Comparison of three chromogenic agar plates for isolation and identification of urinary tract pathogens

Novel Techniques to Unravel Causative Bacterial Ecological Shifts in Chronic Urinary Tract Infection

Chronic urinary tract infection (UTI) presents with protracted lower urinary tract symptoms and elevated urinary leukocyte counts, but its bacterial etiological agents remain obscure. In this cross-sectional investigation, we aimed to unravel the role of the bladder microbiota in chronic UTI pathogenesis by studying the host immune response. Urine samples were collected from healthy controls (HT), chronic UTI patients who had not initiated treatment (PT) and those undergoing treatment (OT), then sorted into white blood cell (WBC) and epithelial cell (EPC) fractions. Bacteria associated with both fractions were identified by chromogenic agar culture coupled with mass spectrometry and 16S rRNA sequencing. Distinct WBC-exclusive bacteria were observed in the healthy population, but this pattern was less obvious in patients, plausibly due to epithelial shedding and breaching of the urothelial barrier. We also described a bacterial fingerprint guided by Escherichia that was able to stratify patients based on symptom severity. Clustering analyses of mean rank changes revealed highly statistically significant upward and downward ecological shifts in communities of bacteria between the healthy and diseased populations. Interestingly, many of the most abundant genera identified in sequencing remained stable when compared between the study cohorts. We concluded that reshuffling of the urinary microbiome, rather than the activity of a single known urinary pathogen, could drive chronic UTI.

Phenotypic and molecular methods of carbapenemase detection: Can we break the chain and preserve the carbapenems?

Background

The World Health Organization (WHO) has declared antimicrobial resistance (AMR) as one of the top ten public health threats faced by humanity. Carbapenems are currently the last option β-lactam antibiotics for treatment of both hospital and community acquired infections. The rapid rise and spread of carbapenem resistant organisms (CRO) is a global concern highlighting the need for early detection and isolation of patients.

Methods

A total of 226 non- repeat, carbapenem resistant Gram-negative isolates were subjected to carbapenemase detection. Three phenotypic methods like Modified Hodge Test (MHT), RAPIDEC® CARBA NP kit (bioMérieux, France) and Chromogenic agar were used and a cartridge based molecular method Xpert® Carba-R (Cepheid) was used on all the study samples for detection of carbapenemases.

Results

The results of MHT, RAPIDEC® CARBA NP and CHROMagar were same for both Enterobacteriaceae and Non Fermenters (except for CHROMagar, which is applicable only for Enterobacteriaceae). Xpert® Carba R could not detect genes in all the phenotypically positive organisms for carbapenemase production. However, there was no statistically significant difference between the three phenotypic tests and Xpert® Carba R used for the detection of carbapenem resistance.

Conclusion

Preserving the last resort antimicrobials is the need of the hour, as there are few therapeutic options for treating infections caused by carbapenem-resistant bacteria. Early detection, followed by strict implementation of infection prevention and control strategies to stall the dissemination of such organisms is the best way and needs to be implemented on a war footing.

The Role of Gram-Negative Bacteria in Urinary Tract Infections: Current Concepts and Therapeutic Options

Urinary tract infections (UTIs) are some of the most common infections in human medicine worldwide, recognized as an important public health concern to healthcare systems around the globe. In addition, urine specimens are one of the most frequently submitted samples for culture to the clinical microbiology laboratory, exceeding the number of most of the other sample types. The epidemiology, species-distribution and susceptibility-patterns of uropathogens vary greatly in a geographical and time-dependent manner and it also strongly correlated with the reported patient population studied. Nevertheless, many studies highlight the fact that the etiological agents in UTIs have changed considerably, both in nosocomial and community settings, with a shift towards "less common" microorganisms having more pronounced roles. There is increasing demand for further research to advance diagnostics and treatment options, and to improve care of the patients. The aim of this review paper was to summarize current developments in the global burden of UTI, the diagnostic aspects of these infectious pathologies, the possible etiological agents and their virulence determinants (with a special focus on the members of the Enterobacterales order), current guidelines and quality indicators in the therapy of UTIs and the emergence of multidrug resistance in urinary pathogens.

A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics

In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including Pseudomonas aeruginosa, group B streptococci, Clostridium difficile, Campylobacter spp., and Yersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant Acinetobacter spp., and Enterobacteriaceae with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics.

Genitourinary Tract Infections

Similarly to the general population, genitourinary tract infections are common conditions in theimmunocompromised host. They can be furthermore divided into infections of the urinary tract and genital tract infections. Transplant recipients are more likely to have infections of the urinary tract infections while persons with human immunodeficiency virus (HIV) are at higher risk for the second group of infections, especially sexually transmitted infections (STIs). Manifestations of these diseases can be associated with more complications and can be more severe. We provide an overview of manifestations, diagnosis, and management of these disorders.

Molecular identification of multi drug resistant bacteria from urinary tract infected urine samples

Urinary tract infections (UTIs) are of great concern in both developing and developed countries all over the world. Even though the infections are more common in women and children, they are at a considerable rate in men and of all ages. The uropathogens causing the infections are spread through various routes. The treatment generally recommended by the physicians is antibiotic usage. But, most of the uropathogens have evolved antibiotic resistance mechanisms. This makes the present situation hectic in control and prevention of UTIs. The present study aims to illustrate the multidrug resistance patterns among isolated bacterial strains from infected urine samples in Odisha state, India. Four bacterial strains were isolated and identified as Proteus sp. SK3, Pseudomonas sp. ADMK77, Proteus sp. BLKB2 and Enterobacter hormaechei strain CW-3 by 16S rRNA gene sequencing. Phylogenetc analysis indicated the strains belong to three various genera namely, Proteus, Pseudomonas and Enterobacter. The evolutionary timeline of the bacteria was studied by constructing phylogenetic trees by Neighborhood Joining method. The presence of ESBL gene and biofilm forming capability were studied for the four strains. Antibiotic susceptibility patterns of the isolates were studied toward the commonly recommended antibiotics. Both the Proteus strains were found commonly susceptible to aminoglycoside and sulphonamide groups. Pseudomonas strain was found to be susceptible to cephems, aminoglycosides and fluoroquinolones. Enterobacter sp was found to be resistant to almost all antibiotic groups and susceptible to only sulphonamides group. The antibiotic susceptibility patterns of the bacteria help in choosing the empirical antibiotic treatment for UTI.

Optical scatter patterns facilitate rapid differentiation of Enterobacteriaceae on CHROMagar™ Orientation medium

Enterobacteriaceae family comprised pathogens and commensals and has a significant impact on food safety and public health. Enterobacteriaceae is often enumerated and presumptively identified on chromogenic media, such as CHROMagar(TM) Orientation medium based on colony profile; however, classification is highly arbitrary, and some could not be differentiated due to similar chromogen production. Here, we investigated the ability of the laser optical sensor, BARDOT (bacterial rapid detection using optical scattering technology) for rapid screening and differentiation of colonies of the major bacterial genera from Enterobacteriaceae on CHROMagar(TM) Orientation. A total of 36 strains representing 12 genera and 15 species were used to generate colony scatter image library that comprised 1683 scatter images. This library was used to differentiate mixed cultures of Enterobacteriaceae family - Klebsiella pneumoniae, Enterobacter spp., Citrobacter freundii and Serratia marcescens (KECS group); Proteus mirabilis, Morganella morganii and Providencia rettgeri (PMP group); and non-Enterobacteriaceae family: Pseudomonas aeruginosa, Acinetobacter spp. and Staphylococcus aureus (PAS group) - and data show high accuracy (83-100%) for intra-group classification of colonies in 10-22 h or even before visible production of chromogens. BARDOT successfully differentiated the major genera, including the ones that do not produce visually distinguishable chromogens on CHROMagar(TM) Orientation, providing a label-free, real-time on-plate colony screening tool for Enterobacteriaceae.

Evaluation of New bioMérieux Chromogenic CPS Media for Detection of Urinary Tract Pathogens

Four chromogenic media were compared for their ability to detect urinary tract pathogens in 299 urine specimens, of which 175 were found positive, allowing the growth of 279 microorganisms. After 18 to 24 h of incubation, the CPS ID4, CPSE, CPSO (bioMérieux), and UriSelect4 (Bio-Rad) media showed sensitivities of 97.1%, 99.3%, 99.6%, and 99.6%, respectively.

Evaluation of two chromogenic media for the isolation and identification of urinary tract pathogens

Chromogenic media (CM) are available for urine specimens (US) to enable rapid identification of common urinary tract pathogens (UTP). Two CM, chromID™ CPS (CPS4) agar (bioMérieux, St. Laurent, QC) and UriSelect™ 4 (URS4) agar (Bio-Rad, Montreal, QC), were compared to the standard media (SM) for the isolation and identification of UTP. Over a 10-day period, US were inoculated to CPS4, URS4, and SM (BAP and MAC). CM interpretation was done according to the product inserts by one person blinded to the results of SM. SM were read by experienced technologists according to protocol and isolates were identified using BD Phoenix™. The results were grouped into significant (SG), mixed (MG), and no significant growth (NSG). A total of 903 US were studied. SM identified 239 SG, 112 MG, and 552 NSG cultures. The most common pathogens were Escherichia coli (38 %) and Enterococcus spp. (11 %). Comparing CM to SM, the exact agreement was 89.3 and 89.5 % for URS4 and CPS4, respectively. When grouped by clinical significance, agreement with SM was 93.0 and 93.1 % for URS4 and CPS4, respectively. CM were equivalent with respect to processing time. Advantages include decreased need for automated identification of certain species, particularly E. coli. In terms of workflow, CM enables same-day identification for almost 50 % of significant UTP. Overall, both CM compared well to SM and allowed for rapid preliminary identification of many UTP.

Rapid detection of urinary tract infections caused by Proteus spp. using PNA-FISH

We developed a fluorescence in situ hybridization (FISH) method for the rapid detection of Proteus spp. in urine, using a novel peptide nucleic acid (PNA) probe. Testing on 137 urine samples from patients with urinary tract infections has shown specificity and sensitivity values of 98 % (95 % CI, 93.2-99.7) and 100 % (95 % CI, 80,8-100), respectively, when compared with CHROMagar Orientation medium. Results indicate that PNA-FISH is a reliable alternative to traditional culture methods and can reduce the diagnosis time to approximately 2 h.

Evaluation of a new chromogenic medium for isolation and identification of common urinary tract pathogens

In the study presented here, a new chromogenic medium (CPS ID 3; bioMérieux, Marcy l'Etoile, France) was compared to routine media for the isolation, identification and antimicrobial susceptibility testing of bacteria recovered from urine specimens, and a cost analysis was performed. Escherichia coli, Proteeae tribe, Pseudomonas aeruginosa, Enterococcus spp. and Streptococcus agalactiae grew on the chromogenic medium as typical differentiated colonies and were accurately identified even in mixed cultures. Although the similarity of colors produced by isolates belonging to the Klebsiella, Enterobacter, Serratia and Citrobacter (KESC) group prevents differentiation among them, members of KESC were easily identified as coliforms. No substantial difference was observed when comparing the results of antimicrobial susceptibility testing performed on colonies selected from reference media versus CPS ID 3. Use of the new medium was associated with a savings of 75% over the conventional methods and the API system. Furthermore, this medium facilitated a remarkable reduction in the laboratory workload and consequently resulted in additional time and cost savings.

Practical bench comparison of BBL CHROMagar Orientation and standard two-plate media for urine cultures

A total of 1023 urine samples sent for routine culture were plated onto sheep blood and MacConkey agars and a BBL CHROMagar Orientation (CO; Becton Dickinson, Cockeysville, Md.) plate, and the results were compared. Of these, 250 urine samples (24%) grew >10000 CFU of one or two putative pathogens/ml and 773 showed no growth (NG), mixed growth of <10000 CFU/ml, or three or more strains (mixed). The CO and conventional medium results agreed completely for 595 cultures with NG or <10000 CFU/ml. An additional 178 urine samples yielded clinically insignificant differences. Both medium sets essentially agreed on quantities and identification for 400 single-pathogen cultures and 9 mixed cultures. With the caveat that CO cannot differentiate Klebsiella, Enterobacter, and Serratia spp., enteric pathogens were identified only by morphology and color on CO. Direct visual differentiation of group B streptococci from lactobacilli is not possible, but lactobacillus cells always exhibited easily recognizable morphology on Gram stain. Of 108 paired organism susceptibility results encompassing 2268 drug-pathogen combinations, there were 3% errors and only 1% very major errors. Use of CO allowed a >50% reduction in inoculation time and a >20% reduction in work-up time. For our laboratory, with 50% "no growth" and ca. 25% significant results (50% Escherichia coli), CO allowed time and workup cost savings for a majority of cultures. A cost analysis (time and supplies for our laboratory) showed that if CO is used alone, the break-even level for CO pricing is US dollars 1.78; if CO and blood agar are both used, the break-even pricing for CO is US dollars 1.53.