Advances in the Prevention and Control of HAIs

Detection of Methicillin-Resistant Staphylococcus aureus (MRSA) From Multiple Body Sites of Residents at Long-Term Care Facilities

Table of Contents

Donna M. Schora, Susan Boehm, Sanchita Das, Parul A. Patel, Kenneth Schora, Kari E. Peterson, Althea Grayes, Carolyn Hines, Deborah Burdsall, Ari Robicsek, Lance R. Peterson


Accurate determination of methicillin-resistant Staphylococcus aureus (MRSA) colonization status can be an important part of any infection control strategy to limit the exposure of MRSA-free residents of long-term care facilities (LTCFs) to these pathogens. The nares are the most commonly sampled body site and the most frequently positive body site for the organism. We compared nasal polymerase chain reaction (PCR) to culture of the nares and four other body sites for detection of MRSA colonization to determine if the nares are still the preferred body site to be tested or if other sites should be included. The study population consisted of asymptomatic, infection-free residents at three LTCFs. A double-headed swab was used to collect nasal samples, and single swabs were used to collect oral, axilla, perineum, and perianal samples. Each swab was plated onto BBL™ CHROMagar™ MRSA (CM). When S. aureus was recovered, identification was confirmed with the Staphaurex® agglutination test. Pulsed-field gel electrophoresis (PFGE) analysis was performed on MRSA isolates recovered from each positive body site. After plating, one of the paired swabs from each nasal specimen was used to perform the BD GeneOhm™ MRSA achromopeptidase (ACP) assay, and the second swab was used for the Cepheid Xpert® MRSA test. Both PCR assays were performed according to the manufacturers' instructions. A total of 291 residents qualified for the study, and 26 (8.9 percent) residents had at least one body site culture positive for MRSA. Twenty-one of 26 (81 percent [95 percent CI, 76 percent to 85 percent]) residents were PCR positive in the nares; of the five that were PCR negative, three had positive perianal samples, and two had positive perineum samples. Our results suggest that nasal PCR testing captures 81 percent of those colonized with MRSA. If greater capture is desired, additional body sites should be considered for testing.


The long-term care facility (LTCF) is a part of the U.S. health care system that presents unique challenges for infection prevention and control. Many residents of LTCFs are vulnerable older adults who are unable to manage independently in the community. They require a range of care, from minimal assistance with activities of daily living to total dependence upon health care personnel. In addition, there are many opportunities for direct interaction among residents, visitors, and health care personnel during group activities and at mealtimes, both in common activity areas and in dining rooms. An important goal of the LTCF is to find effective ways of minimizing the healthcare-associated infection risk while still maintaining the desired interactive lifestyle for these residents, who call the facility their home.

A major challenge in health care organizations today is the spread of drug-resistant bacteria. When residents of an LTCF are admitted to an acute care hospital, they are at risk of becoming colonized and then returning to the LTCF with these organisms. Because it is hard to impose "contact isolation" precautions that restrict resident movement in a home-like living environment, there is considerable risk for the spread of these organisms. To better protect older adults, it is important for hospitals and LTCFs to collaborate on ways to prevent the spread of these organisms in both facilities. We developed a research and demonstration project to create a model of interfacility communication and cooperation between hospitals and LTCFs to facilitate infection prevention and control by developing LTCF-tailored interventions that reduce infection risk in older adults while maintaining their desired lifestyle. The prevention of methicillin-resistant Staphylococcus aureus (MRSA) colonization and disease is the program model proof of concept. Our hypothesis for the study is that one can safely remove the colonization risk from nearly all MRSA-negative residents in a way that does not interfere with the desired lifestyle and thereby reduce their risk of MRSA clinical infection.

Colonization prevalence is an important measure for the success of this program, and accurate determination of colonization status is therefore an important part of the strategy. The nares is the most commonly sampled body site and is the most frequently positive body site for the organism, but not all MRSA carriers harbor MRSA in their nose. Studies have found that the throat and the rectum may provide additional information about true colonization status,1–3 but past studies that have mixed reports of infected and non-infected individuals do not provide an accurate description of colonization sites in the asymptomatic, non-infected person. Our hypothesis was that testing the nares alone, using real-time polymerase chain reaction (PCR), is sufficient in long-term care because this approach led to a 70 percent reduction in clinical disease in our acute care hospitals.4 Therefore, as part of our study, we sampled the nares and four other body sites of 300 non-infected residents at three LTCFs to investigate if sampling the nares is sufficient for determining MRSA colonization. We compared nasal PCR to the culture of all five body sites to determine if nasal PCR is sufficient for surveillance or if other body sites need to be included.


Sample Collection

Samples were collected from residents of three LTCFs from March 15, 2011 to February 22, 2012. The LTCFs are within 15 miles of each other and are served by two different health care systems. Residents selected for the study were able to give written consent and did not have an active infection with MRSA. They were selected from non-dementia units including, but not limited to, assisted-living and hospital/surgical rehabilitation floors.

To obtain consent, the residents were approached by a member of the research team. Research personnel wore street clothes with no lab coats so as not to give the impression of medical authority (i.e., did not look like a nurse or doctor) that would arouse feelings of coercion on the part of the resident. Research personnel read the consent form to the resident; if the resident orally agreed to be sampled and could sign his or her name and the date on the consent form, the investigator proceeded. If at any time the resident asked the researcher to stop, the collection process was discontinued.

Five body sites were sampled for culture: nose, throat, axilla, perineum, and perianal area. Nasal samples were collected using a double-headed swab with Liquid Stuart's transport media (Copan) because two swabs were needed to perform PCR and culture. PCR was only done on the nares, since the test is Food and Drug Administration (FDA)-approved only for that use. The swabs were pre-moistened with the transport media prior to collection, for ease of sample collection, following protocol in our acute care hospital. Single swabs with Liquid Stuart's transport media were used to collect throat, axilla, perineum, and perianal samples. FDA-cleared PCR tests are not available for these sample sites; therefore one swab was sufficient for culture testing. Non-nasal swabs were not pre-moistened prior to sample collection. All samples were immediately transported to the laboratory and processed within 8 hours of collection.

Laboratory Testing

Each body site swab was plated onto BBL™ CHROMagar™ MRSA (CHROMagar). After plating, one of the paired swabs from the nasal specimens was used to perform the BD GeneOhm™ MRSA ACP assay, and the second swab was used for the Cepheid Xpert® MRSA test. Both nasal swab samples were destroyed after the PCR tests were performed, and so no sample existed for broth enrichment culture. For consistency, the other four body site swabs did not receive broth enrichment culture. The CHROMagar cultures were read at 24 and 48 hours. Mauve colonies found growing on the plates were isolated to blood agar, and S. aureus identification was made by performing a Staphaurex® agglutination test (Remel, Lenexa, KS). S. aureus colonies that were mauve on CHROMagar were considered to be MRSA.

The nasal samples were tested for MRSA by two different PCR assays, the BD GeneOhm assay and the Cepheid test. Both assays were performed according to the manufacturers' instructions. Sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) were determined for each PCR method, with positive culture of any single body site as the gold standard.

MRSA isolates recovered from each body site were typed by pulsed-field gel electrophoresis (PFGE) using SmaI restriction enzyme as previously described.5,6 The patterns were identified on BioNumerics version 6.6 (Applied Maths Inc., Austin, TX) using a dendogram generated by the unweighted-pair group method with arithmetic mean based on Dice coefficients, where optimization and band position tolerance were set at 0.8 percent and 1.2 percent, respectively.6,7 A similarity coefficient of 80 percent was selected to define the patterns. Assignment of pulsotype was correlated by comparison to the published literature.8,9


A total of 302 residents were enrolled in the study, and 291 qualified for analysis. The 11 residents who were disqualified included 5 who were mistakenly sampled twice, and 6 whose written consent was deemed invalid by the institutional review board. The results for the residents tested, by LTCF, are shown in Table 1.

Table 1. Residents tested during study period, by long-term care facility

  MRSA Culture Negative (all body sites) ≥1 Culture Positive with MRSA Total Residents Tested Percent Positive Residents Tested/(95% confidence interval)
LTCF 1 90 20 110 18%/(12%–26%)
LTCF 2 101 3 104 2.9%/(1%–-8%)
LTCF 3 74 3 77 3.9%/(1%–11%)
Totals 265 26 291 8.9%/(6%–13%)


Twenty-six (8.9 percent) residents had at least one body site that was culture positive for MRSA, with a total of 63 culture-positive body sites. The number of cultures positive at each body site is listed in Tables 2 and 3. More than two-thirds (69 percent) of the 26 culture-positive residents were positive at two or more body sites. Of note, 21 of the 26 (81 percent) culture-positive residents were MRSA nasal PCR positive. Of the five that were not PCR positive, three were culture positive from the perianal region, two were positive from the throat, two were positive from the perineum, and none had a positive axilla culture. Overall, 13 of the 26 culture-positive residents were positive from their perianal site, 15 were positive from the throat, 11 from the perineum, and 3 from the axilla.


Table 2. Culture of multiple positive body sites vs. BD GeneOhm™ MRSA ACP assay and Cepheid Xpert® MRSA PCR test

Culture Positive Body Site BD Nasal PCR Positive (n=21) BD Nasal PCR Negative (n=5) Cepheid Nasal PCR Positive

Cepheid Nasal PCR Negative

Nasal 20 1 19 2
Throat 13 2 14 1
Axilla 3 0 3 0
Perineum 9 2 9 2
Perianal 10 3 10 3

Table 3. MRSA culture-positive colonization of residents in three long-term care facilities, by body site

No. of Sites with MRSA Carriage No. of Residents Nares Throat Axilla Perineum Perianal
0 265 0 0 0 0 0
1 8 5 1 0 1 1
2 6 4 4 0 1 3
3 6 6 4 1 3 4
4 5 5 5 1 5 4
5 1 1 1 1 1 1


The sensitivity, specificity, PPV, and NPV for each of the nasal MRSA PCR tests are given in Tables 4 and 5. Culture of MRSA from any of the five body sites sampled was used as the reference standard for a positive patient. When the BD GeneOhm assay was used, 21 of 26 (81 percent) MRSA-colonized residents were detected. The results were similar with the Cepheid test: 20 of 26 (77 percent) of residents colonized with MRSA were detected. A total of seven residents had at least one nasal PCR test negative; five had negative results for the BD GeneOhm test, and six for the Cepheid test.


Table 4. BD GeneOhm™ MRSA ACP assay versus all culture sites

  Any Body Site Culture Positive All Body Site Cultures Negative  
PCR Positive 21 34 p=0.42
PCR Negative 5 231  
Sensitivity 81%    
Specificity 87%    
Predictive Value Positive 38%    
Predictive Value Negative 98%    


Table 5. Cepheid Xpert® MRSA PCR versus all culture sites

  Any Body Site Culture Positive All Body Sites Culture Negative  
PCR Positive 20 5 p=0.36
PCR Negative 6 256*  
Sensitivity 77%    
Specificity 98%    
Predictive Value Positive 78%    
Predictive Value Negative 98%    

* Four tests were invalid, and results could not be provided.


The results of the strain typing of the 63 MRSA isolates are depicted in Figure 1. Analysis of the strain typing revealed eight different groups of related isolates that were arbitrarily designated as Groups 1–8. Group 1, with five residents, represents the USA300 pulsotype (community-associated MRSA), and Group 2, with 14 residents, is the USA100 pulsotype (the most common healthcare-associated MRSA clone). An additional five residents had strain types that had PFGE patterns similar or closely related to the USA100 pulsotype. One resident had a MRSA strain that resembled EMRSA-15 (the epidemic MRSA strain that has spread from the United Kingdom to several countries in Europe and Asia but is rarely detected in the United States) when compared to published PFGE images (Figure 2).10,11 This strain type was recovered from the resident's nose, throat, perineum, and perianal area (the axilla did not grow MRSA). No other resident harbored this strain during this study. Two residents had one different strain type each among their MRSA isolates. Of the five residents that were nasal culture negative, no one strain type predominated in the other body sites.

Figure 1. Pulsed-field gel electrophoresis pulsotypes of the 63 MRSA isolates at three long-term care facilities

Figure 1: Pulsed-field gel electgrophoresis pulsotypes of the 63 MRSA isolates at three long-term care facilities – depicts an image of the pulsed-field gel electrophoreses pulsotypes of the 63 methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered at the three long-term care facilities involved in this study.


Figure 2. Pulsed-field gel electrophoresis image of long-term care facility resident's strain resembling EMRSA-15

Figure 2: Pulsed-field gel electrophoresis image of long-term care facility resident’s strain resembling EMRSA-15 – shows the pulsed-field gel electrophoresis image of a long-term care facility resident’s strain that resembles the EMRSA-15 strain that has spread from the United Kingdom to several countries in Europe and Asia but is rarely detected in the United States.

Notes: MBS=multiple body site, N=nasal, O=oral (throat), P=perineum, PR=perianal.


In our health care organization, as in many others, real-time PCR is used to determine the MRSA nasal colonization status of a patient. Tests for nasal colonization with MRSA at an LTCF may also be conducted with PCR, and it was therefore added to the study to make the results applicable. Our results suggest that if we had only performed nasal PCR on the 291 residents in this LTCF population, we would have missed 19 percent of those colonized with MRSA, and that additional sampling with culture is needed to capture all those colonized with MRSA. Upon examination of our data, a good choice for additional sampling in this population might be the culture of the perianal region. In the case of the five residents who were nasal PCR negative with the BD GeneOhm test, three were positive in the perianal area. Likewise, in the six residents that were nasal PCR negative with the Cepheid test, three were positive in the perianal area. Only the nasal PCR and perianal culture combination gave a MRSA colonization rate close to 90 percent.

These findings are similar to Eveillard et al., who also showed that nasal and perirectal sampling captured more than 90 percent of those colonized; however, their study was conducted at a 600-bed teaching hospital rather than at an LTCF.2 Mody and colleagues found that only 65 percent of the residents from 14 nursing homes were nasally colonized with MRSA.1 Of those not colonized in the nose, perianal/groin samples and throat samples added approximately the same number of additional positive cultures. However the authors reported that adding just one body site, either perianal/groin or throat, would not achieve a colonization rate greater than 90 percent, and more than two sites would have to be sampled to achieve it. Interestingly, in our investigation and the Mody study,1 the throat offered no distinct advantage in combination with the nose as some have suggested.12,13 In addition, our study set included only uninfected individuals, providing an accurate description of colonization sites in the asymptomatic, uninfected person. The Mody and Eveillard studies included infected as well as asymptomatic patients.1,2

The predominant MRSA clonal type in this population of 291 non-infected LTCF patients was USA100. We did not detect many USA300 strains. Reports suggest that USA300 can evade detection because it is not a predominant nasal colonizer.14 However, in contrast to these reports, of the five residents who were colonized with the USA300 type, four were found to harbor their MRSA strain only in the nose, and the nasal PCR test was positive for all four residents. This discrepancy may be due to the fact that we excluded clinically infected residents in the study. Interestingly, Shurland et al. found similar results with a study of residents in extended care facilities from one health care system. Eighty-four percent of USA300 MRSA-colonized residents had anterior nares colonization, whereas 86 percent of residents with non-USA300 strains were nasally colonized, and this difference was not significant.14 Unlike our study, however, this study included residents with areas of skin breakdown.

One of the challenges in this investigation was the recruitment of subjects. Our study population was limited to 300 residents, a subset of the LTCF population, where we sought to enroll only residents who could give informed consent and were able to sign the consent forms. This excluded the dementia units. Also, an important consideration in the choice to exclude dementia units was to avoid the risk of undue stress on the residents. Five swabs were used to collect the various samples, and residents might become upset if they saw long, white swabs coming close to their body, especially personal areas like the groin or rectum. Moreover, it might be difficult for these residents to be moved if they were wheelchair bound. On the other hand, they might be combative and not allow anyone to get near the area to be sampled. Still another reason to exclude residents with dementia is the need to involve individuals with power of attorney to sign a consent form. This would require more communication time than speaking directly to a resident. There might also be additional time and expense if forms needed to be handled through the mail.

Another challenge in the recruitment of subjects was their physical availability and mental alertness. Residents were consented mid-morning to afternoon because they were dressed and alert at this time. We found that this time period fostered a successful conversation with the resident, and the consent process went smoothly. However, it was during this time period that the residents were highly mobile and were often gone from their rooms. They could be participating in activities in other parts of the building or even outside the facility, making recruitment difficult. We found that the best time to find residents in their rooms was immediately before or after a meal. Research personnel had to arrange their visits to coincide with these timed events. In addition, we found it helpful to have two research personnel travel together to collect the samples. Often residents needed assistance during the sample collection, so the second person could aid in supporting the resident while the samples were collected.

To avoid potential problems while collecting samples at the LTCF, we found it helpful to have a good rapport with the LTCF personnel responsible for infection control (preferably a dedicated infection preventionist). This person was key to providing ongoing communication to the LTCF staff about the study and acted as a liaison with research personnel for any problems that arose. We relied on the guidance of these individuals because they are the experts when it comes to the framework of their facility, and the execution of the project had fewer problems because we had these study champions. We received no complaints from the residents or health care personnel about the study process.

This study had some limitations. One was the lack of the broth enrichment culture as part of the culture process. It is possible that there would have been more positive cultures had broth enrichment been used. Unfortunately, there was not a nasal swab sample left over for broth enrichment because both swabs were used for the PCR tests. The other potential limitation was the exclusion of the dementia unit. If this population of patients had a higher MRSA colonization rate than the population tested, it could have provided additional positive samples.

There were several lessons learned from this study. Having a good working relationship with the infection preventionist and the leadership staff at the LTCF afforded a smooth path to working with the residents and the health care workers. Knowing the activity patterns of the residents helped to maximize study personnel time and increased sample collection rates. Residents were often at doctors' appointments, physical therapy, or unit activities between meals, so those were time intervals to be avoided for sample collection. Interacting with residents immediately before or after breakfast was very successful. Knowing peak mental and physical fitness time of the day for the residents allowed for less confusion and more willingness to participate in a study.

More than one sample type will likely need to be collected if greater than 90 percent colonization status is to be achieved; for our population, the nose and perianal region represented the best combination. PCR can be a useful test methodology for nasal screening in LTCFs, although test systems vary in sensitivity and specificity. However, in our acute care hospitals, which have a comprehensive MRSA control program, we only test the nares and have achieved a 70 percent reduction in clinical disease using this approach.4 Thus, if colonization and disease in long-term care are reduced using nasal PCR testing, approximately an 80 percent level of capture may be sufficient.


Accurate determination of MRSA colonization status is an important part of any infection control surveillance strategy that has a goal to limit the exposure of non-colonized individuals to this pathogen. In our study the nose proved to be the site most colonized with MRSA, with nasal PCR capturing 81 percent of all those colonized with MRSA. Of interest in this study was that while the two PCR tests had similar sensitivity for the LTCF population, one had superior specificity, which resulted in significantly fewer false positive tests being reported when the Cepheid assay was used (Tables 4 and 5; p <0.001). To capture more than 90 percent of all colonized residents, sampling the nares and additional sites is necessary. Since we used nasal PCR alone to reduce MRSA disease in our acute care facility,4 this level of detection may be sufficient; but if successful control is not achieved in the LTCF setting using nasal swab PCR alone, then the testing of additional body sites should be considered.


This project was funded under Grant No. 1R18HS019968 from the Agency for Healthcare Research and Quality, U.S. Department of Health and Human Services. The BD GeneOhm™ MRSA ACP assay kits were provided by Becton, Dickinson and Company. The findings and conclusions in this document are those of the authors, who are responsible for its content, and do not necessarily represent the views of AHRQ. No statement in this report should be construed as an official position of AHRQ or of the U.S. Department of Health and Human Services.

Authors' Affiliations

NorthShore University HealthSystem, Evanston, IL (DMS, SB, SD, PAP, KS, KEP, AG, AR, LP). University of Chicago, Chicago IL (AR, LP). Whitehall of Deerfield, Deerfield, IL and Glenview Terrace, Glenview, IL (CH). Lutheran Life Communities, Arlington Heights, IL (DB).

Address correspondence to: Donna M. Schora, MT (ASCP), NorthShore University HealthSystem, 2650 Ridge Avenue, Walgreen Building, SB Rm 525, Evanston, IL 60201; Email:


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Page last reviewed June 2014
Page originally created June 2014
Internet Citation: Detection of Methicillin-Resistant Staphylococcus aureus (MRSA) From Multiple Body Sites of Residents at Long-Term Care Facilities. Content last reviewed June 2014. Agency for Healthcare Research and Quality, Rockville, MD.
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