Prevalent Bacterial Pathogens Research Articles

Prevalence study of acute tonsillitis among pediatrics age groups

Tonsils and adenoids are the body’s first line of defense at the oropharyngeal pathway. They “sample” bacteria and viruses that enter the body through the mouth or nose.Tonsillitis is inflammation of tonsils, a common clinical condition often encountered in Pediatrics and E.N.T. practice. The management of this condition is often empirical with the choice of antibiotics not based on any culture reports. The increasing incidence of resistance in many organisms is due to β-lactamase production and resistance transfer factors that leads to unsuccessful medical therapy which results in recurrent or chronic forms of tonsillitis. The present study was conducted to identify the prevalent bacterial pathogens and their antibiotic sensitivity that would indicate the optimum line of treatment and prevent the complications of acute tonsillitis and avoids unnecessary surgical treatment. Study Design: The clinical and laboratory (culture and sensitivity) study on acute tonsillitis was carried in the family medicine, pediatric and ENT outpatient clinic of Al-Raed Health Center in Riyadh K.S.A., The laboratory studies was carried out in the Department of Microbiology. 100 cases of acute tonsillitis were selected 58 males and 42 females aged from 4-18 years at random from the patients attending the outpatient Department of family medicine, pediatrics and ENT durng a period of one year from July 2017 to August 2018; each selected case has been studied as per the standard procedures. The chosen patients were not given antibiotics for one week prior to the study.

Comparative screening of recombinant antigen thermostability for improved leptospirosis vaccine design

Recombinant antigens exhibit targeted protectiveproperties and offer important opportunities in the development of therapeutic technologies. Biophysical and structural methods have become important tools for the rational design and engineering of improved antigen-based vaccines. Vaccines containing Leptospira immunoglobulin-like (Lig) protein-derived antigens are currently the most promising candidates for protective immunity against the globally prevalent bacterial pathogen, Leptospira interrogans; however, vaccine trials using these domains have produced inconsistent results. Here, we compare the thermostability of domains from the main immunogenic regions from major leptospiral antigens, LigA and LigB. By measuring temperature-dependent fluorescence decay of the hydrophobic core tryptophan, 17 individual Lig protein immunoglobulin-like (Ig-like) domains were shown to display a broad range of unfolding temperatures. For a majority of the domains, stability issues begin to occur at physiologically relevant temperatures. A set of chimeric Ig-like domains was used to establish the ability of transplanted domain regions to enhance thermostability. Further insights into the determinants for domain stabilization were explored with nuclear magnetic resonance dynamics and mutational analysis. The current study has yielded a set of thermostable Ig-like domain scaffolds for use in engineering antigen-based vaccines and demonstrates the importance of incorporating thermostability screening as a design parameter.

Bacteriological Investigation of S . Aureus in Urinary Tract Infection in South Port Said City

UTI is characterized by the evidence of uropathogens and pyuria and is accompanied by various clinical manifestations depending on the area of involvement. The aim of this study - was to isolate the bacterial infection to urinary tract infection in men and women at different ages and to investigate the susceptibility of bacteria implicated in urinary tract infection to different antimicrobial drugs (antibiotics).Also to determine minimum inhibitor concentration for resistant bacteria to antibiotic and molecular characterization of S. aureus associated . Materials and methods :One hundred urine specimens were received from patients admitted during January till December 2015. S. aureus isolates were confirmed by typical colonial morphology, and identified by differential tests as well as by the growth on characteristic agar, Susceptibility testing was carried out by disk diffusion method . Among the 100 isolates, 6 bacterial strain was isolated from the urine specimens of infected Patient admitted at Port-said area out-patient clinics, using agar medium and macCkonkey agar, This organism was characterized by biochemical tests and showed similarity with S. aureus . The genomic level confirmation done with 16S rDNA primer by submitting the genomic sequence to Gene Bank under acc.No-GU046545 after comparing, showed 98 % sequence similarity with S. aureus . Antibiotic susceptibility test revealed that Amikacin, Amoxicillin and Imepenem are the lowest resistant rate with percent of 100, 83 and 66%respectively and Ciprofloxacin showed the highest resistant rate with 84% . Pattern on antibiotic susceptibility test showed high resistant rate to some antibiotic that made it difficult for pregnant patients, although its frequency was low. The most prevalent Gram positive bacterial pathogen in Port-saed city was S. aureus and the most sensitive antibiotic against it is Amikacin.

Isolation and identification of prevalent bacterial pathogens from an exotic fish Tilapia zillii and Oreochromis mossambicus

Aim: Fishes are susceptible to a wide variety of bacterial pathogens which are part of the natural microflora of the environment. The aim of the present study was to isolate the pathogenic bacteria in gills, liver, gut, and skin of Tilapia zillii and Oreochromis mossambicus from the lake near Perumbakkam in Chennai. Materials and Methods: The experimental fish T. zillii and O. mossambicus were collected from large lake 2 km length which starts from Perumbakkam through Vengaivasal Chithalapakkam in Chennai. Results and Discussion: Based on the differentiation and characterization of isolates on specific culture media, human bacterial pathogen such as Escherichia coli, Staphylococcus aureus, Salmonella typhi, Pseudomonas aeruginosa, Enterococcus faecalis, and Shigella dysenteriae was isolated. In this study, the total plate count in the tissues of T. zillii ranged between 7.14 × 105 and 23.2 105 cfu/g. Similarly, in O. mossambicus, the total cell count in the tissue ranged between 6.21 × 105 and 21.16 × 105, respectively. The isolation of enteric bacteria in fish serves as indicator organisms of fecal contamination and/or water pollution. Their presences are also hazardous to humans. Conclusion: The association of pathogenic bacteria among the fishes suggests that if fish are handled or prepared improperly it could lead to food safety hazards for consumers.

Antimicrobial resistance and outcomes of community-onset bacterial bloodstream infections in patients with type 2 diabetes.

Antimicrobial resistance of bacterial pathogens in the diabetic population with infection is seldom investigated. This study evaluated the antimicrobial resistance and outcomes of community-onset bloodstream infections (CO-BSIs) in patients with diabetes. From 2007-2014, 1271 monomicrobial CO-BSIs and 178 polymicrobial CO-BSIs were identified in patients with type 2 diabetes from three teaching hospitals in Taiwan. Antimicrobial-resistant strains of the ten most prevalent bacterial pathogens in monomicrobial CO-BSIs were recorded and were defined according to individual drug resistance. The 30-day mortality rate and factors associated with outcome were analysed. Antimicrobial-resistant strains were found in 33.7% (379/1125) of monomicrobial CO-BSIs involving the 10 most prevalent pathogens. The leading pathogens in these monomicrobial CO-BSIs were Staphylococcus spp. (33.8%; 430/1271), Escherichia coli (20.9%; 266/1271) and Klebsiella spp. (9.6%; 122/1271); antimicrobial-resistant strains accounted for 61.9%, 18.4% and 10.7% of each, respectively. A higher overall 30-day mortality rate was observed for patients infected by antimicrobial-resistant strains compared with antimicrobial-susceptible strains (9.5% vs. 5.5%; P=0.011, log-rank test). A lower serum albumin level was a predictor of mortality after adjusting for antimicrobial-resistant strains and C-reactive protein level. Antimicrobial-resistant bacterial pathogens pose a serious threat to diabetic patients with CO-BSIs owing to a higher risk of mortality.

Versatile Bioconjugation Chemistries of ortho-Boronyl Aryl Ketones and Aldehydes.

Biocompatible and bioorthogonal conjugation reactions have proven to be powerful tools in biological research and medicine. While the advent of bioorthogonal conjugation chemistries greatly expands our capacity to interrogate specific biomolecules in situ, biocompatible reactions that target endogenous reactive groups have given rise to a number of covalent drugs as well as a battery of powerful research tools. Despite the impressive progress, limitations do exist with the current conjugation chemistries. For example, most known bioorthogonal conjugations suffer from slow reaction rates and imperfect bioorthogonality. On the other hand, covalent drugs often display high toxicity due to off-target labeling and immunogenicity. These limitations demand continued pursuit of conjugation chemistries with optimal characteristics for biological applications. A spate of papers appearing in recent literature report the conjugation chemistries of 2-formyl and 2-acetyl phenylboronic acids (abbreviated as 2-FPBA and 2-APBA, respectively). These simple reactants are found to undergo fast conjugation with various nucleophiles under physiological conditions, showing great promise for biological applications. The versatile reactivity of 2-FPBA and 2-APBA manifests in dynamic conjugation with endogenous nucleophiles as well as conjugation with designer nucleophiles in a bioorthogonal manner. 2-FPBA/APBA conjugates with amines in biomolecules, such as lysine side chains and aminophospholipids, in a highly dynamic manner to give iminoboronates. In contrast to typical imines, iminoboronates enjoy much improved thermodynamic stability, yet are kinetically labile for hydrolysis due to imine activation bythe boronic acid. Dynamic conjugations as such presenta novel binding mechanism analogous to hydrogen bonding and electrostatic interactions. Implementation of this covalent binding mechanism has yielded reversible covalent probes of prevalent bacterial pathogens. It has also resulted in reversible covalent inhibitors of a therapeutically important protein Mcl-1. Such covalent probes/inhibitors with 2-FPBA/APBA warheads avoid permanent modification of their biological target, potentially able to mitigate off-target labeling and immunogenicity of covalent drugs. The dynamic conjugation of 2-FPBA/APBA has been recently extended to N-terminal cysteines, which can be selectively targeted via formation of a thiazolidino boronate (TzB) complex. The dynamic TzB formation expands the toolbox for site-specific protein labeling and the development of covalent drugs. On the front of bioorthogonal conjugation, 2-FPBA/APBA has been found to conjugate with α-nucleophiles under physiologic conditions with rate constant ( k2) over 1000 M-1 s-1, which overcomes the slow kinetics problems and rekindles the interest of using the conjugation of α-nucleophiles for biological studies. With fast kinetics being a shared feature, this family of conjugation chemistries gives remarkably diverse product structures depending on the choice of nucleophile. Importantly, both dynamic and irreversible conjugations have been developed, which we believe will enable a wide array of applications in biological research. In this Account, we collectively examine this rapidly expanding family of conjugation reactions, seeking to elucidate the unifying principles that would guidefurther development of novel conjugation reactions, as well as their applications in biology.

Aspergillus fumigatus Inhibits Pseudomonas aeruginosa in Co-culture: Implications of a Mutually Antagonistic Relationship on Virulence and Inflammation in the CF Airway.

Many cystic fibrosis (CF) airway infections are considered to be polymicrobial and microbe–microbe interactions may play an important role in disease pathology. Pseudomonas aeruginosa and Aspergillus fumigatus are the most prevalent bacterial and fungal pathogens isolated from the CF airway, respectively. We have previously shown that patients co-colonized with these pathogens had comparable outcomes to those chronically colonized with P. aeruginosa. Our objective was to examine the interactions between A. fumigatus and P. aeruginosa, specifically the effects of co-colonization on biofilm formation, virulence and host pro-inflammatory responses. Our findings suggest that co-infections of A. fumigatus and P. aeruginosa in the Galleria mellonella acute infection model showed that pre-exposure of larvae to sub-lethal inocula of A. fumigatus increased the mortality caused by subsequent P. aeruginosa infection. Co-infection of human bronchial epithelial cells (CFBE41o-) with both pathogens did not enhance IL-6 and IL-8 production beyond the levels observed following single infections. In addition, both pathogens stimulated cytokine secretion via the same two mitogen-activated protein kinases (MAPKs) signaling pathways, ERK and p38. Mixed species biofilms showed overall reduced biofilm development with crystal violet staining. Quantification by species-specific qPCR revealed that both pathogens had mutually antagonistic effects on each other. A. fumigatus supernatants showed strong anti-Pseudomonal activity and gliotoxin was the main active agent. Gliotoxin resulted in varying levels of anti-biofilm activity toward other bacteria commonly found in the CF airways. Gliotoxin produced by A. fumigatus colonizing the CF airways may have a significant impact on the CF airway microbiome composition with potential clinical implications.

Antagonism Against Fish Pathogens by Cellular Components/Preparations of Bacillus coagulans (MTCC-9872) and It’s In Vitro Probiotic Characterisation

Bacterial fish pathogens are pervasive in aquaculture. Control of bacterial fish pathogen is a difficult task among aquaculture practitioners. A large number of antibiotics are used for the control of prevalent bacterial pathogens in aquaculture. This may lead to drug resistance among pathogens and further treatment will be ineffective. Here, we can use probiotic bacteria as a biocontrol agent in fish disease and it is a novel field. In this study, antimicrobial potential of the bacterium Bacillus coagulans (MTCC-9872) has been evaluated through in vitro antagonistic activity of cellular preparations/components against potent pathogens. The cellular preparations/components such as Ethyl acetate extract, whole-cell product, heat-killed whole-cell product, and filtered broth were exhibited bactericidal activity against the tested pathogens. Bactericidal activity varied among different cellular preparation/components. The tested bacterium effectively produced biofilm as significant as tested positive control in a microtitre plate and effectively adhered on to the glass slide. In addition, the bacterium was capable of producing extracellular enzymes necessary for the digestion of food materials and was capable to grow in fish mucus from Oreochromis niloticus. The bacterium tolerated bile juice secreted by the host. Moreover, intraperitoneal injection of the bacterium did not induce any pathological signs, symptoms or mortalities in Oreochromis niloticus and revealed the safety of this bacterium in the fish.

Covering the Cover

Covering the Cover

Characterization of prevalent bacterial pathogens associated with pododermatitis in table egg layers

ABSTRACT Pododermatitis has been observed in several layer flocks in Denmark during 2015. The aetiology is complex, including litter quality, nutrition and management. Bacterial pathogens associated with pododermatitis, however, have not received much attention. The aim of the present study was, therefore, to identify 106 bacterial isolates obtained from pododermatitis in table egg layers in addition to five isolates from spleen/bursa presternalis. Isolates were obtained from layers from six affected flocks. All isolates were identified by standard bacterial methods, species-specific PCRs, 16S rRNA sequencing or matrix-assisted laser desorption-ionization identification. Staphylococcus aureus and Enterococcus faecalis made up 75/111 (68%) and 15/111 (14%) of the isolates from pododermatitis, respectively; the remaining isolates represented Escherichia coli (10), Staphylococcus hyicus (5), Gallibacterium anatis (3), Trueperella pyogenes (2) and Aerococcus urinaeequi (1). All isolates of S. aureus were spa-typed. Spa-type t8646 and t002 made up 72% and 26% of the S. aureus isolates, respectively. The same types were also demonstrated from spleen/bursa presternalis. The same or closely related spa-types were found among 6/11 sepsis-affected day-old chicks included for comparison, indicating that these types of S. aureus are ubiquitous pathogens in poultry. In contrast, isolates of E. faecalis and E. coli showed major population diversity. In conclusion, the results suggest that S. aureus is a major pathogen associated with pododermatitis abscesses, which could be from a common source, whereas the diversity among the E. faecalis and E. coli populations suggests that these bacteria might originate from multiple sources.

Microbiota-Derived Metabolic Factors Reduce Campylobacteriosis in Mice

Campylobacter jejuni, a prevalent foodborne bacterial pathogen, exploits the host innate response to induce colitis. Little is known about the roles of microbiota in C jejuni-induced intestinal inflammation. We investigated interactions between microbiota and intestinal cells during C jejuni infection of mice. Germ-free C57BL/6 Il10-/- mice were colonized with conventional microbiota and infected with a single dose of C jejuni (109 colony-forming units/mouse) via gavage. Conventional microbiota were cultured under aerobic, microaerobic, or anaerobic conditions and orally transplanted into germ-free Il10-/- mice. Colon tissues were collected from mice and analyzed by histology, real-time polymerase chain reaction, and immunoblotting. Fecal microbiota and bile acids were analyzed with 16S sequencing and high-performance liquid chromatography with mass spectrometry, respectively. Introduction of conventional microbiota reduced C jejuni-induced colitis in previously germ-free Il10-/- mice, independent of fecal load of C jejuni, accompanied by reduced activation of mammalian target of rapamycin. Microbiota transplantation and 16S ribosomal DNA sequencing experiments showed that Clostridium XI, Bifidobacterium, and Lactobacillus were enriched in fecal samples from mice colonized with microbiota cultured in anaerobic conditions (which reduce colitis) compared with mice fed microbiota cultured under aerobic conditions (susceptible to colitis). Oral administration to mice of microbiota-derived secondary bile acid sodium deoxycholate, but not ursodeoxycholic acid or lithocholic acid, reduced C jejuni-induced colitis. Depletion of secondary bile acid-producing bacteria with antibiotics that kill anaerobic bacteria (clindamycin) promoted Cjejuni-induced colitis in specific pathogen-free Il10-/- mice compared with the nonspecific antibiotic nalidixic acid; colitis induction by antibiotics was associated with reduced level of luminal deoxycholate. We identified a mechanism by which the microbiota controls susceptibility to C jejuni infection in mice, via bacteria-derived secondary bile acids.

Rapid detection of ESBL, carbapenemases, MRSA and other important resistance phenotypes within 6-8 h by automated disc diffusion antibiotic susceptibility testing.

In principle, automated systems allow rapid reading of disc diffusion AST (rAST) within 6-8 h. This study analysed whether rAST can discriminate resistance phenotypes such as ESBL, carbapenemases and MRSA/methicillin-resistant Staphylococcus epidermidis from WT populations. We describe species-drug combinations that may require clinical breakpoint adaptions for early reading due to zone diameter changes during the incubation period. In total, 1852 clinical strains [Escherichia coli (n = 475), Klebsiella pneumoniae (n = 375), Enterobacter cloacae (n = 301), Staphylococcus aureus (n = 407) and S. epidermidis (n = 294)] were included in this study comprising WT populations and important resistance phenotypes, e.g. ESBL, carbapenemases and MRSA. We assessed (i) separation of resistance phenotypes and WT populations after 6, 8 and 12 h as compared with the 18 h standard, and (ii) diameter changes of WT populations and associated putative epidemiological cut-offs during the incubation period. Disc diffusion plates were automatically streaked, incubated and imaged using the WASPLabTM system. We demonstrated that important resistance phenotypes could reliably be separated from WT populations at early reading times for the most prevalent bacterial pathogens encountered in the clinical laboratory. Current AST expert rules and algorithms for identification of resistance mechanisms can readily be applied for rAST, e.g. EUCAST recommended rules for detection of ESBL, AmpC, carbapenemases and MRSA/methicillin-resistant S. epidermidis. However, several species-drug combinations may require clinical breakpoint adaptations when using rAST as the diameter, and hence the epidemiological cut-off, changes during the incubation period.

Co-colonisation with Aspergillus fumigatus and Pseudomonas aeruginosa is associated with poorer health in cystic fibrosis patients: an Irish registry analysis

BackgroundPulmonary infection is the main cause of death in cystic fibrosis (CF). Aspergillus fumigatus (AF) and Pseudomonas aeruginosa (PA) are the most prevalent fungal and bacterial pathogens isolated from the CF airway, respectively. Our aim was to determine the effect of different colonisation profiles of AF and PA on the clinical status of patients with CF.MethodsA retrospective analysis of data from the Cystic Fibrosis Registry of Ireland from 2013 was performed to determine the effect of intermittent and persistent colonisation with AF or PA or co-colonisation with both microorganisms on clinical outcome measures in patients with CF. Key outcomes measured included forced expiratory volume in one second (FEV1), number of hospitalisations, respiratory exacerbations and antimicrobials prescribed, and complications of CF, including CF related diabetes (CFRD) and allergic bronchopulmonary aspergillosis (ABPA).ResultsThe prevalence of AF and PA colonisation were 11% (5% persistent, 6% intermittent) and 31% (19% persistent, 12% intermittent) in the Irish CF population, respectively. Co-colonisation with both pathogens was associated with a 13.8% reduction in FEV1 (p = 0.016), higher levels of exacerbations (p = 0.042), hospitalisations (p = 0.023) and antimicrobial usage (p = 0.014) compared to non-colonised patients and these clinical outcomes were comparable to those persistently colonised with PA. Intermittent and persistent AF colonisation were not associated with poorer clinical outcomes or ABPA. Patients with persistent PA had a higher prevalence of CFRD diagnosis (p = 0.012).ConclusionsCF patients co-colonised with AF and PA had poor clinical outcomes comparable to patients persistently colonised with PA, emphasising the clinical significance of co-colonisation with these microorganisms.

Enteric pathogens and factors associated with acute bloody diarrhoea, Kenya.

BackgroundShigellosis is the major cause of bloody diarrhoea worldwide and is endemic in most developing countries. In Kenya, bloody diarrhoea is reported weekly as part of priority diseases under Integrated Disease Surveillance and Response System (IDSR) in the Ministry of Health.MethodsWe conducted a case control study with 805 participants (284 cases and 521 controls) between January and December 2012 in Kilifi and Nairobi Counties. Kilifi County is largely a rural population whereas Nairobi County is largely urban. A case was defined as a person of any age who presented to outpatient clinic with acute diarrhoea with visible blood in the stool in six selected health facilities in the two counties within the study period. A control was defined as a healthy person of similar age group and sex with the case and lived in the neighbourhood of the case.ResultsThe main presenting clinical features for bloody diarrhoea cases were; abdominal pain (69 %), mucous in stool (61 %), abdominal discomfort (54 %) and anorexia (50 %). Pathogen isolation rate was 40.5 % with bacterial and protozoal pathogens accounting for 28.2 % and 12.3 % respectively. Shigella was the most prevalent bacterial pathogen isolated in 23.6 % of the cases while Entamoeba histolytica was the most prevalent protozoal pathogen isolated in 10.2 % of the cases. On binary logistic regression, three variables were found to be independently and significantly associated with acute bloody diarrhoea at 5 % significance level; storage of drinking water separate from water for other use (OR = 0.41, 95 % CI 0.20–0.87, p = 0.021), washing hands after last defecation (OR = 0.24, 95 % CI 0.08–.076, p = 0.015) and presence of coliforms in main source water (OR = 2.56, CI 1.21–5.4, p = 0.014). Rainfall and temperature had strong positive correlation with bloody diarrhoea.ConclusionThe main etiologic agents for bloody diarrhoea were Shigella and E. histolytica. Good personal hygiene practices such as washing hands after defecation and storing drinking water separate from water for other use were found to be the key protective factors for the disease while presence of coliform in main water source was found to be a risk factor. Implementation of water, sanitation and hygiene (WASH) interventions is therefore key in prevention and control of bloody diarrhoea.

Stereoselective Synthesis of 1-Tuberculosinyl Adenosine; a Virulence Factor of Mycobacterium tuberculosis.

Despite its status as one of the world's most prevalent and deadly bacterial pathogens, Mycobacterium tuberculosis (Mtb) infection is not routinely diagnosed by rapid and highly reliable tests. A program to discover Mtb-specific biomarkers recently identified two natural compounds, 1-tuberculosinyl adenosine (1-TbAd) and N(6)-tuberculosinyl adenosine (N(6)-TbAd). Based on their association with virulence, the lack of similar compounds in nature, the presence of multiple stereocenters, and the need for abundant products to develop diagnostic tests, synthesis of these compounds was considered to be of high value but challenging. Here, a multigram-scale stereoselective synthesis of 1-TbAd and N(6)-TbAd is described. As a key-step, a chiral auxiliary-mediated Diels-Alder cycloaddition was developed, introducing the three stereocenters with a high exo endo ratio (10:1) and excellent enantioselectivity (>98% ee). This constitutes the first entry into the stereoselective synthesis of diterpenes with the halimane skeleton. Computational studies explain the observed stereochemical outcome.

Synthesis and antimicrobial effects of colloidal gold nanoparticles against prevalent waterborne bacterial pathogens

AbstractGold is being used therapeutically since 2500 BC in Chinese medical history. Red colloidal gold is still used in the Indian Ayurvedic medicine for rejuvenation and revitalization during old age under the name of Swarna Bhasma. The present research describes a more reliable method for assaying growth inhibition of some waterborne bacterial pathogens by gold nanoparticles. The gold nanoparticles were synthesized by chemical method using auric chloride as a precursor salt and sodium citrate as a reducing as well as stabilizing agent. Characterization of Au NPs was performed using UV–Vis, X-ray diffraction (XRD) and TEM (transmission electron microscope). Further, these nanoparticles were tested against four well-explored waterborne bacterial pathogens viz., E. coli, V. cholerae, S. typhimurium, S. dysenteriae, using globally accepted broth microdilution method recommended by CLSI, which exhibited a good antibacterial potency demonstrated in the form of IC50 and MIC. Subsequently, a novel phylogenetic...

Detection of Zoonotic Enteropathogens in Children and Domestic Animals in a Semirural Community in Ecuador.

Animals are important reservoirs of zoonotic enteropathogens, and transmission to humans occurs more frequently in low- and middle-income countries (LMICs), where small-scale livestock production is common. In this study, we investigated the presence of zoonotic enteropathogens in stool samples from 64 asymptomatic children and 203 domestic animals of 62 households in a semirural community in Ecuador between June and August 2014. Multilocus sequence typing (MLST) was used to assess zoonotic transmission of Campylobacter jejuni and atypical enteropathogenic Escherichia coli (aEPEC), which were the most prevalent bacterial pathogens in children and domestic animals (30.7% and 10.5%, respectively). Four sequence types (STs) of C. jejuni and four STs of aEPEC were identical between children and domestic animals. The apparent sources of human infection were chickens, dogs, guinea pigs, and rabbits for C. jejuni and pigs, dogs, and chickens for aEPEC. Other pathogens detected in children and domestic animals were Giardia lamblia (13.1%), Cryptosporidium parvum (1.1%), and Shiga toxin-producing E. coli (STEC) (2.6%). Salmonella enterica was detected in 5 dogs and Yersinia enterocolitica was identified in 1 pig. Even though we identified 7 enteric pathogens in children, we encountered evidence of active transmission between domestic animals and humans only for C. jejuni and aEPEC. We also found evidence that C. jejuni strains from chickens were more likely to be transmitted to humans than those coming from other domestic animals. Our findings demonstrate the complex nature of enteropathogen transmission between domestic animals and humans and stress the need for further studies. We found evidence that Campylobacter jejuni, Giardia, and aEPEC organisms were the most common zoonotic enteropathogens in children and domestic animals in a region close to Quito, the capital of Ecuador. Genetic analysis of the isolates suggests transmission of some genotypes of C. jejuni and aEPEC from domestic animals to humans in this region. We also found that the genotypes associated with C. jejuni from chickens were present more often in children than were those from other domestic animals. The potential environmental factors associated with transmission of these pathogens to humans then are discussed.

Modelling the Impact and Cost-Effectiveness of Biomarker Tests as Compared with Pathogen-Specific Diagnostics in the Management of Undifferentiated Fever in Remote Tropical Settings.

BackgroundMalaria accounts for a small fraction of febrile cases in increasingly large areas of the malaria endemic world. Point-of-care tests to improve the management of non-malarial fevers appropriate for primary care are few, consisting of either diagnostic tests for specific pathogens or testing for biomarkers of host response that indicate whether antibiotics might be required. The impact and cost-effectiveness of these approaches are relatively unexplored and methods to do so are not well-developed.MethodsWe model the ability of dengue and scrub typhus rapid tests to inform antibiotic treatment, as compared with testing for elevated C-Reactive Protein (CRP), a biomarker of host-inflammation. Using data on causes of fever in rural Laos, we estimate the proportion of outpatients that would be correctly classified as requiring an antibiotic and the likely cost-effectiveness of the approaches.ResultsUse of either pathogen-specific test slightly increased the proportion of patients correctly classified as requiring antibiotics. CRP testing was consistently superior to the pathogen-specific tests, despite heterogeneity in causes of fever. All testing strategies are likely to result in higher average costs, but only the scrub typhus and CRP tests are likely to be cost-effective when considering direct health benefits, with median cost per disability adjusted life year averted of approximately $48 USD and $94 USD, respectively.ConclusionsTesting for viral infections is unlikely to be cost-effective when considering only direct health benefits to patients. Testing for prevalent bacterial pathogens can be cost-effective, having the benefit of informing not only whether treatment is required, but also as to the most appropriate antibiotic; this advantage, however, varies widely in response to heterogeneity in causes of fever. Testing for biomarkers of host inflammation is likely to be consistently cost-effective despite high heterogeneity, and can also offer substantial reductions in over-use of antimicrobials in viral infections.

Whole genome analysis of an MDR Beijing/W strain of Mycobacterium tuberculosis with large genomic deletions associated with resistance to isoniazid

Mycobacterium tuberculosis (M.tb) is one of the most prevalent bacterial pathogens in the world. With geographical wide spread and hypervirulence, Beijing/W family is the most successful M.tb lineage. China is a country of high tuberculosis (TB) and high multiple drug-resistant TB (MDR-TB) burden, and the Beijing/W family strains take the largest share of MDR strains. To study the genetic basis of Beijing/W family strains' virulence and drug resistance, we performed the whole genome sequencing of M.tb strain W146, a clinical Beijing/W genotype MDR isolated from Wuxi, Jiangsu province, China. Compared with genome sequence of M.tb strain H37Rv, we found that strain W146 lacks three large fragments and the missing of furA-katG operon confers isoniazid resistance. Besides the missing of furA-katG operon, strain W146 harbored almost all known drug resistance-associated mutations. Comparison analysis of single nucleotide polymorphisms (SNPs) and indels between strain W146 and Beijing/W genotype strains and non-Beijing/W genotype strains revealed that strain W146 possessed some unique mutations, which may be related to drug resistance, transmission and pathogenicity. These findings will help to understand the large sequence polymorphisms (LSPs) and the transmission and drug resistance related genetic characteristics of the Beijing/W genotype of M.tb.

SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs.

BackgroundCampylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5’-GmATC-3’ motifs. This indicates significant differences in DNA methylation between both microbial species.The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C. jejuni and Helicobacter pylori.ResultsUsing one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %.ConclusionsOnly five dominant methylation motifs have been identified in C. jejuni, which have been associated with known RM-systems. C. coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP, methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP RM-system has been described for H. pylori. The remaining methylation motifs are specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor in H. pylori.The results of this study give us new insights into epigenetics of Campylobacteraceae and provide the groundwork to resolve the function of RM-systems in C. coli.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2317-3) contains supplementary material, which is available to authorized users.