Ability of laboratories to detect emerging antimicrobial resistance in nosocomial pathogens: a survey of project ICARE laboratories

Evolutionary druggability for low-dimensional fitness landscapes toward new metrics for antimicrobial applications

The term 'druggability' describes the molecular properties of drugs or targets in pharmacological interventions and is commonly used in work involving drug development for clinical applications. There are no current analogues for this notion that quantify the drug-target interaction with respect to a given target variant's sensitivity across a breadth of drugs in a panel, or a given drug's range of effectiveness across alleles of a target protein. Using data from low-dimensional empirical fitness landscapes composed of 16 β-lactamase alleles and 7 β-lactam drugs, we introduce two metrics that capture (i) the average susceptibility of an allelic variant of a drug target to any available drug in a given panel ('variant vulnerability'), and (ii) the average applicability of a drug (or mixture) across allelic variants of a drug target ('drug applicability'). Finally, we (iii) disentangle the quality and magnitude of interactions between loci in the drug target and the seven drug environments in terms of their mutation by mutation by environment (G x G x E) interactions, offering mechanistic insight into the variant variability and drug applicability metrics. Summarizing, we propose that our framework can be applied to other datasets and pathogen-drug systems to understand which pathogen variants in a clinical setting are the most concerning (low variant vulnerability), and which drugs in a panel are most likely to be effective in an infection defined by standing genetic variation in the pathogen drug target (high drug applicability).

Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications

The term "druggability" describes the molecular properties of drugs or targets in pharmacological interventions and is commonly used in work involving drug development for clinical applications. There are no current analogues for this notion that quantify the drug-target interaction with respect to a given target variant's sensitivity across a breadth of drugs in a panel, or a given drug's range of effectiveness across alleles of a target protein. Using data from low-dimensional empirical fitness landscapes composed of 16 β-lactamase alleles and seven β-lactam drugs, we introduce two metrics that capture (i) the average susceptibility of an allelic variant of a drug target to any available drug in a given panel ("variant vulnerability"), and (ii) the average applicability of a drug (or mixture) across allelic variants of a drug target ("drug applicability"). Finally, we (iii) disentangle the quality and magnitude of interactions between loci in the drug target and the seven drug environments in terms of their mutation by mutation by environment (G × G × E) interactions, offering mechanistic insight into the variant variability and drug applicability metrics. Summarizing, we propose that our framework can be applied to other datasets and pathogen-drug systems to understand which pathogen variants in a clinical setting are the most concerning (low variant vulnerability), and which drugs in a panel are most likely to be effective in an infection defined by standing genetic variation in the pathogen drug target (high drug applicability).

Computational and data mining studies to understand the distribution and dynamics of Temoneria (TEM) β-lactamase and their interaction with β-lactam and β-lactamase inhibitors

β-lactams are large group of antibiotics widely used to suppress the bacterial growth by inhibiting cell wall synthesis. Bacterial resistance against β-lactam antibiotics is primarily mediated through the production of Temoneria (TEM) β-lactamase (BLs), with almost 474 variants identified in Lactamase Engineering Database (LacED). The present study aims to develop a model to track the evolution of TEM BLs and their interactions with β-lactam and BLs inhibitors through data mining and computational approaches. Further, the model will be used to predict the effective combinations of β-lactam and BLs inhibitors to treat the bacterial infection harbouring emerging variants of β-lactamase. The molecular docking study results demonstrated that most TEM mutants recorded the least binding energy to penicillin and cephalosporin (I/II/III/IV/V generations) class of antibiotics. On the contrary, the same mutants recorded higher binding energy to carbapenem and Monobactam class of antibiotics. Among the BLs inhibitors, tazobactam recorded the least binding energy against most of the TEM mutants, indicating that it can lower the catalytic activity of TEM BLs, thereby potentiating antibiotic action. Similarly, data mining work has assisted us in creating a database of TEM mutants that has comprehensive data on mutations, bacterial diversity, Km, MIC, and IRT types. It has been noted that earlier released antibiotics like amoxicillin and ampicillin had lower Km and higher MIC values, which indicates the prevalence of bacterial resistance. By analysing the differential binding energy (ΔBE) of the selected TEM mutants against β-lactam and BLs inhibitors, the most effective combination of β-lactam (carbapenem and monobactam class of antibiotics) and BLs inhibitors (tazobactam) was identified, to cure bacterial diseases/infections and to prevent similar antibiotic resistance outbreaks. Therefore, our study opens a new avenue in developing strategies to manage antibiotic resistance in bacteria.

Prevalence of CTX-M β-Lactamases Producing Multidrug Resistant Escherichia coli and Klebsiella pneumoniae among Patients Attending Bir Hospital, Nepal

The emergence of multidrug resistant (MDR) bacteria which is attributable to extended spectrum β-lactamases (ESBLs) production of CTX-M types is an obvious problem worldwide. This study is aimed at determining the prevalence of CTX-M β-lactamases producing multidrug resistant Escherichia coli and Klebsiella pneumoniae among patients attending Bir Hospital. A cross-sectional study was conducted between April and September 2019 at Bir Hospital, Kathmandu, and Department of Microbiology, National College, Kathmandu, Nepal. A total of 5,690 different clinical specimens were subjected to cultural, microscopic, and biochemical analyses for the identification of the isolates. Antimicrobial susceptibility testing of the isolates was done, and MDR isolates were selected and processed for further ESBL confirmation by the combination disks method. All confirmed ESBL isolates were screened for CTX-M type β-lactamases (bla _CTX-M) by PCR. Of the total 345 isolates (227 Escherichia coli and 118 Klebsiella pneumoniae), 232 were MDR. All 232 (67.24%) MDR isolates were suspected as ESBL producers on the screening test. However, on the phenotypic test, 135 (58.18%) of total MDR bacteria were confirmed as ESBL producers with the highest proportion in K. pneumoniae (59.37%). The major source of ESBL producers was urine. ESBL producing isolates were mostly identified from outpatients and patients belonging to age group 41-60. Gentamicin was found to be effective against ESBL producers. The prevalence of bla _CTX-M was (89.62%) with the highest frequency for E. coli (93.81%). High prevalence of ESBL of CTX-M types among MDR E. coli and K. pneumoniae was detected from clinical specimens of patients in Bir Hospital. This study warrants the need for the judicious use of antibiotics as well as emphasize the use of modern diagnostic tools for the early detection of MDR and ESBL producers to curb the emergence and spread of MDR and ESBL producing bacteria in the clinical settings of Nepal.

Antimicrobial resistance genes are enriched in aerosols near impacted urban surface waters in La Paz, Bolivia

Antibiotic resistance poses a major global health threat. Understanding emergence and dissemination of antibiotic resistance in environmental media is critical to the design of control strategies. Because antibiotic resistance genes (ARGs) may be aerosolized from contaminated point sources and disseminated more widely in localized environments, we assessed ARGs in aerosols in urban La Paz, Bolivia, where wastewater flows in engineered surface water channels through the densely populated urban core. We quantified key ARGs and a mobile integron (MI) via ddPCR and E. coli spp. as a fecal indicator by culture over two years during both the rainy and dry seasons in sites near wastewater flows. ARG targets represented major antibiotic groups-tetracyclines (tetA), fluoroquinolines (qnrB), and beta-lactams (blaTEM)-and an MI (intI1) represented the potential for mobility of genetic material. Most air samples (82%) had detectable targets above the experimentally determined LOD: most commonly blaTEM and intI1 (68% and 47% respectively) followed by tetA and qnrB (17% and 11% respectively). ARG and MI densities in positive air samples ranged from 1.3 × 101 to 6.6 × 104 gene copies/m3 air. Additionally, we detected culturable E. coli in the air (52% of samples <1 km from impacted surface waters) with an average density of 11 CFU/m3 in positive samples. We observed decreasing density of blaTEM with increasing distance up to 150 m from impacted surface waters. To our knowledge this is the first study conducting absolute quantification and a spatial analysis of ARGs and MIs in ambient urban air of a city with contaminated surface waters. Environments in close proximity to urban wastewater flows in this setting may experience locally elevated concentrations of ARGs, a possible concern for the emergence and dissemination of antimicrobial resistance in cities with poor sanitation.

DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases

Beta-lactamases (BLs) are enzymes localized in the periplasmic space of bacterial pathogens, where they confer resistance to beta-lactam antibiotics. Experimental identification of BLs is costly yet crucial to understand beta-lactam resistance mechanisms. To address this issue, we present DeepBL, a deep learning-based approach by incorporating sequence-derived features to enable high-throughput prediction of BLs. Specifically, DeepBL is implemented based on the Small VGGNet architecture and the TensorFlow deep learning library. Furthermore, the performance of DeepBL models is investigated in relation to the sequence redundancy level and negative sample selection in the benchmark dataset. The models are trained on datasets of varying sequence redundancy thresholds, and the model performance is evaluated by extensive benchmarking tests. Using the optimized DeepBL model, we perform proteome-wide screening for all reviewed bacterium protein sequences available from the UniProt database. These results are freely accessible at the DeepBL webserver at http://deepbl.erc.monash.edu.au/.

Review of phenotypic assays for detection of extended-spectrum β-lactamases and carbapenemases: a microbiology laboratory bench guide

Background

Infections caused by gram-negative antibiotic-resistant bacteria continue to increase. Despite recommendations by the Clinical Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) with regards to detection of antibiotic degrading enzymes secreted by these bacteria, the true prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase producers remains a difficult task to resolve. Describing of previously designed phenotypic detection assays for ESBLs and carbapenemases in a single document avails a summary that allows for multiple testing which increases the sensitivity and specificity of detection.

Methods and aims

This review, therefore, defined and classified ESBLs and carbapenemases, and also briefly described how the several previously designed phenotypic detection assays for the same should be performed.

Conclusion

Extended-spectrum β-lactamase and carbapenemase detection assays, once performed correctly, can precisely discriminate between bacteria producing these enzymes and those with other mechanisms of resistance to β-lactam antibiotics.

Occurrence of diverse aminoglycoside modifying enzymes with co-existing extended-spectrum-β-lactamases within Enterobacteriaceae isolated in India

OBJECTIVE

The present study describes aminoglycoside modifying enzymes (AMEs) among clinical isolates with coexisting extended spectrum beta-lactamases.

METHODOLOGY

A total of 227 non duplicate enterobacterial isolates were collected and identified from patients who were admitted to different wards or attended OPD of a tertiary referral hospital of North-East India. Isolates were initially screened for antimicrobial susceptibility testing followed by PCR based screening of aminoglycosides modifying enzymes and co-existing ESBLs and carbapenemases. Horizontal transferability, incompatibility typing and stability of plasmids were also analyzed.

RESULTS

Diverse types of AMEs were observed namely; ant(3″)-I, ant(4')-Ia, aac(3)-IIc, ant(3')-I, aac(6')-Ib, ant(2″)-Ia and aac(6'). Majority of the AME positive isolates harboured bla_TEM followed by bla_CTX-M-15 and a combination of bla_TEM and bla_CTX-M-15 were also observed. Nine isolates were found to harbour carbapenemases genes. AME genes were found to be located within a self conjugative plasmid of Inc FIA, IncY, IncN, IncFIB and IncA/C incompatibility types. It was observed that most AME genes were stable over 50 days of serial passages whereas aph(3')-Via and aph(3')-IIb were completely lost within 50 days.

CONCLUSION

This study underscores the co-existence of AMEs and ESBLs within enterobacteriaceae which emphasize a reassessment of combination therapy in the health settings.

The Growing Genetic and Functional Diversity of Extended Spectrum Beta-Lactamases

The β-lactams-a large class of diverse compounds-due to their excellent safety profile and broad antimicrobial spectrum are considered to be the most widely used therapeutic class of antibacterials prescribed in human and veterinary clinical practices. This, unfortunately, has also given rise to a continuous increased resistance globally in health care settings as well as in the community due to their permanent selective force driving diversification of the resistance mechanism. Resistance against β-lactams is increasing rapidly as novel β-lactamases, enzymes that degrade β-lactams, are being discovered each day such as recent emergence of extended spectrum β-lactamases (ESBL) that have the ability to inactivate most of the cephalosporins. The complexity and diversity of ESBL are increasing so rapidly that more than 170 variants have thus far been described for only a single genotype, the blaCTX-M -encoding ESBL. This review is to organize all the current updated literature describing genomic features, organization, and mechanism of resistance and mode of dissemination of all known ESBLs.

High Emergence of ESBL-Producing E. coli Cystitis: Time to Get Smarter in Cyprus

Background: Widespread prevalence of extended-spectrum βeta-lactamase producing Escherichia coli (ESBL-producing E. coli) limits the infection therapeutic options and is a growing global health problem. In this study our aim was to investigate the antimicrobial resistance profile of the E. coli in hospitalized and out-patients in Cyprus.

Results: During the period 2010–2014, 389 strains of E. coli were isolated from urine samples of hospitalized and out-patients in Cyprus. ESBL-producing E. coli, was observed in 53% of hospitalized and 44% in out-patients, latest one being in 2014. All ESBL-producing E. coli remained susceptible to amikacin, carbapenems except ertapenem (in-patients = 6%, out-patients = 11%).

Conclusion: High emerging ESBL-producing E. coli from urine samples in hospitalized and out-patients is an extremely worrisome sign of development of untreatable infections in the near future on the island. We therefore emphasize the immediate need for establishment of optimal therapy guidelines based on the country specific surveillance programs. The need for new treatment strategies, urgent prescription habit changes and ban of over-the-counter sale of antimicrobials at each segment of healthcare services is also discussed in this research.

Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment

Antibiotic resistance is a problem of deep scientific concern both in hospital and community settings. Rapid detection in clinical laboratories is essential for the judicious recognition of antimicrobial resistant organisms. Production of extended-spectrum β-lactamases (ESBLs) is a significant resistance-mechanism that impedes the antimicrobial treatment of infections caused by Enterobacteriaceae and is a serious threat to the currently available antibiotic armory. ESBLs are classified into several groups according to their amino acid sequence homology. Proper infection control practices and barriers are essential to prevent spread and outbreaks of ESBL producing bacteria. As bacteria have developed different strategies to counter the effects of antibiotics, the identification of the resistance mechanism may help in the discovery and design of new antimicrobial agents. The carbapenems are widely regarded as the drugs of choice for the treatment of severe infections caused by ESBL-producing Enterobacteriaceae, although comparative clinical trials are scarce. Hence, more expeditious diagnostic testing of ESBL-producing bacteria and the feasible modification of guidelines for community-onset bacteremia associated with different infections are prescribed.

Designing antibiotic cycling strategies by determining and understanding local adaptive landscapes

The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore susceptibility after resistance has arisen have been unsuccessful, including restrictions on prescribing [1] and antibiotic cycling [2], [3]. Part of the problem may be that those efforts have implemented different classes of unrelated antibiotics, and relied on removal of resistance by random loss of resistance genes from bacterial populations (drift). Here, we show that alternating structurally similar antibiotics can restore susceptibility to antibiotics after resistance has evolved. We found that the resistance phenotypes conferred by variant alleles of the resistance gene encoding the TEM β-lactamase (bla_TEM) varied greatly among 15 different β-lactam antibiotics. We captured those differences by characterizing complete adaptive landscapes for the resistance alleles bla_TEM-50 and bla_TEM-85, each of which differs from its ancestor bla_TEM-1 by four mutations. We identified pathways through those landscapes where selection for increased resistance moved in a repeating cycle among a limited set of alleles as antibiotics were alternated. Our results showed that susceptibility to antibiotics can be sustainably renewed by cycling structurally similar antibiotics. We anticipate that these results may provide a conceptual framework for managing antibiotic resistance. This approach may also guide sustainable cycling of the drugs used to treat malaria and HIV.

Prevalence of ESBL-Producing Klebsiella pneumoniae Isolates in Tertiary Care Hospital

Extended-spectrum β lactamases (ESBLs) continue to be a major challenge in clinical setups world over, conferring resistance to the expanded-spectrum cephalosporins. An attempt was made to study the prevalence of ESBL-producing Klebsiella pneumoniae clinical isolates in a tertiary care hospital in Kurnool. A total of hundred collected isolates of Klebsiella pneumoniae was studied for their susceptibility patterns to various antibiotics and detection of ESBL producers by double disc synergy test (DDST) and phenotypic confirmatory disc diffusion test (PCDDT). Of the 100 isolates tested for their antibiogram, 61% isolates have shown susceptibility to 3rd-generation cepholosporins and 39% were resistant. Amoxycillin showed the highest percentage of resistance followed by tetracyclins and cotrimoxazole. Among 39 resistant isolates of Klebsiella pneumoniae, 17 were ESBL producers detected by DDST and PCDDT. ESBL producers were more in the hospital isolates (28%) compared to community isolates (6%). Maximum percentage of ESBL producers were noticed from blood sample with 57.14%. In the present study, a large number of isolates were found to be multidrug resistant and ESBL producers. PCDDT was found to be better than DDST in the detection of ESBLs. Continued monitoring of drug resistance is necessary in clinical settings for proper disease management.

Expert systems in clinical microbiology

This review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). It considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. A variety of noncommercial systems is described, and the central role played by the EUCAST is stressed. The need for expert rules in the environment of reset EUCAST breakpoints is also questioned. Commercial automated systems with on-board expert systems are considered, with emphasis being placed on the "big three": Vitek 2, BD Phoenix, and MicroScan. By necessity and in places, the review becomes a general review of automated system performances for the detection of specific resistance mechanisms rather than focusing solely on expert systems. Published performance evaluations of each system are drawn together and commented on critically.

Ertapenem resistance among extended-spectrum-beta-lactamase-producing Klebsiella pneumoniae isolates

Ertapenem resistance in Klebsiella pneumoniae is rare. We report on an ertapenem-nonsusceptible phenotype among 25 out of 663 (3.77%) extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates in a multicenter Israeli study. These isolates originated from six different hospitals and were multiclonal, belonging to 12 different genetic clones. Repeat testing using Etest and agar dilution confirmed ertapenem nonsusceptibility in only 15/663 (2.3%) of the isolates. The molecular mechanisms of ertapenem resistance in seven single-clone resistant isolates was due to the presence of ESBL genes (CTX-M-2 in four isolates, CTX-M-10 and OXA-4 in one isolate, SHV-12 in one isolate, and SHV-28 in one isolate) combined with the absence of OMPK36. Seven of 10 isolates initially reported as ertapenem nonsusceptible and subsequently classified as susceptible showed an inoculum effect with ertapenem but not with imipenem or meropenem. Population analysis detected the presence of an ertapenem-resistant subpopulation at a frequency of 10(-6). These rare resistant subpopulations carried multiple ESBL genes, including TEM-30, SHV-44, CTX-M-2, and CTX-M-10, and they lacked OMPK36. The clinical and diagnostic significance of the results should be further studied.

Accuracy of six antimicrobial susceptibility methods for testing linezolid against staphylococci and enterococci

A challenge panel of enterococci (n = 50) and staphylococci (n = 50), including 17 and 15 isolates that were nonsusceptible to linezolid, respectively, were tested with the Clinical and Laboratory Standards Institute broth microdilution and disk diffusion reference methods. In addition, all 100 isolates were tested in parallel by Etest (AB Biodisk, Solna, Sweden), MicroScan WalkAway (Dade, West Sacramento, CA), BD Phoenix (BD Diagnostic Systems, Sparks, MD), VITEK (bioMérieux, Durham, NC), and VITEK 2 (bioMérieux) by using the manufacturers' protocols. Compared to the results of the broth microdilution method for detecting linezolid-nonsusceptible staphylococci and enterococci, MicroScan results showed the highest category agreement (96.0%). The overall categorical agreement levels for VITEK 2, Etest, Phoenix, disk diffusion, and VITEK were 93.0%, 90.0%, 89.6%, 88.0%, and 85.9%, respectively. The essential agreement levels (results within +/-1 doubling dilution of the MIC determined by the reference method) for MicroScan, Phoenix, VITEK 2, Etest, and VITEK were 99.0%, 95.8%, 92.0%, 92.0%, and 85.9%, respectively. The very major error rates for staphylococci were the highest for VITEK (35.7%), Etest (40.0%), and disk diffusion (53.3%), although the total number of resistant isolates tested was small. The very major error rate for enterococci with VITEK was 20.0%. Three systems (MicroScan, VITEK, and VITEK 2) provided no interpretations of nonsusceptible results for staphylococci. These data, from a challenge panel of isolates, illustrate that the recent emergence of linezolid-nonsusceptible staphylococci and enterococci is providing a challenge for many susceptibility testing systems.

Systems approach to improving antimicrobial susceptibility testing in clinical laboratories in the United States

Laboratory practice in the preanalytical phase of antimicrobial susceptibility testing (AST) was evaluated in 102 hospital, reference, physician office-clinic, and public health laboratories in Washington state. Surveys were sent to evaluate (i) use of NCCLS/CLSI (formerly NCCLS) AST performance standards, (ii) technical competence in AST case studies, challenging knowledge of contemporary testing issues, and (iii) choice of antimicrobial agents to test for Streptococcus pneumoniae. Numerous deficiencies were identified in the survey: (i) initially only 40% of the laboratories surveyed used current NCCLS/CLSI AST performance standards, (ii) the rate of accurate responses for three different case studies ranged from 29% to 69%, and (iii) variation was noted in the choice of antimicrobials tested against invasive isolates of S. pneumoniae. These deficiencies could affect therapy and detection of antimicrobial resistance. Several educational programs were implemented to improve AST policies and practices, and a follow-up survey indicated that four intervention strategies were most effective: (i) regional technical workshops, (ii) National Laboratory Training Network teleconferences, (iii) use of the Centers for Disease Control and Prevention (CDC) CD-ROM on AST, and (iv) the CDC Multilevel Antimicrobial Susceptibility Testing Resource website. The interventions could be implemented more widely in the United States to improve AST knowledge and practices.

Carbapenem resistance in Klebsiella pneumoniae not detected by automated susceptibility testing

Detecting β-lactamase–mediated carbapenem resistance among Klebsiella pneumoniae isolates and other Enterobacteriaceae is an emerging problem. In this study, 15 bla_KPC-positive Klebsiella pneumoniae that showed discrepant results for imipenem and meropenem from 4 New York City hospitals were characterized by isoelectric focusing; broth microdilution (BMD); disk diffusion (DD); and MicroScan, Phoenix, Sensititre, VITEK, and VITEK 2 automated systems. All 15 isolates were either intermediate or resistant to imipenem and meropenem by BMD; 1 was susceptible to imipenem by DD. MicroScan and Phoenix reported 1 (6.7%) and 2 (13.3%) isolates, respectively, as imipenem susceptible. VITEK and VITEK 2 reported 10 (67%) and 5 (33%) isolates, respectively, as imipenem susceptible. By Sensititre, 13 (87%) isolates were susceptible to imipenem, and 12 (80%) were susceptible to meropenem. The VITEK 2 Advanced Expert System changed 2 imipenem MIC results from >16 μg/mL to <2 μg/mL but kept the interpretation as resistant. The recognition of carbapenem-resistant K. pneumoniae continues to challenge automated susceptibility systems.

Susceptibility testing practices for Streptococcus pneumoniae: results of a proficiency testing survey of clinical laboratories

In June 2003, a test sample was sent to 355 laboratories enrolled in a proficiency testing program to assess their ability to detect low-level penicillin resistance in a strain of Streptococcus pneumoniae. One hundred fifty participants reported results for antimicrobial susceptibility testing. Of the 62 respondents using disk diffusion, 34 (55%) failed to report a result that was acceptable for detecting penicillin resistance and 30 (48%) reported a result for one or more drugs not approved for testing S. pneumoniae. Moreover, 12 (14%) of the 88 respondents using minimum inhibitory concentration methods reported results for at least one unapproved drug. These findings support the conclusions of other studies that antimicrobial susceptibility testing practices are suboptimal in many laboratories. Resolution of this problem will require continued educational initiatives, studies to discover the reasons why laboratories fail to follow published standards, and enforcement of the use of standards by regulatory and credentialing agencies.

Implementation of antibiotic management teams in Belgian hospitals

In 2002-03, the Belgian government subsidized in part the activities of local Antibiotic Managers (AMs) in 36 hospitals selected based on the presence of an operational multidisciplinary Antibiotic Management Team (AMT). AMs were trained as Internists (28), Microbiologists (13) and Hospital Pharmacists (13). The hospitals were representative of Belgian hospitals in affiliation, regional origin and size. The financing scheme allowed the implementation of 175 antibiotic management interventions, with a mean of 5 interventions/hospital. The activities reported in the first 9-month progress reports were analyzed according to national guidelines for AMTs. All hospitals irrespective of size or affiliation had undertaken a wide range of measures: review of formulary (29), implementation of new clinical guidelines (24), restricted access to selected antibiotics (25), improvement of antibiotic susceptibility testing methods (12), development of antibiotic consumption database (35) and analysis of antibacterial susceptibility data (31). Advertisement type categorization of communication methods showed that education of prescribers was based on multimodal communication. All hospitals used at least one passive method, 39% at least one active method and 55% at least one personalized method. The quality of communication was higher in hospitals with teaching affiliation. In conclusion, hospitals that received a financial incentive under theAMT pilot phase have developed multimodal antibiotic policy interventions independently of the hospital size and teaching status. Extension to all Belgian hospitals appears warranted. The impact of AMTs and AMs on the quality of use of antibiotics and trends of antibiotic resistance and cost will be monitored based on standardized indicators.

Extended-spectrum beta-lactamases: a clinical update

Extended-spectrum beta-lactamases (ESBLs) are a rapidly evolving group of beta-lactamases which share the ability to hydrolyze third-generation cephalosporins and aztreonam yet are inhibited by clavulanic acid. Typically, they derive from genes for TEM-1, TEM-2, or SHV-1 by mutations that alter the amino acid configuration around the active site of these beta-lactamases. This extends the spectrum of beta-lactam antibiotics susceptible to hydrolysis by these enzymes. An increasing number of ESBLs not of TEM or SHV lineage have recently been described. The presence of ESBLs carries tremendous clinical significance. The ESBLs are frequently plasmid encoded. Plasmids responsible for ESBL production frequently carry genes encoding resistance to other drug classes (for example, aminoglycosides). Therefore, antibiotic options in the treatment of ESBL-producing organisms are extremely limited. Carbapenems are the treatment of choice for serious infections due to ESBL-producing organisms, yet carbapenem-resistant isolates have recently been reported. ESBL-producing organisms may appear susceptible to some extended-spectrum cephalosporins. However, treatment with such antibiotics has been associated with high failure rates. There is substantial debate as to the optimal method to prevent this occurrence. It has been proposed that cephalosporin breakpoints for the Enterobacteriaceae should be altered so that the need for ESBL detection would be obviated. At present, however, organizations such as the Clinical and Laboratory Standards Institute (formerly the National Committee for Clinical Laboratory Standards) provide guidelines for the detection of ESBLs in klebsiellae and Escherichia coli. In common to all ESBL detection methods is the general principle that the activity of extended-spectrum cephalosporins against ESBL-producing organisms will be enhanced by the presence of clavulanic acid. ESBLs represent an impressive example of the ability of gram-negative bacteria to develop new antibiotic resistance mechanisms in the face of the introduction of new antimicrobial agents.

Methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci in rural communities, western United States

The impact and prevalence of antimicrobial drug resistance in rural community healthcare settings is uncertain. Prospective surveillance in 51 rural hospitals in Idaho and Utah examined the epidemiologic features of clinical cases of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Thirty-two cases of VRE were reported; for 6, the patient had no prior healthcare exposure or coexisting condition. Among the 724 MRSA cases available for evaluation, 405 (56%) were healthcare-associated (HA-MRSA), and 319 (44%) were community-associated (CA-MRSA). The characteristics of HA-MRSA and CA-MRSA patients with coexisting factors were similar, which suggests community transmission of healthcare strains. CA-MRSA cases without coexisting factors, however, demonstrated features previously reported for community strains. MRSA infections were substantially more frequent than VRE in rural communities in the western United States. Based on epidemiologic criteria, a large proportion of MRSA cases were community-associated. CA-MRSA rates were predictive of institutional MRSA rates.

Emergence of Enterobacteriaceae producing extended-spectrum beta-lactamases (ESBLs) in the community

Enterobacteriaceae, especially Klebsiella spp. producing extended-spectrum beta-lactamases (ESBLs) such as SHV and TEM types, have been established since the 1980s as a major cause of hospital-acquired infections. Appropriate infection control practices have largely prevented the dissemination of these bacteria within many hospitals, although outbreaks have been reported. However, during the late 1990s and 2000s, Enterobacteriaceae (mostly Escherichia coli) producing novel ESBLs, the CTX-M enzymes, have been identified predominantly from the community as a cause of urinary tract infections. Resistance to other classes of antibiotics, especially the fluoroquinolones, is often associated with ESBL-producing organisms. Many clinical laboratories are still not aware of the importance of screening for ESBL-producing Enterobacteriaceae originating from the community. A heightened awareness of these organisms by clinicians and enhanced testing by laboratories, including molecular surveillance studies, is required to reduce treatment failures, to limit their introduction into hospitals and to prevent the spread of these emerging pathogens within the community.

Update on Resistance among Nosocomial Gram-Negative Pathogens to Extended-Spectrum Cephalosporins and Fluoroquinolones: Results of the Antimicrobial Resistance Management (ARM) Program

Objective

To evaluate trends in antibiotic resistance among Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, and Pseudomonas aeruginosa isolates submitted to the Antimicrobial Resistance Management (ARM) program between 1990 and 2002.

Design

The ongoing Antimicrobial Resistance Management (ARM) program is a queriable Web-based surveillance system that tracks resistance patterns among U.S. inpatient and outpatient isolates. This report represents data from 285 institutions and over 17 million isolates. Using a Web-based analysis tool, antibiogram and sensitivity reports of E. coli, K. pneumoniae, P. mirabilis, and P. aeruginosa isolates were reviewed for resistance to extended-spectrum cephalosporins and fluoroquinolones.

Setting

285 teaching and non-teaching U.S Hospitals nationwide.

Results

For E. coli, resistance was 3.2% to ciprofloxacin (n = 444,947), 5.4% to levofloxacin (n = 201,532), and 0.8% to cefotaxime (n = 107,394), ceftriaxone (n = 464,931), and cefepime (n = 81,980), respectively. K. pneumoniae isolate resistance was 4.6% to ciprofloxacin (n = 144,698), 4.5% to levofloxacin (n = 57,462), 1.9% to cefotaxime (n = 33,189), 2.0% to ceftriaxone (n = 145,328) and 1.9% to cefepime (n = 25,503). For P. mirabilis, resistance was 12.5% to ciprofloxacin (n = 83,186), 12.2% to levofloxacin (n = 35,277), 1.0% to cefotaxime (n = 18,802), 0.7% to ceftriaxone (83,652), and 2.3% to cefepime (n = 13,968). P. aeruginosa resistance was also higher for fluoroquinolones (only 65.2% of isolates were susceptible to ciprofloxacin) compared to extended-spectrum cephalosporins, with ceftazidime exhibiting the greatest antipseudomonal activity. Clinically significant regional variations in the activity of fluoroquinolones and cephalosporins were apparent.

Conclusion

Resistance to the fluoroquinolones is increasing dramatically, whereas the third generation cephalosporins remain inherently more active. P. aeruginosa exhibits the most formidable resistance pattern with neither the antipseudomonal cephalosporins nor fluoroquinolones representing acceptable monotherapy options. Given the association between fluoroquinolone resistance and extended-spectrum β-lactamase production, continued surveillance is vital to preserve the activity of existing therapies.

Phenotypic and molecular detection of CTX-M-beta-lactamases produced by Escherichia coli and Klebsiella spp

Organisms producing CTX-M-beta-lactamases are emerging around the world as a source of resistance to oxyiminocephalosporins such as cefotaxime (CTX). However, the laboratory detection of these strains is not well defined. In this study, a molecular detection assay for the identification of CTX-M-beta-lactamase genes was developed and used to investigate the prevalence of these enzymes among clinical isolates of Escherichia coli and Klebsiella species in the Calgary Health Region during 2000 to 2002. In addition, National Committee for Clinical Laboratory Standards (NCCLS) recommendations were evaluated for the ability to detect isolates with CTX-M extended-spectrum beta-lactamases (ESBLs). The PCR assay consisted of four primer sets and demonstrated 100% specificity and sensitivity for detecting different groups of CTX-M-beta-lactamases in control strains producing well-characterized ESBLs. Using these primer sets, 175 clinical strains producing ESBLs were examined for the presence of CTX-M enzymes; 24 (14%) were positive for bla(CTX-M-1-like) genes, 95 (54%) were positive for bla(CTX-M-14-like) genes, and the remaining 56 (32%) were negative for bla(CTX-M) genes. Following the NCCLS recommendations for ESBL testing, all of the control and clinical strains were detected when screened with cefpodoxime and when both cefotaxime and ceftazidime with clavulanate were used as confirmation tests.

Diagnostic modalities for infectious diseases

The role of the microbiology laboratory is essential to successful provision of patient care. Obtaining appropriate laboratory data allows clinicians the best opportunity to arrive at a definitive diagnosis in a timely manner, eliminates the need for further tests, and can offer specific treatment approaches with maximal potential for success. This article discusses the laboratory procedures useful for diagnosis of oral or maxillofacial infections, including collection and transport of microbial specimens, representative techniques and methods available for culture and diagnostic assays, diagnostic laboratory principles for specific types of microbial etiologies, antimicrobial sensitivity, quality control issues, and evaluation of reported findings.

Extended-spectrum β-lactamases: implications for the clinical microbiology laboratory, therapy, and infection control

Extended-spectrum beta-lactamase (ESBL) producing gram-negative bacilli are a growing concern in human medicine today. When producing these enzymes, organisms (mostly K. pneumoniae and E. coli) become highly efficient at inactivating the newer third-generation cephaloporins (such as cefotaxime, ceftazidime, and ceftriaxone). In addition, ESBL-producing bacteria are frequently resistant to many classes of non-beta-lactam antibiotics, resulting in difficult-to-treat infections. This review gives an introduction into the topic and is focused on various aspects of ESBLs; it covers the current epidemiology, the problems of ESBL detection and the clinical relevance of infections caused by ESBL-producing organisms. Therapeutic options and potential strategies for dealing with this growing problem are also discussed in this article.

Detection of antimicrobial resistance by small rural hospital microbiology laboratories: comparison of survey responses with current NCCLS laboratory standards

Microbiology laboratory personnel from 77 rural hospitals in Idaho, Nevada, Utah, and eastern Washington were surveyed in July 2000 regarding their routine practices for detecting antimicrobial resistance. Their self-reported responses were compared to recommended laboratory practices. Most hospitals reported performing onsite bacterial identification and susceptibility testing. Many reported detecting targeted antimicrobial resistant organisms. While only 5/61 hospitals (8%) described using screening tests capable of detecting all 8 targeted types of resistance, most (57/61, 93%) were capable of accurately screening for at least 6 types. Conversely, most hospitals (58/61, 95%) reported confirmatory testing capable of identifying only 3 or fewer resistance types with high-level penicillin resistance among pneumococci, methicillin and vancomycin resistance among staphylococci and enterococci, and extended spectrum beta-lactamase production by Gram-negative bacilli presenting the greatest difficulties. Furthermore, only 50% of hospitals compiled annual antibiogram reports to help physicians choose initial therapy for suspected infectious illnesses. This survey suggests that the antimicrobial susceptibility testing in many rural hospitals may be unreliable.

Antimicrobial proficiency testing of National Nosocomial Infections Surveillance System hospital laboratories

OBJECTIVE

The National Nosocomial Infections Surveillance (NNIS) System personnel report trends in antimicrobial-resistant pathogens. To validate select antimicrobial susceptibility testing results and to identify test methods that tend to produce errors, we conducted proficiency testing among NNIS System hospital laboratories.

SETTING

NNIS System hospital laboratories in the United States.

METHODS

Each laboratory received five organisms (ie, an imipenem-resistant Serratia marcescens, an oxacillin-resistant Staphylococcus aureus, a vancomycin-resistant Enterococcus faecalis, a vancomycin-intermediate Staphylococcus epidermidis, and an extended-spectrum beta-lactamase (ESbetaL)-producing Klebsiella pneumoniae). Testing results were compared with reference testing results from the Centers for Disease Control and Prevention.

RESULTS

Of 138 laboratories testing imipenem against the Serratia marcescens strain, 110 (80%) correctly reported minimum inhibitory concentrations (MICs) or zone sizes in the resistant range. All 193 participating laboratories correctly reported the Staphylococcus aureus strain as oxacillin resistant Of the 193 laboratories, 169 (88%) reported correct MICs or zone sizes for the vancomycin-resistant Enterococcus faecalis. One hundred sixty-two (84%) of 193 laboratories demonstrated the ability to detect a vancomycin-intermediate strain of Staphylococcus epidermidis, however, disk diffusion performed poorly when testing both staphylococci and enterococci with vancomycin. Although laboratory personnel correctly reported nonsusceptible extended-spectrum cephalosporins and aztreonam results for K. pneumoniae, only 98 (51%) of 193 correctly reported this organism as an ESbetaL producer.

CONCLUSION

Overall, NNIS System hospital laboratory personnel detected most emerging resistance patterns. Disk diffusion continues to be unreliable for vancomycin testing of staphylococci and must be used cautiously for enterococci. Further education on the processing of ESbetaL-producing organisms is warranted.

Quality control for beta-lactam susceptibility testing with a well-defined collection of Enterobacteriaceae and Pseudomonas aeruginosa strains in Spain

Eighteen Enterobacteriaceae and Pseudomonas aeruginosa strains, 16 of them with well-defined beta-lactam resistance mechanisms, were sent to 52 Spanish microbiology laboratories. Interpretative categories for 8 extended-spectrum beta-lactams were collected. Participating laboratories used their own routine susceptibility testing procedures (88% automatic systems, 10% disk diffusion, and 2% agar dilution). Control results were established by two independent reference laboratories by applying the NCCLS microdilution method and interpretative criteria. Interpretative discrepancies were observed in 16% of the results (4.4% for cefepime, 3.0% for aztreonam, 2.8% for piperacillin-tazobactam, 1.7% for cefotaxime [CTX] and ceftazidime, 1.1% for ceftriaxone, 0.9% for meropenem, and 0.3% for imipenem). High consistency with reference values (<5% of major plus very major errors) was observed with (i) American Type Culture Collection quality control strains; (ii) strains with low-efficiency mechanisms inactivating extended-spectrum beta-lactams, such as OXA-1-producing Escherichiacoli or SHV-1-hyperproducing Klebsiella pneumoniae; (iii) strains with highly efficient mechanisms, such as SHV-5 porin-deficient K. pneumoniae, CTX-M-10 in Enterobacter cloacae hyperproducing AmpC, and P. aeruginosa with the MexAB OprM efflux phenotype or hyperproducing AmpC. Low consistency (>30% major plus very major errors) was detected in K1-producing Klebsiella oxytoca, CTX-M-9-producing E. coli, and in OprD(-) P. aeruginosa strains. Extended-spectrum beta-lactamase (ESBL)-producing strains accounted for 86% of very major errors. Recognition of the ESBL phenotype was particularly low in Enterobacter cloacae strains (<35%), due to the lack of NCCLS-specific rules in this genus. A K1-producing K. oxytoca was misidentified by 10% of laboratories as an ESBL producer. The use of well-defined resistant strains is useful for improving proficiency in susceptibility testing in clinical laboratories.

Proficiency testing program for clinical laboratories performing antifungal susceptibility testing of pathogenic yeast species

Antifungal susceptibility testing is expected to facilitate the selection of adequate therapy for fungal infections. The general availability of antifungal susceptibility testing in clinical laboratories is low, even though a number of standard methods are now available. The objective of the present study was to develop and evaluate a proficiency testing program (PTP) for the antifungal susceptibility testing of pathogenic yeasts in laboratories licensed by the New York State Department of Health. A number of quality control standards, and methods for documenting laboratory performance, were developed in consultation with the laboratory directors. The participating laboratories were provided with five American Type Culture Collection strains of pathogenic yeasts for which the minimum inhibitory concentrations (MICs) of amphotericin B and fluconazole were well defined. A majority of laboratories (14 of 17) used broth microdilution, and these were evenly split between the NCCLS M-27A protocol and the Sensititre YeastOne method. The other three laboratories performed susceptibility testing with Etest. Overall, the levels of agreement between MIC reference ranges and the reported MICs were 85 and 74% for amphotericin B and for fluconazole, respectively. All laboratories except one successfully detected fluconazole resistance in a Candida krusei strain. However, amphotericin B resistance in a Candida lusitaniae strain was not detected by any of the participating labs. It is concluded that a suitably designed PTP could adequately monitor the competence of clinical laboratories performing antifungal susceptibility testing.

Antimicrobial susceptibility testing of carbapenems: multicenter validity testing and accuracy levels of five antimicrobial test methods for detecting resistance in Enterobacteriaceae and Pseudomonas aeruginosa isolates

From January 1996 to May 1999, Project ICARE (Intensive Care Antimicrobial Resistance Epidemiology) received 448 nonduplicate clinical isolates of Enterobacteriaceae and Pseudomonas aeruginosa that were reported to be imipenem intermediate or resistant. However, broth microdilution (BMD) confirmatory testing at the Project ICARE central laboratory confirmed this result in only 11 of 123 (8.9%) Enterobacteriaceae isolates and 241 of 325 (74.2%) P. aeruginosa isolates. To investigate this overdetection of imipenem resistance, we tested 204 selected isolates from the Project ICARE collection plus five imipenem-resistant challenge strains at the Centers for Disease Control and Prevention against imipenem and meropenem by agar dilution, disk diffusion, Etest (AB BIODISK North America, Inc., Piscataway, N.J.), two MicroScan WalkAway conventional panels (Neg MIC Plus 3 and Neg Urine Combo 3) (Dade MicroScan, Inc., West Sacramento, Calif.), and two Vitek cards (GNS-116 containing meropenem and GNS-F7 containing imipenem) (bioMérieux Vitek, Inc., Durham, N.C.). The results of each test method were compared to the results of BMD testing using in-house-prepared panels. Seven imipenem-resistant and five meropenem-resistant isolates of Enterobacteriaceae and 43 imipenem-resistant and 21 meropenem-resistant isolates of P. aeruginosa were identified by BMD. For Enterobacteriaceae, the imipenem and meropenem test methods produced low numbers of very major and major errors. All test systems in the study produced low numbers of very major and major errors when P. aeruginosa was tested against imipenem and meropenem, except for Vitek testing (major error rate for imipenem, 20%). Further testing conducted in 11 of the participating ICARE hospital laboratories failed to pinpoint the factors responsible for the initial overdetection of imipenem resistance. However, this study demonstrated that carbapenem testing difficulties do exist and that laboratories should consider using a second, independent antimicrobial susceptibility testing method to validate carbapenem-intermediate and -resistant results.

Temporal changes in prevalence of antimicrobial resistance in 23 US hospitals

Antimicrobial resistance is increasing in nearly all health-care-associated pathogens. We examined changes in resistance prevalence during 1996-1999 in 23 hospitals by using two statistical methods. When the traditional chi-square test of pooled mean resistance prevalence was used, most organisms appear to have increased in prevalence. However, when a more conservative test that accounts for changes within individual hospitals was used, significant increases in prevalence of resistance were consistently observed only for oxacillin-resistant Staphylococcus aureus, ciprofloxacin-resistant Pseudomonas aeruginosa, and ciprofloxacin- or ofloxacin-resistant Escherichia coli. These increases were significant only in isolates from patients outside intensive-care units (ICU). The increases seen are of concern; differences in factors present outside ICUs, such as excessive quinolone use or inadequate infection-control practices, may explain the observed trends.

Monitoring antimicrobial use and resistance: comparison with a national benchmark on reducing vancomycin use and vancomycin-resistant enterococci

To determine if local monitoring data on vancomycin use directed quality improvement and decreased vancomycin use or vancomycin-resistant enterococci (VRE), we analyzed data from 50 intensive-care units (ICUs) at 20 U.S. hospitals reporting data on antimicrobial-resistant organisms and antimicrobial agent use. We compared local data with national benchmark data (aggregated from all study hospitals). After data were adjusted for changes in prevalence of methicillin-resistant Staphylococcus aureus, changes in specific prescriber practice at ICUs were associated with significant decreases in vancomycin use (mean decrease -48 defined daily doses per 1,000 patient days, p<0.001). These ICUs also reported significant decreases in VRE prevalence compared with those not using unit-specific changes in practice (mean decrease of 7.5% compared with mean increase of 5.7%, p<0.001). In this study, practice changes focused towards specific ICUs were associated with decreases in ICU vancomycin use and VRE prevalence.

Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat

Beta-lactamases continue to be the leading cause of resistance to beta-lactam antibiotics among gram-negative bacteria. In recent years there has been an increased incidence and prevalence of extended-spectrum beta-lactamases (ESBLs), enzymes that hydrolyze and cause resistance to oxyimino-cephalosporins and aztreonam. The majority of ESBLs are derived from the widespread broad-spectrum beta-lactamases TEM-1 and SHV-1. There are also new families of ESBLs, including the CTX-M and OXA-type enzymes as well as novel, unrelated beta-lactamases. Several different methods for the detection of ESBLs in clinical isolates have been suggested. While each of the tests has merit, none of the tests is able to detect all of the ESBLs encountered. ESBLs have become widespread throughout the world and are now found in a significant percentage of Escherichia coli and Klebsiella pneumoniae strains in certain countries. They have also been found in other Enterobacteriaceae strains and Pseudomonas aeruginosa. Strains expressing these beta-lactamases will present a host of therapeutic challenges as we head into the 21st century.

Extended-spectrum beta-lactamases: epidemiology, detection, and treatment

Extended-spectrum beta-lactamases (ESBLs) are extremely broad spectrum beta-lactamase enzymes found in a variety of Enterobacteriaceae. Most strains producing these beta-lactamases are Klebsiella pneumoniae, other Klebsiella species (i.e., K. oxytoca), and Escherichia coli. When producing these enzymes, organisms become highly effective at inactivating various beta-lactam antibiotics. In addition, ESBL-producing bacteria are frequently resistant to many classes of antibiotics, resulting in difficult-to-treat infections. Other problems due to ESBL-producing bacteria are difficulty in detecting the presence of ESBLs, limited treatment options, and deleterious impact on clinical outcomes. Clinicians should be familiar with the clinical significance of these enzymes and potential strategies for dealing with this growing problem.

Antimicrobial resistance prevalence rates in hospital antibiograms reflect prevalence rates among pathogens associated with hospital-acquired infections

To determine whether routine antibiograms (summaries reporting resistance of all tested isolates) reflect resistance rates among pathogens associated with hospital-acquired infections, we compared data collected from 2 different surveillance components in the same 166 intensive care units (ICUs). ICUs reported data during the same months to both the infection-based surveillance and the laboratory-based surveillance. Paired comparisons of the percentage of isolates resistant were made between systems within each ICU. No significant differences existed (P>.05) between the percentage of isolates resistant from the infection-based system and laboratory-based system for all antimicrobial-resistant organisms studied, except methicillin resistance in Staphylococcus species. The mean difference in percentage resistance was higher from the infection-based system than the laboratory-based system for S. aureus (mean difference, +8%, P<.001) and coagulase-negative staphylococci (mean difference, +9%, P<.001). Overall, hospital antibiograms reflected susceptibility patterns among isolates associated with hospital-acquired infections. Hospital antibiograms may underestimate the relative frequency of methicillin resistance among Staphylococcus species when associated with hospital-acquired infections.