Real-Time Sequencing To Decipher the Molecular Mechanism of Resistance of a Clinical Pan-Drug-Resistant Acinetobacter baumannii Isolate from Marseille, France

TEXT

Acinetobacter baumannii is an emerging multidrug-resistant (MDR) pathogen that is responsible for community- and hospital-acquired infections that are difficult to control and to treat (1, 2). This bacterium is intrinsically highly resistant to several antimicrobial agents, but increasing resistance to other antibiotics has been reported during the last decade, especially resistance to carbapenems, and the antibiotic resistance of A. baumannii is now recognized as a significant health problem because of the limited options for antibiotic therapy (1, 2). In these MDR strains, colistin is often the last resort for treatment, but colistin-resistant clinical isolates have been reported recently leading to pan-drug-resistant bacteria (1, 3, 4). We have recently reported such clinical pan-drug-resistant bacteria in a French patient with a bloodstream infection occurring after colistin therapy (4). An imipenem-resistant but colistin- and rifampin-susceptible A. baumannii isolate was recovered initially from a bronchoalveolar lavage (BAL) specimen from this French patient who suffered from pneumonia (ABIsac_ColiS). After 4 weeks of treatment with colistin and rifampin, a colistin- and rifampin-resistant isolate was recovered from a tracheal aspirate (ABIsac_ColiR). Here we report the whole-genome sequence comparison of these two clinical isolates to decipher whether the two MDR isolates actually were derived from a single clone of a colistin- and rifampin-resistant isolate being selected by antibiotic treatment.

High-throughput sequencing technologies are now widespread and could be used in a real-time manner to decipher the molecular support of any outbreak and/or MDR bacteria as recently exemplified with whole-genome sequencing as a rapid and powerful tool to elucidate the origin of the huge outbreak of Escherichia coli responsible for hemolytic-uremic syndrome in Germany (5) or the Haitian cholera outbreak (6). Genomic sequences of ABIsac_ColiS and ABIsac_ColiR were sequenced using both paired-end pyrosequencing strategy on the 454-Titanium instrument and with an additive shotgun for ABIsac_ColiR (454 Life Sciences, Branford, CT) (7) and SOLiD version 4 paired-end sequencing technology (Applied Biosystems, Foster City, CA) (8). For genome annotation, all contigs from these two strains were submitted to an online bioserver, the RAST server (RAST stands for Rapid Annotation using Subsystems Technology) (http://www.theseed.org) (9) to predict protein-encoding genes, rRNA and tRNA sequences, and assign function to these genes. Predicted open reading frames (ORFs) by RAST server were confirmed by BLASTP (E value 10^E−8; identity ≥ 30%; coverage ≥ 50%) against no redundant protein (nr) and clusters of orthologous groups of proteins (COG) databases of the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov). tRNA and rRNA genes were also verified on tRNAscan-SE Search Server (http://lowelab.ucsc.edu/tRNAscan-SE) and RFAM (http://rfam.sanger.ac.uk), respectively. Genome comparison was performed by “in silico” DNA-DNA hybridization using BLASTN analysis on a local bioserver to determine the full-length alignment between two genome sequences and the coverage percentage using the cutoff stringency of an E value at 1.00e−5. Genome alignment of both A. baumannii ABIsac_ColiS and ABIsac_ColiR strains was performed using Mauve alignment software (10). All antimicrobial resistance genes and mutated genes involved in antibiotic resistance were retrieved from this functional annotation.

The assembly of the paired-end and shotgun sequences from A. baumannii ABIsac_ColiS gave a chromosome size of 3,771,873 bp with 38.77% GC content assembled into 275 contigs with the length of the contigs ranging from 902 bp to 98,458 bp and two plasmids of 68,612 bp (pABIsac_A) and 9,893 bp (pABIsac_B). With paired-end and shotgun sequences from A. baumannii ABIsac_ColiR, the assembly process gave a chromosome size of 3,785,453 bp with 38.84% GC content assembled into 108 contigs with the length of the contigs ranging from 1,077 bp to 192,975 bp and two plasmids of 68,347 bp (pABIsac_C) and 9.879 bp (pABIsac_D) (Table 1). The two plasmids have 96% sequence identity (small plasmids) and 99% sequence identity (large plasmids) to plasmids p2ABTCDC0715 and p1ABTCDC0715 previously reported in A. baumannii in Taiwan (11). “In silico” DNA-DNA hybridization and Mauve alignment demonstrate that these two strains, ABIsac_ColiS and ABIsac_ColiR, were likely the same clone (Fig. 1 and Table 1) as previously suggested using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) analysis (12). Differences between the two strains consist mainly of the loss of a prophage in A. baumannii ABIsac_ColiR compared to ABIsac_ColiS. The loss of the prophage in ABIsac_ColiR may explain the impaired virulence of this strain (4) as recently demonstrated for Pseudomonas aeruginosa in the context of the Liverpool epidemic strain in cystic fibrosis patients (13). Table 2 lists the antibiotic resistance-encoding genes found in the two A. baumannii genomes. Resistance to sulfonamides (sul1 gene) and aminoglycosides (aadB and aadA2 genes) were located on the chromosome within a 7.8-kb class 1 integron (Fig. 2). Interestingly, the chromosomal bla_OXA23-like gene was located in transposon Tn2006 in a 16.7-kb genomic island (Fig. 2) that completely replaced the 86-kb genomic region previously reported in A. baumannii strain AYE (14) within the comM gene. Finally, resistance to colistin, rifampin, and fluoroquinolones in ABIsac_ColiR were mediated by point mutation on target genes (Table 2). Rifampin resistance was likely due to a D525Y mutation in the rifampin resistance-determining region (RRDR) of the rpoB gene (Table 2). The same mutation responsible for rifampin resistance has recently been found in an A. baumannii strain isolated in Italy (15). This mutation has also been reported in Mycobacterium tuberculosis rifampin-resistant isolates (16, 17). Finally, resistance to colistin in strain ABIsac_ColiR was likely due to mutations in the pmrA gene with E changed to D at position 8 [pmrA(E8D)] (Table 2). These two proteins constitute a two-component system (PmrAB) involved in the modification of lipid A, the major constituent of the lipopolysaccharide (LPS) membrane, and mutations in the PmrAB two-component system have been reported recently in in vitro-selected A. baumannii strains (18). Mutations or disruption of the A. baumannii lipid A biosynthesis genes lpxA and lpxC by insertion sequence ISAba11 resulting in complete loss of lipopolysaccharide production has also been shown to be responsible for colistin resistance in vitro (19, 20) but was not found in our clinical isolate. To the best of our knowledge, the mutation in the PmrAB (18) two-component system is novel and reported for the first time in a clinical isolate that was likely selected because of colistin therapy.

• Open in new tab
• Download powerpoint

Fig 1

Mauve alignment of A. baumannii ABIsac_ColiS and ABIsac_ColiR genomes.

• Open in new tab
• Download powerpoint

Fig 2

Circular representation of A. baumannii ABIsac_ColiR and ABIsac_ColiS chromosomes and antibiotic resistance determinants. The transposon AbaR4 island and class 1 integron were identical in the chromosomes of both strains, whereas pmrA, pmrB, and rpoB mutations were found only in the ABIsac_ColiR chromosome. The genes and the proteins they encode follow: comM, competence protein ComM disrupted/Mg²⁺ chelatase-like protein; tnpA, transposase protein A; tnpB, transposase protein B; tniC, transposition helper protein C; tniD, probable transposition protein; ORF_6, hypothetical protein; ORF_7, hypothetical protein; uspA, universal stress protein; suldelta, sul1delta fusion protein/sulfate permease interrupted by Tn2006; Ab_IS4, IS4 family transposase ORF 1; yeeA, DNA methylase; ORF_12, hypothetical protein; bla_OXA-23, OXA-23 carbapenemase; Ab_IS4, IS4 family transposase ORF 1; suldelta, sul1delta fusion protein/sulfate permease, interrupted by Tn2006; ORF_15, hypothetical protein; comM, competence protein ComM disrupted/Mg²⁺ chelatase-like protein; araC, transcriptional regulator of the AraC family; tnpR, transposon Tn21 resolvase; intI1, IntI1 integrase; aadB, aminoglycoside-2′-adenylyltransferase; aadA2, aminoglycoside adenyltransferase A2; emrE, ethidium bromide-methyl viologen resistance protein EmrE; sul1, dihydropteroate synthase; GCN-5, GCN5-like N-acetyltransferase; tniB, nucleoside triphosphate (NTP)-binding protein; istB, transposon NTP-binding protein; istA, transposase IstA protein; pcaR, regulon regulatory protein; ORF-1373, 4-hydroxybenzoate 3-monooxygenase.

In conclusion, the present work demonstrated that real-time whole-genome sequence comparison is a powerful tool to decipher all antibiotic resistance determinants in clinical microbiology when outbreak and/or novel MDR bacteria are isolated from clinical specimens.