Comparison of agar dilution, disk diffusion, MicroScan, and Vitek antimicrobial susceptibility testing methods to broth microdilution for detection of fluoroquinolone-resistant isolates of the family Enterobacteriaceae

Meta-Analysis of In Vitro Antimicrobial Capacity of Extracts and Essential Oils of Syzygium aromaticum, Citrus L. and Origanum L.: Contrasting the Results of Different Antimicrobial Susceptibility Methods

Diffusion methods, including agar disk-diffusion and agar well-diffusion, as well as dilution methods such as broth and agar dilution, are frequently employed to evaluate the antimicrobial capacity of extracts and essential oils (EOs) derived from Origanum L., Syzygium aromaticum, and Citrus L. The results are reported as inhibition diameters (IDs) and minimum inhibitory concentrations (MICs), respectively. In order to investigate potential sources of variability in antimicrobial susceptibility testing results and to assess whether a correlation exists between ID and MIC measurements, meta-analytical regression models were built using in vitro data obtained through a systematic literature search. The pooled ID models revealed varied bacterial susceptibilities to the extracts and in some cases, the plant species and methodology utilised impacted the measurements obtained (p < 0.05). Lemon and orange extracts were found to be most effective against E. coli (24.4 ± 1.21 and 16.5 ± 0.84 mm, respectively), while oregano extracts exhibited the highest level of effectiveness against B. cereus (22.3 ± 1.73 mm). Clove extracts were observed to be most effective against B. cereus and demonstrated the general trend that the well-diffusion method tends to produce higher ID (20.5 ± 1.36 mm) than the disk-diffusion method (16.3 ± 1.40 mm). Although the plant species had an impact on MIC, there is no evidence to suggest that the methodology employed had an effect on MIC (p > 0.05). The ID–MIC model revealed an inverse correlation (R2 = 47.7%) and highlighted the fact that the extract dose highly modulated the relationship (p < 0.0001). The findings of this study encourage the use of extracts and EOs derived from Origanum, Syzygium aromaticum, and Citrus to prevent bacterial growth. Additionally, this study underscores several variables that can impact ID and MIC measurements and expose the correlation between the two types of results.

A prevalence and molecular characterization of novel pathogenic strains of Macrococcus caseolyticus isolated from external wounds of donkeys in Khartoum State -Sudan

A pathogenic strain of Macrococcus caseolyticus (M. caseolyticus) was isolated from wounds infection during an investigation on donkeys in Khartoum State. (122) samples were collected from external wounds (head, abdomen, back and leg) during different seasons. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified 31 virulent genes of disease and defense, including methicillin-resistant genes, TatR family and ANT(4')-Ib. Plasmid rep22 was identified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel M. caseolyticus strain (DaniaSudan). The MLST-tree-V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain DaniaSudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. Mice modeling showed bacteremia and many clinical signs (swelling, allergy, wounds, and hair loss). Enlargement, hyperemia, adhesions and abscesses were observed in many organs.Constructive conclusionThe prevalence of the strain was 4.73%, with significant differences between collection seasons and locations of wounds. A highly significant association between doses (105 CFU/ml, 102 CFU/ml, Intra-peritoneum and sub-cutaneous) and swelling, developing of allergy and loss of hair (p = 0.001, p = 0.000 and p = 0.005) respectively were seen.This result represents the first report of pathogenic strains of M. caseolyticus worldwide.

Susceptibility testing and reporting of new antibiotics with a focus on tedizolid: an international working group report

Inappropriate use and overuse of antibiotics are among the most important factors in resistance development, and effective antibiotic stewardship measures are needed to optimize outcomes. Selection of appropriate antimicrobials relies on accurate and timely antimicrobial susceptibility testing. However, the availability of clinical breakpoints and in vitro susceptibility testing often lags behind regulatory approval by several years for new antimicrobials. A Working Group of clinical/medical microbiologists from Brazil, Canada, Mexico, Saudi Arabia, Russia and the UK recently examined issues surrounding antimicrobial susceptibility testing for novel antibiotics. While commercially available tests are being developed, potential surrogate antibiotics may be used as marker of susceptibility. Using tedizolid as an example of a new antibiotic, this special report makes recommendations to optimize routine susceptibility reporting.

A cost-saving strategy for processing isolated uropathogens in community-acquired urinary tract infections

Outpatient urine samples are among the most commonly processed in a microbiology laboratory, which involves a high economic burden. The aim of this study was compare cost and efficiency to process uropathogens between MicroScan system (2010-2011) versus a chromogenic medium and the disk diffusion method (2013-2014). In the first period, a total 9918 bacterial populations were isolated from urine samples. Annual estimated costs during 2010 and 2011 for processing were EUR 53,818 and EUR 57,306, respectively (EUR 111,124 total). In the second period, a total 11,728 bacterial isolates were processed, with annual estimated costs of EUR 21,078 and EUR 23,248, respectively (EUR 44,326 total). We included the cost for a laboratory technician (252h worked per year), estimated at EUR 2500 per year. The mean estimated savings were EUR 66,797 (60%).The identification by chromogenic media and antibiotic susceptibility patterns by disk diffusion method was similar to MicroScan in both study periods. Only some isolated Citrobacter spp., Enterobacter spp., Morganella morganii, and Providencia spp. were misidentified. The strategy reported here did not affect the quality of the results and yielded substantial cost savings.

Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli

For Enterobacteriaceae such as Salmonella spp. and Escherichia coli, no unified interpretive resistance criteria exist for streptomycin, an epidemiologically important antibiotic. As part of the National Antimicrobial Resistance Monitoring System, we had previously used a minimum inhibitory concentration of ≥ 64 μg mL(-1) as an epidemiological cutoff value (ECV) to define non-wild-type isolates. To identify whether this ECV correlated with genetic determinants of resistance, we performed whole-genome sequencing of 463 Salmonella and E. coli isolates to identify streptomycin resistance genotypes. From this analysis, we found that using a streptomycin resistance breakpoint of ≥ 64 μg mL(-1) classified over 20% of strains possessing aadA or strA/strB resistance genes as wild-type. Therefore, to improve the concordance between genotypic and phenotypic data, we propose reducing the phenotypic cutoff values to ≥ 32 μg mL(-1) for both Salmonella and E. coli, to be used widely as ECVs to categorize non-wild-type isolates.

Serotype distribution and antimicrobial susceptibilities of Streptococcus agalactiae isolated from infected cultured tilapia (Oreochromis niloticus) in Thailand: Nine-year perspective

Streptococcus agalactiae (group B Streptococcus, GBS) infection remains a major problem associated with high mortality of cultured tilapia worldwide. The present study reports the serotype distribution and antimicrobial susceptibilities of GBS isolated from infected tilapia cultured in Thailand. One hundred and forty-four GBS isolates were identified by biochemical, serological and molecular analyses. Of these 144 GBS isolates, 126 were serotype Ia and 18 were serotype III. Antimicrobial susceptibilities of the 144 GBS isolates were determined by the disc diffusion method. Most GBS isolates were susceptible to lincomycin, norfloxacin, oxytetracycline, ampicillin, erythromycin and chloramphenicol, but resistant to oxolinic acid, gentamicin, sulfamethoxazole and trimethoprim. However, 17 isolates displayed an oxytetracycline-resistant phenotype and harboured the tet(M) gene. The broth microdilution method was used to determine the minimal inhibitory concentrations (MICs) of 17 oxytetracycline-resistant GBS isolates, and then minimal bactericidal concentrations (MBCs) of these isolates were evaluated. Oxytetracyline-resistant isolates were found to be susceptible to ampicillin, lincomycin, norfloxacin, erythromycin and chloramphenicol, with the MIC and MBC ranging from ≤ 0.125 to 0.5 μg ml- 1 and ≤ 0.125 to 2 μg ml- 1, respectively. Moreover, all 17 oxytetracycline-resistant isolates demonstrated resistance to trimethoprim, oxolinic acid, gentamicin, sulfamethoxazole and oxytetracycline, with the MIC and MBC ranging from 16 to ≥ 128 μg ml- 1 and ≥ 128 μg ml- 1, respectively. These findings are useful information for antibiotic usage in fish aquaculture.

Bioautography detection in thin-layer chromatography

Bioautography is a microbial detection method hyphenated with planar chromatography techniques. It is based mainly on antimicrobial or antifungal properties of analyzed substances. The review discusses three versions of bioautography, i.e. contact, immersion and direct bioautography. The more concern is given to the last one. Many applications are quoted, not only for testing various groups of compounds, but also for investigating biochemical processes and factors influencing bacterial growth. Additionally, related methods, which can be included into direct bioautography, are discussed. The most promising among them seems to be TLC-bioluminescence screening.

Role of azithromycin against clinical isolates of family enterobacteriaceae: A comparison of its minimum inhibitory concentration by three different methods

PURPOSE

To determine the effect of azithromycin, a new azalide antibiotic, on clinical isolates of the family Enterobacteriaceae and to determine and compare its minimum inhibitory concentration (MIC) by disk diffusion, agar dilution and E-test methods.

MATERIALS AND METHODS

One hundred fifty-nine bacterial strains belonging to the family Enterobacteriaceae, isolated from different clinical samples, were tested for their susceptibility to azithromycin by disk diffusion, agar dilution and E-test methods. The MIC values were analysed and the percentages of agreement between the different methods were mentioned.

RESULTS

Of the 159 isolates of the family Enterobacteriaceae, 60.37% were E. coli followed by Klebsiella species 28.3%, Salmonella and Shigella species 3.77% and Enterobacter and Citrobacter species 1.88% each. Maximum isolates were obtained from urine 117/159 (73.58%). Azithromycin was found to be more active against Salmonella and Shigella species, showing 100% sensitivity the by E-test and 83.33% by the disk diffusion methods. In the agar dilution method, 83.33% of Salmonella and 66.66% of Shigella species were sensitive to azithromycin. The overall agreement between disk diffusion and agar dilution method was 96.8%, between agar dilution and E-test was 88% and between disk diffusion and E-test was 91.2%.

CONCLUSION

Azithromycin may become an important addition to our antimicrobial strategies, especially for the treatment of bacterial diarrhoea and infections caused by Salmonella typhi.

Increased fluoroquinolone resistance with time in Escherichia coli from >17,000 patients at a large county hospital as a function of culture site, age, sex, and location

Background

Escherichia coli infections are common and often treated with fluoroquinolones. Fluoroquinolone resistance is of worldwide importance and is monitored by national and international surveillance networks. In this study, we analyzed the effects of time, culture site, and patient age, sex, and location on fluoroquinolone resistance in E. coli clinical isolates.

Methods

To understand how patient factors and time influenced fluoroquinolone resistance and to determine how well data from surveillance networks predict trends at Ben Taub General Hospital in Houston, TX, we used Perl to parse and MySQL to house data from antibiograms (n ≅ 21,000) for E. coli isolated between 1999 to 2004 using Chi Square, Bonferroni, and Multiple Linear Regression methods.

Results

Fluoroquinolone resistance (i) increased with time; (ii) exceeded national averages by 2- to 4-fold; (iii) was higher in males than females, largely because of urinary isolates from male outpatients; (iv) increased with patient age; (v) was 3% in pediatric patients; (vi) was higher in hospitalized patients than outpatients; (vii) was higher in sputum samples, particularly from inpatients, than all other culture sites, including blood and urine, regardless of patient location; and (viii) was lowest in genital isolates than all other culture sites. Additionally, the data suggest that, with regard to susceptibility or resistance by the Dade Behring MicroScan system, a single fluoroquinolone suffices as a "surrogate marker" for all of the fluoroquinolone tested.

Conclusion

Large surveillance programs often did not predict E. coli fluoroquinolone resistance trends at a large, urban hospital with a largely indigent, ethnically diverse patient population or its affiliated community clinics.

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.

Detection of decreased susceptibility to fluoroquinolones in Salmonella spp. by five different methods including real-time polymerase chain reaction (PCR)

Detection of Salmonella spp. isolates showing decreased susceptibility to fluoroquinolones has become important owing to the increasing prevalence of these strains and their association with treatment failure. Nalidixic acid agar dilution, nalidixic acid disk diffusion, MicroScan automated system and real-time polymerase chain reaction (PCR) (LightCycler) followed by melting temperature (Tm) analysis are compared with ciprofloxacin agar dilution as suitable methods to detect decreased susceptibility to fluoroquinolones in 100 Salmonella spp. isolates. Three minor discrepancies were found for nalidixic acid disk diffusion, one minor discrepancy was found for nalidixic acid agar dilution and Tm analysis, and one major discrepancy was found for MicroScan. Nalidixic acid disk diffusion was confirmed as a good screening method. Tm analysis is a rapid and accurate method for detecting decreased susceptibility to fluoroquinolones due to gyrA mutations in Salmonella spp.

Two-center collaborative evaluation of performance of the BD phoenix automated microbiology system for identification and antimicrobial susceptibility testing of gram-negative bacteria

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, MD) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) of the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 494 bacterial isolates including various species of the Enterobacteriaceae and 110 nonfermentative gram-negative bacteria were investigated: of these, 385 were single patient isolates, and 109 were challenge strains tested at one center. The performance of the Phoenix extended-spectrum beta-lactamase (ESBL) test was also evaluated for 203 strains of Escherichia coli, Klebsiella pneumoniae, and Klebsiella oxytoca included in the study. Forty-two antimicrobial drugs were tested, including members of the following drug classes: aminoglycosides, beta-lactam antibiotics, beta-lactam/beta-lactamase inhibitors, carbapenems, cephems, monobactams, folate antagonists, quinolones, and others. Phoenix system ID results were compared to those of the laboratories' routine ID systems (API 20E and API CHE, ATB ID32E, ID32GN, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS (now CLSI) guidelines (NCCLS document M100-S9, approved standard M7-A4). Discrepant results were repeated in duplicate. Concordant IDs of 98.4 and 99.1% were observed for the Enterobacteriaceae and the nonfermentative group, respectively. For AST results, the overall essential agreement was 94.2%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.6, 0.6, and 1.9%, respectively. In terms of ESBL detection, Phoenix results were 98.5% concordant with those of the reference system, with 98.0% sensitivity and 98.7% specificity. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared: the AST performance was highly equivalent to that of the SBM reference method, and the system proved to be very accurate for the detection of ESBL producers.

Evaluation of the BD Phoenix automated microbiology system for identification and antimicrobial susceptibility testing of staphylococci and enterococci

We evaluated the Phoenix automated microbiology system (BD Diagnostic Systems, Sparks, MD) for the identification (ID) and antimicrobial susceptibility testing (AST) of challenge and clinical staphylococci and enterococci recovered from patients in a tertiary-care medical center. In total, 424 isolates were tested: 90 enterococci; 232 Staphylococcus aureus isolates, including 14 vancomycin-intermediate S. aureus isolates; and 102 staphylococci other than S. aureus (non-S. aureus). The Phoenix panels were inoculated according to the manufacturer's instructions. The reference methods for ID comparisons were conventional biochemicals and cell wall fatty acid analysis with the Sherlock microbial identification system (v 3.1; MIDI, Inc. Newark, DE). Agar dilution was the reference AST method. The overall rates of agreement for identification to the genus and the species levels were 99.7% and 99.3%, respectively. All S. aureus isolates and enterococci were correctly identified by the Phoenix panels. For the non-S. aureus staphylococci, there was 98.0% agreement for the ID of 16 different species. The AST results were stratified by organism group. For S. aureus, the categorical agreement (CA) and essential agreement (EA) were 98.2% and 98.8%, respectively. Three of three very major errors (VMEs; 1.7%) were with oxacillin. For non-S. aureus staphylococci, the CA, EA, VME, major errors, and minor error rates were 95.7%, 96.8%, 0.7%, 1.7%, and 2.9%, respectively. The two VMEs were with oxacillin. For the enterococci, there was 100% CA and 99.3% EA. All 36 vancomycin-resistant enterococci were detected by the Phoenix system. The Phoenix system compares favorably to traditional methods for the ID and AST of staphylococci and enterococci.

Antibiotic susceptibility tests directly on urine samples using Uro-Quick, a rapid automated system

During the period June 2003-March 2004, 12,579 urine samples were examined employing the Uro-Quick system. Positive samples (1,948) were subsequently Gram-stained and processed by standard procedures for microorganism identification and antibiotic susceptibility determination by the disk diffusion method. Results of this latter test were compared with those obtained employing the new rapid Uro-Quick method. Antibiotics were introduced in vials containing 2 ml of Mueller-Hinton broth, then 0.5 ml of urine or a bacterial suspension in broth were added; a vial without drug was used as control. After 3 and 5 hours of incubation (for Gram-negative and Gram-positive strains respectively) the instrument showed the results. No growth and a growth curve like the control indicated susceptible and resistant strains respectively. Overall 1,590 Gram-negative strains were tested against ciprofloxacin, nitrofurantoin, amoxicillin-clavulanate, ceftazidime, fosfomycin, imipenem, amikacin, trimethoprim-sulfamethoxazole, and piperacillin-tazobactam, while 358 Gram-positive bacteria were assessed against ciprofloxacin, nitrofurantoin, amoxicillin-clavulanate, ampicillin, fosfomycin, gentamicin, oxacillin and trimethoprim-sulfamethoxazole. Against the major urinary tract pathogens (Escherichia. coli, enterococci, Klebsiella spp. and Proteus spp.) agreement between the Uro-Quick system and the disk diffusion test generally was >90% for all antibiotics tested. On the basis of these results the system appears useful not only for bacteriuria screening, but also to rapidly test the antibiotic susceptibility of common uropathogens.

[Antimicrobial susceptibility of the uropathogens in out patients in Goiânia City, Goiás State]

Due to the fact that the number of multiresistant microorganisms which cause cystitis is increasing, the objective of this study was to identify the pathogens that cause urinary tract infection in women and determine antimicrobial susceptibility. We analyzed 442 urine samples from June 2002 to August 2003. Identification through biochemical and enzymatic assays, and the antibiogram by Disk diffusion method were performed. Out of these samples, 78 were positive for urinary tract infection (17.6%). Escherichia coli were the microorganisms that most frequently caused infections (67.9%). Gram-negative bacteria exhibited resistance to amoxicillin in 74.6% of the cases. Most were ceftazidime and gentamicin sensitive. Gram-positive bacteria were resistant in 72.7% of the samples to ampicillin, and they were trimethoprim/sulfamethoxazole, vancomycin and linezolid sensitive. It was concluded that investigation of bacterial resistance is necessary to provide information for new therapeutic options.

Association between antibiotic resistance and community prescribing: a critical review of bias and confounding in published studies

The reported association between antibiotic prescribing and resistance may be subject to bias or confounding. Bias describes any effect at any stage of investigation or inference tending to produce results that depart systematically from the true value. A confounding variable is one that is associated independently with both exposure and outcome. Confounding variables may create an apparent association or mask a real association. Pharmacoepidemiology is the study of the use and the effects of drugs in large numbers of people. We have used standard pharmacoepidemiological methods to investigate sources of bias and confounding in the association between prescribing and resistance. We conclude that the association is statistically valid and that the consistency of evidence supports a cause-effect relationship. Nonetheless, several important sources of bias and confounding must be taken into account in future studies that analyze the impact of prescribing policies on resistance.

Differences in antimicrobial susceptibility among hospitals in an integrated health system

We evaluated the differences in antimicrobial susceptibility among hospitals in three different integrated healthcare systems. Each system provided antibiogram-susceptibility reports from representative hospitals. Reports were analyzed for statistically significant differences between hospitals in a given system for nine important organisms. We found numerous significant interhospital differences in antimicrobial-susceptibility patterns within health systems. For this reason, the practice of combining antibiotic-susceptibility data into a systemwide antibiogram should be discouraged.