Diversity and Distribution of β-Lactamase Genes Circulating in Indian Isolates of Multidrug-Resistant Klebsiella pneumoniae

Suraj Shukla; Siddhi Desai; Ashutosh Bagchi; Pushpendra Singh; Madhvi Joshi; Chaitanya Joshi; Jyoti Patankar; Geeti Maheshwari; Ekadashi Rajni; Manali Shah; Devarshi Gajjar

doi:10.3390/antibiotics12030449

Diversity and Distribution of β-Lactamase Genes Circulating in Indian Isolates of Multidrug-Resistant Klebsiella pneumoniae

Antibiotics (Basel). 2023 Feb 23;12(3):449. doi: 10.3390/antibiotics12030449.

Authors

Affiliations

¹ Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India.
² Amity Institute of Biotechnology, Amity University of Noida, Noida 201313, Uttar Pradesh, India.
³ ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, Madhya Pradesh, India.
⁴ Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, Gujarat, India.
⁵ Sterling Hospital, Vadodara 390007, Gujarat, India.
⁶ Toprani Advanced Lab Systems, Vadodara 390020, Gujarat, India.
⁷ Department of Microbiology, Mahatma Gandhi University of Medical Sciences & Technology, Jaipur 302015, Rajasthan, India.
⁸ Desai Metropolis Health Service Pvt. Ltd., Surat 395001, Gujarat, India.

Abstract

Klebsiella pneumoniae (Kp) has gained prominence in the last two decades due to its global spread as a multidrug-resistant (MDR) pathogen. Further, carbapenem-resistant Kp are emerging at an alarming rate. The objective of this study was (1) to evaluate the prevalence of β-lactamases, especially carbapenemases, in Kp isolates from India, and (2) determine the most prevalent sequence type (ST) and plasmids, and their association with β-lactamases. Clinical samples of K. pneumoniae (n = 65) were collected from various pathology labs, and drug susceptibility and minimum inhibitory concentrations (MIC) were detected. Whole genome sequencing (WGS) was performed for n = 22 resistant isolates, including multidrug-resistant (MDR) (n = 4), extensively drug-resistant (XDR) (n = 15), and pandrug-resistant (PDR) (n = 3) categories, and genomic analysis was performed using various bioinformatics tools. Additional Indian MDRKp genomes (n = 187) were retrieved using the Pathosystems Resource Integration Center (PATRIC) database. Detection of β-lactamase genes, location (on chromosome or plasmid), plasmid replicons, and ST of genomes was carried out using CARD, mlplasmids, PlasmidFinder, and PubMLST, respectively. All data were analyzed and summarized using the iTOL tool. ST231 was highest, followed by ST147, ST2096, and ST14, among Indian isolates. bla_ampH was detected as the most prevalent gene, followed by bla_CTX-M-15 and bla_TEM-1. Among carbapenemase genes, bla_OXA-232 was prevalent and associated with ST231, ST2096, and ST14, which was followed by bla_NDM-5, which was observed to be prevalent in ST147, ST395, and ST437. ST231 genomes were most commonly found to carry Col440I and ColKP3 plasmids. ST16 carried mainly ColKP3, and Col(BS512) was abundantly present in ST147 genomes. One Kp isolate with a novel MLST profile was identified, which carried bla_CTX-M-15, bla_OXA-1, and bla_TEM-1. ST16 and ST14 are mostly dual-producers of carbapenem and ESBL genes and could be emerging high-risk clones in India.

Keywords: Klebsiella pneumoniae; MLST; plasmid replicons; whole genome sequencing; β-lactamases.

Grants and funding

GSBTM/JDRD/584/2018/199/Gujarat State Biotechnology Mission (GSBTM)