Antonio Carlos Campos Pignatari

Rapid Detection and Identification of Metallo-β-Lactamase-Encoding Genes by Multiplex Real-Time PCR Assay and Melt Curve Analysis

ABSTRACT Metallo-β-lactamase enzymes (MβL) are encoded by transferable genes, which appear to spread rapidly among gram-negative bacteria. The objective of this study was to develop a multiplex real-time PCR assay followed by a melt curve step for rapid detection and identification of genes encoding MβL-type enzymes based on the amplicon melting peak. The reference sequences of all genes encoding IMP and VIM types, SPM-1, GIM-1, and SIM-1 were downloaded from GenBank, and primers were designed to obtain amplicons showing different sizes and melting peak temperatures (Tm). The real-time PCR assay was able to detect all MβL-harboring clinical isolates, and the Tm-assigned genotypes were 100% coincident with previous sequencing results. This assay could be suitable for identification of MβL-producing gram-negative bacteria by molecular diagnostic laboratories.

Rapid detection of carbapenemase genes by multiplex real-time PCR

OBJECTIVES To develop a single multiplex real-time PCR assay to detect six different genetic types of carbapenemases already identified in Enterobacteriaceae (KPC, GES, NDM, IMP, VIM and OXA-48). METHODS A total of 58 bacterial isolates were tested. Thirty were previously characterized as resistant to carbapenems and documented by PCR and sequencing analysis to carry the following genes: bla(KPC) type, bla(GES) type, bla(IMP) type, bla(VIM) type, bla(OXA-48) and bla(NDM-1). These positive strains included 21 Enterobacteriaceae, 1 Acinetobacter baumannii and 8 Pseudomonas aeruginosa isolates. The remaining 28 isolates previously tested susceptible to carbapenems and were negative for these genes. Bacterial DNA was extracted using the easyMag extractor (bioMérieux, France). The real-time PCR was performed using the Rotor-Gene 6000 instrument (Corbett Life Science, Australia) and specific primers for each carbapenemase target were designed using the DNAStar software (Madison, WI, USA). RESULTS Each one of the six carbapenemase genes tested presented a different melting curve after PCR amplification. The melting temperature (T(m)) analysis of the amplicons identified was as follows: bla(IMP) type (T(m) 80.1°C), bla(OXA-48) (T(m) 81.6°C), bla(NDM-1) (T(m) 84°C), bla(GES) type (T(m) 88.6°C), bla(VIM) type (T(m) 90.3°C) and bla(KPC) type (T(m) 91.6°C). No amplification was detected among the negative samples. The results showed 100% concordance with the genotypes previously identified. CONCLUSIONS The new assay was able to detect the presence of six different carbapenemase gene types in a single 3 h PCR.

SENTRY antimicrobial surveillance program report: latin american and brazilian results for 1997 through 2001

The alarming emergence and spread of antimicrobial resistance among common bacteria threatens the effectiveness of therapy for many infections. Surveillance of antimicrobial resistance is essential to identify the major problems and guide adequate control measures. Several resistance surveillance programs have been implemented in North America and Europe in the last decade; however, very few programs have assessed antimicrobial resistance in Latin American countries. The SENTRY Antimicrobial Surveillance Program was initiated in 1997 and represents the most comprehensive surveillance program in place at the present time worldwide. The SENTRY Program collects consecutive isolates from clinically documented infections in more than 80 medical centers worldwide (10 in Latin America). The isolates are collected according to the type of infection (objectives) and susceptibility tested in a central microbiology laboratory by reference broth microdilution methods according to NCCLS guidelines. The Program also incorporated molecular typing (ribotyping and PFGE) and resistance mechanism analysis of selected isolates. In this report we present a very broad analysis of the data generated by testing almost 20,000 bacterial isolates against more than 30 antimicrobial agents. The susceptibility results (MIC(50), MIC(90) and % susceptible) are presented in 11 tables according to the organism and site of infection. The data from Brazil, as well as the data from isolates collected in 2001, are analyzed separately. This report allows the evaluation of the activities numerous antimicrobial agents against clinical isolates collected in Latin American countries.

Nosocomial Bloodstream Infections in Brazilian Hospitals: Analysis of 2,563 Cases from a Prospective Nationwide Surveillance Study

ABSTRACT Nosocomial bloodstream infections (nBSIs) are an important cause of morbidity and mortality. Data from a nationwide, concurrent surveillance study, Brazilian SCOPE (Surveillance and Control of Pathogens of Epidemiological Importance), were used to examine the epidemiology and microbiology of nBSIs at 16 Brazilian hospitals. In our study 2,563 patients with nBSIs were included from 12 June 2007 to 31 March 2010. Ninety-five percent of BSIs were monomicrobial. Gram-negative organisms caused 58.5% of these BSIs, Gram-positive organisms caused 35.4%, and fungi caused 6.1%. The most common pathogens (monomicrobial) were Staphylococcus aureus (14.0%), coagulase-negative staphylococci (CoNS) (12.6%), Klebsiella spp. (12.0%), and Acinetobacter spp. (11.4%). The crude mortality was 40.0%. Forty-nine percent of nBSIs occurred in the intensive-care unit (ICU). The most frequent underlying conditions were malignancy, in 622 patients (24.3%). Among the potential factors predisposing patients to BSI, central venous catheters were the most frequent (70.3%). Methicillin resistance was detected in 157 S. aureus isolates (43.7%). Of the Klebsiella sp. isolates, 54.9% were resistant to third-generation cephalosporins. Of the Acinetobacter spp. and Pseudomonas aeruginosa isolates, 55.9% and 36.8%, respectively, were resistant to imipenem. In our multicenter study, we found high crude mortality and a high proportion of nBSIs due to antibiotic-resistant organisms.

Increased resistance to first-line agents among bacterial pathogens isolated from urinary tract infections in Latin America: time for local guidelines?

Emerging resistance phenotypes and antimicrobial resistance rates among pathogens recovered from community-acquired urinary tract infections (CA-UTI) is an increasing problem in specific regions, limiting therapeutic options. As part of the SENTRY Antimicrobial Surveillance Program, a total of 611 isolates were collected in 2003 from patients with CA-UTI presenting at Latin American medical centers. Each strain was tested in a central laboratory using Clinical Laboratory Standard Institute (CLSI) broth microdilution methods with appropriate controls. Escherichia coli was the leading pathogen (66%), followed by Klebsiella spp. (7%), Proteus mirabilis (6.4%), Enterococcus spp. (5.6%), and Pseudomonas aeruginosa (4.6%). Surprisingly high resistance rates were recorded for E. coli against first-line orally administered agents for CA-UTI, such as ampicillin (53.6%), TMP/SMX (40.4%), ciprofloxacin (21.6%), and gatifloxacin (17.1%). Decreased susceptibility rates to TMP/SMX and ciprofloxacin were also documented for Klebsiella spp. (79.1 and 81.4%, respectively), and P. mirabilis (71.8 and 84.6%, respectively). For Enterococcus spp., susceptibility rates to ampicillin, chloramphenicol, ciprofloxacin, and vancomycin were 88.2, 85.3, 55.9, and 97.1%, respectively. High-level resistance to gentamicin was detected in 24% of Enterococcus spp. Bacteria isolated from patients with CA-UTI in Latin America showed limited susceptibility to orally administered antimicrobials, especially for TMP/SMX and fluoroquinolones. Our results highlight the need for developing specific CA-UTI guidelines in geographic regions where elevated resistance to new and old compounds may influence prescribing decisions.

Antimicrobial susceptibility of gram-positive bacteria isolated in brazilian hospitals participating in the SENTRY Program (2005-2008)

We report the antimicrobial susceptibility patterns of the most frequently isolated Gram-positive bacteria in the Brazilian hospitals participating in the SENTRY Antimicrobial Surveillance Program. The strains were consecutively collected (one per patient) between January 2005 and September 2008 and susceptibility tested by reference broth microdilution methods at the JMI Laboratories (North Liberty, Iowa, USA). A total of 3,907 Gram-positive cocci were analyzed. The Gram-positive organisms most frequently isolated from bloodstream infections were Staphylococcus aureus (2,218 strains; 20.2% of total), coagulase-negative staphylococci (CoNS; 812 strains [14.7%]), and Enterococcus spp. (754 strains; 5.0%). S. aureus ranked first (28.1%) and Enterococcus faecalis ranked 7th (4.5%) among cases of skin and soft tissue infections. S. aureus was also the second most frequently isolated pathogen from patients with lower respiratory tract infections (24.9% of cases) after Pseudomonas aeruginosa (30.5%). Resistance to oxacillin was observed in 31.0% of S. aureus and the vast majority of oxacillin-resistant (MRSA) strains were also resistant to clindamycin, ciprofloxacin and levofloxacin. Vancomycin, linezolid and daptomycin were all very active against S. aureus strains tested (>99.9-100.0% susceptible), but daptomycin (MIC(50), 0.25 g/mL and MIC(90), 0.5 g/mL) was four- to eight-fold more potent than vancomycin (MIC(50) and MIC(90) of 1 g/mL) and linezolid (MIC(50), 1 g/mL and MIC(90), 2 g/mL). Vancomycin resistance increased significantly among enterococci during the study period, but it was restrict to only one medical center until 2007 and emerged in a second medical center in 2008. Daptomycin was the most active antimicrobial tested against enterococci in general (100.0% susceptible), followed by linezolid (99.9% susceptible), ampicillin (87.4%) and vancomycin (84.6%). In conclusion, daptomycin and linezolid showed excellent in vitro activity against contemporary Gram-positive organisms (3,907) collected in Brazilian hospitals monitored by the SENTRY Program, including MRSA, vancomycin-resistant enterococci (VRE) and other multi-drug-resistant organisms. Although vancomycin resistance rates in Brazil appears to be relatively low compared to those reported in the USA, VRE has emerged and rapidly disseminated in some Brazilian medical centers.

Epidemiologic typing of multiply drug-resistant Pseudomonas aeruginosa isolated from an outbreak in an intensive care unit

From June to August 1991, there was an outbreak of Pseudomonas aeruginosa infections in an intensive care unit in a general hospital in Sao Paulo, Brazil. We obtained 14 isolates from 14 patients, 11 from tracheal aspirate, and 3 from surgical wound exudates. These strains were typed by serotyping, pyocin typing, and pulsed-field electrophoresis (CHEF) of chromosomal DNA (chrDNA), and the different typing methods were analyzed. These three methods demonstrated seven identical strains. We also performed an extensive antibiogram (33 drugs) in all 14 isolates. The incidence of resistance to aminoglycosides, extended-spectrum beta-lactams, and quinolones was very high among the seven identical isolates; however, the antibiogram profile differed significantly among the isolates. Our results suggest that a unique strain caused several cross-transmitted infections during this period of time, and the emergence of antimicrobial resistance has been occurring before and after the establishment of the epidemic strain by selective drug use. The chrDNA fingerprinting proved to be versatile and precise for epidemiologic investigations of P. aeruginosa infections.

Evaluation of interhospital spread of methicillin-resistant Staphylococcus aureus in Sao Paulo, Brazil, using pulsed-field gel electrophoresis of chromosomal DNA.

To evaluate the interhospital spread of methicillin-resistant Staphylococcus aureus (MRSA) clone in Sao Paulo, we analyzed the restriction fragment length polymorphisms (RFLP) of chromosomal DNA from isolates from nine Sao Paulo hospitals. Restriction digestion of genomic DNA was performed with SmaI and the fragments were separated by pulsed-field gel electrophoresis. Only six different RFLP patterns were demonstrated among 30 MRSA isolates. Isolates possessing an identical RFLP pattern were demonstrated in eight of the nine Sao Paulo hospitals evaluated. Our results documented the widespread dissemination of a single clone of MRSA in several hospitals. Furthermore, the small clonal variability among multidrug-resistant MRSA coupled with the wide spread of this clone could make the intrahospital epidemiological evaluation of RMSA outbreaks very difficult.

Phenotypic and molecular characterization of Salmonella Enteritidis strains isolated in São Paulo, Brazil

In São Paulo State, Brazil, the epidemic increase in isolation of Salmonella Enteritidis has been observed since 1994. A total of 105 S. Enteritidis strains (72 from human and 33 from non-human sources) isolated during the period 1975-1995, previously characterized by phage typing, was analyzed by antimicrobial susceptibility, plasmid profile, and ribotyping. Over 70% of the strains were susceptible to all antimicrobial agents tested, however, multiple resistance to antimicrobials was observed among the studied strains, mainly those from hospitalized patients. Phage type 8 (PT-8) was predominant among the strains isolated during the period of 1975-1992, but in the following years, PT-4 was the most frequent phage type identified. Seven different plasmid profiles were detected and 96% of the isolates harbored a plasmid of approximately 36 MDa. Ribotyping discriminated fourteen ribotypes (R1 to R14) among the strains examined. By analysis of dendrogram the strains were included in three groups with similarity level of 60%. The obtained results indicate that, a single ribotype (R11), determined for PT-4 strains isolated from 1993, characterizes the epidemic clone of S. Enteritidis in our region.

Epidemiology and Microbiologic Characterization of Nosocomial Candidemia from a Brazilian National Surveillance Program.

Candidemia is a growing problem in hospitals all over the world. Despite advances in the medical support of critically ill patients, candidiasis leads to prolonged hospitalization, and has a crude mortality rate around 50%. We conducted a multicenter surveillance study in 16 hospitals distributed across five regions of Brazil to assess the incidence, species distribution, antifungal susceptibility, and risk factors for bloodstream infections due to Candida species. From June 2007 to March 2010, we studied a total of 2,563 nosocomial bloodstream infection (nBSI) episodes. Candida spp. was the 7th most prevalent agent. Most of the patients were male, with a median age of 56 years. A total of 64 patients (46.7%) were in the ICU when candidemia occurred. Malignancies were the most common underlying condition (32%). The crude mortality rate of candidemia during the hospital admission was 72.2%. Non-albicans species of Candida accounted for 65.7% of the 137 yeast isolates. C. albicans (34.3%), Candida parapsilosis (24.1%), Candida tropicalis (15.3%) and Candida glabrata (10.2%) were the most prevalent species. Only 47 out of 137 Candida isolates were sent to the reference laboratory for antifungal susceptibility testing. All C. albicans, C. tropicalis and C. parapsilosis isolates were susceptible to the 5 antifungal drugs tested. Among 11 C. glabrata isolates, 36% were resistant to fluconazole, and 64% SDD. All of them were susceptible to anidulafungin and amphotericin B. We observed that C. glabrata is emerging as a major player among non-albicans Candida spp. and fluconazole resistance was primarily confined to C. glabrata and C. krusei strains. Candida resistance to echinocandins and amphotericin B remains rare in Brazil. Mortality rates remain increasingly higher than that observed in the Northern Hemisphere countries, emphasizing the need for improving local practices of clinical management of candidemia, including early diagnosis, source control and precise antifungal therapy.