Computational protocol: Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri

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Protocol publication

[…] Acinetobacter species can be found in any environment: water, soil, body surface, etc., and is one of the most dangerous nosocomial pathogens in the world (), being found principally in intensive care units (ICUs) (). In the last few years, it was discovered that members of the genus Acinetobacter can be transmitted by air (), although it is true that air contamination when there are any patients infected is rare. However, some researchers refer to intense Acinetobacter species air contamination when there are infected patients around (, ). Nowadays, little is known about this method of transmission; therefore, many researchers are studying this transmission method.In this study, we report the genome sequence of airborne Acinetobacter sp. strain 5-2Ac02, which was collected from the air in an ICU of a hospital in Rio de Janeiro, Brazil. Genomic DNA was isolated using the Wizard genomic DNA kit (Promega). Genome sequencing was determined using an Ilumina MiSeq system. The final draft genome was annotated using the RAST server to identify the protein-coding genes, rRNA, and tRNA genes, and to assign functions to these genes. The predicted open reading frames (ORFs) were confirmed using BlastP in the Protein Data Bank (PDB) and COG databases from NCBI and InterProScan. Using the Antibiotic Resistance Database, we could predict the antibiotic resistance genes. The insertion sequences (IS) were analyzed by IS Finder software. Antimicrobial susceptibility testing was performed according to CLSI methods (2014), and disinfectant susceptibility testing was performed by microdilution. Phylogenetic analysis was carried out by average nucleotide identity (ANI), single nucleotide polymorphism analysis (snpTree), and RNA polymerase beta subunit sequence (rpoB) analysis. A matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) dendrogram was generated (Bruker Daltonics).The genome includes a chromosome of 2,951,447 bp, with a 40.9% G+C content. The functional annotation of the circular chromosome showed a total of 2,795 predicted coding sequences (CDSs) and suggests that 1,281 (46%) of these CDSs could be assigned a biological function included in 380 subsystems (RAST software). There were a total of 97 RNAs genes identified. We studied the rhizome of this genome (). In the analysis of the resistome, we found the presence of TerC family proteins from the ter operon (terZABCDEF); we also found klaA and klaB genes from the kil operon, which is in association with the previous one, as said by O’Gara et al. (). One arsenic operon, arsC1-arsR-arsC2-ACR3-arsH was studied. This operon organization has only been described in the Pseudomona stutzeri TS44 (). Moreover, this strain showed an MIC to arsenic of >2,048 mg/liter. Finally, an ISAba3-like transposase was present upstream of blaOXA-58, which determines its silence state (MICs to imipenem and meropenem, 0.06 and 0.03 mg/liter, respectively) (). For the persistome, we found four different toxin-antitoxin systems: RelEB (4 gene cassettes), ParDE, HipBA, and HigBA, with all of them related to persistence, among other things (). For the mobilome, the percentage of insertion sequences (ISs) in this strain was about 5%, which is higher than that of clinical Acinetobacter species. Finally, posterior phylogenetic analysis suggested that Acinetobacter sp. 5-2Ac02 is a new species of Acinetobacter, with A. towneri eing the most closely related one (94.39 by ANI score, 90% by rpoB score gene, and 2.127 MALDI-TOF MS score). […]

Pipeline specifications

Software tools RAST, BLASTP, InterProScan, snpTree
Application Phylogenetics