ORIGINAL RESEARCH published: 17 December 2019 doi: 10.3389/fmicb.2019.02865 Edited by: Raffaele Zarrilli, University of Naples Federico II, Italy Reviewed by: Gokhlesh Kumar, University of Veterinary Medicine Vienna, Austria Rita Berisio, Italian National Research Council (CNR), Italy *Correspondence: Asad U. Khan asad.k@rediffmail.com † Present address: Divakar Sharma, Central Research Facility, Mass Spectrometry Laboratory, Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India Specialty section: This article was submitted to Antimicrobials, Resistance and Chemotherapy, a section of the journal Frontiers in Microbiology Received: 17 August 2019 Accepted: 27 November 2019 Published: 17 December 2019 Citation: Sharma D, Garg A, Kumar M, Rashid F and Khan AU (2019) Down-Regulation of Flagellar, Fimbriae, and Pili Proteins in Carbapenem-Resistant Klebsiella pneumoniae (NDM-4) Clinical Isolates: A Novel Linkage to Drug Resistance. Front. Microbiol. 10:2865. doi: 10.3389/fmicb.2019.02865 Down-Regulation of Flagellar, Fimbriae, and Pili Proteins in Carbapenem-Resistant Klebsiella pneumoniae (NDM-4) Clinical Isolates: A Novel Linkage to Drug Resistance Divakar Sharma 1† , Anjali Garg 2 , Manish Kumar 2 , Faraz Rashid 3 and Asad U. Khan 1 * 1 Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India, 2 Department of Biophysics, University of Delhi, New Delhi, India, 3 SCIEX Pvt. Ltd., Gurgaon, India The emergence and spread of carbapenem-resistant Klebsiella pneumoniae infections have worsened the current situation worldwide, in which totally drug-resistant strains (bad bugs) are becoming increasingly prominent. Bacterial biofilms enable bacteria to tolerate higher doses of antibiotics and other stresses, which may lead to the drug resistance. In the present study, we performed proteomics on the carbapenem- resistant NDM-4-producing K. pneumoniae clinical isolate under meropenem stress. Liquid chromatography coupled with mass spectrometry (LC–MS/MS) analysis revealed that 69 proteins were down-regulated (≤0.42-fold change) under meropenem exposure. Within the identified down-regulated proteome (69 proteins), we found a group of 13 proteins involved in flagellar, fimbriae, and pili formation and their related functions. Further, systems biology approaches were employed to reveal their networking pathways. We suggest that these down-regulated proteins and their interactive partners cumulatively contribute to the emergence of a biofilm-like state and the survival of bacteria under drug pressure, which could reveal novel mechanisms or pathways involved in drug resistance. These down-regulated proteins and their pathways might be used as targets for the development of novel therapeutics against antimicrobial-resistant (AMR) infections. Keywords: Klebsiella pneumoniae (NDM-4), proteomics, bioinformatics, pathway enrichment, biofilm, carbapenem resistance INTRODUCTION Klebsiella pneumoniae is a gram-negative bacteria of the family Enterobacteriaceae. In clinical settings, the emergence and spread of drug-resistant K. pneumoniae are worsening the medical situation worldwide. Carbapenems have been considered the last line of defense in the treatment of drug-resistant infections (Paterson, 2000; Paterson and Bonomo, 2005). Interrupted use of Abbreviations: CLSI, Clinical and Laboratory Standards Institute; ESBLs, extended spectrum beta-lactamases; LB, Luria– Bertani; MIC, minimum inhibitory concentration; STRING, Search Tool for the Retrieval of Interacting Genes/Proteins. Frontiers in Microbiology | www.frontiersin.org 1 December 2019 | Volume 10 | Article 2865