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Phenotypic and genotypic assays for detecting the prevalence of metallo-β-lactamases in clinical isolates of Acinetobacter baumannii from a South Indian tertiary care hospital

R. Uma Karthika, R. Srinivasa Rao, Suchismita Sahoo, P. Shashikala, Reba Kanungo, S. Jayachandran, K. Prashanth

  • 1Department of Biotechnology, School of Life Sciences, Pondicherry University, R. Venkataraman Nagar, Kalapet, Puducherry 605 014, India
  • 2Department of Clinical Microbiology, Pondicherry Institute of Medical Sciences, Puducherry 605 014, India
  • Correspondence
    Prashanth K.
    prashi2k{at}gmail.com

    • Journal of Medical Microbiology 2009; 58(4):430–435 · https://doi.org/10.1099/jmm.0.002105-0

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    Abstract

    Nosocomial infections caused by Acinetobacter baumannii often prove difficult to treat owing to their multiple drug resistance. Carbapenems play a pivotal role in the management of severe Acinetobacter infections. However, reports of carbapenem resistance have been increasing alarmingly due to production of a variety of carbapenemases including metallo-β-lactamases (MBLs). This study investigated by both phenotypic and genotypic assays the prevalence of MBLs in a total of 55 A. baumannii strains isolated from a South Indian tertiary care hospital. Random amplified polymorphic DNA (RAPD) genotyping and antimicrobial susceptibility testing for nine clinically relevant antibiotics was done for characterization of isolates. Phenotypic expression of MBLs was examined by a simple double disc synergy (DDS) test, and the presence of the most frequent MBL coding genes, blaIMP1 and blaVIM2, was checked by PCR. RAPD analysis generated six clusters of isolates and there was very little correlation between RAPD clusters and resistant profiles. Most of the isolates showed complete or high resistance to imipenem (100 %), meropenem (89 %), amikacin (80 %), cefotaxime (89 %) and ciprofloxacin (72 %). In addition, 44 % of isolates showed a high MIC level (≥16 μg ml−1) for meropenem. Thirty-nine isolates (70.9 %) were positive for MBL production by the DDS test while blaIMP1 gene amplification was seen only in 23 isolates (42 %). Interestingly, none of the isolates showed amplification of blaVIM2. Further investigations on DDS-positive/PCR-negative isolates by spectrophotometric assay showed MBL activity in most of the isolates, suggesting involvement of other genes. The high incidence of isolates possessing MBL activity in the present study represents an emerging threat of complete resistance to carbapenems among Acinetobacter spp. in India.

    INTRODUCTION

    Acinetobacter baumannii, one of the most important nosocomial pathogens with multiple drug resistance (MDR), is of great concern because of its intrinsic and acquired resistance mechanisms, limiting the treatment options (Navon-Venezia et al., 2005). Carbapenems are the drugs of choice for A. baumannii infections and are often used as a last resort (Yano et al., 2001). However, carbapenem-resistant A. baumannii producing carbapenemases has been isolated increasingly in recent times (Jones et al., 2005) and in particular a variety of IMP and VIM type metallo-β-lactamases (MBLs) have been detected and grouped under the class B carbapenemases (Jeong et al., 2006; Yum et al., 2002; Da Silva et al., 2002). Since the first descriptions of MBLs in Acinetobacter spp., IMP and VIM types have been found to have a wide geographical occurrence (Walsh et al., 2005; Jones et al., 2005). Recently, a new type of MBL, SIM-1, has also been reported (Lee et al., 2005). MBL genes also have the propensity to disseminate quickly to other species of Gram-negative bacilli (Navon-Venezia et al., 2005; Peleg et al., 2005). Therefore, it is essential to rapidly screen and detect MBLs in Acinetobacter, which could help in modifying therapy and initiate effective infection control to prevent further dissemination (Hirakata et al., 1998).

    Numerous Indian studies have documented the presence of MBLs in Pseudomonas aeruginosa (Jesudason et al., 2005; Mendiratta et al., 2005; Sarkar et al., 2006); however, to our knowledge only one study for phenotypic detection of MBLs in A. baumannii has been done in India (Gupta et al., 2006). The aim of this study was to determine both phenotypically and genotypically the prevalence of MBL-producing strains among MDR A. baumannii isolated from clinical specimens in this geographical region.

    METHODS

    Bacterial isolates.

    All the Acinetobacter isolates were obtained from a South Indian tertiary care hospital (Pondicherry Institute of Medical Sciences, Puducherry, India) from various clinical specimens, such as endotracheal aspirates, cerebrospinal fluid, wound swabs, urine and blood culture specimens, from patients admitted to the intensive care and acute medical care units from January to April 2007. All the replicates were excluded from the study. A total of 55 Acinetobacter isolates were identified and grouped into the Acinetobacter calcoaceticus–baumannii complex (Acb complex) using phenotypic tests as described elsewhere (Gerner-Smidt et al., 1991; Prashanth & Badrinath, 2000; Kenchappa & Sreenivasmurthy, 2003). A simple molecular method, namely amplified rDNA restriction analysis (ARDRA), was used to further identify genomic groups within the Acb complex as described elsewhere (Chandra et al., 2002). ARDRA identified all the isolates from our collection as A. baumannii.

    Antimicrobial susceptibility testing.

    Antimicrobial susceptibility testing was performed for nine different therapeutically relevant antibiotics by the Kirby–Bauer disc diffusion method according to Clinical Laboratory Standards Institute guidelines (CLSI, 2006). Antibiotics tested included amikacin (10 μg), ceftazidime (30 μg), cefotaxime (30 μg), ceftriaxone (30 μg), ciprofloxacin (5 μg), cefepime (30 μg), imipenem (10 μg), meropenem (10 μg) and netilmicin (30 μg). A. baumannii ATCC 19606T was used as control. Isolates showing MDR were further tested for MBL production. MDR was defined as resistance to two or more drugs or drug classes of therapeutic relevance (Prashanth & Badrinath, 2004; Navon-Venezia et al., 2005).

    RAPD typing.

    Genotyping of A. baumannii isolates was performed using random amplified polymorphic DNA (RAPD) analysis for 48 isolates using arbitrary hexamers (H series) obtained from Operon Technologies. The PCR mixtures (10 μl) contained 1 μl PCR buffer with 1.5 mM MgCl2, 50 μM each dNTP, 50 pmol primer, 1 U Taq polymerase (Bangalore Genei) and 50 ng DNA template. PCR amplifications were performed using a thermal cycler (Eppendorf) as follows: (i) initial denaturation step of 5 min at 94 °C; (ii) 35 cycles of PCR, with each cycle consisting of 30 s at 94 °C, 45 s at 45 °C and 2 min at 72 °C; and (iii) a final extension step of 5 min at 72 °C. Amplified products from the isolates were analysed by electrophoresis on 1.2 % (w/v) agarose gels, stained with ethidium bromide and the banding patterns were analysed using the Quantity One Gel Doc 2000 (Bio-Rad) computer software system.

    MIC determination and MBL detection.

    The MIC for meropenem was determined by the agar dilution method as recommended by the CLSI (2006). The organisms were considered susceptible to meropenem if the MIC was ≤4 μg ml−1 and resistant if the MIC was ≥16 μg ml−1 (CLSI, 2006). For phenotypic detection of MBLs among the A. baumannii strains, we used the imipenem EDTA-double disc synergy (DDS) test developed by Yong et al. (2002). All the MBL-positive isolates were repeatedly checked for reproducibility. All the isolates were checked for MBL genotypically by PCR for the presence of the predominant genes blaIMP1 and blaVIM2. PCR conditions and blaIMP1 and blaVIM2 primers used for PCR amplification were according to previously described studies (Poirel et al., 2000; Yum et al., 2002). Isolates which were positive for MBL by the DDS test but PCR-negative were further tested for enzyme activity by spectrophotometry. The spectrophotometric assay for assessing MBL activity was performed as described previously (Edwards et al., 1998; Lauretti et al., 1999).

    RESULTS AND DISCUSSION

    In recent years, there have been numerous reports on MDR A. baumannii from hospital settings in India (Prashanth & Badrinath, 2005, 2006; Sinha et al., 2007; Joshi et al., 2003b). In our earlier studies, we characterized isolates obtained mainly from intensive care units (Prashanth & Badrinath, 2000, 2005), while this study attempted to determine the resistance among isolates obtained from various other medical wards also. In particular, 36 strains were isolated from wards outside the intensive care unit. Antibiotic susceptibility testing showed that the majority of the isolates were resistant to three or more antibiotics (Table 1⇓). While all the isolates were resistant to imipenem, 89 %, 80 %, 89 % and 72 % of isolates were resistant to meropenem, amikacin, cefotaxime and ciprofloxacin, respectively. A. baumannii isolates also showed moderate resistance to ceftriaxone (42 %) and ceftazidime (36 %). Unfortunately, these are the antibiotics that are currently being prescribed in the hospital. However, a few antimicrobials, those that were not used frequently in the hospital, such as cefepime and netilmicin, continued to show low resistance, i.e. 30 % and 27 %, respectively. Such observations have also been witnessed by other investigators wherein susceptibility is attributed to decreased usage of the antimicrobial (Manikal et al., 2000).

    Table 1.

    Origin, resistogram, MBLs and RAPD cluster of all the isolates of A. baumannii

    RAPD analysis of the A. baumannii isolates examined showed fragments ranging from 500 to 1500 bp (Fig. 1)⇓. An UPGMA dendrogram (data not shown) constructed using binary data generated six clusters from the isolates (designated A–F), revealing the genetic relatedness among the isolates. Two major clusters depicted in the dendrogram, namely D and F, comprised 17 and 13 isolates, respectively. Cluster E had a total of nine isolates. The A, B and C clusters constituted only a few isolates (one to five isolates). RAPD results did not correlate with those of the antibiotypes since our isolates showed highly divergent resistance profiles and only a few correlations could be made in this regard. A few isolates belonging to certain clusters (A: P31, P49, P51; C: P39, P56; E: P46, P47; F: P15, P16) had identical resistograms (Table 1⇑). Interestingly, cluster D had seven isolates showing two kinds of identical resistograms specific for the site of isolation [D1 (P5, P53, P55 all from endotracheal aspirates) and D2 (P32, P33, P36, P38 all from wounds)]. Such associations were also found in clusters C (wound) and E (urine), suggesting that distinct clones may be responsible for specific disease or infection caused by this organism. Although the discriminatory power of PFGE genotyping was found to be higher than that of PCR-based techniques, the present study employed RAPD because of its simplicity and feasibility (Liu & Wu, 1997). PFGE, though more efficient in analysing Acinetobacter epidemiology in complex endemic settings (Vila et al., 1996; Liu & Wu, 1997; D'Agata et al., 2001), is cumbersome as well as expensive and many less well-equipped laboratories may not be able to use this technique routinely.

    Figure image not available in archive
    Fig. 1.

    RAPD fingerprinting of representative clinical isolates of A. baumannii including the reference strain A. baumannii ATCC 19606T. Lanes: 1, 500 bp molecular mass marker (Bangalore Genei); 2–14 and 16–51, clinical isolates of A. baumannii (1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 49, 51, 53, 55, 56 and 57). Lane 15, A. baumannii ATCC 19606T.

    Carbapenems are the drugs of choice for nosocomial Acinetobacter infections in India. However, in recent years, it has been reported that there is reduced susceptibility to imipenem (Taneja et al., 2003; Joshi et al., 2003a; Sinha et al., 2007; Sinha & Srinivasa, 2007). Interestingly, many of these reports have documented only moderate resistance to imipenem (Taneja et al., 2003; Sinha & Srinivasa, 2007). The present study showed high levels of imipenem and meropenem resistance among A. baumannii isolates. Forty-four per cent of isolates were resistant to meropenem with MIC levels ranging from 16 μg ml−1 to 128 μg ml−1. However, there was low agreement among the disc diffusion and MIC results for meropenem. Meropenem MIC results showed 60 % of isolates having moderate to complete resistance, while the disc diffusion test showed 89 % resistance. In the present study, 29 % of isolates detected as resistant by disc diffusion were found to have their MICs in the sensitive range. A similar observation was witnessed in a recent study from India (Sinha & Srinivasa, 2007).

    Detection of resistance in pathogens by molecular testing is gaining momentum in India. Many Indian studies have checked for carbapenem resistance in bacteria other than A. baumannii by looking for the presence of extended-spectrum β-lactamase and MBL genes by PCR (Mendiratta et al., 2005; Sarkar et al., 2006). Amid various MBL-encoding genes thus far discovered, blaIMP and blaVIM appear to be the most clinically important due to their ability to spread among other major pathogens (Da Silva et al., 2002). In India, recently a high percentage of P. aeruginosa strains producing MBL has been reported (Jesudason et al., 2005; Mendiratta et al., 2005; Sarkar et al., 2006). A similarly significant increase in the percentage of A. baumannii isolates (70.9 %) positive for MBL production by the EDTA-DDS test was observed in the present study, which is in contrast to the 7.5 % reported in the only other Indian study on MBL production in A. baumannii (Gupta et al., 2006), reflecting the evolving scenario in India.

    PCR revealed amplification of an 862 bp fragment corresponding to the blaIMP1 gene in 42 % of isolates and no isolates showing the presence of blaVIM2 (510 bp) when tested for MBL genes. Thirteen isolates were positive for MBLs by both the DDS assay and blaIMP1 amplification. There were 10 isolates that were PCR-positive, but negative in the DDS test. Since blaIMP gene cassettes have been associated with integrons, it is possible that blaIMP alleles could be carried by Acinetobacter strains but do not phenotypically express the IMP β-lactamases (Da Silva et al., 2002). Besides, the DDS test showed 26 isolates positive for MBL which did not show amplification for blaIMP1. These isolates were further tested for MBL activity by spectrophotometry, which was positive for 24 isolates wherein cell extracts caused breakdown of imipenem. Specific activity ranged from 41.4 to 60 nmol imipenem hydrolysed min−1 (mg protein)−1, compared to 1.9–13.2 nmol imipenem hydrolysed min−1 (mg protein)−1 by the two MBL-negative isolates used as controls (Table 1⇑). The remaining two DDS-positive isolates displayed no enzyme activity. In the presence of EDTA, hydrolysis measured by spectrophotometry was greatly reduced. These results suggest that other genes might be responsible for encoding MBLs. The DDS test thus proved to be quite reliable and easy to perform.

    The carbapenem-resistant strains with no MBL detectable by the DDS test in this study may possess other enzymes mediating carbapenem resistance, such as OXA-type lactamases (class D) or AmpC β-lactamases, and/or other mechanisms such as outer-membrane permeability and efflux mechanisms that were not checked. The isolates that were MBL-positive by the DDS test but negative for either blaIMP1 or blaVIM2 amplification may have variant blaIMP or blaSIM genes. MBL genes are mostly detected in class 1 integron structures and these integrons are detected in a high percentage of Acinetobacter isolates (Seward, 1999; Gallego & Towner, 2000). The blaVIM-2 gene cassette has been identified throughout the world as part of class 1 integrons and is noted to be the most prevalent carbapenemase gene (Poirel et al., 2000; Yum et al., 2002; Walsh et al., 2005). Surprisingly, blaVIM-2 was not detected in our A. baumannii isolates. Interestingly, one of the latest studies showed blaVIM-2 only in imipenem-resistant Acinetobacter genomic species 13TU isolates, and not in imipenem-resistant A. baumannii isolates, which produced the OXA type of β-lactamase (Lee et al., 2007). Possibly there may be specific genotypic traits against antimicrobial agents in our A. baumannii isolates too that could lack blaVIM-2. By acquiring various kinds of resistance mechanisms, A. baumannii has developed into one of the most difficult hospital pathogens to control and treat. The alarming increase in the frequency of MBLs presents an emerging threat of complete resistance to the useful drugs against Acinetobacter spp. in India. Hence restrained and careful use of antibiotics, as well as strict hygiene practices, are critical for preventing the emergence of complete resistance and spread of this pathogen in this country.

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