Gender differences in non-cystic fibrosis bronchiectasis severity and bacterial load: the potential role of hormones.

Non cystic-fibrosis bronchiectasis (NCFB) is a complex chronic respiratory disease, characterised by excessive sputum production and abnormal permanent dilation of bronchi. Mucus accumulation leads to recurrent bacterial infections and increased bacterial load, causing vicious cycles of structural damage and decreased lung function. Respiratory physiotherapy management of NCFB includes airway clearance techniques and use of nebulised, hypertonic saline. Despite advances in treatment, a consistent relationship has been observed between gender and disease occurrence, with a higher prevalence amongst females. Furthermore, NCFB presents most aggressively amongst post-menopausal females, a group likely exposed to higher levels of progesterone (P4) over a longer period of time. The effects of gender-specific hormones on bacterial load and physiotherapy management of people living with NCFB remain unknown. The aim of this narrative review was to discuss the potential influence of gender specific hormones on NCFB disease progression and influence on physiotherapy, medical management and future research. SCOPUS and PUBMED electronic databases were used to conduct searches for relevant studies using specific inclusion and exclusion criteria. Secondary inclusion of relevant literature was obtained from primary paper references. Previous literature suggests that P4 may impair Cilia Beat Frequency (CBF) in airway epithelium. Reduction in CBF may further reduce ability to expectorate amongst individuals with NCFB, increasing bacterial load and likelihood of exacerbations, negatively impacting on disease progression. Furthermore, coadministration of Estrogen has been suggested to offer opposing effects to that of P4 only. These findings question whether hormonal levels may be monitored, controlled and optimised within management and treatment of females with NCFB to improve airway clearance, reduce exacerbations and improve quality of life. Larger scale, long-term trials are required to further explore the effects of gender specific hormones on NCFB and the viability of treatment with hormone replacement therapy.The reviews of this paper are available via the supplemental material section.

Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children.

BACKGROUND: Exposure to particulate matter has been shown to increase the adhesion of bacteria to human airway epithelial cells. However, the impact of traffic-related air pollution (TRAP) on the respiratory microbiome is unknown. METHODS: Forty children were recruited through the Cincinnati Childhood Allergy and Air Pollution Study, a longitudinal cohort followed from birth through early adolescence. Saliva and induced sputum were collected at age 14 years. Exposure to TRAP was characterized from birth through the time of sample collection using a previously validated land-use regression model. Sequencing of the bacterial 16S and ITS fungal rRNA genes was performed on sputum and saliva samples. The relative abundance of bacterial taxa and diversity indices were compared in children with exposure to high and low TRAP. We also used multiple linear regression to assess the effect of TRAP exposure, gender, asthma status, and socioeconomic status on the alpha diversity of bacteria in sputum. RESULTS: We observed higher bacterial alpha diversity indices in sputum than in saliva. The diversity indices for bacteria were greater in the high TRAP exposure group than the low exposure group. These differences remained after adjusting for asthma status, gender, and mother's education. No differences were observed in the fungal microbiome between TRAP exposure groups. CONCLUSION: Our findings indicate that exposure to TRAP in early childhood and adolescence may be associated with greater bacterial diversity in the lower respiratory tract. Asthma status does not appear to confound the observed differences in diversity. These results demonstrate that there may be a TRAP-exposure related change in the lower respiratory microbiota that is independent of asthma status.

Bacterial load slopes represent biomarkers of tuberculosis therapy success, failure, and relapse.

There is an urgent need to discover biomarkers that are predictive of long-term TB treatment outcomes, since treatment is expense and prolonged to document relapse. We used mathematical modeling and machine learning to characterize a predictive biomarker for TB treatment outcomes. We computed bacterial kill rates, γf for fast- and γs for slow/non-replicating bacteria, using patient sputum data to determine treatment duration by computing time-to-extinction of all bacterial subpopulations. We then derived a γs-slope-based rule using first 8 weeks sputum data, that demonstrated a sensitivity of 92% and a specificity of 89% at predicting relapse-free cure for 2, 3, 4, and 6 months TB regimens. In comparison, current methods (two-month sputum culture conversion and the Extended-EBA) methods performed poorly, with sensitivities less than 34%. These biomarkers will accelerate evaluation of novel TB regimens, aid better clinical trial designs and will allow personalization of therapy duration in routine treatment programs.

Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application.

Populations of genetically identical bacteria are phenotypically heterogeneous, giving rise to population functionalities that would not be possible in homogeneous populations. For instance, a proportion of non-dividing bacteria could persist through antibiotic challenges and secure population survival. This heterogeneity can be studied in complex environmental or clinical samples by spreading the bacteria on agar plates and monitoring time to growth resumption in order to infer their metabolic state distribution. We present ColTapp, the Colony Time-lapse application for bacterial colony growth quantification. Its intuitive graphical user interface allows users to analyze time-lapse images of agar plates to monitor size, color and morphology of colonies. Additionally, images at isolated timepoints can be used to estimate lag time. Using ColTapp, we analyze a dataset of Staphylococcus aureus time-lapse images including populations with heterogeneous lag time. Colonies on dense plates reach saturation early, leading to overestimation of lag time from isolated images. We show that this bias can be corrected by taking into account the area available to each colony on the plate. We envision that in clinical settings, improved analysis of colony growth dynamics may help treatment decisions oriented towards personalized antibiotic therapies.

Investigating alternative materials to EPDM for automatic taps in the context of Pseudomonas aeruginosa and biofilm control.

BACKGROUND: Automatic taps use solenoid valves (SVs) which incorporate a rubber (typically EPDM) diaphragm to control water flow. Contaminated SVs can be reservoirs of opportunistic pathogens such as Pseudomonas aeruginosa; an important cause of healthcare-associated infection. AIMS: To investigate the attachment and biofilm formation of P. aeruginosa on EPDM and relevant alternative rubbers to assess the impact on water hygiene in a laboratory model. METHODS: Biofilm formation on EPDM, silicone and nitrile rubber coupons was investigated using a CDC biofilm reactor. SVs incorporating EPDM or nitrile rubber diaphragms were installed on to an experimental water distribution system (EWDS) and inoculated with P. aeruginosa. P. aeruginosa water levels were monitored for 12-weeks. SVs incorporating diaphragms (EPDM, silicone or silver ion-impregnated silicone rubber), pre-colonized with P. aeruginosa, were installed and the effect of flushing as a control measure was investigated. The concentration of P. aeruginosa in the water was assessed by culture and biofilm assessed by culture and microscopy. FINDINGS: Bacterial attachment was significantly higher on nitrile (6.2 × 105 cfu/coupon) and silicone (5.4 × 105 cfu/coupon) rubber than on EPDM (2.9 ×105 cfu/coupon) (P<0.05, N = 17). Results obtained in vitro did not translate to the EWDS where, after 12-weeks in situ, there was no significant difference in P. aeruginosa water levels or biofilm levels. Flushing caused a superficial reduction in bacterial counts after <5 min of stagnation. CONCLUSION: This study did not provide evidence to support replacement of EPDM with (currently available) alternative rubbers and indicated the first sample of water dispensed from a tap should be avoided for use in healthcare settings.

Gender-neutral bathroom surfaces recolonized by microbes more quickly than single-gender bathrooms.

As humans become increasingly urban and spend more time inside the built environment, there will be increased interactions between humans and shared public surface microbiomes. Recent cultural changes in the United States have led to increased numbers of gender-neutral bathrooms. Given that bathroom surfaces are frequently sanitized, we used this increased availability of gender-neutral bathrooms to examine how single-gender or gender-neutral surfaces are recolonized with microbes. Given that male and female microbiomes vary, we hypothesized that rates of recolonization would differ between male, female and gender-neutral bathroom surfaces. We collected swabs from common hand-contacted surfaces in bathrooms and cultured microbes on selective and rich media to determine microbial abundance after cleaning. Recolonization was dominated by Gram-positive bacteria and was slowest on male, intermediate on female and fastest on gender-neutral surfaces. These results imply that gender-neutral surfaces approach normal climax microbial communities more quickly than single-gender bathrooms. SIGNIFICANCE OF IMPACT OF THE STUDY: Humans now spend substantial amount of time within the built environment, and as a consequence the human microbiome interacts frequently with indoor surfaces. Social changes are making gender-neutral public bathrooms more common, so it is important to study how humans and microbiomes interact with these bathroom surfaces. We found that the gender-neutral bathroom surfaces recolonize more quickly than single-gender, which suggests that there are more potential human-surface microbiome connections in these public spaces. These results will potentially add a new layer to our understanding of the interactions of humans, our microbiomes and how we design our built environment.

Intravesical Antibiotic Administration in the Treatment of Recurrent Urinary Tract Infections: Promising Results From a Case Series.

OBJECTIVE: Intravesical antibiotic administration for the treatment of recurrent urinary tract infections (UTIs) provides targeted therapy that may be a useful alternative to oral antibiotics. The objective of the study was to assess the rate of UTIs before and after intravesical antibiotic instillations in community-dwelling postmenopausal women with recurrent UTIs. METHODS: Patients with recurrent UTI who underwent antibiotic bladder instillations were included. Instillation was performed in the office by trained nursing staff using either gentamycin or tobramycin. Every instillation was preceded by bladder irrigation with sterile water. Retrospective chart review was performed to compare rates of UTIs for 6 months before and after intervention. Descriptive and nonparametric statistics were used for data analysis. RESULTS: Twelve patients were evaluated. The average rate of UTIs decreased from a median of 2.5 to 1.5 infections (P = 0.025) after intravesical instillations. The number of pathogen types decreased from a median of 2.5 to 1.5 after therapy (P = 0.025). There was a reduction in bacterial antibiotic resistance after completion of instillations, with an estimated median difference of -5.250 (P = 0.065). There were no adverse effects reported during instillations. CONCLUSIONS: Intravesical instillations offer a promising therapy for the treatment of recurrent UTIs in postmenopausal women who failed oral antibiotic therapy. Future prospective studies are needed to further elucidate the clinical utility and long-term benefits of antibiotic instillations.

Optimizing Contact Precautions to Curb the Spread of Antibiotic-resistant Bacteria in Hospitals: A Multicenter Cohort Study to Identify Patient Characteristics and Healthcare Personnel Interactions Associated With Transmission of Methicillin-resistant Staphylococcus aureus.

BACKGROUND: Healthcare personnel (HCP) acquire antibiotic-resistant bacteria on their gloves and gowns when caring for intensive care unit (ICU) patients. Yet, contact precautions for patients with methicillin-resistant Staphylococcus aureus (MRSA) remains controversial despite existing guidelines. We sought to understand which patients are more likely to transfer MRSA to HCP and to identify which HCP interactions are more likely to lead to glove or gown contamination. METHODS: This was a prospective, multicenter cohort study of cultured HCP gloves and gowns for MRSA. Samples were obtained from patients' anterior nares, perianal area, and skin of the chest and arm to assess bacterial burden. RESULTS: Among 402 MRSA-colonized patients with 3982 interactions, we found that HCP gloves and gowns were contaminated with MRSA 14.3% and 5.9% of the time, respectively. Contamination of either gloves or gowns occurred in 16.2% of interactions. Contamination was highest among occupational/physical therapists (odds ratio [OR], 6.96; 95% confidence interval [CI], 3.51, 13.79), respiratory therapists (OR, 5.34; 95% CI, 3.04, 9.39), and when any HCP touched the patient (OR, 2.59; 95% CI, 1.04, 6.51). Touching the endotracheal tube (OR, 1.75; 95% CI, 1.38, 2.19), bedding (OR, 1.43; 95% CI, 1.20, 1.70), and bathing (OR, 1.32; 95% CI, 1.01, 1.75) increased the odds of contamination. We found an association between increasing bacterial burden on the patient and HCP glove or gown contamination. CONCLUSIONS: Gloves and gowns are frequently contaminated with MRSA in the ICU. Hospitals may consider using fewer precautions for low-risk interactions and more for high-risk interactions and personnel.

The Microflora of Chronic Diabetic Foot Ulcers Based on Culture and Molecular Examination: A Descriptive Study

Infection of chronic diabetic foot ulcers (DFUs) is a major concern in patients with diabetes mellitus. Purpose: This prospective, descriptive study was conducted to evaluate clinical wound parameters and to determine the aerobic and anaerobic microflora of DFUs with 1 or more clinical signs of infection using culture and molecular methods. Methods: Patients with a DFU and clinical signs of infection receiving care at a tertiary care hospital in Varanasi, India, were consecutively enrolled. Patient and wound characteristics were assessed, and the cultures obtained were analyzed quantitatively to detect aerobes/facultative anaerobes and by polymerase chain reaction for common anaerobes. If no organisms were found using these methods, sequence analysis of bacterial 16S ribosomal RNA (16SrRNA) was used. Clinical, demographic, and microbial flora variables were compared using the chi-squared test, and predictors of culture results were ascertained using multiple logistic regressions. Results: Forty (40) patients participated. Of those, 30 (75%) had positive culture results with a total of 64 isolates (2.13 isolates/ulcer). The ratio of aerobes to anaerobes was 1.24:1 (35/29); Peptococcus spp was the most frequent isolate (15, 23.4%). Proteobacteria and Firmicutes were detected by 16SrRNA in 6 of the 10 samples (60%), their presence not detected by other methods. Ulcer size <11.84 cm2 (OR: 4.71; 95% CI: 0.93-23.68) and ulcer on the dorsum of the foot (OR: 0.92; 95% CI: 0.05-16.42) were significantly associated (P <.05) with monomicrobial microflora. Conclusion: Gram-negative aerobic/facultative anaerobes predominated in the 30 DFUs that exhibited clinical signs of infection. Further experimental studies are required to understand the diverse microorganisms present in DFUs and their potential role in wound infections.

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.

Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects ("bottle effect") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called "bottle effect," which is well known to occur during enclosure experiments.

Flagellin attenuates experimental sepsis in a macrophage-dependent manner.

BACKGROUND: Sepsis is the leading cause of death among critically ill patients, and no specific therapeutic agent is currently approved for the treatment of sepsis. METHODS: We assessed the effects of flagellin administration on survival, bacterial burden, and tissue injury after sepsis. In addition, we examined the effects on phagocytosis and bacterial killing in monocytes/macrophages. RESULTS: Therapeutic administration of flagellin increased bacterial clearance, decreased organ inflammation and injury, and reduced immune cell apoptosis after experimental sepsis, in a Toll-like receptor 5 (TLR5)-dependent manner. Macrophages, but not neutrophils, mediated the beneficial effects of flagellin on experimental sepsis, and flagellin induced macrophage polarization into M1 in septic mice. Flagellin treatment could directly enhance phagocytosis and bacterial killing of macrophages, but not neutrophils. Subsequent studies demonstrated that flagellin could promote phagosome formation and increase reactive oxygen species (ROS) levels in macrophages. Finally, we found that the expression of TLR5 was significantly elevated on the surface of circulating monocytes, but not neutrophils, from patients with sepsis. Higher expression levels of TLR5 on monocytes were associated with increased mortality, documented bacteremia, and higher Sequential Organ Failure Assessment scores of the septic patients. Moreover, flagellin treatment rescued the impaired phagocytosis and bacterial killing ability of monocytes/macrophages from patients who died of sepsis. CONCLUSIONS: These novel findings not only established the potential value of application of flagellin as an immunoadjuvant in treating sepsis, but also provided new insights into targeted therapeutic strategy on the basis of monocyte TLR5 expression in septic patients.

Food safety on board tankers. Results of analysis from 'Healthy Ship' project.

BACKGROUND: Microbiological monitoring of surfaces used for food preparation, as required by the Hazard Analysis and Critical Control Points (HACCP) plan, is important in risky conditions as those observed in the kitchens of ships. Limits to introduce a classification of risk levels and methods to adopt in conditions as those occurring in tankers have not been investigated. This paper presents the results of the "Healthy Ship" project on HACCP monitoring of surfaces used in food preparation on Italian flag tankers. MATERIALS AND METHODS: Microbiological monitoring was carried out on 19 tankers between 2013 and 2017. Food handlers were also trained on board ship according to HACCP standards. Contact plates (ISO 18593:2004 compliant) were used to determine the colonies and bacterial charge according to the Wirtanen and Salo's method. RESULTS: A total of 1074 samples, 108 before the first course, 168 after the first course, 390 during the period of refresher (2015-2016), and 408 after the refresher training, were obtained from the three main kitchen surfaces: the worktop, cutting board, and kitchen sink. A good level of hygiene was observed in 56.9% of all samples, 0.1% were classified as adequate, and the remaining 43% as poor. The highest contamination was observed on the cutting board and kitchen sink and involved the total aerobic count. The only surface with inadequate levels of hygiene was the worktop. A reduction of contaminated samples was noted after training. CONCLUSIONS: Our results suggest that continuous training should be provided for personnel responsible for handling foodstuffs on board ships.

Microbiological colonization of healthcare workers' mobile phones in a tertiary-level Italian intensive care unit.

BACKGROUND: Careful hand hygiene of healthcare workers is recommended to reduce transmission of pathogenic microorganisms to patients. Mobile phones are commonly used during work shifts and may act as vehicles of pathogens. OBJECTIVE: To assess the colonizsation rate of intensive care unit healthcare workers' mobile phones before and after work shifts. METHODS: Prospective observational study conducted in an academic, tertiary-level intensive care unit. Healthcare workers (including doctors, nurses and healthcare assistants) had their mobile phones sampled for microbiology before and after work shifts. Samples were taken with a swab in a standardizsed modality. RESULTS: Fifty healthcare workers participated in the study (91% of the department staff). One hundred swabs were taken from 50 mobile phones. Forty-three healthcare workers (86%) reported a habitual use of their phones during the work shift. All phones (100%) were positive for bacteria. The most frequently isolated bacteria were Coagulase Negative Staphylococci, Bacillus sp. and Methicillin-resistant Staphylococcus aureus (97%, 56%, 17%, respectively). No patient admitted to the intensive care unit during the study period was positive for bacteria found on healthcare workers' mobile phones. No difference in bacteria types and burden was found between the beginning and the end of work shifts. CONCLUSION: Healthcare workers' mobile phones are colonized even before the work shift and irrespective of the patients' microbiological flora.

Microbial contamination of moose (Alces alces) and white-tailed deer (Odocoileus virginianus) carcasses harvested by hunters.

Hunting is currently a very popular activity, and interest in game meat is increasing. However, only limited research is available on the bacterial quality and safety of moose (Alces alces) and white-tailed deer (Odocoileus virginianus) harvested by hunters. Poor hunting hygiene can spread bacteria onto the carcasses, and inadequate chilling of the carcasses may increase the bacterial load on the carcass surface. We studied the bacterial contamination level on carcasses of 100 moose and 100 white-tailed deer shot in southern Finland. Hunters eviscerated carcasses in the field and skinned them in small slaughter facilities. During the sampling, same person visited 25 facilities located in 12 municipalities of four provinces. Moose carcasses had mean mesophilic aerobic bacteria (MAB), Enterobacteriaceae (EB) and Escherichia coli (EC) values of 4.2, 2.6 and 1.2 log10 cfu/cm2, respectively, while deer carcass values were 4.5, 1.5 and 0.7 log10 cfu/cm2, respectively. Moose carcasses were significantly more contaminated with EB and EC than deer carcasses. High bacterial counts (MAB>5.0 log10 cfu/cm2 and EB > 2.5 log10 cfu/cm2) on the carcasses were associated with the smallest facilities having only one room. The outdoor temperature and days between hunting and sampling affected the bacterial counts. High EB counts on the carcasses indicated a gut hit. Male gender was significantly more contaminated by EC and meat-borne pathogenic bacteria: Campylobacter spp., Salmonella spp., enteropathogenic Yersinia spp., stx-harbouring EC (STEC) and Listeria monocytogenes. STEC (28/200) and L. monocytogenes (20/200) were the most commonly detected bacteria by PCR. L. monocytogenes isolates of different sequence types (ST7, 18, 29, 37, 249, 412, 451 and 611) belonged to serotypes 1/2a (seven isolates) and 4b (three isolates). The virulence gene ail was detected in four Yersinia enterocolitica biotype 1A isolates and one Yersinia kristensenii isolate. The bacterial counts on the moose and deer carcasses varied highly, and more attention should be paid to hunting hygiene and training of hunters. Game meat may be a source of meat-borne pathogens, and close attention should therefore be paid when handling and preparing game.

Effect of Polyhexamethylene Biguanide Solution on Bacterial Load and Biofilm in Venous Leg Ulcers: A Randomized Controlled Trial.

PURPOSE: The purpose of this study was to investigate the effect of polyhexamethylene biguanide (PHMB) solution as a wound cleanser on bacterial load and bacterial biofilm in venous leg ulcers. DESIGN: Randomized controlled trial. SUBJECTS AND SETTING: The target population was adults attending the dermatology outpatient clinic of the Clinical Hospital of the Federal University of Minas Gerais, Brazil. The sample comprised 44 patients with venous leg ulcers recruited over a 6-month period. METHODS: Participants were divided into 2 groups: the intervention group had their wounds cleansed with PHMB, and the control group had their wound cleansed with a 0.9% saline solution. Tissue fragments of the wounds were collected for bacteriological analysis; transmission electron microscopy was used to identify the presence of biofilm. RESULTS: The bacterial load was reduced in both groups compared to baseline values; no significant difference was found when groups were compared. Correlation analysis between wound duration (months), wound area (cm²), necrosis (%), variables, and bacterial count (colony forming units [CFUs]/g) after cleansing showed a significant relationship between area of the wound and CFUs/g (P = .0070, r = 0.51). Transmission electron microscopy revealed the presence of bacterial biofilm in the wounds after cleansing with both solutions. CONCLUSIONS: The results of this study indicate that both PHMB and saline solution are effective in reducing the bacterial load in venous leg ulcers. However, bacterial biofilm was present after cleansing with both solutions. These findings provide important evidence regarding effectiveness of 2 common wound cleansers on bacterial presence in wounds.

Bacterial Load and Molecular Markers Associated With Early-onset Group B Streptococcus: A Systematic Review and Meta-analysis.

BACKGROUND: The natural history of neonatal group B Streptococcus (GBS) is poorly understood. Little is known about the bacterial factors influencing the transmission of GBS from mother to neonate, or the development of invasive early-onset GBS disease (EOGBS) in colonized neonates. We reviewed whether bacterial load and molecular markers are associated with GBS vertical transmission and progression to EOGBS. METHODS: We searched Medline, Embase, Cochrane and Web of Science from inception to October 10, 2016, for observational studies in English. We also hand-searched reference lists of relevant publications and experts cross-checked included studies. Two reviewers independently screened studies, extracted data and appraised the quality of included studies using the Quality in Prognosis Studies tool. We conducted random-effects meta-analyses where possible and narratively synthesized the evidence in text and tables. RESULTS: Seventeen studies were included from 1107 records retrieved from electronic databases and publication references. Meta-analyses of 3 studies showed that neonates colonized by serotype III had a higher risk of developing EOGBS than serotype Ia (pooled risk ratio: 1.51, 95% confidence interval: 1.12-2.03) and serotype II (risk ratio: 1.95, 95% confidence interval: 1.10-3.45). Eleven studies showed that in heavily colonized mothers, 2-3 times more neonates were colonized, and in heavily colonized neonates, up to 15 times more neonates had EOGBS, compared with light colonization. Most evidence was published before 2000 and was at risk of bias. CONCLUSIONS: Acknowledging the difficulty of natural history studies, well-controlled studies are needed to assess the predictive value of pathogen subtype and heavy load; they may be useful for better-targeted prevention.

Development of a biosensor protein bullet as a fluorescent method for fast detection of Escherichia coli in drinking water.

Drinking water can be exposed to different biological contaminants from the source, through the pipelines, until reaching the final consumer or industry. Some of these are pathogenic bacteria and viruses which may cause important gastrointestinal or systemic diseases. The microbiological quality of drinking water relies mainly in monitoring three indicator bacteria of faecal origin, Escherichia coli, Enterococcus faecalis and Clostridium perfringens, which serve as early sentinels of potential health hazards for the population. Here we describe the analysis of three chimeric fluorescent protein bullets as biosensor candidates for fast detection of E. coli in drinking water. Two of the chimeric proteins (based on GFP-hadrurin and GFP-pb5 chimera proteins) failed with respect to specificity and/or sensitivity, but the GFP-colS4 chimera protein was able to carry out specific detection of E. coli in drinking water samples in a procedure encompassing about 8 min for final result and this biosensor protein was able to detect in a linear way between 20 and 103 CFU of this bacterium. Below 20 CFU, the system cannot differentiate presence or absence of the target bacterium. The fluorescence in this biosensor system is provided by the GFP subunit of the chimeric protein, which, in the case of the better performing sensor bullet, GFP-colS4 chimera, is covalently bound to a flexible peptide bridge and to a bacteriocin binding specifically to E. coli cells. Once bound to the target bacteria, the excitation step with 395 nm LED light causes emission of fluorescence from the GFP domain, which is amplified in a photomultiplier tube, and finally this signal is converted into an output voltage which can be associated with a CFU value and these data distributed along mobile phone networks, for example. This method, and the portable fluorimeter which has been developed for it, may contribute to reduce the analysis time for detecting E. coli presence in drinking water.

Robust fit of Bayesian mixed effects regression models with application to colony forming unit count in tuberculosis research.

Early bactericidal activity of tuberculosis drugs is conventionally assessed using statistical regression modeling of colony forming unit (CFU) counts over time. Typically, most CFU counts deviate little from the regression curve, but gross outliers due to erroneous sputum sampling are occasionally present and can markedly influence estimates of the rate of change in CFU count, which is the parameter of interest. A recently introduced Bayesian nonlinear mixed effects regression model was adapted to offer a robust approach that accommodates both outliers and potential skewness in the data. At its most general, the proposed regression model fits the skew Student t distribution to residuals and random coefficients. Deviance information criterion statistics and compound Laplace-Metropolis marginal likelihoods were used to discriminate between alternative Bayesian nonlinear mixed effects regression models. We present a relatively easy method to calculate the marginal likelihoods required to determine compound Laplace-Metropolis marginal likelihoods, by adapting methods available in currently available statistical software. The robust methodology proposed in this paper was applied to data from 6 clinical trials. The results provide strong evidence that the distribution of CFU count is often heavy tailed and negatively skewed (suggesting the presence of outliers). Therefore, we recommend that robust regression models, such as those proposed here, should be fitted to CFU count.

Integrating running water monitoring tools with the Micro Biological Survey (MBS) method to improve water quality assessment.

Running water habitats are among the most altered aquatic systems by human activities driving an increase in the organic components and the associated bacterial load as well. To contribute in improving the monitoring activities in running waters, here we tested the validity of the new Micro Biological Survey (MBS) method to specifically assess the bacterial load in running waters focusing on Total Viable Counts (at 22°C and 37°C) and Escherichia coli (at 44°C) in order to propose a new prognostic tool for watercourses. MBS method is an alternative colorimetric method for counting bacterial load in water and food samples that is easy to use and leads to a reliable and simple interpretation of results, being also faster and less expensive than traditional methods. Then, we compared MBS with the traditionally used reference method for the bacterial load, and with the most used biotic index for Italian watercourses based on the benthic invertebrates: the Extended Biotic Index (EBI). The last comparison was performed to validate the use of MBS in biomonitoring activities since the benthic invertebrate multi-species assemblage (and then EBI) alter own structure mainly depending on the organic component variation. During the first part of the study, the assessment of both linearity (regressions among bacterial concentrations) and accuracy (significant correlation between a measured value and a value used as reference) confirmed the validity of the MBS method. Second, the linear regressions between the three investigated microbial parameters vs. both physical-chemical descriptors and EBI, revealed the usefulness of MBS as a valid tool for routine microbiological analyses involved in rapid and easy field monitoring activities. This represents the first attempt to evaluate the river microbial status by exploiting the innovative MBS on running waters to propose it as new valuable monitoring tool in the biomonitoring field.

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome.

The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions.