Integration of molecular characterization of microorganisms in a global antimicrobial resistance surveillance program

Application of Next-Generation Sequencing for Characterization of Surveillance and Clinical Trial Isolates: Analysis of the Distribution of β-lactamase Resistance Genes and Lineage Background in the United States

Background

Sequencing technologies and techniques have seen remarkable transformation and innovation that have significantly affected sequencing capability. Data analyses have replaced sequencing as the main challenge. This paper provides an overview on applying next-generation sequencing (NGS) and analysis and discusses the benefits and challenges. In addition, this document shows results from using NGS and bioinformatics tools to screen for β-lactamase genes and assess the epidemiological structure of Escherichia coli– and Klebsiella pneumoniae–causing bloodstream (BSIs) and urinary tract (UTIs) infections in patients hospitalized in the United States during the SENTRY Antimicrobial Surveillance Program for 2016.

Methods

A total of 3525 isolates (2751 E. coli and 774 K. pneumoniae) causing BSIs (n = 892) and UTIs (n = 2633) in hospitalized patients in the United States were included. Isolates were tested for susceptibility by broth microdilution, and those that met a minimum inhibitory concentration (MIC)–based screening criteria had their genomes sequenced and analyzed.

Results

A total of 11.6% and 16.1% of E. coli–causing UTIs and BSIs, respectively, met the MIC-based criteria, whereas 11.0% and 13.7% of K. pneumoniae isolates causing UTIs and BSIs, respectively, met the criteria. Among E. coli, bla_CTX-M variants (87.6% overall) prevailed (60.5% of CTX-M group 1 and 26.9% of group 9). A total of 60.3% of K. pneumoniae isolates carried bla_CTX-M variants (52.7% and 7.6% of groups 1 and 9, respectively). Two E. coli (0.6%) and 13 K. pneumoniae (12.9%) isolates harbored bla_KPC. Among KPC-producing K. pneumoniae (2 from BSIs and 11 from UTIs), 84.6% (11/13) were ST258 (CC258). Seventeen and 38 unique clonal complexes (CCs) were noted in E. coli that caused BSIs and UTIs, respectively, and CC131 (or ST131) was the most common CC among BSI (53.6%) and UTI (58.2%) isolates. Twenty-three and 26 CCs were noted among K. pneumoniae–causing BSIs and UTIs, respectively. CC258 (28.3%) prevailed in UTI pathogens, whereas CC307 (15.0%) was the most common CC among BSI isolates.

Conclusions

This study provides a benchmark for the distribution of β-lactamase genes and the population structure information for the most common Enterobacteriaceae species responsible for BSIs and UTIs in US medical centers during the 2016 SENTRY Program.

Antimicrobial Resistance Surveillance and New Drug Development

Surveillance represents an important informational tool for planning actions to monitor emerging antimicrobial resistance. Antimicrobial resistance surveillance (ARS) programs may have many different designs and can be grouped in 2 major categories based on their main objectives: (1) public health ARS programs and (2) industry-sponsored/product-oriented ARS programs. In general, public health ARS programs predominantly focus on health care and infection control, whereas industry ARS programs focus on an investigational or recently approved molecule(s). We reviewed the main characteristics of industry ARS programs and how these programs contribute to new drug development. Industry ARS programs are generally performed to comply with requirements from regulatory agencies responsible for commercial approval of antimicrobial agents, such as the US Food and Drug Administration, European Medicines Agency, and others. In contrast to public health ARS programs, which typically collect health care and diverse clinical data, industry ARS programs frequently collect the pathogens and perform the testing in a central laboratory setting. Global ARS programs with centralized testing play an important role in new antibacterial and antifungal drug development by providing information on the emergence and dissemination of resistant organisms, clones, and resistance determinants. Organisms collected by large ARS programs are extremely valuable to evaluate the potential of new agents and to calibrate susceptibility tests once a drug is approved for clinical use. These programs also can provide early evaluations of spectrum of activity and postmarketing trends required by regulatory agencies, and the programs may help drug companies to select appropriate dosing regimens and the appropriate geographic regions in which to perform clinical trials. Furthermore, these surveillance programs provide useful information on the potency and spectrum of new antimicrobial agents against indications and organisms in which clinicians have little or no experience. In summary, large ARS programs, such as the SENTRY Antimicrobial Surveillance Program, contribute key data for new drug development.

Ceftobiprole activity when tested against contemporary bacteria causing bloodstream infections in the United States (2016-2017)

Ceftobiprole medocaril, the prodrug of ceftobiprole, is an advanced-generation cephalosporin that is approved in many European and non-European countries for the treatment of adults with hospital-acquired pneumonia (excluding ventilator-associated pneumonia) and community-acquired pneumonia and is currently being evaluated in a global phase 3 clinical trial of patients with Staphylococcus aureus bacteremia. This study investigated the in vitro activity of ceftobiprole and comparators against a total of 5466 gram-positive and -negative isolates from bloodstream infections (BSIs) that were collected in the United States during 2016 and 2017 as part of the SENTRY Antimicrobial Surveillance Program. Ceftobiprole was highly active (isolates were >99% susceptible) against S. aureus (including methicillin-resistant S. aureus), coagulase-negative staphylococci, Enterococcus faecalis, streptococci, and non-extended-spectrum β-lactamase (non-ESBL) phenotype Enterobacteriaceae. As expected, lower activities were observed against Enterococcus faecium, ESBL-phenotype Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. These results support further clinical evaluation of ceftobiprole for the treatment of BSIs caused by susceptible organisms.

Molecular characterization of multidrug-resistant Klebsiella pneumoniae isolates

Klebsiella pneumoniae is an important cause of healthcare-associated infections worldwide. Selective pressure, the extensive use of antibiotics, and the conjugational transmission of antibiotic resistance genes across bacterial species and genera facilitate the emergence of multidrug-resistant (MDR) K. pneumoniae. Here, we examined the occurrence, phenotypes and genetic features of MDR K. pneumoniae isolated from patients in intensive care units (ICUs) at the First Affiliated Hospital of Xiamen University in Xiamen, China, from January to December 2011. Thirty-eight MDR K. pneumoniae strains were collected. These MDR K. pneumoniae isolates possessed at least seven antibiotic resistance determinants, which contribute to the high-level resistance of these bacteria to aminoglycosides, macrolides, quinolones and β-lactams. Among these isolates, 24 strains were extended-spectrum β-lactamase (ESBL) producers, 2 strains were AmpC producers, and 12 strains were both ESBL and AmpC producers. The 38 MDR isolates also contained class I (28/38) and class II integrons (10/38). All 28 class I-positive isolates contained aacC1, aacC4, orfX, orfX' and aadA1 genes. β-lactam resistance was conferred through bla SHV (22/38), bla TEM (10/38), and bla CTX-M (7/38). The highly conserved bla KPC-2 (37/38) and bla OXA-23(1/38) alleles were responsible for carbapenem resistance, and a gyrAsite mutation (27/38) and the plasmid-mediated qnrB gene (13/38) were responsible for quinolone resistance. Repetitive-sequence-based PCR (REP-PCR) fingerprinting of these MDR strains revealed the presence of five groups and sixteen patterns. The MDR strains from unrelated groups showed different drug resistance patterns; however, some homologous strains also showed different drug resistance profiles. Therefore, REP-PCR-based analyses can provide information to evaluate the epidemic status of nosocomial infection caused by MDR K. pneumoniae; however, this test lacks the power to discriminate some isolates. Thus, we propose that both genotyping and REP-PCR typing should be used to distinguish genetic groups beyond the species level.

Evaluation of Three Molecular Typing Techniques for Nonfermentative Gram-Negative Bacilli

Objective:

To evaluate three different DNA techniques for typing nonfermentative gram-negative bacilli isolated from Latin American hospitals.

Design:

One hundred twenty-six nonfermentative gram-negative bacilli were typed.

Participants:

Pseudomonas aeruginosa(n = 64) andAcinetobacter baumannii(n = 42) samples were obtained from blood cultures of patients admitted to 10 medical centers in Latin America during 1998 andStenotrophomonas maltophilia(n = 20) samples were obtained from patients admitted to the Hospital São Paulo between 1999 and 2001.

Methods:

All samples were typed using automated ribotyping, PFGE, and ERIC-PCR. The discriminatory power for each technique was calculated using Hunter's generalized formula.

Results:

All strains could be typed by automated ribotyping and ERIC-PCR, but two strains (1.6%) were not typeable by PFGE. All three techniques showed 100% reproducibility. The time to obtain the results was shorter for automated ribotyping and ERIC-PCR compared with PFGE. Likewise, the costs for ERIC-PCR and PFGE were lower than those for automated ribotyping. The interpretation of results was more complicated and more difficult with ERIC-PCR than with both PFGE and automated ribotyping. All techniques presented excellent discriminatory power forP. aeruginosa(0.98). PFGE presented the highest discriminatory power (0.94) forA. baumannii,and both PFGE and ERIC-PCR showed higher discriminatory power (0.90 for both) than automated ribotyping (0.82) for S.maltophilia.

Conclusions:

PFGE showed the highest discriminatory power for typing these nonfermentative gram-negative bacilli. However, automated ribotyping and ERIC-PCR can provide results in a shorter time period with similar discriminatory power.

Presence of fimH, mrkD, and irp2 virulence genes in KPC-2-producing Klebsiella pneumoniae isolates in Recife-PE, Brazil

Klebsiella pneumoniae strains can produce different virulence factors, such as fimbrial adhesins and siderophores, which are important in the colonization and development of the infection. The aims of this study were to determine the occurrence of fimH, mrkD, and irp2 virulence genes in 22 KPC-2-producing K. pneumoniae isolates as well as 22 not producing-KPC isolates, from patients from different hospitals in Recife-PE, Brazil, and also to analyze the clonal relationship of the isolates by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The genes were detected by PCR and DNA sequencing. The bla KPC-2 gene was identified in 22 KPC-positive isolates. On analyzing the antimicrobial susceptibility profile of the isolates, it was detected that polymyxin and amikacin were the antimicrobials of best activity against K. pneumoniae. On the other hand, five isolates exhibited resistance to polymyxin. In the KPC-positive group, was observed a high rate of resistance to cephalosporins, followed by carbapenems. Molecular typing by ERIC-PCR detected 38 genetic profiles, demonstrating a multiclonal spread of the isolates analyzed. It was observed that the virulence genes irp2, mrkD, and fimH were seen to have together a higher frequency in the KPC-positive group. The accumulation of virulence genes of KPC-positive K. pneumoniae isolates, observed in this study, along with the multi-resistance impose significant therapeutic limitations on the treatment of infections caused by K. pneumoniae.

Unexpected Multidrug Resistance of Methicillin-Resistant Staphylococcus aureus in Urine Samples: A Single-Center Study

PURPOSE

Infections of methicillin-resistant Staphylococcus aureus (MRSA) are becoming an increasingly concerning clinical problem. The aim of this study was to assess the development of MRSA in urine cultures in a major public university-affiliated hospital and the therapeutical and hygiene-related possibilities for reducing resistance.

MATERIALS AND METHODS

This study included 243 samples from patients diagnosed with MRSA infection over a period of 6 years. An agar diffusion test measured the effects of antimicrobial agents against bacteria grown in culture. The analyses were based on the guidelines of the Clinical and Laboratory Standards Institute.

RESULTS

A regression analysis was performed, which showed 100% resistance to the following antibiotics throughout the entire testing period: carbapenem, cephalosporin (1st-4th generation), penicillin G, aminopenicillin, β-lactamase, and isoxazolyl penicillin. However, a significant decrease in resistance was found for amikacin, gentamicin, clindamycin, levofloxacin, erythromycin, and mupirocin.

CONCLUSIONS

MRSA showed a decreasing trend of antimicrobial resistance, except against carbapenem, cephalosporin (1st-4th generation), penicillin G, aminopenicillin, β-lactamase, and isoxazolyl penicillin, for which complete resistance was observed.

The fluoroquinolones: How long will their utility last?

Injudicious use of the fluoroquinolones may result in treatment failure, increased patient morbidity, increased health care cost, and possible patient fatality. Fluoroquinolone-resistant bacteria may also adversely impact the microbiological environment in the hospital, the local community and eventually large geographical regions. Fluoroquinolone resistance develops in a stepwise fashion, and current susceptibility testing methods and recommended MIC susceptible breakpoint values for the United States may fail to identify some bacteria that are resistant due to first step mutations at the fluoroquinolone target site gene sequences. C-8 methoxy- fluoroquinolone compounds are more active against resistant bacteria than the older compounds. Fluoroquinolone resistance relates directly to human and veterinary usage and emerging bacterial resistance poses the single greatest threat to the future survival of the fluoroquinolone drugs as an antibiotic class.

Microbiological and epidemiological characterization of imipenem-resistant Pseudomonas aeruginosa strains from a Brazilian tertiary hospital: report from the SENTRY Antimicrobial Surveillance Program

OBJECTIVES

To evaluate the antimicrobial susceptibility profile, the genetic similarity, and the mechanisms of carbapenem resistance among imipenem-resistant Pseudomonas aeruginosa isolates collected from a Brazilian tertiary teaching hospital.

METHODS

Seventy-eight consecutive samples of P. aeruginosa were evaluated during 2000 and 2001. The antimicrobial susceptibility was evaluated by reference broth microdilution methods and the imipenem-resistant isolates were screened for metallo-beta-lactamase (MbetaL) production throughout disc approximation test and MbetaL Etest strips and isolates with positive screen test result were submitted to PCR assays using primers blaIMP-1, bla VIM-1, blaVIM-2 e blaSPM-1. The genetic similarity of MbetaL-producing strains was evaluated by automated ribotyping for epidemiological typing purpose.

RESULTS

Resistance rates were high to the majority of antimicrobial agents tested except polymyxin B, which inhibited all samples at the Clinical and Laboratory Standards Institute breakpoint (< or = 2 microg/ml). Twenty-nine (37.2%) isolates were resistant to imipenem and these isolates showed great genomic variability. MbetaL production was demonstrated in two imipenem-resistant isolates, which were detected using blaSPM-1 and blaIMP-2-specific primers. Sequence analysis revealed the presence of blaSPM-1 and a novel blaIMP-type gene, blaIMP-16.

CONCLUSION

The results of this study showed high resistance rates to the majority of antimicrobial agents among P. aeruginosa samples. High imipenem resistance rates were probably due to continuous selection of resistant mutants. The production of MbetaL did not represent a frequent mechanism of carbapenem resistance in this medical center; but a novel MbetaL was identified. Continued antimicrobial surveillance and infection control measures should be emphasized to minimize the emergence and dissemination of antimicrobial resistance.

The molecular epidemiology of Stenotrophomonas maltophilia bacteraemia in a tertiary referral hospital in the United Arab Emirates 2000-2004

Background

Stenotrophomonas maltophilia is recognised as an important cause of nosocomial infection, especially in immunocompromised patients, resulting in significant morbidity and mortality. The treatment of S. maltophilia infection presents a therapeutic challenge. The precise modes of transmission of S. maltophilia in the hospital environment are not known and such knowledge is essential to target interventions to prevent spread. There are few published data on the patterns of nosocomial infection in the United Arab Emirates (UAE). A recent study showed that S. maltophilia is an established cause of bloodstream infection in Tawam Hospital in the UAE. Little is known about its epidemiology in the hospital.

Methods

We describe the clinical characteristics of 25 episodes of S. maltophilia bacteraemia which occurred from 2000–2004. The strains were characterised using pulsed field gel electrophoresis (PFGE).

Results

All episodes were hospital-acquired and malignancy and central venous catheters were predisposing factors. Catheter-associated infection comprised 88% infection. Catheter removal was important for the successful management of catheter-associated infection. The results of PFGE suggested that there were as many strains as patients. S. maltophilia strains isolated from the same patient had indistinguishable PFGE profiles.

Conclusion

PFGE is a valid and reproducible typing method for S. maltophilia. The precise sources and modes of spread of S. maltophilia in the hospital are still not known. Knowledge that person to person transmission was not a major mode of transmission enabled infection control interventions for S. maltophilia to be targeted more effectively.

Microbiologic characterization of isolates from a dalbavancin clinical trial for catheter-related bloodstream infections

Dalbavancin, a new-generation semisynthetic lipoglycopeptide in phase 3 clinical development, has been documented to be more active than vancomycin or teicoplanin against Gram-positive bacteria, including multidrug-resistant strains, by in vitro testing and in animal models. The human pharmacokinetics of dalbavancin predicts efficacy at weekly dosing intervals. In a phase 2 open-label clinical trial, dalbavancin exhibited superiority when compared with vancomycin against catheter-related bloodstream infection (CR-BSI). The majority of pathogens identified in this study as in clinical practice were coagulase-negative staphylococci (CoNS), necessitating rigorous characterization of duplicate isolates to rule out contaminants and to validate cases for study evaluations. At follow-up for the intent-to-treat population, overall pathogen eradication was 92.3% for dalbavancin and 75.9% for vancomycin. We describe the details of organisms isolated, their epidemiologic/genetic characterization, susceptibility patterns against glycopeptides, and the eradication rates by organism group. In conclusion, dalbavancin was active against all isolated pathogens associated with CR-BSI (CoNS, Staphylococcus aureus and Enterococcus faecalis; all MIC results, < or = 0.25 microg/mL) and achieved significant (P < 0.05) clinical success when compared with vancomycin.

Emerging Metallo‐β‐Lactamase–Mediated Resistances: A Summary Report from the Worldwide SENTRY Antimicrobial Surveillance Program

The rates of occurrence of metallo-beta-lactamase-mediated resistances in Pseudomonas aeruginosa, Acinetobacter species, and Serratia marcescens, among other gram-negative bacilli, have escalated since 2000, severely limiting treatment options in Asia, Europe, and Latin America to non-beta-lactam antimicrobial classes. Clinical isolates harboring metallo-beta-lactamases have also recently been reported in western Canada and in Texas, signaling the need for development of accurate diagnostic tests by clinical laboratories to detect their presence and for new, and more potent, antimicrobial agents.

Dissemination and diversity of metallo-β-lactamases in Latin America: report from the SENTRY Antimicrobial Surveillance Program

Carbapenem resistance among Pseudomonas aeruginosa and Acinetobacter spp. is becoming a critical therapeutic problem worldwide. The SENTRY Antimicrobial Surveillance Program monitors pathogen frequency and antimicrobial resistance patterns of nosocomial and community-acquired infections through sentinel hospitals on five continents. Pseudomonas spp. and Acinetobacter spp. strains resistant to imipenem (MIC, >/=16 mg/l), meropenem (MIC, >/=16 mg/l), and ceftazidime (MIC, >/=32 mg/l) collected from January 2001 to December 2003 were routinely screened for antimicrobial resistance genes. Resistant isolates were initially tested for metallo-beta-lactamase (MbetaL) production by phenotypic tests (disk approximation or MbetaL Etest strip) and then characterization of the MbetaL (hydrolysis assays, PCR for bla(IMP), bla(VIM), bla(SPM), gene sequencing). Eighty-nine isolates (33 Acinetobacter spp., 54 Pseudomonas aeruginosa, and 2 P. fluorescens) had positive phenotypic screening tests. Among those, 34 isolates producing MbetaL were identified, including 7 Acinetobacter spp., 25 P. aeruginosa and 2 P. fluorescens. The MbetaLs identified were IMP-1, VIM-2 and two newly described enzymes: SPM-1 and IMP-16. The greatest concentration of MbetaL strains was in Brazil, where imipenem-resistant P. aeruginosa increased significantly in the time period evaluated by the SENTRY Program. MbetaL-producing P. aeruginosa was detected in São Paulo (SPM-1) and Brasilia (SPM-1 and IMP-16), Brazil and Caracas, Venezuela (VIM-2); while MbetaL-producing Acinetobacter spp. isolates were detected in São Paulo, Brazil (IMP-1). P. fluorescens isolates producing IMP-1 and VIM-2 were detected in São Paulo, Brazil and Santiago, Chile, respectively. The emergence and dissemination of mobile MbetaL-producing isolates represent an alarming factor for increasing resistance to carbapenems in several medical centres evaluated by the SENTRY Program in Latin America.

Molecular diversity and characterization of tetracycline-resistant Staphylococcus aureus isolates from a poultry processing plant

DNA fingerprinting and molecular characterization showed that the tetracycline-resistant Staphylococcus aureus population of a South African poultry processing plant comprised one or possibly several tet(K)-containing endemic clones that contaminated chicken and machinery surfaces at all sampled processing stages. The tet(K) gene was transferable by filter mating to S. aureus recipient 80CR5 and was located on a pT181-like plasmid.

Occurrence and antimicrobial resistance pattern comparisons among bloodstream infection isolates from the SENTRY Antimicrobial Surveillance Program (1997-2002)

The empiric treatment of patients with bloodstream infections (BSI) has become more complicated in an era of increasing antimicrobial resistance. The SENTRY Antimicrobial Surveillance Program has monitored BSI from patients in medical centers worldwide since 1997. During 1997-2002, a total of 81,213 BSI pathogens from North America, Latin America, and Europe were tested for antimicrobial susceptibility. S. aureus, E. coli, and coagulase-negative staphylococci were the three most common BSI pathogens in all three regions each year. Prevalence variability was noted in regions for some species, including higher rates of isolation of E. coli in Europe, Enterococcus spp. in North America, and Gram-negative enteric and nonenteric species in Latin America. Patient age analysis showed the most common BSI pathogen among neonates was coagulase-negative staphylococci and among elderly patients, E. coli. Resistance among BSI pathogens was much more prevalent in nosocomial infections and in patients in intensive care units (ICUs); age differences were also noted. Geographically, oxacillin-resistant S. aureus (39.1%, 2002) and vancomycin-resistant enterococci (17.7%, 2002) were highest in North America, and extended-spectrum beta-lactamase-producing Klebsiella spp. (35.8-46.7%) and multidrug-resistant P. aeruginosa (18.7%, 2002) were highest in Latin America. Activity of commonly used antimicrobial agents remained relatively stable in North America, except in the case of vancomycin-resistant enterococci (20% decline between 1997 and 2002). An epidemiologic investigation of oxacillin-resistant S. aureus in North America identified 10 significant clones (ribotypes) and the common resistance patterns associated with them. Surveillance of BSI pathogens is needed to determine trends of resistance and provide useful information regarding patient risk factors and geographic differences.

An international multicenter study of antimicrobial resistance and typing of hospital Staphylococcus aureus isolates from 21 laboratories in 19 countries or states

During 1996, 4065 consecutive Staphylococcus aureus strains from different patients were collected in 21 worldwide hospital laboratories. The strains, their resistance pattern, and hospital demographic data were forwarded to Statens Serum Institut where the strains were typed and data analyzed. Resistance patterns varied by region and resistance to other antibiotics than methicillin were mainly related to the occurrence of methicillin resistance, except for mupirocin, rifampicin, and fusidic acid. Methicillin-resistant S. aureus (MRSA) occurred with low levels in hospitals in Northern Europe (<1%), increasing levels in middle-European countries, United States, New Zealand, and Australia (6-22%), and very high levels in Southern European countries as well as in parts of the United States, Asia, and South Africa (28-63%). MRSA found in large hospitals were more resistant to other antibiotics than MRSA found in smaller hospitals serviced by the same laboratory. No difference in resistance levels was seen for methicillin-susceptible S. aureus (MSSA) isolated in large or small hospitals. Intensive Care Units had the highest level of MRSA. Strains from the lower respiratory tract showed the highest resistance levels and blood isolates the lowest. A dominating MRSA clone was found in hospitals with an MRSA frequency of more than 10%. Pulsed-field gel electrophoresis (PFGE) typing recognized several of these clones as international epidemic MRSA (E-MRSA). All MSSA isolates were phage typed (typeability 85.4%) and divided in seven major phage patterns. Isolates of all patterns were found in all hospitals except one, indicating that the MSSA seldom represented the spread of clones within the hospital. The comparison should evaluate the prevalence of community-acquired MRSA and identify internationally E-MRSA. The present study gives a snapshot of the MRSA situation, but it is important to build up a continuous national and international surveillance, because MRSA is a global socioeconomic problem. Global infection control procedures, including rational antibiotic use, should be agreed on. The accompanying paper will address the issue of antibiotic consumption and MRSA.

Molecular epidemiology of selected multidrug-resistant bacteria: A global report from the SENTRY Antimicrobial Surveillance Program

The SENTRY Antimicrobial Surveillance Program was initiated in 1997 as a global network for the longitudinal tracking of antimicrobial resistance and has incorporated a molecular typing protocol to detect and monitor emerging resistances in participant medical centers. Isolates with similar resistance profiles and patient demographics that were temporally related or those exhibiting emerging resistance phenotypes were routinely compared. Isolates were initially analyzed using the automated Riboprinter Microbial Characterization System (Qualicon, Inc., Wilmington, DE). Isolates with identical ribotype patterns were further characterized by pulsed field gel electrophoresis. During 2001, a total of 647 bacterial isolates were processed using this typing protocol; 36% were Staphylococcus aureus with multidrug-resistant, mupirocin- or quinupristin/dalfopristin-resistant phenotypes. Five ribotypes were predominant in this species with some occurring on more than one continent (184.5), whereas others were restricted to a single geographic region (893.2). Among S. aureus, 51 clusters demonstrating dissemination among patients were identified (31 medical centers). Twenty-three outbreaks/clusters were found among Enterobacteriaceae producing either extended-spectrum beta-lactamases or demonstrating resistance to fluoroquinolones. Carbapenem-resistant Pseudomonas aeruginosa and Acinetobacter spp. strains were also analyzed, some of which produced metallo-beta-lactamase enzymes. Clusters of carbapenem-resistant Acinetobacter were identified in Argentina and Israel, whereas metallo-beta-lactamase-producing P. aeruginosa epidemic strains were observed in Italy (three sites) and Brazil. The coupling of molecular epidemiologic investigations with global surveillance such as the SENTRY program adds significant value to participating medical centers and has proven to be effective in tracking changing trends and distribution of resistance genotypes both locally and globally.

Antimicrobial-resistance and enterotoxin-encoding genes among staphylococci isolated from expressed human breast milk

Resistance traits and the presence of enterotoxin-encoding genes were investigated in staphylococcus isolates obtained from expressed human breast milk. A total of 54 staphylococcal isolates identified as Staphylococcus epidermidis (53.6 %), Staphylococcus warneri (20.4 %), Staphylococcus haemolyticus (13 %) and Staphylococcus aureus (13 %) were investigated. By using a disc-diffusion method, higher rates of resistance, including intermediate resistance, were observed for penicillin (87 %) and erythromycin (59.3 %). All strains were susceptible to clindamycin and vancomycin. Minimal inhibitory concentration (MIC) was determined by a macrodilution method for four clinically relevant antimicrobial drugs. High rates of resistance or intermediate resistance were observed for erythromycin, gentamicin and oxacillin. Additionally, three isolates showed reduced susceptibility to vancomycin (MIC, 8 microg ml(-1)). Genetic determinants of resistance were detected by using PCR and the results showed good correlation with the macrodilution tests. Moreover, in four staphylococcus isolates, the presence of enterotoxin-encoding genes (seg, seh and sea) was identified. The results demonstrated that expressed human breast milk can be a reservoir of multiresistant staphylococci that may also harbour important virulent determinants.

Typing and Molecular Characterization ofStreptococcus pneumoniaewith Reduced Susceptibility to Cefotaxime Isolated in Latin America

The treatment of systemic infections, especially meningitis, caused by Streptococcus pneumoniae nonsusceptible to third-generation cephalosporins, is extremely difficult due to the paucity of therapeutic options. The main objective of this study was to characterize isolates of S. pneumoniae with reduced susceptibility to cefotaxime (MICs, > or = 1 microg/ml) by different typing methods and to evaluate whether clonal dissemination of this pathogen had occurred among Latin American medical centers. A total of 46 isolates collected from respiratory tract specimens, blood cultures, cerebrospinal fluid, eye, and other sources were analyzed. The isolates were collected from Latin American medical centers located in Argentina, Brazil, Chile, Colombia, Mexico, and Uruguay through two multicenter surveillance programs, in 1997 and 1998. Isolates were serotyped and molecular typed by pulsed-field gel electrophoresis (PFGE) and automated ribotyping. Antimicrobial susceptibilities were determined to 19 drugs by reference broth microdilution methods. Ten isolates (21.7%) had cefotaxime MICs > or = 2 microg/ml, whereas 36 (78.3%) had cefotaxime MIC results at 1 microg/ml. All isolates were susceptible to gatifloxacin, levofloxacin, and vancomycin. The isolates were distributed among five major serotypes (%): 23F (39.1%), 14 (32.6%), 19F (23.9%), 9V (2.2%), and 6B (2.2%). However, distinct molecular patterns were detected among isolates with a unique serotype. Six and four PFGE patterns were identified among isolates with serotype 23F and 19F, respectively. When PFGE and automated ribotyping analyses were combined, four clusters were identified. The largest cluster (10 isolates) was represented by isolates with ribotype 18-2, major PFGE pattern I, and serotype 14. ATCC 700671 (international clone Spain 9V-3) also showed ribotype 18-2. This clone was detected in four countries: Argentina, Brazil, Chile, and Uruguay. A second cluster (8 isolates) were characterized by isolates with ribotype 17-4, PFGE type D, and serotype 23F, similar to ATCC 700669 (international clone Spain23F-1). Isolates from this cluster were identified in three countries: Brazil, Chile, and Mexico. Our results indicated that clonal dissemination of S. pneumoniae with reduced susceptibility to cefotaxime has occurred in Latin America mainly among serogroups 14, 19F, and 23F.

Moving from recommendation to implementation and audit: part 2. Review of interventions and audit

There are multiple interventions available that may help to control the development and spread of resistance to antimicrobial agents in bacteria implicated in community-acquired respiratory tract infections. Unfortunately, very few studies have assessed the effectiveness of these interventions using objective end-points, such as reduction in resistance rates and improvement in clinical outcomes. Most interventions are centered on reducing inappropriate or unnecessary use of antibiotics; others focus on reducing disease burden and bacterial colonization. With regard to antibiotic use, efforts should be concentrated at both the prescriber and consumer levels. Interventions that target prescribers include: provision of educational materials; strategies and tools to improve diagnosis; implementation of practice guidelines; personalized interactive sessions with feedback on the practice profile; and use of delayed prescription and alternative prescribing strategies. Optimal results are usually obtained when these interventions are combined with consumer education. Regulatory interventions (e.g. licensing regulations and controlled access to drugs), restrictions in the use of agents for growth promotion in animals, and use of nonantimicrobial therapies (e.g. probiotics) may help further to reduce inappropriate antibiotic use and thereby decrease the selective pressure for development of resistance. Infection-control strategies, public health measures, vaccination programs, and new antibiotics all have a role in minimizing the spread of resistant organisms. Ideally, resistance-control programs should include predefined criteria for success and integral audit processes based on objective end-points (antibiotic use, resistance trends, and health outcomes). Standardization of data collection is imperative so that the relative merits of various interventions can be compared. Effective implementation and audit of interventions is often difficult in developing countries owing to poor health-care infrastructures, lack of resources, poor education/training, and minimal regulatory controls on the supply and quality of antimicrobials. Substantial support from governments and health-care organizations across the globe is required to initiate and sustain effective intervention programs to control antimicrobial resistance.

Widespread use of fluoroquinolones versus emerging resistance in pneumococci

During the past decade, respiratory-tract pathogens have shown an increase in resistance to all classes of antimicrobial agents. Although the increasing prevalence of penicillin-resistant Streptococcus pneumoniae has resulted in an increased reliance on newer classes of agents, such as the fluoroquinolones, the broad use of these agents has contributed to increasing prevalence of strains with in vitro fluoroquinolone resistance, which are associated with treatment failures, nosocomial outbreaks, and patient fatalities. Strategies to limit this emerging dilemma and preserve the clinical utility of these agents are needed.

Molecular detection and genotyping of pathogens: more accurate and rapid answers

Rapid molecular methods have enhanced the capabilities of laboratories to identify and characterize microbial pathogens in greater detail. Nucleic acid amplification strategies and advances in amplicon detection have been key aspects in the progress of molecular microbiology. Sophisticated new amplification-detection combinations are resulting in many applications in laboratory testing for infectious diseases. These applications include qualitative detection, sub-species-level DNA fingerprinting, molecular resistance testing and genotyping, and quantitative (viral load) testing. When applied selectively in the laboratory, these applications can enhance diagnostic approaches and clinical management and will probably evolve into standard laboratory and point-of-care testing protocols.

Prevalence of single mutations in topoisomerase type II genes among levofloxacin-susceptible clinical strains of Streptococcus pneumoniae isolated in the United States in 1992 to 1996 and 1999 to 2000

Levofloxacin resistance in Streptococcus pneumoniae is rare, requiring at least two mutations in the quinolone resistance-determining region (QRDR) of topoisomerase IV and DNA gyrase. The prevalence of single QRDR mutations in these genes is unknown. Of 9,438 levofloxacin-susceptible pneumococci from the TRUST 4 surveillance study (1999-2000), 528 strains (MICs of 0.5 to 2.0 microg/ml) were selected for analysis. For comparison, 214 levofloxacin-susceptible strains (MICs of 0.5 to 1 microg/ml) isolated between 1992 and 1996 were analyzed. Oligonucleotide probe assay and DNA sequencing were used to detect QRDR mutations leading to changes at Ser79 and Asp83 in ParC, Ser81 in GyrA, and Asp435 in ParE, the most frequently found substitutions among levofloxacin-resistant strains. Among the 1992 to 1996 isolates only one strain (levofloxacin MIC, 1 microg/ml) had a mutation (Ser79 to Phe in ParC). No single mutations were found among 270 TRUST 4 strains with levofloxacin MICs of 0.5 microg/ml. Among 244 strains for which levofloxacin MICs were 1 microg/ml, 15 strains (6.1%) had a parC mutation and 3 strains (1.2%) had a parE mutation. Of 14 strains for which levofloxacin MICs were 2 microg/ml, 10 strains (71%) had a parC mutation; no parE mutations were found. No gyrA mutations were detected. It was estimated that 4.5% of the 9,438 levofloxacin-susceptible TRUST 4 isolates (MICs, < or =0.06 to 2 microg/ml) had a single parC or parE QRDR mutation. Although there has been an increase in the prevalence of single-step mutants, the increase may have been overestimated due in part to differences in geographical distribution for the two sets of isolates.

Antimicrobial resistance trends in medical centers using carbapenems: report of 1999 and 2000 results from the MYSTIC program (USA)

Trends in susceptibility to antimicrobials were assessed from United States participants using 4488 isolates in the MYSTIC Program, 1999 (10 centers) through 2000 (15 centers). Diverse types of hospitals (general service, university, cancer, federal, pediatric, cystic fibrosis) were enrolled from 13 states. In 2000, oxacillin-susceptible staphylococci were 100% susceptible to meropenem, imipenem, and cefepime; but only 88% of strains were susceptible to ceftazidime. Among Enterobacteriaceae, > or = 96% of Enterobacter spp., Citrobacter spp., and Serratia spp. were susceptible to meropenem, imipenem, and cefepime; but ceftazidime, ceftriaxone, and piperacillin/tazobactam had 5-20% resistance rates. Extended-spectrum beta-lactamase resistance rates in Klebsiella spp. and Escherichia coli (6-7% and 3-5%, respectively) were stable over 2 years. Acinetobacter spp. were 78-81% susceptible to carbapenems but only 63-72% susceptible to ciprofloxacin. Meropenem, tobramycin, and piperacillin/tazobactam were the most active against Pseudomonas aeruginosa, but ciprofloxacin inhibited only 74% in 2000. Overall, meropenem remained the most potent agent, especially against ceftazidime- or piperacillin/tazobactam-resistant strains.