Search

Background and Aims: Outbreaks of severe and chronic tick-borne diseases (TBDs) are on the rise. This is through the transmission of infectious disease agents to humans during tick feeding. The transmission rate and extent of microbial exchange, however, vary based on the tick microbiome composition. While select microbes are determined to be members of the normal tick microbiome and others are clearly recognized mammalian and/or avian pathogens, the status of many other members of the tick microbiota with respect to human and alternate host pathogenesis remains unclear. Moreover, the species-level 16S microbiome of prominent TBD vectors, including Ixodes pacificus, have not been extensively studied. To elucidate the I. pacificus microbiome composition, we performed a pan-domain species-specific characterization of the bacterial microbiome on adult I. pacificus ticks collected from two regional parks within Western California. Our methods provide for characterizing nuances within cohort microbiomes and their relationships to geo-locale of origin, surrounding fauna, and prevalences of known and suspected pathogens in relation to current TBD epidemiological zones. Methods: Ninety-two adult I. pacificus bacterial microbiomes were characterized using a high-fidelity, pan-domain, species-specific, full-length 16S rRNA amplification method using circular consensus sequencing performed on the Pacific Biosciences Sequel platform. Data analyses were performed with the MCSMRT data analysis package and database. Results: The species-specific I. pacificus microbiome composition illustrates a complex assortment of microflora, including over 900 eubacterial species with high taxonomic diversity, which was revealed to vary by sex and geo-locale, though the use of full-length 16S gene sequencing. The TBD-associated pathogens, such as Borrelia burgdorferi, Anaplasma phagocytophilum, and Rickettsia monacensis, were identified along with a host of bacteria previously unassociated with ticks. Conclusion: Species-level taxonomic classification of the I. pacificus microbiome revealed that full-length bacterial 16S gene sequencing is required for the granularity to elucidate the microbial diversity within and among ticks based on geo-locale.

Objective To undertake the first comprehensive evaluation of the urinary microbiota associated with Hunner lesion (HL) interstitial cystitis/bladder pain syndrome (IC/BPS). Despite no previous identification of a distinct IC/BPS microbial urotype, HL IC/BPS, an inflammatory subtype of IC/BPS, was hypothesized most likely to be associated with a specific bacterial species or microbial pattern. Participants and methods The bacterial microbiota of midstream urine specimens from HL IC/BPS and age- and gender-matched IC/BPS patients without HL (non-HL IC/BPS) were examined using the pan-bacterial domain clinical-level molecular diagnostic Pacific Biosciences full-length 16S gene sequencing protocol, informatics pipeline and database. We characterized the differential presence, abundances, and diversity of species, as well as gender-specific differences between and among HL and non-HL IC/BPS patients. Results A total of 59 patients with IC/BPS were enrolled (29 HL, 30 non-HL; 43 women, 16 men) from a single centre and the microbiota in midstream urine specimens was available for comparison. The species abundance differentiation between the HL and non-HL groups (12 species) was not significantly different after Bonferroni adjustments for multiple comparisons. Similarly, the nine differentiating species noted between female HL and non-HL patients were not significantly different after similar statistical correction. However, four species abundances (out of the 10 species differences identified prior to correction) remained significantly different between male HL and non-HL subjects: Negativicoccus succinivorans, Porphyromonas somerae, Mobiluncus curtisii and Corynebacterium renale. Shannon diversity metrics showed significantly higher diversity among HL male patients than HL female patients (P = 0.045), but no significant diversity differences between HL and non-HL patients overall. Conclusions We were not able to identify a unique pathogenic urinary microbiota that differentiates all HL from all non-HL IC/BPS. It is likely that the male-specific differences resulted from colonization/contamination remote from the bladder. We were not able to show that bacteria play an important role in patients with HL IC/BPS.

BackgroundOver the last few decades, a growing body of evidence suggests a role for various infectious agents in Alzheimer’s Disease (AD) pathogenesis. Despite diverse pathogens (virus, bacteria, or fungi) being detected in AD subjects’ brains, most research has focused on individual pathogens and only a few studies investigated the hypothesis of a bacterial brain microbiome. We profiled the bacterial communities present in non-demented controls and AD subjects’ brains.ResultsWe obtained post-mortem samples from the brains of 32 individual subjects, comprising 16 AD and 16 control aged-matched subjects with a total of 130 samples from the frontal and temporal lobes and entorhinal cortex. We used full-length 16S rRNA gene amplification with Pacific Biosciences sequencing technology to identify the bacteria.We detected bacteria in the brains of both cohorts with the principal bacteria comprising Propionibacterium acnes (recently renamed Cutibacterium acnes) and two species each of Acinetobacter and Comamonas genera. We used a hierarchical Bayesian method to detect differences in relative abundance among AD and control groups. Because of large abundance variances we also employed an unconventional analysis approach that utilized Latent Dirichlet Allocation, often used in computational linguistics. This allowed us to identify 5 classes of samples, each revealing a different microbiome. Assuming that samples represented infections that potentially began at different times, we ordered these classes in time, finding that the last class exclusively explained the existence or non-existence of AD.ConclusionsThe AD-related pathogenicity of the brain microbiome seems to be based on a complex polymicrobial dynamic. The time ordering revealed a rise and fall of the abundance of Propionibacterium acnes with pathogenicity occurring for an off-peak abundance level in association with at least one other bacterium from a set of genera that included: Methylobacterium, Bacillus, Caulobacter, Delftia, and Variovorax. P. acnes may also be involved with outcompeting the Comamonas species, which were strongly associated with non-demented brain microbiome, whose early destruction could be the first stage of the disease. The statistical results are also consistent with a leaky blood brain barrier or lymphatic network that allows bacteria, viruses, fungi, or other pathogens to enter the brain.

PURPOSE: To correlate the presence of fungi with symptom flares, pain and urinary severity in a prospective, longitudinal study of women with IC/BPS enrolled in the MAPP Research Network. METHODS: Flare status, pelvic pain, urinary severity, and midstream urine were collected at baseline, 6, 12 months from female IC/BPS participants with at least one flare and age-matched participants with no reported flares. Multilocus PCR coupled with electrospray ionization/mass spectrometry was used for identification of fungal species and genus. Associations between “mycobiome” (species/genus presence, relative abundance, Shannon’s/Chao1 diversity indices) and current flare status, pain, urinary severity were evaluated using generalized linear mixed models, permutational multivariate analysis of variance, Wilcoxon’s Rank Sum test. RESULTS: The most specific analysis detected 13 fungal species from 8 genera in 504 urine samples from 202 females. A more sensitive analysis detected 43 genera. No overall differences were observed in fungal species/genus composition or diversity by flare status or pain severity. Longitudinal analyses suggested greater fungal diversity (Chao1 Mean Ratio 3.8, 95% CI 1.3–11.2, p=0.02) and a significantly greater likelihood of detecting any fungal species (OR=5.26, 95% CI 1.1–25.8, p=0.04) in high versus low urinary severity participants. Individual taxa analysis showed a trend toward increased presence and relative abundance of Candida (OR=6.63, 95% CI 0.8–58.5, p=0.088) and Malassezia (only identified in ‘high’ urinary severity phenotype) for high vs. low urinary symptoms. CONCLUSION: This analysis suggests the possibility that greater urinary symptom severity is associated the urinary mycobiome urine in some females with IC/BPS.

Background and Aims: Outbreaks of severe and chronic tick-borne diseases (TBDs) are on the rise. This is through the transmission of infectious disease agents to humans during tick feeding. The transmission rate and extent of microbial exchange, however, vary based on the tick microbiome composition. While select microbes are determined to be members of the normal tick microbiome and others are clearly recognized mammalian and/or avian pathogens, the status of many other members of the tick microbiota with respect to human and alternate host pathogenesis remains unclear. Moreover, the species-level 16S microbiome of prominent TBD vectors, including Ixodes pacificus, have not been extensively studied. To elucidate the I. pacificus microbiome composition, we performed a pan-domain species-specific characterization of the bacterial microbiome on adult I. pacificus ticks collected from two regional parks within Western California. Our methods provide for characterizing nuances within cohort microbiomes and their relationships to geo-locale of origin, surrounding fauna, and prevalences of known and suspected pathogens in relation to current TBD epidemiological zones. Methods: Ninety-two adult I. pacificus bacterial microbiomes were characterized using a high-fidelity, pan-domain, species-specific, full-length 16S rRNA amplification method using circular consensus sequencing performed on the Pacific Biosciences Sequel platform. Data analyses were performed with the MCSMRT data analysis package and database. Results: The species-specific I. pacificus microbiome composition illustrates a complex assortment of microflora, including over 900 eubacterial species with high taxonomic diversity, which was revealed to vary by sex and geo-locale, though the use of full-length 16S gene sequencing. The TBD-associated pathogens, such as Borrelia burgdorferi, Anaplasma phagocytophilum, and Rickettsia monacensis, were identified along with a host of bacteria previously unassociated with ticks. Conclusion: Species-level taxonomic classification of the I. pacificus microbiome revealed that full-length bacterial 16S gene sequencing is required for the granularity to elucidate the microbial diversity within and among ticks based on geo-locale.

Current genetic detection methods require gene isolation, gene amplification and detection with a fluorescent-tagged probe. They typically require sophisticated equipment and expensive fluorescent probes, rendering them not widely available for rapid acute infection diagnoses at the point of care to ensure timely treatment of the diseases. Here we report a rapid genetic detection method that can detect the bacterial gene directly from patient stools using a piezoelectric plate sensor (PEPS) in conjunction with a continuous flow system with two temperature zones. With stools spiked with sodium dodecyl sulfate (SDS) in situ bacteria lysing and DNA denaturation occurred in the high-temperature zone whereas in situ specific detection of the denatured DNA by the PEPS occurred in the lower-temperature zone. The outcome was a rapid genetic detection method that directly detected bacterial genes from stool in < 40 min without the need of gene isolation, gene amplification, or expensive fluorescent tag but with polymerase chain reaction (PCR) sensitivity. In 40 blinded patient stools, it detected the toxin B gene of Clostridium difficile with 95% sensitivity and 95% specificity. The all-electrical, label-free nature of the detection further supports its potential as a low-cost genetic test that can be used at the point of care.

Streptococcus pneumoniae displays increased resistance to antibiotic therapy following biofilm formation. A genome-wide search revealed that SP 0320 and SP 0675 (respectively annotated as 5-keto-D-gluconate-5-reductase and glucose dehydrogenase) contain the highest degree of homology to CsgA of Myxococcus xanthus, a signaling factor that promotes cell aggregation and biofilm formation. Single and double SP 0320 and SP 0675 knockout mutants were created in strain BS72; however, no differences were observed in the biofilm-forming phenotypes of mutants compared to the wild type strain. Using the chinchilla model of otitis media and invasive disease, all three mutants exhibited greatly increased virulence compared to the wild type strain (increased pus formation, tympanic membrane rupture, mortality rates). The SP 0320 gene is located in an operon with SP 0317, SP 0318 and SP 0319, which we bioinformatically annotated as being part of the Entner-Doudoroff pathway. Deletion of SP 0317 also resulted in increased mortality in chinchillas; however, mutations in SP 0318 and SP 0319 did not alter the virulence of bacteria compared to the wild type strain. Complementing the SP 0317, SP 0320 and SP 0675 mutant strains reversed the virulence phenotype. We prepared recombinant SP 0317, SP 0318, SP 0320 and SP 0675 proteins and confirmed their functions. These data reveal that disruption of genes involved in the degradation of ketogluconate, the Entner-Doudoroff pathway, and glucose dehydrogenase significantly increase the virulence of bacteria in vivo; two hypothetical models involving virulence triggered by reduced in carbon-flux through the glycolytic pathways are presented.

BackgroundPan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy. Moreover, sequencing errors often inflate the number of taxa present. Pacific Biosciences’ (PacBio’s) long-read technology in particular suffers from high error rates per base. Herein we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome dataResultsAnalysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity. Examination of a 250-plus species mock community demonstrated correct species-level classification of >90% of taxa and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed.Propiniobacterium acnes(recently renamedCutibacterium acnes[1]) was the predominant species throughout, but was found at distinct relative abundances by site.ConclusionsOur microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT,https://github.com/jpearl01/mcsmrt) overcomes deficits of standard marker gene based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.

Iron acquisition mechanisms in Francisella tularensis, the causative agent of tularemia, include the Francisella siderophore locus (fsl) siderophore operon and a ferrous iron-transport system comprising outer-membrane protein FupA and inner-membrane transporter FeoB. To characterize these mechanisms and to identify any additional iron uptake systems in the virulent subspecies tularensis, single and double deletions were generated in the fsl and feo iron acquisition systems of the strain Schu S4. Deletion of the entire fsl operon caused loss of siderophore production that could be restored by complementation with the biosynthetic genes fslA and fslC and Major Facilitator Superfamily (MFS) transporter gene fslB. (55) Fe-transport assays demonstrated that siderophore-iron uptake required the receptor FslE and MFS transporter FslD. A ΔfeoB' mutation resulted in loss of ability to transport ferrous iron ((55) Fe(2+) ). A ΔfeoB' ΔfslA mutant that required added exogenous siderophore for growth in vitro was unable to grow within tissue culture cells and was avirulent in mice, indicating that no compensatory cryptic iron uptake systems were induced in vivo. These studies demonstrate that the fsl and feo pathways function independently and operate in parallel to effectively support virulence of F. tularensis.

Figure S1. Effect of primary filters on the number of reads. Figure S2. Insert size distribution. Figure S3. Effects of Host DNA on bacterial 16S yield. Figure S4. Total CCS yield vs. DNA yield vs. PCR yields. Figure S5. CCS reads mapping to the human genome from the sinonasal samples. Figure S6. Primer matching filters. Figure S7. Primer matching truncation and nucleotide variability against positive control E.coli forward and reverse primer matches. Figure S8. Primer matching truncation and nucleotide variability against positive control A.tumefaciens forward and reverse primer matches. Figure S9. Histogram of the number of species per DB cluster in NCBI. Figure S10. The effect of PCR cycle number and polymerase choice on OTU abundances in the BEI mock community. Figure S11. The effect of PCR cycles and polymerase on abundances of chimeric molecules in the BEI mock community. Figure S12. Substitution errors in BEI mock community. Figure S13. E.coli MG1655 16S copies and MED analysis. Figure S14. Phylogenetic trees of well---resolved multi---species genera Clostridium and Desulfovibrio. Figure S15. Phylogenetic trees of poorly---resolved multi---species genera Azotobacter and Nonlabens. Figure S16. Phylogenetic trees of multi---species genera with improved species resolution using FL16S for Algoriphagus and Salegentibacter. Figure S17. Phylogeny of AnaerococcusMED nodes from the sinonasal communities plus NCBI database entries. Figure S18. Relationship between species---level confidence in centroid assignments and the number of species in the matching dbOTU. Figure S19. Effective Number of Species as a function of sample read depth. (PDF 3167 kb)

Supplementary Text. (DOCX 56 kb)

AIM To understand the underlying cellular mechanisms during inactivation of Escherichia coli in response to antimicrobial solution of nonthermal plasma-activated N-acetylcysteine (NAC). METHODS AND RESULTS The recommended techniques were used to demonstrate E. coli cellular and transcriptomic changes caused associated with peroxynitrite and compared with plasma-treated NAC solution. The findings demonstrate that E. coli cells respond to plasma-treated NAC and undergo severe oxidative and nitrosative stress, and leading to stress-induced damages to different components of bacterial cells, which includes loss of membrane potential, formation of oxidized glutathione (GSSG), formation of nitrotyrosine (a known marker of nitrosative stress), DNA damage, and generated a prominent pool of peroxynitrite. Reverse-transcriptase (RT)-polymerase chain reaction analysis of reactive nitrogen species (RNS) responsive genes indicated their differential expressions. CONCLUSION For the first time, we report that the plasma-treated NAC solution activates predominantly nitrosative stress-responsive genes in E. coli and is responsible for cell death. SIGNIFICANCE AND IMPACT OF THE STUDY The reactive species generated in solutions by nonthermal plasma treatment depends on the type of solution or solvent used. The plasma-treated NAC solution rapidly inactivates E. coli, mostly involving highly RNS generated in NAC solution, and has high potential as disinfectant.

Background Acinetobacter baumannii is a nosocomial pathogen which is establishing as a major cause of morbidity and mortality within the healthcare community. The success of this pathogen is largely due to its ability to rapidly gain resistance to antimicrobial therapies and its capability to persist in an abiotic environment through the production of a biofilm. Our tertiary-care hospital has showed high incidence of carbapenem-resistant Acinetobacter baumannii (CRAB) isolates. Methods In this study we explore both genotypic and phenotypic properties of 26 CRAB isolates: 16 isolates were collected from January 2010 to March 2011, and 10 were collected between February and May 2015. Results We determined that all 26 CRAB isolates possessed multiple β-lactamase genes, including genes from Groups A, C, and D. Specifically, 42% of the isolates possesses the potentially plasmid-borne genes of OXA-23-like or OXA-40-like β-lactamase. The presence of mobile gene element integron cassettes and/or integrases in 88% of the isolates suggests a possible mechanism of dissemination of antibiotic resistance genes. Additionally, the location of insertion sequence (IS) ISAba1 in promotor region of of the OXA-51-like, ADC-7, and ampC genes was confirmed. Multilocus sequence typing (MLST) demonstrated that all 26 CRAB isolates were either sequence type (ST)-229 or ST-2. Interestingly, ST-2 went from being the minority CRAB strain in the 2010–2011 isolates to the predominant strain in the 2015 isolates (from 32 to 90%). We show that the ST-2 strains have an enhanced ability to produce biofilms in comparison to the ST-229 strains, and this fact has potentially led to more successful colonization of the clinical environment over time. Conclusions This study provides a longitudinal genetic and phenotypic survey of two CRAB sequence types, and suggests how their differing phenotypes may interact with the selective pressures of a hospital setting effecting strain dominance over a 5-year period. Electronic supplementary material The online version of this article (10.1186/s12941-017-0248-3) contains supplementary material, which is available to authorized users.

Francisella tularensisis a highly infectious Gram-negative pathogen that replicates intracellularly within the mammalian host. One of the factors associated with virulence ofF. tularensisis the protein FupA that mediates high-affinity transport of ferrous iron across the outer membrane. Together with its paralogue FslE, a siderophore–ferric iron transporter, FupA supports survival of the pathogen in the host by providing access to the essential nutrient iron. The FupA orthologue in the attenuated live vaccine strain (LVS) is encoded by the hybrid genefupA/B, the product of an intergenic recombination event that significantly contributes to attenuation of the strain. We used55Fe transport assays with mutant strains complemented with the different paralogues to show that the FupA/B protein of LVS retains the capacity for high-affinity transport of ferrous iron, albeit less efficiently than FupA of virulent strain Schu S4.55Fe transport assays using purified siderophore and siderophore-dependent growth assays on iron-limiting agar confirmed previous findings that FupA/B also contributes to siderophore-mediated ferric iron uptake. These assays further demonstrated that the LVS FslE protein is a weaker siderophore–ferric iron transporter than the orthologue from Schu S4, and may be a result of the sequence variation between the two proteins. Our results indicate that iron-uptake mechanisms in LVS differ from those in Schu S4 and that functional differences in the outer membrane iron transporters have distinct effects on growth under iron limitation.

Additional file 2: Table S2. Primer sequences used for A. baumannii in present study.

Additional file 1: Table S1. Quality control (QC) organisms used in this study.

Additional file 3: Table S3. Antimicrobial typing of A. baumannii study isolates, showing individual isolates against commonly used drugs.

Fibrocystic Breast Disease (FBD) or Fibrocystic change (FC) affects about 60% of women at some time during their life. Although usually benign, it is often associated with pain and tenderness (mastalgia). The synthetic steroid danazol has been shown to be effective in reducing the pain associated with FBD, but the cellular and molecular mechanisms for its action have not been elucidated. We investigated the hypothesis that danazol acts by affecting energy metabolism. Effects of danazol on Mcf10A cells homeostasis, including mechanisms of oxidative phosphorylation, cytosolic calcium signaling and oxidative stress, were assessed by high-resolution respirometry and flow cytometry. In addition to fast physiological responses the associated genomic modulations were evaluated by Affimetrix microarray analysis. The alterations of mitochondria membrane potential and respiratory activity, downregulation of energy metabolism transcripts result in suppression of energy homeostasis and arrest of Mcf10A cells growth. The data obtained in this study impacts the recognition of direct control of mitochondria by cellular mechanisms associated with altered energy metabolism genes governing the breast tissue susceptibility and response to medication by danazol.

Francisella tularensis subsp. tularensis is a highly infectious bacterium causing acute disease in mammalian hosts. Mechanisms for the acquisition of iron within the iron-limiting host environment are likely to be critical for survival of this intracellular pathogen. FslE (FTT0025) and FupA (FTT0918) are paralogous proteins that are predicted to form β-barrels in the outer membrane of virulent strain Schu S4 and are unique to Francisella species. Previous studies have implicated both FupA, initially identified as a virulence factor and FslE, encoded by the siderophore biosynthetic operon, in iron acquisition. Using single and double mutants, we demonstrated that these paralogs function in concert to promote growth under iron limitation. We used a (55)Fe transport assay to demonstrate that FslE is involved in siderophore-mediated ferric iron uptake, whereas FupA facilitates high affinity ferrous iron uptake. Optimal replication within J774A.1 macrophage-like cells required at least one of these uptake systems to be functional. In a mouse model of tularemia, the ΔfupA mutant was attenuated, but the ΔfslE ΔfupA mutant was significantly more attenuated, implying that the two systems of iron acquisition function synergistically to promote virulence. These studies highlight the importance of specific iron acquisition functions, particularly that of ferrous iron, for virulence of F. tularensis in the mammalian host.

The Gram-negative pathogen Francisella tularensis secretes a siderophore to obtain essential iron by a TonB-independent mechanism. The fslABCDE locus, encoding siderophore-related functions, is conserved among different Francisella strains. In the virulent strain Schu S4, fslE is essential for siderophore utilization and for growth under conditions of iron limitation. In contrast, we found that deletion of fslE did not affect siderophore utilization by the attenuated live vaccine strain (LVS). We found that one of the fslE paralogs encoded in the LVS genome, FTL _ 0439 ( fupA/B ), was able to partially complement a Schu S4 Δ fslE mutant for siderophore utilization. We generated a deletion of fupA/B in LVS and in the LVS Δ fslE background. The Δ fupA/B mutant showed reduced growth under conditions of iron limitation. It was able to secrete but was unable to utilize siderophore. Mutation of both fupA/B and fslE resulted in a growth defect of greater severity. The Δ fupA/B mutants showed a replication defect in J774.1A cells and decreased virulence following intraperitoneal infection in mice. Complementation of the Δ fupA/B mutation in cis restored the ability to utilize siderophore and concomitantly restored virulence. Our results indicate that fupA/B plays a significant role in the siderophore-mediated iron uptake mechanism of LVS whereas fslE appears to play a secondary role. Variation in iron acquisition mechanisms may contribute to virulence differences between the strains.

Shigella species represent one of the growing numbers of antimicrobial-resistant bacteria in developing countries. Fluoroquinolone-resistant strains of Shigella dysenteriae type 1 and Shigella flexneri type 2a emerged in India during 2002 and 2003, respectively. Sixty strains of Shigella from different parts of India were analysed for antimicrobial susceptibility, the presence of the qnr plasmid, mutations in the quinolone resistance determining regions (QRDRs), fluoroquinolone accumulation, and the presence of other genes encoding resistance to various antimicrobials. Fluoroquinolone-resistant strains had mutations in gyrA and parC genes and had an active efflux system. They were also resistant to several other antimicrobials but were susceptible to azithromycin and ceftriaxone. The majority of the strains harboured genes encoding resistance to ampicillin (97 %), tetracycline (95 %), streptomycin (95 %) and chloramphenicol (94 %). PFGE analysis revealed clonality among strains of S. dysenteriae types 1 and 5, S. flexneri type 2a and Shigella boydii type 12.

We demonstrate herein the novel finding of occluded sweat ducts in healing wounds. We also show these occlusions are from biofilms because they are periodic acid Schiff positive which indicates they are polysaccharides and Congo red positive which shows they contain amyloid, which forms the infrastructure of biofilms. Further, from the skin immediately adjacent to the wounds, we have cultured staphylococci, all of which have the capability of forming biofilms as indicated by a colorimetric assay. These findings are similar to the findings in eczema, and we believe trigger the same response of the innate immune system in healing wounds, just as in eczema. The activated immune system (Toll-like receptor 2) then initiates the pathway leading to pruritus.

Aims Characterize the genetic type and resistance mechanisms of 16 carbapenem-resistant Acinetobacter baumannii (CRAB) isolates recovered between January 2010 and March 2011 from US tertiary-care hospital. Methods and Results A modified Hodge test demonstrated the presence of carbapenemases, but meropenem and ethylenediaminetetraacetic acid (EDTA) double-disc synergy tests and PCR for metallo-β-lactamase (MBL) genes were negative. The genes of ampC β-lactamase and efflux pump of adeABC and adeIJK were detected. The presence of oxacillinase (OXA)-like genes, blaOXA-51-like, blaOXA-23-like and blaOXA-40-like genes, and insertion sequence ISAba1 in promoter region of blaOXA-51-like and blaOXA-23-like genes were detected; and confirmed by RT-PCR analyses. The sequencing of blaOXA-51-like genes revealed two major alleles, blaOXA-66-like (blaOXA-82) and blaOXA-113 from 31·2 to 68·8% of isolates respectively. The blaOXA-23 and blaOXA-72 genes showed high expression and found co-harbouring blaOXA-51-like gene preceded by ISAba-1. All CRAB isolates revealed significant reduction in carO transcription, indicated downregulation of CarO porin system, a potentially independent mechanism of carbapenam resistance. Sequencing of carO gene from representative isolates showed no ISAba1 insertional inactivation. Pulsed-field gel electrophoresis revealed a clonal relationship. Conclusions CRAB exhibited diversity of mechanisms of carbapenem resistance, and clonal relationship. Significance and Impact of the Study Studies on distinct outbreaks of CRAB are alarming situation for clinicians.

Prostate cancer cells reprogram their metabolism, so that they support their elevated oxidative phosphorylation and promote a cancer friendly microenvironment. This work aimed to explore the mechanisms that cancer cells employ for fueling themselves with energy rich metabolites available in interstitial fluids. The mitochondria oxidative phosphorylation in metastatic prostate cancer DU145 cells and normal prostate epithelial PrEC cells were studied by high-resolution respirometry. An important finding was that prostate cancer cells at acidic pH 6.8 are capable of consuming exogenous succinate, while physiological pH 7.4 was not favorable for this process. Using specific inhibitors, it was demonstrated that succinate is transported in cancer cells by the mechanism of plasma membrane Na(+)-dependent dycarboxylic acid transporter NaDC3 (SLC13A3 gene). Although the level of expression of SLC13A3 was not significantly altered when maintaining cells in the medium with lower pH, the respirometric activity of cells under acidic condition was elevated in the presence of succinate. In contrast, normal prostate cells while expressing NaDC3 mRNA do not produce NaDC3 protein. The mechanism of succinate influx via NaDC3 in metastatic prostate cancer cells could yield a novel target for anti-cancer therapy and has the potential to be used for imaging-based diagnostics to detect non-glycolytic tumors.

Solute carriers are membrane proteins that play an important role in cancer homeostasis by supplying cancer cells with essential building blocks and signaling molecules. Different types of membrane transporters were shown to be overexpressed in tumors in support of tumor growth and survival. Due to high affinity interaction with anticancer drugs they can also significantly contribute to the rapid chemoresistance. There is a limited number of studies on the role of solute carriers in reprogramming of cancer metabolism and signaling, especially in metastatic prostate cancer. Our study enabled us to establish the identity of the prostate cancer solute carrier that supports uptake of succinate and possibly similar energy rich metabolites from tumor microenvironment to promote an elevated energy metabolism of cancer cells. We demonstrated that prostate metastatic DU145 cells acquire Na+-dependent dycarboxylic acid carrier SLC13A3 but normal prostate PrEC cells do not express this protein. An important finding was that only at acidic pH 6.8 prostate cancer cells are capable of consuming exogenous succinate, while physiological pH 7.4 was not favorable for this process. Importantly, succinate transported by SLC13A3 not only accelerates the oxidative phosphorylation of prostate cancer mitochondria but it is also known to stabilize onco-factor HIF-1α. The HIF-involved signaling pathways have been linked to prostate tumorigenesis and chemoresistance and therefore, targeting these pathways by inhibiting cancer specific SLC13A3 has great potential for clinical benefit. In addition, the mechanism of succinate influx via SLC13A3 transporter in metastatic prostate cancer cells could also yield a novel metabolic onco-marker and has the potential to be used for imaging-based diagnostics to detect non-glycolytic tumors. Citation Format: Aigul Zhunussova, Zhanar Irgebayeva, Bhaswati Sen, Leah Friedman, Saniya Ossikbayeva, Sultan Tuleukhanov, Ari Brooks, Richard Sensenig, Zulfiya Orynbayeva. Tumor promoting activity of SLC13A3 in metastatic prostate cells. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B07.

Antimicrobial therapy is the mainstay for the treatment of typhoid fever. In 1948, Woodward et al. successfully used chloramphenicol to treat patients who had typhoid fever (8). After this accomplishment, the first choice therapy for typhoid fever was chloramphenicol, until the 1970s when the first outbreaks of infection by antibiotic-resistant bacteria appeared (5). There has been an increase in the resistance of strains of Salmonella enterica serotype Typhi to chloramphenicol as well as to other drugs, like ampicillin and trimethoprim-sulfamethoxazole, and this emerging multiple drug resistance (MDR) is a major problem in the control of typhoid fever (6, 7). Fluoroquinolones have been proven to be effective for the treatment of typhoid fever caused by MDR strains (1). Recently, reports of patients for whom fluoroquinolone treatment has clinically failed have become the subject of worldwide attention. Due to the emergence of MDR Salmonella serotype Typhi in countries where typhoid fever is endemic, the search for alternative antibiotics for treatment is required. Expanded-spectrum cephalosporins such as cefpodoxime proxetil, ceftriaxone, and cefixime have shown promise as therapies for the treatment of pediatric typhoid (2, 3). However, only cefixime and cefpodoxime proxetil allow oral administration, while ceftriaxone is administered parenterally, for use in ambulatory patients. Also, cefpodoxime proxetil has a favorable pharmacokinetic profile, which allows twice-daily administration. A representative collection of 90 Salmonella serotype Typhi strains were analyzed in this study. These strains were isolated during the period 2003 to 2005 from a prospective surveillance conducted for typhoid fever in two urban slums in eastern Kolkata, India. Identification and characterization of organisms were carried out according to conventional procedures (9). Antimicrobial susceptibility testing was determined following the Kirby and Bauer disk diffusion method, in accordance with the Clinical and Laboratory Standards Institute (formerly National Committee for Clinical Laboratory Standards), using commercially available antimicrobial disks (Difco, Detroit, MI) (4). All the Salmonella serotype Typhi strains were uniformly susceptible to cefpodoxime, ceftriaxone, and cefixime according to the zone size criterion of the manufacturer. A comparison of ceftriaxone and cefixime zone size data, geometric mean and range, is provided in Table ​Table1.1. It appears that ceftriaxone is the best choice for the treatment of typhoid fever, but as it is a parenterally administered drug, the choice of cefpodoxime or cefixime as an orally administered agent is preferred for the pediatric population. To date, the fluoroquinolones are the agents of choice for the treatment of MDR typhoid fever. However, the role of this agent in the treatment of children is controversial because of concerns about quinolone-induced arthropathy and cartilage damage. In this setting, cefpodoxime delivers the desired characteristics of an antibiotic and may be the treatment of choice for MDR typhoid fever, particularly with children from areas with a high prevalence of MDR typhoid fever. A study from Pakistan reported about 86% efficacy for cefpodoxime in the treatment of typhoid fever. In Bangladesh, where typhoid fever is also endemic, a clinical trial showed cefpodoxime to be highly efficacious in the treatment of typhoid fever, and it was reported that the cost of cefpodoxime is less than that of cefixime. Our in vitro study shows that oral cefpodoxime provides an effective alternative for the treatment of typhoid fever, particularly for children, even in cases of multidrug-resistant Salmonella serotype Typhi, because of its excellent activity. TABLE 1. Comparison of three antimicrobial agents against Salmonella serotype Typhia

Kolkata and its suburbs in eastern India are known to be endemic for typhoid fever. The objective of this study was to determine phage types, biotypes and antimicrobial resistance patterns of Salmonella enterica serotype Typhi isolated during the period 2003-2005 from a prospective surveillance for typhoid fever in two urban slums in Kolkata.A total of 195 Salmonella enterica serotype Typhi isolated from blood cultures were phage typed, biotyped and tested for their antimicrobial susceptibility profile.Phage type E1 was the most common (60.3%) followed by phage type A among five phage types identified. Biotype I (95%) was predominant, 28 isolates were multidrug resistant (MDR) and most of the MDR strains belonged to phage type E1 and biotype I.A single phage type and biotype were prevalent among the Salmonella enterica serotype Typhi isolates studied from Kolkata, India.

Although typhoid fever is confirmed by culture of Salmonella enterica serotype Typhi, rapid and simple diagnostic serologic tests would be useful in developing countries. We examined the performance of Widal test in a community field site and compared it with Typhidot and Tubex tests for diagnosis of typhoid fever. Blood samples were collected from 6697 patients with fever for > or =3 days for microscopy, culture, and serologic testing and from randomly selected 172 consenting healthy individuals to assess the baseline Widal anti-Typhi O lipopolysaccharide antibody (anti-TO) and anti-Typhi H flagellar antibody (anti-TH) titers. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the 3 serologic tests were calculated using culture-confirmed typhoid fever cases as "true positives" and paratyphoid fever and malaria cases as "true negatives". Comparing cutoff values for the Widal test, an anti-TO titer of 1/80 was optimal with 58% sensitivity, 85% specificity, 69% PPV, and 77% NPV. Sensitivity was increased to 67% when the Widal test was done on the 5th day of illness and thereafter. The sensitivity, specificity, PPV, and NPV of Typhidot and Tubex were not better than Widal test. There is a need for more efficient rapid diagnostic test for typhoid fever especially during the acute stage of the disease. Until then, culture remains the method of choice.