Development of a real-time PCR for Escherichia coli based on gadE, an acid response regulatory gene

Revolutionizing chronic endometritis diagnosis: real-time polymerase chain reaction unveils microbial pathogens in Indian women with abnormal bleeding and reproductive challenges

Background

This study aimed to assess the utility of real-time-polymerase chain reaction (PCR) for diagnosing chronic endometritis (CE) by targeting 11 prevalent pathogens and to compare the outcomes with conventional culture-based diagnosis.

Study Design

A retrospective analysis was conducted on 500 patients with clinical conditions such as abnormal bleeding, in vitro fertilization failure, recurrent implantation failure, recurrent miscarriage, and recurrent pregnancy loss. The prevalence of 11 key pathogens associated with CE was evaluated in endometrial biopsy samples.

Results

In our study, PCR identified 318 cases (63.6%) positive for at least one of the 11 investigated pathogens, while culture-based methods detected 115 cases (23%). Predominant pathogens detected by PCR included Enterococcus faecalis (E. faecalis) (19%), Escherichia coli (E. coli) (6.8%), Staphylococcus aureus (S. aureus) (9%), Mycoplasma hominis (5%), Mycoplasma genitalium (6.2%), Streptococcus agalactiae (S. agalactiae) (4.2%), Ureaplasma urealyticum (4%), nontuberculous Mycobacterium (5.2%), Mycobacterium tuberculosis (1.2%), Neisseria gonorrhoeae (0.6%), and Chlamydia trachomatis (2.4%). Standard culture methods identified E. faecalis (10.8%), S. aureus (6.2%), E. coli (3.8%), and S. agalactiae (2.2%).

Conclusion

The DICE panel proves itself as a swift, precise, and cost-effective diagnostic tool for detecting both culturable and nonculturable endometrial pathogens in CE. Demonstrating superiority, the Molecular method outshines microbial culture, ensuring accurate and sensitive detection of CE-associated pathogens, harmonizing seamlessly with histology and hysteroscopy findings.

Pantoprazole promotes sustained intestinal carriage of multidrug-resistant Escherichia coli in amoxicillin-treated mice

AIMS

The main objective of this study was to compare extended-spectrum β-lactamase (ESBL) Escherichia coli fecal titers during 12 days between two groups: mice who received proton pump inhibitors (PPIs) and those that did not.

METHODS AND RESULTS

We tested three different in vivo models: model 1, high inoculum (106 CFU ml-1); model 2, low inoculum (102 CFU ml-1); and model 3, low inoculum and 2-day amoxicillin wash-out. There was no significant difference between the two groups in fecal ESBL E. coli titers in models 1 and 2. The fecal titers of ESBL E. coli were probably too high to show differences in colonization related to PPI treatment. By introducing a 2-day wash-out period after stopping amoxicillin (model 3), the fecal ESBL E. coli titers were higher in the PPI-treated mice during 12 days (3 log versus 11 log day CFU g-1; P < 0.05). This result highlighted that PPIs promote stable ESBL E. coli digestive carriage in mice. Fecal quantitative PCR showed that mice with low ESBL E. coli fecal titers had a much higher concentration of equol-producing bacteria, Muribaculum sp., and Adlercreutzia caecimuris.

CONCLUSIONS

Pantoprazole treatment promotes sustained digestive carriage of ESBL E. coli in amoxicillin-treated mice.

Rapid Reverse Purification DNA Extraction Approaches to Identify Microbial Pathogens in Wastewater

Wastewater monitoring became a promising solution in the early detection of outbreaks. Despite the achievements in the identification of pathogens in wastewater using real-time PCR, there is still a lack of reliable rapid nucleic acid extraction protocols. Therefore, in this study, samples were subjected to alkali, proteinase K and/or bead-beating followed by reverse purification magnetic beads-based separation. Wastewater samples spiked with S. aureus, E. coli and C. parvum were used as examples for Gram-positive and -negative bacteria and protozoa, respectively. All results were compared with a spin column technology as a reference method. Proteinase K with bead beating (vortexing with 0.1 mm glass beads for three minutes) was particularly successful for bacterial DNA extraction (three- to five-fold increase). The most useful extraction protocol for protozoa was pre-treatment with proteinase K (eight-fold increase). The selected methods were sensitive as far as detecting one bacterial cell per reaction for S. aureus, ten bacterial cells for E. coli and two oocysts for C. parvum. The extraction reagents are cold chain independent and no centrifuge or other large laboratory equipment is required to perform DNA extraction. A controlled validation trial is needed to test the effectiveness at field levels.

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

Background

Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative, have been developed to identify them. Some of these methods are explicitly designed to work in single strains, while others make use of multiple strains. In general, existing methods do not identify islands in the context of the phylogeny in which they evolved. Even multiple strain approaches are best suited to identifying genomic islands that are present in one strain but absent in others. They do not automatically recognize islands which are shared between some strains in the clade or determine the branch on which these islands inserted within the phylogenetic tree.

Results

We have developed a software package, xenoGI, that identifies genomic islands and maps their origin within a clade of closely related bacteria, determining which branch they inserted on. It takes as input a set of sequenced genomes and a tree specifying their phylogenetic relationships. Making heavy use of synteny information, the package builds gene families in a species-tree-aware way, and then attempts to combine into islands those families whose members are adjacent and whose most recent common ancestor is shared. The package provides a variety of text-based analysis functions, as well as the ability to export genomic islands into formats suitable for viewing in a genome browser. We demonstrate the capabilities of the package with several examples from enteric bacteria, including an examination of the evolution of the acid fitness island in the genus Escherichia. In addition we use output from simulations and a set of known genomic islands from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree.

Conclusions

xenoGI is an effective tool for studying the history of genomic island insertions in a clade of microbes. It identifies genomic islands, and determines which branch they inserted on within the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive path that has produced living species.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2038-0) contains supplementary material, which is available to authorized users.