Phoenix 100 versus Vitek 2 in the identification of gram-positive and gram-negative bacteria: a comprehensive meta-analysis

Prevalence and In Vivo Assessment of Virulence in Shiga Toxin-Producing Escherichia coli Clinical Isolates from Greater Cairo Area

Background: Shiga toxin-producing Escherichia coli (STEC) has been identified as an important etiologic agent of human disease in Egypt. Aims: To investigate the occurrence and describe the characterization as well as prevalence of STEC in Greater Cairo hospitals as well as molecular characterization of virulence and resistance genes. Methods: Four hundred seventy E. coli clinical isolates were collected from eight hospitals and analyzed by genotypic and phenotypic methods for STEC, followed by histopathological examination and scoring of different organs lesions. Results: The highest proportion of isolates was from urine (151 isolates), whereas the lowest was from splenic drain (3 isolates). In tandem, when serogrouping was performed, 15 serogroups were obtained where the most prevalent was O157 and the least prevalent was O151. All isolates were positive when screened for identity gene gad A, while only typable strains were screened for seven virulence genes stx1 (gene encoding Shiga toxin 1), stx2 (gene encoding Shiga toxin 2), tsh (gene encoding thermostable hemagglutinin), eaeA (gene encoding intimin), invE (gene encoding invasion protein), aggR (gene encoding aggregative adherence transcriptional regulator), and astA (aspartate transaminase) where the prevalence was 48%, 30%, 50%, 57%, 7.5%, 12%, and 58%, respectively. Of 254 typable isolates, 152 were STEC carrying stx1 or stx2 genes or both. Conclusions: Relying on in vivo comparison between different E. coli pathotypes via histopathological examination of different organs, E. coli pathotypes could be divided into mild virulent, moderate virulent, and high virulent strains. Statistical analysis revealed significant correlation between different serogroups and presence of virulence genes.

Plant growth promoting rhizobacterial diversity in potato grown soil in the Gwalior region of India

There seems to be meager studies with regards to rhizo and non-rhizo microbial association with potato plant from the central India. Present study was undertaken to evaluate the microbial diversity of rhizospheric and non-rhizospheric isolates from three varieties of potato viz Kufri sindhuri, Kufri lauvkar and Kufri chipsona-3 procured from the Central Potato Research Station, Maharajpura, Gwalior. A total of 130 bacterial forms were isolated, and amongst these forty isolates were further characterized on their morphological basis, and those showing some of PGPR characteristics were identified to species level using VITEK-2 method. Various bacterial populations were found in potato rhizosphere and dominant presence was those of Bacillus subtilis, Bacillus Megaterium and Lysinibacillus sphaericus. The non-rhizospheric soil was dominant in the forms like Aeromonas salmonicida, Morxella group and Bacillus coagulans. Highest bacterial diversity was found in the rhizosphere soil of different potato cultivars than in the non-rhizospheric soil of potato.

Staphylococcus lugdunensis Bacteremia with an Infected Aortic Thrombus in a Preterm Infant

Staphylococcus lugdunensis is a rare cause of late-onset sepsis in preterm infants. To our best knowledge, we report the fourth case of a male preterm infant who developed fulminant late-onset sepsis due to Staphylococcus lugdunensis with persistent bacteremia secondary to an infected aortic thrombus confirmed with two positive blood cultures. Our patient was an extremely low birth weight growth-restricted infant born at 27 weeks gestation and initially required an umbilical arterial catheter for blood pressure and blood gas monitoring. The course of this neonate was complicated by severe respiratory distress syndrome that evolved into chronic lung disease along with multiple episodes of tracheitis. Hemodynamically, the infant had a significant patent ductus arteriosus, and an episode of medical necrotizing enterocolitis followed by Staphylococcus lugdunensis septicemia. He was diagnosed with an infected aortic thrombus, probably the occult focus responsible for the persistent bacteremia. After a 6-week course of intravenous antibiotics and 4-week course of anticoagulant therapy, the infant responded and recovered without complications.

Bacteria cultured from the gut of Meccus pallidipennis (Hemiptera: Reduviidae), a triatomine species endemic to Mexico

The study of intestinal microbiota in vector insects like triatomines is paramount in parasitology because many parasitic species inhabit the vector's gut. Although knowledge on the gut microbiota in various vectors of the parasitic flagellate Trypanosoma cruzi has grown, research efforts have focused on South American triatomines. This study reports the isolation of bacterial microbiota in the anterior and posterior gut of Meccus pallidipennis (a triatomine species endemic to Mexico) by culture, as well as its identification by phenotypic and biochemical tests and its quantification by counting colony-forming units. The study was performed on fifth-instar nymph and adult specimens of M. pallidipennis, either laboratory-bred or collected in the field and either infected or not with T. cruzi. Overall, 17 bacterial species were identified, with the genera Bacillus and Staphylococcus being the most prevalent regardless of the origin of the insects. No differences were observed in the number of bacterial species in the gut of laboratory-bred and field-collected insects, neither with respect to life stage or infection status. In general, the Shannon-Weaver diversity index was higher in non-infected insects than in infected ones. Further studies using non-culture methods are required to determine whether bacterial species diversity is modified by laboratory breeding.

A Study on Multidrug-Resistant Escherichia coli Clinical Isolates from Different Hospitals in Greater Cairo

The biological fitness cost of antibiotic resistance is a key parameter in determining the rate of appearance and spread of antibiotic-resistant bacteria in Egypt. Our study aimed to investigate the prevalence of antibiotic resistance among Escherichia coli clinical isolates from Greater Cairo area hospitals. A total of 537 clinical isolates were recovered from samples of urine, diarrheal specimen, pus, wound culture, gastric wound, blood, drain culture, sputum, high vaginal swab, abscess, amniotic fluid, ventilator, burn swab, splenic drain culture, and unknown site of infection during different seasons. All isolates were subjected to phenotypic and genotypic susceptibility testing for colistin, nitrofurantoin, fosfomycin, and trimethoprim, quinolones, and β-lactam resistance. Our results revealed that 42.7% of the isolates harbored at least one resistance encoding gene, 10% harboring 2, 0.6% harboring 3, and 0.85% harboring 4 resistance-encoding genes. PCR reported the prevalence of resistance genes as follows: bla-SHV 13.4%, mcr-1 0.6%, qnr-A 23.8%, fos-A 1.06%, nfs-A 3.6%, and dfr-A 25.5%. We reported that three isolates carried the mcr-1 gene encoding colistin resistance from three different hospitals. Upon performing sequencing and phylogenetic analysis on the three positive mcr-1 isolates (MT890587, MT890588, and MT890589), the three isolates showed 100% identity with themselves, with some strains from Egypt and Japan, and 99.9% identity with an isolate from China.

Evaluation of MicroScan Bacterial Identification Panels for Low-Resource Settings

Bacterial identification is challenging in low-resource settings (LRS). We evaluated the MicroScan identification panels (Beckman Coulter, Brea, CA, USA) as part of Médecins Sans Frontières' Mini-lab Project. The MicroScan Dried Overnight Positive ID Type 3 (PID3) panels for Gram-positive organisms and Dried Overnight Negative ID Type 2 (NID2) panels for Gram-negative organisms were assessed with 367 clinical isolates from LRS. Robustness was studied by inoculating Gram-negative species on the Gram-positive panel and vice versa. The ease of use of the panels and readability of the instructions for use (IFU) were evaluated. Of species represented in the MicroScan database, 94.6% (185/195) of Gram-negative and 85.9% (110/128) of Gram-positive isolates were correctly identified up to species level. Of species not represented in the database (e.g., Streptococcus suis and Bacillus spp.), 53.1% out of 49 isolates were incorrectly identified as non-related bacterial species. Testing of Gram-positive isolates on Gram-negative panels and vice versa (n = 144) resulted in incorrect identifications for 38.2% of tested isolates. The readability level of the IFU was considered too high for LRS. Inoculation of the panels was favorably evaluated, whereas the visual reading of the panels was considered error-prone. In conclusion, the accuracy of the MicroScan identification panels was excellent for Gram-negative species and good for Gram-positive species. Improvements in stability, robustness, and ease of use have been identified to assure adaptation to LRS constraints.

Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus

The urgent need to develop a detection system for Staphylococcus aureus, one of the most common causes of infection, is prompting research towards novel approaches and devices, with a particular focus on point-of-care analysis. Biosensors are promising systems to achieve this aim. We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. We show that the displacement of fluorescent peptides upon the competitive binding of S. aureus to immobilized aptamers can be detected and quantified through fluorescence loss. This approach could be also applied to the detection of other bacterial species once aptamers interacting with specific antigens will be identified, allowing the development of a platform for easy detection of a pathogen without requiring access to a healthcare environment.

Specimen Collection, Processing, Culture, and Biochemical Identification of Acinetobacter spp

Specimen collection and processing is an important aspect of clinical microbiology laboratory. The reports are dependent on the quality of the specimen and the time between the collection and processing. Appropriate methodology needs to be followed for the collection, amount, type, labeling, transportation, and processing of the specimens especially for organism like Acinetobacter species. Various biochemical tests are used for identification of various organisms. Such identification depends on the ability of organisms to produce certain enzymes or to utilize certain compound to be identified by biochemical tests.

From days to hours: Can MALDI-TOF MS system replace both conventional and molecular typing methods with new cut off level for Vancomycin Resistant Enterococcus faecium

Vancomycin-Resistant E. faecium (VRE) strains from clinical specimens were identified by conventional methods before. Following the phenotype-based identification, all strains were also identified using both BD Phoenix and VITEK MS bioMérieux System. Strains were typed with the Bruker MALDI-TOF MS system, pulsed field gel electrophoresis (PFGE) and 16S rRNA gene sequencing analysis and then the sensitivity compared for each. A cut off value of 850 assigned with Bruker MALDI-TOF MS system was found to give equal sensitivity to that of PFGE. Results obtained were compared with those of molecular typing. The main advantage of MALDI-TOF MS technology over the others was the much shorter analysis time which lasted only a few hours rather than days or a whole week. Also, the Bruker MALDI-TOF MS system was used for typing and compared with the gold standard method and this study is first to report the determined cut off level for typing of VRE strains.

The emergence of multi-resistant Enterococcus faecalis clonal complex, CC4, causing nosocomial infections

PURPOSE

Enterococcus faecalis is commonly found as a commensal gut bacteria, but some linages have caused increasing extra-gastrointestinal infections. In particular, strains with high-level virulence or antimicrobial resistance are prevalent in healthcare settings as nosocomial pathogens. This study was performed to elucidate the epidemiological characteristics and antimicrobial susceptibility profiles of E. faecalis causing nosocomial infections in a Chinese general hospital over a 4-year period.

METHODOLOGY

We collected 77 isolates causing extra-gastrointestinal infections from patients at 14 different wards in a tertiary hospital from 2011 to 2014. The population relationship was assessed by multilocus sequence typing and multilocus variable-number tandem repeat analysis. The Kirby-Bauer disk diffusion method was used to evaluate susceptibility against 11 antimicrobial agents.

RESULTS

The isolates showed high-level resistance to tetracycline (86.5 %), erythromycin (78.4 %), rifampin (62.2 %), etc. The major clonal complexes (CCs) included CC4, CC16 and CC21. As the most dominant subtype, CC16 was identified in almost all of the wards and all types of samples, but the isolation rate decreased continually. In contrast, the isolation rates of CC4 and CC21 increased and the proportion of these two CCs in 2014 was more than three times that in 2011. In addition, CC4 showed higher resistance than CC16.

CONCLUSIONS

This study demonstrated the prevalent subtypes and resistance profiles of E. faecalis causing nosocomial infection, and indicated that CC4 may be a newly emerging high-risk, multi-resistant cluster. More surveillance is urgently needed, which will increase our understanding of the prevention and treatment of such infections.

Improved Discrimination of Bacillus anthracis from Closely Related Species in the Bacillus cereus Sensu Lato Group Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Discrimination of highly pathogenic bacteria, such as Bacillus anthracis, from closely related species based on molecular biological methods is challenging. We applied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to a collection of B. anthracis strains and close relatives in order to significantly improve the statistical confidence of identification results for this group of bacteria. Protein mass spectra of 189 verified and diverse Bacillus strains of the Bacillus cereus sensu lato group were generated using MALDI-TOF MS and subsequently analyzed with supervised and unsupervised statistical methods, such as shrinkage discriminant analysis (SDA) and principal-component analysis (PCA). We aimed at identifying specific biomarkers in the protein spectra of B. anthracis not present in closely related Bacillus species. We could identify 7, 10, 18, and 14 B. anthracis-specific biomarker candidates that were absent in B. cereus, B. mycoides, B. thuringiensis, and B. weihenstephanensis strains, respectively. Main spectra (MSP) of a defined collection of Bacillus strains were compiled using the Bruker Biotyper software and added to an in-house reference library. Reevaluation of this library with 15 hitherto untested strains of B. anthracis and B. cereus yielded improved score values. The B. anthracis strains were identified with score values between 2.33 and 2.55 using the in-house database, while the same strains were identified with scores between 1.94 and 2.37 using the commercial database, and no false-positive identifications occurred using the in-house database.

Nanomotion Detection Method for Testing Antibiotic Resistance and Susceptibility of Slow-Growing Bacteria

Infectious diseases are caused by pathogenic microorganisms and are often severe. Time to fully characterize an infectious agent after sampling and to find the right antibiotic and dose are important factors in the overall success of a patient's treatment. Previous results suggest that a nanomotion detection method could be a convenient tool for reducing antibiotic sensitivity characterization time to several hours. Here, the application of the method for slow-growing bacteria is demonstrated, taking Bordetella pertussis strains as a model. A low-cost nanomotion device is able to characterize B. pertussis sensitivity against specific antibiotics within several hours, instead of days, as it is still the case with conventional growth-based techniques. It can discriminate between resistant and susceptible B. pertussis strains, based on the changes of the sensor's signal before and after the antibiotic addition. Furthermore, minimum inhibitory and bactericidal concentrations of clinically applied antibiotics are compared using both techniques and the suggested similarity is discussed.

The pyogenic potential of the different Streptococcus anginosus group bacterial species: retrospective cohort study

Streptococcus anginosus Group (SAG) bacteria are common causes of pyogenic infections (PIs). We examined the association between SAG species and the presence of a PI through a retrospective, observational, cohort study, between the years 2009 and 2015. All adults with clinically significant SAG infections in one hospital in Israel were assessed for association between SAG species and the presence of a PI defined as an abscess, empyema, or deep/organ space surgical site infection. Risk factors for PI were assessed using multivariate backward stepwise logistic regression analysis. We identified 263 patients with significant SAG infections, 182 (69%) of which were caused by S. anginosus, 45 (17·1%) by S treptococcus constellatus and 36 (13·7%) by S treptococcus intermedius. The mean age of the patients was 56·8 ± 19·1 years. PIs were identified among 160 (60%) of the patients and were mostly non-bacteraemic (147/160, 91·8%), while most non-PI patients had bacteraemia (70/103, 68%). S. anginosus and S. constellatus were associated with a significantly lower incidence of PI than S. intermedius, OR 0·18 (95% CI 0·06-0·53) and 0·14 (0·04-0·48), respectively. Patients with PI were younger and, in general, had less co-morbidities. S. intermedius was associated with pyogenic non-bacteraemic infections, while S. anginosus and S. constellatus were associated with bacteraemia with no abscess or empyema formation. These data may indicate differences in virulence mechanisms of these SAG bacteria.

Rapid phenotypic stress-based microfluidic antibiotic susceptibility testing of Gram-negative clinical isolates

Bacteremia is a life-threatening condition for which antibiotics must be prescribed within hours of clinical diagnosis. Since the current gold standard for bacteremia diagnosis is based on conventional methods developed in the mid-1800s-growth on agar or in broth-identification and susceptibility profiling for both Gram-positive and Gram-negative bacterial species requires at least 48-72 h. Recent advancements in accelerated phenotypic antibiotic susceptibility testing have centered on the microscopic growth analysis of small bacterial populations. These approaches are still inherently limited by the bacterial growth rate. Our approach is fundamentally different. By applying environmental stress to bacteria in a microfluidic platform, we can correctly assign antibiotic susceptibility profiles of clinically relevant Gram-negative bacteria within two hours of antibiotic introduction rather than 8-24 h. The substantial expansion to include a number of clinical isolates of important Gram-negative species-Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa-reported here underscores the broad utility of our approach, complementing the method's proven utility for Gram-positive bacteria. We also demonstrate that the platform is compatible with antibiotics that have varying mechanisms of action-meropenem, gentamicin, and ceftazidime-highlighting the versatility of this platform.

Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm

Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcusmitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae, whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper.

Microfluidic advances in phenotypic antibiotic susceptibility testing

A strong natural selection for microbial antibiotic resistance has resulted from the extensive use and misuse of antibiotics. Though multiple factors are responsible for this crisis, the most significant factor - widespread prescription of broad-spectrum antibiotics - is largely driven by the fact that the standard process for determining antibiotic susceptibility includes a 1-2-day culture period, resulting in 48-72 h from patient sample to final determination. Clearly, disruptive approaches, rather than small incremental gains, are needed to address this issue. The field of microfluidics promises several advantages over existing macro-scale methods, including: faster assays, increased multiplexing, smaller volumes, increased portability for potential point-of-care use, higher sensitivity, and rapid detection methods. This Perspective will cover the advances made in the field of microfluidic, phenotypic antibiotic susceptibility testing (AST) over the past two years. Sections are organized based on the functionality of the chip - from simple microscopy platforms, to gradient generators, to antibody-based capture devices. Microfluidic AST methods that monitor growth as well as those that are not based on growth are presented. Finally, we will give our perspective on the major hurdles still facing the field, including the need for rapid sample preparation and affordable detection technologies.

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in immunocompromised patients. In most cases only few data, mostly published as case reports, are available which investigate the role of such pathogens as an infectious agent. Therefore, in order to clarify the pathogenic character of such microorganisms, it is necessary to conduct epidemiologic studies which include large numbers of these bacteria. The methods used in such a surveillance study have to meet the following criteria: the identification of the strains has to be accurate according to the valid nomenclature, they should be easy to handle (robustness), economical in routine diagnostics and they have to generate comparable results among different laboratories. Generally, there are three strategies for identifying bacterial strains in a routine setting: 1) phenotypic identification characterizing the biochemical and metabolic properties of the bacteria, 2) molecular techniques such as 16S rRNA gene sequencing and 3) mass spectrometry as a novel proteome based approach. Since mass spectrometry and molecular approaches are the most promising tools for identifying a large variety of bacterial species, these two methods are described. Advances, limitations and potential problems when using these techniques are discussed.

Nanotools and molecular techniques to rapidly identify and fight bacterial infections

Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

Rapid antimicrobial susceptibility testing of clinical isolates by digital time-lapse microscopy

Rapid antimicrobial susceptibility testing (AST) is essential for early and appropriate therapy. Methods with short detection time enabling same-day treatment optimisation are highly favourable. In this study, we evaluated the potential of a digital time-lapse microscope system, the oCelloScope system, to perform rapid AST. The oCelloScope system demonstrated a very high accuracy (96 % overall agreement) when determining the resistance profiles of four reference strains, nine clinical isolates, including multi-drug-resistant isolates, and three positive blood cultures. AST of clinical isolates (168 antimicrobial agent–organism combinations) demonstrated 3.6 % minor, no major and 1.2 % very major errors of the oCelloScope system compared to conventional susceptibility testing, as well as a rapid and correct phenotypic detection of strains with methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL) profiles. The net average time-to-result was 108 min, with 95 % of the results being available within 180 min. In conclusion, this study strongly indicates that the oCelloScope system holds considerable potential as an accurate and sensitive AST method with short time-to-result, enabling same-day targeted antimicrobial therapy, facilitating antibiotic stewardship and better patient management. A full-scale validation of the oCelloScope system including more isolates is necessary to assess the impact of using it for AST.

Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy

Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 isolates), and Vitek 2 (2,853 isolates) systems. The random-effects pooled identification ratios at the species level were 0.89 (95% confidence interval [CI], 0.80 to 0.95) for the API ID32C system, 0.89 (95% CI, 0.83 to 0.93) for the AuxaColor system, and 0.93 (95% CI, 0.89 to 0.96) for the Vitek 2 system (P for heterogeneity, 0.255). Overall, the accuracy of studies using phenotypic analysis-based comparison methods was comparable to that of studies using molecular analysis-based comparison methods. Subanalysis of studies conducted on Candida yeasts showed that the Vitek 2 system was significantly more accurate (pooled ratio, 0.94 [95% CI, 0.85 to 0.99]) than the API ID32C system (pooled ratio, 0.84 [95% CI, 0.61 to 0.99]) and the AuxaColor system (pooled ratio, 0.76 [95% CI, 0.67 to 0.84]) with respect to uncommon species (P for heterogeneity, <0.05). Subanalysis of studies conducted on non-Candida yeasts (i.e., Cryptococcus, Rhodotorula, Saccharomyces, and Trichosporon) revealed pooled identification accuracies of ≥98% for the Vitek 2, API ID32C (excluding Cryptococcus), and AuxaColor (only Rhodotorula) systems, with significant low or null levels of heterogeneity (P > 0.05). Nonetheless, clinical microbiologists should reconsider the usefulness of these systems, particularly in light of new diagnostic tools such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, which allow for considerably shortened turnaround times and/or avoid the requirement for additional tests for species identity confirmation.

Occurrence of Multidrug Resistant Extended Spectrum Beta-Lactamase-Producing Bacteria on Iceberg Lettuce Retailed for Human Consumption

Antibiotic resistance in bacteria is a global problem exacerbated by the dissemination of resistant bacteria via uncooked food, such as green leafy vegetables. New strains of bacteria are emerging on a daily basis with novel expanded antibiotic resistance profiles. In this pilot study, we examined the occurrence of antibiotic resistant bacteria against five classes of antibiotics on iceberg lettuce retailed in local convenience stores in Rochester, Michigan. In this study, 138 morphologically distinct bacterial colonies from 9 iceberg lettuce samples were randomly picked and tested for antibiotic resistance. Among these isolates, the vast majority (86%) demonstrated resistance to cefotaxime, and among the resistant bacteria, the majority showed multiple drug resistance, particularly against cefotaxime, chloramphenicol, and tetracycline. Three bacterial isolates (2.17%) out of 138 were extended spectrum beta-lactamase (ESBL) producers. Two ESBL producers (T1 and T5) were identified as Klebsiella pneumoniae, an opportunistic pathogen with transferable sulfhydryl variable- (SHV-) and TEM-type ESBLs, respectively. The DNA sequence analysis of the bla SHV detected in K. pneumoniae isolate T1 revealed 99% relatedness to bla SHV genes found in clinical isolates. This implies that iceberg lettuce is a potential reservoir of newly emerging and evolving antibiotic resistant bacteria and its consumption poses serious threat to human health.

Performance of the Vitek 2 system software version 5.03 in the bacterial identification and antimicrobial susceptibility test: evaluation study of clinical and reference strains of Gram-positive cocci

INTRODUCTION

The genera Enterococcus, Staphylococcus and Streptococcus are recognized as important Gram-positive human pathogens. The aim of this study was to evaluate the performance of Vitek 2 in identifying Gram-positive cocci and their antimicrobial susceptibilities.

METHODS

One hundred four isolates were analyzed to determine the accuracy of the automated system for identifying the bacteria and their susceptibility to oxacillin and vancomycin.

RESULTS

The system correctly identified 77.9% and 97.1% of the isolates at the species and genus levels, respectively. Additionally, 81.8% of the Vitek 2 results agreed with the known antimicrobial susceptibility profiles.

CONCLUSION

Vitek 2 correctly identified the commonly isolated strains; however, the limitations of the method may lead to ambiguous findings.

Accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinical pathogenic fungi: a meta-analysis

Fungal infections in the clinic have become increasingly serious. In many cases, the identification of clinically relevant fungi remains time-consuming and may also be unreliable. Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) is a newly developed diagnostic tool that is increasingly being employed to rapidly and accurately identify clinical pathogenic microorganisms. The present meta-analysis aimed to systematically evaluate the accuracy of MALDI-TOF MS for the identification of clinical pathogenic fungi. After a rigorous selection process, 33 articles, involving 38 trials and a total of 9,977 fungal isolates, were included in the meta-analysis. The random-effects pooled identification accuracy of MALDI-TOF MS increased from 0.955 (95% confidence interval [CI], 0.939 to 0.969) at the species level to 0.977 (95% CI, 0.955 to 0.993) at the genus level (P < 0.001; χ(2) = 15.452). Subgroup analyses were performed at the species level for several categories, including strain, source of strain, system, system database, and modified outcomes, to calculate the accuracy and to investigate heterogeneity. These analyses revealed significant differences between the overall meta-analysis and some of the subanalyses. In parallel, significant differences in heterogeneity among different systems and among different methods for calculating the identification ratios were found by multivariate metaregression, but none of the factors, except for the moderator of outcome, was significantly associated with heterogeneity by univariate metaregression. In summary, the MALDI-TOF MS method is highly accurate for the identification of clinically pathogenic fungi; future studies should analyze the comprehensive capability of this technology for clinical diagnostic microbiology.

Emerging organisms in a tertiary healthcare set up

BACKGROUND

One-tenth of all infectious diseases are attributable to emerging organisms. As emerging organisms sporadically affect a relatively small percentage of population they are not studied at large. This study was aimed at studying the characteristics of emerging organisms encountered from various clinical samples in an apex tertiary care multispeciality teaching and research hospital.

METHODS

16,918 positive isolates obtained from 66,323 culture samples processed in the clinical microbiology lab of an apex multispeciality hospital during 2011-2012 were included after a pilot study. Both manual and automated systems were used for identification and antimicrobial susceptibility. The frequency of isolation, sources, referring centers, resistance and susceptibility profiles, phenotypic characteristics and number of reports in PubMed were studied.

RESULTS

Out of 16,918 isolates, 13,498 (79.78%) were Gram negative bacteria, 3254 (19.23%) were Gram positive bacteria and 166 (0.98%) were yeasts. A total of 483 (2.85%, 95% CI 2.6%-3.1%) emerging organisms including 116 (0.69%, 95% CI 0.57%-0.81%) emerging species were identified comprising 54 genera.

CONCLUSION

Emerging organisms are likely to evade routine identification or be disregarded as non-contributory. Astute efforts directed at identification of emerging isolates, decisions by clinical microbiologists and treating physicians and containment of infection are required.

Multi-center evaluation of the VITEK® MS system for mass spectrometric identification of non-Enterobacteriaceae Gram-negative bacilli

Studies have demonstrated that matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, accurate method for the identification of clinically relevant bacteria. The purpose of this study was to evaluate the performance of the VITEK MS v2.0 system (bioMérieux) for the identification of the non-Enterobacteriaceae Gram-negative bacilli (NEGNB). This multi-center study tested 558 unique NEGNB clinical isolates, representing 18 genera and 33 species. Results obtained with the VITEK MS v2.0 were compared with reference 16S rRNA gene sequencing and when indicated recA sequencing and phenotypic analysis. VITEK MS v2.0 provided an identification for 92.5 % of the NEGNB isolates (516 out of 558). VITEK MS v2.0 correctly identified 90.9 % of NEGNB (507 out of 558), 77.8 % to species level and 13.1 % to genus level with multiple species. There were four isolates (0.7 %) incorrectly identified to genus level and five isolates (0.9 %), with one incorrect identification to species level. The remaining 42 isolates (7.5 %) were either reported as no identification (5.0 %) or called "mixed genera" (2.5 %) since two or more different genera were identified as possible identifications for the test organism. These findings demonstrate that the VITEK MS v2.0 system provides accurate results for the identification of a challenging and diverse group of Gram-negative bacteria.

Comparison of the epidemiological behavior of mastitis pathogens by applying time-series analysis in results of milk samples submitted for microbiological examination

The objective of this study is to examine and compare the trends of mastitis pathogens in quarter milk samples (n = 240,232) submitted for microbiological examination at the Milk Analysis Laboratory (L.I.G.A.L.) at Galicia, Spain from June 2005 to September 2011. Autoregressive Integrated Moving Average (ARIMA) models and multivariate statistical techniques such as Cluster Analysis were used in order to detect seasonal trends and similarities between the series trends and to classify mastitis pathogens into relatively homogeneous groups. The decrease of bulk milk somatic cell counts achieved by the mastitis control program, developed in recent years in this region, is the result of the decrease in IMI caused by a limited number of mastitis pathogens. The obtained results reflect a greater complexity in the behavior of mastitis pathogens, unlike the traditional classification into contagious or environmental. Staphylococcus aureus showed a trend similar to Streptococcus dysgalactiae, a mastitis pathogen can behave in both a contagious and an environmental manner. Among the traditionally considered environmental mastitis pathogens, Strep. uberis showed a different behavior to Escherichia coli and Klebsiella pneumoniae. Coagulase-negative staphylococci (CNS) species and Streptococcus other than Strep. agalactiae showed differences in the trend model. Time-series analysis and multivariate statistical techniques, such as Cluster Analysis, could be powerful tools to assess the isolation trend of mastitis pathogens because of their ability to cope with stochastic dependence of consecutive data. Furthermore, they could be used to identify the epidemiological behavior of mastitis pathogens using the results of milk samples submitted for routine microbiological examination, by classifying them into relatively homogeneous groups.

Development of rapid phenotypic system for the identification of Gram-negative oxidase-positive bacilli in resource-limited settings

Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology. The diagnosis and surveillance of diseases is dependent, to a great extent, on laboratory services, which cannot function without effective reliable reagents and diagnostics. Despite the advancement in microbiology diagnosis globally, resourcelimited countries still struggle to provide an acceptable diagnosis quality which helps in clinical disease management and improve their mortality and morbidity data. During this study an indigenous product, Quick Test Strip (QTS) NE, was developed for the rapid identification of biochemically slower group of Gram-negative oxidase-positive bacilli that covers 19 different bacterial genera. Some of the members belonging to these groups are well-established human pathogens, e.g. various species of Vibrio, Pseudomonas, Burkholderia, Aeromonas, Achromobacter and Stenotrophomonas. This study also evaluates the performance of QTS-NE by comparing with genotypic characterization methods. A total of 232 clinical and reference bacterial isolates were tested by three different methods. QTSNE provides 100 percent concordant results with other rapid identification and molecular characterization methods and confirms the potential to be used in clinical diagnosis.

Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting.

Real-time optical antimicrobial susceptibility testing

Rapid antibiotic susceptibility testing is in high demand in health care fields as antimicrobial-resistant bacterial strains emerge and spread. Here, we describe an optical screening system (oCelloScope) which, based on time-lapse imaging of 96 bacteria-antibiotic combinations at a time, introduces real-time detection of bacterial growth and antimicrobial susceptibility with imaging material to support the automatically generated graphs. Automated antibiotic susceptibility tests of a monoculture showed statistically significant antibiotic effects within 6 min and within 30 min in complex samples from pigs suffering from catheter-associated urinary tract infections. The oCelloScope system provides a fast high-throughput screening method for detecting bacterial susceptibility that might entail an earlier diagnosis and introduction of appropriate targeted therapy and thus combat the threat from multidrug-resistant pathogenic bacteria. The oCelloScope system can be employed for a broad range of applications within bacteriology and might present new vistas as a point-of-care instrument in clinical and veterinary settings.

Comparison of the accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry with that of other commercial identification systems for identifying Staphylococcus saprophyticus in urine

Among 30 urinary isolates of Staphylococcus saprophyticus identified by sequencing methods, the rate of accurate identification was 100% for Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), 86.7% for the Phoenix PID and Vitek 2 GP systems, 93.3% for the MicroScan GP33 system, and 46.7% for the BBL CHROMagar Orientation system.

Resistance trends in gram-negative bacteria: surveillance results from two Mexican hospitals, 2005-2010

BACKGROUND

Hospital-acquired infections caused by multiresistant gram-negative bacteria are difficult to treat and cause high rates of morbidity and mortality. The analysis of antimicrobial resistance trends of gram-negative pathogens isolated from hospital-acquired infections is important for the development of antimicrobial stewardship programs. The information obtained from antimicrobial resistant programs from two hospitals from Mexico will be helpful in the selection of empiric therapy for hospital-acquired gram-negative infections.

FINDINGS

Two thousand one hundred thirty two gram-negative bacteria collected between January 2005 and December 2010 from hospital-acquired infections occurring in two teaching hospitals in Mexico were evaluated. Escherichia coli was the most frequently isolated gram-negative bacteria, with >50% of strains resistant to ciprofloxacin and levofloxacin. Klebsiella spp. showed resistance rates similar to Escherichia coli for ceftazidime (33.1% vs 33.2%), but exhibited lower rates for levofloxacin (18.2% vs 56%). Of the samples collected for the third most common gram-negative bacteria, Pseudomonas aeruginosa, >12.8% were resistant to the carbapenems, imipenem and meropenem. The highest overall resistance was found in Acinetobacter spp. Enterobacter spp. showed high susceptibility to carbapenems.

CONCLUSIONS

E. coli was the most common nosocomial gram-negative bacilli isolated in this study and was found to have the second-highest resistance to fluoroquinolones (>57.9%, after Acinetobacter spp. 81.2%). This finding represents a disturbing development in a common nosocomial and community pathogen.