Susceptibility Testing System Research Articles

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning‐enabled molecular diagnostics

Limited therapy options due to antibiotic resistance underscore the need for optimization of current diagnostics. In some bacterial species, antimicrobial resistance can be unambiguously predicted based on their genome sequence. In this study, we sequenced the genomes and transcriptomes of 414 drug‐resistant clinical Pseudomonas aeruginosa isolates. By training machine learning classifiers on information about the presence or absence of genes, their sequence variation, and expression profiles, we generated predictive models and identified biomarkers of resistance to four commonly administered antimicrobial drugs. Using these data types alone or in combination resulted in high (0.8–0.9) or very high (> 0.9) sensitivity and predictive values. For all drugs except for ciprofloxacin, gene expression information improved diagnostic performance. Our results pave the way for the development of a molecular resistance profiling tool that reliably predicts antimicrobial susceptibility based on genomic and transcriptomic markers. The implementation of a molecular susceptibility test system in routine microbiology diagnostics holds promise to provide earlier and more detailed information on antibiotic resistance profiles of bacterial pathogens and thus could change how physicians treat bacterial infections.

Proportion of bacterial isolates, their antimicrobial susceptibility profile and factors associated with puerperal sepsis among post-partum/aborted women at a referral Hospital in Bahir Dar, Northwest Ethiopia

BackgroundPuerperal sepsis is any bacterial infection of the genital tract that occurs after childbirth. It is among the leading causes of maternal morbidity and mortality especially in low-income countries including Ethiopia. The aim of this study was to determine the proportion of bacterial isolates, their antimicrobial susceptibility profile and factors associated with puerperal sepsis among post-partum/aborted women at a Referral Hospital in Bahir Dar, Northwest Ethiopia.MethodsA cross sectional study was conducted from January to May 2017 among 166 post-partum/aborted women admitted to Felege Hiwot Referral Hospital for medical services and suspected for puerperal sepsis.. Socio-demographic data and associated factors were collected using structured questionnaire. Bacteria were isolated and identified from blood samples on Trypton soya broth, blood, Chocolate and MacConkey agars following standard bacteriological procedures. The VITEK 2 identification and susceptibility testing system was used to determine the antimicrobial susceptibility profiles of bacterial isolates. Data were entered and analyzed using SPSS version 20. Factors associated with puerperal sepsis were considered statistically significant at P-value < 0.05.ResultsThe overall proportion of bacterial isolates among post-partum/aborted women was 33.7% (56/166); of which 55.4% was caused by Gram-negative and 44.6% was by Gram-positive bacteria. The most frequently isolated bacteria were Escherichia coli (32.1%) from Gram-negatives and Staphylococcus aureus (33.9%) from Gram-positives. The proportion of other isolates was (7.2%) for Coagulase Negative Staphylococci (CoNS), (12.5%) for Klebsiella pneumoniae, (10.7%) for Acinetobacter baumanni and (3.6%) for Raoultella ornithinolytica. All isolates of Gram-positive and Gram-negative bacteria were resistant to tetracycline (100%). The gram negatives show resistance to Cefazolin (72.7%), Tetracycline (93.9%) and Ampicillin (100%). The overall prevalence of multidrug resistance (MDR) was 84%. Women having multiparous parity were more likely to develop puerperal sepsis than primiparous parity (AOR 4.045; 95% CI: 1.479–11.061; P < 0.05). Other socio-demographic and clinical factors had no significant association with puerperal sepsis.ConclusionAbout one third of post-partum/aborted women suspected for puerperal sepsis were infected with one or more bacterial isolates. Significant proportion of bacterial isolates showed mono and multi-drug resistance for the commonly prescribed antibiotics. Women with multiparous parity were more likely to develop puerperal sepsis than primiparous parity.

Prevalence and antimicrobial resistance of Staphylococcus species isolated from cats and dogs.

Background:Methicillin-resistant staphylococci (MRS) are an emerging global problem with serious public health concern.Aims:This study investigated the prevalence and antimicrobial susceptibility of commensal Staphylococcus species isolated from healthy and clinical cats and dogs.Methods:Nasal swab samples were collected from animals and processed using selective and semi-selective mediums. Presumptive isolates were subjected to biochemical testing and analyzed using the Phoenix automated identification and susceptibility testing system. PCRs protocols were used to screen for mecA and pvl genes.Results:In total, 151 pets (103 cats and 48 dogs) were enrolled, of which 14 dogs (29%) and 24 cats (23%) were colonized with various Staphylococcus species mainly originated from healthy animals. A total of 38 staphylococci isolates were collected and distributed between 24 coagulase-negative and 14 coagulase-positive staphylococci. Only 13 staphylococci strains were identified as MRS, out of which only five isolates expressed that the mecA gene exclusively originated from healthy pets.Conclusion: This is the first study reporting the prevalence and colonization status of staphylococci species and MRS strains isolated from cats and dogs in Libya. The study reports important information of medical and clinical importance on antimicrobial and multidrug resistance of different staphylococci strains, particularly the coagulase negative species.

Impact of Efflux Pump Inhibitor Carbonyl-Cyanide M-Chlorophenylhydrazone in Multidrug Resistant AcinetobacterSpecies Isolates from Sterile Body Fluids

Introduction: Antimicrobial resistance of Acinetobacter baumannii(A. baumannii) are rapidly emerging, becoming non-responsive to most of the commonly prescribed antibiotics and leaving us with few treatment options and galloping treatment costs. Aim: To study the effect of Efflux Pump Inhibitor (EPI) Carbonyl Cyanide 3-Chlorophenylhydrazone (CCCP) on Multidrug Resistance (MDR) A. baumannii isolates from different sterile body fluids. Materials and Methods: A total of 40 Acinetobacter species isolates from different sterile body fluids i.e., Cerebrospinal Fluid (CSF), ascitic fluid, pleural fluid, and peritoneal fluid were collected and identified by Matrix Assisted Laser Desorption/Ionisation-Time Of Flight (MALDI-TOF), Biomerieux, France. Minimum Inhibitory Concentration (MIC) of A. baumannii was determined by automated VITEK-2 Antimicrobial Susceptibility Testing (AST) system (Biomerieux, France). In addition, MIC of the isolates, grown on Mueller-Hinton Agar (MHA) plate with 15 μg/mL with EPI CCCP (Sigma Aldrich, US) was determined. For Tigecycline, MIC was determined by Broth Microdilution (BMD) method. Results: Out of 40 isolates, 34 (85%) were A. baumannii and 6 (15%) were Acinetobacter junii. Most of the Acinetobacter spps were MDR and only susceptible to few antibiotics. Most effective antibiotic was Tigecycline 25 (73.52%) followed by Co-trimoxazole 10 (29.41%). Similarly, Out of 40 isolates, 2 to 64 folds reductions in MIC was observed due to CCCP in 10 (25%) isolates for various antibiotics. Likewise, for Tigecycline, 2 to 4 folds reductions in MIC value (One strain changed from intermediate to sensitive) was observed by VITEK-2 AST which corroborated with reduction in MIC by BMD after addition of CCCP. Conclusion: MDR A. baumannii are spreading rapidly. There is the need to overcome the antimicrobial resistance by investigating resistance inhibiting substance that will help to restore antimicrobial susceptibility and bringing back the existing antibiotics in prescription.

A high-throughput cell culture system based on capillary and centrifugal actions for rapid antimicrobial susceptibility testing.

Antibiotic resistance is a global threat to modern society. Rapid determination of suitable antibiotics that inhibit bacterial growth can effectively reduce antibiotic resistance and improve clinical treatment. The conventional methods of antimicrobial susceptibility testing (AST) depend on optical density measurements, which require long-time incubation. Various kinds of rapid AST systems which utilize various technologies from the field of lab on a chip have promised a great reduction in measurement time, but cannot achieve high-throughput, user-friendly testing due to the complexity of the testing system. Here, we introduce a capillary and centrifuge-based rapid AST system that reduces the time of loading the sample and culture media while achieving a high-throughput testing capacity. The capability of the proposed system is validated in a systematic analysis that includes sample loading characteristics and AST trials with standard strains. The proposed system provides a useful tool for drug testing in cell-culture systems with user-friendly and high-throughput analysis.

Egyptian consensus for the use of antimicrobial therapy in Preoperative prophylaxis, surgical site infections and diabetic foot infections

Use of antimicrobials in surgical prophylaxis These consensuses focus on primary perioperative prophylaxis for the prevention of an initial infection, the administration of the first dose of antimicrobial beginning within 60 min before surgical incision is recommended, but administration of vancomycin and fluoroquinolones should begin within 120 min before surgical incision because of the prolonged infusion times required for these drugs. Dosing In general, it is advisable to administer prophylactic agents in a manner that will ensure adequate levels of drug in serum and tissue for the interval during which the surgical site is open, If the duration of the procedure exceeds two half-lives of the antimicrobial or there is excessive blood loss (>1500 ml), the re-dosing interval should be measured from the time of administration of the preoperative dose, not from the beginning of the procedure. The selection of certain antimicrobial in most of the surgeries is shown in Table 2, and the special dosing of antimicrobials in patients with renal impairment is shown in Table 3. Surgical site infections “SSI” SSIs or wound infections are the most common adverse events affecting hospitalized surgical patients. The most important therapy for an SSI is to open the incision, evacuate the infected material, and continue dressing changes until the wound heals by secondary intention. Before starting an empiric antibiotics course, culture should be done. The antibiotic choice is usually empiric but can be supported by Gram stain, culture of the wound contents, the site of surgery, and the hospital antimicrobial susceptibility test system ‘Hospital Biogram’. The selection of Antibiotics for treatment of incisional surgical site infections is summarized in table 4. Diabetic foot infections Diabetic Foot infections typically begin in a wound, most often a neuropathic ulceration, while all wounds are colonized with microorganisms, and the presence of infection is defined by greater than or equal to 2 classic findings of inflammation or purulence. Most DFIs are polymicrobial, with aerobic gram-positive cocci, and especially Staphylococci spp., the most common causative organisms. Clinicians should consider the possibility of infection occurring in any foot wound in a patient with diabetes. Clinicians should evaluate a diabetic patient presenting with a foot wound at three levels: the patient as a whole, the affected foot or limb, and the infected wound. The clinically noninfected wounds should not be treated with antibiotic therapy. Prescription of antibiotic therapy for all infected wounds should be done, but with caution, as it is often insufficient unless combined with appropriate wound debridement. The clinicians need to select an empiric antibiotic regimen on the basis of the severity of the infection and the likely etiologic agent(s) (shown in Table 6).

Rapid pathogen identification and antimicrobial susceptibility testing in in vitro endophthalmitis with matrix assisted laser desorption-ionization Time-of-Flight Mass Spectrometry and VITEK 2 without prior culture.

Prompt clinical diagnosis and initiation of treatment are critical in the management of infectious endophthalmitis. Current methods used to identify causative agents of infectious endophthalmitis are mostly inefficient, owing to suboptimal sensitivity, length, and cost. Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) can be used to rapidly identity pathogens without a need for culture. Similarly, automated antimicrobial susceptibility test systems (AST, VITEK 2) provide accurate antimicrobial susceptibility profiles. In this proof-of-concept study, we apply these technologies for the direct identification and characterization of pathogens in vitreous samples, without culture, as an in vitro model of infectious endophthalmitis. Vitreous humor aspirated from freshly enucleated porcine eyes was inoculated with different inocula of Staphylococcus aureus (S. aureus) and incubated at 37°C. Vitreous endophthalmitis samples were centrifuged and pellets were directly analyzed with MALDI-TOF MS and VITEK 2 without prior culture. S. aureus colonies that were conventionally grown on culture medium were used as control samples. Time-to-identification, minimum concentration of bacteria required for identification, and accuracy of results compared to standard methods were determined. MALDI-TOF MS achieved accurate pathogen identification from direct analysis of intraocular samples with confidence values of up to 99.9%. Time from sample processing to pathogen identification was <30 minutes. The minimum number of bacteria needed for positive identification was 7.889x106 colony forming units (cfu/μl). Direct analysis of intraocular samples with VITEK 2 gave AST profiles that were up to 94.4% identical to the positive control S. aureus analyzed per standard protocol. Our findings demonstrate that the direct analysis of vitreous samples with MALDI-TOF MS and VITEK 2 without prior culture could serve as new, improved methods for rapid, accurate pathogen identification and targeted treatment design in infectious endophthalmitis. In vivo models and standardized comparisons against other microbiological methods are needed to determine the value of direct analysis of intraocular samples from infectious endophthalmitis with MALDI-TOF MS and VITEK 2.

Molecular Detection of Bacterial Etiologies Causing Meningitis in Pediatric Pateints in Taif City, Saudi Arabia

Bacterial meningitis is prevalent in pediatric populations worldwide and associated with mortality and neurological complications in tropical and subtropical regions. This study aimed to evaluate in-use clinical diagnostic approaches against two PCR method in detection of bacterial pathogens implicated in pediatric meningitis in Taif city (Saudi Arabia). The tested PCR method were real-time and multiplex polymerase chain-reaction (RT-PCR and mPCR).One hundred and fifteen CSF samples were collected from suspected pediatric patients with acute meningitis admitted to Taif children’s hospital between January and December 2016. Bacterial identification and antimicrobial susceptibility testing were performed by the automated BD Phoenix™ identification and susceptibility testing system. Culture-based detection identified Citrobacter freundii (in one sample) and Salmonella spp. (in one sample). However, molecular detection by PCR approach of 113 culture-negative samples identified; N. meningitidis , (A serotype), H. influenzae (2-strains), and S. pneumoniae (19A and 23F strains). PCR-based detection approach is more efficient in microbiological diagnosis of bacterial etiologies in CSF specimens.

Evaluation of the impact of the Accelerate Pheno\u2122 system on time to result for differing antimicrobial stewardship intervention models in patients with gram-negative bloodstream infections

BackgroundInitiating early effective antimicrobial therapy is the most important intervention demonstrated to decrease mortality in patients with gram-negative bacteremia with sepsis. Rapid MIC-based susceptibility results make it possible to optimize antimicrobial use through both escalation and de-escalation.MethodWe prospectively evaluated the performance of the Accelerate Pheno™ system (AXDX) for identification and susceptibility testing of gram-negative species and compared the time to result between AXDX and routine standard of care (SOC) using 82 patient samples and 18 challenge organisms with various confirmed resistance mechanisms. The potential impact of AXDX on time to antimicrobial optimization was investigated with various simulated antimicrobial stewardship (ASTEW) intervention models.ResultsThe overall positive and negative percent agreement of AXDX for identification were 100 and 99.9%, respectively. Compared to VITEK® 2, the overall essential agreement was 96.1% and categorical agreement was 95.4%. No very major or major errors were detected. AXDX reduced the time to identification by an average of 11.8 h and time to susceptibility by an average of 36.7 h. In 27 patients evaluated for potential clinical impact of AXDX on antimicrobial optimization, 18 (67%) patients could potentially have had therapy optimized sooner with an average of 18.1 h reduction in time to optimal therapy.ConclusionUtilization of AXDX coupled with simulated ASTEW intervention notification substantially shortened the time to potential antimicrobial optimization in this cohort of patients with gram-negative bacteremia. This improvement in time occurred when ASTEW support was limited to an 8-h coverage model.

2159. Accurate Carbapenem Susceptibility Testing Within 5–6 Hours

BackgroundPatients infected with multi-drug-resistant (MDR) pathogens may experience long delays to targeted therapies due to the incomplete antimicrobial menus and/or breakpoints tested on current commercial antimicrobial susceptibility testing (AST) systems. Detection of carbapenem resistance poses a challenge to rapid, accurate, minimum inhibitory concentrations (MIC) determinations because some resistant organisms may be inhibited by a carbapenem antibiotic until sufficient carbapenemase production has been achieved and traditional AST platforms must wait to make MIC calls. More accurate carbapenem MICs can be determined by implementing a carbapenemase test alongside rapid AST.MethodsWe demonstrate a novel, proprietary test to detect carbapenemase production that enables rapid MIC testing for carbapenem antibiotics. The test is processed in parallel with the Selux next-generation phenotyping (NGP) AST method, enabling rapid, <6-hour, accurate MIC determinations. The carbapenemase assay utilizes high concentrations of intact bacteria. After 3 hours of incubation, a fluorescent pH indicator is read spectroscopically. The solution pH is lowered by carbapenemase-mediated imipenem degradation and is indicative of enzyme activity.ResultsThis assay accurately identifies carabapenemases across multiple enzyme classes and bacterial species. Figure 1 shows the accuracy and speed of NGP AST at determining MICs for representative isolates from the FDA-CDC antimicrobial resistance bank compared with results from overnight broth microdilution (BMD). To date, over 100 challenge strains of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii have been tested with no very major errors and an average time-to-result of 5.3 hours.ConclusionBy incorporating a rapid, on-board carbapenemase activity assay, the NGP AST platform rapidly delivers accurate carbapenem results. Combined with NGP’s comprehensive antibiotic menus, this platform will therefore ensure prompt delivery of personalized antibiotic therapies for all patients, including those infected with MDROs, and enable streamlined antibiotic stewardship coordination. Disclosures All authors: No reported disclosures.

586. Multidrug-Resistant Organisms from Three Pedaitric Inpatient Units in the Domincan Republic

BackgroundMultidrug-resistant organisms (MDRO) are a major global public health threat. Antimicorbial consumption and resistance in low- and middle-income countries (LMICs) are rising. This trend can be consequential for vulnerable populations such as children who have high rates of febrile illnesses. The aim of our study is to asses the burden of MDRO in hospitalized pediatric patients in the Dominican Republic (DR).MethodsRetrospective review of all positive cultures in patients ages 0–17 at three tertiary referral centers in Santiago, DR. Culture-positive cases from January 2016 to December 2017 were reviewed. Repeat cultures from the same patient were excluded. Phenotypic susceptibility data were collected from automated susceptibility testing systems using WHOnet interface.ResultsA total of 1,584 cultures were reviewed, of which 1,041 (65%) were Gram-negative and 514 (32%) Gram-positive. The most common microorganisms were E. coli (23%)and S. aureus (11%). Sample were obtained from stool (26.9%), blood (23.5%), urine (16.2%), secretions (5.4%), and central line catheters (7.2%). Phenotypic resistance consistent with extended-spectrum β-lactamase (ESBL) and carbapenem-resistant Enterobacteriaceae (CRE) was found in 524 (50.3%) and 179 (17.2%) of Gram-negatives, respectively. MDRO rates by organism are in Figure 2. A total of 72 (21.0%) S aureusisolates were methicillin resistant (MRSA) and 62 (18%) showed suspected inducible resistance to clindamycin (Figure 3).ConclusionData from automated culture systems suggests a high prevalence of ESBL and CRE in this city-wide cohort from three pediatric facilities. Prospective confirmatory studies with manual susceptibility testing may help clarify the true prevalence of MDRO. Further studies are needed to understand the epidemiology and risk factors pediatric patients colonized or infected with MDROs in LMICs and in the DR. Exposure to antimicrobials may be an important risk factor. Understanding antimicrobial use in children and possible exposure to antimicrobials in the environment may help identify antimicrobial stewardship targets and help curb antimicrobial pressure and resistance. Disclosures All authors: No reported disclosures.

Identification of Gram negative non-fermentative bacteria: How hard can it be?

IntroductionThe prevalence of bacteremia caused by Gram negative non-fermentative (GNNF) bacteria has been increasing globally over the past decade. Many studies have investigated their epidemiology but focus on the common GNNF including Pseudomonas aeruginosa and Acinetobacter baumannii. Knowledge of the uncommon GNNF bacteremias is very limited. This study explores invasive bloodstream infection GNNF isolates that were initially unidentified after testing with standard microbiological techniques. All isolations were made during laboratory-based surveillance activities in two rural provinces of Thailand between 2006 and 2014.MethodsA subset of GNNF clinical isolates (204/947), not identified by standard manual biochemical methodologies were run on the BD Phoenix automated identification and susceptibility testing system. If an organism was not identified (12/204) DNA was extracted for whole genome sequencing (WGS) on a MiSeq platform and data analysis performed using 3 web-based platforms: Taxonomer, CGE KmerFinder and One Codex.ResultsThe BD Phoenix automated identification system recognized 92% (187/204) of the GNNF isolates, and because of their taxonomic complexity and high phenotypic similarity 37% (69/187) were only identified to the genus level. Five isolates grew too slowly for identification. Antimicrobial sensitivity (AST) data was not obtained for 93/187 (50%) identified isolates either because of their slow growth or their taxa were not in the AST database associated with the instrument. WGS identified the 12 remaining unknowns, four to genus level only.ConclusionThe GNNF bacteria are of increasing concern in the clinical setting, and our inability to identify these organisms and determine their AST profiles will impede treatment. Databases for automated identification systems and sequencing annotation need to be improved so that opportunistic organisms are better covered.

Evolución de la resistencia antimicrobiana en aislados clínicos de Pseudomonas aeruginosa productores de infecciones invasivas en el sur de España

IntroductionThe aim of this study was to determine the antimicrobial resistance rates and their evolution in clinical isolates of Pseudomonas aeruginosa causing invasive infections in the south of Spain between 2012 and 2017. MethodsRetrospective study consisting of the collection of microbiological data from 20 hospitals (14 from Andalucía, 5 from Extremadura and 1 from Ceuta) between 2012 and 2017. The main variables studied were the antimicrobial susceptibility testing system used, interpretation criteria (CLSI or EUCAST) and the rate or percentage of resistant isolates. ResultsThe most widely used antimicrobial susceptibility testing system was MicroScan (58%). The global resistance rates varied between 25% (ciprofloxacin) and 4% (colistin) using EUCAST, and between 19% (ciprofloxacin and imipenem) and 3% (amikacin) using CLSI. The antimicrobial resistance rates were relatively stable throughout the period 2012-2017. 14% of isolates were MDR and 7% were XDR. Respiratory isolates were more resistant, particularly to ciprofloxacin and colistin, than isolates from urine or blood. ConclusionsThe antimicrobial resistance rates in P. aeruginosa are not particularly high in the south of Spain. The highest resistance rates were observed with ciprofloxacin, piperacillin/tazobactam and meropenem, whereas the more active antimicrobials were colistin, tobramycin and amikacin. The highest resistance rates were seen in respiratory isolates. In general, the resistance rates remained stable during the study period for most of the antimicrobials studied.

Evaluation of the BD Phoenix M50 Automated Microbiology System for Antimicrobial Susceptibility Testing with Clinical Isolates in Korea.

The objectives of this study were to evaluate the performance of the BD Phoenix™ M50 system with two antimicrobial susceptibility testing (AST) panels against clinical isolates in South Korea and the accuracy of determining carbapenem and colistin susceptibility compared with reference methods. A total of 825 nonduplicated clinical isolates were included in this study. Bacterial identification was performed using Bruker Biotyper and 16S rDNA sequencing. Antimicrobial susceptibilities were tested by disk diffusion, broth microdilution, and agar dilution methods. AST with the Phoenix system was performed following the manufacturer's instructions. The categorical agreement (CA), very major error (VME), major error (ME), and minor error (mE) rates were calculated for each antibiotic. CA rates between the results of the Phoenix system and reference methods were more than 90% for most antibiotics except for ciprofloxacin in enterococci (82.7%, 163/197) and cefepime in Acinetobacter species (88.9%, 88/99). VME and ME rates were less than 3% for all the antibiotics tested in this study. Minimum inhibitory concentration (MIC) values for carbapenem and colistin determined by the Phoenix system were highly correlated with those of dilution methods, exhibiting 99.2% (384/387), 96.7% (374/387), and 98.5% (129/131) of the agreement rate within onefold dilution difference for imipenem, meropenem, and colistin, respectively. The BD Phoenix M50™ system showed reliable performance for AST in clinical microbiology laboratories and for detecting carbapenem and colistin resistance in Gram-negative clinical isolates.

Evaluation of the Alfred AST® system for rapid antimicrobial susceptibility testing directly from positive blood cultures

To assess the concordance of antimicrobial susceptibility testing results obtained by the Alfred AST® system performed directly from positive blood cultures in comparison with the standard susceptibility test results performed from isolated colonies by an automated broth microdilution method and to determine the applicability of Alfred AST® system in the routine of our blood culture laboratory. This system is based on the detection of growth by turbidimetry through a technology based on light scattering. Antimicrobial susceptibility testing was performed directly from positive bottles by the Alfred AST® system (Alifax, Padova, Italy). The broth microdilution method (MicroScan, Beckman Coulter, CA, USA) performed to the isolates was considered the standard for comparison. We evaluated 115 significant episodes of bacteremia produced by 51 Gram-negative Enterobacterales, 8 Pseudomonas spp., 2 non-fermenting Gram-negative rods, 7 Staphylococcus aureus, 23 coagulase-negative Staphylococcus, 12 Enterococcus spp., and 12 Streptococcus spp. We performed 828 susceptibility determinations with a categorical agreement with the standard method of 97.1%. Only 24 errors (2.9%) were detected. It should be pointed out that for staphylococci and glycopeptides the correlation was only 87% and for non-fermenting Gram-negative rods and piperacillin/tazobactam was only 88.9%. Time to get antibiogram results by Alfred AST® system was 5 versus 48h for the standard microdilution method from the isolated colonies. The Alfred AST® system is a useful and rapid method to obtain antimicrobial susceptibility results within the same work shift after blood culture positivity.

Adaptable microfluidic system for single-cell pathogen classification and antimicrobial susceptibility testing

Infectious diseases caused by bacterial pathogens remain one of the most common causes of morbidity and mortality worldwide. Rapid microbiological analysis is required for prompt treatment of bacterial infections and to facilitate antibiotic stewardship. This study reports an adaptable microfluidic system for rapid pathogen classification and antimicrobial susceptibility testing (AST) at the single-cell level. By incorporating tunable microfluidic valves along with real-time optical detection, bacteria can be trapped and classified according to their physical shape and size for pathogen classification. By monitoring their growth in the presence of antibiotics at the single-cell level, antimicrobial susceptibility of the bacteria can be determined in as little as 30 minutes compared with days required for standard procedures. The microfluidic system is able to detect bacterial pathogens in urine, blood cultures, and whole blood and can analyze polymicrobial samples. We pilot a study of 25 clinical urine samples to demonstrate the clinical applicability of the microfluidic system. The platform demonstrated a sensitivity of 100% and specificity of 83.33% for pathogen classification and achieved 100% concordance for AST.

Quality Assurance In The Medical Microbiology Laboratory

Abstract In each laboratory, a quality assurance program should be developed in order to obtain reliable results and to fulfil the requirements of quality standards in the field of microbiological laboratory tests. Microbiological diagnostics makes it possible to determine the etiological agent of infection and allow the selection of an appropriate therapy. The quality of test results are affected by pre-laboratory, laboratory and post-laboratory steps, which should be checked regularly. Constant internal quality control of performance in the laboratory and participation in external quality control programmes may ensure the quality of results. Internal quality control of the tests at all stages of routine microbiological diagnostics in the laboratory facilitates constant monitoring of the quality of results. Participation in interlaboratory external quality control programmes permits the quality of performance of tests routinely used in a laboratory to be assessed. 1. Introduction. 2. Quality assurance programme. 2.1. Factors affecting quality. 3. Internal quality control. 3.1. Quality control of identification tests. 3.2. Internal quality control of antimicrobial susceptibility testing and detecting resistance mechanisms. 3.3. Internal quality control of automated systems for identification and susceptibility testing. 4. External quality control. 4.1. External quality assurance programme participation rules. 5. Summary

An integrated microfluidic system for antimicrobial susceptibility testing with antibiotic combination.

Polypharmacy is routinely administered to fight severe infections, though it has led to rampant multi-drug resistance in many bacterial strains. Preferably, antimicrobial susceptibility testing (AST) would be carried out prior to antibiotic prescription, though it is generally thought to be too complex and labor-intensive. In order to assist clinicians with better antibiotic administration for the effective treatment of bacterial infections, an integrated microfluidic system (IMS) capable of automating AST for 1-2 antibiotics against clinical bacterial pathogens was developed herein. Accurate determination of the minimum and fractional inhibitory concentrations of vancomycin, gentamicin, and linezolid were determined by assaying growth of two clinical methicillin-resistant Staphylococcus aureus isolates via a colorimetric assay on-chip. By applying various antibiotic combinations against a single pathogen in multiple chambers, the IMS could identify the optimal drug combination and the minimum effective dosage by evaluating the fractional inhibitory concentration index. This IMS possessed several advantages over conventional methods, including (1) a 50% reduction in bacterial sample and reagent volume (<50 μL per well), (2) less potential for human error due to its automatic nature, (3) faster liquid manipulation time by integrating the microfluidic components rather than labor-intensive process, and (4) straightforward result interpretation via colorimetric change instead of turbidity degree. Personalized medicine for treatment of bacterial infections may therefore be realized using this IMS.

Performance of the Accelerate Pheno™ system for Early identification and antimicrobial susceptibility testing for Sepsis diagnosis from positive blood cultures. (First Evaluation from Middle East)

Performance of the Accelerate Pheno™ system for Early identification and antimicrobial susceptibility testing for Sepsis diagnosis from positive blood cultures. (First Evaluation from Middle East)

Conjunctival microflora and its antibiotic sensitivity after serial intravitreal injections

The approach to post-procedure management of patients undergoing intravitreal injections should be unified and consistent. Frequent use of antibiotic drugs leads to generation of resistant conjunctival strains. To study the composition of conjunctival microflora and its antibiotic susceptibility in patients who received 20 or more intravitreal injections and concomitant antibiotic therapy, and in a group of patients of the same age without history of intravitreal injections or ophthalmological operations. A total of 40 inoculations were performed (20 patients in each group, 40 eyes). In case of culture growth, species identification and antibiotic sensitivity of the microorganisms were investigated using automated identification and susceptibility testing system BD Phoenix 100. Culture growth was observed in 70% of the control group patients. All isolated microorganisms were different types of staphylococci - Staphylococcus epidermidis (78.57%), S. caprae (7.14%), S. hominis (7.14%), and S. aureus (7.14%). In the second group, we observed culture growth in 55% of cases. Eleven cultures were Gram-positive bacteria: S. epidermidis (72.73%), S. haemolyticus (18.18%), S. aureus (9.09%). Gram-negative Pseudomonas aeruginosa was detected in 1 patient. In the control group, multi-resistant cultures accounted for 42.86%. In the group of patients with multiple intravitreal injections, 75% of cases showed multiresistance (9 out of 12 isolates). In the group of patients who have undergone 20 or more injections, greatest resistance was observed to penicillin G, doxycycline, gentamicin, erythromycin, clindamycin, moxifloxacin, fusidic acid, chloramphenicol, and trimethoprim/sulfamethoxazole compared to the control group. Overuse of antibiotics in the management of patients receiving intravitreal injections leads to selection of resistant strains.