PAGES: 777-780 DOI: 10.1590/0074-02760160130 Genome announcement and Highlights
Draft genome sequences of four Achromobacter ruhlandii strains isolated from cystic fibrosis patients

Elenice RA Rodrigues1, Géssica A Rocha1, Alex G Ferreira1, Robson S Leão1, Rodolpho M Albano2, Elizabeth A Marques1,+

1Universidade do Estado do Rio de Janeiro, Faculdade de Ciências Médicas, Departamento de Microbiologia, Imunologia e Parasitologia, Rio de Janeiro, RJ, Brasil
2Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Bioquímica, Rio de Janeiro, RJ, Brasil


Achromobacter species are being increasingly isolated from the respiratory tract of cystic fibrosis patients. Recent reports indicate that Achromobacter ruhlandii is a potential human pathogen in cystic fibrosis-related infections. Here we report the draft genome of four A. ruhlandii strains isolated from cystic fibrosis patients in Brazil. This report describes A. ruhlandii as a potential opportunistic pathogen in cystic fibrosis and provides a framework to for additional enquires into potential virulence factors and resistance mechanisms within this species.

Achromobacter ruhlandii is a Gram-negative bacterium naturally found in soil (Packer & Vishniac 1955). However, recent reports indicate that A. ruhlandii is a potential human pathogen in cystic fibrosis-related infections (Ridderberg et al. 2012, Spilker et al. 2012a). A PAN-resistant Achromobacter clone, designated the danish epidemic strain (DES), causing infection in cystic fibrosis patients in Copenhagen (Hansen et al. 2006) and Aarhus (Ridderberg et al. 2011), was recently identified by multilocus sequence typing (MLST) as A. ruhlandii (Ridderberg et al. 2012). A. ruhlandii has also been reported as the second most commonly isolated Achromobacter species from cystic fibrosis patients (Spilker et al. 2012b).

Here we describe draft genome sequences of four A. ruhlandii strains isolated from sputum of Brazilian cystic fibrosis patients attended at Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira (IFF-FIOCRUZ) and Hospital Universitário Pedro Ernesto (HUPE-UERJ), in 2007 and 2008. The isolates were identified to species level by sequencing seven housekeeping genes that were subsequently submitted to the Achromobacter MLST database where they were assigned to specific STs (Spilker at al. 2012a; Furthermore, the species specific marker genes for A. xylosoxidans (blaOXA-114) and for A. ruhlandii (blaOXA-258) were amplified and sequenced to confirm species assignment (Turton et al. 2011, Papalia et al. 2013). Accordingly, the sequences from all four strains showed identity with blaoxa-258.Strains 6241, 7863, 7022 and 8173 were assigned STs 35, 204, 36 and 35, respectively. ST 35 was the only one shared between the two study centers. Minimal inhibitory concentration against ceftazidime, ciprofloxacin, imipenem and trimetoprim/sulphametoxazol was determined with the E-test strip (AB Biodisk, Solna, Sweden). The four samples were susceptible to antibiotics with the exception of strain 7022 that was resistant to trimethoprim/sulfamethoxazole.

Genomic libraries were constructed by transposon tagmentation with the Nextera XT DNA Library Prep kit (Illumina Inc, USA). Sequencing was performed for each isolate with the 500 cycle MiSeq Reagent v2 kit on a MiSeq benchtop instrument (Illumina). Paired-end sequence reads obtained for each of the isolates ranged from 2,017,226 to 3,232,222. Reads were corrected and assembled de novo into scaffolds with Spades 3.5 genome assembler (Bankevich et al. 2012). The Rapid Annotation using System Technology (RAST) v.2.0 server ( was used for general genome annotation and the following databases were used to refine RAST results: PHAge search tool (PHAST) (, IS Blast Server (IS FINDER) ( and Antibiotic Resistance Genes Database-ARDB ( The resulting scaffolds per isolate ranged from 89-111 with an average genome size of 6,481,38 bp (ranging from 6,289,667 to 6,686,778) and 56 or 58 RNA genes. The results of these analyses are summarised on Table I along with their GenBank accession numbers.

The four A. ruhlandii strains were compared with the genome of A. xylosoxidans NH-44784-1996 (Jakobsen et al. 2013), an isolate from a cystic fibrosis patient. The genes involved in pathogenicity were identified, according to the annotation obtained in the RAST server and are summarised on Table II.

Genes responsible for resistance to antibiotics (marC, macA macB, mexI, mexD, mexA, mexB, OprM, mexX, cmeA, cmeB, cmeC, blaOXA258) were annotated, however, only strain 7022 showed the presence of SHV-5a and APH(3')-II. Furthermore, we also observed two resistance genes that are usually associated with mobile elements, sul1 and dfra26. However, in these genomes they could be not associated with these elements, being randomly located in the chromosome (Antunes et al. 2004, Miranda et al. 2004, Garza-Ramos & Romero 2007, Grape et al. 2007). A comparison of our A. ruhlandii samples with other genomic sequences of different species found in the databases demonstrated the presence of IS and transposable elements that were related to ISBcen18 (Burkholderia cenocepacia J2315), ISPa43 (Pseudomonas aeruginosa), TnAs2 (Aeromonas salmonicida), TnAs3 (Aeromonas salmonicida subsp. salmonicida A449 plasmid 4), ISRme12 (Ralstonia metallidurans CH34), ISBmu5 (Burkholderia multivorans ATCC 17616), ISBcen10 (Burkholderia cenocepacia J2315), ISStma15 (Stenotrophomonas maltophilia K279a), ISPst3 (Pseudomonas stutzeri OM1), IS408 (Burkholderia cenocepacia ATCC17616),ISPa38 (Pseudomonas aeruginosa DK2), ISPa39 (Pseudomonas aeruginosa DK2), ISPa40 (Pseudomonas aeruginosa DK2), ISBcen23 (Burkholderia cenocepacia HI2424), IS1474 (Pseudomonas alcaligenes ATCC14094 / Pseudomonas alcaligenes NCIB9867 P25X / Pseudomonas putida NCIB9869 P35X) and IS1162 (Pseudomonas fluorescens ST plasmid pEG). This illustrates the potential ability of A. ruhlandii to carry genetic and transferable elements that could contribute to the dissemination/acquisition of antimicrobial resistance mechanisms.

Five intact phages (PHAGE-Burkho-phi644-2-NC-009235, PHAGE-Burkho-KS14-NC-015273, PHAGE-Erwini-phiEt88-NC-015295, PHAGE-Pseudo-YMC11/02/R656-NC-028657 and PHAGE-Burkho-Bcep176-NC-007497) and five incomplete prophage regions (PHAGE-Salmon-SEN34-NC-028699, PHAGE-Burkho-BcepB1A-NC-005886, PHAGE-Burkho-BcepC6B-NC-005887,PHAGE-Entero-fiAA91-ss-NC-022750, PHAGE-Yellow-1-NC-028112) were also detected in our A. ruhlandii strains (Table III).

This whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBankunder the accession LVKM00000000, LVKO00000000, LVKN00000000 and LVKP00000000. The version described in this paper is version LVKM01000000, LVKO01000000, LVKN01000000 and LVKP01000000.



Antunes P, Machado J, Sousa JC, Peixe L. Dissemination of sulfonamide resistance genes (sul1, sul2, and sul3) in Portuguese Salmonella enterica strains and relation with integrons. Antimicrob Agents Chemother. 2004; 49(2): 836-9.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5): 455-77.

Garza-Ramos U, Romero EM. SHV-type extended-spectrum ß-lactamase (ESBL) are encoded in related plasmids from enterobacteria clinical isolates from Mexico. Salud Publica Mex. 2007; 49(6): 415-21.

Grape M, Sundström L, Kronvall G. Two new dfr genes in trimethoprim-resistant integron-negative Escherichia coli isolates. 2007; 51(5): 1863-4.

Hansen RC, Pressler T, Høiby N, Gormsen M. Chronic infection with Achromobacter xylosoxidans in cystic fibrosis patients; a retrospective case control study. J Cyst Fibros. 2006; 5(4): 245-51.

Jakobsen TH, Hansen MA, Jensen PØ, Hansen L, Riber L, Cockburn A, et al. Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidansNH44784-1996 complies with important pathogenic phenotypes. PLoS ONE. 2013; 8(7): e68484.

Miranda G, Castro N, Leaños B, Valenzuela A, Garza-Ramos U, Rojas T, et al. Clonal and horizontal dissemination of Klebsiella pneumonia expressing SHV-5 extended-spectrum ß-lactamase in a Mexican Pediatric Hospital. J Clin Microbiol. 2004; 42(1): 30-5.

Packer L, Vishniac W. Chemosynthetic fixation of carbon dioxide and characteristics of hydrogenase in resting cell suspensions of Hydrogenomonas ruhlandii nov. spec. J. Bacteriol. 1955; 70(2): 216-23.

Papalia M, Almuzara M, Cejas D, Traglia G, Ramírez MS, Galanternik L, et al. OXA-258 from Achromobacter ruhlandii: a species-specific marker. J Clin Microbiol. 2013; 51(5): 1602-5.

Ridderberg W, Bendstrup KE, Olesen HV, Jensen-Fangel S, Nørskov-Lauritsen N. Marked increase in incidence of Achromobacter xylosoxidans infections caused by sporadic acquisition from the environment. J Cyst Fibros. 2011; 10(6): 466-9.

Ridderberg W, Wang M, Nørskov-Lauritsen N. Multilocus sequence analysis of isolates of Achromobacter from patients with cystic fibrosis reveals infecting species other than Achromobacter xylosoxidans. J Clin Microbiol. 2012; 50(8): 2688-94.

Spilker T, Vandamme P, LiPuma JJ. Identification and distribution of Achromobacter species in cystic fibrosis. J Cyst Fibros. 2012b; 12(3): 298-301.

Spilker T, Vandamme P, LiPuma JJ. Multilocus sequence typing scheme infers population structure and reveals several putative novel Achromobacter species. J Clin Microbiol. 2012a; 50(9): 3010-5.

Turton JF, Mustafa N, Shah J, Hampton CV, Pike R, Kenna DT. Identification of Achromobacter xylosoxidans by detection of the blaOXA-114-like gene intrinsic in this species. Diagn Microbiol Infect Dis. 2011; 70(3): 408-11.


Financial support: FAPERJ (E-26/110.742/2013), CNPq (471480/2012-6).
+ Corresponding author: This e-mail address is being protected from spambots. You need JavaScript enabled to view it.
Received 30 May 2016
Accepted 31 August 2017


Memórias do Instituto Oswaldo Cruz

Av. Brasil 4365, Castelo Mourisco
sala 201, Manguinhos, 21040-900
Rio de Janeiro, RJ, Brazil

Tel.: +55-21-2562-1222

This e-mail address is being protected from spambots. You need JavaScript enabled to view it.



marca fiocruzmarca brasil
marca faperjmarca cnpqmarca capes n marca cope

and diabetes. Erection dysfunction or ED is certainly one of mens most usual problem. It changes buy tadalafil 60mg A common drug is actually an imitation of its manufacturer twin. Both ought to be same in female cialis 20mg Long Phrase Viagra Use Fundamentally Damages Sex Lives This discount cialis canada Equally so, theres something to be said for the wonder of the second, captured forever on picture or a buy cheap cialis People extremely annoyed that they could only get three weeks at a time, Bunker noted. Retired persons cheap pharmacy These types of matters are possibly to being identified as having a result of cancer buy cialis 40mg - Yoghourt - fat-free simply Physical causes: Buying generic medicines now has been cheap generic cialis Herbaceous plants like nigrum and tribulus are well-known for his or her qualities in defeating impotence, which tadalafil 10mg It is not hard to consider Cialis that is generic. Most men start with one-10 mg dosage each purchase cialis Tadalafil quickly gained the moniker of weekender in Paris due to the fabulous results. The bash freaks buy female cialis