Direct detection of extended-spectrum beta-lactamases (CTX-M) from blood cultures by LC-MS/MS bottom-up proteomics

Rapid bacterial species identification and antibiotic susceptibility testing in positive blood cultures have an important impact on the antibiotic treatment for patients. To identify extended-spectrum beta-lactamases (ESBL) directly in positive blood culture bottles, we developed a workflow of saponin extraction followed by a bottom-up proteomics approach using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The workflow was applied to positive blood cultures with Escherichia coli and Klebsiella pneumoniae collected prospectively in two academic hospitals over a 4-month period. Of 170 positive blood cultures, 22 (12.9%) contained ESBL-positive isolates based on standard susceptibility testing. Proteomic analysis identified CTX-M ESBLs in 95% of these isolates directly in positive blood cultures, whereas no false positives were found in the non-ESBL producing positive blood cultures. The results were confirmed by molecular characterisation of beta-lactamase genes. Based on this proof-of-concept study, we conclude that LC-MS/MS-based protein analysis can directly identify extended-spectrum beta lactamases in E. coli and K. pneumoniae positive blood cultures, and could be further developed for application in routine diagnostics.

Antimicrobial resistance trends in blood culture positive Salmonella Paratyphi A isolates from Pondicherry, India

Enteric fever is a public health problem with the upsurge in the occurrence of Salmonella isolates that are resistant to ciprofloxacin. In this study, a total of 284 blood culture isolates of S. Paratyphi A were investigated. Of these isolates, 281 (98.9%) were nalidixic acid resistant. A high rate (6.3%) of high-level resistance (≥ 4 μg/mL) was found to ciprofloxacin. The isolates with ciprofloxacin minimum inhibitory concentrations (MICs) of ≥ 12 μg/mL had 4 mutations, 2 mutations within the quinolone resistance-determining region of gyrA and 2 mutations also in parC. According to the Clinical Laboratory Standards Institute 2012 MIC breakpoints, 75.0% of isolates were resistant to ciprofloxacin. Finally, 3 major pulsed-field gel electrophoresis patterns were observed among the S. Paratyphi A isolates. The spread of fluoroquinolone resistant S. Paratyphi A necessitates a change toward 'evidence-based' treatment for enteric fever. The research provides a perspective on the increasing prevalence of antimicrobial resistant S. Paratyphi A isolates in this region of India.

Molecular characterization of antimicrobial resistance in non-typhoidal salmonellae associated with systemic manifestations from India

Extended-spectrum cephalosporins and fluoroquinolones are essential antimicrobials for treating invasive salmonellosis, although emerging resistance to these antimicrobials is of growing concern, especially in India. Therefore, a study was conducted to characterize the antimicrobial susceptibility phenotypes, types of extended-spectrum β-lactamase (ESBL) gene plasmids and serological relationships of 21 non-typhoidal Salmonella isolates from patients who attended three different hospitals in India from 2006 to 2008. The isolates were cultured from stool, blood and cerebrospinal fluid samples obtained from patients presenting with diarrhoea and accompanying systemic manifestations such as fever, vomiting and meningism. Non-typhoidal Salmonella isolates were investigated using serotyping and antimicrobial susceptibility testing. PCR screening was also performed to detect the β-lactamase, qnr and aac(6′)-Ib-cr genes and class 1 integrons. Sequencing for quinolone resistance mutations and plasmid replicon typing were also performed. An antimicrobial resistance microarray was used for preliminary screening and identification of bla TEM and bla SHV genes, and phenotypic testing for the presence of efflux pumps was also performed. Ten out of 21 isolates (48 %) possessed the extended-spectrum cephalosporin resistance phenotype, with PCR amplification and sequencing revealing that isolates possessed TEM-1, SHV-12, DHA-1, OXA-1-like and CTX-M-15 ESBL genes. FIIs plasmid replicons were detected in seven isolates (33 %). The involvement of efflux pumps was detected in four isolates (19 %) resistant to ciprofloxacin. It was concluded that SHV-12-carrying Salmonella serotype Agona may play an important role in ESBL-mediated resistance in non-typhoidal salmonellae in India. The very high percentage (48 %) of ESBL-producing non-typhoidal salmonellae isolated from these patients represents a real and immediate challenge to the effective antimicrobial therapy of Salmonella infections associated with systemic manifestations. Continued surveillance for the presence of ESBL-producing (non-typhoidal) salmonellae in India is essential.

Rapid identification and antimicrobial susceptibility testing reduce antibiotic use and accelerate pathogen-directed antibiotic use

INTRODUCTION

Rapid bacterial identification and susceptibility tests can lead to earlier microbiological diagnosis and pathogen-directed, appropriate therapy. We studied whether accelerated diagnostics affected antibiotic use and patient outcomes.

PATIENTS AND METHODS

A prospective randomized clinical trial was performed over a 2-year period. Inpatients were selected on the basis of a positive culture from normally sterile body fluids and randomly assigned to either a rapid intervention arm or the control arm. The intervention arm used the Vitek 2 automated identification and susceptibility testing device, combined with direct inoculation of blood cultures. In the control arm, the Vitek 1 system inoculated from subcultures was used. Follow-up was 4 weeks after randomization.

RESULTS

A total of 1498 patients were randomized: 746 in the intervention arm and 752 in the control arm. For susceptibility testing, the rapid arm was 22 h faster than the control arm, and for identification, it was 13 h faster (P < 0.0001). In the rapid arm, antibiotic use was 6 defined daily doses lower per patient than in the control arm (P = 0.012). Whereas antibiotics were switched more in the rapid group on the day of randomization (P = 0.006), in the control group they were switched more on day two (P = 0.02). Mortality rates did not differ significantly between the two groups (17.6% versus 15.2%).

CONCLUSIONS

While rapid bacterial identification and susceptibility testing led to earlier changes and a significant reduction in antibiotic use, they did not reduce mortality.

Accuracy of the VITEK 2 system to detect glycopeptide resistance in enterococci

We evaluated the accuracy of the VITEK 2 fully automated system to detect and identify glycopeptide-resistant enterococci (GRE) compared to a reference agar dilution method. The sensitivity of vancomycin susceptibility testing with VITEK 2 for the detection of vanA, vanB, and vanC1 strains was 100%. The sensitivity of vancomycin susceptibility testing of vanC2 strains was 77%. The sensitivity of teicoplanin susceptibility testing of vanA strains was 90%. Of 80 vanC enterococci, 78 (98%) were correctly identified by VITEK 2 as Enterococcus gallinarum/Enterococcus casseliflavus. Since the identification and susceptibility data are produced within 3 and 8 h, respectively, VITEK 2 appears a fast and reliable method for detection of GRE in microbiology laboratories.

Rapid emergence of ciprofloxacin-resistant enterobacteriaceae containing multiple gentamicin resistance-associated integrons in a Dutch hospital

In a hematology unit in the Netherlands, the incidence of ciprofloxacin-resistant Enterobacter cloacae and Escherichia coli increased from from 1996 to 1999. Clonal spread of single genotypes of both ciprofloxacin-resistant E. coli and Enterobacter cloacae from patient to patient was documented by pulsed-field gel electrophoresis and random amplification of polymorphic DNA. In addition, genetically heterogeneous strains were isolated regularly. Integrons associated with gentamicin resistance were detected in Enterobacter cloacae and E. coli strains. Integron-containing E. coli were detected in all hematology wards. In contrast, in Enterobacter cloacae strains two integron types were encountered only in the isolates from one ward. Although in all patients identical antibiotic regimens were used for selective decontamination, we documented clear differences with respect to the nosocomial emergence of ciprofloxacin-resistant bacterial strains and gentamicin resistance-associated integrons.

Multicenter evaluation of a modified protocol for the RAPIDEC staph system for direct identification of Staphylococcus aureus in blood cultures

A modified protocol for the RAPIDEC Staph system (bioMérieux, Marcy-l'Etoile, France) for direct identification of Staphylococcus aureus in blood cultures was evaluated in a multicenter study. A total of 129 blood cultures (BACTEC 9000 Blood Culture System; Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) containing gram-positive cocci in clusters were analyzed by conventional methods and by RAPIDEC Staph in accordance with the manufacturer's protocol and in accordance with a modified protocol. The sensitivity, specificity, and positive and negative predictive values obtained with the manufacturer's protocol were 90.5, 97.7, 95. 0, and 95.5%, respectively, and those obtained with the modified protocol were 100, 96.6, 93.3, and 100%, respectively. The modified protocol for the RAPIDEC Staph is easier to perform than the manufacturer's protocol and is very reliable.

Detection of antigen in sera of patients with invasive aspergillosis: intra- and interlaboratory reproducibility. The Dutch Interuniversity Working Party for Invasive Mycoses

The intra- and interlaboratory reproducibilities of a commercial sandwich enzyme-linked immunosorbent assay (ELISA) for the detection of Aspergillus galactomannan in serum (Platelia Aspergillus; Sanofi Diagnostics Pasteur, Marnes-La-Coquette, France) were evaluated in six laboratories of university hospitals. Twenty serum samples were obtained from 12 neutropenic patients including 6 with invasive aspergillosis. These samples were blinded and sent to each center together with eight blinded ELISA-negative serum samples spiked with known concentrations of galactomannan. The centers were provided with ELISA microtiter plates from a single batch and a detailed protocol. Ten clinical samples showed ELISA reactivity, while 10 samples were ELISA negative. The mean coefficient of variation (CV) of the optical density values was 4.24% within a single assay and 25.6% between runs. The interassay CV of the ratios for the serum samples tested was 18.6%. Analysis of ordinal interpretation of the ELISA result (i.e., negative, gray zone, or positive) showed excellent reproducibility. Recalculation of the cutoff values for positive and negative samples suggested that the cutoff level recommended by the manufacturer could be lowered from 1.0 to 0.8 for negative samples and from 1.5 to 1.0 for positive samples. The intra- and interlaboratory reproducibilities were excellent when the ELISA results were interpreted as ordinal data, but considerable variation in optical density values and, to a lesser extent, in the ratios for the serum samples tested, was observed between runs. High assay variability was also found for serum samples spiked with known concentrations of galactomannan. Therefore, antigen titers in serum samples from a single patient, measured in different runs, should be compared with caution.

Towards a better diagnosis of throat infections (with group A beta-haemolytic streptococcus) in general practice

BACKGROUND

Sore throat is a common complaint in general practice. However, management strategies are not very clear. A better diagnostic procedure is needed to prevent the overuse of antibiotics.

AIM

To assess the diagnostic value of a rapid streptococcal antigen detection test in addition to four clinical features in patients with sore throat, using throat culture and antibody titres as reference tests.

METHOD

Four clinical features [fever (history) > or = 38.0 degrees C, lack of cough, tonsillar exudate, and anterior cervical lymphadenopathy] were registered in 558 patients aged 4 to 60 years presenting with sore throat of no more than 14 days' duration. A rapid diagnostic test was performed, as well as a throat culture and antibody titres [fourfold increase in anti-streptolysin-O (ASO) and/or anti-deoxyribonuclease B (anti-DNAase B)] in patients aged 11 years and older.

RESULTS

Throat cultures were positive for group A beta-haemolytic streptococcus (GABHS) in 33% of the patients. Rapid tests were positive in 24%. Compared with the throat culture, the sensitivity of the rapid test was 65%, the specificity 96%, the positive predictive value 88%, and the negative predictive value 85%. However, for patients with three or four clinical features, the sensitivity of the rapid test was considerably higher at 75%. Children (< or = 14 years) had a slightly raised specificity and raised positive predictive value and prevalence. With the antibody titres as a reference, the rapid test performed as well as the throat culture with regard to its predictive value.

CONCLUSION

For the management of patients with sore throat in general practice, a rapid test may have an additional value, especially in patients with a high chance of having GABHS infection. However, as the sensitivity of the test studied is low, tests with a higher sensitivity are needed.

Monitoring persistence of coagulase-negative staphylococci in a hematology department using phenotypic and genotypic strategies

OBJECTIVE

To determine persistence of coagulase-negative staphylococci (CNS) on a hematology-oncology ward and to determine the value of phenotypic and genotypic procedures for establishing clonality among CNS isolates.

DESIGN

Strains of CNS isolated from bacteremic patients (n = 139) were typed by biochemical reactivity, antibiotic susceptibility, DNA macrorestriction analysis by pulsed-field gel electrophoresis (PFGE), and arbitrary primed polymerase chain reaction (AP PCR). Coagulase-negative staphylococci were subgrouped in a random collection (n = 20) used for the evaluation of the typing procedures and a collection of 119 CNS isolates from hematologic patients displaying multiple bacteremic episodes.

RESULTS

Analysis of the reference collection demonstrated the usefulness of the DNA typing procedures, indicating that AP PCR and PFGE can be used for epidemiologic typing of CNS in a concordant fashion. Certain strains appeared to be permanent colonizers of the hematology ward or ward-related personnel. In individual patients, persistent colonization by a single type was demonstrated. However, a number of patients also experienced bacteremic episodes caused by CNS belonging to different types.

CONCLUSION

We conclude that monitoring of CNS infections on a hematology ward by various genotypic techniques provides insight into nosocomial epidemiology and elucidates the complexity of the infections taking place. DNA typing is preferred over phenotypic procedures and can identify persistent CNS strains in a given location.

Contribution of molecular typing methods and antifungal susceptibility testing to the study of a candidemia cluster in a burn care unit

We investigated a cluster of cases of Candida septicemia diagnosed in four burn patients. Twenty clinical isolates of Candida albicans and two of Candida parapsilosis, plus eight isolates of C. albicans recovered from nurses' clothes, were analyzed by antifungal susceptibility testing and three genotyping methods (restriction fragment length polymorphism analysis with EcoRI and HinfI, arbitrarily primed PCR, and karyotyping). The high MICs of the azoles for all of the C. albicans isolates tested suggest either a natural resistance of the endogenous flora or the transmission of isolates with acquired resistance. The genotyping methods demonstrated the involvement of four different strains, cross-infections with one C. albicans strain and one C. parapsilosis strain, and identity between some of the strains from the patients and nurses. The origins of the strains remain unclear. Our results show that the use of a combination of at least two different methods such as those used in the present study is recommended for C. albicans typing.

Investigation into the repeated recovery of coagulase-negative staphylococci from blood taken at the end of cardiopulmonary by-pass

Forty-six strains of coagulase-negative staphylococci (CNS) were typed by biochemical reactivity, antibiotic susceptibility pattern, macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) and arbitrary primed polymerase chain reaction (AP PCR). Twenty-four strains were obtained in 1993 from blood cultures of as many patients coupled to a heart-lung machine during cardiac surgery. Since over 30% of the latter belonged to a single type, it was concluded that during the year of analysis a single clone of CNS persisted in this hospital setting. Subsequent epidemiological surveillance putatively identified four possible carriers among surgical personnel. For this reason, 22 strains collected from the hands and nose of two cardiac surgeons and two perfusionists were also tested; none were identical to the persistent clone. Thus either the operation equipment was colonized longitudinally or the causative CNS had disappeared from the suspect individuals' flora. Longitudinal monitoring of CNS infections by various techniques gives a valuable insight into nosocomial epidemiology and elucidates the complexity of the CNS colonization.

Food-initiated outbreak of methicillin-resistant Staphylococcus aureus analyzed by pheno- and genotyping

An outbreak of methicillin-resistant Staphylococcus aureus (MRSA) involving 27 patients and 14 health-care workers (HCW) was studied. The outbreak started in the hematology unit of the University Hospital Rotterdam, Dijkzigt, The Netherlands, and spread to the surgical unit. Twenty-one patients (77.8%) developed clinical disease, and five died. Subsequently, MRSA was detected in food and in the throat of one of the HCW who prepared food for hematology patients. Food contaminated by an HCW most likely caused the first case of MRSA septicemia. This route of transmission has not been described before. The outbreak strain was probably transmitted to the surgical unit by a colonized nurse, where it caused an explosive outbreak. Airborne probably transmitted to the surgical unit by a colonized nurse, where it caused an explosive outbreak. Airborne MRSA transmission played an important role in disseminating the organism. The outbreak was controlled within 6 months by intensifying surveillance, temporarily closing the affected wards, treating carriers, and instituting an MRSA ward outside the hospital. Phage typing, insertion sequence probing, protein A gene typing, and DNA fingerprinting by PCR revealed that all outbreak-related isolates were identical. By pulsed-field gel electrophoresis, all but one of the outbreak-related isolates were determined to be identical. Protein A gene typing identified numerous (11) repeat units in all outbreak-related isolates, which supports the suggestion that the outbreak strain may have been more virulent and more transmissible than other MRSA strains. Pheno- and genotyping studies underlined the value of DNA fingerprinting methods for investigation of MRSA epidemiology. Optimal discriminatory power was achieved by combining the results of four genotyping methods.