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Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine antibiotic resistance genotypes

Background

Multi-drug resistant (MDR) Acinetobacter baumannii is an important cause of hospital acquired infection and often increases mortality and length of stay[13]. The mechanisms of resistance include: (1) antimicrobial-inactivating enzymes such as □-lactamases, (2) alteration of membrane porin channels, and (3) mutations that change cellular functions [4]. Accurate genotyping and correlation to antimicrobial susceptibility will help prevent and treat outbreaks of Acinetobacter.

The genome of A. baumannii ranges from 3.2 Megabases (Mb) in the drug sensitive SDF strain up to 3.9 Mb in the MDR AYE strain. A surprisingly high proportion of baumannii ORFs, (15%-20%), are located in resistance islands or “alien islands” - long stretches of DNA acquired from a foreign source. The MDR AYE strain has an 86Kb island containing 45-50 drug resistance genes located in an insertion hotspot [5]. Our study aims to sequence several A. baumanni i isolates from Metro Nashville General (NGH) Hospital and conduct a strain-to-reference genomic characterization of clinical virulence factors.

Materials and methods

A retrospective review of the NGH hospital epidemiology data base included 247 isolates of A. baumannii from 164 patients (submitted, BMC Infectious Disease). Cluster Software version 2.11 and TreeView software grouped resistance phenotypes into six categories (see Figure 1) [6].

Figure 1
figure 1

Clustered baumannii groups. Left Side: full clustergram of all isolate phenotypes. Right Side: zoom in of resistance group 4: meripenem/imipenum and aminoglycoside sensitive.

Legend: red = resistant, green = sensitive, yellow = intermediate, black/gray = no data.

1.Pan resistant

2.Pan sensitive

3.Sensitive to meropenem /imipenem only.

4.Sensitive to meropenem/imipenem and aminoglycoside only.

5.Sensitive to cephalosporins only.

6.Resistant to aminoglycosides only.

We chose a meripenum/imepenum and aminoglycosides sensitive baumanii isolate for strain-to-reference sequencing on an Illumina Genome Analyzer II system at the Vanderbilt University Genome Technology Core (https://gtc.vanderbilt.edu/gtc/tech).

Conclusion

Initial sequencing yielded 5,250,420 reads of 43bp each, yielding 225.76 Mb of total sequence. The reads from our isolate were aligned to MDR baumannii reference strain ACICU (NC_010611.1). Alignment was done with the Bowtie Aligner [7]. Of the 5.2 million total reads, 4,004,012 (76.26%) aligned to AICIU, with a mean coverage depth of 43.96 fold. Roughly 58% of the ACICU genome was covered by at least one read. We will next align the reads further with other baumannii reference strains including MDR AYE (NC_010410) and non-resistant strain SDF (NC_010400) in order to further characterize and annotate our isolate at the genomic level.

References

  1. Garcia-Garmendia J, Ortiz-Leyba C, Garmacho-Montero J, Jimenez-Jimenez FJ, Monterrubio-Villar J, Gili-Miner M: Mortality and the increase in length of stay attributable to the acquisition of Acinetobacter in critically ill patients. Crit Care Med 1999, 27(9):1794–1799. 10.1097/00003246-199909000-00015

    Article  CAS  PubMed  Google Scholar 

  2. Falagas ME, Rafailidis PI: Attributable mortality of Acinetobacter baumannii : no longer a controversial issue. Critical Care (London, England) 2007, 11(3):134. 10.1186/cc5911

    Article  Google Scholar 

  3. Jamulitrat S, Arunpan P, Phainuphong P: Attributable mortality of imipenem-resistant nosocomial Acinetobacter baumannii bloodstream infection. J Med Assoc Thai 2009, 92(3):413–419.

    PubMed  Google Scholar 

  4. Bonomo RA, Szabo D: Mechanisms of multidrug resistance in Acinetobacter species and Pseudomonas aeruginosa. Clin Infect Dis 2006, 43(Suppl 2):S49-S56. 10.1086/504477

    Article  CAS  PubMed  Google Scholar 

  5. Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, Nordmann P, Weissenbach J, Raoult D, Claverie JM: Comparative genomics of multidrug resistance in Acinetobacter baumannii . Plos Genet 2006, 2(1):e7. 10.1371/journal.pgen.0020007

    Article  PubMed Central  PubMed  Google Scholar 

  6. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. PNAS 1998, 95: 14863–14868. 10.1073/pnas.95.25.14863

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10: R25. doi:10.1186/gb-2009–10–3-r25 doi:10.1186/gb-2009-10-3-r25 10.1186/gb-2009-10-3-r25

    Article  PubMed Central  PubMed  Google Scholar 

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Acknowledgements

Experiment design and data analysis performed through the use of the Meharry Medical College Microarray and Bioinformatics Core, which is supported in part by NIH grants G12RR03032-19 and P20RR011792. (http://www.mmc.edu/bioinformatics/)

Sequencing and alignment was performed at the Vanderbilt University Genome Technology Core (https://gtc.vanderbilt.edu/gtc/tech).

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Correspondence to Leon Dent.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Dent, L., Marshall, D., Hulette, R. et al. Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine antibiotic resistance genotypes. BMC Bioinformatics 11 (Suppl 4), P16 (2010). https://doi.org/10.1186/1471-2105-11-S4-P16

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