Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma

Dogs across the globe are afflicted by diverse blood- and vector-borne bacteria (VBB), many of which cause severe disease and can be fatal. Diagnosis of VBB infections can be challenging due to the low concentration of bacteria in the blood, the frequent occurrence of coinfections, and the wide range of known, emerging, and potentially novel VBB species encounterable. Therefore, there is a need for diagnostics that address these challenges by being both sensitive and capable of detecting all VBB simultaneously. We detail the first employment of a nanopore-based sequencing methodology conducted on the Oxford Nanopore Technologies (ONT) MinION device to accurately elucidate the "hemobacteriome" from canine blood through sequencing of the full-length 16S rRNA gene. We detected a diverse range of important canine VBB, including Ehrlichia canis, Anaplasma platys, Mycoplasma haemocanis, Bartonella clarridgeiae, "Candidatus Mycoplasma haematoparvum", a novel species of hemotropic mycoplasma, and Wolbachia endosymbionts of filarial worms, indicative of filariasis. Our nanopore-based protocol was equivalent in sensitivity to both quantitative PCR (qPCR) and Illumina sequencing when benchmarked against these methods, achieving high agreement as defined by the kappa statistics (k > 0.81) for three key VBB. Utilizing the ability of the ONT' MinION device to sequence long read lengths provides an excellent alternative diagnostic method by which the hemobacteriome can be accurately characterized to the species level in a way previously unachievable using short reads. We envision our method to be translatable to multiple contexts, such as the detection of VBB in other vertebrate hosts, including humans, while the small size of the MinION device is highly amenable to field use. IMPORTANCE Blood- and vector-borne bacteria (VBB) can cause severe pathology and even be lethal for dogs in many regions across the globe. Accurate characterization of all the bacterial pathogens infecting a canine host is critical, as coinfections are common and emerging and novel pathogens that may go undetected by traditional diagnostics frequently arise. Deep sequencing using devices from Oxford Nanopore Technologies (ONT) provides a solution, as the long read lengths achievable provide species-level taxonomic identification of pathogens that previous short-read technologies could not accomplish. We developed a protocol using ONT' MinION sequencer to accurately detect and classify a wide spectrum of VBB from canine blood at a sensitivity comparable to that of regularly used diagnostics, such as qPCR. This protocol demonstrates great potential for use in biosurveillance and biosecurity operations for the detection of VBB in a range of vertebrate hosts, while the MinION sequencer's portability allows this method to be used easily in the field.

Detection and hazard assessment of pathogenic microorganisms in medical wastes

This study was undertaken to investigate the types and concentrations of microbial agents in various medical wastes as well as to characterize their survivals in these wastes at different temperatures for microbial risk assessment. Medical wastes collected from 5 major hospitals in South Korea were classified and stored at three different temperatures (-20, 6, and 30 degrees C). Presence of various microorganisms such as pathogenic viruses and bacteria were investigated by both cultivation and by (RT)-PCR assays. A number of (opportunistic) pathogenic bacteria, including Pseudomonas spp., Lactobacillus spp., Staphylococcus spp., Micrococcus spp., Kocuria spp., Brevibacillus spp., Microbacterium oxydans, and Propionibacterium acnes, were identified from the various medical wastes. In addition, pathogenic viruses such as noroviruses and hepatitis B virus were also detected in one of the human tissue wastes. Commonly identified bacterial and viral pathogens such as Pseudomonas spp., Corynebacterium diphtheriae, Escherichia coli, Staphylococcus spp., and respiratory synctial virus (RSV) were inoculated into either gauzes or diapers, and their survivals were characterized. Viral agents such as RSV showed poor survival in most environmental conditions, and demonstrated that various pathogens could be present in medical wastes but that the associated health risk appeared to be low. However, medical waste should be carefully controlled and monitored to prevent nosocomial infection associated with the exposure to these wastes.

Multiplexed identification of blood-borne bacterial pathogens by use of a novel 16S rRNA gene PCR-ligase detection reaction-capillary electrophoresis assay

We have developed a novel high-throughput PCR-ligase detection reaction-capillary electrophoresis (PCR-LDR-CE) assay for the multiplexed identification of 20 blood-borne pathogens (Staphylococcus epidermidis, Staphylococcus aureus, Bacillus cereus, Enterococcus faecalis, Enterococcus faecium, Listeria monocytogenes, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, Escherichia coli, Klebsiella pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Acinetobacter baumannii, Neisseria meningitidis, Bacteroides fragilis, Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella abortus), the last four of which are biothreat agents. The method relies on the amplification of two regions within the bacterial 16S rRNA gene, using universal PCR primers and querying the identity of specific single-nucleotide polymorphisms within the amplified regions in a subsequent LDR. The ligation products vary in color and size and are separated by CE. Each organism generates a specific pattern of ligation products, which can be used to distinguish the pathogens using an automated software program we developed for that purpose. The assay has been verified on 315 clinical isolates and demonstrated a detection sensitivity of 98%. Additionally, 484 seeded blood cultures were tested, with a detection sensitivity of 97.7%. The ability to identify geographically variant strains of the organisms was determined by testing 132 isolates obtained from across the United States. In summary, the PCR-LDR-CE assay can successfully identify, in a multiplexed fashion, a panel of 20 blood-borne pathogens with high sensitivity and specificity.

Infection risks following accidental exposure to blood or body fluids in health care workers: a review of pathogens transmitted in published cases

Hospital staff and all other human or veterinary health care workers, including laboratory, research, emergency service, or cleaning personnel are exposed to the risk of occupational infection following accidental exposure to blood or body fluids (BBF) contaminated with a virus, a bacteria, a parasite, or a yeast. The human immunodeficiency virus (HIV) or those of hepatitis B (HBV) or C (HCV) account for most of this risk in France and worldwide. Many other pathogens, however, have been responsible for occupational infections in health care workers following exposure to BBF, some with unfavorable prognosis. In developed countries, a growing number of workers are referred to clinicians responsible for the evaluation of occupational infection risks following accidental exposure. Although their principal task remains the evaluation of the risks of HIV, HBV, or HCV transmission and the possible usefulness of postexposure prophylaxis, these experts are also responsible for evaluating risks of occupational infection with other emergent or more rare pathogens and their possible timely prevention. The determinants of the risks of infection and the characteristics of described cases are discussed in this article.

Seroprevalence of human immunodeficiency virus, hepatitis B and C viruses and syphilis infections among blood donors at the Muhimbili National Hospital in Dar es Salaam, Tanzania

Background

According to the latest Tanzanian National AIDS Control Programme (NACP) report a total of 147,271 individuals donated blood during the year 2002. However, blood safety remains an issue of major concern in transfusion medicine in Tanzania where national blood transfusion services and policies, appropriate infrastructure, trained personnel and financial resources are inadequate. Most of the donated blood is screened for HIV alone.

Methods

We determined among blood donors at Muhimbili National Hospital (MNH), the seroprevalence of human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B surface antigen (HBsAg) and syphilis by donor type, sex and age and to determine association, if any, in the occurrence of the pathogens. The sample included 1599 consecutive donors, 1424(89.1%) males and 175 (10.9%) females, who donated blood between April 2004 and May, 2005. Most of them 1125 (70.4%) were replacement donors and a few 474 (29.6%) voluntary donors. Their age (in years) ranged from 16 to 69, and most (72.2%) were between 20–39 years.

Results

Two hundred and fifty four (15.9%) of the donated blood had serological evidence of infection with at least one pathogen and 28 (1.8%) had multiple infections. The current seroprevalence of HIV, HBsAg, HCV and syphilis among blood donors at MNH in Dar es Salaam was found to be 3.8%, 8.8%, 1.5% and 4.7%, respectively. Respective seroprevalences among HIV seronegative blood donors were 8.7% for HBV, 1.6% for HCV and 4.6% for syphilis. The differences in the prevalence of HIV and syphilis infections between replacement and voluntary donors were statistically significant (P < 0.05). Syphilis was the only infection that occurred more frequently among HIV infected (12.1%) than non-infected (4.6%) blood donors (P < 0.05), and whose prevalence increased with age (X² = 58.5 df = 5, P < 0.001). There were no significant sex differences in the occurrence of pathogens. Finally, there were significant associations in the occurrence of HBsAg and syphilis (OR = 2.2, 95% CI 1.1.-4.2) and HIV and syphilis (OR = 2.2, 95% CI 1.0–5.3).

Conclusion

The high (15.9%) seroprevalence of blood-borne infections in blood donated at MNH calls for routine screening of blood donors for HBV, HCV, HIV and syphilis and for strict selection criteria of donors, with emphasis on getting young voluntary donors and for establishment of strict guidelines for blood transfusions.

Ensuring the biologic safety of plasma-derived therapeutic proteins: detection, inactivation, and removal of pathogens

Human plasma-derived proteins, such as immunoglobulins, coagulation factors, α₁-antitrypsin, fibrin sealants, and albumin, are widely used as therapeutics for many serious and life-threatening medical conditions. The human origin of these proteins ensures excellent efficacy and compatibility but may also introduce the risk of unintentional disease transmission. Historically, only viruses, particularly hepatitis and HIV, have posed serious threats to the safety of these therapeutics. Fortunately, between 1970 and 1990, the molecular biology of each of the major viruses was elucidated. These advances led to the development and implementation of effective donor screening tests, mainly based on immunoassays and nucleic acid testing, which resulted in a significant reduction of disease transmission risk. In addition, viral inactivation and removal steps were implemented and validated by manufacturers, further reducing the risk associated with known, as well as unidentified, viruses. Since the late 1990s, a different class of transmissible agent, referred to as prions, has been identified as a new risk for disease transmission. However, prion diseases are very rare, and prion transmission through plasma-derived proteins has not been reported to date. The prion-related risk is minimized by deferring donors with certain key risk factors, and by the manufacturing processes that are capable of removing prions. Advances in science and pathogen safety-related technology, compliance with good manufacturing practices by manufacturers, and increasingly stringent regulatory oversight, has meant that plasma-derived proteins have been developed into today’s highly effective therapeutics with very low risk of disease transmission.

Virus safety of human blood, plasma, and derived products

The reconstitution of blood and its components is hampered by factors of compatibility, availability, and the risk of transmission of infectious diseases. Protozoal agents such as plasmodium malariae and trypanosoma cruzi are only regionally relevant. Bacterial transmissions are easy to prevent and treat. Antibody, antigen, and nucleic acid screening have been implemented to prevent transmission of blood-borne viruses. Transfusion-relevant viruses include hepatitis B and C virus (HBV and HCV), human immunodeficiency virus (HIV), human T leukemia virus (HTLV-I), and in certain circumstances, parvovirus B19, hepatitis A virus (HAV), and cytomegalovirus (CMV). Of great concern is the possible transmission of prion protein causing transmissible spongiform encephalopathy. Of future interest will be whether other viruses such as Nipah and Hendra virus are blood-borne and whether viruses such as TT, SEN, and GBV-C are involved in diseases or their progression, while not causing hepatitis.

[TT (TTV) Virus]

Characterization of TT virus (TTV), the history of its discovery, taxonomy and identification are reviewed as update on the diagnostics of TTV infection with PCR. The variability of the virus and resulting difficulties in the selection of a TTV DNA fragment for amplification are described. Data on the virus prevalence, replication and persistence are given. The pathogenetic importance of TTV is discussed with the account of different concepts.