Evaluation of the BIOGRAM antimicrobial susceptibility test system

Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA

Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements.

A review of the current state of digital plate reading of cultures in clinical microbiology

Digital plate reading (DPR) is increasingly being adopted as a means to facilitate the analysis and improve the quality and efficiency within the clinical microbiology laboratory. This review discusses the role of DPR in the context of total laboratory automation and explores some of the platforms currently available or in development for digital image capturing of microbial growth on media. The review focuses on the advantages and challenges of DPR. Peer-reviewed studies describing the utility and quality of these novel DPR systems are largely lacking, and professional guidelines for DPR implementation and quality management are needed. Further development and more widespread adoption of DPR is anticipated.

Methodological comparisons for antimicrobial resistance surveillance in feedlot cattle

BACKGROUND

The purpose of this study was to objectively compare methodological approaches that might be utilized in designing an antimicrobial resistance (AMR) surveillance program in beef feedlot cattle. Specifically, four separate comparisons were made to investigate their potential impact on estimates for prevalence of AMR. These included investigating potential differences between 2 different susceptibility testing methods (broth microdilution and disc diffusion), between 2 different target bacteria (non-type-specific E. coli [NTSEC] and Mannheimia haemolytica), between 2 strategies for sampling feces (individual samples collected per rectum and pooled samples collected from the pen floor), and between 2 strategies for determining which cattle to sample (cattle that were culture-positive for Mannheimia haemolytica and those that were culture-negative).

RESULTS

Comparing two susceptibility testing methods demonstrated differences in the likelihood of detecting resistance between automated disk diffusion (BioMIC®) and broth microdilution (Sensititre®) for both E. coli and M. haemolytica. Differences were also detected when comparing resistance between two bacterial organisms within the same cattle; there was a higher likelihood of detecting resistance in E. coli than in M. haemolytica. Differences in resistance prevalence were not detected when using individual animal or composite pen sampling strategies. No differences in resistance prevalences were detected in E. coli recovered from cattle that were culture-positive for M. haemolytica compared to those that were culture-negative, suggesting that sampling strategies which targeted recovery of E. coli from M. haemolytica-positive cattle would not provide biased results.

CONCLUSIONS

We found that for general purposes, the susceptibility test selected for AMR surveillance must be carefully chosen considering the purpose of the surveillance since the ability to detect resistance appears to vary between these tests depending upon the population where they are applied. Continued surveillance of AMR in M. haemolytica recovered by nasopharyngeal swab is recommended if monitoring an animal health pathogen is an objective of the surveillance program as results of surveillance using fecal E. coli cannot be extrapolated to this important respiratory pathogen. If surveillance of E. coli was pursued in the same population, study populations could target animals that were culture-positive for M. haemolytica without biasing estimates for AMR in E. coli. Composite pen-floor sampling or sampling of individuals per-rectum could possibly be used interchangeably for monitoring resistance in E. coli.

Prolonged infusion antibiotics for suspected gram-negative infections in the ICU: a before-after study

BACKGROUND

ß-Lactam antibiotics demonstrate time-dependent killing. Prolonged infusion of these agents is commonly performed to optimize the time the unbound concentration of an antibiotic remains greater than the minimum inhibitory concentration and decrease costs, despite limited evidence suggesting improved clinical results.

OBJECTIVE

To determine whether prolonged infusion of ß-lactam antibiotics improves outcomes in critically ill patients with suspected gram-negative infection.

METHODS

We conducted a single-center, before-after, comparative effectiveness trial between January 2010 and January 2011 in the intensive care units at Barnes-Jewish Hospital, an urban teaching hospital affiliated with the Washington University School of Medicine in St. Louis, MO. Outcomes were compared between patients who received standardized dosing of meropenem, piperacillin-tazobactam, or cefepime as an intermittent infusion over 30 minutes (January 1, 2010, to June 30, 2010) and patients who received prolonged infusion over 3 hours (August 1, 2010, to January 31, 2011).

RESULTS

A total of 503 patients (intermittent infusion, n = 242; prolonged infusion, n = 261) treated for gram-negative infection were included in the clinically evaluable population. Approximately 50% of patients in each group received cefepime and 20% received piperacillin-tazobactam. More patients in the intermittent infusion group received meropenem (35.5% vs 24.5%; p = 0.007). Baseline characteristics were similar between groups, with the exception of a greater occurrence of chronic obstructive pulmonary disease (COPD) in the intermittent infusion group. Treatment success rates in the clinically evaluable group were 56.6% for intermittent infusion and 51.0% for prolonged infusion (p = 0.204), and in the microbiologically evaluable population, 55.2% for intermittent infusion and 49.5% for prolonged infusion (p = 0.486). Fourteen-day, 30-day, and inhospital mortality rates in the clinically evaluable population for the intermittent and prolonged infusion groups were 13.2% versus 18.0% (p = 0.141), 23.6% versus 25.7% (p = 0.582), and 19.4% versus 23.0% (p = 0.329).

CONCLUSIONS

Routine use of prolonged infusion of time-dependent antibiotics for the empiric treatment of gram-negative bacterial infections offers no advantage over intermittent infusion antibiotic therapy with regard to treatment success, mortality, or hospital length of stay. These results were confirmed after controlling for potential confounders in a multivariate analysis.

Resistance to empiric antimicrobial treatment predicts outcome in severe sepsis associated with Gram-negative bacteremia

BACKGROUND

Gram-negative bacteria are an important cause of severe sepsis. Recent studies have demonstrated reduced susceptibility of Gram-negative bacteria to currently available antimicrobial agents.

METHODS

We performed a retrospective cohort study of patients with severe sepsis who were bacteremic with Pseudomonas aeruginosa, Acinetobacter species, or Enterobacteriaceae from 2002 to 2007. Patients were identified by the hospital informatics database and pertinent clinical data (demographics, baseline severity of illness, source of bacteremia, and therapy) were retrieved from electronic medical records. All patients were treated with antimicrobial agents within 12 hours of having blood cultures drawn that were subsequently positive for bacterial pathogens. The primary outcome was hospital mortality.

RESULTS

A total of 535 patients with severe sepsis and Gram-negative bacteremia were identified. Hospital mortality was 43.6%, and 82 (15.3%) patients were treated with an antimicrobial regimen to which the causative pathogen was resistant. Patients infected with a resistant pathogen had significantly greater risk of hospital mortality (63.4% vs 40.0%; P < 0.001). In a multivariate analysis, infection with a pathogen that was resistant to the empiric antibiotic regimen, increasing APACHE II scores, infection with Pseudomonas aeruginosa, healthcare-associated hospital-onset infection, mechanical ventilation, and use of vasopressors were independently associated with hospital mortality.

CONCLUSIONS

In severe sepsis attributed to Gram-negative bacteremia, initial treatment with an antibiotic regimen to which the causative pathogen is resistant was associated with increased hospital mortality. This finding suggests that rapid determination of bacterial susceptibility could influence treatment choices in patients with severe sepsis potentially improving their clinical outcomes.

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.

Left-sided endocarditis caused by Pseudomonas aeruginosa: successful treatment with meropenem and tobramycin

Medical treatment alone is rarely successful in left-sided infective endocarditis caused by Pseudomonas aeruginosa. We report the cure of such a case with high-dose meropenem in combination with tobramycin.

Survey of antimicrobial susceptibility testing practices of veterinary diagnostic laboratories in the United States

OBJECTIVE

To describe antimicrobial susceptibility testing practices of veterinary diagnostic laboratories in the United States and evaluate the feasibility of collating this information for the purpose of monitoring antimicrobial resistance in bacterial isolates from animals.

DESIGN

Cross-sectional study.

PROCEDURES

A questionnaire was mailed to veterinary diagnostic laboratories throughout the United States to identify those laboratories that conduct susceptibility testing. Nonrespondent laboratories were followed up through telephone contact and additional mailings. Data were gathered regarding methods of susceptibility testing, standardization of methods, data management, and types of isolates tested.

RESULTS

Eighty-six of 113 (76%) laboratories responded to the survey, and 64 of the 86 (74%) routinely performed susceptibility testing on bacterial isolates from animals. Thirty-four of the 36 (94%) laboratories accredited by the American Association of Veterinary Laboratory Diagnosticians responded to the survey. Laboratories reported testing > 160,000 bacterial isolates/y. Fifty-one (88%) laboratories reported using the Kirby-Bauer disk diffusion test to evaluate antimicrobial susceptibility; this accounted for 65% of the isolates tested. Most (87%) laboratories used the NCCLS (National Committee for Clinical Laboratory Standards) documents for test interpretation. Seventy-five percent of the laboratories performed susceptibility testing on bacterial isolates only when they were potential pathogens.

CONCLUSIONS

The veterinary diagnostic laboratories represent a comprehensive source of data that is not easily accessible in the United States. Variability in testing methods and data storage would present challenges for data aggregation, summary, and interpretation.

Evaluation of the BIOMIC video reader system for routine use in the clinical microbiology laboratory

The BIOMIC Video Reader System (Giles Scientific, New York, NY, USA) is a semi-automated AST method that combines disk diffusion testing with automated reading and data interpretation. We evaluated this system with 497 strains comprising a total of 5821 drug organism combinations (DOC) from our routine diagnostic laboratory. Additionally, we compared the time required of the manual and the automated method. The overall agreement of interpretative categories of all DOC was 96.1%. However, comparing complete tests the agreement was only 70.8%. The average time required of the BIOMIC system to complete a test was more than twice as long as that of the manual method. Our data suggest that the tested version of the BIOMIC system cannot be recommended for routine use in diagnostic laboratories.

Evaluation of a computerized antimicrobial susceptibility system with bacteria isolated from animals

The BIOMIC is a computerized system used to calculate the minimal inhibitory concentration (MIC) of an antimicrobial agent from a zone of inhibition generated by a disk diffusion test. This system was developed using bacterial pathogens of human origin. This study investigated the use of the BIOMIC system for determining MICs for bacterial pathogens from animals. The MICs generated by the BIOMIC system were compared with the MICs generated using a broth microdilution testing method. A total of 663 drug-organism combinations was tested. These combinations included 3 species of gram-positive bacteria, 5 species of gram-negative bacteria, and the antimicrobial agents ampicillin, gentamicin, cephalothin, ciprofloxacin, enrofloxacin, trimethoprim/sulfamethoxazole, tetracycline, and erythromycin. Overall, the MICs generated by the BIOMIC system correlated with the broth microdilution MICs for 72% of the total drug-organism combinations tested. The Pseudomonas aeruginosa strains tested showed the highest agreement between the 2 systems, with 100% for all antibacterial agents tested, whereas Pasteurella haemolytica, Pasteurella multocida, and enterococci showed the least agreement (76%, 57%, and 47%, respectively). Among these organisms, trimethoprim-sulfa showed the least agreement (31%) and ciprofloxacin showed the greatest (91%). These results indicate that the BIOMIC system could be a useful tool in veterinary medicine for producing quantitative antimicrobial susceptibility results. However, it is currently unreliable for some drug-bacteria combinations. This discrepancy possibly could be corrected by modification of the software using data points generated by a large-scale study.

Determination of penicillin MICs for Streptococcus pneumoniae by using a two- or three-disk diffusion procedure

The potential for the use of the disk diffusion method to accurately predict penicillin MICs for Streptococcus pneumoniae was investigated with penicillin (6 microg), methicillin (5 microg), and oxacillin (1 microg) disks. A total of 183 S. pneumoniae isolates were tested by three MIC procedures (agar dilution, microdilution, and E-test). Regression analyses of the geometric mean of the three MIC results against (i) the sum of the zone diameters for methicillin, penicillin, and oxacillin disks; (ii) the sum of the zone diameters for methicillin and penicillin disks; and (iii) each of the three individual zone diameters were performed. Calculated MICs were determined from each of these regression analyses and compared to the mean reference MICs. A high level of correlation was obtained with both the two- and the three-disk procedures (r = 0.97), with essential agreement rates (+/-1 doubling dilution) between MICs calculated by the three-disk procedure and the two-disk procedure and the mean reference MICs of 98.4 and 98.9%, respectively. No major or very major errors were obtained with the two- or three-disk procedures. The accuracy of the disks used individually was lower (r = 0.84 to 0.93). However, oxacillin and methicillin disk testing remain excellent for screening strains, with all penicillin-susceptible strains having zones of >21 and >22 mm, respectively. The combination disk procedure, which involves the use of three disks (methicillin, oxacillin, and penicillin) or two disks (methicillin and penicillin) for testing S. pneumoniae, can provide accurate penicillin MICs and qualitative category results that are comparable to results obtained by the E-test, agar, and microdilution MIC methods.

Laboratory issues in the detection and reporting of antibacterial resistance

The emergence of antimicrobial resistance among several common bacterial pathogens requires that clinical microbiology laboratories have the ability to promptly and accurately recognize resistance in patients' isolates. Laboratories have several options for performing routine susceptibility testing, including the broth microdilution procedure (with or without instrumentation for test reading), automated instrument systems that provide rapid results, antibiotic gradient diffusion, and disk diffusion procedures. In addition, there are definitive screening tests capable of recognizing resistance to drugs of choice among several common bacterial species based on single drug concentration tests or rapid spot tests. The likely emergence of still newer resistance mechanisms will provide a challenge to clinical microbiologists to devise accurate, yet cost-effective strategies for use in the future.

Comparison of efficacy and cost-effectiveness of BIOMIC VIDEO and Vitek antimicrobial susceptibility test systems for use in the clinical microbiology laboratory

Antimicrobial susceptibility testing expense may be a significant portion of a clinical microbiology laboratory's budget. This study compares the BIOMIC VIDEO system (Giles Scientific, Inc., New York, N.Y.) with the Vitek system (bioMérieux Vitek, Inc., Hazelwood, Mo.), an established automated method of antimicrobial susceptibility testing with the ability to generate MIC data. The BIOMIC system is relatively inexpensive and automates the reading of the classical disk agar diffusion test to provide both qualitative (susceptibility interpretation) and quantitative (MIC) data. The overall MIC correlation between the two systems for the 2,913 drug-organism combinations tested was 92.6%. The overall agreement for susceptibility interpretation was 97.4%. The BIOMIC system offers a 57.4% savings per test over the Vitek system. The BIOMIC system utilizes an older technology which is more efficient and yet yields results comparable to those of established automated MIC methods. The savings achievable in laboratories and hospitals nationwide may contribute significantly to the containment of national health care expenditures.

Established antimicrobial susceptibility testing methods with a new twist--points to consider and a glimpse of the future

The developments seen in these systems allow speculation about future trends in antimicrobial susceptibility testing methods. Microbiology system manufacturers seem to be heeding the call of all industry, for greater automation, enhanced data management capabilities and increased flexibility (see Table 2 below). [table: see text] Cost seems to be less of an issue. This may be due to the decrease in the availability of medical technologists and the need to find systems with better throughput and increased productivity. Increased automation, data management capabilities, and walkaway technology may justify the additional cost of some of these systems. The computer software package provided with these systems is becoming increasingly important with the focus on quality assurance and utilization. Computer generated data analysis gives the microbiologist the tools to educate physicians through the use of selective reporting functions, antibiograms, cost analysis and drug effectiveness comparisons. Each of the four systems is unique and will probably find a niche among the various markets that exist in the United States, European and other specialized markets. The lack of automation in the ALAMAR system may be its selling point in those areas where automation is not affordable, but new ways are being sought for ease of interpretation of results. BIOMIC and CATHRA systems may be more beneficial to those microbiologists who do not want to stop doing traditional Bauer-Kirby or agar dilution methods, but require computer enhancements. ALADIN, may fill a niche to which other walkaway systems have not adapted, but because of its expense, will face more demands than the other three systems covered in this review.

Automated interpretation of disk diffusion antibiotic susceptibility tests with the radial profile analysis algorithm

An original algorithm referred to as the radial profile analysis algorithm was implemented on a Macintosh Quadra 700 computer to provide an automatic determination of the inhibition zone diameters of antibiotic susceptibility tests performed with the disk diffusion method. After digitization of the petri plate image, each antibiotic disk is recognized and labeled. Pixels of the local zone around each disk are then used for generating a profile pattern that is subjected to decision rules. The resulting estimate of the inhibition zone diameter is then automatically compared with conventional breakpoints for classifying the tested strain in one of the clinical categories of antibiotic susceptibility. The program is also able to request a human reading for some rare plates difficult to interpret. The algorithm accuracy was tested by comparing the results with a combination of independent human measurements performed on the tested plates. The test sample was composed of 98 strains, and 2,552 tests of 40 distinct antibiotics were subjected to the analysis. The difference between the automatic and human diameter estimates was less than 4 mm in 90% of the tests. The agreement between the automatic and human clinical categorizations amounted to 95.5%, and severe (major and very major) disagreements were found in 5.6% of the tests performed with staphylococci but only 0.3% of the tests with gram-negative rods. We conclude that the radial profile analysis algorithm is a solid backbone for an automatic system dedicated to the clinical interpretation of disk diffusion antibiotic susceptibility tests.

Comparison of BIOGRAM and commercial microdilution antimicrobial susceptibility test systems

The BIOGRAM (Difco Laboratories, Detroit, Mich.) system, which is designed to calculate MICs from disk diffusion zone diameters, was compared with two commercial microdilution antimicrobial susceptibility systems. A total of 111 clinical isolates were evaluated with each test system. Six additional isolates were tested in a comparison between BIOGRAM and Sceptor (Johnston Laboratories, Inc. Towson, Md.) systems. BIOGRAM demonstrated an overall correlation with the Sceptor microdilution method of 95.7% for 1,287 organism-antimicrobial susceptibility combinations. The BIOGRAM and UniScept (Analytab Products, Inc., Plainview, N.Y.) systems were in agreement in 90.3% of 1,048 organism-antimicrobial susceptibility combinations tested. All methicillin-resistant staphylococci were detected by the standard disk agar diffusion method used with the BIOGRAM system. The BIOGRAM system provides an acceptable alternative to these commercial systems for the determination of quantitative susceptibility.