Role of Xpert PCR kit in assessing MRSA colonization in medical and surgical units of a tertiary care teaching hospital

Abstract

Background and rationale

Methicillin resistant Staphylococcus aureus (MRSA) colonization increases the risk of MRSA infection. Detecting MRSA colonization can influence postoperative outcomes and prolong hospital stay. The conventional standard culture method for detecting MRSA colonization has limitations in terms of sensitivity and turnaround time. Hence, we sought out use of Xpert PCR kit for prompt evaluation of MRSA colonization to support MRSA prevention in a tertiary care hospital in Karachi, Pakistan.

Materials and methods

During 1st April-31st December 2022, 290 nasal and skin swab samples were collected from 257 patients and processed using routine culture (as gold standard method) and PCR-based MRSA detection assay (MRSA Xpert).

Results

A total of two hundred and ninety (290) swab samples from 257 patients were obtained, 33 of which were paired. The overall prevalence of MRSA colonization was 12% by both methods, with 90% of cases classified as community-associated (CA-MRSA) whereas 10% as hospital-acquired (HA-MRSA). The colonized group showed a higher subsequent MRSA infection rate (11% vs. 3.5%) compared to the noncolonized group. Culture identified 11% of screening samples as MRSA positive, Xpert MRSA assay showed 100% sensitivity and 95% specificity. The cost of a single MRSA Xpert assay was $50 while MRSA culture cost around $7.50.

Conclusion

Our study findings suggest that the presence of MRSA colonization in our cohort of patients is consistent with the existing trends in hospital epidemiology. Both conventional culture and Xpert MRSA methods showed comparable efficacy for detection of MRSA colonization. Larger-scale studies are recommended to validate these findings conclusively.

Introduction

Methicillin-resistant Staphylococcus aureus (MRSA) is a significant pathogen both in community and hospital settings, responsible for a wide variety of invasive and toxin-mediated infections [1]. MRSA can spread through direct contact, contaminated instruments, and healthcare personnel, causing infections that are often difficult to treat [2, 3]. The high prevalence of MRSA colonization in hospitalized patients poses significant challenges for the infection control team and healthcare budget. In recent years, there has been an increase in hospital-acquired bacteremia and pneumonia attributable to MRSA [4]. Several studies have demonstrated the role of MRSA colonization in the development of surgical site infections (SSIs) [5]. Furthermore, MRSA nasal decolonization has demonstrated a significant protective effect against SSIs associated with MRSA [6]. In Pakistan, the prevalence of MRSA has shown significant variation over recent years, ranging from 6 to 52% reflecting a concerning trend [7,8,9] To prevent the spread of these infections, several strategic measures have been implemented in healthcare settings. Infection control programs unambiguously benefit from a method of MRSA surveillance that is both rapid and more sensitive. In addition to broth microdilution, the Clinical and Laboratory Standards Institute (CLSI) recommends many other techniques of MRSA screening like the cefoxitin disc diffusion test and, the use of a plate containing 6 µg/ml oxacillin. Furthermore, commercially available chromogenic agars, latex agglutination, or immunochromatographic membrane tests for PBP2a can be used to detect MRSA. However, all these methods typically require 2–3 days [10]. Furthermore, an automated MRSA identification system (i.e., Microscan^® and Vitek^®) can also be utilized for MRSA surveillance screening. Finally, the use of real-time polymerase chain reaction (RT‒PCR) for detecting and monitoring organisms in clinical specimens has been made possible [11]. The Xpert MRSA assay is one such modality modeled on the principle of RT-PCR and was recently developed for the detection of MRSA in wound swab samples by detecting specific DNA sequences within the staphylococcal cassette chromosome mec (SCCmec); this method automates and integrates all the steps of SCCmec detection from DNA extraction to detection of the target organism within 2 h [12]. Our study sought to validate the clinical utility of wound swab Xpert MRSA assay kit as MRSA screening tool from nasal and skin swab, by comparing with gold-standard culture technique and assessing the sensitivity, specificity, positive and negative predictive value (PPV, NPV) of this kit in clinical settings.

The current study was aimed to determine the frequency of patients with MRSA colonization/ infection at admission and discharge at Aga Khan University Hospital (AKUH) and the potential risk factors in both groups. In addition, the sensitivity, and specificity of a PCR-based MRSA kit used as a MRSA screening tool were evaluated.

Definitions

Community-acquired MRSA (CA-MRSA)

CA-MRSA infections are defined as an MRSA infection in an individual who has had: MRSA identified within 48 h of admission to a hospital having no history of hospitalization, surgery, dialysis, or residence in a long-term care facility within 1 year of the MRSA culture date, having no permanent indwelling catheter or percutaneous medical device (e.g., tracheostomy tube, gastrostomy tube, or Foley catheter) and no known prior positive culture for MRSA.

Hospital-acquired MRSA (HA-MRSA)

Hospital-acquired Methicillin-resistant Staphylococcus aureus (HA-MRSA) is characterized as an infection caused by MRSA that is identified more than 48 h after a patient has been admitted to a healthcare facility, and the patient did not have MRSA infection or colonization upon admission to the healthcare setting.

MRSA colonization

Positive MRSA culture from any body site (e.g., nasal swab, forehead, respiratory tract sample, wound culture) without signs or symptoms of infection.

MRSA infection

Positive MRSA culture from a normally sterile site (e.g., blood, cerebrospinal fluid, joint fluid, deep tissue biopsy) along with clinical signs and symptoms of infection such as fever, localized pain, inflammation, or systemic signs of infection along with a positive MRSA culture from an affected site.

Materials & methods

This was a cross-sectional study conducted at Aga Khan University Hospital (AKUH), a 650-bed tertiary care private setting. The hospital has a well-organized Department of Infection Prevention and Hospital Epidemiology (DIPHE). The study population included patients ≥ 18 years to 85 years of age, admitted to medical/surgical units of Aga Khan University Hospital, Karachi between 1st April and31st December 2022.

Inclusion criteria

Patients aged ≥ 18 years were included in the study.

Exclusion criteria

(i) critically ill/patients for whom nasal swab sampling was difficult, (ii) patients who were transferred from other hospitals, and (iii) patients with known MRSA colonization or infection.

At Aga Khan University Hospital, routine infection prevention and control practices include hand hygiene audits, performed by trained infection control nurses, using a World Health Organization-based methodology. In addition, routine environmental cleaning is conducted according to the hospital’s infection control policy. MRSA surveillance is part of the routine surveillance for multidrug-resistant organisms at AKUH, using the Centers for Disease Control and Prevention (CDC) Infection Surveillance methodology type B, which involves selected locations within the facility (one or more). Daily MDRO colonized/infected patients are identified by automated generated lab-based details through an online Integrated lab management system (ILMS). Once MRSA detection is reported in any clinical sample, contact isolation precautions are initiated. Unit-wise MDRO is calculated as per admission days and patient days.

Sample size calculation

The sample size for this study was calculated using World Health Organization sample size software. In a locally conducted MRSA prevalence study, MRSA frequency of 52% has been reported in Staphylococcus aureus clinical isolates [2]. We estimated that a minimum sample size of 180 patient samples would be needed to detect 52% of MRSA isolates, keeping a 95% confidence interval and 6.1% margin of error and using the equation below:

$$\eqalign{& n { = ^{{{1.96}^2}p(1{\rm{ }} - p) = {{\left( {1.96} \right)}^2} \times {\rm{ }}0.52{\rm{ }} \times {\rm{ }}\left( {1{\rm{ }} - {\rm{ }}0.52} \right)}} \cr & \,\,\, = {\rm{ }}257\,patient\,samples \cr}$$

A sample size of 257 was drawn from the above equation.

Data analysis

For evaluating sensitivity and specificity of a PCR-based method sample size was calculated using Open EPI with expected sensitivity of 0.76, expected specificity of 0.96, expected prevalence of 0.52, desired precision of 0.07, and confidence level of 95%. A minimum sample size of 254 was drawn from the above equation. Finally sample size of 257 was selected to include both objectives.

Ethical approval

The study was approved by the Ethics Review Committee of the Agha Khan University Hospital, Karachi, Pakistan (ERC Reference No2022-6593-20783.Dated 24-Februray-2022).

Sampling and testing protocols

Before sampling, informed written consent was obtained from those patients fulfilling the inclusion and exclusion criteria. In the case of affirmative consent, the sample was taken, and patient data were entered into as standardized questionnaire. At admission, the first screening sample (Admission sample) was collected. The second screening sample was obtained before the patient’s discharge. This excluded those patients who had less than 48 h stay. If a first screening specimen grew MRSA, the patient was classified as CA-MRSA, whereas if a second screening specimen grew MRSA, the patient was classified as HA-MRSA. MRSA infection in a patient was labelled if physician had clinical suspicion supported by MRSA growth in clinical specimens.

For each study participant, two different swabs according to manufacturer’s recommendation for culture (as gold standard method) and MRSA Xpert were collected from the sampling site (from the forehead and both nostrils): one for standard MRSA screening culture and the other for the MRSA assay. The swab specimens were transferred to a zip lock bag and transported to the clinical microbiology laboratory at room temperature for further processing.

Culture screening method

One of the paired swabs was processed for MRSA screening culture as per the Manual of Clinical Microbiology (3rd edition). Cefoxitin (30 µg) disc results were interpreted using CLSI guidelines [13]. Costing for single culture testing was done.

Xpert MRSA assay

Xpert MRSA demonstrates cost-effectiveness and faster turnaround time compared to conventional culture methods, enhancing efficiency and reducing healthcare costs associated with MRSA detection. The second swab of the pair was processed directly using the GeneXpert system (Cepheid) with an Xpert Methicillin-resistant S. aureus (MRSA) cartridge (Cepheid) according to manufacturer’s protocol [14]. Costing for single Xpert MRSA testing was done.

Results

During the study period, a total of 257 patients were included in the study. Two hundred and ninety (290) MRSA screening samples were obtained, 33 of which were paired. The cost of a single MRSA Xpert assay was $50 while MRSA culture cost around $7.50.

Table 1 Shows the demographic characteristics of the patient population whereas Fig. 1 shows the MRSA colonization status of the study patients

Table 1 Demographic characteristics of the patient population

During the study period (April-December 2022) hand hygiene compliance rate in medical and surgical units was 85% and 87% respectively. MDRO surveillance report for the study duration showed a hospital-acquired MRSA rate of 14%. The median age of the 257 enrolled patients was 47 years (IQR: 32-61 years), and the mean age was 48years (SD: ±17.7 years). Sixteen (53%) of the 30 MRSA isolates were from male gender. Among the age groups, patients aged between 30 and 44 years had the highest prevalence (15%). Patients with diabetes mellitus had the highest MRSA colonization rate (8%), followed by those with cancer (6%).

Samples from 72 patients were selected for MRSA Xpert screening based on randomization using software. The selection criteria ensured random and unbiased sampling due to financial limitations. MRSA colonization by either method was present in 30 (12%) patients, 28 (11%) identified via culture method whereas 30 (12%) patients were detected via the Xpert MRSA assay as shown in Table 2

Table 2 Comparison of the culture and Gene Xpert results for MRSA

Fig. 1

Shows the MRSA colonization status of the study patients

Discussion

To the best of our knowledge, this is the first analytical study from Pakistan and other regional countries documenting the efficacy of the Xpert MRSA assay for MRSA screening. Similarly, limited research on the incidence of MRSA colonization and the outcomes of infection in hospitalized patients from Pakistan or regional countries, such as India and Bangladesh, is available. Current study revealed a high rate (11%) of MRSA colonized patients upon admission to a large, urban private hospital in Karachi. The prevalence of community-acquired MRSA(CA-MRSA) is found to be higher than that published in previous reports (1.3%) [15]. According to current investigation, diabetes and other comorbidities were identified as risk factors for MRSA colonization; these findings have been documented in other studies [16, 17]. Amongst MRSA colonization, 90% (n=27) were categorized as CA-MRSA colonization while 10% (n=3) were as HA-MRSA. The low prevalence of hospital-acquired MRSA colonization can be related to effective infection control measures, such as hand hygiene, isolation precautions, and environmental cleaning, which can reduce the transmission of MRSA in healthcare settings. None of the statistically significant factors contributed to the high incidence of CA-MRSA in comparison with HA-MRSA. While assessing subsequent MRSA infection amongst the study population, a total of 11/257 (4%) patients developed subsequent infection during their hospital stay. This included 3/27 (11%) CA-MRSA colonization and 8/227 patients (3.5%) in whom no colonization was detected at admission and discharge. The overall rate of subsequent MRSA infections was greater in the colonized group (11% vs. 3.5%) than in the non-colonized group. No patient with HA-MRSA colonization developed subsequent MRSA infection.

Our study demonstrated significant findings regarding the MRSA screening via the use of an Xpert MRSA kit that is recommended for MRSA detection in wound swabs and pus specimens [18, 19]. We evaluated this kit for MRSA colonization screening. A high concordance was observed between the two modalities used for MRSA isolation in this study. In a study from Australia, Xpert MRSA kit was used for assessing nasal and groin colonization, kit showed 87% and 94% sensitivity and specificity respectively [20]. Early MRSA detection and decolonization before major surgery are important as postoperative outcomes can be influenced by MRSA infections, which may prolong hospital stays, slow recovery from primary surgery, and worsen prognosis. [21, 22]. The Xpert MRSA assay is a quick and clinically convenient test for the early detection of MRSA. One such study done in patients with major heart surgery showed that 42% of patients had a negative culture and positive PCR result [21]. Overall, the study’s findings suggest that the GeneXpert MRSA screening is extremely sensitive and precise, with very low false-positive rates. The turnaround times for the culture and Xpert MRSA tests were approximately 18–48 h and 1.25 h, respectively. Since Pakistan is a lower-middle-income nation, the clinical use of MRSA Xpert assay ($50 per test) for detecting MRSA colonization should be compared with culture-based techniques ($7.50 per test) in terms of cost-effectiveness as > 60% of patients in Pakistan are uninsured and resort to out-of-pocket payments for medical expenses [22].

Our study has certain limitations like single-site study, hence the results obtained may not be generalizable to the rest of the population. Analytical studies from other parts of Pakistan are required for the wide implementation of the Xpert MRSA assay for the detection of MRSA colonization. Due to financial constraints, molecular typing to characterize MRSA was not achievable. Finally, it is possible that some of the study patients might have received vancomycin during the study period, which may have influenced the results. Nonetheless, our findings are robust, with high concordance between the two diagnostic modalities and a sensitivity of 100% and specificity of 96%. Our study is anticipated to pave the way for further multicenter studies involving larger sample sizes and a longer study duration that could contribute to validating the generalizability of the findings, advocating the use of molecular diagnostics to identify colonization by MRSA.

Conclusion

Our study findings suggest that the presence of MRSA colonization in our cohort of patients is consistent with the existing trends in hospital epidemiology. Additionally, we reported comparable efficacy of conventional culture and Xpert MRSA method for the determination of MRSA colonization and prompt deployment of infection control measures. However, to validate our findings we recommend future studies with a larger sample size.