Eubacterium bacteremia - a retrospective observational study of a seldom found anaerobic pathogen

BACKGROUND

Human infections due to Eubacterium are rare and knowledge of the condition is limited. This study aimed to describe clinical characteristics and outcome in patients with Eubacterium bacteremia.

METHODS

Episodes of Eubacterium bacteremia were identified through the clinical microbiology laboratory in Lund, Sweden. Medical records were retrospectively reviewed. Blood isolates of Eubacterium were collected and antibiotic susceptibility testing was performed with agar dilution.

RESULTS

Seventeen patients with Eubacterium bacteremia were identified of whom six had monomicrobial bacteremia. The incidence was 1.7 cases of Eubacterium bacteremia per million inhabitants and year. The median age was 67 years (interquartile range 63-79 years), and six patients had some form of malignancy. Most of the patients an abdominal focus of infection and the 30-day mortality was low (n = 1).

CONCLUSIONS

Invasive infections with Eubacterium have a low incidence. The condition has a low mortality and an abdominal focus of infection, and malignancy, is common.

Genomic analysis of Fosfomycin resistance in multi-drug resistant uropathogens and comparison of in-vitro susceptibility methods uropathogens

BACKGROUND AND OBJECTIVES

Urinary tract infection is one of the most common bacterial infections causing high morbidity and mortality. The alarming rise of multidrug-resistant uropathogens worldwide forced the clinician to rethink the old drugs like Fosfomycin for its therapeutic management. Our objective was to compare agar dilution, disc diffusion and E-test method for antimicrobial susceptibility testing of Fosfomycin against different drug-resistant uropathogens.

MATERIALS AND METHODS

Consecutive 181 uropathogens were tested for Fosfomycin susceptibility using agar dilution, disc diffusion and E-test. Results were interpreted using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. Whole genome sequencing analysis was done on the 4 XDR/PDR Fosfomycin resistant Klebsiella pneumoniae isolates.

RESULTS

Escherichia coli was found as the most common (62.4%) uropathogen followed by Klebsiella pneumoniae (21%). Considering agar dilution as the gold standard, 6.1% of isolates were resistant to Fosfomycin. Following CLSI breakpoints, the susceptibility of Escherichia coli, Klebsiella pneumoniae, other Enterobacterales and Pseudomonas aeruginosa were 92.9%, 92.1%, 100%, 100%; whereas using EUCAST breakpoints the susceptibility rates were 85.7%, 86.9%, 92.9%, and 100%, respectively. The essential agreement, categorical agreement, major error, and very major error for E-test/disc diffusion for all the organisms were 91.2%/Not Applicable, 95%/93.9%, 1.8%/4.7%, 9.1%/9.1%, respectively. Whole-genome sequencing showed mutation UhpT gene as well as the presence of plasmid-mediated fosA5 or fosA6 genes conferring Fosfomycin resistance.

CONCLUSION

This result supports very low resistance of Enterobacterales against Fosfomycin; hence should be considered a valuable option to treat multidrug-resistant uropathogens. Disc diffusion was observed to be a convenient method for Fosfomycin susceptibility testing compared to agar dilution.

Efficacy of Disc Diffusion and Agar Dilution Methods in Evaluating Helicobacter pylori Susceptibility to Antibiotics

BACKGROUND: In this study, efficacy and consistency of disc diffusion (DD) and agar dilution (AD) methods in determining Helicobacter pylori susceptibility to antibiotics were evaluated using Brucella blood agar (BBA) in both methods and tetrazolium egg yolk agar (TEYA) in AD. METHODS: Twenty H. pylori isolates were tested for susceptibility to nine antibiotics; metronidazole (MTZ), clarithromycin (CLR), amoxicillin (AMX), tetracycline (TET), ofloxacin (OFX), levofloxacin (LVX), ciprofloxacin (CIP), furazolidone (FRZ), and rifampin (RIF). Antibiotics solutions were impregnated into blank paper disks on BBA in the DD method or added to BBA (ADB) or TEYA (ADT) media in the AD method. Suspensions of H. pylori isolates were surface or spot inoculated on solid media. Plates were incubated in CO₂ incubator at 37°C for 5-7 days. RESULTS: The highest rate of susceptibility to MTZ (65%) was determined by DD method compared with AD method (ADB: 40%, ADT: 30%). Both methods showed similar CLR (85%) and AMX (100%) susceptibility rates. Susceptibility to remaining antibiotics, determined by DD and ADB/ADT media were in respective order as 95%, 75% / 75% for TET, 100%, 95% / 85% for FRZ, 85%, 85% / 75% for OFX, 90%, 95% / 85% for LVX, 90%, 85% / 85% for CIP, and 100%, 85% / 75% for RIF. CONCLUSION: DD and AD methods showed consistency in determining 161 (89.4%) susceptibility and resistance and inconsistency in determining 19 (10.6%) susceptibility and resistance (P < 0.05). DD is recommended as a cheap and easy method with the efficacy and precision comparable to the AD method in determining H. pylori susceptibility to antibiotics.

Evaluating the performance characteristics of different antimicrobial susceptibility testing methodologies for testing susceptibility of gram-negative bacteria to tigecycline

Background

The current emergence of multi-drug resistance among nosocomial pathogens has led to increased use of last-resort agents including Tigecycline (TGC). Availability of reliable methods for testing TGC susceptibility is crucial to accurately predict clinical outcomes. We evaluated the influence of different methodologies and type of media on TGC susceptibility of different gram-negative bacteria of clinical origin.

Methods

The TGC susceptibility of 84 clinical isolates of Klebsiella pneumoniae (n = 29), Escherichia coli (n = 30), and Acinetobacter baumannii (n = 25) was tested by broth microdilution (BMD), Etest, agar dilution (AD) and disk diffusion (DD) methods using Mueller Hinton agar from Difco and Mueller Hinton broth (MHB) from two different manufacturers (Difco and Condalab). FDA TGC susceptibility breakpoints issued for Enterobacteriaceae were used for interpretation of the results.

Results

MICs determined by BMD using MHB from two suppliers showed a good correlation with overall essential agreement (EA) and categorical agreement (CA) being 100% and 95% respectively. However, a twofold rise in BMD-Condalab MICs which was detected in 50% of the isolates, resulted in changes in susceptibility categories of few isolates with MICs close to susceptibility breakpoints leading to an overall minor error (MI) rate of 4.7%. Among the tested methods, Etest showed the best correlation with BMD, being characterized with the lowest error rates (only 1% MI) and highest overall EA (100%) and CA (98.8%) for all subsets of isolates. AD yielded the lowest overall agreement (EA 77%, CA 81%) with BMD in a species dependent manner, with the highest apparent discordance being found among the A. baumannii isolates. While the performance of DD for determination of TGC susceptibility among Enterobacteriaceae was excellent, (CA:100% with no errors), the CA was lower (84%) when it was used for A. baumannii where an unacceptably high minor-error rate was noted (16%). No major error or very major error was detected for any of the tested methods.

Conclusions

Etest can be reliably used for TGC susceptibility testing in the three groups of studied bacteria. For the isolates with close-to-breakpoint MICs, testing susceptibility using the reference method is recommended.

Accurate detection of oxacillin-resistant Staphylococcus lugdunensis by use of agar dilution

BACKGROUND/PURPOSE

Staphylococcus lugdunensis is a Gram-positive coagulase-negative bacterium and is recognized as a critical pathogenic species recently. Here, we aimed to evaluate the cefoxitin disk diffusion (CDD), oxacillin agar dilution (OAD), and mecA PCR for detecting oxacillin-resistant S. lugdunensis (ORSL) isolates.

METHODS

Multilocus sequence typing (MLST) analysis was performed to determine the clonality of 117 S. lugdunensis isolates isolated between May 2009 and Jul 2014. CDD, OAD, and mecA PCR were used to identify oxacillin-resistant S. lugdunensis (ORSL).

RESULTS

MLST results showed that the most common sequence type (ST) of our S. lugdunensis isolates was ST6 (35.9%) followed by ST3 (28.2%), ST27 (17.9%), and ST4 (6.8%). CDD and OAD showed that 39 and 43 isolates were ORSL, respectively. 4 ST3 CDD-susceptible S. lugdunensis (OSSL) isolates had MIC values ≥ 4 for oxacillin. mecA PCR results showed that 43 OAD-resistant S. lugdunensis and 3 OAD-susceptible ST27 S. lugdunensis had the mecA gene. Therefore, OAD was used as the gold standard to evaluate the performance of CDD and mecA PCR for identifying ORSL. The overall sensitivity, specificity, and accuracy of CCD for ORSL detection was 90.7%, 100%, and 96.8%, respectively. The sensitivity, specificity, and accuracy of mecA PCR for identifying ORSL was 100%, 95.9%, and 97.44%, respectively.

CONCLUSION

Our results indicate that OAD shows higher accuracy for ORSL detection compared with CDD and mecA PCR.

False amoxicillin/clavulanic acid susceptibility in Bacteroides fragilis using gradient strip tests

BACKGROUND

Repeatedly, too low MIC results were obtained in Bacteroides fragilis quality assessment strains, using gradient strip tests with a ratio of amoxicillin:clavulanic acid of 2:1. We aimed to find the most accurate available gradient strip tests for susceptibility testing of amoxicillin/clavulanic acid in B. fragilis in comparison with agar dilution with EUCAST methodology and breakpoints.

METHODS

Twenty-seven clinical B. fragilis isolates were investigated using gold standard EUCAST amoxicillin/clavulanic acid agar dilution (fixed clavulanic acid concentration at 2 mg/L, with increasing amoxicillin concentrations) as well as three commercial gradient strip tests: XL (ratio), AUG (ratio) or AMC (fixed concentration).

RESULTS

Using agar dilution (fixed concentration), 19 isolates were susceptible, 1 isolate was susceptible increased exposure (I) and 7 isolates were resistant. Categorical agreement of the gradient strip tests with agar dilution (fixed concentration) was 70% for XL (ratio), 71% for AUG (ratio) and 89% for AMC (fixed concentration). Very major error rates in comparison with agar dilution (fixed concentration) were 100%, 0%, and 0%, respectively.

CONCLUSIONS

EUCAST breakpoint usage in amoxicillin/clavulanic acid susceptibility tests for B. fragilis should be accompanied by EUCAST methodology. When using alternative methods such as gradient strip tests, a higher degree of alignment with EUCAST methodology, such as using fixed clavulanic acid concentrations, improves precision.

Evaluation of the commercial AD fosfomycin test for susceptibility testing of multidrug-resistant Enterobacterales and Pseudomonas aeruginosa

OBJECTIVES

To compare fosfomycin susceptibility testing with the commercial agar dilution (AD) test, AD Fosfomycin (Liofilchem, Roseto degli Abruzzi, Italy) and the reference AD method, using a collection of multidrug-resistant (MDR) Enterobacterales and Pseudomonas aeruginosa clinical isolates.

METHODS

The collection included 119 carbapenemase-producing Enterobacterales, 53 Enterobacterales producing acquired AmpC-type and/or extended-spectrum β-lactamases and 38 carbapenemase-producing P. aeruginosa, including representatives of different high-risk clones. AD Fosfomycin and AD reference method (ISO 20776-1:2019) were performed starting from the same microbial suspension. Results were interpreted according to EUCAST clinical breakpoints (10.0). Essential agreement (EA), category agreement (CA) and error rates were calculated as described by the International Organization for Standardization.

RESULTS

Of 172 Enterobacterales, 143 (83.1%, including 92.9% (52 of 56) of the NDM-producers and 84.2% (48 of 57) of the KPC-producers) were susceptible to fosfomycin using reference AD. A CA of 91.9% (158 of 172; 95% CI 87.1%-95.3%) and an EA of 92.5% (136 of 147; 95% CI 87.4%-96.0%), respectively, were calculated for the commercial AD Fosfomycin test, with 9.8% (14 of 128) of major errors and no very major errors (0 of 29). Overall, 86.8% (33 of 38) of P. aeruginosa showed a fosfomycin MIC ≤128 mg/L using reference AD. An EA of 84.8% (95% CI 66.3%-92.0%) was calculated for the commercial AD Fosfomycin test, with a CA of 100% (95% CI 93.6%-100%) when considering a tentative breakpoint at 128 mg/L.

CONCLUSIONS

AD Fosfomycin showed an overall good concordance compared with reference AD.

Comparison of minimum inhibitory concentration results for gepotidacin obtained using agar dilution and broth microdilution methods

Gepotidacin (GSK2140944) is a first in class, novel triazaacenaphthylene bacterial type II topoisomerase inhibitor in Phase 3 clinical development for the treatment of gonorrhea and uncomplicated urinary tract infections (acute cystitis). This study tested the equivalency of minimal inhibitory concentrations (MICs) obtained by two reference susceptibility testing methods, agar dilution and broth microdilution, for gepotidacin when tested against various gram-positive and gram-negative organisms. Equivalency, measured as the essential agreement >89.9%, was established between the two methods for determining gepotidacin susceptibility results against Staphylococcus spp., Streptococcus spp., and Escherichia coli. However, for Neisseria gonorrhoeae and Haemophilus influenzae, equivalency was not established. Agar dilution remains the sole dilution reference method for determining gepotidacin MICs against N. gonorrhoeae.

In vitro activity of fosfomycin against mucoid and non-mucoid Pseudomonas aeruginosa strains

OBJECTIVES

Pseudomonas aeruginosa is the most frequent infectious agent in cystic fibrosis patients. P. aeruginosa resistance to first line antibiotics limits therapeutic options, but the therapeutic potential of older generation antibiotics, such as fosfomycin is under investigation. Fosfomycin does not belong to any other antibiotic class and acts by inhibiting the biosynthesis of the bacterial cell wall during the initial phases. A major problem for the use of fosfomycin against P. aeruginosa is the absence of a clinical breakpoint, the last one of 32 μg/mL was proposed in 2013 by the CA-SFM (Comité de l'Antibiogramme de la Société Française de Microbiologie).

METHODS

Sixty-one strains of P. aeruginosa (thirty mucoid and thirty-one non mucoid) were collected from respiratory samples of cystic fibrosis patients. All isolates were identified by MALDI-TOF (Bruker, Bremen, Germany). Fosfomycin MICs against P. aeruginosa were measured using an automated system and confirmed by the gold standard method.

RESULTS

There was no significant difference between mucoid and non-mucoid strains. MIC distribution and susceptibility rates were obtained by agar dilution method and from this data we measured MIC50 and MIC90 which were equal to 32 μg/mL and 64 μg/mL, respectively. From automated method results we measured a very major error (VME), major error (ME) and categorical agreement (CA) which were equal to 0%, 11% and 89%, respectively. Comparing automated and agar dilution methods, a Cohen's kappa equal to 73% (0.726) was measured.

CONCLUSIONS

Our data suggest that fosfomycin has good effect against mucoid and non-mucoid strains of P. aeruginosa and automated systems can be implemented in clinical microbiology laboratories to assess fosfomycin with rapid and reproducible results.

E-test versus agar dilution for antibiotic susceptibility testing of Helicobacter pylori: a comparison study

OBJECTIVE

For evaluating the antibiotic resistance of Helicobacter pylori, the agar dilution method is the gold standard; however, using this method in daily practice is laborious. E-test has been proposed to be an uncomplicated method. This study was aimed at validating the E-test and detecting the presence of any bias between the agar dilution method and E-test.

RESULTS

The agar dilution method and E-test were performed using five antibiotics for 72 strains of H. pylori obtained from clinical patients in Indonesia. The E-test's results showed a higher prevalence of resistance to all the antibiotics tested but the difference was not significant. Results showed high essential agreement (> 90.0%) for all the antibiotics, but only 84.7% for metronidazole. The agreement for MIC value was acceptable for levofloxacin, clarithromycin, and metronidazole. For amoxicillin, it showed only fair agreement (0.25) by the Kappa analysis and significant difference by Passing-Bablok regression. Even though some discrepancies were found, the E-test has an acceptable agreement for levofloxacin, metronidazole, tetracycline, and clarithromycin but further confirmation may be necessary for amoxicillin.

Detection of Overexpression of Efflux Pump Expression in Fluoroquinolone-Resistant Pseudomonas aeruginosa Isolates

Context:

Fluoroquinolones are the most effective antibiotics against Pseudomonas aeruginosa; many strains, however, have shown resistance due to mutations in DNA gyrase, topoisomerase IV, or in the efflux pumps. Little is known about P. aeruginosa efflux pump resistance mechanisms in the Kingdom of Bahrain.

Aim:

The aim was to study efflux pump-mediated fluoroquinolone resistance among P. aeruginosa isolates using phenotypic (E-test and agar dilution) and genotypic (real-time-polymerase chain reaction [RT-PCR]) methods.

Materials and Methods:

Fifty ciprofloxacin-resistant P. aeruginosa isolates were included in this study. Genus and species of P. aeruginosa were confirmed by conventional PCR. The minimum inhibitory concentration (MIC) of ciprofloxacin with and without carbonyl cyanide 3-chlorophenylhydrazone (CCCP) was determined by E-test and agar dilution test. The overexpression of genes MexB, MexD, MexF, and MexY was measured by RT-PCR.

Results:

All isolates were confirmed as P. aeruginosa. Among the fifty isolates, four showed reduction in ciprofloxacin MIC after addition of CCCP. These four isolates showed upregulation of expression of at least one of the four genes by RT-PCR. The mean gene expression of MexB, MexD, MexF, and MexY increased by 1.6, 4.65, 3.4, and 3.68-fold, respectively.

Conclusion:

The results demonstrate the presence and type of efflux pump overexpression, mandating for large multicentric studies.

Quality assurance for genotyping and resistance testing of Clostridium (Clostridioides) difficile isolates - Experiences from the first inter-laboratory ring trial in four German speaking countries

Clostridium (Clostridioides) difficile is a major cause of nosocomial diarrhoea. A first inter-laboratory ring trial was performed in four European countries to evaluate the genotyping and antibiotic susceptibility testing (AST) accuracy. Six C. difficile isolates representing the epidemiologic important ribotypes (RT), RT001, RT002, RT010, RT014, RT027, and RT078 were blinded and send to 21 participating laboratories. Participants tested the samples with their genotyping and AST methods in use for concordance with reference. A total of 21 genotyping- and 14 antimicrobial susceptibility data sets were obtained. Ribotyping (11 participants) correctly identified most RTs (median 91% concordance rate) except for RT002, which was misidentified in 4/11 reports. However, this isolate was correctly asserted to RT002 after an update of a publicly available ribotyping database. Multilocus sequence typing, surface layer sequence typing, DNA microarray based genotyping, and whole genome sequencing, which were used by 1-3 participants, identified all six isolates correctly. AST was done by epsilometry by the participants and compared to agar dilution data determined by the coordinating reference centre. Susceptibilities against metronidazole, moxifloxacin, and vancomycin were correctly identified in 235 of 237 cases and in accordance to agar dilution as the gold standard. Genotyping of the C. difficile test strains revealed a remarkable high concordance on the level of ribotypes with a wide variety of methods. Epsilometry appears to be a reliable method for AST of C. difficile isolates in routine clinical microbiology laboratories.

Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods

Background

UK public health organisations perform routine antimicrobial susceptibility tests (ASTs) to characterise the potential for antimicrobial resistance in Salmonella enterica serovars. Genetic determinants of these resistance mechanisms are detectable by whole genome sequencing (WGS), however the viability of WGS-based genotyping as an alternative resistance screening tool remains uncertain. We compared WGS-based genotyping, disk diffusion and agar dilution to the broth microdilution reference AST for 102 Salmonella enterica serovar Typhimurium (S. Typhimurium) isolates across 11 antimicrobial compounds.

Results

Genotyping concordance, interpreted using epidemiological cut-offs (ECOFFs), was 89.8% (1007/1122) with 0.83 sensitivity and 0.96 specificity. For seven antimicrobials interpreted using Salmonella clinical breakpoints, genotyping produced 0.84 sensitivity and 0.88 specificity. Although less accurate than disk diffusion (0.94 sensitivity, 0.93 specificity) and agar dilution (0.83 sensitivity, 0.98 specificity), genotyping performance improved to 0.89 sensitivity and 0.97 specificity when two antimicrobials with relatively high very major error rates were excluded (streptomycin and sulfamethoxazole).

Conclusions

An 89.8% concordance from WGS-based AST predictions using ECOFF interpretations suggest that WGS would serve as an effective screening tool for the tracking of antimicrobial resistance mechanisms in S. Typhimurium. For use as a standalone clinical diagnostic screen, further work is required to reduce the error rates for specific antimicrobials.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1520-9) contains supplementary material, which is available to authorized users.

High primary resistance to metronidazole and levofloxacin, and a moderate resistance to clarithromycin in Helicobacter pylori isolated from Karnataka patients

Background

Due to increased prevalence of H. pylori antimicrobial resistance worldwide and more importantly the resistance patterns vary between different geographical regions, it is important to survey local H. pylori antibiotic resistance profile to provide physicians with more informed drug choices to better treat H. pylori infection. To our knowledge, this is the first study to examine the prevalence of antimicrobial resistance of H. pylori in Karnataka state of South India.

Results

A total of 113 H. pylori strains were isolated from gastric biopsies and tested: 81.4% were resistant to metronidazole, 54.9% were resistant to levofloxacin, 20.4% were resistant to clarithromycin, 5.3% were resistant to tetracycline and 7.1% were resistant to amoxicillin. Multidrug resistance was detected in 59.3% of total isolated strains, among which 86.6% were resistant to at least both metronidazole and levofloxacin. In this study, 38 out of 113 H. pylori strains had been whole-genome sequenced. Based on the draft genomes, RdxA and/or FrxA inactivation mutations were found to present in 75% of metronidazole-resistant strains. Clarithromycin-resistant strains had mainly A2143G and G2224A mutations in the 23 rRNA gene. While 87.1% levofloxacin-resistant strains had amino acid substitution mutations occurring predominantly at N87 and D91 in GyrA, novel mutations in the same protein including an insertion of five amino acid residues (QDNSV), immediately after the start codon, and a substitution mutation at R295 were identified.

Conclusion

High primary resistance to metronidazole and levofloxacin, and a modest occurrence of clarithromycin resistance were revealed in H. pylori strains isolated from Karnataka patients. Therefore metronidazole-, levofloxacin- and clarithromycin-based triple therapies are not suitable as first-line treatment in Karnataka. Both amoxicillin and tetracycline can still be used to eradicate H. pylori infection in this region. We also revealed novel mutations in GyrA protein that possibly contribute to H. pylori resistance in levofloxacin, which merit further investigations.

Combining VITEK® 2 with colistin agar dilution screening assist timely reporting of colistin susceptibility

OBJECTIVES

The rise in carbapenem resistance among Gram-negative bacteria has renewed interest in colistin. Recently, the EUCAST-CLSI Polymyxin Breakpoints Working Group declared that broth microdilution (BMD) is the only valid method for colistin susceptibility testing. BMD is not easily incorporated into the routine work of clinical laboratories, and usually this test is incorporated serially, resulting in delayed susceptibility reporting. We tested a strategy of combining VITEK^® 2 with a 2 μg/mL colistin agar dilution (VITEK^® 2/AD) screening plate to improve performance and time to reporting of colistin susceptibility.

METHODS

Colistin susceptibility for 364 clinical isolates was determined by VITEK^® 2/AD and compared with the reference standard BMD according to the ISO 20776-1:2007 and CLSI guidelines. The EUCAST colistin susceptibility breakpoint of ≤2 μg/mL was used. Escherichia coli NCTC 13846 served as quality control strain. Agreement, very major error (VME) and major error rates were determined using ISO 20776-2:2007.

RESULTS

The VME rate for VITEK^® 2 alone was 30.6% (15/49, 95% CI 18.3-45.4%), and was reduced to 10.2% (5/49, 95% CI 3.4-22.2%) using the VITEK^® 2/AD combined testing. The combined testing had categorical agreement with BMD of 97% (354/364, 95% CI 95.0-98.7%), and a major error (ME) rate of 1.6% (5/315, 95% CI 0.5-3.7%). Using the combined testing, even against challenging strains, 349 (95.8%, 95% CI 93.3-97.7%) colistin susceptibility results could be reported, and only 15 isolates required further analysis by BMD.

DISCUSSION

Our method is simple to apply and allows rapid reporting of colistin susceptibility.

clinical isolates and update of their susceptibility

OBJECTIVES

Although Corynebacterium spp. are part of the microbiota of the skin and mucous membranes, human infections caused by Corynebacterium spp. have been reported and the multidrug resistance pattern of the recovered isolates was emphasised. Due to the usefulness of disk diffusion in daily practice, the purpose of this study was to compare disk diffusion with agar dilution to determine disk diffusion breakpoints and to review the antimicrobial susceptibility of the most frequent Corynebacterium spp. isolated in clinical samples.

METHODS

Susceptibility to 20 antimicrobial agents of 143 Corynebacterium spp. isolates recovered from relevant clinical samples was determined. Comparison between the disk diffusion and agar dilution methods for eight antimicrobial agents was performed to establish new breakpoints using simple linear regression analysis.

RESULTS

All of the isolates tested were susceptible to vancomycin, minocycline and linezolid. A typical susceptibility profile to β-lactam antibiotics among the different species included was not observed. Almost all isolates showed resistance to macrolides and lincosamides. Using a simple linear regression method, it was possible to establish breakpoints for penicillin, erythromycin, clindamycin, gentamicin and ciprofloxacin. However, the low correlation coefficient obtained for vancomycin, minocycline and trimethoprim/sulfamethoxazole did not allow establishment of breakpoints for the disk diffusion method.

CONCLUSION

The disk diffusion method could only be used to evaluate susceptibility to penicillin, erythromycin, clindamycin, gentamicin and ciprofloxacin. These data show that the presence of a Corynebacterium spp. isolate in a clinical sample demands the performance of antimicrobial susceptibility testing since the susceptibility profile is not predictable.

Evaluation of colistin stability in agar and comparison of four methods for MIC testing of colistin

Susceptibility testing for colistin remains challenging primarily due to its inherent properties. We evaluated colistin stability in agar and reproducibility of colistin MICs obtained by agar dilution, broth macro- and micro-dilution and MIC gradient strips on 3–7 iterations of each method using clinical Klebsiella pneumoniae (susceptible-CS, and resistant-CR, n = 2 each), mcr-harboring Escherichia coli (n = 2), and reference strains E. coli ATCC25922 and Pseudomonas aeruginosa ATCC27853. MICs for reference strains were not in the given range using Etest and broth microdilution (ATCC25922, 0.125 and 4 μg/ml, respectively). MICs of CR-1 and CR-2, and of the mcr-harboring E. coli showed high concordance between agar and broth dilution varying up to one 2-fold dilution. However, remarkable variations were observed on broth dilution with CS-1 and CS-2 (MIC range 0.25–32 and 0.5–64 μg/ml, respectively); whereas for agar dilution the MIC for both CS strains was 0.5 μg/ml in all the runs. MICs obtained by MIC gradient strips were lower than those obtained by dilution methods (1–2 dilutions for CS and mcr strains, and up to five dilutions for CR strains). To confirm uniform distribution of colistin in agar, a single strain was spotted in five different regions of the same plate. All spots showed concordant growth with maximum one dilution difference. No effect on MIC was found due to storage of colistin-containing agar plates for 7 days at 4 °C. In our hands, agar dilution was superior in terms of reproducibility and robustness, compared to broth dilution methods, for colistin MIC determination.

Antimicrobial susceptibility of Brazilian Clostridium difficile strains determined by agar dilution and disk diffusion

Clostridium difficile is a leading cause of diarrhea in hospitalized patients worldwide. While metronidazole and vancomycin are the most prescribed antibiotics for the treatment of this infection, teicoplanin, tigecycline and nitazoxanide are alternatives drugs. Knowledge on the antibiotic susceptibility profiles is a basic step to differentiate recurrence from treatment failure due to antimicrobial resistance. Because C. difficile antimicrobial susceptibility is largely unknown in Brazil, we aimed to determine the profile of C. difficile strains cultivated from stool samples of inpatients with diarrhea and a positive toxin A/B test using both agar dilution and disk diffusion methods. All 50 strains tested were sensitive to metronidazole according to CLSI and EUCAST breakpoints with an MIC90 value of 2μg/mL. Nitazoxanide and tigecycline were highly active in vitro against these strains with an MIC90 value of 0.125μg/mL for both antimicrobials. The MIC90 were 4μg/mL and 2μg/mL for vancomycin and teicoplanin, respectively. A resistance rate of 8% was observed for moxifloxacin. Disk diffusion can be used as an alternative to screen for moxifloxacin resistance, nitazoxanide, tigecycline and metronidazole susceptibility, but it cannot be used for testing glycopeptides. Our results suggest that C. difficile strains from São Paulo city, Brazil, are susceptible to metronidazole and have low MIC90 values for most of the current therapeutic options available in Brazil.

A comparison of agar dilution with the Calibrated Dichotomous Sensitivity (CDS) and Etest methods for determining the minimum inhibitory concentration of ceftriaxone against Neisseria gonorrhoeae

OBJECTIVES

The objective of this study was to compare the Calibrated Dichotomous Sensitivity (CDS) based agar dilution (CDS AD) method with the Etest (bioMérieux SA) methods using 2 method protocols for determining the minimum inhibitory concentration (MIC) of ceftriaxone against Neisseria gonorrhoeae. The two method protocols were the manufacturer's protocol for which the Clinical and Laboratory Standards Institute (CLSI) interpretative criteria for Neisseria gonorrhoeae could be applied, and the CDS-adapted protocol. Comparability of MIC data is critical for situation analysis and monitoring trends in global antimicrobial analysis.

METHODS

Two hundred and forty eight clinical isolates of N. gonorrhoeae and the World Health Organisation (WHO) N. gonorrhoeae reference strains were tested using the three methods.

RESULTS

When compared, CDS AD and CDS Etest gave a regression R(2) value of 94%, the Pearson's correlation coefficient was 97% and a paired comparison within one log2 dilution was 98%. The CDS AD and the Etest (CLSI) comparison gave a regression R(2) value of 90%, a Pearson's correlation coefficient of 95% and a paired comparison within one log2 dilution was 98%. The comparison of the CDS Etest and CLSI Etest gave a regression R(2) value of 91%, a Pearson's correlation coefficient of 95% and a paired comparison within one log2 dilution of 99%. Importantly, there was robust agreement between all three methods for the categorization of susceptibility of Neisseria gonorrhoeae isolates using the WHO nominated breakpoint for decreased susceptibility to ceftriaxone (≥0.125 μg/mL).

CONCLUSIONS

The CDS Etest method is comparable to agar dilution and the Etest methods for determining the MIC of ceftriaxone against N. gonorrhoeae.

Improved allele-specific PCR assays for detection of clarithromycin and fluoroquinolone resistant of Helicobacter pylori in gastric biopsies: identification of N87I mutation in GyrA. Diagn Microbiol Infect Dis. 2015;81:251-255. [PMID: 25600075 DOI: 10.1016/j.diagmicrobio.2014.12.003]

Molecular testing can rapidly detect Helicobacter pylori susceptibility using gastric biopsies. Allele-specific polymerase chain reaction (ASP-PCR) was used to identify H. pylori 23S rRNA and gyrA mutation using gastric biopsies from Colombian patients and confirmed by PCR and sequencing of the 23S rRNA and gyrA genes. The sensitivity and specificity of ASP-PCR were compared with susceptibilities measured by agar dilution. Samples included gastric biopsies from 107 biopsies with H. pylori infections and 20 H. pylori negative. The sensitivity and specificity of ASP-PCR for the 23S rRNA gene were both 100%. The sensitivity and specificity of ASP-PCR for the gyrA gene, published in 2007 by Nishizawa et al., were 52% and 92.7%, respectively; the lower sensitivity was due to the presence of mutation N87I in our samples, which were not detected by the test. In this study, we designed new primers to detect the mutation N87I in GyrA. The ASP-PCR was performed with the original primers plus the new primers. The molecular test with the new primers improved the sensitivity to 100%. In conclusion, ASP-PCR provides a specific and rapid means of predicting resistance to clarithromycin and levofloxacin in gastric biopsies.

Can ampicillin/sulbactam resistance in Acinetobacter baumannii be predicted accurately by disk diffusion?

The objective of this study was to compare the performance of disk diffusion and agar dilution for the determination of susceptibility to ampicillin/sulbactam (SAM), ceftazidime, cefepime, imipenem, meropenem, polymyxin B and tigecycline of 121 Acinetobacter baumannii clinical isolates. The antimicrobial susceptibility testing methods were performed as recommended by the Clinical and Laboratory Standards Institute (CLSI). For SAM, in addition the Etest method was performed according to the manufacturer's instructions. The error rates for the antimicrobial agents for 121 isolates tested were within the acceptable ranges established by the CLSI, with the exception of SAM and polymyxin B. For polymyxin B, there were 1.7% very major errors and for SAM there were 15% comparing disk diffusion with agar dilution. The very major error rate of SAM comparing the Etest with agar dilution was 10%. These high observed rates of very major error cast doubt on the disk diffusion and Etest techniques as appropriate methods for detecting resistance to SAM.

Resistance of Helicobacter pylori to antibiotics from 2000 to 2009 in Shanghai

AIM: To investigate the resistance of Helicobacter pylori (H. pylori) to 6 commonly used antibiotics from 2000 to 2009 in Shanghai.

METHODS: A total of 293 H. pylori strains were collected from 2000 to 2009 in Shanghai and tested for their susceptibility to metronidazole, clarithromycin, amoxicillin, furazolidone, levofloxacin and tetracycline using agar dilution.

RESULTS: The resistant rates of H. pylori to clarithromycin (8.6%, 9.0% and 20.7%) and levofloxacin (10.3%, 24.0% and 32.5%) increased from 2000 to 2009 in Shanghai. The resistant rate of H. pylori to metronidazole remained stable (40%-50%). Only one strain of H. pylori isolated in 2005 was resistant to tetracycline. All strains were sensitive to amoxicillin and furazolidone. The resistant rate of H. pylori to antibiotics was not related with the sex, age and clinical outcome of patients.

CONCLUSION: Resistance of H. pylori to antibiotics plays an important role in making treatment strategies against H. pylori-associated diseases.