Milk Contamination by Mycobacterium tuberculosis Complex, Implications for Public Health in Amazonas, Brazil.

ABSTRACT: In Brazil, contamination of raw milk with Mycobacterium tuberculosis complex (MTC) has been reported in several states. The highest rate of consumption of raw milk and its derivatives in Brazil occurs in Amazonas. This state also has the highest prevalence of tuberculosis in both humans and livestock. We assessed the contamination of cow's milk and buffalo's milk with MTC in Amazonas, focusing on Mycobacterium bovis, the species most commonly found in cattle and buffalo. In 2019, 250 samples of raw milk (91 from cattle, 159 from buffalo) were collected before processing from three milk plants in the state of Amazonas. The samples were placed into 21 pools and analyzed using shotgun metagenomic sequencing and taxonomic classification with Kraken 2 and MegaBLAST. To confirm the identity of mycobacterial species found, BLASTN was used to identify specific genomic positions in the TbD1 and RD1 regions and flanking RD4 region. MTC genetic material was identified in all pools of raw milk. Genetic material consistent with M. bovis was identified in seven pools of raw milk (1 from cattle, 6 from buffalo). Buffalo's milk had significantly higher MTC reads than did cow's milk. The common practice of consumption of raw milk and its derivatives in Amazonas presents a risk to public health. Urgent measures to prevent transmission of foodborne tuberculosis are needed in the Amazon region. Greater efforts and resources also should be directed toward elimination of bovine tuberculosis in cattle and buffalo herds in Amazonas and the rest of Brazil.

Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems.

The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels.IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities.

BACKGROUND: The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To expand our understanding of subsurface CPR microorganisms, we sampled four separate groundwater wells over 2 years across three Ohio counties. RESULTS: Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised between 2 and 20% of the microbial communities with relative abundances stable through time in Athens and Greene samples but dynamic in Licking groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and 2 putative new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored metabolic characteristics of known CPR members, some features were previously uncharacterized. For instance, nitrite reductase, encoded by nirK, was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a potentially undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our 71 genomes and over 2000 other CPR genomes were analyzed to characterize their carbon-processing potential. Although common trends were present throughout the radiation, differences highlighted potential mechanisms that could allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. CONCLUSIONS: CPR members are present across a range of environments and often constitute a significant fraction of the microbial population in groundwater systems, particularly. Further sampling of such environments will resolve this portion of the tree of life at finer taxonomic levels, which is essential to solidify functional differences between members that populate this phylogenetically broad region of the tree of life.

Solvent immersion imprint lithography.

We present Solvent Immersion Imprint Lithography (SIIL), a technique for polymer functionalization and microsystem prototyping. SIIL is based on polymer immersion in commonly available solvents. This was experimentally and computationally analyzed, uniquely enabling two practical aspects. The first is imprinting and bonding deep features that span the 1 to 100 µm range, which are unattainable with existing solvent-based methods. The second is a functionalization scheme characterized by a well-controlled, 3D distribution of chemical moieties. SIIL is validated by developing microfluidics with embedded 3D oxygen sensors and microbioreactors for quantitative metabolic studies of a thermophile anaerobe microbial culture. Polystyrene (PS) was employed in the aforementioned applications; however all soluble polymers - including inorganic ones - can be employed with SIIL under no instrumentation requirements and typical processing times of less than two minutes.

Survival of HIV-positive individuals with hepatitis B and C infection in Michigan.

We sought to estimate mortality and associated factors in HIV-hepatitis co-infected individuals in Michigan using a retrospective cohort study. For the study period of 1 January 2006 to 31 December 2009, all HIV-infected individuals were matched to hepatitis B and C cases. In the final Cox proportional hazards regression model, individuals of other [hazard ratio (HR) 2·2, 95% confidence interval (CI) 1·4-3·2] and black (HR 1·3, 95% CI 1·1-1·6) race had decreased survival compared to white race. Similarly, injecting drug users (IDUs) (HR 2·1, 95% CI 1·6-2·6), men who have sex with men (MSM)/IDUs (HR 1·5, 95% CI 1·1-2·2), individuals with undetermined risk (HR 1·5, 95% CI 1·2-1·9) and heterosexual practices (HR 1·4, 95% CI 1·1-1·8) had decreased survival compared to MSM. Additionally, an interaction was found between current HIV status and co-infection. Mortality in HIV-hepatitis co-infected individuals remains a continuing problem. Our study can help in planning interventions to reduce mortality in HIV-infected individuals.

Hepatitis B and C co-infection in HIV/AIDS population in the state of Michigan.

A retrospective cohort study was conducted from 1 January 2006 to 31 December 2009 in Michigan to estimate the prevalence of HIV and hepatitis co-infection and identify associated factors. The prevalence of co-infection was 4.1% [95% confidence interval (CI) 3.8-4.5]. Multivariable logistic regression analysis revealed a significant association between co-infection and being male and: of Black race [odds ratio (OR) 2.0, 95% CI 1.2-3.6] and of Other race (OR 3.5, 95% CI 1.7-7.0) compared to Hispanic race. A significant association was found between co-infection and risk categories of blood products (OR 11.1, 95% CI 6.2-20.2), injecting drug user (IDU) (OR 3.6, 95% CI 2.7-4.8) and men who have sex with men/IDU (OR 3.4, 95% CI 2.4-4.9) in addition to two interactions; one between sex and current HIV status and the other between current HIV status and age at HIV diagnosis. Our results document the changing epidemiology of HIV-hepatitis co-infection which can guide preventive measures and interventions to reduce the prevalence of hepatitis co-infection.

The role of exposures to animals and other risk factors in sporadic, non-typhoidal Salmonella infections in Michigan children.

Salmonellosis is largely a major foodborne disease. However, contact with animals particularly reptiles, has been increasingly recognized as a risk factor for Salmonella infection among children. The major risk factors for salmonellosis in Michigan children have not been assessed. Therefore, we have evaluated the association between Salmonella infections and contact with animals among Michigan children aged ≤ 10 years by conducting a population-based case-control study. A total of 123 children with laboratory-confirmed Salmonella infections and 139 control children, who had not experienced symptoms of gastrointestinal illness during the month prior to the interviews, were enrolled. A multivariable analysis matched on age group revealed that children with Salmonella infections had reported more commonly than controls contact with reptiles [adjusted matched odds ratio (MOR) = 7.90, 95% confidence interval (CI): 1.52-41.01] and cats (MOR = 2.53, 95% CI: 1.14-5.88). Results of this study suggest an association between salmonellosis and contact with cats and reptiles in Michigan children. Additional efforts are needed to educate caretakers of young children about the risk of Salmonella transmission through animal contact.

Use of multiple-locus variable number tandem repeat analysis and phage typing for subtyping of Salmonella Enteritidis from sporadic human cases in the United States.

AIMS: To investigate the genetic diversity among S. Enteritidis isolates from different geographic regions to evaluate the relationship between phage types (PTs) and variable number tandem repeat analysis (VNTR) loci. METHODS AND RESULTS: We performed multiple-locus variable number tandem repeat analysis (MLVA) and phage typing on 245 S. Enteritidis isolates collected from sporadic human clinical cases in Michigan, Minnesota, New York, and Washington states between 2000 and 2007. Ninety-four MLVA types and 22 different PTs were identified. Specific PTs were associated with a predominant allele for certain VNTR loci. Cluster analysis using a minimum-spanning tree demonstrated two major clusters (I, II) and one minor cluster of isolates. PTs 8, 13a, 13 and 34 were significantly associated with MLVA cluster I. Phage types 1, 4, 6a, and 18 were significantly associated with MLVA cluster II. CONCLUSIONS: We found significant association between MLVA-based clusters and PTs. Certain VNTR loci were associated with specific PTs and could serve as useful molecular markers for S. Enteritidis in epidemiological investigations. SIGNIFICANCE AND IMPACT OF THE STUDY: MLVA genotyping in combination with phage typing can be used for effective characterization of S. Enteritidis isolates. It can also be useful for tracing possible sources during investigations of sporadic and outbreak cases of S. Enteritidis.

Absence of Mycobacterium bovis infection in dogs and cats residing on infected cattle farms: Michigan, 2002.

A cross-sectional field study was performed to evaluate infection in dogs and cats living on farms with Mycobacterium bovis-infected cattle. The purpose was to determine pet infection status and assess their risk to farm families and/or tuberculosis-free livestock. Data and specimens were collected from 18 cats and five dogs from nine participating farms. ELISA testing for M. bovis and M. avium was conducted. Fifty-one biological samples were cultured; all were negative for M. bovis, although other Mycobacterium species were recovered. No radiographic, serological or skin test evidence of mycobacterial infection was found. These negative results may be due to the low level of M. bovis infection in the cattle and the limited duration of exposure of pets to infected cattle residing on the same farm. No evidence was found to indicate that pets residing on M. bovis-infected Michigan cattle farms pose a risk to humans or M. bovis-free livestock; however, precautionary advice for farm owners was provided.

Mycobacterium bovis (bovine TB) exposure as a recreational risk for hunters: results of a Michigan Hunter Survey, 2001.

SETTING: Tuberculosis caused by Mycobacterium bovis (bovine TB) is endemic in the white-tailed deer population of north-eastern Michigan. Hunters may be exposed to M. bovis via cutaneous inoculation while field dressing deer or by ingestion of undercooked venison. Michigan hunters have received inconsistent messages about their risk of acquiring tuberculosis from recreational exposure to deer. The most common health advice offered has been to wear gloves while field dressing deer and to cook venison products thoroughly. OBJECTIVE: Data were collected to quantify these self-protective activities and to characterize hunters practicing these activities. DESIGN: In 2001, we surveyed 1833 hunters who had successfully harvested deer in or near Michigan's bovine TB endemic area in 2000. RESULTS: The survey response rate was 78%. Most hunters (89%) reported field dressing deer, 43% of whom wore gloves. Most hunters (95%) reported eating venison, 55% of whom reported their venison was always cooked thoroughly. Several hunter characteristics, including older age, female sex, higher awareness level, and area of residence, were significantly associated with the practice of these self-protective activities. CONCLUSION: The survey results suggest that hunters should receive consistent advice encouraging glove use while field dressing deer and the thorough cooking of venison products before consumption.

Human salmonellosis associated with young poultry from a contaminated hatchery in Michigan and the resulting public health interventions, 1999 and 2000.

Although approximately 95% of disease caused by nontyphoidal salmonella is transmitted by foodborne vehicles, four documented salmonella outbreaks in the 1990s have been traced to contact with young poultry. No environmental studies of source hatcheries were completed. This case-control study was performed by comparing culture-confirmed Salmonella Infantis in Michigan residents, identified between May and July 1999, with two age- and neighbourhood-matched controls. Eighty environmental and bird tissue samples were collected from an implicated hatchery; all salmonella isolates underwent pulsed-field gel electrophoresis (PFGE) analysis. The study included 19 case-patients sharing the same PFGE subtype and 37 matched controls. Within 5 days before illness onset, 74% of case-patients resided in households raising young poultry compared with 16% of controls (matched OR 19.5; 95% CI 2.9, 378.1). Eight hatchery samples yielded Salmonella Infantis with PFGE subtypes matching the patients' isolates. This investigation identified birds from a single hatchery as the source of human illness and confirmed the link by matching PFGE patterns from humans, birds and the hatchery environment. Subsequent public health interventions reduced, but did not eliminate, transmission of poultry-associated salmonellosis. Five additional PFGE-linked cases were identified in Spring 2000, necessitating quarantine of the hatchery for depopulation, cleaning and disinfection.

An in situ dissolution study of aspirin crystal planes (100) and (001) by atomic force microscopy.

PURPOSE: To observe in situ and on individual aspirin crystal faces the comparative rates and processes of dissolution of the dominant faces. METHODS: The kinetics of the dissolution rate of two aspirin crystal planes (001) and (100) under 0.05M HCl are studied in situ at room temperature using Atomic Force Microscopy. The dissolution process of each crystal plane was followed by observed changes in topographic features. RESULTS: The results revealed that crystal plane (001) dissolves by receding step edges, and has a dissolution rate of 0.45 nm s(-1). Conversely. plane (100) displays crystal terrace sinking at an average rate of 2.93 nm s(-1). Calculated intrinsic dissolution values (g s(-1) cm(-2)) for planes (001) and (100) are 1.37 x 10(-7) gs(-1) cm(-2) and 8.36 x 10(-7) gs(-1) cm(-2), respectively. CONCLUSIONS: These values indicate that the rate of flux of material from plane (100) is approximately six times greater than that from plane (001), under 0.05M HCl. Interpretation of the data, based upon intrinsic dissolution rates and dissolution rate velocities, correlate with reported variations in the dissolution behavior of commercial aspirin products. These observations illustrate the suitability of the technique for characterizing the dissolution behavior of crystalline drugs.

Surface characterization of aspirin crystal planes by dynamic chemical force microscopy.

Tapping mode (TM) atomic force microscopy (AFM) has been applied in a novel fashion to characterize and distinguish the (001) and (100) surfaces of individual aspirin crystals. The surface characterization was achieved by amplitude-phase, distance (a-p,d) measurements employing gold-coated AFM probes functionalized with self-assembled monolayers (SAM). Experiments using model probes coated with -CH3 and -COOH terminated SAMs have been performed on the two aspirin crystal planes (001) and (100). Results indicate that the hydrophobic -CH3 terminated AFM probes had a greater degree of interaction with the crystal plane (001), whereas the -COOH terminated AFM probes had a larger interaction with the crystal plane (100). Interpretation of these data, based upon the chemistries of the probes, correlates with current understanding of the crystal surface chemistry derived from X-ray diffraction data and dissolution rate studies.

Discrimination of polymorphic forms of a drug product by localized thermal analysis.

In chemical processing, it is important to distinguish between and identify polymorphic forms. We demonstrate the novel use of scanning thermal microscopy (SThM) and localized thermal analysis to distinguish and identify polymorphic forms of the drug cimetidine. These forms cannot be resolved by classical bulk thermal analysis. SThM reveals a sample consisting of a 50 : 50 mixture of the polymorphs contains regions of different thermal conductivity, corresponding to the different polymorphs. Localized thermal analysis of small volumes of pure polymorphic samples (approximately 50 microm3) shows that the origin of the thermal conductivity contrast lies, at least in part, with the presence of a surface water layer on the more hydrophilic polymorph.

Extracranial giant cell arteritis.

Although giant cell arteritis (GCA) of the extracranial arteries is said to be relatively frequent, clinical manifestations are rarely recognized. We describe a case presenting with intestinal perforation who subsequently died with active GCA of the coronary, mesenteric and temporal vessels.

Giant cell reparative granuloma of the cricoid cartilage.

Giant cell reparative granuloma (GCRG) is an uncommon benign lesion which has been reported at several sites in the head and neck. We present a case of a GCRG of the cricoid cartilage not previously described in the literature. It must be differentiated from the brown tumour of hyperparathyroidism and true giant cell tumours of bone. These were excluded on clinical, biochemical, radiological and histological grounds. The lesion responded well to surgical debulking and curettage and the patient remained disease-free 15 months after treatment.

Pathologist variation in reporting cervical borderline epithelial abnormalities and cervical intraepithelial neoplasia.

AIMS: To evaluate the interobserver variation in the diagnosis of cervical intraepithelial lesions, including the new category "borderline abnormalities of uncertain significance" (BAUS) which has not been tested before. METHODS: Biopsy specimens of 122 patients were reviewed by five histopathologists and the diagnoses subjected to kappa statistical analysis. RESULTS: There was poor interobserver agreement in all categories, particularly between BAUS and normal tissue. CONCLUSIONS: The current guidelines for the histological diagnosis of cervical intraepithelial neoplasia and BAUS are poorly reproducible.