Evaluation of the Etest ESBL and the BD Phoenix, VITEK 1, and VITEK 2 automated instruments for detection of extended-spectrum beta-lactamases in multiresistant Escherichia coli and Klebsiella spp

Molecular Screening of Carbapenem-Resistant K. pneumoniae (CRKP) Clinical Isolates for Concomitant Occurrence of Beta-Lactam Genes (CTX-M, TEM, and SHV) in the Kingdom of Bahrain

The emergence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae, including CRKP infections, has resulted in significant morbidity and mortality worldwide. We aimed to explore the presence of bla genes (CTX-M, TEM, and SHV) in CRKP isolates. A total of 24 CRKP isolates were randomly selected from the Salmaniya Medical Complex Microbiology Laboratory. These isolates, which were positive for carbapenemases, were further explored for CTX-M, TEM, and SHV genes using PCR. All the CTX-M PCR amplicons were sent for sequencing. To determine genetic relatedness, molecular typing by ERIC-PCR was performed. The bla gene testing demonstrated that a significant proportion of these isolates harbored SHV, CTX-M, and TEM genes (100%, 91.6%, and 45.8%), respectively. Bioinformatic analyses confirmed CTX-M-15 in these isolates. ERIC-PCR analysis showed three clusters demonstrating genetic relatedness. The study findings reveal the concomitant carriage of the SHV and CTX-M-15 and a comparatively lower carriage of TEM genes in CRKP isolates. Our findings highlight the significance of routinely reporting the presence of antibiotic resistance genes along with regular antibiotic sensitivity reports, as this will aid clinicians in prescribing appropriate antibiotics.

Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates

BACKGROUND

Klebsiella pneumoniae strains have been divided into two major categories: classical K. pneumoniae, which are frequently multidrug-resistant and cause hospital-acquired infections in patients with impaired defenses, and hypervirulent K. pneumoniae, which cause severe community-acquired and disseminated infections in normal hosts. Both types of infections may lead to bacteremia and are associated with significant morbidity and mortality. The relative burden of these two types of K. pneumoniae among bloodstream isolates within the United States is not well understood.

METHODS

We evaluated consecutive K. pneumoniae isolates cultured from the blood of hospitalized patients at Northwestern Memorial Hospital (NMH) in Chicago, Illinois between April 2015 and April 2017. Bloodstream isolates underwent whole genome sequencing, and sequence types (STs), capsule loci (KLs), virulence genes, and antimicrobial resistance genes were identified in the genomes using the bioinformatic tools Kleborate and Kaptive. Patient demographic, comorbidity, and infection information, as well as the phenotypic antimicrobial resistance of the isolates were extracted from the electronic health record. Candidate hypervirulent isolates were tested in a murine model of pneumonia, and their plasmids were characterized using long-read sequencing. We also extracted STs, KLs, and virulence and antimicrobial resistance genes from the genomes of bloodstream isolates submitted from 33 United States institutions between 2007 and 2021 to the National Center for Biotechnology Information (NCBI) database.

RESULTS

Consecutive K. pneumoniae bloodstream isolates (n = 104, one per patient) from NMH consisted of 75 distinct STs and 51 unique capsule loci. The majority of these isolates (n = 58, 55.8%) were susceptible to all tested antibiotics except ampicillin, but 17 (16.3%) were multidrug-resistant. A total of 32 (30.8%) of these isolates were STs of known high-risk clones, including ST258 and ST45. In particular, 18 (17.3%) were resistant to ceftriaxone (of which 17 harbored extended-spectrum beta-lactamase genes) and 9 (8.7%) were resistant to meropenem (all of which harbored a carbapenemase genes). Four (3.8%) of the 104 isolates were hypervirulent K. pneumoniae, as evidenced by hypermucoviscous phenotypes, high levels of virulence in a murine model of pneumonia, and the presence of large plasmids similar to characterized hypervirulence plasmids. These isolates were cultured from patients who had not recently traveled to Asia. Two of these hypervirulent isolates belonged to the well characterized ST23 lineage and one to the re-emerging ST66 lineage. Of particular concern, two of these isolates contained plasmids with tra conjugation loci suggesting the potential for transmission. We also analyzed 963 publicly available genomes of K. pneumoniae bloodstream isolates from locations within the United States. Of these, 465 (48.3%) and 760 (78.9%) contained extended-spectrum beta-lactamase genes or carbapenemase genes, respectively, suggesting a bias towards submission of antibiotic-resistant isolates. The known multidrug-resistant high-risk clones ST258 and ST307 were the predominant sequence types. A total of 32 (3.3%) of these isolates contained aerobactin biosynthesis genes and 26 (2.7%) contained at least two genetic features of hvKP strains, suggesting elevated levels of virulence. We identified 6 (0.6%) isolates that were STs associated with hvKP: ST23 (n = 4), ST380 (n = 1), and ST65 (n = 1).

CONCLUSIONS

Examination of consecutive isolates from a single center demonstrated that multidrug-resistant high-risk clones are indeed common, but a small number of hypervirulent K. pneumoniae isolates were also observed in patients with no recent travel history to Asia, suggesting that these isolates are undergoing community spread in the United States. A larger collection of publicly available bloodstream isolate genomes also suggested that hypervirulent K. pneumoniae strains are present but rare in the USA; however, this collection appears to be heavily biased towards highly antibiotic-resistant isolates (and correspondingly away from hypervirulent isolates).

Evaluation of Rapid Immunochromatographic Tests for the Direct Detection of Extended Spectrum Beta-Lactamases and Carbapenemases in Enterobacterales Isolated from Positive Blood Cultures

NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech) are two rapid in vitro immunochromatographic assays that are widely used for the detection of the most common extended spectrum beta-lactamases (ESBL) and carbapenemases in Enterobacterales. ESBL and carbapenemases are leading causes of morbidity and mortality worldwide and their rapid detection from positive blood cultures is crucial for early initiation of effective antimicrobial therapy in bloodstream infections (BSI) involving antibiotic-resistant organisms. In this study, we developed a rapid workflow for positive blood cultures for direct identification of Enterobacterales by MALDI-TOF mass-spectrometry, followed by detection of ESBL and carbapenemases using NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech). The workflow was evaluated using Enterobacterales isolates (n = 114), primarily Klebsiella species (n = 50) and Escherichia coli (n = 40). Compared to the standard testing approach in our institution using BD Phoenix, our new testing approach demonstrates 100% sensitivity and specificity for organism identification and detection of ESBL and carbapenemases. Implementation of a rapid workflow in diagnostic microbiology laboratories will enable more effective antimicrobial management of patients with BSI due to ESBL- and carbapenemase-producing Enterobacterales.

IMPORTANCE The incidence of bloodstream infections (BSI) with extended spectrum beta-lactamase (ESBL) producing and carbapenemase producing Enterobacterales (CPE) is increasing at an alarming rate, for which only limited therapeutic options remain available. Rapid identification of these bacteria along with their antibiotic resistance mechanisms in positive blood cultures with Gram-negative bacteria will allow for early initiation of effective therapy and limit the overuse of broad-spectrum antibiotics in BSI (1). In this study we evaluated a combined approach of testing positive blood cultures directly, using MALDI-TOF MS followed by rapid immunochromatographic tests, for the detection of ESBLs and CPEs. Our approach demonstrates 100% sensitivity and specificity for the identification of Enterobacterales and detection of ESBLs and CPEs in positive blood culture with a turnaround time (TAT) of ≤60 min compared to a TAT of 48 h required by conventional culture and susceptibility testing methods.

Antibacterial and antibiofilm efficacy of Ag NPs, Ni NPs and Al2O3 NPs singly and in combination against multidrug-resistant Klebsiella pneumoniae isolates

BACKGROUND

Although traditional antibiotic therapy provided an effective approach to combat pathogenic bacteria, the long-term and widespread use of antibiotic results in the evolution of multidrug-resistant bacteria. Recent progress in nanotechnology offers an alternative opportunity to discover and develop novel antibacterial agents.

METHODS

A total of 51 K. pneumoniae strains were collected from several specimens of hospitalized patients and identified by two parallel methods (biochemical tests and Vitek-2 system). The antibiotic sensitivity of isolates was evaluated by disk diffusion antibiogram and Vitek-2 system. The biofilms formation ability of antibiotic-resistant strains was examined by microtiter plate and tube methods based on crystal violet staining. The molecular technique was used to determine key genes responsible for biofilms formation of clinical isolates. The antibacterial and antibiofilm activities of Ag NPs, Ni NPs, Al₂O₃ NPs singly (NPs) and in combination (cNPs) were investigated against selected strains using standard methods. Moreover, the cytotoxicity of NPs was evaluated on mouse neural crest-derived (Neuro-2A) cell line.

RESULTS

The results of bacterial studies revealed that more than 80 % of the isolates were resistant to commonly used antibiotics and about 95 % of them were able to form biofilms. Moreover, the presence of fimA and mrkA genes were determined in all biofilm-producing strains. The results of antibacterial and antibiofilm activities of NPs and cNPs demonstrated the lower MIC and MBEC values for Al₂O₃ NPs singly as well as for Ag/Ni cNPs and Ag/Al₂O₃ cNPs in combination, respectively. Overall, the inhibitory effects of cNPs were superior to NPs against all strains. Furthermore, the results of the checkerboard assays showed that Ag NPs act synergistically with two other NPs against multidrug-resistant Klebsiella pneumoniae (MDR-K. pneumoniae) isolates. The in vitro cytotoxicity assay revealed no significant toxicity of NPs against Neuro-2A cells.

CONCLUSION

In the present study, the combination of Ag NPs, Ni NPs, and Al₂O₃ NPs were used against MDR-K. pneumoniae strains and antibacterial and antibiofilm activities were observed for Ag/Ni cNPs and Ag/Al₂O₃ cNPs.

Prevalence and molecular characterization of antibiotic resistance and associated genes in Klebsiella pneumoniae isolates: A clinical observational study in different hospitals in Chattogram, Bangladesh

Objective

This study was performed to investigate the prevalence of multidrug resistance and molecular characterization of Klebsiella pneumoniae (KPN) from clinical isolates in the southern region of Bangladesh. Additional analysis of the prevalence of bla_NDM-1, bla_SHV-11, uge genes of KPN was also carried out among these clinical isolates.

Method

The study was carried out using 1000 clinical isolates collected from two different hospitals of Chattogram. A drug susceptibility test was performed by the disk diffusion method to detect KPN’s response to 16 antibiotics. The presence of antibiotic-resistant and (or) virulent genes bla_NDM-1, bla_SHV-11, uge were investigated using the PCR technique. Isolates having bla_NDM-1, bla_SHV-11, uge gene were further validated by sequencing followed by phylogenetic analysis. Phylogenetic relationships among these isolates were determined by Clustal omega and MEGA7.

Result

A total of 79%, 77%, 74.9%, 71%, 66% and 65% isolates exhibited resistance against cefuroxime, cefixime, cefotaxime, ceftazidime, cefepime and ceftriaxone respectively. The frequency of resistance to other antibiotics varied from 26.5% to 61.8%. PCR analysis showed that 64% of strains harbored bla_NDM-1 gene, and 38% strains harbored bla_SHV-11 gene. Moreover, 47% of samples were carrying uge gene, and 19% of samples carried bla_NDM-1, bla_SHV-11, uge genes together.

Conclusion

In this study, we’ve analysed the pattern of expression as well as prevalence of bla_NDM-1, bla_SHV-11, and uge genes in Klebsiella isolates. Upon molecular and statistical analysis, we found a high prevalence of multi-drug resistance KPN strains in the isolates. The Klebsiella isolates were confirmed to harbor multiple ESBL genes and 64% of the isolates were found to be producing NDM-1. As multidrug resistance is an alarming issue, continuous surveillance and routine clinical detection of resistant bacteria and plasmids are necessary to prevent catastrophic public health incidents.

Intestinal colonization with extended-spectrum beta-lactamase producing Enterobacterales (ESBL-PE) during long distance travel: A cohort study in a German travel clinic (2016-2017)

BACKGROUND

Intercontinental travel contributes to the spread of extended-spectrum beta-lactamase producing Enterobacterales (ESBL-PE). We assessed risk factors for intestinal ESBL-PE colonization in people travelling to low and middle income countries in the tropics and subtropics to better understand how travel affects ESBL-PE spread.

METHOD

This prospective cohort study in travellers attending a travel clinic in Leipzig, Germany was conducted in 2016-2017. Information on risk factors related to travel, symptoms, antibiotic use, health care usage, accommodation, destination, diet and hygiene was collected by questionnaire after travel. Stools were phenotypically tested for ESBL-PE before and after travel. Risk factors for ESBL-PE colonization were identified using logistic regression.

RESULTS

Of the 230 travellers that were ESBL-PE negative before travelling, 23% (n = 53) travellers returned positive. Multivariable analyses showed that age, type of accommodation and travelling to Asia were associated with ESBL-PE colonization.

CONCLUSIONS

Given that a considerable amount of travellers returned with ESBL-PE, we recommend raising awareness in returning high-risk travellers, e.g. those returning from high-risk areas. They should be aware that they may carry antimicrobial-resistant bacteria after travel, and how they can prevent its spread. The role of the type of accommodation as a factor favouring intestinal colonization with ESBL-PE requires further investigation.

The accuracy of extended-spectrum beta-lactamase detection in Escherichia coli and Klebsiella pneumoniae in South African laboratories using the Vitek 2 Gram-negative susceptibility card AST-N255

Background

Phenotypic detection of extended-spectrum beta-lactamases (ESBLs) is based on the inhibition of ESBL enzymes by β-lactamase inhibitors and on the comparison of cephalosporin activity with or without a β-lactamase inhibitor. Many South African diagnostic laboratories rely on the Vitek 2 for automated susceptibility testing and for ESBL detection. However, the Gram-negative susceptibility card currently used locally (AST-N255) has been modified and its accuracy for ESBL detection is not known.

Methods

We randomly selected 50 isolates of Klebsiella pneumoniae and Escherichia coli from a collection of clinical bloodstream isolates from Groote Schuur Hospital from 2015 to 2016, including ESBL-producing and non-ESBL-producing strains. We used standardised phenotypic (disc diffusion and broth microdilution) and genotypic (conventional polymerase chain reaction (PCR) for bla_CTX-M, bla_SHV and bla_TEM) methods for detection of ESBLs. We compared ESBL detection by Vitek 2 to a composite reference standard comprising ESBL detection either by both phenotypic methods or by one phenotypic method together with genotypic detection.

Results

The sensitivity of Vitek 2 system for detection of ESBLs was 33/36 or 92% (78% – 97%) for E. coli, and 40/40 or 100% (91% – 100%) for K. pneumoniae, whilst specificity was 10/10 or 100% (72% – 100%) and 9/10 or 90% (60% – 98%), respectively. This is comparable with previous studies.

Conclusion

Using a composite reference standard of the phenotypic and genotypic methods employed in this study, no Vitek-categorised ESBL E. coli or K. pneumoniae was found to be a non-ESBL with the exception of possible misinterpretation with K. pneumoniae SHV-hyper-producing isolates.

Phenotypic and Molecular Characterization of Multidrug Resistant Klebsiella pneumoniae Isolated from Different Clinical Sources in Al-Najaf Province-Iraq

BACKGROUND AND OBJECTIVE

Burns infections and urinary tract infections are the most important prevalent diseases in Asian countries, such as Iraq. Klebsiella pneumoniae is one of the most important bacteria cause this type of infections especially in hospitals. Therefore, the aim of this study was to investigate the prevalence of multi-drug resistance K. pneumoniae and extended-spectrum beta-lactamases producing K. pneumoniae isolates from inpatients with urinary tract infection and burns infections in Al-Kufa hospital in Al-Najaf province, Iraq.

MATERIALS AND METHODS

A total of 285 clinical samples were collected from in-patients infected with urinary tract infection (141 urine samples) and burns infections (144 burns swabs). Fourteen different antibiotics were used by disc diffusion method and 13 antimicrobials resistance genes were used by PCR technique.

RESULTS

A total of 43 K. pneumoniae strains were isolated. The highest resistance rate was observed for amoxicillin 25 μg and amoxicillin+clavulanic acid 20+10 μg (97.67%) while the lowest resistance rate was observed for imipenem 10 μg (9.30%). The most common resistance associated-genes were blaSHV (86.04%) and at lower prevalence were IMP (9.30%).

CONCLUSION

Klebsiella pneumoniae strains isolated from burns infections were more virulent than those isolated from urinary tract infections.

Antibacterial resistance patterns of pediatric community-acquired urinary infection: Overview

BACKGROUND

Urinary tract infection (UTI) is common in children. The aim of this study was therefor to construct a guide for the empirical antibiotic treatment of community-acquired UTI by investigating the etiology and antimicrobial resistance patterns of uropathogens and analyzing the epidemiological and clinical patient characteristics.

METHODS

A total of 158 children with positive urine culture were included in the study. Antibiotic susceptibility testing was performed with Vitek 2 Compact for 28 commonly used antimicrobials.

RESULTS

Mean age was 3.36 ± 3.38 years (range, 45 days-15 years). Escherichia coli (60.1%), and Klebsiella spp. (16.5%) were the most common uropathogens. For all Gram-negative isolates, a high level of resistance was found against ampicillin/sulbactam (60.1%), trimethoprim/sulfamethoxazole (44.2%), cefazolin (36.2%), cefuroxime sodium (33.5%), and amoxicillin/clavulanate (31.5%). A low level of resistance was noted against cefepime (8.7%), ertapenem (4.6%), norfloxacin (1.3%), and meropenem (0.7%). There was no resistance against amikacin.

CONCLUSIONS

There is high antibiotic resistance in children with UTI. The patterns of uropathogen antimicrobial resistance vary in susceptibility to antimicrobials depending on region and time. Thus, the trends of antibiotic susceptibility patterns should be analyzed periodically to select the appropriate regimen for UTI treatment.

High Heterogeneity of Escherichia coli Sequence Types Harbouring ESBL/AmpC Genes on IncI1 Plasmids in the Colombian Poultry Chain

Background

Escherichia coli producing ESBL/AmpC enzymes are unwanted in animal production chains as they may pose a risk to human and animal health. Molecular characterization of plasmids and strains carrying genes that encode these enzymes is essential to understand their local and global spread.

Objectives

To investigate the diversity of genes, plasmids and strains in ESBL/AmpC-producing E. coli from the Colombian poultry chain isolated within the Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars).

Methods

A total of 541 non-clinical E. coli strains from epidemiologically independent samples and randomly isolated between 2008 and 2013 within the Coipars program were tested for antimicrobial susceptibility. Poultry isolates resistant to cefotaxime (MIC ≥ 4 mg/L) were screened for ESBL/AmpC genes including bla_CTX-M, bla_SHV, bla_TEM, bla_CMY and bla_OXA. Plasmid and strain characterization was performed for a selection of the ESBL/AmpC-producing isolates. Plasmids were purified and transformed into E. coli DH10B cells or transferred by conjugation to E. coli W3110. When applicable, PCR Based Replicon Typing (PBRT), plasmid Multi Locus Sequence Typing (pMLST), plasmid Double Locus Sequence Typing (pDLST) and/or plasmid Replicon Sequence Typing (pRST) was performed on resulting transformants and conjugants. Multi Locus Sequence Typing (MLST) was used for strain characterization.

Results

In total, 132 of 541 isolates were resistant to cefotaxime and 122 were found to carry ESBL/AmpC genes. Ninety-two harboured bla_CMY-2 (75%), fourteen bla_SHV-12 (11%), three bla_SHV-5 (2%), five bla_CTX-M-2 (4%), one bla_CTX-M-15 (1%), one bla_CTX-M-8 (1%), four a combination of bla_CMY-2 and bla_SHV-12 (4%) and two a combination of bla_CMY-2 and bla_SHV-5 (2%). A selection of 39 ESBL/AmpC-producing isolates was characterized at the plasmid and strain level. ESBL/AmpC genes from 36 isolates were transferable by transformation or conjugation of which 22 were located on IncI1 plasmids. These IncI1 plasmids harboured predominantly bla_CMY-2 (16/22), and to a lesser extend bla_SHV-12 (5/22) and bla_CTX-M-8 (1/22). Other plasmid families associated with ESBL/AmpC-genes were IncK (4/33), IncHI2 (3/33), IncA/C (2/33), IncΒ/O (1/33) and a non-typeable replicon (1/33). Subtyping of IncI1 and IncHI2 demonstrated IncI1/ST12 was predominantly associated with bla_CMY-2 (12/16) and IncHI2/ST7 with bla_CTX-M-2 (2/3). Finally, 31 different STs were detected among the 39 selected isolates.

Conclusions

Resistance to extended spectrum cephalosporins in E. coli from Colombian poultry is mainly caused by bla_CMY-2 and bla_SHV-12. The high diversity of strain Sequence Types and the dissemination of homogeneous IncI1/ST12 plasmids suggest that spread of the resistance is mainly mediated by horizontal gene transfer.

Extended-spectrum beta-lactamase- and carbapenemase-producing Enterobacteriaceae among Ethiopian children

BACKGROUND

Infections by extended-spectrum beta-lactamase- (ESBL) and carbapenem-resistant Enterobacteriaceae (CRE) are an emerging problem in children nowadays. Hence, the aim of this study was to determine the prevalence of ESBL- and carbapenemase-producing Enterobacteriaceae among children suspected of septicemia and urinary tract infections (UTIs).

METHODS

A cross-sectional study was conducted from January to March 2014. A total of 322 study participants suspected of septicemia and UTIs were recruited. All blood and urine samples were cultured on blood and MacConkey agar. All positive cultures were characterized by colony morphology, Gram stain, and standard biochemical tests. Antimicrobial susceptibility test was performed on Muller-Hinton agar using disk diffusion. ESBL was detected using combination disk and double-disk synergy methods, and the results were compared. Carbapenemase was detected by modified Hodge method using meropenem. Data were analyzed using SPSS version 20.

RESULTS

The overall prevalence of ESBL- and carbapenemase-producing Enterobacteriaceae was 78.57% (n=22/28) and 12.12%, respectively. Among the Enterobacteriaceae tested, Klebsiella pneumoniae (84.2%, n=16/19), Escherichia coli (100%, n=5/5), and Klebsiella oxytoca (100%, n=1/1) were positive for ESBL. Double-disk synergy method showed 90.9% sensitivity, 66.7% specificity, 95.2% positive predictive value, and 50% negative predictive value. Carbapenemase-producing Enterobacteriaceae were K. pneumoniae (9.09%, n=3/33) and Morganella morganii (3.03%, n=1/33).

CONCLUSION

Screening Enterobacteriaceae for ESBL production is essential for better antibiotics selection and preventing its further emergence and spread. In resource-limited settings, double-disk synergy method can be implemented for screening and confirming ESBL production. Moreover, occurrence of CRE in countries where no carbapenems are sold is worrying microbiologists as well as clinicians. Hence, identifying factors that induce carbapenemase production in the absence of carbapenems prescription is essential for control of CRE dissemination within the community.

Epidemiology and Resistance Patterns of Bacterial and Fungal Colonization of Biliary Plastic Stents: A Prospective Cohort Study

Background

Plastic stents used for the treatment of biliary obstruction will become occluded over time due to microbial colonization and formation of biofilms. Treatment of stent-associated cholangitis is often not effective because of inappropriate use of antimicrobial agents or antimicrobial resistance. We aimed to assess the current bacterial and fungal etiology of stent-associated biofilms, with particular emphasis on antimicrobial resistance.

Methods

Patients with biliary strictures requiring endoscopic stent placement were prospectively enrolled. After the retrieval of stents, biofilms were disrupted by sonication, microorganisms were cultured, and isolates were identified by matrix-associated laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and/or biochemical typing. Finally, minimum inhibitory concentrations (MICs) were determined for various antimicrobial agents. Selected stents were further analyzed by fluorescence in situ hybridization (FISH).

Results

Among 120 patients (62.5% males, median age 64 years) with biliary strictures (35% malignant, 65% benign), 113 double pigtail polyurethane and 100 straight polyethylene stents were analyzed after a median indwelling time of 63 days (range, 1–1274 days). The stent occlusion rate was 11.5% and 13%, respectively, being associated with a significantly increased risk of cholangitis (38.5% vs. 9.1%, P<0.001). Ninety-five different bacterial and 13 fungal species were detected; polymicrobial colonization predominated (95.8% vs. 4.2%, P<0.001). Enterococci (79.3%), Enterobacteriaceae (73.7%), and Candida spp. (55.9%) were the leading pathogens. Candida species were more frequent in patients previously receiving prolonged antibiotic therapy (63% vs. 46.7%, P = 0.023). Vancomycin-resistant enterococci accounted for 13.7%, extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae with co-resistance to ciprofloxacin accounted for 13.9%, and azole-resistant Candida spp. accounted for 32.9% of the respective isolates.

Conclusions

Enterococci and Candida species play an important role in the microbial colonization of biliary stents. Therefore, empirical antimicrobial treatment of stent-associated cholangitis should be guided toward enterococci, Enterobacteriaceae, streptococci, anaerobes, and Candida. To determine causative pathogens, an accurate microbiological analysis of the extracted stent(s) may be helpful.

A qPCR and multiplex pyrosequencing assay combined with automated data processing for rapid and unambiguous detection of ESBL-producers Enterobacteriaceae

Rapid and specific detection of extended-spectrum β-lactamase-producing (ESBL) bacteria is crucial both for timely antibiotic therapy when treating infected patients as well as for appropriate infection control measures aimed at curbing the spread of ESBL-producing isolates. Whereas a variety of phenotypic methods are currently available for ESBL detection, they remain time consuming and sometimes difficult to interpret while being also affected by a lack of sensitivity and specificity. Considering the longer turnaround time (TAT) of susceptibility testing and culture results, DNA-based ESBL identification would be a valuable surrogate for phenotypic-based methods. Putative ESBL-positive Enterobacteriaceae isolates (n = 330) from clinical specimen were prospectively collected in Bulgaria, Romania and Democratic Republic of Congo and tested in this study. All isolates were assessed for ESBL-production by the E-test method and those giving undetermined ESBL status were re-tested using the combination disk test. A genotypic assay successively combining qPCR detection of blaCTX-M, blaTEM and blaSHV genes with a multiplex pyrosequencing of blaTEM and blaSHV genes was developed in order to detect the most common ESBL-associated TEM and SHV single nucleotides polymorphisms, irrespective of their plasmid and/or chromosomal location. This assay was applied on all Enterobacteriaceae isolates (n = 330). Phenotypic and genotypic results matched in 324/330 (98.2%). Accordingly, real-time PCR combined with multiplex pyrosequencing appears to be a reliable and easy-to-perform assay with high-throughput identification and fast TAT (~5 h).

Sequence analysis of genes mediating extended-spectrum beta-lactamase (ESBL) production in isolates of Enterobacteriaceae in a Lagos Teaching Hospital, Nigeria

Background

Extended-spectrum β-lactamases (ESBLs) in Gram-negative organisms is now a major concern in Enterobacteriaceae worldwide. This study determined a point-prevalence and genetic profiles of ESBL-producing isolates among members of the family Enterobacteriaceae in Lagos State University Teaching Hospital Ikeja, Nigeria.

Methods

Consecutive non-repetitive invasive multidrug-resistant isolates of the family Enterobacteriaceae obtained over a period of 1 month (October 2011) were studied. The isolates were identified using VITEK-2/VITEK MS Systems. Susceptibility testing was performed using E test technique; results were interpreted according to the criteria recommended by the Clinical and Laboratory Standards Institute (CLSI, 2012). ESBL production was detected by E test ESBL method and confirmed by polymerase chain reaction (PCR).

Results

During the one-month study period, 38 isolates with ESBL phenotypic characteristics were identified and confirmed by PCR. Of these, 21 (55.3 %) were E. coli, 12 (31.6 %) K. pneumoniae, 3 (7.9 %) Proteus spp., 1 (2.6 %) each M. morganii and C. freundii. Thirty (79 %) harbored bla_CTX-M genes. Sequence analysis revealed that they were all bla_CTX-M-15 genes. Twenty-nine (96.7 %) of these, also harbored bla_TEM genes simultaneously. All the CTX-M-15-producing isolates carried insertion sequence bla_ISEcP1 upstream of bla_CTX-M-15 genes. The E. coli isolates were genetically heterogeneous, while the K. pneumoniae had 98 % homology.

Conclusions

Our point-prevalence surveillance study revealed a high prevalence of Enterobacteriaceae isolates harboring bla_CTX-M-15 in the Hospital. Urgent implementation of antibiotic stewardship and other preventive strategies are necessary at this time in our hospital.

Bacterial nanoscale cultures for phenotypic multiplexed antibiotic susceptibility testing

An optimal antimicrobial drug regimen is the key to successful clinical outcomes of bacterial infections. To direct the choice of antibiotic, access to fast and precise antibiotic susceptibility profiling of the infecting bacteria is critical. We have developed a high-throughput nanowell antibiotic susceptibility testing (AST) device for direct, multiplexed analysis. By processing in real time the optical recordings of nanoscale cultures of reference and clinical uropathogenic Escherichia coli strains with a mathematical algorithm, the time point when growth shifts from lag phase to early logarithmic phase (Tlag) was identified for each of the several hundreds of cultures tested. Based on Tlag, the MIC could be defined within 4 h. Heatmap presentation of data from this high-throughput analysis allowed multiple resistance patterns to be differentiated at a glance. With a possibility to enhance multiplexing capacity, this device serves as a high-throughput diagnostic tool that rapidly aids clinicians in prescribing the optimal antibiotic therapy.

Detection and fate of antibiotic resistant bacteria in wastewater treatment plants: a review

Antibiotics are among the most successful group of pharmaceuticals used for human and veterinary therapy. However, large amounts of antibiotics are released into municipal wastewater due to incomplete metabolism in humans or due to disposal of unused antibiotics, which finally find their ways into different natural environmental compartments. The emergence and rapid spread of antibiotic resistant bacteria (ARB) has led to an increasing concern about the potential environmental and public health risks. ARB and antibiotic resistant genes (ARGs) have been detected extensively in wastewater samples. Available data show significantly higher proportion of antibiotic resistant bacteria contained in raw and treated wastewater relative to surface water. According to these studies, the conditions in wastewater treatment plants (WWTPs) are favourable for the proliferation of ARB. Moreover, another concern with regards to the presence of ARB and ARGs is their effective removal from sewage. This review gives an overview of the available data on the occurrence of ARB and ARGs and their fate in WWTPs, on the biological methods dealing with the detection of bacterial populations and their resistance genes, and highlights areas in need for further research studies.

TEM-187, a new extended-spectrum β-lactamase with weak activity in a Proteus mirabilis clinical strain

A Proteus mirabilis clinical strain (7001324) was isolated from urine sample of a patient hospitalized in a long-term-care facility. PCR and cloning experiments performed with this strain identified a novel TEM-type β-lactamase (TEM-187) differing by four amino acid substitutions (Leu21Phe, Arg164His, Ala184Val, and Thr265Met) from TEM-1. This characterization provides further evidence for the diversity of extended-spectrum β-lactamases (ESBL) produced by P. mirabilis and for their potential spread to other Enterobacteriaceae due to a lack of sensitive detection methods used in daily practice.

Transmission dynamics of extended-spectrum β-lactamase-producing Enterobacteriaceae in the tertiary care hospital and the household setting

Transmission of extended-spectrum β-lactamase (ESBL)–producing Enterobacteriaceae in households outweighs nosocomial dissemination in the non-outbreak setting. Importation of ESBL producers into the hospitals is as frequent as transmission during hospital stay. ESBL–Klebsiella pneumoniae might be more efficiently transmitted within the hospital than ESBL–Escherichia coli.

Background. Studies about transmission rates of extended-spectrum β-lactamase (ESBL)–producing Enterobacteriaceae in hospitals and households are scarce.

Methods. Eighty-two index patients with new carriage of ESBL-producing Escherichia coli (ESBL-Ec; n = 72) or ESBL-producing Klebsiella pneumoniae (ESBL-Kp; n = 10) and their hospital (n = 112) and household (n = 96) contacts were studied prospectively from May 2008 through September 2010. Isolates were phenotypically and molecularly characterized (sequencing of bla genes, repetitive extragenic palindromic polymerase chain reaction, pulse-field gel electrophoresis, and multilocus sequence typing). Transmission was defined as carriage of a clonally-related ESBL producer with identical bla_ESBL gene(s) in the index patient and his or her contact(s).

Results. CTX-M-15 was the most prevalent ESBL in ESBL-Ec (58%) and ESBL-Kp (70%) in the index patients. Twenty (28%) ESBL-Ec isolates were of the hyperepidemic clone ST131. In the hospital, transmission rates were 4.5% (ESBL-Ec) and 8.3% (ESBL-Kp) and the incidences of transmissions were 5.6 (Ec) and 13.9 (Kp) per 1000 exposure days, respectively. Incidence of ESBL-Kp hospital transmission was significantly higher than that of ESBL-Ec (P < .0001), despite implementation of infection control measures in 75% of ESBL-Kp index patients but only 22% of ESBL-Ec index patients. Detection of ESBL producers not linked to an index patient was as frequent (ESBL-Ec, 5.7%; ESBL-Kp, 16.7%) as nosocomial transmission events. In households, transmission rates were 23% for ESBL-Ec and 25% for ESBL-Kp.

Conclusions. Household outweighs nosocomial transmission of ESBL producers. The effect of hospital infection control measures may differ between different species and clones of ESBL producers.

Expert systems in clinical microbiology

This review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). It considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. A variety of noncommercial systems is described, and the central role played by the EUCAST is stressed. The need for expert rules in the environment of reset EUCAST breakpoints is also questioned. Commercial automated systems with on-board expert systems are considered, with emphasis being placed on the "big three": Vitek 2, BD Phoenix, and MicroScan. By necessity and in places, the review becomes a general review of automated system performances for the detection of specific resistance mechanisms rather than focusing solely on expert systems. Published performance evaluations of each system are drawn together and commented on critically.

Extended-spectrum β-lactamases in Gram Negative Bacteria

Extended-spectrum β-lactamases (ESBLs) are a group of plasmid-mediated, diverse, complex and rapidly evolving enzymes that are posing a major therapeutic challenge today in the treatment of hospitalized and community-based patients. Infections due to ESBL producers range from uncomplicated urinary tract infections to life-threatening sepsis. Derived from the older TEM is derived from Temoniera, a patient from whom the strain was first isolated in Greece. β-lactamases, these enzymes share the ability to hydrolyze third-generation cephalosporins and aztreonam and yet are inhibited by clavulanic acid. In addition, ESBL-producing organisms exhibit co-resistance to many other classes of antibiotics, resulting in limitation of therapeutic option. Because of inoculum effect and substrate specificity, their detection is also a major challenge. At present, however, organizations such as the Clinical and Laboratory Standards Institute (formerly the National Committee for Clinical Laboratory Standards) provide guidelines for the detection of ESBLs in Klebsiella pneumoniae, K. oxytoca, Escherichia coli and Proteus mirabilis. In common to all ESBL-detection methods is the general principle that the activity of extended-spectrum cephalosporins against ESBL-producing organisms will be enhanced by the presence of clavulanic acid. Carbapenems are the treatment of choice for serious infections due to ESBL-producing organisms, yet carbapenem-resistant isolates have recently been reported. ESBLs represent an impressive example of the ability of gram-negative bacteria to develop new antibiotic-resistance mechanisms in the face of the introduction of new antimicrobial agents. Thus there is need for efficient infection-control practices for containment of outbreaks; and intervention strategies, e.g., antibiotic rotation to reduce further selection and spread of these increasingly resistant pathogens.

[Extended-spectrum beta-lactamases in enterobacteria other than Escherichia coli and Klebsiella]

Methods for detecting ESBL-producing Enterobacteriaceae begin by a correct interpretation of the susceptibility profiles, applying the usual criteria for interpretative reading of the antibiogram. Appropriate confirmatory methods will be consequently chosen, based on the inhibition of the enzyme by betalactamases inhibitors, generally clavulanic acid. In case of non-AmpC-producing Enterobacteriaceae, at least two substrates should be used -cefotaxime or ceftriaxone and ceftazidime- to detect enzymes with a low hydrolytic activity against both substrates. Cefepime or AmpC-inhibitors should be recommended for AmpC-producing microorganisms. The identification of the enzymes responsible for the confirmed ESBL phenotype can be performed, either in the clinical laboratory or in reference centres, following a protocol of biochemical and molecular reactions able to detect and characterize, at least, those genes more frequently related to the predominant phenotypic profiles in our region. It is important to know which are the most prevalent combinations enzyme-microorganism, the vehicles for the genetic transmission involved in their dissemination, and the main epidemiological characteristics of the infections that they produce, in order to establish the dimensions of the problem and conduct surveillance studies, with the aim of achieving measures to control the wide spread.

Comparison of different methods of determining β-lactam susceptibility in clinical strains of Pseudomonas aeruginosa

One hundred and one randomly selected (2003–2005) clinical isolates ofPseudomonas aeruginosawere used to assess the quantitative (MIC) and qualitative (susceptibility category) agreement between the microdilution broth reference method (RM) and disc diffusion (DD), Etest and the VITEK 2 automated susceptibility test system for determination of the susceptibility ofP. aeruginosato piperacillin (PIP), PIP–tazobactam (TZP), ceftazidime (CAZ), aztreonam (ATM) cefepime (FEP) and imipenem (IMP). The results obtained by the RM were compared with those obtained by the other methods. The RM and DD were performed according to CLSI criteria. Etest and VITEK 2 were according to the manufacturer's instructions. The Advanced Expert System (AES), which interprets MICs generated by VITEK 2, was modified with new rules of interpretation. Overall, VITEK 2 showed the lowest MIC90values for the six antibiotics. The RM categorical testing (susceptibility and resistance) rates withP. aeruginosawere 11.8 and 88.1 for PIP, 22.7 and 77.2 for TZP, 14.8 and 78.2 for CAZ, 12.8 and 54.4 for ATM, 16.8 and 75.3 for FEP, and 7.9 and 90.1 for IMP, respectively. Very major errors (false susceptible) were only detected for ATM and FEP with DD and for IMP with three methods. Major errors (false resistant) were generally acceptable for all antibiotics except TZP. VITEK 2 yielded a high level of minor errors (trends toward false susceptibility), mainly with CAZ and FEP. A good agreement was obtained for all antibiotics/methods assayed, thus highlighting the importance of the AES for categorization ofβ-lactam susceptibility inP. aeruginosa.

[Evaluation of the Phoenix automated microbiology system for detecting extended-spectrum beta-lactamase in Escherichia coli, Klebsiella species and Proteus mirabilis]

BACKGROUND

The aim of this study was to compare the BD Phoenix (Beckton Dickinson Diagnostic Systems, USA) extended-spectrum beta-lactamase (ESBL) test with the Clinical and Laboratory Standards Institute (CLSI) ESBL phenotypic confirmatory test by disk diffusion (CLSI ESBL test) in Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca and Proteus mirabilis.

METHODS

We tested 224 clinical isolates of E. coli, K. pneumoniae, K. oxytoca and P. mirabilis during May 2006 to March 2007. These isolates were examined by the Phoenix and the CLSI ESBL tests simultaneously. For the isolates showing discordant results between the two tests, boronic acid disk test was performed to differentiate AmpC beta-lactamase and ESBL.

RESULTS

Among the 224 clinical isolates, 75 and 79 isolates were positive for ESBL by CLSI ESBL test and Phoenix test, respectively. Having detected 4 more isolates as ESBL-producers, Phoenix test showed a 98.2% agreement with a 100% sensitivity and 97.3% specificity compared with CLSI ESBL test. Among the four false positive isolates, three were AmpC-positive but ESBL-negative.

CONCLUSIONS

The BD Phoenix ESBL test was sensitive and specific, and can be used as a rapid and reliable method to detect ESBL production in E. coli, Klebsiella species, and P. mirabilis.

The technical aspects and clinical significance of detecting extended-spectrum beta-lactamase-producing Enterobacteriaceae at a tertiary-care hospital in Kuwait

Extended-spectrum beta-lactamase (ESBL) production by Enterobacteriaceae is an emerging problem. This 3-year prospective study was undertaken to determine the prevalence of such enzymes among the clinically significant isolates of the Enterobacteriaceae family gathered from patients, and to evaluate the different techniques for their detection as well as their clinical significance. Members of the Enterobacteriaceae family isolated from blood, inhibited by the third-generation cephalosporins with minimum inhibitory concentrations (MICs) of < or =2 microg/ml and MIC < or =8 microg/ml and isolates from other sources inhibited by MIC < or =8 microg/ml were also investigated for ESBL production by VITEK2 and E test. Their clinical significance in septicemic patients was analyzed. Out of 3,215 isolates, 1018 (31.7%) were ESBL-producers by both VITEK2 and E test. Of these, 428 (42%) were Klebsiella pneumoniae and 376 (37.0%) were Escherichia coli with overall prevalence rates of 13.3% and 11.7%, respectively. There were a total of 184 septicemic patients infected by ESBL-producing Enterobacteriaceae out of which 134 (73%) needed modification of therapy; most (58%) of these patients were initially on third-generation cephalosporin therapy. A total of 58 (31.5%) patients were infected by ESBL-producing blood isolates which were inhibited by cefotaxime/ceftriaxone at MICs =8 microg/ml (within the susceptibility range). Resistance to both aminoglycosides and quinolones were significantly higher among ESBLproducing isolates compared to non-producers (P <0.05). This study highlights a high prevalence of ESBL-producing Enterobacteriaceae in a major tertiary teaching hospital in our country and demonstrates that almost a third of the ESBL-producing Enterobacteriaceae blood isolates would have been released as susceptible by routine susceptibility testing; a finding inimical to optimal therapeutic success.

Extended-spectrum Beta-lactamase detection with different panels for automated susceptibility testing and with a chromogenic medium

Infections caused by extended-spectrum beta-lactamase (ESBL)- and ampC beta-lactamase-producing gram-negative bacteria complicate therapy and limit treatment options. Several different panels for ESBL detection with automated systems exist. In addition, a chromogenic agar medium is available for ESBL screening. We compared two automated identification and susceptibility testing systems with regard to their effectiveness in detecting ESBL production in Enterobacteriaceae: the BD Phoenix system (BD Diagnostic Systems, Sparks, MD) and the Vitek 2 system (bioMerieux, Marcy l'Etoile, France). We tested 114 strains using the Etest as the standard, various available panels for both automated systems (for BD Phoenix, the NMIC/ID-50 and NMIC/ID-70 GN Combo panels for combined identification and susceptibility testing of gram-negative bacilli, and for Vitek 2, the ID-GNB panel for identification of gram-negative bacilli and the AST-N020, AST-N041, and AST-N062 panels for susceptibility testing), and a chromogenic agar medium (bioMérieux, Marcy l'Etoile, France). PCR for common ESBL gene families (encoding TEM, SHV, OXA, and CTX-M) and for chromosomal or plasmid-mediated ampC beta-lactamase genes was conducted to complete the study design. For the tested specimens overall, the chromID ESBL agar showed the highest sensitivity (95.8%) but the lowest specificity (10.5%) compared to the sensitivity and specificity of the Etest (chosen as reference by the authors) for the detection of ESBL-producing strains. The BD Phoenix system showed sensitivities of 77.1% and 84.2% and specificities of 61.5% and 75.0%, respectively, for the NMIC/ID-50 andNMIC/ID-70 panels. The sensitivity of the Vitek 2 system ranged from 78.8% (AST-N020) to 80.6% (AST-N062) and up to 84.2% (AST-N041). The specificities of the respective panels were 50.0% (AST-N041 and AST-N062) and 55.6% (AST-N020). In conclusion, the sensitivities and specificities of ESBL detection by the different methods differ depending on the microorganisms under study.

Evaluation of the VITEK 2 AST N-054 test card for the detection of extended-spectrum beta-lactamase production in Escherichia coli with CTX-M phenotypes

OBJECTIVES

A new VITEK 2 antibiotic susceptibility testing (AST) card, AST N-054, was introduced for aerobic gram-negative bacilli in 2007 and has been widely adopted for routine use in the UK. We evaluated its performance for detecting extended-spectrum beta-lactamase (ESBL) production in Escherichia coli.

METHODS

ESBL-producing faecal isolates of E. coli (n = 137) from residents in nursing homes were tested using the AST N-054 card on VITEK 2 and with MASTDISCS ID ESBL detection disc diffusion tests (Mast Diagnostics, Bootle, UK). The susceptibility result recommended by the VITEK 2 software was also recorded.

RESULTS

The AST N-054 card detected ESBL production in 93 of the 137 isolates tested [test sensitivity 67.9% (95% CI, 59.7-75.1)]. E. coli strain A, a widespread lineage in the UK with a low-level CTX-M enzyme production, accounted for most of the detection failures, with 35/73 strain A isolates incorrectly reported versus 9/64 non-strain A isolates (P < 0.0001). The MASTDISCS correctly detected ESBL in 135/137 isolates [test sensitivity 98.5% (95% CI, 94.5-99.9)]. Of the 44 isolates found to be negative for ESBL production by VITEK 2, the Advanced Expert System misreported 29 as susceptible to cefotaxime and all as susceptible to ceftazidime and aztreonam.

CONCLUSIONS

These data suggest that the AST N-054 card for the VITEK 2 system is less reliable than other previously reported cards for the detection of CTX-M beta-lactamase-producing E. coli circulating in the UK, particularly strain A isolates.

Direct comparison of the BD phoenix system with the MicroScan WalkAway system for identification and antimicrobial susceptibility testing of Enterobacteriaceae and nonfermentative gram-negative organisms

The Phoenix automated microbiology system (BD Diagnostics, Sparks, MD) is designed for the rapid identification (ID) and antimicrobial susceptibility testing (AST) of clinically significant human bacterial pathogens. We evaluated the performance of the Phoenix instrument in comparison with that of the MicroScan WalkAway system (Dade Behring, West Sacramento, CA) in the ID and AST of gram-negative clinical strains and challenge isolates of Enterobacteriaceae (n = 150) and nonfermentative gram-negative bacilli (NFGNB; 45 clinical isolates and 8 challenge isolates). ID discrepancies were resolved with the API 20E and API 20NE conventional biochemical ID systems (bioMerieux, Durham, NC). The standard disk diffusion method was used to resolve discordant AST results. The overall percentages of agreement between the Phoenix ID results and the MicroScan results at the genus and species levels for clinical isolates of Enterobacteriaceae were 98.7 and 97.7%, respectively; following resolution with conventional biochemical testing, the accuracy of the Phoenix system was determined to be 100%. For NFGNB, the levels of agreement were 100 and 97.7%, respectively. Both systems incorrectly identified the majority of the uncommon nonfermentative nonpseudomonal challenge isolates recovered from cystic fibrosis patients; these isolates are not included in the databases of the respective systems. For AST of Enterobacteriaceae, the rate of complete agreement between the Phoenix results and the MicroScan results was 97%; the rates of very major, major, and minor errors were 0.3, 0.2, and 2.7%, respectively. For NFGNB, the rate of complete agreement between the Phoenix results and the MicroScan results was 89.1%; the rates of very major, major, and minor errors were 0, 0.5, and 7.7%, respectively. Following the confirmatory testing of nine clinical isolates initially screened by the MicroScan system as possible extended-spectrum-beta-lactamase (ESBL)-producing organisms (seven Klebsiella pneumoniae isolates and two Escherichia coli isolates), complete agreement was achieved for eight isolates (one ESBL positive and seven negative); one false positive was obtained with the Phoenix instrument. The MicroScan system correctly detected the 10 ESBL challenge isolates, versus the 6 detected by the Phoenix system. Overall, there was good correlation between the Phoenix instrument and the MicroScan system for the ID and AST of Enterobacteriaceae and common NFGNB. The Phoenix system is a reliable method for the ID and AST of the majority of clinical strains encountered in the clinical microbiology laboratory. Until additional performance data are available, results for all Klebsiella pneumoniae or Klebsiella oxytoca and E. coli isolates screened and confirmed as ESBL producers by any automated system should be confirmed by alternate methods prior to the release of final results.

Activities of the frog skin peptide, ascaphin-8 and its lysine-substituted analogs against clinical isolates of extended-spectrum beta-lactamase (ESBL) producing bacteria

Extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacteria are becoming increasingly prevalent and their antibiotic resistance necessitates novel therapeutic intervention. Ascaphin-8 is a cationic alpha-helical peptide that shows broad-spectrum antibacterial activity but is also toxic to human erythrocytes (LC(50)= 55 microM). This study assesses the activity of ascaphin-8, and a series of l-lysine-substituted analogs, against a range of clinical isolates of ESBL-producing bacteria. All ESBL-producing Escherichia coli (MIC=1.5-6 microM) and Klebsiella pneumoniae (MIC=12.5-25 microM) strains tested were susceptible to ascaphin-8, as well as a group of miscellaneous ESBL-producing strains (Citrobacter, Salmonella, Serratia, Shigella spp.) (MIC< or = 25 microM). The Lys4- and Lys8-substituted analogs were generally the most potent against bacteria but showed the highest hemolytic activity. However, the Lys10, Lys14, and Lys18 analogs also displayed potent antibacterial activity while showing very low hemolytic activity (LC50> 500 microM). An unexpected finding was the susceptibility of ESBL-producing Proteus mirabilis strains to ascaphin-8 (MIC=12.5-25 microM) and its Lys4-substituted analog (MIC= 6 microM), although non-ESBL isolates of this organism were resistant to these peptides (MIC> 100 microM).

Comparison of Phoenix and VITEK 2 extended-spectrum-beta-lactamase detection tests for analysis of Escherichia coli and Klebsiella isolates with well-characterized beta-lactamases

The VITEK 2 and Phoenix extended-spectrum beta-lactamase (ESBL) detection systems, which comprise confirmatory tests and expert systems, were evaluated for their ability to discriminate between 102 well-characterized strains of ESBL-positive or -negative Escherichia coli, Klebsiella pneumoniae, and Klebsiella oxytoca. At least 38 distinct ESBLs were included. The strains were chosen to include some known to cause false-positive and false-negative CLSI ESBL confirmatory test results. Therefore, enzyme characterizations, rather than CLSI tests, were the reference methods for the Phoenix and VITEK 2 evaluations. A third arm of the study was conducted with the Phoenix test using two normally inactive expert rules intended to enhance ESBL detection, in addition to using the currently available software. The Phoenix ESBL confirmatory test and unmodified expert system exhibited 96% sensitivity and 81% specificity for ESBL detection. Activation of the two additional rules increased sensitivity to 99% but reduced the specificity to 58%. The VITEK 2 ESBL confirmatory test exhibited 91% sensitivity, which was reduced to 89% sensitivity by its expert system, while its specificity was 85%. Many of the expert system interpretations of both instruments were helpful, but some were suboptimal. The VITEK 2 expert system was potentially more frustrating because it provided more inconclusive interpretations of the results. Considering the high degree of diagnostic difficulty posed by the strains, both ESBL confirmatory tests were highly sensitive. The expert systems of both instruments require modification to update and enhance their utility.

Metallo-beta-lactamase or extended-spectrum beta-lactamase: a wolf in sheep's clothing

Diagnostic algorithms in commonly used automated bacterial identification systems fail to reliably identify a metallo-beta-lactamase in the Enterobacteriaceae. Misidentification as an extended-spectrum beta-lactamase may result in inappropriate dismissal of drugs such as aztreonam in favor of carbapenems, which may in turn select for a highly carabapenem resistant phenotype.

Detection of extended-spectrum beta-lactamases among Enterobacteriaceae by use of semiautomated microbiology systems and manual detection procedures

Three commercially available microbiology identification and susceptibility testing systems were compared with regard to their ability to detect extended-spectrum beta-lactamase (ESBL) production in Enterobacteriaceae, i.e., the Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, MD), the VITEK 2 System (bioMérieux, Marcy l'Etoile, France), and the MicroScan WalkAway-96 System (Dade Behring, Inc., West Sacramento, CA), using routine testing panels. One hundred fifty putative ESBL producers were distributed blindly to three participating laboratories. Conventional phenotypic confirmatory tests such as the disk approximation method, the CLSI double-disk synergy test, and the Etest ESBL were also evaluated. Biochemical and molecular characterization of beta-lactamases performed at an independent laboratory was used as the reference method. One hundred forty-seven isolates of Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Citrobacter freundii, Serratia marcescens, Proteus mirabilis, Proteus vulgaris, and Morganella morganii were investigated. Of these isolates, 85 were identified as ESBL producers by the reference method. The remaining isolates were identified as non-ESBL producers; they were either hyperproducers of their chromosomal AmpC, Koxy, or SHV enzymes or lacked any detectable beta-lactamase activity. The system with the highest sensitivity for the detection of ESBLs was the Phoenix (99%), followed by the VITEK 2 (86%) and the MicroScan (84%); however, specificity was more variable, ranging from 52% (Phoenix) to 78% (VITEK 2). The performance of the semiautomated systems differed widely with the species investigated. The sensitivities of the conventional test methods ranged from 93 to 94%. The double-disk synergy test showed the highest specificity and positive predictive value among all test methods, i.e., 97% and 98%, respectively.

Molecular characterization of extended-spectrum beta-lactamases in Enterobacteriaceae from patients of two hospitals in Saxony, Germany

Between January and September 2003, 39 isolates of the family Enterobacteriaceae with phenotypically positive Vitek 1 extended-spectrum beta-lactamase (ESBL) test results were collected, originating from patients of two hospitals in Saxony, Germany. Plasmid DNA was isolated and screened by PCR for the presence of genes encoding beta-lactamases of SHV, TEM and CTX-M types. To differentiate ESBL and non-ESBL among SHV and TEM genes, detailed analysis of PCR products was performed. Twenty-four strains carried SHV-2, SHV-5 or SHV-12 genes. In a further 11 strains a CTX-M gene was detected. The CTX-M genes could be affiliated to the CTX-M-1 and CTX-M-9 cluster by RFLP analysis. In the case of four Klebsiella oxytoca isolates, hyperproduction of the chromosomal beta-lactamase K1 was inferred, because genes of the above-mentioned types were not detected. The strains contained plasmid DNA between 45 and 160 kb in size. Common plasmid restriction patterns among SHV-5 producers provided evidence of horizontal spread. Twenty strains had a MIC for cefotaxime of ⩽4 mg l−1, 18 strains had the same MIC for ceftazidime, and nine strains had this MIC of >4 mg l−1 for both antibiotics. The ESBL phenotypes often coincided with ciprofloxacin or gentamicin resistance.

Extended-spectrum β-lactamase-producing Shigella strains in Israel, 2000–2004

Routine susceptibility testing of 5,616 Shigella isolates at the National Shigella Reference Centre in Israel over a 5-year period (2000-2004) revealed resistance to ceftriaxone in one strain of Shigella boydii 2 and in two strains each of Shigella flexneri 2a, S. flexneri 6, and Shigella sonnei. All seven isolates were confirmed as producers of extended-spectrum beta-lactamase (ESBL) by the combination disk method, the Vitek 1 system, and a modification of the double-disk synergy test, which is based on the inhibitory properties of clavulanic acid, tazobactam, and sulbactam. Tazobactam had the strongest effect in all seven strains. Molecular characterization of the ESBLs identified CTX-M-type enzymes, consisting of the CTX-M-9 group (n = 3), CTX-M-3 (n = 2), CTX-M-39 (n = 1), and CTX-M-2 group (n = 1). Three of the strains also carried bla-(OXA) genes and a bla-(TEM) gene. Although the prevalence of ESBLs in this study was low, further research is needed on the spread and transfer of resistance genes, both in hospitals and in the community.

Occurrence of a novel SHV-type enzyme (SHV-55) among isolates of Klebsiella pneumoniae from Portuguese origin in a comparison study for extended-spectrum β-lactamase–producing evaluation

Fifty-five isolates of Klebsiella pneumoniae were evaluated for extended-spectrum beta-lactamase (ESBL) detection and confirmation, using MIC testing by agar dilution, broth microdilution, and the ESBL E-Test (AB Biodisk, Solna, Sweden), according to reference laboratory criteria (RLC) and Clinical and Laboratory Standards Institute (CLSI) guidelines. The RLC classify as ESBL producers those strains for which any MIC of cephalosporins is 3-fold lower in the presence of 2 mug/mL of clavulanate. The E-Test was the only to show 100% sensitivity and specificity to detect ESBL-producer strains with either set of guidelines. MIC determination by agar dilution or broth microdilution, using NCCLS guidelines, showed sensitivity of 92.9%. Nucleotide sequencing allowed the identification of a new ESBL (SHV-55). Overall, this gold standard method confirmed the production of 18 ESBL producers, 36 non-ESBL producers, from which 9 were false ESBL producers (suggesting hyperproduction) and 1 presumptive ESBL TEM-derived. New guidelines for ESBL detection and reliable methods of ESBL identification are required.

Endocarditis caused by extended-spectrum-beta-lactamase-producing Klebsiella pneumoniae: emergence of resistance to ciprofloxacin and piperacillin-tazobactam during treatment despite initial susceptibility

Three episodes of bacteremia occurred in the course of prosthetic valve endocarditis caused by an extended-spectrum-beta-lactamase (ESBL)-producing Klebsiella pneumoniae strain. The second isolate developed resistance to ciprofloxacin and the third isolate to piperacillin-tazobactam (PIP-TZ) following sequential therapy with each agent. The first isolate was resistant to PIP-TZ only at high inocula, the second isolate acquired increased transcription of the acrA gene, and the third isolate became resistant to PIP-TZ due to loss of beta-lactamase inhibition by TZ. We question if and how PIP-TZ susceptibility should be reported for ESBL-producing Enterobacteriaceae.

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

We evaluated the accuracy of the BD Phoenix system for the identification (ID) and antimicrobial susceptibility testing (AST) of 251 isolates of the family Enterobacteriaceae representing 31 species. Organisms were inoculated onto the Phoenix panel according to the manufacturer's instructions. The results from conventional biochemical tests were used for the reference method for ID. Agar dilution, performed according to the CLSI guidelines, was the reference AST method. Essential and categorical agreements were determined. The overall levels of agreement for the genus- and species-level identifications were 95.6% and 94.4%, respectively. Fourteen isolates were incorrectly identified by the Phoenix system; 10 of these were incorrectly identified to the species level. Three of these were Enterobacter (Pantoea) species and four of these were Shigella spp. misidentified as Escherichia coli. For AST results, the essential and categorical agreements were 98.7% and 97.9%, respectively. The very major error, major error, and minor error rates were 0.38%, 0.33%, and 1.8%, respectively. Six isolates (three E. coli isolates and three Klebsiella isolates) were extended-spectrum beta-lactamase producers. All six were flagged by the Phoenix system expert rules. The Phoenix system compares favorably to traditional methods for ID and AST of Enterobacteriaceae.

Evaluation of the new VITEK 2 extended-spectrum beta-lactamase (ESBL) test for rapid detection of ESBL production in Enterobacteriaceae isolates

Extended-spectrum beta-lactamases (ESBLs) are a large, rapidly evolving group of enzymes that confer resistance to oxyimino cephalosporins and monobactams and are inhibited by clavulanate. Rapid reliable detection of ESBL production is a prerequisite for successful infection management and for monitoring resistance trends and implementation of intervention strategies. We evaluated the performance of the new VITEK 2 ESBL test system (bioMérieux, Inc, Hazelwood, Mo.) in the identification of ESBL-producing Enterobacteriaceae isolates. We examined a total of 1,129 clinically relevant Enterobacteriaceae isolates (including 218 that had been previously characterized). The ESBL classification furnished by the VITEK 2 ESBL test system was concordant with that of the comparison method (molecular identification of beta-lactamase genes) for 1,121 (99.3%) of the 1,129 isolates evaluated. ESBL production was correctly detected in 306 of the 312 ESBL-producing organisms (sensitivity, 98.1%; positive predictive value, 99.3%). False-positive results emerged for 2 of the 817 ESBL-negative isolates (specificity, 99.7%; negative predictive value, 99.3%). VITEK 2 ESBL testing took 6 to 13 h (median, 7.5 h; mean +/- SD, 8.2 +/- 2.39 h). This automated short-incubation system appears to be a rapid and reliable tool for routine identification of ESBL-producing isolates of Enterobacteriaceae.

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.

Accuracy of three automated systems (MicroScan WalkAway, VITEK, and VITEK 2) for susceptibility testing of Pseudomonas aeruginosa against five broad-spectrum beta-lactam agents

One hundred recent clinical Pseudomonas aeruginosa isolates were used to assess the quantitative (MIC) and qualitative (susceptibility category) accuracies of the MicroScan WalkAway, VITEK, and VITEK 2 automated susceptibility test systems when five-broad spectrum beta-lactams, aztreonam, cefepime, ceftazidime, imipenem, and piperacillin-tazobactam, were tested. Isolates were selected so that the MICs for the isolates overrepresented the MICs near the breakpoints to assess precisely the agreement between the results obtained with the automated systems and the results obtained by the reference tests. The categorical and MIC results from the automated systems were compared to the consensus result of three reference methods: broth microdilution, agar dilution, and disk diffusion. The consensus categorical testing (susceptibility and resistance) rates were 47 and 27%, respectively, for aztreonam; 59 and 14%, respectively, for cefepime; 44 and 43%, respectively, for ceftazidime; 71 and 19%, respectively, for imipenem; and 50 and 50%, respectively, for piperacillin-tazobactam. All systems tested exhibited a high, unacceptable level of very major (false-susceptible) errors for piperacillin-tazobactam (19 to 27%). Major (false-resistant) error rates were generally acceptable (0 to 3%), but minor error rates were elevated (8 to 32%) for cefepime (VITEK 2 and VITEK) and for aztreonam (all three systems), leading to consistent trends toward false resistance. Manufacturer reevaluation of these automated systems for the testing of selected beta-lactams with current clinical isolates of P. aeruginosa that exhibit contemporary resistance mechanisms would be prudent to minimize the potential for serious reporting errors.

Overview of the epidemiological profile and laboratory detection of extended-spectrum beta-lactamases

Extended-spectrum beta-lactamases (ESBLs) are plasmid-mediated bacterial enzymes that confer resistance to a broad range of beta-lactams. They are descended by genetic mutation from native beta-lactamases found in gram-negative bacteria, especially infectious strains of Escherichia coli and Klebsiella species. Genetic sequence modifications have broadened the substrate specificity of the enzymes to include third-generation cephalosporins, such as ceftazidime. Because ESBL-producing strains are resistant to a wide variety of commonly used antimicrobials, their proliferation poses a serious global health concern that has complicated treatment strategies for a growing number of hospitalized patients. Another resistance mechanism, also common to Enterobacteriaceae, results from the overproduction of chromosomal or plasmid-derived AmpC beta-lactamases. These organisms share an antimicrobial resistance pattern similar to that of ESBL-producing organisms, with the prominent exception that, unlike most ESBLs, AmpC enzymes are not inhibited by clavulanate and similar beta-lactamase inhibitors. Recent technological improvements in testing and in the development of uniform standards for both ESBL detection and confirmatory testing promise to make accurate identification of ESBL-producing organisms more accessible to clinical laboratories.

Utility of the VITEK 2 Advanced Expert System for identification of extended-spectrum beta-lactamase production in Enterobacter spp

Forty clinical isolates of Enterobacter spp. were identified as extended-spectrum beta-lactamase (ESBL) producers by disk diffusion. The VITEK 2 Advanced Expert System (AES) identified the ESBL phenotype in only 25 isolates (62.5%), and erroneously reported cephalosporin susceptibility in 11 isolates (28%). Refinements in the AES are required in order to improve ESBL detection in Enterobacter.

Detection and genotyping of SHV beta-lactamase variants by mass spectrometry after base-specific cleavage of in vitro-generated RNA transcripts

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR-amplified and in vitro-transcribed bla(SHV) genes was used for the identification and genotyping of SHV beta-lactamases. For evaluation, bla(SHV) stretches of 21 clinical Enterobacteriaceae isolates were PCR amplified using T7 promoter-tagged forward and reverse primers, respectively. In vitro transcripts were generated with T7 RNA and DNA polymerase in the presence of modified analogues replacing either CTP or UTP. Using RNase A, the in vitro transcripts were base-specifically cleaved at every "T" or "C" position. Resulting cleavage products were analyzed by MALDI-TOF MS, generating a characteristic signal pattern based on the fragment masses. All 21 individual SHV genes were identified unambiguously using reference sequences, and the results were in perfect concordance with those obtained by fluorescent dideoxy sequencing, which represents the current standard method. As multiple point mutations can be detected in a single assay and newly emerged mutations which are not yet described in public databases can be identified too, MALDI-TOF MS appears to be an ideal tool for analysis of sequence polymorphisms in resistance-associated gene loci.