The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits

Deermice of the genus Peromyscus are well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and their ability to serve as disease vectors. Here, we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a nontraditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals and subsequently maintained for ∼40-60 generations. From 405 low-pass short-read sequenced deermice we accurate impute genotypes at 16 million single nucleotide polymorphisms. Conditional on observed genotypes simulations were conducted in which three different sized quantitative trait loci contribute to a complex trait under three different genetic models. Using a stringent significance threshold power was modest, largely a function of the percent variation attributable to the simulated quantitative trait loci, with the underlying genetic model having only a subtle impact. We additionally simulated 2,000 pseudo-individuals, whose genotypes were consistent with those observed in the genotyped cohort and carried out additional power simulations. In experiments employing more than 1,000 mice power is high to detect quantitative trait loci contributing greater than 2.5% to a complex trait, with a localization ability of ∼100 kb. We finally carried out a Genome-Wide Association Study on two demonstration traits, bleeding time and body weight, and uncovered one significant region. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice and similar colonies in other systems using easily obtained genotypes from low-pass sequencing.

An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin

Animals that are competent reservoirs of zoonotic pathogens commonly suffer little morbidity from the infections. To investigate mechanisms of this tolerance of infection, we used single-dose lipopolysaccharide (LPS) as an experimental model of inflammation and compared the responses of two rodents: Peromyscus leucopus, the white-footed deermouse and reservoir for the agents of Lyme disease and other zoonoses, and the house mouse Mus musculus Four hours after injection with LPS or saline, blood, spleen, and liver samples were collected and subjected to transcriptome sequencing (RNA-seq), metabolomics, and specific reverse transcriptase quantitative PCR (RT-qPCR). Differential expression analysis was at the gene, pathway, and network levels. LPS-treated deermice showed signs of sickness similar to those of exposed mice and had similar increases in corticosterone levels and expression of interleukin 6 (IL-6), tumor necrosis factor, IL-1β, and C-reactive protein. By network analysis, the M. musculus response to LPS was characterized as cytokine associated, while the P. leucopus response was dominated by neutrophil activity terms. In addition, dichotomies in the expression levels of arginase 1 and nitric oxide synthase 2 and of IL-10 and IL-12 were consistent with type M1 macrophage responses in mice and type M2 responses in deermice. Analysis of metabolites in plasma and RNA in organs revealed species differences in tryptophan metabolism. Two genes in particular signified the different phenotypes of deermice and mice: the Slpi and Ibsp genes. Key RNA-seq findings for P. leucopus were replicated in older animals, in a systemic bacterial infection, and with cultivated fibroblasts. The findings indicate that P. leucopus possesses several adaptive traits to moderate inflammation in its balancing of infection resistance and tolerance.IMPORTANCE Animals that are natural carriers of pathogens that cause human diseases commonly manifest little or no sickness as a consequence of infection. Examples include the deermouse, Peromyscus leucopus, which is a reservoir for Lyme disease and several other disease agents in North America, and some types of bats, which are carriers of viruses with pathogenicity for humans. Mechanisms of this phenomenon of infection tolerance and entailed trade-off costs are poorly understood. Using a single injection of lipopolysaccharide (LPS) endotoxin as a proxy for infection, we found that deermice differed from the mouse (Mus musculus) in responses to LPS in several diverse pathways, including innate immunity, oxidative stress, and metabolism. Features distinguishing the deermice cumulatively would moderate downstream ill effects of LPS. Insights gained from the P. leucopus model in the laboratory have implications for studying infection tolerance in other important reservoir species, including bats and other types of wildlife.

Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses

The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines.

The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections

The rodent Peromyscus leucopus is the natural reservoir of several tick-borne infections, including Lyme disease. To expand the knowledge base for this key species in life cycles of several pathogens, we assembled and scaffolded the P. leucopus genome. The resulting assembly was 2.45 Gb in total length, with 24 chromosome-length scaffolds harboring 97% of predicted genes. RNA sequencing following infection of P. leucopus with Borreliella burgdorferi, a Lyme disease agent, shows that, unlike blood, the skin is actively responding to the infection after several weeks. P. leucopus has a high level of segregating nucleotide variation, suggesting that natural resistance alleles to Crispr gene targeting constructs are likely segregating in wild populations. The reference genome will allow for experiments aimed at elucidating the mechanisms by which this widely distributed rodent serves as natural reservoir for several infectious diseases of public health importance, potentially enabling intervention strategies.

Genotyping Strains of Lyme Disease Agents Directly From Ticks, Blood, or Tissue

The tick-borne spirochetes that cause Lyme disease in North America and Eurasia display strong linkage disequilibrium between certain chromosomal and plasmid loci within each three major geographic areas of their distribution. For strain typing for epidemiologic and ecologic purposes, the commonly used genotypes based on a single locus are the spacer between the 16S-23S ribosomal RNA and the ospC gene of a plasmid. A simple genotyping scheme based on the two loci allows for discrimination between strains representing all the areas of distribution. The methods presented here are meant for genotyping directly from ticks and from blood and tissue samples from vertebrates.

Chest radiography for active tuberculosis case finding in the homeless: a systematic review and meta-analysis

SETTING

In low-incidence regions, tuberculosis (TB) often affects vulnerable populations. Guidelines recommend active case finding (ACF) in homeless populations, but there is no consensus on a preferred screening method.

OBJECTIVE

We performed a systematic review and meta-analysis to evaluate the use of chest X-ray (CXR) screening in ACF for TB in homeless populations.

DESIGN

Articles were identified through EMBASE, Medline and the Cochrane Library. Studies using symptom screens, CXRs, sputum sweeps, tuberculin skin tests and/or interferon-gamma release assays to detect active TB in homeless populations were sought. Data were extracted using a standardised method by two reviewers and validated with an objective tool.

RESULTS

Sixteen studies addressing CXR screening of homeless populations for active TB in low-incidence regions were analysed. The pooled prevalence of active TB in the 16 study cohorts was 931 per 100 000 population screened (95%CI 565-1534) and 782/100 000 CXR performed (95%CI 566-1079). Six of seven longitudinal screening programs reported a reduction in regional TB incidence after implementation of the CXR-based ACF programme.

CONCLUSION

Our data suggest that CXR screening is a good tool for ACF in homeless populations in low-incidence regions.

Is the delay in diagnosis of pulmonary tuberculosis related to exposure to fluoroquinolones or any antibiotic?

BACKGROUND

Delays in diagnosis of tuberculosis (TB) have been associated with previous use of antibiotics, and in particular fluoroquinolones (FQ), for suspected pulmonary infections.

METHODS

We conducted a population-based cohort study with 2232 patients who had active TB between 1997 and 2006 (records obtained from the British Columbia Linked Health Databases). Patients with a record of an initial health care contact preceding the diagnosis of TB were identified for inclusion. Health care delay was defined as the time between initial health care contact and the initiation of anti-tuberculosis medication, and was compared between patients prescribed antibiotics and those not exposed to any antibiotics.

RESULTS

A total of 1544 patients were included. After adjusting for covariates, average health care delay for patients exposed to antibiotics was found to be significantly greater, by a factor of 2.10 (95%CI 1.80-2.44), with a median delay of 41 days in the antibiotic group compared to 14 days in the non-antibiotic group. Sex, age, foreign-born status and socio-economic status were non-significant factors. Health care delay increased with the number of antibiotic courses received, but not with the type of antibiotic.

CONCLUSIONS

Previous treatment with any antibiotic, and not only a FQ, is associated with a delay in TB diagnosis.

Risk of tuberculosis in screened subjects without known risk factors for active disease

SETTING

Tuberculosis (TB) referral clinic in Vancouver, British Columbia, Canada.

BACKGROUND

Screening for and treatment of latent TB infection (LTBI) in at-risk populations are the cornerstone of TB control in low-incidence countries. Persons at low risk often undergo the tuberculin skin test (TST) for reasons other than contact. Little information exists on the actual risk of TB in this population.

OBJECTIVE

To determine the risk of TB in screened subjects without known risk factors.

DESIGN

Retrospective descriptive analysis of demographics, TST reaction size and TB disease occurrence in 98333 low-risk subjects screened from 1990 to 2002.

RESULTS

The average annual disease rate was 0.4 per 100000 population (cumulative rate 7.4/100000) from 1990 to 2006, and TB was diagnosed only in the foreign-born. Risk of TB in the foreign-born increased with larger TST reaction size (P < 0.03). Completion of treatment for LTBI was not documented for any of the subsequent active TB cases.

CONCLUSION

In a low-risk screened population, active TB disease was found only in the foreign-born. Treatment of LTBI is not recommended in persons with a positive TST and no additional risk factors. Local screening programs should focus on populations with confirmed risk factors for disease.

Investigation of suspected laboratory cross-contamination: interpretation of single smear-negative, positive cultures for Mycobacterium tuberculosis

Restriction fragment length polymorphism (RFLP) analysis can be used to assess genetic relatedness of Mycobacterium tuberculosis isolates. This study reports a collaborative investigation of false-positive cultures for M. tuberculosis, suspected when the DNA fingerprint from an index case matched an epidemiologically improbable source case. RFLP analysis matched fingerprints in ten of 16 cases of suspected laboratory contamination to four separate smear-positive sources that were processed on the same day in the same laboratory. All single smear-negative, positive cultures processed on the same day as smear-positive specimens should be reviewed on a case-by-case basis to identify possible false-positive cultures.

BCG vaccination and the prevalence of latent tuberculosis infection in an aboriginal population

SETTING

Estimations of prevalence of latent tuberculous infection (LTBI) are confounded by factors known to influence the results of the tuberculin skin test (TST) such as age, contact history and bacille Calmette-Guerin (BCG) vaccination. Appropriate interpretation of TST results is necessary to ensure LTBI treatment for those at greatest risk.

OBJECTIVE

To document the prevalence of LTBI in Aboriginal people living on a reserve in British Columbia (BC) and to determine the influence of BCG.

DESIGN

A population-based, retrospective descriptive analysis of all epidemiological data collected for the on-reserve Aboriginal programme in BC (1951-1996).

RESULTS

Of 17615 persons who received a TST during the study period, 42% had received BCG. During the study period, an average of 2517 TSTs were completed per year (SD = 1228) among persons with an average age of 26 years (SD = 16). Among all subjects, the average prevalence of LTBI was 25% (95 %CI 24-25). The presence of BCG (OR = 3.1, 95%CI 2.8-3.4) and multiple BCGs (OR = 10.2, 95%CI 7.7-13.6) were both associated with a positive TST. A positive TST was also associated with a shorter duration in years between the most recent BCG and the TST.

CONCLUSION

The average prevalence of LTBI in a sequential sample of Aboriginal people living on a reserve in BC was estimated at 25%. BCG, especially in multiple doses, increased the likelihood of a positive TST.

Risk of tuberculosis in children from smear-negative source cases

SETTING

British Columbia, Canada.

OBJECTIVE

To determine the frequency of smear-negative tuberculosis (TB) transmission events from adults to children in epidemiologically linked pairs and to determine the predictors for identifying the source case.

DESIGN

We extracted demographic, clinical and mycobacteriology information of 190 children with TB and their 83 source cases reported from 1990 to 2001 in the province of British Columbia. Smear-negative transmission events from adults to children were determined by identifying the smear results of epidemiologically linked source cases. We compared the sex, age, ethnicity, contact history, site of disease and tuberculin skin test (TST) results of children who had a source case identified with those who had not.

RESULTS

Smear-negative source cases transmitted the disease to 10% of children (95%CI 5-17). Aboriginals (OR 4.9, 95%CI 1.5-13.4), those with primary TB (OR 7.3, 95%CI 3.3-16.0) and those with a positive TST (OR 2.9, 95%CI 1.2-7.0) were independent predictors for source case identification.

CONCLUSION

This study suggests lower rates of transmission of disease to children from smear-negative sources compared to other studies involving all ages. Ethnicity of children, site of disease and a positive TST predict source case identification.

Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae

A group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (=ATCC BAA-614T=DSM 44648T).

Mycobacterium saskatchewanense sp. nov., a novel slowly growing scotochromogenic species from human clinical isolates related to Mycobacterium interjectum and Accuprobe-positive for Mycobacterium avium complex

A pigmented, slowly growing Mycobacterium avium complex AccuProbe-positive organism was isolated from the sputum and pleural fluid of a 72-year-old female with bronchiectasis. The unusual morphology of the organism prompted further identification by 16S rRNA gene sequencing, revealing a perfect identity with previously uncharacterized strain Mycobacterium sp. MCRO 8 (GenBank accession no. X93034), with the closest established species by 16S rDNA analysis being Mycobacterium interjectum. HPLC of the organism corresponded to previously obtained patterns identified as M. interjectum-like and, upon sequence evaluation of a selection of strains with a similar profile, more were subsequently identified as MCRO 8. A total of 16 strains isolated from human respiratory samples were evaluated in the characterization of this novel species, for which the name Mycobacterium saskatchewanense sp. nov. is proposed. The type strain is strain 00-250T (=ATCC BAA-544T=DSM 44616T=CIP 108114T).

Bullae, bronchiectasis and nutritional emphysema in severe anorexia nervosa

STUDY OBJECTIVES

Pulmonary complications of anorexia nervosa are rarely documented. The case of a patient with anorexia nervosa and pulmonary disease is presented, a new quantitative computed tomography (CT) method for the detection of emphysema is employed, the literature is reviewed and the concept of 'nutritional' emphysema is discussed.

RESULTS

The case of a 34-year-old, nonsmoking woman with long-standing severe anorexia nervosa who was evaluated for cough and progressive shortness of breath is reported. Pulmonary function testing showed a predominant restrictive pattern with a marked reduction in carbon monoxide transfer and respiratory muscle strength, and an elevated residual volume. Imaging revealed bullae and bronchiectasis, and quantitative analysis of the CT scan was consistent with mild, generalized emphysema. Bronchial washings grew Pseudomonas aeruginosa. Known causes for bronchiectasis were excluded. A literature review disclosed few reported noninfectious pulmonary complications of anorexia nervosa.

CONCLUSIONS

To the authors' knowledge, this is the first report of bullae and bronchiectasis in a patient with anorexia nervosa, and the CT analysis was consistent with mild emphysema. Malnutrition has been associated with emphysematous changes in animals and may be the primary insult in the development of emphysema, bullae and bronchiectasis in the present patient.