a different healthcare setting (tertiary hospital ICU), data from a large study clearly showing higher risk of MRSA and VRE acquisition when the previous occupant of a room was colonized,
which prompted us to investigate the likelihood of persistence and the molecular epidemiology of strains involved. Interestingly, a follow up to that study confirmed that a one-size-fits-all approach may not be optimal, with interventions focused on cleaning proving much more effective in limiting MRSA acquisitions than VRE acquisitions.
Such differences may be due to a number of reasons ranging from different patient behavior and levels of precaution, to different likelihood and characteristics of environmental biofilms formation. Importantly, recent research shows that in many cases, daily cleaning may not be sufficient, and improved outcomes may be obtained with multiple cleaning sessions a day, as well as by performing additional targeted disinfection following specific high-transmission risk situations, regardless of the timing of the lates room cleaning.
. Additionally, when appropriate, patient participation in cleaning (e.g.: personal objects) could be encouraged and facilitated by making disinfecting wipes and other non-harmful tools readily available.
We chose to use WGS for molecular typing of our isolates of interest due to its advantages over other traditional typing techniques.
Time to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology: Comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013-2015.
Meticillin-resistant Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing.
Indeed, WGS with SNV analysis has higher discriminatory power than traditional MLST, with the degree of difference depending in part on the specific pathogen addressed.
As sequencing and data analysis methods improve, new strategies are and will become available to obtain a better discrimination between strains when comparing numerous and complex populations of closely related organisms.
In our case, we observed several strains belonging to the same MLST type or complex but diverging enough, in terms of accumulated SNV, to study persistence and horizontal transfer events on a room-by-room and occupancy-by-occupancy basis. As WGS becomes more widely adopted in the future, we expect expansion of strain databases allowing us to better study the evolution of pathogens. For example, in our case it will be important to understand the origin, evolution and geographical spread of the strains ultimately found in our facility. This will help inform the most likely mechanisms and avenues of further MRSA and VRE spread and make an informed choice of the optimal measures to prevent harm to our patients.
Author Contribution
Concept and design: Cassone, Wang, Lansing, and Mody.
Acquisition, analysis, and interpretation of data: Cassone, Wang, Lansing, Gibson, Gontjes, Mantey, Mody.
Drafting of the manuscript: Cassone, Wang, Mantey, Mody.
Dr. Cassone and Dr. Wang have accessed and verified the underlying data reported in the manuscript. All authors had full access to all the study data and accept responsibility to submit for publication
Funding
This work was supported by the National Institutes of Health [grant number K24AG050685 to Mody], University of Michigan Pepper Older Americans Independence Center [REC Scholarship to Cassone].
Data Sharing
The authors will make microbiological and sequence data freely available upon reasonable request.
Declaration of Competing Interest
The authors declare no conflicts of interest.
Acknowledgments
We thank the facility leadership, employees, patients and visitors for their assistance and patience. We thank the University of Michigan Advanced Genomics Core.for performing Whole Genome Sequencing.
Appendix A. Supplementary data
The following is the Supplementary data to this article.
Interplay Between Patient Colonization and Environmental Contamination with Vancomycin-Resistant Enterococci and Their Association With Patient Health Outcomes in Postacute Care.
Environmental Panels as a Proxy for Nursing Facility Patients with Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus Colonization.
The evolution of methicillin resistance in Staphylococcus aureus: similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones.
Private patient rooms and hospital-acquired methicillin-resistant Staphylococcus aureus: A hospital-level analysis of administrative data from the United States.
Time to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology: Comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013-2015.
Meticillin-resistant Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing.
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