Syphilis, a genital ulcerative disease caused by the bacterium Treponema pallidum, is associated with significant complications if left untreated. Syphilis rates in the United States have been increasing.

Syphilis is a sexually transmitted infection that remains a global health threat. The World Health Organization estimates that more than 12 million new cases are reported in adults annually worldwide. Syphilis rates are rising domestically as well. The rapid plasma reagin (RPR) test (including automated version) and the Venereal Disease Research Laboratory (VDRL) test are commercially available and used to detect/screen active infection.

According to 2010-2014 World Health Organization (WHO) research, dog-transmitted human rabies was present or suspected in 150 countries and territories worldwide. Domestic dogs were the most common reservoir of the rabies virus in these countries, and more than 99% of human deaths were caused by dog-transmitted rabies. Rabies is 100% preventable in dogs with appropriate administration of vaccines.

Within recent years, point-of-care (POC) testing has allowed for many individuals to be screened for and provided with HIV test results. It is critical to be able to accurately detect acute HIV infections as this is a stage where the risk of transmission is great. Additionally, early HIV detection could lead to less high-risk behavior, thereby reducing transmission. Currently, there are no rapid, cost-effective diagnostic tests sensitive enough to detect acute HIV-1 infections for the POC setting.

Zika virus infection during pregnancy can cause microcephaly and other severe birth defects. The CDC Zika MAC-ELISA (IgM antibody capture enzyme-linked immunosorbent assay) currently used for diagnosis detects antibodies produced to fight a Zika virus infection. However, reactivity of flavivirus antibodies (from exposure to other mosquito-borne infections such as dengue or West Nile virus) can complicate the interpretation of these results.

Streptococcus pneumoniae (S. pneumoniae) bacteria, or pneumococcus, can cause many types of illnesses. These range from ear and sinus infections to life-threatening conditions such as pneumonia, bloodstream infections, and meningitis. Pneumococci are surrounded by a polysaccharide capsule, which is thought to help it evade the immune system. Presently, over 90 known serotypes of S. pneumoniae have been identified, of which only a minority produce the majority of pneumococcal infections; a serotype is defined by a unique pneumococcal capsule structure.

Scrub typhus is a bacterial disease caused by Orientia tsutsugamushi (O. tsutsugamushi or Ots) that is spread to people through bites of infected chiggers (larval mites). The most common symptoms can include fever, headache, body aches, and sometimes rash. Severe illness can lead to organ failure and bleeding which can be fatal if left untreated. Most cases of scrub typhus occur in Asia Pacific countries, however, recent reports document establishment in the Arabian Peninsula, Chile, and possibly Kenya.

The U.S. Food and Drug Administration and World Health Organization (WHO) approved the antiretroviral drug emtricitabine (FTC)/ tenofovir disoproxil fumurate (TDF) combination for HIV pre-exposure prophylaxis (PrEP) in high risk populations. Efficacy of PrEP depends strongly on adherence to taking the FTC/TDF pill daily. In the US, the Centers for Disease Control and Prevention (CDC) estimates that 1.2 million Americans will benefit from PrEP. FTC is also a key component of antiretroviral therapy (ART) regimens of HIV-infected persons and significantly associated with adherence.

Clinical and biological specimens often contain microbial nucleic acid in extremely low quantities, presenting a significant challenge for the detection of viral and bacterial pathogens. This also prevents direct sequencing of non-culturable samples using next-generation sequencing (NGS). Currently, NGS library preparation on most platforms requires 0.1 ng to 10 µg of DNA or cDNA, while microbial or viral nucleic acids in clinically relevant specimens, such as blood, serum, respiratory secretions, cerebral spinal fluid, and stool, often contain less than 0.1 ng.

CDC researchers have developed a patented set of RT-PCR and sequencing primers based on HIV-1 group M sequences. Evaluation of the primers using samples collected around the world demonstrated broad detection capacity for multiple HIV-1 group subtypes and predominant circulating recombinant forms. Commercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limited ability to detect non-B subtypes. This optimized assay is broadly sensitive in genotyping HIV-1 group M viral strains and more sensitive than other assays in detecting mixed viral populations.