Method for inducing experimental pneumococcal meningitis in outbred mice

Background  

Streptococcus pneumoniae is the leading cause of bacterial meningitis. Pneumococcal meningitis is associated with the highest mortality among bacterial meningitis and it may also lead to neurological sequelae despite the use of antibiotic therapy. Experimental animal models of pneumococcal meningitis are important to study the pathogenesis of meningitis, the host immune response induced after infection, and the efficacy of novel drugs and vaccines.     

Insects in confined swine operations carry a large antibiotic resistant and potentially virulent enterococcal community

Background  

Extensive use of antibiotics as growth promoters in the livestock industry constitutes strong selection pressure for evolution and selection of antibiotic resistant bacterial strains. Unfortunately, the microbial ecology and spread of these bacteria in the agricultural, urban, and suburban environments are poorly understood. Insects such as house flies (Musca domestica) and German cockroaches (Blattella germanica) can move freely between animal waste and food and may play a significant role in the dissemination of antibiotic resistant bacteria within and between animal production farms and from farms to residential settings.     

Few amino acid positions in <Emphasis Type="Italic">rpoB</Emphasis> are associated with most of the rifampin resistance in <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis>

Background  

Mutations in rpoB, the gene encoding the β subunit of DNA-dependent RNA polymerase, are associated with rifampin resistance in Mycobacterium tuberculosis. Several studies have been conducted where minimum inhibitory concentration (MIC, which is defined as the minimum concentration of the antibiotic in a given culture medium below which bacterial growth is not inhibited) of rifampin has been measured and partial DNA sequences have been determined for rpoB in different isolates of M. tuberculosis. However, no model has been constructed to predict rifampin resistance based on sequence information alone. Such a model might provide the basis for quantifying rifampin resistance status based exclusively on DNA sequence data and thus eliminate the requirements for time consuming culturing and antibiotic testing of clinical isolates.     

RecET driven chromosomal gene targeting to generate a RecA deficient Escherichia coli strain for Cre mediated production of minicircle DNA

Background  

Minicircle DNA is the non-replicating product of intramolecular site-specific recombination within a bacterial minicircle producer plasmid. Minicircle DNA can be engineered to contain predominantly human sequences which have a low content of CpG dinucleotides and thus reduced immunotoxicity for humans, whilst the immunogenic bacterial origin and antibiotic resistance marker gene sequences are entirely removed by site-specific recombination. This property makes minicircle DNA an excellent vector for non-viral gene therapy. Large-scale production of minicircle DNA requires a bacterial strain expressing tightly controlled site-specific recombinase, such as Cre recombinase. As recombinant plasmids tend to be more stable in RecA-deficient strains, we aimed to construct a recA ^- bacterial strain for generation of minicircle vector DNA with less chance of unwanted deletions.     

Characteristics of phenotypic antibiotic resistance of Helicobacter pylori and its correlation with genotypic antibiotic resistance: A retrospective study in Ningxia

Background

Geographic differences exist in the antibiotic resistance patterns of Helicobacter pylori. Personalized treatment regimens based on local or individual resistance data are essential. We evaluated the current status of H. pylori resistance in Ningxia, analyzed resistance-related factors, and assessed the concordance of phenotypic and genotypic resistance.

Methods

Strains were isolated from the gastric mucosa of patients infected with H. pylori in Ningxia and relevant clinical information was collected. Phenotypic antibiotic susceptibility assays (Kirby–Bauer disk diffusion) and antibiotic resistance gene detection (Sanger sequencing) were performed.

Results

We isolated 1955 H. pylori strains. The resistance rates of H. pylori to amoxicillin, levofloxacin, clarithromycin, and metronidazole were 0.9%, 42.4%, 40.4%, and 94.2%, respectively. Only five tetracycline-resistant and one furazolidone-resistant strain were identified. Overall, 3.3% of the strains were sensitive to all six antibiotics. Multidrug-resistant strains accounted for 22.9%, of which less than 20% were from Wuzhong. Strains isolated from women and patients with nonulcerative disease had higher rates of resistance to levofloxacin and clarithromycin. Higher rates of resistance to metronidazole, levofloxacin, and clarithromycin were observed in the older age group than in the younger age group. The kappa coefficients of phenotypic resistance and genotypic resistance for levofloxacin and clarithromycin were 0.830 and 0.809, respectively, whereas the remaining antibiotics showed poor agreement.

Conclusion

H. pylori antibiotic resistance is severe in Ningxia. Therefore, furazolidone, amoxicillin, and tetracycline are better choices for the empirical therapy of H. pylori infection in this region. Host sex, age, and the presence of ulcerative diseases may affect antibiotic resistance of the bacteria. Personalized therapy based on genetic testing for levofloxacin and clarithromycin resistance may be a future direction for the eradication therapy of H. pylori infection in Ningxia.     

Susceptibility of Pediococcus isolates to antimicrobial compounds in relation to hop-resistance and beer-spoilage

Background  

Though important in the context of food microbiology and as potential pathogens in immuno-compromised humans, bacterial isolates belonging to the genus Pediococcus are best known for their association with contamination of ethanol fermentation processes (beer, wine, or fuel ethanol). Use of antimicrobial compounds (e.g., hop-compounds, Penicillin) by some industries to combat Pediococcus contaminants is long-standing, yet knowledge about the resistance of pediococci to antimicrobial agents is minimal. Here we examined Pediococcus isolates to determine whether antibiotic resistance is associated with resistance to hops, presence of genes known to correlate with beer spoilage, or with ability to grow in beer.     

Interaction of bacteria isolated from clinical biofilms with cardiovascular prosthetic devices and eukaryotic cells

Purpose

To identify the relationships between some infectious agents implicated in cardiovascular diseases with the cellular substrate and prosthetic devices in the presence of antibiotics.

Specific objectives

Strains isolation and identification, comparative study of antibiotic resistance of planktonic (disk diffusion, E-test, automatic systems) and sessile (using original experimental models for in vitro development of monospecific biofilms) bacterial cells, virulence assays (adherence and invasion of HeLa cells, slime test, soluble virulence factors expression), dynamic study of biofilm development on inert substrata, under the influence of antibiotics, the influence of cellular and soluble bacterial fractions on HeLa cells (by flow cytometry and real-time PCR).

Results

The identified strains were isolated from different sources, the etiology being dominated by Gram-negative non-fermentative bacilli, Gram-positive cocci and yeasts, harboring invasion enzymes responsible for development of systemic infections. The isolated strains exhibited a high level of antibiotic resistance to beta-lactams, aminoglycosides and quinolones, and an evident tendency of colonizing the cellular and inert substrate, the degree of colonization depending on the physico-chemical nature of the substrate. By comparison with planktonic ones, the sessile bacterial strains expressed a changed profile of antibiotic resistance, this aspect being very important for the readjustment of the treatment and prevention of infections associated with prosthetic devices. In vitro experiments suggested that different fractions of S. aureus cultures could trigger the release of proinflammatory (TNF-α, IL-1b, IL-6) and anti-inflammatory (IL-8) cytokines and induced apoptosis in HeLa cells.     

Assessment of three Resistance-Nodulation-Cell Division drug efflux transporters of Burkholderia cenocepacia in intrinsic antibiotic resistance

Background  

Burkholderia cenocepacia are opportunistic Gram-negative bacteria that can cause chronic pulmonary infections in patients with cystic fibrosis. These bacteria demonstrate a high-level of intrinsic antibiotic resistance to most clinically useful antibiotics complicating treatment. We previously identified 14 genes encoding putative Resistance-Nodulation-Cell Division (RND) efflux pumps in the genome of B. cenocepacia J2315, but the contribution of these pumps to the intrinsic drug resistance of this bacterium remains unclear.     

Antibiotics resistance of Helicobacter pylori in children with upper gastrointestinal symptoms in Hangzhou,China

Background

The decreasing eradication rate of Helicobacter pylori is mainly because of the progressive increase in its resistance to antibiotics. Studies on antimicrobial susceptibility of H. pylori in children are limited. This study aimed to investigate the resistance rates and patterns of H. pylori strains isolated from children.

Materials and Methods

Gastric mucosa biopsy samples obtained from children who had undergone upper gastrointestinal endoscopy were cultured for H. pylori, and susceptibility to six antibiotics (clarithromycin, amoxicillin, gentamicin, furazolidone, metronidazole, and levofloxacin) was tested from 2012‐2014.

Results

A total of 545 H. pylori strains were isolated from 1390 children recruited. The total resistance rates of H. pylori to clarithromycin, metronidazole, and levofloxacin were 20.6%, 68.8%, and 9.0%, respectively. No resistance to amoxicillin, gentamicin, and furazolidone was detected. 56.1% strains were single resistance, 19.6% were resistant to more than one antibiotic, 16.7% for double resistance, and 2.9% for triple resistance in 413 strains against any antibiotic. And the H. pylori resistance rate increased significantly from 2012‐2014. There was no significant difference in the resistance rates to clarithromycin, metronidazole, and levofloxacin between different gender, age groups, and patients with peptic ulcer diseases or nonulcer diseases.

Conclusions

Antibiotic resistance was indicated in H. pylori strains isolated from children in Hangzhou, and it increased significantly during the 3 years. Our data strongly support current guidelines, which recommend antibiotic susceptibility tests prior to eradication therapy.     

Antibiotic susceptibility profiles of some <Emphasis Type="Italic">Vibrio</Emphasis> strains isolated from wastewater final effluents in a rural community of the Eastern Cape Province of South Africa

Background  

To evaluate the antibiogram and antibiotic resistance genes of some Vibrio strains isolated from wastewater final effluents in a rural community of South Africa. V. vulnificus (18), V. metschnikovii (3), V. fluvialis (19) and V. parahaemolyticus (12) strains were isolated from final effluents of a wastewater treatment plant (WWTP) located in a rural community of South Africa. The disk diffusion method was used for the characterization of the antibiogram of the isolates. Polymerase chain reaction (PCR) was employed to evaluate the presence of established antibiotic resistance genes using specific primer sets.     

Superoxide dismutase is upregulated in <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> following protoporphyrin-mediated photodynamic inactivation and does not directly influence the response to photodynamic treatment

Background  

Staphylococcus aureus, a major human pathogen causes a wide range of disease syndromes. The most dangerous are methicillin-resistant S. aureus (MRSA) strains, resistant not only to all β-lactam antibiotics but also to other antimicrobials. An alarming increase in antibiotic resistance spreading among pathogenic bacteria inclines to search for alternative therapeutic options, for which resistance can not be developed easily. Among others, photodynamic inactivation (PDI) of S. aureus is a promising option. Photodynamic inactivation is based on a concept that a non toxic chemical, called a photosensitizer upon excitation with light of an appropriate wavelength is activated. As a consequence singlet oxygen and other reactive oxygen species (e.g. superoxide anion) are produced, which are responsible for the cytotoxic effect towards bacterial cells. As strain-dependence in photodynamic inactivation of S. aureus was observed, determination of the molecular marker(s) underlying the mechanism of the bacterial response to PDI treatment would be of great clinical importance. We examined the role of superoxide dismutases (Sod) in photodynamic inactivation of S. aureus as enzymes responsible for oxidative stress resistance.     

Inactivation of staphylococcal virulence factors using a light-activated antimicrobial agent

Background  

One of the limitations of antibiotic therapy is that even after successful killing of the infecting microorganism, virulence factors may still be present and cause significant damage to the host. Light-activated antimicrobials show potential for the treatment of topical infections; therefore if these agents can also inactivate microbial virulence factors, this would represent an advantage over conventional antibiotic therapy. Staphylococcus aureus produces a wide range of virulence factors that contribute to its success as a pathogen by facilitating colonisation and destruction of host tissues.     

Azithromycin effectiveness against intracellular infections of <Emphasis Type="Italic">Francisella</Emphasis>

Background  

Macrolide antibiotics are commonly administered for bacterial respiratory illnesses. Azithromycin (Az) is especially noted for extremely high intracellular concentrations achieved within macrophages which is far greater than the serum concentration. Clinical strains of Type B Francisella (F.) tularensis have been reported to be resistant to Az, however our laboratory Francisella strains were found to be sensitive. We hypothesized that different strains/species of Francisella (including Type A) may have different susceptibilities to Az, a widely used and well-tolerated antibiotic.     

Prenatal household size and composition are associated with infant fecal bacterial diversity in Cebu,Philippines

Objectives

The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members.

Materials and Methods

As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition.

Results

Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables.

Conclusions

Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM.

     

Subinhibitory concentrations of antibiotics affect stress and virulence gene expression in Listeria monocytogenes and cause enhanced stress sensitivity but do not affect Caco‐2 cell invasion

Aims

Antibiotics can act as signal molecules and affect bacterial gene expression, physiology and virulence. The purpose of this study was to determine whether subinhibitory antibiotic concentrations alter gene expression and physiology of Listeria monocytogenes.

Methods and Results

Using an agar‐based screening assay with promoter fusions, 14 of 16 antibiotics induced or repressed expression of one or more stress and/or virulence genes. Despite ampicillin‐induced up‐regulation of PinlA‐lacZ expression, Caco‐2 cell invasion was not affected. Subinhibitory concentrations of ampicillin and tetracycline caused up‐ and down‐regulation of stress response genes, respectively, but both antibiotics caused increased sensitivity to acid stress. Six combinations of gene‐antibiotic were quantified in broth cultures and five of the six resulted in the same expression pattern as the agar‐based assay.

Conclusions

Antibiotics affect virulence and/or stress gene expression; however, altered expression could not predict changes in phenotypic behaviour. Subinhibitory concentrations of antibiotics led to increased acid sensitivity, and we speculate that this is attributed to changes in cell envelope or reduced σ^B‐dependent gene expression.

Significance and Impact of the Study

Although subinhibitory concentrations of antibiotics affect gene expression in L. monocytogenes, the changes did not increase virulence but did enhance the acid sensitivity.     

Differential proteomic analysis highlights metabolic strategies associated with balhimycin production in <Emphasis Type="Italic">Amycolatopsis balhimycina</Emphasis> chemostat cultivations

Background  

Proteomics was recently used to reveal enzymes whose expression is associated with the production of the glycopeptide antibiotic balhimycin in Amycolatopsis balhimycina batch cultivations. Combining chemostat fermentation technology, where cells proliferate with constant parameters in a highly reproducible steady-state, and differential proteomics, the relationships between physiological status and metabolic pathways during antibiotic producing and non-producing conditions could be highlighted.     

Predictive analysis of transmissible quinolone resistance indicates <Emphasis Type="Italic">Stenotrophomonas maltophilia</Emphasis> as a potential source of a novel family of Qnr determinants

Background  

Predicting antibiotic resistance before it emerges at clinical settings constitutes a novel approach for preventing and fighting resistance of bacterial pathogens. To analyse the possibility that novel plasmid-encoded quinolone resistance determinants (Qnr) can emerge and disseminate among bacterial pathogens, we searched the presence of those elements in nearly 1000 bacterial genomes and metagenomes.     

Properties and identification of antibiotic drug targets

Background  

We analysed 48 non-redundant antibiotic target proteins from all bacteria, 22 antibiotic target proteins from E. coli only and 4243 non-drug targets from E. coli to identify differences in their properties and to predict new potential drug targets.     

Soil moisture effect on bacterial and fungal community in Beilu River (Tibetan Plateau) permafrost soils with different vegetation types

Aim

This study investigated the effects of environmental variables on the bacterial and fungal communities of the Beilu River (on the Tibetan Plateau) permafrost soils with different vegetation types.

Methods and Results

Microbial communities were sampled from meadow, steppe and desert steppe permafrost soils during May, June, August and November, and they were analysed by both pyrosequencing and the use of Biolog EcoPlates. The dominant bacterial and fungal phyla in meadow and steppe soils were Proteobacteria and Ascomycota, whereas Actinobacteria and Basidiomycota predominated in desert steppe soils. The bacterial communities in meadow soils degraded amines and amino acids very rapidly, while polymers were degraded rapidly by steppe communities. The RDA patterns showed that the microbial communities differed greatly between meadow, steppe and desert steppe, and they were related to variations in the soil moisture, C/N ratio and pH. A UniFrac analysis detected clear differences between the desert steppe bacterial community and others, and seasonal shifts were observed. The fungal UniFrac patterns differed significantly between meadow and steppe soils. There were significant correlations between the bacterial diversity (H′) and soil moisture (r = 0·506) and C/N (r = 0·527). The fungal diversity (Hf′) was significantly correlated with the soil pH (r = 0·541).

Conclusion

The soil moisture, C/N ratio and pH were important determinants of the microbial community structure in Beilu River permafrost soils.

Significance and Impact of the Study

These results may provide a useful baseline for predicting the variation in microbial communities in response to climate changes.     

Heart valve allograft decontamination with antibiotics: impact of the temperature of incubation on efficacy

Heart valve allografts are typically processed at 4°C in North America, including the step of antibiotic decontamination. In our own experience with heart valve banking, we often observe persistent positive cultures following decontamination at wet ice temperature. We hypothesized that warmer temperatures of incubation might increase the efficacy of the decontamination procedure. In a first series of experiments, 12 different bacterial species were grown overnight, frozen in standardized aliquots and used directly to inoculate antibiotic cocktail aliquots at 10⁵ colony-forming units (CFU)/ml. The antibiotic cocktail contains vancomycin (50 μg/ml), gentamicin (80 μg/ml) and cefoxitin (240 μg/ml) in Dulbecco’s Modified Eagle’s Medium. Inoculated aliquots were incubated at 4, 22 and 37°C and CFUs were determined at regular intervals up to 24 h post-inoculation. In a second set of experiments, 10 heart valves were spiked with 5000 CFU/ml and incubated with antibiotics at 4 and 37°C for 24 h. The final rinse solutions of these heart valves were filtered and tested for bacterial growth. After 24 h of incubation, CFUs of all 12 bacterial species were reduced by a factor of only one to two logs at 4°C whereas log reductions of 3.7 and 5.0 or higher were obtained at 22 and 37°C, respectively. Most microorganisms, including Staphylococcus epidermidis, Lactococcus lactis lactis and Propionibacterium acnes survived well the 24-h antibiotic treatment at 4°C (<1 Log reduction). All 10 heart valves that were spiked with microorganisms had positive final rinse solutions after antibiotic soaking at 4°C, whereas 8 out of 10 cultures were negative when antibiotic decontamination was done at 37°C. These experiments show that a wet ice temperature greatly reduces the efficacy of the allograft decontamination process as microorganisms survived well to a 24-h 4°C antibiotic treatment. This could explain the high rate of positive post-processing cultures obtained with our routine tissue decontamination procedure. Increasing the decontamination temperature from 4 to 37°C may significantly reduce the incidence of post-disinfection bacterial contamination of heart valves.