Improved diagnostic stewardship in carbapenem-resistant Enterobacterales gene detection helps in early initiation of targeted therapy

Abstract

Introduction. Antimicrobial resistance (AMR) is an escalating global health crisis, leading to ~700,000 deaths annually. Without significant containment efforts, this number could surge to 10 million by 2050. Carbapenem-resistant organisms, particularly carbapenem-resistant Enterobacterales (CRE), Pseudomonas aeruginosa, and Acinetobacter baumannii, present a critical challenge due to their ability to evade potent carbapenem antibiotics.Hypothesis and Aim. This study aimed to determine the prevalence of CRE among 1,317 culture-positive patients and to assess the impact of advanced diagnostic techniques, such as RT-PCR, modified carbapenem inactivation method (mCIM), EDTA carbapenem inactivation method (eCIM) and Vitek susceptibility testing, on improving diagnostic stewardship and patient outcomes.Methodology. A retrospective cross-sectional study was conducted at Peerless Hospitex Hospital and Research Centre Limited, Kolkata, from June 2023 to May 2024. CRE isolates were identified from various clinical samples and subjected to phenotypic (Vitek 2, mCIM and eCIM) and genotypic real time polymerase chain reaction (RT-PCR) testing for carbapenemase genes. Data on demographics, specimen types, bacterial isolates, comorbidities, etc. were analysed.Results. Out of 20,129 inpatient samples sent for culture during this 1-year period, 3,124 (15.51%) had culture-proven infections. A total of 1,317 Enterobacterales isolates were processed for carbapenem resistance (CR) detection PCR, with 354 (26.88%) identified as CRE. Klebsiella pneumoniae was the predominant isolate (60.17%), followed by Escherichia coli (26.55%). New Delhi metallo-β-lactamase (MBL) (NDM) and OXA-48-like co-production (33.75%) were most commonly seen, followed by NDM gene alone (32.50%). The concordance between phenotypic susceptibility and genotypic PCR method for CRE was 85.88%. Targeted antibiotic therapy could be initiated based on PCR results, in 70.90% of cases. Synergy test guided effective combination therapy of ceftazidime-avibactam and aztreonam for MBL-producing CRE isolates.Conclusion. The study highlights a significant prevalence of CRE, particularly among older adults. Advanced diagnostic techniques improved diagnostic stewardship, allowing timely and accurate detection of CR. However, discrepancies between phenotypic and genotypic methods and the high cost of certain therapies are notable limitations. Enhanced infection control and early initiation of targeted therapy are crucial to combat AMR.

Keywords: EDTA carbapenem inactivation method (eCIM); New Delhi metallo-β-lactamase (NDM); OXA-48 like; RT-PCR; Vitek 2; carbapenem-resistant Enterobacterales (CRE); diagnostic stewardship; modified carbapenem inactivation method (mCIM); synergy test.

Fig. 1.. Details of the workflow in this study.

Fig. 2.. Age-wise gender distribution of CRE patients in the study population.

Fig. 3.. (a) Duration of hospital stay of CRE patients in relation to the bacterial isolates obtained from clinical samples; others include Klebsiella aerogenes, Klebsiella oxytoca, Proteus vulgaris and Pantoea species. (b) Comparison of hospital stays between CRE-positive K. pneumoniae (KP) and E. coli (EC)-positive cases. The differences in <1 week (P value 0.0031) and >1 month (P value 0.0329) are statistically significant, while differences in 1–2 weeks (P value 0.3298) and 3 weeks–1 month (P value 0.9836) are not statistically significant.

Fig. 4.. Distribution of different Enterobacterales species obtained from clinical samples; others include Klebsiella aerogenes, Klebsiella oxytoca, Proteus vulgaris and Pantoea species.

Fig. 5.. Sample-wise distribution of CRE obtained from the study population.

Fig. 6.. Prevalence of carbapenemase gene detected by open system RT-PCR from clinical isolates.

Fig. 7.. Antibiotic therapy modification as per CR detection PCR report.

Fig. 8.. Modified E test/disc with CZA E test and ATM disc (30 µg) placed 15 mm apart: synergy demonstrated by inverse D.