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

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.

Readiness for antimicrobial resistance (AMR) surveillance in Pakistan; a model for laboratory strengthening

BACKGROUND

Limited capacity of laboratories for antimicrobial susceptibility testing (AST) presents a critical diagnostic bottleneck in resource limited countries. This paper aims to identify such gaps and to explore whether laboratory networks could contribute towards improving AST in low resource settings.

METHODS

A self-assessment tool to assess antimicrobial susceptibility testing capacity was administered as a pre-workshop activity to participants from 30 microbiology laboratories in 3 cities in Pakistan. Data from public and private laboratories was analyzed and capacity of each scored in percentage terms. Laboratories from Karachi were invited to join a support network. A cohort of five laboratories that consented were provided additional training and updates sessions over a period of 15 months. Impact of training activities in these laboratories was evaluated using a point scoring (0-11) tool.

RESULTS

Results of self-assessment component identified a number of areas that required strengthening (scores of ≤60%). These included; readiness for AMR surveillance; 38 and 46%, quality assurance; 49 and 55%, and detection of specific organisms; 56 and 60% for public and private laboratories respectively. No significant difference was detected in AST capacity between public and private laboratories [ANOVA; p > 0.05]. Scoring tool used to assess impact of training within the longitudinal cohort showed an increase from a baseline of 1-5.5 (August 2015) to improved post training scores of 7-11 (October 2016) for the 5 laboratories included. Moreover, statistical analysis using paired t-Test Analysis, assuming unequal variance, indicated that the increase in scored noted represents a statistically significant improvement in the components evaluated [p < 0.05].

CONCLUSION

Strengthening of laboratory capacity for AMR surveillance is important. Our data shows that close mentoring and support can help enhance capacity for antimicrobial sensitivity testing in resource limited settings. Our study further presents a model wherein laboratory networks can be successfully established and used towards improving diagnostic capacity in such settings.

Analysis and Presentation of Cumulative Antimicrobial Susceptibility Data (Antibiograms): Substantial Variability Across Medical Centers in the United States

We found substantial variability in approaches to constructing antibiograms at 65 United States medical centers. Laboratories in teaching hospitals and those with more personnel were significantly more likely to offer sophisticated antibiogram approaches, including the compiling of unit-specific susceptibility data and the reporting of temporal trends in susceptibility data.

Klebsiella pneumoniae bloodstream infection: epidemiology and impact of inappropriate empirical therapy

Multidrug resistance associated with extended-spectrum beta-lactamase (ESBL) and Klebsiella pneumoniae carbapenemase (KPC) among K. pneumoniae is endemic in southern Europe. We retrospectively analyzed the impact of resistance on the appropriateness of empirical therapy and treatment outcomes of K. pneumoniae bloodstream infections (BSIs) during a 2-year period at a 1420-bed tertiary-care teaching hospital in northern Italy. We identified 217 unique patient BSIs, including 92 (42%) KPC-positive, 49 (23%) ESBL-positive, and 1 (0.5%) metallo-beta-lactamase-positive isolates. Adequate empirical therapy was administered in 74% of infections caused by non-ESBL non-KPC strains, versus 33% of ESBL and 23% of KPC cases (p < 0.0001). To clarify the impact of resistance on BSI treatment outcomes, we compared several different models comprised of non-antibiotic treatment-related factors predictive of patients' 30-day survival status. Acute Physiology and Chronic Health Evaluation (APACHE) II score determined at the time of positive blood culture was superior to other investigated models, correctly predicting survival status in 83% of the study cohort. In multivariate analysis accounting for APACHE II, receipt of inadequate empirical therapy was associated with nearly a twofold higher rate of death (adjusted hazard ratio 1.9, 95% confidence interval 1.1-3.4; p = 0.02). Multidrug-resistant K. pneumoniae accounted for two-thirds of all K. pneumoniae BSIs, high rates of inappropriate empirical therapy, and twofold higher rates of patient death irrespective of underlying illness.

Whole genome mapping of the first reported case of KPC-2-positive Klebsiella pneumoniae ST258 in Nebraska

Three ertapenem-resistant Klebsiella pneumoniae carrying bla(KPC-2) were isolated from a single patient in Nebraska over a span of 5 months. A comparative analysis of the genetic relatedness of these isolates was investigated using pulsed-field gel electrophoresis, multilocus sequence typing, and whole genome mapping.

Agar disk diffusion and automated microbroth dilution produce similar antimicrobial susceptibility testing results for Salmonella serotypes Newport, Typhimurium, and 4,5,12:i-, but differ in economic cost

Data generated using different antimicrobial testing methods often have to be combined, but the equivalence of such results is difficult to assess. Here we compared two commonly used antimicrobial susceptibility testing methods, automated microbroth dilution and agar disk diffusion, for 8 common drugs, using 222 Salmonella isolates of serotypes Newport, Typhimurium, and 4,5,12:i-, which had been isolated from clinical salmonellosis cases among cattle and humans. Isolate classification corresponded well between tests, with 95% overall category agreement. Test results were significantly negatively correlated, and Spearman's correlation coefficients ranged from -0.98 to -0.38. Using Cox's proportional hazards model we determined that for most drugs, a 1 mm increase in zone diameter resulted in an estimated 20%-40% increase in the hazard of growth inhibition. However, additional parameters such as isolation year or serotype often impacted the hazard of growth inhibition as well. Comparison of economical feasibility showed that agar disk diffusion is clearly more cost-effective if the average sample throughput is small but that both methods are comparable at high sample throughput. In conclusion, for the Salmonella serotypes and antimicrobial drugs analyzed here, antimicrobial susceptibility data generated based on either test are qualitatively very comparable, and the current published break points for both methods are in excellent agreement. Economic feasibility clearly depends on the specific laboratory settings, and disk diffusion might be an attractive alternative for certain applications such as surveillance studies.

Extended-spectrum beta-lactamase-producing Enterobacteriaceae: an emerging public-health concern

The medical community relies on clinical expertise and published guidelines to assist physicians with choices in empirical therapy for system-based infectious syndromes, such as community-acquired pneumonia and urinary-tract infections (UTIs). From the late 1990s, multidrug-resistant Enterobacteriaceae (mostly Escherichia coli) that produce extended-spectrum beta lactamases (ESBLs), such as the CTX-M enzymes, have emerged within the community setting as an important cause of UTIs. Recent reports have also described ESBL-producing E coli as a cause of bloodstream infections associated with these community-onset UTIs. 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. Thus, more rapid diagnostic testing of ESBL-producing bacteria and the possible modification of guidelines for community-onset bacteraemia associated with UTIs are required.

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.

Performance in detection and reporting beta-lactam resistance phenotypes in Enterobacteriaceae: a nationwide proficiency study in Italian laboratories

We evaluated the ability of 60 Italian clinical microbiology laboratories in detecting and reporting beta-lactam resistance phenotypes in Enterobacteriaceae. Laboratories received 5 well-characterized isolates producing extended-spectrum beta-lactamases (ESBLs), 2 hyperproducers of chromosomal enzymes, and 3 quality control strains. The performances in antimicrobial susceptibility testing (AST) were different depending on the species and type of ESBL produced. High rates of very major errors (up to 56%) were observed for ESBL producers when testing cephalosporins and aztreonam, especially in the case of CTX-M-1-producing Escherichia coli and TEM-52-producing Proteus mirabilis. Isolates hyperproducing chromosomal enzymes were erroneously reported as ESBL producers in approximately 20% of cases. Detection of ESBLs is still a problem for clinical microbiology laboratories. Overall, performances in AST appear to be better with Klebsiella spp. producing well-known enzymes (e.g., SHV type) than with strains producing emerging enzymes (e.g., CTX-M type) or organisms not well recognized as ESBL producers (e.g., P. mirabilis).

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.

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.

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.

Are United States hospitals following national guidelines for the analysis and presentation of cumulative antimicrobial susceptibility data?

The National Committee for Clinical Laboratory Standards recently published guidelines for analysis and presentation of cumulative antimicrobial susceptibility test data (antibiograms). We sought to determine how well US hospitals already adhere to standards for antibiogram compilation, and to examine the relationship between hospital characteristics and guideline adherence. We surveyed laboratory directors at 670 hospitals and examined 3 guideline criteria: compilation of an antibiogram, annual updating, and distribution to infection control staff and medical staff yearly; 494 surveys were returned (74%). Almost all of the hospitals surveyed publish an antibiogram (95%, n = 481); however, only 60% (n = 296) met all three criteria. Hospital laboratories meeting criteria were more likely to serve as referral laboratories (OR = 1.82; 95% CI = 1.26-2.63), perform susceptibility testing on site (OR = 4.47; 95% CI = 1.84-10.84), use confirmatory tests to detect extended-spectrum beta-lactamases (OR = 1.8; 95% CI = 1.2-2.6), and have more laboratory personnel per bed (3.0 vs. 2.0 FTEs/bed, p = 0.0031). Adherence to guidelines for preparation and dissemination of antibiograms could be improved. Institutional commitment to high quality, on-site microbiology laboratory services will improve adherence to these guidelines.