Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections

Abstract

Background Osteoarticular infections (OAI) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children. Methods This was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children’s hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon’s discretion per standard care (fluid or tissue) and based on imagining and operative findings. We compared mNGS to culture and usual care testing (culture and PCR) from the same site. Results We recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In four subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS. Conclusion In this single site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.

Case report: A prosthetic valve endocarditis caused by Legionella bozemanae in an immunocompetent patient

“…Unfortunately, as of today no such method has shown satisfactory performance. Metagenomic next-generation sequencing of plasma is suggested as a promising aid in systemic infections, although both false positive and false negative results, as well as the noise of polymicrobial identification can make interpretation of results challenging ( 30 – 32 ). Our 16S Nanopore sequencing of the patient’s serum were not able to detect any Legionella .…”

Enhancing Diagnostics in Orthopedic Infections

“…Metagenomic next-generation sequencing has also been evaluated as a diagnostic tool for bone and joint infection in the pediatric population, an area of significant importance for enhancing diagnostics, given the relative frequency of bone and joint infections and the challenges with invasive sampling. In their single site study of 42 operative culture samples, Ramchandar et al ( 40 ) found that the overall performance of mNGS was similar to that of usual care testing, with mNGS identifying a pathogen in 26 cases (61.9%) and usual care identifying a pathogen in 24 cases (57.1%). There were 4 cases in which mNGS identified a pathogen (2 cases of Neisseria gonorrhoeae arthritis, 1 case of Brevundimonas vesicularis osteomyelitis, and 1 case of Kingella kingae osteomyelitis) where usual care testing (culture and PCR) was negative.…”

The Past, Present, and Future of Kingella kingae Detection in Pediatric Osteoarthritis

“…In theory, mNGS can detect any pathogen, and currently, this technology can unambiguously identify > 1400 species, and the turnaround time has been shortened to 1–2 days [ 56 ]. The detection and identification can be performed without a priori knowledge of the suspected etiologic agent, and, providing a comprehensive database grounded on single nucleotide polymorphisms is available, a resolution at the subspecies or strain level can be achieved [ 57 ].…”

“…Therefore, reports on the use of mNGS in diagnosing pediatric skeletal system infections, in general, and the specific detection of Kingella kingae , in particular, are scarce. Ramchandar performed mNGS on joint and bone samples of 42 children with suspected acute skeletal system infections and compared the results with those obtained by cultures and NAATs [ 56 ]. Overall, 26 (61.9%) children had a putative pathogen detected by mNGS vs. 24 (57.1%) detected by the comparators.…”

“…However, a timely mNGS diagnosis may avoid the performance of less informative tests and costly risky diagnostic procedures and shorten hospital stays. The sensitivity of mNGS remains suboptimal and only comparable, but not superior, to that of NAATs [ 60 ], and microorganisms detected by routine microbiological methods can be overlooked by mNGS [ 56 ]. Although unbiased testing can be an advantage because it may reveal unexpected pathogens, mNGS provides no information on antimicrobial susceptibility and resistance.…”