Deciphering Multifactorial Resistance Phenotypes in Acinetobacter baumannii by Genomics and Targeted Label-free Proteomics

• Published in: Molecular & cellular proteomics Vol. 17; no. 3; pp. 442 - 456
• Main Authors: Cecchini, Tiphaine, Yoon, Eun-Jeong, Charretier, Yannick, Bardet, Chloé, Beaulieu, Corinne, Lacoux, Xavier, Docquier, Jean-Denis, Lemoine, Jerome, Courvalin, Patrice, Grillot-Courvalin, Catherine, Charrier, Jean-Philippe
• Format: Journal Article Web Resource
• Language: English
• Published: United States Elsevier Inc 01.03.2018; American Society for Biochemistry and Molecular Biology; American Society for Biochemistry and Molecular Biology Inc; The American Society for Biochemistry and Molecular Biology
• Subjects: Acinetobacter baumannii; Acinetobacter baumannii - drug effects; Acinetobacter baumannii - genetics; Acinetobacter baumannii - metabolism; Amides; Analytical chemistry; Anti-Bacterial Agents; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacterial Proteins; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; beta-Lactamases - genetics; beta-Lactamases - metabolism; beta-Lactams - pharmacology; Chemical Sciences; Clinical isolates; Coefficient of variation; Drug Resistance, Microbial; Drug Resistance, Microbial - physiology; Efflux; Gene sequencing; Genes; Genomics; Life sciences; Mass spectrometry; Mass spectroscopy; Microbiologie; Microbiology; Peptides; Phenotype; Polymerase chain reaction; Proteins; Proteomics; Quantitation; Sciences du vivant
• ISSN: 1535-9476; 1535-9484; 1535-9484
• DOI: 10.1074/mcp.RA117.000107

Resistance to β-lactams in Acinetobacter baumannii involves various mechanisms. To decipher them, whole genome sequencing (WGS) and real-time quantitative polymerase chain reaction (RT-qPCR) were complemented by mass spectrometry (MS) in selected reaction monitoring mode (SRM) in 39 clinical isolates. The targeted label-free proteomic approach eNAbled, in one hour and using a single method, the quantitative detection of 16 proteins associated with antibiotic resistance: eight acquired β-lactamases (i.e. GES, NDM-1, OXA-23, OXA-24, OXA-58, PER, TEM-1, and VEB), two resident β-lactamases (i.e. ADC and OXA-51-like) and six components of the two major efflux systems (i.e. AdeABC and AdeIJK). Results were normalized using “bacterial quantotypic peptides,” i.e. peptide markers of the bacterial quantity, to obtain precise protein quantitation (on average 8.93% coefficient of variation for three biological replicates). This allowed to correlate the levels of resistance to β-lactam with those of the production of acquired as well as resident β-lactamases or of efflux systems. SRM detected enhanced ADC or OXA-51-like production and absence or increased efflux pump production. Precise protein quantitation was particularly valuable to detect resistance mechanisms mediated by regulated genes or by overexpression of chromosomal genes. CombiNAtion of WGS and MS, two orthogoNAl and complementary techniques, allows thereby interpretation of the resistance phenotypes at the molecular level.