Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients.

BACKGROUND: Underlying coinfections may complicate infectious disease states but commonly go unnoticed because an a priori clinical suspicion is usually required so they can be detected via targeted diagnostic tools. Shotgun metagenomics is a broad diagnostic tool that can be useful for identifying multiple microbes simultaneously especially if coupled with lymph node aspirates, a clinical matrix known to house disparate pathogens. The objective of this study was to analyze the utility of this unconventional diagnostic approach (shotgun metagenomics) using clinical samples from human tularemia cases as a test model. Tularemia, caused by the bacterium Francisella tularensis, is an emerging infectious disease in Turkey. This disease commonly manifests as swelling of the lymph nodes nearest to the entry of infection. Because swollen cervical nodes are observed from many different types of human infections we used these clinical sample types to analyze the utility of shotgun metagenomics. METHODS: We conducted an unbiased molecular survey using shotgun metagenomics sequencing of DNA extracts from fine-needle aspirates of neck lymph nodes from eight tularemia patients who displayed protracted symptoms. The resulting metagenomics data were searched for microbial sequences (bacterial and viral). RESULTS: F. tularensis sequences were detected in all samples. In addition, we detected DNA of other known pathogens in three patients. Both Hepatitis B virus (HBV) and Human Parvovirus B-19 were detected in one individual and Human Parvovirus B-19 alone was detected in two other individuals. Subsequent PCR coupled with Sanger sequencing verified the metagenomics results. The HBV status was independently confirmed via serological diagnostics, despite evading notice during the initial assessment. CONCLUSION: Our data highlight that shotgun metagenomics of fine-needle lymph node aspirates is a promising clinical diagnostic strategy to identify coinfections. Given the feasibility of the diagnostic approach demonstrated here, further steps to promote integration of this type of diagnostic capability into mainstream clinical practice are warranted.

Acquisition of meningococcal serogroup W-135 carriage in Turkish Hajj pilgrims who had received the quadrivalent meningococcal polysaccharide vaccine.

Invasive meningococcal disease is a recognized public health problem worldwide, with a dynamic and changeable epidemiology. In Turkey, the second most common pathogenic meningococcal serogroup (after serogroup B) is W-135, including an epidemic in 2005, which has been strongly associated with Hajj pilgrims and their close contacts. In two studies conducted in 2010, we assessed meningococcal carriage in intending Turkish pilgrims to the Hajj when they attended to receive a plain polysaccharide vaccine against serogroups A, C, W-135, and Y and, upon their return, to determine the acquisition of meningococcal carriage by the pilgrims themselves and subsequently their household contacts. Nasopharyngeal swabs were obtained from pilgrims before the Hajj and upon their return. Swabs were then obtained from 39 household contacts of pilgrims who were shown to have acquired carriage during the Hajj. Of the 472 pilgrims before the Hajj, 63 (13%) were positive for meningococcal carriage, of which 52 cases (83%) were serogroup W-135. In the 296 pilgrims tested after the Hajj, 81 (27%) were positive for meningococcal carriage, including 74 (91%) with W-135. In 11 family members of pilgrims who acquired W-135 carriage at the Hajj, 10 (91%) had acquired carriage of serogroup W-135. This study illustrates the acquisition of meningococcal carriage, predominantly of serogroup W-135 by pilgrims attending the Hajj, and the transmission of this carriage to their family members on their return, explaining the source of W-135 meningococcal disease in Turkey.