Diagnostic Microbiology and Infectious Disease 80 (2014) 330–333

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Microbiological characterization of Delftia acidovorans clinical isolates from patients in an intensive care unit in Brazil☆,☆☆ Carlos Henrique Camargo a,⁎, Adriano Martison Ferreira b,c, Edvaldo Javaroni b, Brígida Aparecida Rosa Reis b, Maria Fernanda Campagnari Bueno a, Gabriela Rodrigues Francisco a, Juliana Failde Gallo a, Doroti de Oliveira Garcia a a b c

Instituto Adolfo Lutz, Sao Paulo, Brazil Hospital Amaral Carvalho, Jau, Brazil Botucatu Medical School, Botucatu, Brazil

a r t i c l e

i n f o

Article history: Received 3 August 2014 Accepted 1 September 2014 Available online 6 September 2014 Keywords: Delftia acidovorans Drug resistance Electrophoresis Gel Pulsed-field Microbial sensitivity tests Molecular epidemiology Cross infection

a b s t r a c t Delftia acidovorans is an opportunistic agent in several types of infections, both in immunocompromised and immune-competent individuals; its resistance to aminoglycosides and polymyxin, choice drugs for empirical treatment of Gram-negative infections, is remarkable. We report the antimicrobial susceptibility and the genetic relatedness of 24 D. acidovorans strains recovered from tracheal aspirates of 21 adult inpatients hospitalized in an intensive care unit at a Brazilian hospital, from 2012 to 2013. All of the isolates were recovered as pure cultures and in counts above 1,000,000 CFU/mL. None of them were susceptible to polymyxin B, amikacin, gentamicin, or tobramycin; quinolones and trimethoprim-sulfamethoxazole presented varied activities against the isolates, while β-lactam resistance was not detected. Four clusters were verified in pulsed-field gel electrophoresis analysis, and a major pulsotype comprised 10 strains. A possible, but undetermined common source, can be responsible for this strain dissemination, underscoring the need of reinforcing the adherence to disinfection and infection control standard techniques. © 2014 Elsevier Inc. All rights reserved.

1. Introduction Delftia acidovorans (formerly belonging to Pseudomonas and Comamonas genus) is an opportunistic non-fermentative Gramnegative bacillus, classified in the Pseudomonas rRNA homology group III (LiPuma et al., 2011), sporadically reported in human infections (Steinberg and Burd, 2009). Epidemiology of D. acidovorans infections is not easy to elucidate. When determined, the source of infection can be river water (Reina et al., 1991), various devices and equipment in hospitals and clinics (Miño de Kaspar et al., 2000; Stampi et al., 1999; Stiegler et al., 2003; Weinstein et al., 1976), and paraphernalia contaminated with water used by intravenous drug abusers (Horowitz et al., 1990; Mahmood et al., 2012; Perla and Knutson, 2005), demonstrating the environmental origin of these bacteria (Steinberg and Burd, 2009). Bacteremia due to bacterial translocation from the bowel (Hagiya et al., 2013) or ascending urinary tract infection (Kam et al., 2012) or following a thoraco-abdominal gunshot wound (Oliver et al., 2005) has been reported as well as intravascular dispositive-related bloodstream infections (Castagnola et al., 1994; Chotikanatis et al., 2011; ☆ Financial support: None to declare. ☆☆ Conflict of interest: None to declare. ⁎ Corresponding author. Tel.: +55-11-3068-2876. E-mail address: [email protected] (C.H. Camargo). http://dx.doi.org/10.1016/j.diagmicrobio.2014.09.001 0732-8893/© 2014 Elsevier Inc. All rights reserved.

Kawamura et al., 2011; Lang et al., 2012). There have been reports of relapse peritoneal dialysis-related peritonitis (López-Menchero et al., 1998), urine tract infection (del Mar Ojeda-Vargas et al., 1999), and ocular infections (Brinser and Torczynski, 1977; Lee et al., 2008; Stonecipher et al., 1991) related to this agent. Pulmonary infections attributed to D. acidovorans are rarely reported, e.g., a case of pneumonia in an immunocompromised HIV-positive patient (Franzetti et al., 1992) and a case of chronic empyema in the pleural cavity of an immunocompetent man (Chun et al., 2009). A report of D. acidovorans isolated from intercostal drainage tube tip and repeated samples of endotracheal tube aspirates from an immunocompetent child presenting pulmonary infection and empyema that evolved to death (Khan et al., 2012) underscores the relevance of this pathogen from respiratory tract specimens. Prevalence of D. acidovorans infections may be underestimated because it is an unusual agent in clinical laboratories and, when isolated, may be wrongly reported as a contaminant. To facilitate the identification of this sporadically isolated species, the presence of orange indole reaction was recommended as a simple screening tool for this microorganism (Khan et al., 2012); detection of polymyxin resistance also can help in its identification (Khan et al., 2012; Laffineur et al., 2002). In addition to polymyxin B (PO) resistance, strains of D. acidovorans usually present resistance to amynoglycosides (Steinberg and Burd, 2009). In addition to the antimicrobial susceptibility observed in vitro, D. acidovorans strains can present minimal bactericidal concentration

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up to 8-fold higher than MIC for imipenem (IP) and ceftazidime (TZ) (Higgins et al.). Molecular typing of D. acidovorans has been reported only twice: Kawamura et al. (2011) verified the occurrence of identical Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) profiles in D. acidovorans strains isolated in serial blood cultures from an immune-compromised patient, and recently, Kam et al. (2012) employed pulsed-field gel electrophoresis (PFGE) to confirm the occurrence of bacteremia associated with ascending urinary tract infection. From August 2012 to June 2013, 24 D. acidovorans isolates were recovered from routine cultures of tracheal aspirate of 21 inpatients of the adult intensive care unit in a regional reference hospital in the State of São Paulo, Brazil. Due to this high number of isolates from a single ward, we investigated the antimicrobial susceptibility and the clonal relatedness of these strains. To the best of our knowledge, this is the first study employing molecular typing of D. acidovorans strains from different patients to determine their clonal relatedness. 2. Materials and methods Isolates were recovered from routine cultures of tracheal aspirate (N1,000,000 CFU/mL), from inpatients of the adult intensive care unit in a regional reference hospital in the State of São Paulo, Brazil, between 2012 and 2013. Clinical specimens were seeded onto MacConkey agar and blood agar plates (Oxoid Ltd., Hampshire, UK) (Camargo et al., 2004). Identification was carried out by Vitek2 automatized equipment (bioMérieux, Durham, NC, USA) and confirmed by conventional manual methods (LiPuma et al., 2011; Weyant et al., 1995), API 20NE (bioMérieux), or Matrix Assisted Laser Desorption Ionization–Time of Flight–Mass Spectrometry system (Bruker Daltonics, Billerica, MA, USA). Antimicrobial susceptibility was determined by MIC verified by E-test (bioMérieux), according to the manufacturer's instructions, for the drugs amikacin (AK), gentamicin (GM), tobramycin (TM), PO, cefotaxime (CTX), cefepime (PM), trimethoprimsulfamethoxazole (TS), ciprofloxacin (CI), levofloxacin (LE), IP, and TZ. MIC values were categorized adopting the breakpoints determined by CLSI (2013) for non-Enterobacteriaceae strains. 16S rRNA methylases encoding genes rmtD and rmtG, which confer a high level of resistance to aminoglycosides, prevalent in Brazilian Gramnegative isolates, were assessed by PCR (Bueno et al., 2013; Doi and Arakawa, 2007). PFGE was carried out to evaluate the clonal relatedness among the isolates, using a CHEF-DR III system (Bio-Rad Laboratories Inc., Hercules, CA, USA) after extraction (Ribot et al., 2006) and digestion of whole bacterial DNA with SpeI restriction enzyme (10 units; New England Biolabs, London, UK); running parameters were initial switch, 2.2 s; final switch, 54.2 s; length, 20 h; temperature 14 °C; and 200 V (6 V/cm). After an electrophoresis run with 50 μmol/L thiourea (Sigma-Aldrich, St. Louis, MO, USA), the gel was stained with ethidium bromide solution (1 μg/mL; Sigma-Aldrich) for 20 minutes, destained in fresh distilled water for 30 minutes, and visualized under UV light in Gel Doc XR (Bio-Rad Laboratories Inc.). Acquired images were submitted to BioNumerics v.5.0 (Applied Maths, Sint-Martens-Latem, Belgium) analysis, and a dendrogram was generated by the unweighted pair group method with arithmetic mean (UPGMA); Dice coefficients (N80% similarity) defined the clusters that were represented by capital letters. A pulsotype was defined as a restriction profile, which can comprise more than 1 isolate in a cluster with 100% similarity and represented by a capital letter followed by a sequential number. 3. Results Twenty-four D. acidovorans isolates were recovered from tracheal aspirate samples of 21 patients in the period evaluated; they were confirmed to be D. acidovorans according to the methodologies employed. All strains were non-susceptible to PO, and high-level aminoglycoside resistance rates were observed for all the 3 drugs evaluated. TS presented a

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Table 1 MIC range, MIC50, MIC90 (μg/mL), and percentage of susceptibility, intermediate, and resistance of clinical isolates of D. acidovorans evaluated by E-test. Antimicrobial drug

MIC range

MIC50

MIC90

AK GM TM PO CTX PM TS CI LE IP TZ

48 to N256 48 to N1024 32 to N1024 4–128 0.06–4 0.75–6 0.012 to N32 0.032–12 0.032–6 0.094–1 0.19–1.5

N256 N1024 N1024 48 0.5 2 N32 8 3 0.25 0.38

N256 N1024 N1024 64 1 4 N32 12 4 0.75 0.5

Susceptibility categoriesa %S

%I

%R

0.0 0.0 0.0 0.0 100.0 100.0 45.8 16.7 29.2 100.0 100.0

4.2 0.0 0.0 8.3 0.0 0.0 0.0 4.2 70.8 0.0 0.0

95.8 100 100 91.7 0.0 0.0 54.2 79.2 0.0 0.0 0.0

S = susceptibility; I = intermediate; R = resistance. a Categorized according to the CLSI (2013) breakpoints for non-Enterobacteriaceae strains. bimodal distribution with 11 strains with MIC ≤0.047, and the remaining 13 strains, with MIC N32 μg/mL. LE (resistant strains not detected) presented better activity against the isolates than CI (83.4% of strains non-susceptible). β-Lactams presented great activity; none of the isolates evaluated was categorized as intermediate or resistant. Neither rmtD nor rmtG was detected in the strains. Summarized data on antimicrobial susceptibility are presented in Table 1. Regarding the clonal relatedness assessed by PFGE, a similarity of 51% was observed amongst all isolates. Ten different pulsotypes were observed, but the predominance of isolates was in cluster A (91% similarity), which comprised pulsotypes A1 (10 isolates); A2 (3 isolates); A3 and A4 (2 isolates each); and A5, A6, and A7 (a single strain each) (Fig. 1). Cluster B comprised 2 isolates (100% similarity, pulsotype B), and clusters C and D included only 1 strain, each. Antimicrobial susceptibility was not sufficiently discriminatory for categorizing strains as PFGE did. For instance, resistance profile AK, GM, TM, and PO was observed in 3 strains belonging to pulsotypes B, C, and D. On the other hand, strains belonging to pulsotype A1 showed 3 different resistance patterns: AK, GM, TM, PO, CI, LE* (5 strains); AK, GM, TM, PO, TS, CI (1 strain); and AK, GM, TM, PO, TS, CI, LE* (4 strains). These results indicate that susceptibility patterns can differ even in isolates presenting the same pulsotype.

4. Discussion To the best of our knowledge, this is the first report of clonal dissemination of D. acidovorans in hospital settings confirmed by molecular methods. In this case series, although one may speculate that this bacterium may be considered contaminant because it was recovered from tracheal aspirate cultures, we are highly inclined to believe that they are not simple saprophytes because of the high count in isolation procedures and the absence of another pathogen in the clinical specimens. The recovery of a pure culture of D. acidovorans from sputum is enough to suggest its role as a pathogenic agent (Brinser and Torczynski, 1977; von Graevenitz, 1985). Moreover, previous reports found that D. acidovorans strains were the etiological agents of pulmonary infection and empyema (Franzetti et al., 1992; Khan et al., 2012). The lack of clinical data and patient follow-up, however, arguably challenges our assertions. Even though no D. acidovorans was recovered from environmental culture samples, the fact that this bacteria was isolated from different inpatients of the same hospital ward in a determined period of time, presenting high genetic similarity determined by PFGE, may suggest the presence of a common but unidentified source. Previous reports have identified several putative environmental sources for D. acidovorans infections (Horowitz et al., 1990; Mahmood et al., 2012; Miño de Kaspar et al., 2000; Perla and Knutson, 2005; Reina et al., 1991; Stiegler et al., 2003). Stampi et al. (1999) identified the presence of D. acidovorans in dental-unit water associated with residual chlorine and higher ambient temperatures, which alerts to the potential importance of this agent in locations with warmer climates, such as Brazil. Antimicrobial susceptibility patterns observed in strains herein studied are consistent with previous reports: in vitro susceptibility to

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Fig. 1. Dendrogram and PFGE typing of SpeI restricted D. acidovorans strains isolated from tracheal aspirate samples of inpatients in an intensive care unit of a hospital in the state of Sao Paulo, Brazil (2012–2013). Clusters (represented by capital letters) were defined based on an 80% Dice similarity cutoff value of the UPGMA clustering method (1.25% optimization; 1.25% tolerance). Resistance patterns were determined by MICs according to E-test results, following CLSI (2013) breakpoints. Asterisks denote intermediate susceptibility.

β-lactams and resistance to aminoglycosides and polymyxin is common (Chotikanatis et al., 2011; Kam et al., 2012). The polymyxin and aminoglycoside resistance can be speculated to result from the combination of the rather simple protein composition of D. acidovorans outer membrane (Gerbl-Rieger et al., 1992) and of ionic characteristics of those antimicrobial agents. D. acidovorans presents constitutive porin Omp32 as the major protein compound (Gerbl-Rieger et al., 1992) and 2 less prominent proteins, Omp37 and Omp21 (Baldermann et al., 1998) in its outer membrane composition. Omp32 is recognized to be a porin presenting strong anion selectivity, with positive surface potential at both the external and periplasmic surfaces of the outer membrane (Zeth et al., 2000). Thus, repulsion of positive charged compounds, such as polycationic antimicrobial polymyxins and aminoglycosides, may be very likely. In addition, absence of 16S rRNA methylases RmtD and RmtG reinforces this hypothesis, although the presence of other enzymes was not tested. On the other hand, antibiotics with zwitteronic, neutral or negatively charged species, such as the quinolones, TS, and the β-lactams may preserve their activity, as we verified in the strains we evaluated. Resistance to β-lactams was previously reported but not associated with the extended spectrum β-lactamase CTX-M, a common source of β-lactam resistance in Gram-negative bacteria (Chotikanatis et al., 2011). However, the development of cephalosporin resistance in a D. acidovorans strain from a patient with recurrent vascular catheter-related bacteremia treated initially with PM (Chotikanatis et al., 2011) suggests the evolvement of an adaptive mechanism, such as the presence of inducible β-lactamases. In fact, Ravaoarinoro et al. (1992) and Ravaoarinoro and Therrien (1999) verified that IP induced the in vitro production of β-lactamases in 2 clinical D. acidovorans isolates and that those β-lactamases were inhibited by cloxacillin and p-chloromercuribenzoate. Kawamura et al. (2011) also observed the manifestation of different susceptibility profiles of genetically identical (confirmed by ERIC-PCR) D. acidovorans strains isolated from serial blood samples from an immune-compromised patient;

cefpirome (a broad-spectrum cephalosporin) therapy was initiated, but subsequent isolates developed resistance to piperacillin and fourth-generation cephalosporins (PM and cefozopran) during the treatment. Taken together, these findings very likely indicate the presence of an inducible AmpC β-lactamase (Bush et al., 1995), as previously suggested by Ravaoarinoro et al. (1992). Thus, the presence of different susceptibility patterns in strains presenting the same PFGE pulsotype does not seem contradictory, since manifestation of resistance may be determined by regulatory pathways, inducible mechanisms and by the presence of mobile genetic elements (such as plasmids) not detectable in this typing technique. Indeed, the finding of the resistance profile AK, GM, TM, and PO in 3 strains belonging to pulsotypes B, C, and D suggests non-clonal dissemination of this resistance pattern. 5. Conclusion Since reports on different infections attributed to D. acidovorans have become more common and since antimicrobial resistance may appear during treatment, attention must be given to this unusual opportunistic agent in populations with potential higher risk factors, such as patients using invasive medical devices and intravenous drug abusers. Resistance to antimicrobial agents employed in empirical treatment of Gram-negative infections also alerts to the importance of monitoring this seldom reported bacterium. The presence of a predominant clone determined by molecular technique also underscores the need of continuous surveillance and reinforcement of infection control standard techniques. References Baldermann C, Lupas A, Lubieniecki J, Engelhardt H. The regulated outer membrane protein Omp21 from Comamonas acidovorans is identified as a member of a new family

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Microbiological characterization of Delftia acidovorans clinical isolates from patients in an intensive care unit in Brazil.

Delftia acidovorans is an opportunistic agent in several types of infections, both in immunocompromised and immune-competent individuals; its resistan...
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