Quantitative reverse transcription-PCR assay for the rapid detection of methicillin-resistant Staphylococcus aureus

Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.

Multidrug resistant and multivirulent avian bacterial pathogens: tackling experimental leg disorders using phytobiotics and antibiotics alone or in combination

Locomotor disorders caused by multidrug-resistant (MDR) bacterial pathogens denote one of the most detrimental issues that collectively threaten the poultry industry leading to pronounced economic losses across the world. Hence, searching for effective alternatives, especially those extracted from plant origins became of great priority targeting a partial or complete replacement of chemical antimicrobials to tackle their developing resistance. Therefore, we aimed to determine the prevalence and antimicrobial resistance of Staphylococcus aureus (S. aureus), Salmonella species, Mycoplasma synoviae (M. synoviae), and Escherichia coli (E. coli) recovered from 500 broilers and ducks (250 each) with locomotor disorders in various farms in Dakahlia and Sharkia Governorates, Egypt. Additionally, we assessed, for the first time, the in vitro antimicrobial effectiveness of marjoram, garlic, ginger and cinnamon essential oils (EOs) against MDR and multivirulent bacterial isolates as well as the in vivo efficiency of the most effective antibiotics and EOs either separately or in combination in the treatment of experimentally induced poultry leg disorders. The overall prevalence rates of S. aureus, E. coli, Salmonella species, and M. synoviae were 54, 48, 36, and 2%, respectively. Salmonella species and S. aureus prevailed among ducks and broilers (36 and 76%, respectively). Notably, MDR was observed in 100, 91.7, 81.1, and 78.5% of M. synoviae, E. coli, Salmonella, and S. aureus isolates, respectively. Our in vitro results displayed that marjoram was the most forceful EO against MDR and multivirulent chicken vancomycin-resistant S. aureus (VRSA) and duck S. Typhimurium isolates. The current in vivo results declared that marjoram in combination with florfenicol or amoxicillin/clavulanic acid succeeded in relieving the induced duck and chicken leg disorders caused by S. Typhimurium and VRSA, respectively. This was evidenced by improvement in the clinical and histopathological pictures with a reduction of bacterial loads in the experimental birds. Our encountered successful in vitro and in vivo synergistic effectiveness of marjoram combined with florfenicol or amoxicillin/clavulanic acid recommends their therapeutic application for leg disorders and offers opportunities for reducing the antibiotics usage in the poultry industry.

Organelle 16S rRNA amplicon sequencing enables profiling of active gut microbiota in murine model

High-throughput sequencing of ribosomal RNA (rRNA) amplicons has served as a cornerstone in microbiome studies. Despite crucial implication of organelle 16S rRNA measurements to host gut microbial activities, genomic DNA (gDNA) was overwhelmingly targeted for amplicon sequencings. Although gDNA could be a reliable resource for gene existing validation, little information is revealed in regard to the activity of microorganisms owing to the limited changes gDNA undertaken in inactive, dormant, and dead bacteria. We applied both rRNA- and gDNA-derived sequencings on mouse cecal contents. Respective experimental designs were verified to be suitable for nucleic acid (NA) purification. Via benchmarking, mainstream 16S rRNA hypervariable region targets and reference databases were proven adequate for respective amplicon sequencing study. In phylogenetic studies, significant microbial composition differences were observed between two methods. Desulfovibrio spp. (an important group of anaerobic gut microorganisms that has caused analytical difficulties), Pediococcus spp., and Proteobacteria were drastically lower as represented by gDNA-derived compositions, while microbes like Firmicutes were higher as represented by gDNA-derived microbiome compositions. Also, using PICRUSt2 as an example, we illustrated that rRNA-derived sequencing might be more suitable for microbiome function predictions since pathways like sugar metabolism were lower as represented by rRNA-derived results. The findings of this study demonstrated that rRNA-derived amplicon sequencing could improve identification capability of specific gut microorganisms and might be more suitable for in silico microbiome function predictions. Therefore, rRNA-derived amplicon sequencings, preferably coupled with gDNA-derived ones, could be used as a capable tool to unveil active microbial components in host gut. KEY POINTS: • Conventional pipelines were adequate for the respective amplicon sequencing study • Groups, such as Desulfovibrio spp., were differently represented by two methods • Comparative amplicon sequencings could be useful in host active microbiota studies.

Flavonolignans from silymarin modulate antibiotic resistance and virulence in Staphylococcus aureus

Antibiotic resistance is currently a serious health problem. Since the discovery of new antibiotics no longer seems to be a sufficient tool in the fight against multidrug-resistant infections, adjuvant (combination) therapy is gaining in importance as well as reducing bacterial virulence. Silymarin is a complex of flavonoids and flavonolignans known for its broad spectrum of biological activities, including its ability to modulate drug resistance in cancer. This work aimed to test eleven, optically pure silymarin flavonolignans for their ability to reverse the multidrug resistance phenotype of Staphylococcus aureus and reduce its virulence. Silybin A, 2,3-dehydrosilybin B, and 2,3-dehydrosilybin AB completely reversed antibiotic resistance at concentrations of 20 µM or less. Both 2,3-dehydrosilybin B and AB decreased the antibiotic-induced gene expression of representative efflux pumps belonging to the major facilitator (MFS), multidrug and toxic compound extrusion (MATE), and ATP-binding cassette (ABC) families. 2,3-Dehydrosilybin B also inhibited ethidium bromide accumulation and efflux in a clinical isolate whose NorA and MdeA overproduction was induced by antibiotics. Most of the tested flavonolignans reduced cell-to-cell communication on a tetrahydrofuran-borate (autoinducer-2) basis, with isosilychristin leading the way followed by 2,3-dehydrosilybin A and AB, which halved communication at 10 µM. Anhydrosilychristin was the only compound that reduced communication based on acyl-homoserine lactone (autoinducer 1), with an IC₅₀ of 4.8 µM. Except for isosilychristin and anhydrosilychristin, all of the flavonolignans inhibited S. aureus surface colonization, with 2,3-dehydrosilybin A being the most active (IC₅₀ 10.6 µM). In conclusion, the selected flavonolignans, particularly derivatives of 2,3-dehydrosilybin B, 2,3-dehydrosilybin AB, and silybin A are non-toxic modulators of S. aureus multidrug resistance and can decrease the virulence of the bacterium, which deserves further detailed research.

Analysis of Staphylococcus aureus Molecules in Non-Treated Blood Using Mercury Immobilized Carbon Nanotube Sensor

Staphylococcus aureus bacteria is a ubiquitous Gram-positive microorganism that causes infections related to the sudden infant death syndrome. Recently, basic detection methods depend on complicated PCR amplification, electric separation, spectric adsorption and other detection systems. However, in this study, simplified sensitive voltammetric skills are developed. To identify an effective diagnostic method for Staphylococcus aureus (SA), a voltammetric sensing probe was sought using mercury immobilized on a carbon nanotube sensor (MCN). The voltammetric MCN conditions were optimized through stripping and cyclic voltammetry. Diagnostic electrolyte was used on non-treated blood sera as an electrolyte solution. The optimum cyclic and stripping analytical working range was 0.5–4.0 mL (3 × 102~5 × 102 CFU/0.5 mL) SA. The statistic relative standard deviation of 0.1 mL SA was observed to be 0.0078 (n = 5). Using the optimum parameters, a diagnostic test was performed by the direct assay of SA in non-treated human blood and patient sera. Here, the developed results can be used for the direct assay of non-treated blood sera, organ monitoring, in-vivo diagnosis, and other assays requiring SA detection.

Quantitative flow chamber system for evaluating in vitro biofilms and the kinetics of S. aureus biofilm formation in human plasma media

Background

It has been well established that biofilm formation on orthopaedic implants is a critical event in the pathogenesis of orthopaedic infections, yet the natural history of this process with respect to bacterial adhesion, proliferation, and glycocalyx matrix production remains poorly understood. Moreover, there are no quantitative methods yet available to assess the differences in biofilm formation between different bacterial strains or implant materials. Consequently, this study aimed to investigate the natural history of S. aureus in in vitro biofilm formation in human plasma media using a flow chamber system. Bioluminescent S. aureus strains were used to better understand the bacterial growth and biofilm formation on orthopaedic materials. Also, the effects of human plasma media were assessed by loading the chamber with Tryptic Soy Broth with 10% human plasma (TSB + HP).

Results

Scanning electron microscopy (SEM) was utilized to assess the morphological appearance of the biofilms, revealing that S. aureus inoculation was required for biofilm formation, and that the phenotypes of biofilm production after 24 h inoculation with three tested strains (SH1000, UAMS-1, and USA300) were markedly different depending on the culture medium. Time course study of the bioluminescence intensity (BLI) and biofilm production on the implants due to the UAMS-1 and USA300 strains revealed different characteristics, whereby UAMS-1 showed increasing BLI and biofilm growth until peaking at 9 h, while USA300 showed a rapid increase in BLI and biofilm formation at 6 h. The kinetics of biofilm formation for both UAMS-1 and USA300 were also supported and confirmed by qRT-PCR analysis of the 16S rRNA gene. Biofilms grown in our flow chamber in the plasma media were also demonstrated to involve an upregulation of the biofilm-forming-related genes icaA, fnbA, and alt. The BLI and SEM results from K-wire experiments revealed that the in vitro growth and biofilm formation by UAMS-1 and USA300 on stainless-steel and titanium surfaces were virtually identical.

Conclusion

We demonstrated a novel in vitro model for S. aureus biofilm formation with quantitative BLI and SEM outcome measures, and then used this model to demonstrate the presence of strain-specific phenotypes and its potential use to evaluate anti-microbial surfaces.

Transcriptional analysis of prsA and vraTS regulatory system in methicillin resistant Staphylococcus aureus against oxacillin stress

PURPOSE

The prsA and vraTSR regulatory systems play a unique role in methicillin resistance by modifying the peptidoglycan cell wall PBP2 and involving cell wall stress response in Staphylococcus aureus. This study was designed to observe the transcriptional response of prsA and vraTSR system under oxacillin stress in S.aureus.

METHODS

In this study, three clinical isolates of Staphylococcus aureus and a laboratory strain were examined. All the isolates were tested for mecA gene by PCR assay and were also tested for prsA, vraT, vraS and vraR gene. The transcriptional responses of the prsA gene along with the vraTSR regulatory system in these isolates was observed under normal conditions and exposed to 2 ​μg/ml and 4 ​μg/ml of oxacillin stress by quantitative real-time PCR assay.

RESULTS

The result of transcriptional analysis confirmed that under oxacillin stress, the expressions of vraS and vraT are increased with the increase in the concentration of oxacillin. However, prsA has shown no significant expression under oxacillin stress.

CONCLUSION

Although prsA did not show any specific expressional pattern, the study highlights the role of vraS and vraT regulatory system in conferring a methicillin-resistant phenotype when exposed to subinhibitory concentrations of oxacillin, which could act as a potential target for the next-generation antimicrobials.

Carvacrol Essential Oil: A Natural Antibiotic against Zoonotic Multidrug-Resistant Staphylococcus Species Isolated from Diseased Livestock and Humans

Staphylococcus species cause diseases in animals and humans. The prevalence and antimicrobial profiles of Staphylococcus spp. in animals and human samples in the Minya Governorate, Egypt, were determined, and resistance- and virulence-associated genes were observed in multidrug-resistant (MDR) isolates. Moreover, the antibacterial effect of carvacrol essential oil (EO) on the MDR isolates was studied. A total of 216 samples were aseptically collected from subclinically mastitic cow's milk (n = 100), sheep abscesses (n = 25) and humans (n = 91). Out of 216 samples, a total of 154 single Staphylococcus species (71.3%) were isolated. The most frequent bacterial isolates were S. aureus (43%), followed by S. schleiferi (25%), S. intermedius (12%), S. xylosus (12%), S. haemolyticus (4.5%), S. epidermidis (2%) and S. aurecularis (1%). Haemolytic activity and biofilm production were detected in 77 and 47% of isolates, respectively. Antimicrobial susceptibility testing showed a high degree of resistance to the most commonly used antimicrobials in human and veterinary practices. The mecA, vanA, vanC1 and ermC resistance genes were detected in 93, 42, 83 and 13% of isolates, respectively. Moreover, hla, icaA and icaD virulence genes were detected in 50, 75 and 78% of isolates, respectively. Carvacrol effectively inhibited the growth of all tested isolates at concentrations of 0.1, 0.05 and 0.04% while a concentration of 0.03% inhibited 75% of isolates. Interestingly, some phenotypic changes were observed upon treatment with a carvacrol oil concentration of 0.03%. All the treated MDR Staphylococcus isolates changed from multidrug resistant to either susceptible or intermediately susceptible to 2-3 antimicrobials more than parental bacterial isolates. Real-time PCR was applied for the detection of the differential expression of mecA and vanC1 genes before and after treatment with carvacrol which revealed a mild reduction in both genes' expression after treatment. Staphylococcus spp. Containing MDR genes are more likely to spread between humans and animals. From these results, carvacrol EO is a promising natural alternative to conventional antimicrobials for pathogens impacting human health and agriculture due to its potential antimicrobial effect on MDR pathogens; even in sub-lethal doses, carvacrol EO can affect their phenotypic properties and genes' expression.

Graphene-based fluorometric determination of agrD gene transcription in methicillin-resistant Staphylococcus aureus using exonuclease III-aided target recycling and DNA walker cascade amplification

A graphene-based bioassay is described for the fluorometric determination of agrD gene transcription (mRNA) in methicillin-resistant Staphylococcus aureus (MRSA). This method includes exonuclease III (Exo III)-assisted target recycling and DNA walker cascade amplification. Hairpin1 (HP1) consists of a capture probe (CP) and DNA walker sequence. In the absence of the target, 5'-amino modified hairpin2 (HP2) labeled with carboxyfluorescein (FAM) at its 3' terminus is covalently linked to graphene via 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS) catalysis, resulting in the quenching of the FAM signal. The stem-loop structure of HP1 opens when the target is added to form partially complementary DNA/RNA hybrids. Exo III then initiates the target recycling process by cleaving the CP and DNA walker cascade reaction by automatic walking. This iterative reaction causes the FAM to dissociate from the graphene, and the fluorescence can be measured at excitation/emission wavelengths of 480/514 nm. Therefore, the target can be assayed by fluorescence. This method has a linear relationship with the concentration of target within the range 1 fM to 100 pM with a detection limit of 1 fM. The developed bioassay was used to monitor biofilm formation and investigate the mechanism of drug action with satisfactory results. Schematic representation of the graphene-based fluorescent bioassay for agrD gene transcription in methicillin-resistant Staphylococcus aureus by using exonuclease III-aided target recycling and DNA walker cascade amplification.

SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus

Background

Molecular assays are important tools for pathogen detection but need to be periodically re-evaluated with the discovery of additional genetic diversity that may cause assays to exclude target taxa or include non-target taxa. A single well-developed assay can find broad application across research, clinical, and industrial settings. Pathogen prevalence within a population is estimated using such assays and accurate results are critical for formulating effective public health policies and guiding future research. A variety of assays for the detection of Staphylococcus aureus are currently available. The utility of commercial assays for research is limited, given proprietary signatures and lack of transparent validation.

Results

In silico testing of existing peer-reviewed assays show that most suffer from a lack of sensitivity and specificity. We found no assays that were specifically designed and validated for quantitative use. Here we present a qPCR assay, SaQuant, for the detection and quantification of S. aureus as might be collected on sampling swabs. Sensitivity and specificity of the assay was 95.6 and 99.9 %, respectively, with a limit of detection of between 3 and 5 genome equivalents and a limit of quantification of 8.27 genome equivalents. The presence of DNA from non-target species likely to be found in a swab sample, did not impact qualitative or quantitative abilities of the assay.

Conclusions

This assay has the potential to serve as a valuable tool for the accurate detection and quantification of S. aureus collected from human body sites in order to better understand the dynamics of prevalence and transmission in community settings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02247-6.

Impact of Preoperative Occult-Bacterial Translocation on Surgical Site Infection in Patients Undergoing Pancreatoduodenectomy

BACKGROUND

Occult-bacterial translocation (O-BT) has been reported as the condition in which microorganisms are detected in blood or lymph nodes by a highly sensitive method. However, the clinical impact of preoperative O-BT on postoperative complication is unclear.

STUDY DESIGN

A prospective observational study with patients undergoing pancreatoduodenectomy for periampullary diseases was conducted. Blood samples were collected immediately after induction of anesthesia. The status of O-BT was investigated using bacterium-specific ribosomal RNA-targeted reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). The impact of O-BT on surgical site infection (SSI) was analyzed.

RESULTS

A total of 155 patients were included. The positive rate in preoperative blood samples detected by RT-qPCR was significantly higher than that obtained by the culture method (32 of 155 vs 4 of 155, p < 0.001). Preoperative blood samples were contaminated with 1.0 to 19.2 bacterial cells/mL in positive patients, and 30 of the 41 detected microorganisms were obligate anaerobes. No differences in preoperative factors were observed between patients with positive and negative RT-qPCR results. The incidence of any SSI was significantly higher in patients with contaminated preoperative blood (≥1.2 bacterial cells/mL) than in other patients (14 of 27 vs 35 of 128, p = 0.013). Multivariable analysis indicated that contaminated preoperative blood was identified as one of the independent risk factors for SSI (odds ratio 2.71, 95% CI 1.04 to 7.24, p = 0.041).

CONCLUSIONS

O-BT, predominantly with obligate anaerobes, was commonly observed in preoperative blood samples. In addition to the previously known risk factors, O-BT may be one of the risk factors for SSI after pancreatoduodenectomy.

Ultra-sensitive and rapid detection of nucleic acids and microorganisms in body fluids using single-molecule tethering

Detection of microbial nucleic acids in body fluids has become the preferred method for rapid diagnosis of many infectious diseases. However, culture-based diagnostics that are time-consuming remain the gold standard approach in certain cases, such as sepsis. New culture-free methods are urgently needed. Here, we describe Single MOLecule Tethering or SMOLT, an amplification-free and purification-free molecular assay that can detect microorganisms in body fluids with high sensitivity without the need of culturing. The signal of SMOLT is generated by the displacement of micron-size beads tethered by DNA probes that are between 1 and 7 microns long. The molecular extension of thousands of DNA probes is determined with sub-micron precision using a robust and rapid optical approach. We demonstrate that SMOLT can detect nucleic acids directly in blood, urine and sputum at sub-femtomolar concentrations, and microorganisms in blood at 1 CFU mL⁻¹ (colony forming unit per milliliter) threefold faster, with higher multiplexing capacity and with a more straight-forward protocol than amplified methodologies. SMOLT’s clinical utility is further demonstrated by developing a multiplex assay for simultaneous detection of sepsis-causing Candida species directly in whole blood.

Culture-based diagnostic methods for microorganism detection are time-consuming but still the gold standard for conditions such as sepsis. Here the authors present an amplification and purification-free method to detect microorganisms in bodily fluids with high sensitivity: Single MOLecule Tethering (SMOLT).

Clinical importance of "occult-bacterial translocation" in patients undergoing highly invasive gastrointestinal surgery: A review

In the clinical setting, mild bacteremia cannot be detected by conventional culture methods, only by a highly sensitive bacterial detection system. One of the major causes of mild bacteremia is bacterial translocation (BT) induced by a dysregulated intestinal microenvironment and increased intestinal epithelial permeability. This condition is called "occult-bacterial translocation (O-BT)"; however, the concept of O-BT is not yet fully recognized. In our previous studies, done using a highly sensitive bacterial detection system such as bacterium-specific ribosomal RNA-targeted reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), O-BT was commonly observed in patients who underwent highly invasive surgery. We collected blood and mesenteric lymph node (MLN) samples from patients undergoing esophagectomy for esophageal cancer, before and after they were subjected to surgical stress. The detection rate of bacteria in these samples increased from approximately 20% before surgical stress to more than 50% after surgical stress. Moreover, positivity for bacteria in the blood or MLN samples was associated with the incidence of postoperative infectious complications (POICs). Using the RT-qPCR system, it is possible to detect the specific bacteria that cause O-BT immediately after surgery. This may allow us to select the exact antibiotic that targets possible pathogenic bacteria of POICs.

Prevalence, the antibiogram and the frequency of virulence genes of the most predominant bacterial pathogens incriminated in calf pneumonia

The purpose of this study was to investigate the prevalence, antibiotic resistance and certain virulence genes of the most predominant bacterial pathogens causing BRD. A total of 225 calves; 55 apparently healthy and 170 diseased; were sampled. Bacteriological examination, antimicrobial susceptibility testing and PCR based detection of some virulence genes were performed. In addition, the serotyping of E. coli was performed using the slide agglutination test. The most predominant bacterial pathogens retrieved from apparently healthy calves were E. coli (16.4%) and S. aureus (10.9%), and in pneumonic calves were E. coli (23.5%), P. vulgaris (12.4%) and S. aureus (11.8%). The most prevalent virulence gene in E. coli was the fimH gene (100%), followed by eaeA gene (24.5%) and hly gene (20.4%). All the examined S. aureus strains harbored spa and coa genes; likewise, all P. multocida strains harbored toxA gene. The majority of the isolated strains displayed remarkable sensitivity to norfloxacin and enrofloxacin; furthermore, the retrieved E. coli strains exhibited multidrug-resistance to gentamicin, erythromycin, streptomycin and trimethoprim-sulphamethoxazole, in addition, the isolated S. aureus and P. aeruginosa strains showed multidrug-resistance to amoxicillin, ampicillin and tetracycline. E. coli serogroups including O18, O143, O1, and O6 were retrieved from pneumonic calves as the first report in Egypt. In conclusion, the synergism between the conventional and genotypic analysis is an effective gadget for the characterization of bacterial pathogens causing BRD. Continuous surveillance of antimicrobial susceptibility is essential to select the drug of choice due to the development of multidrug-resistant strains.

Biosynthesis of Fe3O4@Ag Nanocomposite and Evaluation of Its Performance on Expression of norA and norB Efflux Pump Genes in Ciprofloxacin-Resistant Staphylococcus aureus

At present, the universal health problem with Staphylococcus aureus is the emergence of multidrug-resistant strains due to the overuse of antibiotics. Drug extrusion through efflux pumps is one of the bacterial mechanisms to neutralize the bactericidal effect of antibiotics. The antibacterial activity of silver nanoparticle as well as Fe₃O₄ nanoparticle had been previously studied and widely described. Today, the development of green methods for nanomaterial synthesis is an important aspect of research in the field of nanotechnology. Here, we report the biosynthesis and characterization of Fe₃O₄@Ag nanocomposite by Spirulina platensis cyanobacterium and it impacts on the expression of efflux pump genes in ciprofloxacin-resistant S. aureus (CRSA). The physical properties of biosynthesized nanocomposite measured and confirmed by ultraviolet-visible spectroscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, energy-dispersive X-ray spectroscopy, and scanning and transmission electron microscopy. The minimum inhibitory concentration (MIC) of ciprofloxacin in CRSA strains was determined in the presence of Fe₃O₄@Ag nanoparticles by broth microdilution method. The effect of Fe₃O₄@Ag nanocomposite on the expression of norA and norB genes was evaluated by real-time PCR. The physical analysis confirmed well-dispersed, highly stable, and mostly spherical Fe₃O₄/Ag NPs with the average size of 30-68 nm. The results of antibacterial tests showed the synergistic effects of nanocomposite and antibiotics in MIC reduction. Additionally, in the presence of Fe₃O₄@Ag nanocomposite, the expression of norA and norB genes was decreased more than twofold compared to control. In conclusion, the Fe₃O₄/Ag nanocomposite can use as an effective inhibitor of antibiotic resistance in medicine.

Prevalence, molecular typing, and antimicrobial resistance of bacterial pathogens isolated from ducks

Aim:

This study aimed to investigate the prevalence of different bacterial species affecting ducks as well as demonstrating the antimicrobial susceptibility and molecular typing of the isolated strains.

Materials and Methods:

A total of 500 samples were randomly collected from different duck farms at Ismailia Governorate, Egypt. The collected samples were subjected to the bacteriological examination. Polymerase chain reaction (PCR) was applied for amplification of Kmt1 gene of Pasteurella multocida and X region of protein-A (spA) gene of the isolated Staphylococcus aureus strains to ensure their virulence. The antibiotic sensitivity test was carried out.

Results:

The most common pathogens isolated from apparently healthy and diseased ducks were P. multocida (10.4% and 25.2%), Escherichia coli (3.6% and 22.8%), Staphylococcus epidermidis (10% and 8.8%), Pseudomonas aeruginosa (2% and 10%), and Proteus vulgaris (0.8% and 10%), respectively. In addition, S. aureus and Salmonella spp. were isolated only from the diseased ducks with prevalence (12.2%) and (2.8%), respectively. Serotyping of the isolated E. coli strains revealed that 25 E. coli strains were belonged to five different serovars O1, O18, O111, O78, and O26, whereas three strains were untypable. Salmonella serotyping showed that all the isolated strains were Salmonella Typhimurium. PCR revealed that four tested P. multocida strains were positive for Kmt1 gene with specific amplicon size 460 bp, while three strains were negative. In addition, all the tested S. aureus strains were positive for spA gene with specific amplicon size 226 bp. The antibiotic sensitivity test revealed that most of the isolated strains were sensitive to enrofloxacin, norfloxacin, and ciprofloxacin.

Conclusion:

P. multocida is the most predominant microorganism isolated from apparently healthy and diseased ducks followed by E. coli and Staphylococci. The combination of both phenotypic and genotypic characterization is more reliable an epidemiological tool for identification of bacterial pathogens affecting ducks.

The effects of the Lactobacillus casei strain on obesity in children: a pilot study

There are few data regarding the role of probiotics as a dietary intervention in the management of obesity in children. An open prospective examination was conducted to clarify the effects of Lactobacillus casei strain Shirota (LcS)-containing beverages in obese children. We compared the intestinal microbiota and organic acid levels between 12 obese (average age, 10.8 years; body mass index (BMI) Z score, 2.7±1.7) and 22 control children(average age, 8.5 years; BMI Z score, 0.1±0.7), and pre- and post-intervention in the obese children. The obese group underwent diet and exercise therapy for 6 months and then were given an LcS beverage daily for another 6 months and the body weight and serological markers were monitored. Significant reductions in the faecal concentrations of Bifidobacterium (obese group, 7.9±1.5 vs non-obese group, 9.8±0.5 Log10cells/g; P<0.01) along with a significant decline in the Bacteroides fragilis group, Atopobium cluster and Lactobacillus gasseri subgroup, and acetic acid (obese group, 45.1±16.9 vs non-obese group, 57.9±17.6 μmol/g; P<0.05) were observed in the obese group at baseline. A significant decline in body weight (-2.9±4.6%; P<0.05) and an elevation in the high density lipoprotein cholesterol level (+11.1±17.6%; P<0.05) were observed 6 months after ingestion of the LcS beverage compared to baseline. Furthermore, a significant increase in the faecal concentration of Bifidobacterium (7.0±1.2 before ingestion vs 9.1±1.2 Log10cells/g after ingestion; P<0.01) and an apparent increase in the acetic acid concentration (7.0±1.2 before ingestion vs 9.1±1.2 Log10cells/g after ingestion; P<0.01) were observed 6 months after ingestion. LcS contributed to weight loss while also improving the lipid metabolism in obese children via a significant increase in the faecal Bifidobacterium numbers and the acetic acid concentration.

Persistent Staphylococcus aureus isolates from two independent cases of bacteremia display increased bacterial fitness and novel immune evasion phenotypes

Staphylococcus aureus bacteremia cases are complicated by bacterial persistence and treatment failure despite the confirmed in vitro susceptibility of the infecting strain to administered antibiotics. A high incidence of methicillin-resistant S. aureus (MRSA) bacteremia cases are classified as persistent and are associated with poorer patient outcomes. It is still unclear how S. aureus evades the host immune system and resists antibiotic treatment for the prolonged duration of a persistent infection. In this study, the genetic changes and associated phenotypic traits specific to S. aureus persistent bacteremia were identified by comparing temporally dispersed isolates from persistent infections (persistent isolates) originating from two independent persistent S. aureus bacteremia cases with the initial infection isolates and with three resolved S. aureus bacteremia isolates from the same genetic background. Several novel traits were associated specifically with both independent sets of persistent S. aureus isolates compared to both the initial isolates and the isolates from resolved infections (resolved isolates). These traits included (i) increased growth under nutrient-poor conditions; (ii) increased tolerance of iron toxicity; (iii) higher expression of cell surface proteins involved in immune evasion and stress responses; and (iv) attenuated virulence in a Galleria mellonella larva infection model that was not associated with small-colony variation or metabolic dormancy such as had been seen previously. Whole-genome sequence analysis identified different single nucleotide mutations within the mprF genes of all the isolates with the adaptive persistence traits from both independent cases. Overall, our data indicate a novel role for MprF function during development of S. aureus persistence by increasing bacterial fitness and immune evasion.

Intermittent Pringle maneuver is unlikely to induce bacterial translocation to the portal vein: a study using bacterium-specific ribosomal RNA-targeted reverse transcription-polymerase chain reaction

BACKGROUND

The occurrence of bacterial translocation (BT) to the mesenteric lymph nodes following the Pringle maneuver is well established; however, the incidence of BT to the portal circulation remains unclear.

METHODS

Portal blood of patients with suspected hilar malignancy who underwent major hepatobiliary resection with cholangiojejunostomy was sampled three times during surgery: immediately after laparotomy (PV-1); before liver transection and after skeletonization of the hepatoduodenal ligament (PV-2); and after completion of the liver transection (PV-3). The samples were analyzed for microbes with a bacterium-specific ribosomal RNA-targeted reverse transcription-polymerase chain reaction method.

RESULTS

Fifty patients were enrolled in the study, with a mean total Pringle time of 86 min. Microbes in the portal blood were detected in 11 (22%) of the 50 patients. The occurrence of microbes was not different among the PV-1 samples (8% = 4/50), PV-2 samples (14% = 7/50), and PV-3 samples (14% = 7/50) (P = 0.567). Obligate anaerobes were predominantly detected. The positivity of the PV-3 samples showed no correlation with the total Pringle time or with the occurrence of postoperative infectious complications. The total Pringle time did not affect the surgical outcomes, including infectious complications, liver failure, or mortality. The concentrations of aspartate aminotransferase and alanine aminotransferase on postoperative day 1 significantly correlated with the total Pringle time.

CONCLUSIONS

The intermittent Pringle maneuver is unlikely to induce BT to the portal circulation and is safe, even in difficult, complicated hepatobiliary resections requiring long clamping times.

Inhibiting the growth of methicillin-resistant Staphylococcus aureus in vitro with antisense peptide nucleic acid conjugates targeting the ftsZ gene

BACKGROUND

The increasing emergence of clinical infections caused by methicillin-resistant Staphylococcus aureus (MRSA) challenges existing therapeutic options and highlights the need to develop novel treatment strategies. The ftsZ gene is essential to bacterial cell division.

METHODS

In this study, two antisense peptide nucleic acids (PNAs) conjugated to a cell-penetrating peptide were used to inhibit the growth of MRSA. PPNA1, identified with computational prediction and dot-blot hybridization, is complementary to nucleotides 309-323 of the ftsZ mRNA. PPNA2 was designed to target the region that includes the translation initiation site and the ribosomal-binding site (Shine-Dalgarno sequence) of the ftsZ gene. Scrambled PPNA was constructed with mismatches to three bases within the antisense PPNA1 sequence.

RESULTS

PPNA1 and PPNA2 caused concentration-dependent growth inhibition and had bactericidal effects. The minimal bactericidal concentrations of antisense PPNA1 and PPNA2 were 30μmol/l and 40μmol/l, respectively. The scrambled PPNA had no effect on bacterial growth, even at higher concentrations, confirming the sequence specificity of the probes. RT-PCR showed that the antisense PPNAs suppressed ftsZ mRNA expression in a dose-dependent manner.

CONCLUSION

Our results demonstrate that the potent effects of PNAs on bacterial growth and cell viability were mediated by the down-regulation or even knock-out of ftsZ gene expression. This highlights the utility of ftsZ as a promising target for the development of new antisense antibacterial agents to treat MRSA infections.

The detection of intraoperative bacterial translocation in the mesenteric lymph nodes is useful in predicting patients at high risk for postoperative infectious complications after esophagectomy. Ann Surg. 2014;259:477-484. [PMID: 23549427 DOI: 10.1097/SLA.0b013e31828e39e8]

OBJECTIVE

To investigate the incidence of BT in the mesenteric lymph node and bacteremia after an esophagectomy using a bacterium-specific ribosomal RNA-targeted reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR).

BACKGROUND

There is little evidence regarding the occurrence of bacterial translocation (BT) and its correlation to postoperative infectious complications after an esophagectomy.

METHODS

Eighteen patients with esophageal cancer were studied. Mesenteric lymph nodes were harvested from the jejunal mesentery before surgical mobilization (MLN-1) and after the restoration of bowel continuity (MLN-2). Blood and sputum were also sampled before surgery (Blood-1 and Sputum-1) and on postoperative day 1 (Blood-2 and Sputum-2).

RESULTS

The detection rates of bacteria in the MLN-2 (56%) and Blood-2 (56%) were significantly higher than those in the MLN-1 (17%) and Blood-1 (22%), indicating that surgical stress induces BT. The detection rate was not different between Sputum-1 (80%) and Sputum-2 (78%). There was an 80% sequence homology between the RT-qPCR products in the MLN-2 and Blood-2, whereas the homology was only 20% between Blood-2 and Sputum-2. In the patients with positive bacteria in the MLN-2 sample, there was a greater incidence of postoperative infectious complications than in patients without bacteria in the MLN-2 sample (P = 0.04). The postoperative hospital stay was also longer (P = 0.037) for patients with positive bacteria in the MLN-2 sample.

CONCLUSIONS

BT frequently occurs during esophagectomies, and postoperative bacteremia is likely to be gut-derived. Patients with positive bacteria in the MLN-2 sample should be carefully managed because these patients are more susceptible to postoperative infectious complications.

Randomized clinical trial of the effect of perioperative synbiotics versus no synbiotics on bacterial translocation after oesophagectomy

BACKGROUND

The impact of perioperative synbiotics on bacterial translocation and subsequent bacteraemia after oesophagectomy is unclear. This study investigated the effect of perioperative synbiotic administration on the incidence of bacterial translocation to mesenteric lymph nodes (MLNs) and the occurrence of postoperative bacteraemia.

METHODS

Patients with oesophageal cancer were randomized to receive perioperative synbiotics or no synbiotics (control group). MLNs were harvested from the jejunal mesentery before dissection (MLN-1) and after the restoration of digestive tract continuity (MLN-2). Blood and faeces samples were taken before and after operation. Microorganisms in each sample were detected using a bacterium-specific ribosomal RNA-targeted reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) method.

RESULTS

Some 42 patients were included. There was a significant difference between the two groups in detection levels of microorganisms in the MLN-1 samples. Microorganisms were more frequently detected in MLN-2 samples in the control group than in the synbiotics group (10 of 18 versus 3 of 18; P = 0·035). In addition, bacteraemia detected using RT-qPCR 1 day after surgery was more prevalent in the control group than in the synbiotics group (12 of 21 versus 4 of 21; P = 0·025). Neutrophil counts on postoperative days 1, 2 and 7 after surgery were all significantly higher in the control group than in the synbiotics group.

CONCLUSION

Perioperative use of synbiotics reduces the incidence of bacteria in the MLNs and blood. These beneficial effects probably contribute to a reduction in the inflammatory response after oesophagectomy.

REGISTRATION NUMBER

ID 000003262 (University Hospital Medical Information Network, http://www.umin.ac.jp).

Enhanced nucleic acid amplification with blood in situ by wire-guided droplet manipulation (WDM)

There are many challenges facing the use of molecular biology to provide pertinent information in a timely, cost effective manner. Wire-guided droplet manipulation (WDM) is an emerging format for conducting molecular biology with unique characteristics to address these challenges. To demonstrate the use of WDM, an apparatus was designed and assembled to automate polymerase chain reaction (PCR) on a reprogrammable platform. WDM minimizes thermal resistance by convective heat transfer to a constantly moving droplet in direct contact with heated silicone oil. PCR amplification of the GAPDH gene was demonstrated at a speed of 8.67 s/cycle. Conventional PCR was shown to be inhibited by the presence of blood. WDM PCR utilizes molecular partitioning of nucleic acids and other PCR reagents from blood components, within the water-in-oil droplet, to increase PCR reaction efficiency with blood in situ. The ability to amplify nucleic acids in the presence of blood simplifies pre-treatment protocols towards true point-of-care diagnostic use. The 16s rRNA hypervariable regions V3 and V6 were amplified from Klebsiella pneumoniae genomic DNA with blood in situ. The detection limit of WDM PCR was 1 ng/μL or 10(5)genomes/μL with blood in situ. The application of WDM for rapid, automated detection of bacterial DNA from whole blood may have an enormous impact on the clinical diagnosis of infections in bloodstream or chronic wound/ulcer, and patient safety and morbidity.

A magneto-DNA nanoparticle system for rapid detection and phenotyping of bacteria

So far, although various diagnostic approaches for pathogen detection have been proposed, most are too expensive, lengthy or limited in specificity for clinical use. Nanoparticle systems with unique material properties, however, circumvent these problems and offer improved accuracy over current methods. Here, we present novel magneto-DNA probes capable of rapid and specific profiling of pathogens directly in clinical samples. A nanoparticle hybridization assay, involving ubiquitous and specific probes that target bacterial 16S rRNAs, was designed to detect amplified target DNAs using a miniaturized NMR device. Ultimately, the magneto-DNA platform will allow both universal and specific detection of various clinically relevant bacterial species, with sensitivity down to single bacteria. Furthermore, the assay is robust and rapid, simultaneously diagnosing a panel of 13 bacterial species in clinical specimens within 2 h. The generic platform described could be used to rapidly identify and phenotype pathogens for a variety of applications.

Methicillin-resistant Staphylococcus aureus (MRSA) detected at four U.S. wastewater treatment plants

BACKGROUND

The incidence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infections is increasing in the United States, and it is possible that municipal wastewater could be a reservoir of this microorganism. To date, no U.S. studies have evaluated the occurrence of MRSA in wastewater.

OBJECTIVE

We examined the occurrence of MRSA and methicillin-susceptible S. aureus (MSSA) at U.S. wastewater treatment plants.

METHODS

We collected wastewater samples from two Mid-Atlantic and two Midwest wastewater treatment plants between October 2009 and October 2010. Samples were analyzed for MRSA and MSSA using membrane filtration. Isolates were confirmed using biochemical tests and PCR (polymerase chain reaction). Antimicrobial susceptibility testing was performed by Sensititre® microbroth dilution. Staphylococcal cassette chromosome mec (SCCmec) typing, Panton-Valentine leucocidin (PVL) screening, and pulsed field gel electrophoresis (PFGE) were performed to further characterize the strains. Data were analyzed by two-sample proportion tests and analysis of variance.

RESULTS

We detected MRSA (n = 240) and MSSA (n = 119) in 22 of 44 (50%) and 24 of 44 (55%) wastewater samples, respectively. The odds of samples being MRSA-positive decreased as treatment progressed: 10 of 12 (83%) influent samples were MRSA-positive, while only one of 12 (8%) effluent samples was MRSA-positive. Ninety-three percent and 29% of unique MRSA and MSSA isolates, respectively, were multidrug resistant. SCCmec types II and IV, the pvl gene, and USA types 100, 300, and 700 (PFGE strain types commonly found in the United States) were identified among the MRSA isolates.

CONCLUSIONS

Our findings raise potential public health concerns for wastewater treatment plant workers and individuals exposed to reclaimed wastewater. Because of increasing use of reclaimed wastewater, further study is needed to evaluate the risk of exposure to antibiotic-resistant bacteria in treated wastewater.

Quantitative PCR for Etiologic Diagnosis of Methicillin-Resistant Staphylococcus aureus Pneumonia in Intensive Care Unit

Background

Ventilator-associated pneumonia (VAP) requires prompt and appropriate treatment. Since methicillin-resistant Staphylococcus aureus (MRSA) is a frequent pathogen in VAP, rapid identification of it, is pivotal. Our aim was to evaluate the utility of quantitative polymerase chain reaction (qPCR) as a useful method for etiologic diagnoses of MRSA pneumonia.

Methods

We performed qPCR for mecA, S. aureus-specific femA-SA, and S. epidermidis-specific femA-SE genes from bronchoalveolar lavage or bronchial washing samples obtained from clinically-suspected VAP. Molecular identification of MRSA was based on the presence of the mecA and femA-SA gene, with the absence of the femA-SE gene. To compensate for the experimental and clinical conditions, we spiked an internal control in the course of DNA extraction. We estimated number of colony-forming units per mL (CFU/mL) of MRSA samples through a standard curve of a serially-diluted reference MRSA strain. We compared the threshold cycle (Ct) value with the microbiologic results of MRSA.

Results

We obtained the mecA gene standard curve, which showed the detection limit of the mecA gene to be 100 fg, which corresponds to a copy number of 30. We chose cut-off Ct values of 27.94 (equivalent to 1×10⁴ CFU/mL) and 21.78 (equivalent to 1×10⁵ CFU/mL). The sensitivity and specificity of our assay were 88.9% and 88.9% respectively, when compared with quantitative cultures.

Conclusion

Our results were valuable for diagnosing and identifying pathogens involved in VAP. We believe our modified qPCR is an appropriate tool for the rapid diagnosis of clinical pathogens regarding patients in the intensive care unit.

Viable Staphylococcus aureus quantitation using ¹⁵N metabolically labeled bacteriophage amplification coupled with a multiple reaction monitoring proteomic workflow

A multiple reaction monitoring liquid chromatography method with tandem mass spectrometric detection for quantitation of Staphylococcus aureus via phage amplification detection is described. This phage amplification detection method enables rapid and accurate quantitation of viable S. aureus by detecting an amplified capsid protein from a specific phage. A known amount of metabolically labeled (15)N reference bacteriophage, utilized as the input phage and as the internal standard for quantitation, was spiked into S. aureus samples. Following a 2-h incubation, the sample was subjected to a 3-min rapid trypsin digest and analyzed by high-throughput liquid chromatography tandem mass spectrometric detection targeting peptides unique to both the (15)N (input phage) and (14)N (progeny phage) capsid proteins. Quantitation was achieved by comparing peak areas of target peptides from the metabolically labeled (15)N bacteriophage peptide internal standard with that of the wild-type (14)N peptides that were produced by phage amplification and subsequent digestion when the host bacteria was present. This approach is based on the fact that a labeled species differs from the unlabeled one in terms of its mass but exhibits almost identical chemical properties such as ion yields and retention times. A 6-point calibration curve for S. aureus concentration was constructed with standards ranging from 5.0 × 10(4) colony forming units (CFU) ml(-1) to 2.0 × 10(6) CFU ml(-1), with the (15)N reference phage spiked at a concentration of 1.0 × 10(9) plaque forming units (PFU) ml(-1). Amplification with (15)N bacteriophage coupled with LC-MS/MS detection offers speed (3 h total analysis time), sensitivity (LOD: < 5.0 × 10(4) CFU ml(-1)), accuracy, and precision for quantitation of S. aureus.

Effect of the continuous intake of probiotic-fermented milk containing Lactobacillus casei strain Shirota on fever in a mass outbreak of norovirus gastroenteritis and the faecal microflora in a health service facility for the aged

For conducting effective risk management in long-stay elderly people at a health service facility, we performed an open case-controlled study to evaluate the effect of the intake of probiotic-fermented milk containing Lactobacillus casei strain Shirota (LcS-fermented milk) on norovirus gastroenteritis occurring in the winter season during the intake period. A total of seventy-seven elderly people (mean age 84 years) were enrolled in the study. During a 1-month period, there was no significant difference in the incidence of norovirus gastroenteritis between the LcS-fermented milk-administered (n 39) and the non-administered (n 38) groups; however, the mean duration of fever of >37°C after the onset of gastroenteritis was 1·5 (sd 1·7) d in the former and 2·9 (sd 2·3) d in the latter group, showing a significant shortening in the former group (P < 0·05). RT-quantitative PCR analysis targeting ribosomal RNA showed both Bifidobacterium and Lactobacillus to be significantly dominant, whereas Enterobacteriaceae decreased in faecal samples from the administered group (n 10, mean age 83 years), with a significant increase in faecal acetic acid concentration. Continuous intake of LcS-fermented milk could positively contribute to the alleviation of fever caused by norovirus gastroenteritis by correcting the imbalance of the intestinal microflora peculiar to the elderly, although such consumption could not protect them from the disease.

Efficacy of bacterial ribosomal RNA-targeted reverse transcription-quantitative PCR for detecting neonatal sepsis: a case control study

Background

Neonatal sepsis is difficult to diagnose and pathogens cannot be detected from blood cultures in many cases. Development of a rapid and accurate method for detecting pathogens is thus essential. The main purpose of this study was to identify etiological agents in clinically diagnosed neonatal sepsis using bacterial ribosomal RNA-targeted reverse transcription-quantitative PCR (BrRNA-RT-qPCR) and to conduct comparisons with the results of conventional blood culture. Since BrRNA-RT-qPCR targets bacterial ribosomal RNA, detection rates using this approach may exceed those using conventional PCR.

Methods

Subjects comprised 36 patients with 39 episodes of suspected neonatal sepsis who underwent BrRNA-RT-qPCR and conventional blood culture to diagnose sepsis. Blood samples were collected aseptically for BrRNA-RT-qPCR and blood culture at the time of initial sepsis evaluation by arterial puncture. BrRNA-RT-qPCR and blood culture were undertaken using identical blood samples, and BrRNA-RT-qPCR was performed using 12 primer sets.

Results

Positive rate was significantly higher for BrRNA-RT-qPCR (15/39, 38.5%) than for blood culture (6/39, 15.4%; p = 0.0039). BrRNA-RT-qPCR was able to identify all pathogens detected by blood culture. Furthermore, this method detected pathogens from neonates with clinical sepsis in whom pathogens was not detected by culture methods.

Conclusions

This RT-PCR technique is useful for sensitive detection of pathogens causing neonatal sepsis, even in cases with negative results by blood culture.