A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI ("sequence-based ultrarapid pathogen identification"), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.

Fatal Plasmodium falciparum, Clostridium perfringens, and Candida spp. Coinfections in a Traveler to Haiti.

Malaria is one of the most common causes of febrile illness in travelers. Coinfections with bacterial, viral, and fungal pathogens may not be suspected unless a patient fails to respond to malaria treatment. Using novel immunohistochemical and molecular techniques, Plasmodium falciparum, Clostridium perfringens, and Candida spp. coinfections were confirmed in a German traveler to Haiti. Plasmodium falciparum-induced ischemia may have increased this patient's susceptibility to C. perfringens and disseminated candidiasis leading to his death. When a patient presents with P. falciparum and shock and is unresponsive to malaria treatment, secondary infections should be suspected to initiate appropriate treatment.

Neuroinvasion by Mycoplasma pneumoniae in acute disseminated encephalomyelitis.

We report the autopsy findings for a 45-year-old man with polyradiculoneuropathy and fatal acute disseminated encephalomyelitis after having Mycoplasma pneumoniae pneumonia. M. pneumoniae antigens were demonstrated by immunohistochemical analysis of brain tissue, indicating neuroinvasion as an additional pathogenetic mechanism in central neurologic complications of M. pneumoniae infection.

Fatal malaria infection in travelers: novel immunohistochemical assays for the detection of Plasmodium falciparum in tissues and implications for pathogenesis.

Plasmodium falciparum is a significant cause of morbidity and mortality in travelers to areas where the parasite is endemic. Non-specific clinical manifestations may result in failure to recognize malaria until autopsy, when it is often too late to obtain whole blood for microscopic evaluation. The use of immunohistochemical (IHC) assays in the detection of three P. falciparum antigens, histidine rich protein-2 (HRP-2), aldolase, and Plasmodium lactate dehydrogenase (pLDH), was evaluated in formalin-fixed paraffin-embedded autopsy tissues from five travelers to malaria-endemic areas, whose deaths were initially suspected to have been caused by other bacterial or viral hemorrhagic fevers. The HRP-2 assay was specific for P. falciparum, whereas the aldolase and pLDH assays also reacted with P. vivax. Immunostaining patterns were predominately cytoplasmic and membranous. P. falciparum antigens were detected in a variety of organs but were most abundant in the blood vessels of brain, heart, and lung tissues.

A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice.

No single animal model for severe acute respiratory syndrome (SARS) reproduces all aspects of the human disease. Young inbred mice support SARS-coronavirus (SARS-CoV) replication in the respiratory tract and are available in sufficient numbers for statistical evaluation. They are relatively inexpensive and easily accessible, but their use in SARS research is limited because they do not develop illness following infection. Older (12- to 14-mo-old) BALB/c mice develop clinical illness and pneumonitis, but they can be hard to procure, and immune senescence complicates pathogenesis studies. We adapted the SARS-CoV (Urbani strain) by serial passage in the respiratory tract of young BALB/c mice. Fifteen passages resulted in a virus (MA15) that is lethal for mice following intranasal inoculation. Lethality is preceded by rapid and high titer viral replication in lungs, viremia, and dissemination of virus to extrapulmonary sites accompanied by lymphopenia, neutrophilia, and pathological changes in the lungs. Abundant viral antigen is extensively distributed in bronchial epithelial cells and alveolar pneumocytes, and necrotic cellular debris is present in airways and alveoli, with only mild and focal pneumonitis. These observations suggest that mice infected with MA15 die from an overwhelming viral infection with extensive, virally mediated destruction of pneumocytes and ciliated epithelial cells. The MA15 virus has six coding mutations associated with adaptation and increased virulence; when introduced into a recombinant SARS-CoV, these mutations result in a highly virulent and lethal virus (rMA15), duplicating the phenotype of the biologically derived MA15 virus. Intranasal inoculation with MA15 reproduces many aspects of disease seen in severe human cases of SARS. The availability of the MA15 virus will enhance the use of the mouse model for SARS because infection with MA15 causes morbidity, mortality, and pulmonary pathology. This virus will be of value as a stringent challenge in evaluation of the efficacy of vaccines and antivirals.

Utility of the aged BALB/c mouse model to demonstrate prevention and control strategies for severe acute respiratory syndrome coronavirus (SARS-CoV).

The causative agent of Severe Acute Respiratory Syndrome (SARS) was identified as a coronavirus (CoV) following the outbreak of 2002-2003. There are currently no licensed vaccines or treatments for SARS-CoV infections. Potential prevention and control strategies that show promise in vitro must be evaluated in animal models. The aged BALB/c mouse model for SARS supports a high level of viral replication in association with clinical illness and disease that mimics SARS in the elderly. We tested two preventive strategies, vaccination and passive transfer of serum antibody, to determine the extent of protection achieved against SARS-CoV challenge in this model. These approaches were able to achieve or induce antibody titers sufficient to reduce viral load, protect from weight loss and reduce or eliminate histopathologic changes in the lungs of aged mice. This study validates the utility of the aged BALB/c mouse model for evaluation of the efficacy of vaccines and immunoprophylaxis.

Response of religious groups to HIV/AIDS as a sexually transmitted infection in Trinidad.

BACKGROUND: HIV/AIDS-related stigma and discrimination are significant determinants of HIV transmission in the Caribbean island nation of Trinidad and Tobago (T&T), where the adult HIV/AIDS prevalence is 2.5%. T&T is a spiritually-aware society and over 104 religious groups are represented. This religious diversity creates a complex social environment for the transmission of a sexually transmitted infection like HIV/AIDS. Religious leaders are esteemed in T&T's society and may use their position and frequent interactions with the public to promote HIV/AIDS awareness, fight stigma and discrimination, and exercise compassion for people living with HIV/AIDS (PWHA). Some religious groups have initiated HIV/AIDS education programs within their membership, but previous studies suggest that HIV/AIDS remains a stigmatized infection in many religious organizations. The present study investigates how the perception of HIV/AIDS as a sexually transmitted infection impacts religious representatives' incentives to respond to HIV/AIDS in their congregations and communities. In correlation, the study explores how the experiences of PWHA in religious gatherings impact healing and coping with HIV/AIDS. METHODS: Between November 2002 and April 2003, in-depth interviews were conducted with 11 religious representatives from 10 Christian, Hindu and Muslim denominations. The majority of respondents were leaders of religious services, while two were active congregation members. Religious groups were selected based upon the methods of Brathwaite. Briefly, 26 religious groups with the largest followings according to 2000 census data were identified in Trinidad and Tobago. From this original list, 10 religious groups in Northwest Trinidad were selected to comprise a representative sample of the island's main denominations. In-depth interviews with PWHA were conducted during the same study period, 2002-2003. Four individuals were selected from a care and support group located in Port of Spain based upon their perceived willingness to discuss religious affiliation and describe how living with a terminal infection has affected their spiritual lives. The interviewer, a United States Fulbright Scholar, explained the nature and purpose of the study to all participants. Relevant ethical procedures associated with the collection of interview data were adopted: interviews were conducted in a non-coercive manner and confidentiality was assured. All participants provided verbal consent, and agreed to be interviewed without financial or other incentive. Ethics approval was granted on behalf of the Caribbean Conference of Churches Ethics Committee. Interview questions followed a guideline, and employed an open-ended format to facilitate discussion. All interviews were recorded and transcribed by the interviewer. RESULTS: Religious representatives' opinions were grouped into the following categories: rationale for the spread of HIV/AIDS, abstinence, condom use, sexuality and homosexuality, compassion, experiences with PWHA, recommendations and current approach to addressing HIV/AIDS in congregations. Religious representatives expressed a measure of acceptance of HIV/AIDS and overwhelmingly upheld compassion for PWHA. Some statements, however, suggested that HIV/AIDS stigma pervades Trinidad's religious organizations. For many representatives, HIV/AIDS was associated with a promiscuous lifestyle and/or homosexuality. Representatives had varying levels of interaction with PWHA, but personal experiences were positively associated with current involvement in HIV/AIDS initiatives. All 4 PWHA interviewed identified themselves as belonging to Christian denominations. Three out of the 4 PWHA described discriminatory experiences with pastors or congregation members during gatherings for religious services. Nonetheless, PWHA expressed an important role for faith and religion in coping with HIV. CONCLUSION: Religious groups in Trinidad are being challenged to promote a clear and consistent response to the HIV/AIDS epidemic; a response that may reflect personal experiences and respect religious doctrine in the context of sex and sexuality. The study suggests that (1) religious leaders could improve their role in the fight against HIV/AIDS with education and sensitization-specifically aimed at dismantling the myths about HIV transmission, and the stereotyping of susceptible sub-populations, and (2) a consultative dialogue between PWHAs and religious leaders is pivotal to a successful faith-based HIV intervention in Trinidad.

Response of religious groups to HIV/AIDS as a sexually transmitted infection in Trinidad

BACKGROUND: HIV/AIDS-related stigma and discrimination are significant determinants of HIV transmission in the Caribbean island nation of Trinidad and Tobago (T&T), where the adult HIV/AIDS prevalence is 2.5%. T&T is a spiritually-aware society and over 104 religious groups are represented. This religious diversity creates a complex social environment for the transmission of a sexually transmitted infection like HIV/AIDS. Religious leaders are esteemed in T&T's society and may use their position and frequent interactions with the public to promote HIV/AIDS awareness, fight stigma and discrimination, and exercise compassion for people living with HIV/AIDS (PWHA). Some religious groups have initiated HIV/AIDS education programs within their membership, but previous studies suggest that HIV/AIDS remains a stigmatized infection in many religious organizations. The present study investigates how the perception of HIV/AIDS as a sexually transmitted infection impacts religious representatives' incentives to respond to HIV/AIDS in their congregations and communities. In correlation, the study explores how the experiences of PWHA in religious gatherings impact healing and coping with HIV/AIDS. METHODS: Between November 2002 and April 2003, in-depth interviews were conducted with 11 religious representatives from 10 Christian, Hindu and Muslim denominations. The majority of respondents were leaders of religious services, while two were active congregation members. Religious groups were selected based upon the methods of Brathwaite. Briefly, 26 religious groups with the largest followings according to 2000 census data were identified in Trinidad and Tobago. From this original list, 10 religious groups in Northwest Trinidad were selected to comprise a representative sample of the island's main denominations. In-depth interviews with PWHA were conducted during the same study period, 2002-2003. Four individuals were selected from a care and support group located in Port of Spain based upon their perceived willingness to discuss religious affiliation and describe how living with a terminal infection has affected their spiritual lives. The interviewer, a United States Fulbright Scholar, explained the nature and purpose of the study to all participants. Relevant ethical procedures associated with the collection of interview data were adopted: interviews were conducted in a non-coercive manner and confidentiality was assured. All participants provided verbal consent, and agreed to be interviewed without financial or other incentive. Ethics approval was granted on behalf of the Caribbean Conference of Churches Ethics Committee. Interview questions followed a guideline, and employed an open-ended format to facilitate discussion. All interviews were recorded and transcribed by the interviewer. RESULTS: Religious representatives' opinions were grouped into the following categories: rationale for the spread of HIV/AIDS, abstinence, condom use, sexuality and homosexuality, compassion, experiences with PWHA, recommendations and current approach to addressing HIV/AIDS in congregations. Religious representatives expressed a measure of acceptance of HIV/AIDS and overwhelmingly upheld compassion for PWHA. Some statements, however, suggested that HIV/AIDS stigma pervades Trinidad's religious organizations. For many representatives, HIV/AIDS was associated with a promiscuous lifestyle and/or homosexuality. Representatives had varying levels of interaction with PWHA, but personal experiences were positively associated with current involvement in HIV/AIDS initiatives. All 4 PWHA interviewed identified themselves as belonging to Christian denominations. Three out of the 4 PWHA described discriminatory experiences with pastors or congregation members during gatherings for religious services. Nonetheless, PWHA expressed an important role for faith and religion in coping with HIV. CONCLUSION: Religious groups in Trinidad are being challenged to promote a clear and consistent response to the HIV/AIDS epidemic; a response that may reflect personal experiences and respect religious doctrine in the context of sex and sexuality. The study suggests that (1) religious leaders could improve their role in the fight against HIV/AIDS with education and sensitization-specifically aimed at dismantling the myths about HIV transmission, and the stereotyping of susceptible sub-populations, and (2) a consultative dialogue between PWHAs and religious leaders is pivotal to a successful faith-based HIV intervention in Trinidad.