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Revista Pan-Amazônica de Saúde

versão impressa ISSN 2176-6223versão On-line ISSN 2176-6223

Rev Pan-Amaz Saude v.5 n.2 Ananindeua jun. 2014



A preliminary molecular epidemiologic study using analysis of variable number of tandem repeats of Acinetobacter baumannii OXA-23 producing strains isolated from hospitals in Rio de Janeiro State, Brazil


Estudo epidemiológico molecular preliminar usando a análise de número variável de repetições em tandem (VNTR) de cepas de Acinetobacter baumannii produtoras de OXA-23 isoladas em hospitais no Rio de Janeiro, Brasil


Estudio epidemiológico molecular preliminar usando el análisis de número variable en tándem de repeticiones (VNTR) de cepas de Acinetobacter baumannii productoras de OXA-23 aisladas en hospitales de Rio de Janeiro, Brasil



Isabel Nogueira CarramachiI; Karyne Rangel CarvalhoII; Jéssica Gonçalves Vieira da CruzI; Viviane ZahnerI

ILaboratório de Transmissores de Leishmaniose, Setor de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brasil
IIDepartamento de Microbiologia, Laboratório de Saneantes, Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brasil

Endereço para correspondência
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The Gram-negative multidrug-resistant (MDR) bacterium Acinetobacter baumannii constitutes a serious cause of nosocomial infections in Brazilian hospitals. A panel of 36 strains, belonging to five pre-determined pulsed-field gel electrophoresis (PFGE) genotypes from four different hospitals in the City of Rio de Janeiro, Rio de Janeiro State, Brazil, was submitted to simple agarose gel electrophoresis to determine the variation of nine variable number tandem repeats (VNTR) band profiles. Based on published data VNTR were classified in two categories, long (L) and short (S) repeats with different evolutionary implications. The results demonstrated the superior discrimination of VNTR over PFGE. The VNTR Abaum_3002 marker was the least discriminatory with only one allele, while VNTR10 and Abaum_2240 each presented four alleles. The use of a combination of the nine VNTR resulted in a refined genotyping tool that provides valuable epidemiological information.

Keywords: Acinetobacter baumannii; VNTR; Public Health; Epidemiology.


A bactéria Gram-negativa Acinetobacter baumannii multirresistente (AbMR) constitui uma séria causa de infecções nosocominais em hospitais brasileiros. Um painel de 36 cepas, pertencentes a cinco genótipos pré-determinados por eletroforese em gel de campo pulsado (PFGE) de quatro diferentes hospitais na Cidade do Rio de Janeiro, Estado do Rio de Janeiro, Brasil, foi submetido à eletroforese em gel de agarose simples para determinar a variação de nove perfis de número variável de repetições em tandem (VNTR). Com base em dados publicados, os VNTR foram classificados em duas categorias, longa (L) e curta (C) repetições com diferentes implicações evolucionárias. Os resultados demonstraram a discriminação superior de VNTR sobre PFGE. O marcador VNTR Abaum_3002 era o menos discriminatório com apenas um alelo, enquanto VNTR10 e Abaum_2240, cada um, apresentaram quatro alelos. O uso da combinação de nove VNTR resultou em uma aperfeiçoada ferramenta de genotipagem que fornece relevantes informações epidemiológicas.

Palavras-chave: Acinetobacter baumannii; VNTR; Saúde Pública; Epidemiologia.


La bacteria Gram negativa Acinetobacter baumannii multirresistente (AbMR) es una seria causa de infecciones nosocomiales en hospitales brasileños. Un panel de 36 cepas, pertenecientes a cinco genotipos predeterminados por electroforesis en gel de campo pulsado (PFGE) de cuatro diferentes hospitales en la Ciudad de Rio de Janeiro, Estado de Rio de Janeiro, Brasil, fue sometido a electroforesis en gel de agarosa simple para determinar la variación de nueve perfiles de número variable de repeticiones en tándem (VNTR). Con base en datos publicados, los VNTR fueron clasificados en dos categorías, larga (L) y corta (C) repeticiones con distintas implicaciones evolutivas. Los resultados demostraron la discriminación superior de VNTR sobre PFGE. El marcador VNTR Abaum_3002 era el menos discriminatorio con un solo alelo apenas, mientras que VNTR10 y Abaum_2240, cada uno, presentaron cuatro alelos. El uso de la combinación de nueve VNTR resultó en una herramienta de genotipado perfeccionada que suministra relevantes informaciones epidemiológicas.

Palabras clave: Acinetobacter baumannii; VNTR; Salud Pública; Epidemiología.



The Gram-negative bacterium, multidrug-resistant (MDR) Acinetobacter baumannii1 constitutes a signficant cause of nosocomial infections in Brazilian hospitals. According to the MYSTIC Program Brazil2 it features considerably among the total number of nosocomial bacterial isolates recorded in intensive care units. Moreover, the carbapenemases OXA-23 and OXA-143 continue to be observed in Brazilian hospitals3. Recently Zarrilli et al4 reviewed the phenotypic and genotypic methods for typing of A. baumannii. In 1996, Dijkshoorn et al5 reported the development of a rapid and simple detection method, based on analysis of variable number tandem repeats (VNTR), for clonal types of important nosocomial bacteria, that could potentially overcome the limitations and reduce the financial burden associated with pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). PFGE has a limited level of discrimination and is time consuming while MLST, although it is a portable technique, is a costly being restricted primarily to research laboratories6. VNTR have been found in the genomes of several bacteria including Staphylococcus aureus, Bacillus anthracis, Bacillus cereus and Neisseria7,8,9,10,11. Turton et al12 and Pourcel et al6 suggested the use of VNTR as a complement or even for substitution of the other methodologies. VNTR is a technique based on the PCR detection of specific repetitive sequence(s) active in different individuals, which results in an electrophoretic fingerprint. Multiple-locus VNTR analysis, also known as MLVA, presents the polymorphism among different tandemly repeated DNA sequences12. The division of VNTR markers into two groups is made according to their size and rate of evolution. Thus, Short repeats (S-repeats) are 6 to 9 bp in length and appear to have a high rate of evolution, while Long repeats (L-repeats) are 26 to 99 bp in length and show a slower rate of evolution6. This rationale was proposed to aid in phylogenetic studies, outbreak investigations and epidemiological surveillance6.

The occurrence of different PFGE types among OXA-23 producing A. baumannii in different hospitals in Rio de Janeiro State, Brazil, was reported in 2011, and more recently Carvalho13 studied some phenotypic characteristics such as, adherence to epithelial cells and biofilm formation in the same set of strains used in the present study. In addition, the strains were subjected to PCR and phenotypic detection of carbapenemases genes and characterization by MLST for population studies3. In light of the existing classification, we decided to investigate the potential utility of VNTR analysis using a small, but representative, panel of 36 strains of this collection of OXA-23-producing A. baumannii clinical isolates which were recovered from four different hospitals in Rio de Janeiro between January 2006 and September 2007 and that represented five PFGE types3,14. The 36 strains belong to the five previously defined PFGE genotypes (A, B, C, D and E) and S (non-producing OXA-23) (Table 1)3. The VNTR profile (string numbers) was obtained by simple agarose gel electrophoresis of PCR amplicons according to previously described methodology6.



As reported by Grosso et al3, strains from PFGE type A, B, C and D were classified as ST131, ST132, ST133 and ST134 in accordance with the MLST-OD scheme (associated with the Oxford Database) and ST79, ST15 and two new allelic profiles within the MLST-IP scheme (developed by the Institute Pasteur). The genotypes E and S were not submitted to multilocus sequence typing (MLST) schemes.

In the present study we included nine VNTR primer pairs; Abaum_2240, Abaum_3002, Abaum_1988, Abaum_3530 (long-repeats), Abaum_3468, Abaum_0845, Abaum_0826, VNTR1 and VNTR10 (short-repeats). The amplification conditions used were as described by Pourcel et al6. The PCR amplicons were submitted to electrophoresis in 3.2% (S-repeats) and 2% (L-repeats) agarose gels. Following electrophoresis the molecular weight (MW) of each band was estimated using the LabImage 1D gel analysis program (Loccus Biotecnologia, Brazil). In the present study a dendrogram based on VNTR profiles (Figure 1) was created and comparison of the banding patterns was accomplished employing the unweighted pair-group method with arithmetic averages using the Dice similarity coefficient. Computer-assisted analysis was performed using BioNumerics v.4.0 (Applied Maths, Sint-Martens-Latem, Belgium).



Table 1 shows the VNTR alleles for each VNTR maker used in the study. The analysis of the 36 A. baumannii strains, detected 30 different VNTR profiles, each represented by string of numbers (Figure 1). The superior discrimination of VNTR relative to PFGE is clearly demonstrated in figure 1 where strains belonging to the same PFGE type presented variation in VNTR, with the exception of the strains LGB380, LGB382, LGB401, and LGB501 (genotype A), LGB317-LGB405 (genotype A), LGB386-LGB396 (genotype B) and LGB473-LGB480 (genotype B). As a specific example, the strains LGB130 and LGB305, both classified as PFGE type A isolated in the same year from the same hospital at the same time, demonstrated differences in four VNTR (VNTR1, Abaum_3468, Abaum_0826 and Abaum_2240).

Top et al15 studying Enterococccus faecium demonstrated the discriminatory power of six VNTR-MLVA. More recently strains of A. baumannii, producers of CHDL belonging to ICL-II, were typed by MLVA-816. In addition, Hauck et al17 utilized an automated VNTR protocol in the investigation of A. calcoaceticus-A. baumannii complex strains from different hospitals. Moreover, Hu et al18 compared a VNTR based analysis with PFGE typing of A. baumannii in China and observed a remarkable congruence between MLVA-7 and PFGE-based strain clustering.

Taken as a whole our results are in congruence with data presented in the literature and support the use of VNTR analysis for discrimination of isolates of A. baumannii. According to table 1 it can be inferred that the similarity of MLVA is greater within PFGE profiles than between them. As such the use of VNTR does not undermine to PFGE data, but it does show a greater power for detecting genetic variation in clonal groups than can be achieved by PFGE. It was noted that the marker Abaum_1988, except in the case of strain LGB350 (which seems to have a null allele for this VNTR), was conserved among strains of PFGE type A. Nevertheless, more strains should be analyzed in order to confirm if these loci could be employed as a molecular marker of Brazilian PFGE type A. Interestingly, no genetic variation was observed among our samples using the VNTR Abaum_3002, which is in contrast with data reported by Pourcel et al6 which showed that this marker generated three numbers of alleles or types.

It was suggested previously that determination of the number of repeats in VNTR1 and VNTR10 could be valuable in cross-infection studies, with VNTR1 providing the greatest level of discrimination12, at least among the isolates of OXA-23 clone 1 that were included in that study. It is clear that the discriminatory power of this technique depends on the choice of locus. In this context, our data based on the number of alleles showed that VNTR10 was the most polymorphic among the S-repeats while Abaum_2240 were the most polymorphic among the L-repeats, both produced four alleles each (bands) among our strains. Moreover, within the same PFGE group, the VNTR10 and Abaum_2240 markers revealed more differences, an observation which may prove useful in studies that need to be simple, faster and cheaper. In addition, strains with the same PFGE type from different hospitals but from the same hospital chain, e.g. strains LGB382 and LGB130 or strains LGB386 and LGB387 presented a single loci difference: Abaum_3468 and VNTR 10, respectively, S-repeat (Table 1), suggesting that the traffic of employees and material between hospitals may serve to promote dissemination of this bacterium. In this context, the analysis of a group of isolates from the same hospital and belonging to the same PFGE group showed higher rates of evolution in the S-repeat in comparison to L-repeat markers. Indeed, with the exception of Abaum_2240 the pattern of L-repeats was maintained among PFGE-types, while the pattern of S-repeats was highly polymorphic.

The dissemination of A. baumannii in Rio de Janeiro is reflected by the detection of the same VNTR genotype in different hospitals. This observation calls for improvements in the procedures for prevention of hospital infection and prudence in the use of carbapenems. Improved recognition and early detection of potentially epidemic isolates that show a propensity to emerge in hospital wards can be determined by MLST, and also, based on our data, by VNTR. In light of these data we contend that VNTR should be considered as an important tool for infection control.

Although a VNTR data bank ( exists, we did not use this resource since our intention was to facilitate the routine of laboratories which receive samples from hospitals for screening. In conclusion, our results corroborate the impressive discriminatory power of VNTR, as reported by numerous authors and importantly, provide the first report of the applicability of this technique in Brazil. In light of the fact that both MLST and PFGE are technically demanding, expensive and time consuming, the use of VNTR, specifically VNTR10 (due the fact of being a short repeat marker) may be a candidate for further studies on the characterization of strains that belong to an outbreak and to the same PFGE genotype.



To Dr. Douglas Mcintosh for English revision. To the Laboratório de Pesquisa em Infecção Hospitalar of the Instituto Oswaldo Cruz who provided the strains of Coleção de Culturas de Bactérias de Origem Hospitalar used in the present study.



Conselho Nacional de Desenvolvimento Científico e Tecnológico and Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro.



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Correspondence / Correspondência / Correspondencia:
Viviane Zahner
Instituto Oswaldo Cruz, Fundação Oswaldo Cruz
Laboratório de Transmissores de Leishmaniose
Setor de Entomologia Médica e Forense
Av. Brasil, 4365. Bairro: Manguinhos

CEP: 21045-900 Rio de Janeiro-Rio de Janeiro-Brazil
Phone#: +55 (21) 2562-1953 / (21) 2562-1915

Received / Recebido em / Recibido en: 2/10/2013
Accepted / Aceito em / Aceito en: 10/3/2014