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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., Competing Interests: The authors have declared that no competing interests exist.

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, γ f for fast- and γ s 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 γ s- 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.

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 .

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 × 10 5 cfu/coupon) and silicone (5.4 × 10 5 cfu/coupon) rubber than on EPDM (2.9 ×10 5 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., (Copyright © 2020 The Healthcare Infection Society. All rights reserved.)

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.

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., (© 2020 The Society for Applied Microbiology.)

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.

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 Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

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., (Copyright © 2019 American Society for Microbiology.)

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., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

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.

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.

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 log 10  cfu/cm 2 , respectively, while deer carcass values were 4.5, 1.5 and 0.7 log 10  cfu/cm 2 , respectively. Moose carcasses were significantly more contaminated with EB and EC than deer carcasses. High bacterial counts (MAB>5.0 log 10  cfu/cm 2 and EB > 2.5 log 10  cfu/cm 2 ) 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., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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.

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.

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.

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., (Copyright © 2017 John Wiley & Sons, Ltd.)

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.

Objective: To investigate the relationship of pathogen DNA copies with clinic and laboratory features among children with Mycoplasma pneumoniae (MP) pneumonia., Methods: A total of 95 enrolled children with MP pneumonia were assigned into the high-MP-load group (>10 6 /mL) and the low-MP-load group (≤10 6 /mL) according to MP-DNA copies in bronchoalveolar lavage fluid (BALF). Clinical characteristics and any allergy history were collected. Aeroallergens and food allergens were detected with a skin test. Serum IgE and eosinophil cationic protein (ECP) were assessed using enzyme immunoassay. BALF levels of IL-4, IFN-γ, IL-8 and TNF-α were assessed by ELISA., Results: Compared with the low-MP-load group, 72.7% in the high-MP-load group developed refractory MP pneumonia who failed to respond to at least 1-week treatment with macrolides (72.7% vs 41.9%, P = 0.005). More children in the high-load group than those in the low-load group presented with extrapulmonary manifestations, lung consolidation, pleural effusion and atopic conditions including any allergy history, positive findings of aeroallergen test and increased serum IgE and ECP (P < 0.05). A significant higher BALF IL-4 level was seen in the high-load group versus the low-load group (23.00 ± 11.24 vs 14.68 ± 7.12; pg/mL; P < 0.01). There were no significant differences in BALF levels of IFN-γ, IL-8 and TNF-α between the two groups (P > 0.05)., Conclusion: Atopy may be a risk factor for the presence and severity of refractory MP pneumonia due to the high pathogen load in airway., (© 2016 John Wiley & Sons Ltd.)

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.

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.

For deep carious lesions, a more conservative treatment modality ("selective caries removal") has been proposed, where only the heavily contaminated dentine is removed. In this regard, effective adjuncts for cavity disinfection such as the antimicrobial photodynamic therapy (aPDT) can be valuable clinically prior to definitive restoration. Therefore, the aim of this study was to systematically assess clinical studies on the effectiveness of aPDT as a supplementary tool in the treatment of deep caries lesions. Searches were performed in four databases (PubMed, EMBASE, ISI Web of Science, ClinicalTrials.gov) from 1st January, 2011 until 21st June, 2016 for search terms relevant to the observed parameters, pathological condition, intervention and anatomic entity. The pooled information was evaluated according to PRISMA guidelines. At first, 1651 articles were recovered, of which 1249 full-text articles were evaluated, 270 articles thereof were reviewed for eligibility and finally 6 articles met all inclusion criteria. The aPDT protocols involved Methylene Blue, Toluidine Blue and aluminium-chloride-phthalocyanine as photosensitizers and diode lasers, light-emitting diodes and halogen light-sources. The data from five reports, utilizing both culture-dependent and -independent methods, disclosed significant reduction of cariogenic bacterial load after mechanical caries removal with adjunct aPDT. As these studies exhibit some methodological limitations, e.g. lack of positive controls, this systematic review can support the application of aPDT to a limited extent only in terms of reducing the microbial load in deep carious lesions before restorative treatment., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Background: Surfaces in the patient environment may play a role in microbial transmission if they become colonized by bacteria. Patient privacy curtains are one such surface that may pose a high risk for transmission because they are high-contact surfaces, are infrequently cleaned, and healthcare workers are less likely to wash their hands after contacting inanimate objects such as curtains., Aim: To determine the amount and type of bacterial colonization of patient privacy curtains at a regional burns/plastic surgery unit., Methods: Privacy curtain contamination on the burns/plastic surgery ward was determined for two separate occasions six months apart: 23 curtains on August 2015 and 26 curtains on January 2016. Dey-Engley neutralizing agar (DENA) replicate organism detection and counting (RODAC) contact plates were used daily to sample curtains near the edge hem where they are most frequently touched. Microbial contamination was reported as cfu/cm 2 and the presence of meticillin-resistant Staphylococcus aureus (MRSA) was determined. Swabs were also taken of any open wounds and from tracheostomy sites on the ward., Findings: Curtain contamination in August 2015 was 0.7-4.7 cfu/cm 2 with 22% testing positive for MRSA, whereas contamination on January 2016 was 0.6-13.3 cfu/cm 2 with 31% of curtains testing positive for MRSA., Conclusion: Curtains on the burns/plastic surgery ward become colonized with significant quantities of bacteria. Future studies will need to address the rate of colonization and the clinical impact of this colonization to better inform cleaning protocols., (Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Background: Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses., Results: Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average library size, rarefying lowers the false discovery rate. DESeq2, without addition of a constant, increased sensitivity on smaller datasets (<20 samples per group) but tends towards a higher false discovery rate with more samples, very uneven (~10×) library sizes, and/or compositional effects. For drawing inferences regarding taxon abundance in the ecosystem, analysis of composition of microbiomes (ANCOM) is not only very sensitive (for >20 samples per group) but also critically the only method tested that has a good control of false discovery rate., Conclusions: These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.

Objective: This study aimed to assess the levels of microbial contamination in semen samples before and after the micro swim-up (MSU) procedure in intra-cytoplasmic sperm injection (ICSI). The new method is an upgrade to the classic wash swim-up procedure., Methods: Semen analysis and microbiological tests were carried out before and after the MSU procedure. A total of twenty semen samples were analyzed., Results: Pathogens were observed in semen samples only before MSU and never after ICSI. Microbiological tests revealed a large prevalence of gram-positive cocci [Staphylococcus spp. (n=16, 80%) and viridans streptococci (n=10, 50%)]. The results of this study indicate that direct MSU in ICSI improved the ICSI workflow., Conclusion: The new workflow is faster and more affordable, and is likely to prevent infection problems that could arise from the normal microbial flora of the semen., Competing Interests: CONFLICT OF INTERESTS No conflict of interests have been declared.

In a fluctuation experiment, the number of cells existing in a culture immediately before plating (commonly known as Nt) varies across the parallel cultures. However, most existing mathematical models for fluctuation assay data do not recognize the variation in Nt. Despite repeated attempts in the past to integrate this source of variability in the estimation of microbial mutation rates, several questions of practical importance remain unanswered. The present investigation finds that the variation needs accounting for only when the coefficient of variation for Nt is large, and experimental data suggest that the coefficient of variation is often moderate or small. Moreover, an increase in the inoculum size can reduce the coefficient of variation. Through extensive simulation, several existing methods that accommodate the variation in Nt are compared. It was found that a newly devised likelihood method based on the existing gamma mixture model outperforms other existing methods. The investigation focuses on the estimation of mutation rates using the Lea-Coulson model, under which mutation is selectively neutral; however, the paper also explores the major findings' implications for the comparison of mutation rates using the likelihood ratio test, and for the estimation of mutation rates using the Mandelbrot-Koch model that allows for non-neutral mutations., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Background: In several studies, different risk factors other than antibiotic resistance have been documented with Helicobacter pylori eradication failure. We aimed in this study to investigate the relationship of gastric density of H. pylori, the occurrence/degree of gastric atrophy, and intestinal metaplasia (IM) with success rate of H. pylori eradication., Methods: Two hundred consecutive treatment naive patients who received bismuth containing standart quadruple treatment due to H. pylori infection documented by histopathological examination of two antral or two corpal biopsies entered this retrospective study. The updated Sydney system was used to grade the activity of gastritis, density of H. pylori colonization, atrophy, and IM. Stages III and IV of operative link for gastritis assessment (OLGA) or the operative link on gastric intestinal metaplasia assessment (OLGIM) stages was considered as severe gastritis. H. pylori eradication was determined via stool H. pylori antigen test performed 4 weeks after the end of therapy., Results: The presence of gastric atrophy and IM was significantly higher in patients with eradication failure (p = 0.001 and 0.01, respectively). Severe gastritis (OLGA III-IV and OLGIM III-IV) rates were higher in eradication failure group. A multiple linear regression analysis showed that OLGA and OLGIM stages were to be independent risk factors for eradication failure (p = 0.03 and 0.01, respectively)., Conclusion: Our results suggested that histopathologically severe gastritis may cause H. pylori eradication failure. In addition, we found that H. pylori density was not a risk factor for treatment failure in patients who receive quadruple treatment.

Background and Aim: The aim of this study was to evaluate the efficacy of bismuth-based quadruple regiment as a first-line treatment for Helicobacter pylori (H. pylori) eradication in patients with unexplained iron deficiency anemia (IDA). The serum hepcidin-25, iron, ferritin levels and total iron-binding capacity were evaluated at baseline and after H. pylori eradication in order to assess whether H. pylori eradication plays a role in IDA related to H. pylori infection., Methods: The study included 80 patients with unexplained IDA and H. pylori infection. All patients received pantoprazole (40 mg b.i.d.), bismuth subcitrate (120 mg q.i.d.), tetracycline (500 mg q.i.d.) and metronidazole (500 mg t.i.d.) over 14 days as H. pylori eradication regimen. In all patients, blood samples were drawn at baseline and 1 month after eradication therapy. In all patients, serum hepcidin-25 levels were determined by using commercially available enzyme-linked immunosorbent assay kits., Results: There was an improvement in hemoglobin, iron, total iron-binding capacity and ferritin values after H. pylori eradication in all subjects. Serum hepcidin-25 levels significantly decreased after H. pylori eradication (p < 0.001)., Conclusion: Gastric H. pylori infection is a common cause of IDA of unknown origin in adult patients. Our results provide evidence indicating that hepcidin level decreases after successful H. pylori eradication with improvement in IDA.

Objectives: The aim of the study was to assess the usefulness of gastric biopsy-based quantitative real-time polymerase chain reaction (qPCR) for the detection of Helicobacter pylori infection and the identification of clarithromycin-resistant strains in children., Methods: A gastric biopsy-based qPCR for the detection of H pylori infection and the identification of clarithromycin-resistant strains in children was evaluated in 62 children with infection and 341 children without infection. H pylori infection was considered by the "reference method" when culture was positive for both histology and rapid urease test (RUT). Results were compared with those obtained using the qPCR., Results: The reference method versus H pylori qPCR positivity showed 95% confidence interval sensitivity 100% versus 100%, specificity 93.2% (86.9-99.4) versus 100%, positive predictive value 59.7% (47.4-71.9) versus 100%, negative predictive value 100% versus 100%, and, finally, test accuracy of 59.6% (47.3-71.8) versus 100%. Sixty-two children were found to be H pylori positive, based on the qPCR results. Among those, 31 children had both positive qPCR and culture with concordant antimicrobial susceptibility testing results, whereas 31 children had negative culture and positive qPCR. The qPCR showed a bacterial load ≥10 copies per milliliter when culture, histology, and RUT were all positive (29/31 children) versus <10 copies per milliliter when culture, histology, and RUT were all negative (25/31 children). Grades 2 and 3 histological gastritis were associated with a bacterial load ≥10 copies per milliliter for 28/35 of children versus 27/27 of grade 0 to 1 <10 copies per milliliter., Conclusions: H pylori qPCR positivity is a more precise test than the routine culture, histology, RUT alone and allows detecting low bacterial loads.

This is a report of a multidisciplinary project conducted at Karolinska University Hospital in Stockholm. The aim was to study and reduce potential risk factors for the spread of health-care associated infections in the near-patient environment. A process beginning with an observation study conducted by two observers of which one was an industrial designer or a psychologist was used. Bacterial screenings were used to verify factors identified during the observations. The main focus of activities to reduce the identified risks was mainly to improve the cleaning. Improved cleaning routines reduced the microbiological level significantly.

Legionella spp. is considered an emerging microorganism involved in aquatic environments contamination and cause of Legionnaires' disease. The aims of the study are to evaluate the level of contamination of Legionella spp. in the water system of the largest Hospital of Apulia region during a 4-year surveillance and to establish, by molecular method, the presence of a predominant genotype of L. pn. sg 1. The results showed that Legionella spp. was present in 36% of water samples with Legionella pneumophila serogroup 1 (L. pn. sg 1) the most prevalent species and serogroup and the wards most contaminated are the high risk units. In addition, despite four main clones of L. pn. sg 1 were identified, a predominant genotype existed. In conclusion the study demonstrates the necessity for periodic evaluation on hospitals water system to assess the potential contamination of Legionella spp., performing decontamination in the presence of bacterial contamination, even low, in particular in high risk wards. Moreover, the switching of the disinfection methods may be suggested in order to prevent resistance phenomenon by some L. pn. sg 1 clones.

Objectives: To study and compare the number of colony forming units of Streptococcus mutans, Streptococcus sanguis, Streptococcus salivarius, Streptococcus mitis and Streptococcus milleri in dentulous, edentulous and in those wearing partial and complete dentures by using semi-quantitative culture method of saliva samples with calibrated standard loop., Materials: Sterile specimen collection bottles, Mitis salivarius agar plates, Standard loop, Candle jar, Incubator, Colony counter., Methodology: Study population consisted of 100 subjects with 25 in each group, with an age range of 40 to 80 years, who were attending the Department of Community Dentistry and Prosthodontics at MNR Dental College, Sangareddy, Hyderabad. Unstimulated saliva samples were collected from patients and inoculated on to Mitis salivarius agar plates using calibrated standard loop. The plates were then incubated anaerobically at 37°C for 24 hours and left at room temperature for further 24 hours. Using a colony counter, the number of colonies of each species was counted., Results: Streptococcus mutans and Streptococcus mitis predominates in the dentulous group, Streptococcus sanguis in complete denture group, Streptococcus salivarius in edentulous group and Streptococcus milleri in removable partial denture group., Conclusion: The results of our study are in accordance with the previous studies, which have sought to differentiate different groups of mutans streptococci using a simple calibrated standard loop.

Background: Chronic rhinosinusitis (CRS) is an idiosyncratic and multifactorial disease process. Bacteria play a role in some patients, by infection or stimulation of inflammation. Staphylococcus aureus (SA) appears to be implicated in a number of infectious and inflammatory mechanisms, and may be particularly relevant in CRS patients with nasal polyps and asthma., Methods: Middle meatus swabs from control and CRS patients collected during endoscopic sinus surgery were analyzed by quantitative polymerase chain reaction (QPCR). Total bacterial count, SA prevalence, and SA abundance were examined with respect to patient demographics and disease characteristics., Results: Total bacteria, as measured by QPCR, was not statistically different between controls, CRS without nasal polyps (CRSsNP), CRS with nasal polyps (CRSwNP), or CRS with asthma groups (p < 0.09). Total bacterial counts did not correlate with disease severity as measured by Lund-Mackay computed tomography (CT) scores (p = 0.65). The prevalence of SA was similar between groups (15-25%); however, the abundance increased in CRS patients with allergic rhinitis, nasal polyps, and asthma., Conclusion: The paranasal sinuses are not sterile. SA is implicated in a subset of CRS patients with nasal polyps and/or asthma. Further study is required to predict this subset of patients, and to define the mechanisms of SA pathogenesis., (© 2013 ARS-AAOA, LLC.)

Background: Microbiological screening (MS) is standard on neonatal intensive care units (NICU). Objectives are the collection of information regarding bacterial pathogens of the individual patient as well as of the NICU, especially of multidrug-resistant pathogens (MRE). The role of microbiological screening for preterm infants ≤32 weeks of gestational age has not been fully evaluated., Patients and Methods: For preterm infants ≤32 weeks of gestational age admitted during a 41-month period the results of microbiological screening during the first 2 weeks of life were analysed retrospectively. The results were associated with documented septic episodes., Results: Bacteria were isolated in 215/972 of postnatal and 416/862 of later swabs. Detection of bacteria in the initial MS was associated with vaginal birth, low gestational age, low APGAR values at 5 and 10 min and mechanical ventilation. The proportion of patients with positive microbiological screening in subsequent swabs was not influenced by gestational age, birth weight, sex, mode of delivery and APGAR score. During the observation period 52 cases of sepsis (28 clinic, 24 microbiological) occurred. The sepsis rate was increased in patients with positive postnatal swabs, low gestational age, low birth weight, low 5 min APGAR score, male sex or need for mechanical ventilation., Conclusions: Microbiological screening provides an overview of the NICU-specific pathogens but is of limited value in the prediction of septicaemias in preterm infants ≤32 weeks gestational age., (© Georg Thieme Verlag KG Stuttgart · New York.)

The indices of Doppler laser flowmetery are proposed to be used for determination of the readiness of a granulating wound for free autoplasty. An analysis of capillary blood flow in the groups under test showed the information value of indicators of microcirculation obtained by Doppler laser flowmetery for determination of the granulating wound condition before autotransplantation and prediction of the results of skin engraftment. It is stated, that the disorder of microcirculation has been developed against the background of progression of wound invasive infection. The obtained data can allow the development of an algorithm of treatment and the preparation of the patients to surgery, determination of the terms of operation, the development the strategy of postoperative management of the patients, which can reduce unfavorable results of operations.

In this paper we report a stable, label-free, bacteriophage-based detection of Escherichia coli (E. coli) using ultra sensitive long-period fiber gratings (LPFGs). Bacteriophage T4 was covalently immobilized on optical fiber surface and the E. coli binding was investigated using the highly accurate spectral interrogation mechanism. In contrast to the widely used surface plasmon resonance (SPR) based sensors, no moving part or metal deposition is required in our sensor, making the present sensor extremely accurate, very compact and cost effective. We demonstrated that our detection mechanism is capable of reliable detection of E. coli concentrations as low as 10(3)cfu/ml with an experimental accuracy greater than 99%., (Copyright © 2012 Elsevier B.V. All rights reserved.)

The applications of conventional culture-dependent assays to quantify bacteria populations are limited by their dependence on the inconsistent success of the different culture-steps involved. In addition, some bacteria can be pathogenic or a source of endotoxins and pose a health risk to the researchers. Bacterial quantification based on the real-time PCR method can overcome the above-mentioned problems. However, the quantification of bacteria using this approach is commonly expressed as absolute quantities even though the composition of samples (like those of digesta) can vary widely; thus, the final results may be affected if the samples are not properly homogenized, especially when multiple samples are to be pooled together before DNA extraction. The objective of this study was to determine the correlation coefficients between four different methods of expressing the output data of real-time PCR-based bacterial quantification. The four methods were: (i) the common absolute method expressed as the cell number of specific bacteria per gram of digesta; (ii) the Livak and Schmittgen, ΔΔCt method; (iii) the Pfaffl equation; and (iv) a simple relative method based on the ratio of cell number of specific bacteria to the total bacterial cells. Because of the effect on total bacteria population in the results obtained using ΔCt-based methods (ΔΔCt and Pfaffl), these methods lack the acceptable consistency to be used as valid and reliable methods in real-time PCR-based bacterial quantification studies. On the other hand, because of the variable compositions of digesta samples, a simple ratio of cell number of specific bacteria to the corresponding total bacterial cells of the same sample can be a more accurate method to quantify the population.

The relatively small perceived probability associated with retesting a food for the presence of Salmonella at low levels is often considered as one of the reasons that a confirmatory or check-analysis tends to disagree in practice with the results of an original test. Given a retesting process where a retest is only performed to confirm an original positive Salmonella test, the probability that both the original and retest will test positive for Salmonella has been traditionally determined by some as the product of the probabilities of a positive Salmonella test for the original and retest samples. When examining the probabilities associated with the retesting process, we found that our results disagreed with those based on intuitions apparently held by others concerning how these probabilities should be calculated. For Salmonella testing, operating characteristic values were computed to demonstrate the protections afforded by the Salmonella sampling plans presented in the U.S. Food and Drug Administration's Bacteriological Analytical Manual and to obtain the probability of a positive Salmonella test. The geometric distribution was examined for possible utility in determining the probabilities associated with testing amounts, i.e., the number of Salmonella tests needed to obtain a positive test.