www.nature.com/scientificreports OPEN Disentangling etiologies of CNS infections in Singapore using multiple correspondence analysis and random forest Raphaël M. Zellweger1,2, Sophie Yacoub3, Yvonne F. Z. Chan4, Derek Soon5, Humaira Shaf6, Say Tat Ooi7, Monica Chan8, Leslie Jacobson9, October M. Sessions1,10,11, Angela Vincent9, Jenny Guek Hong Low1,4, Eng Eong Ooi1,2,3,10,12, Linfa Wang1, Limin Wijaya4,14, Kevin Tan 13,14* & the Singapore Neurologic Infections Program (SNIP) Central nervous system (CNS) infections cause substantial morbidity and mortality worldwide, with mounting concern about new and emerging neurologic infections. Stratifying etiologies based on initial clinical and laboratory data would facilitate etiology-based treatment rather than relying on empirical treatment. Here, we report the epidemiology and clinical outcomes of patients with CNS infections from a prospective surveillance study that took place between 2013 and 2016 in Singapore. Using multiple correspondence analysis and random forest, we analyzed the link between clinical presentation, laboratory results, outcome and etiology. Of 199 patients, etiology was identifed as infectious in 110 (55.3%, 95%-CI 48.3–62.0), immune-mediated in 10 (5.0%, 95%-CI 2.8–9.0), and unknown in 79 patients (39.7%, 95%-CI 33.2–46.6). The initial presenting clinical features were associated with the prognosis at 2 weeks, while laboratory-related parameters were related to the etiology of CNS disease. The parameters measured were helpful to stratify etiologies in broad categories, but were not able to discriminate completely between all the etiologies. Our results suggest that while prognosis of CNS is clearly related to the initial clinical presentation, pinpointing etiology remains challenging. Bio-computational methods which identify patterns in complex datasets may help to supplement CNS infection diagnostic and prognostic decisions. Abbreviations ADEM Acute disseminated encephalomyelitis CASPR2 Contactin-associated protein 2 CNS Central nervous system CSF Cerebrospinal fuid GABAAR​ Gamma-aminobutyric acidA receptor GAD Glutamic acid decarboxylase HIV Human immunodefciency virus HSV Herpes simplex virus 1Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore. 2Viral Research and Experimental Medicine Center, SingHealth/Duke-NUS, Singapore, Singapore. 3Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance in Research and Technology, Singapore, Singapore. 4Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore. 5Department of Neurology, National University Hospital, Singapore, Singapore. 6Department of General Medicine, Changi General Hospital, Singapore, Singapore. 7Department of Medicine, Khoo Teck Puat Hospital, Singapore, Singapore. 8Infectious Diseases Department, Tan Tock Seng Hospital, Singapore, Singapore. 9Nufeld Department of Clinical Neurosciences, John Radclife Hospital, University of Oxford, Oxford, UK. 10Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore. 11Department of Pharmacy, National University of Singapore, Singapore, Singapore. 12Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore. 13Department of Neurology, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore. 14These authors contributed equally: Limin Wijaya and Kevin Tan. *email: [email protected] Scientifc Reports | (2020) 10:18219 | https://doi.org/10.1038/s41598-020-75088-4 1 Vol.:(0123456789) www.nature.com/scientificreports/ JEV Japanese encephalitis virus LGI1 Leucine-rich glioma inactivated 1 MCA Multiple correspondence analysis mRS Modifed Rankin Scale NMDAR N-Methyl-d-aspartate receptor PCA Principal component analysis RF Random forest TB Tuberculosis VGKC Voltage-gated potassium channel VZV Varicella zoster virus WBC White blood cells Infections of the central nervous system (CNS) cause substantial morbidity and mortality worldwide1. Tey can be caused by bacteria, viruses, fungi, protozoa and parasites, but ofen the etiology remains unknown 2. Patients with CNS infections may present with fever, headache, photophobia, and/or neck stifness, seizures, altered consciousness and/or focal neurological signs or a combination of these features3. Encephalitis, most commonly of viral etiology, is associated with poor outcomes4. In a subset of cases, the presence of autoantibodies to cell- surface neuronal or glial proteins suggest an autoimmune etiology2,5. Concern is growing about novel neurologic infections6, due to the emergence of new pathogens, the spread of existing pathogens to new regions as a consequence of globalization, climate change, increased virulence of existing pathogens and increasing numbers of immunocompromised patients 7–9. Tis is particularly true for Southeast Asia, a focal point for zoonotic and vector-borne diseases emergence 10,11. Singapore, a global transit hub, has recently experienced outbreaks of CNS infections of public health importance, including encephalitis from Nipah virus12,13, H1N1 infuenza with neurological complications 14,15 and meningoencephalitis from Group B Streptococcal infection16,17. However, etiological data of CNS infections in Singapore remain limited. A better understanding of CNS infection epidemiology would improve clinical management and public health. Te diagnosis of CNS infection is notoriously difcult, and early treatment is ofen empirical. Timely identi- fcation of the etiologic agent is crucial to optimize clinical care, as disease outcome ofen depends on tailoring treatment for the infectious agent18. Tis challenge is compounded by (1) the limited accessibility of the tis- sue where pathogen replication occurs, (2) the absence, in most clinical laboratories, of sensitive methods for molecular and serological detection of infection and (3) the lack of consensus on case defnitions and standard- ized diagnostic approaches 19. Categorizing patients into the types of CNS infections and postulating stratifed etiologies based on initial clinical presentation and laboratory results would help rationalize early investigations and target treatments for the most likely etiologies. Here, we report the epidemiology and clinical outcomes of patients with CNS infections from the Singapore Neurologic Infections Program (SNIP), a prospective surveillance study. We used multiple correspondence analy- sis (MCA) and random forest (RF) to uncover patterns in our complex dataset 20,21 and explore the relationship between initial clinical presentation, laboratory results, outcome at 2 weeks, and the etiology of CNS infections. Results Etiology, demographics and epidemiology. In this study, 2061 patients were screened; 277 were recruited and 199 were included in the analysis (Fig. 1). An infectious agent was identifed in 110/199 patients (55.3%, 95%-CI 48.3–62.0), an immune-mediated etiology in 10/199 (5.0%, 95%-CI 2.8–9.0), and 79/199 patients (39.7%, 95%-CI 33.2–46.6) had unknown etiology. Among the 110 cases with an infectious etiology, bacteria (excluding tuberculosis, TB) was the most common (50/110, 45.5%, 95%-CI 36.5–54.8), followed by virus (33/110, 30.0%, 95%-CI 22.2–39.1), TB (22/110, 20.0%, 95%-CI 13.6–28.4) and fungus (5/110, 4.5%, 95%- CI 2.0–10.2) (Table 1). Te most common specifc infectious cause was Mycobacterium tuberculosis (22/199, 11.1%, 95%-CI 7.4–16.1), followed by Group B Streptococcus (17/199, 8.5%, 95%-CI 5.4–13.3), Treponema pal- lidum (13/199, 6.5%, 95%-CI 3.9–10.9), varicella zoster virus (VZV) (12/199, 6.0%, 95%-CI 3.5–10.2), Strep- tococcus pneumoniae (11/199, 5.5%, 95%-CI 3.1–9.6) and herpes simplex virus (HSV) (10/199, 5.0%, 95%-CI 2.8–9.0). Te demographic characteristics of the patients were not signifcantly diferent across etiologies, except for the presence of comorbidities and the HIV status (Supplementary Table 1). In the 14 HIV-positive patients, Treponema pallidum was the most common etiology, followed by cytomegalovirus (CMV) and Cryptococcus neo- formans (Supplementary Table 2). Cerebrospinal fuid (CSF) results are summarized in Supplementary Table 3. Of the 10 immune-mediated cases, 7 were diagnosed locally based on clinico-serological data: 3 N-methyl- D-aspartate receptor (NMDAR) encephalitis, and 1 each of voltage-gated potassium channel (VGKC) complex encephalitis, glutamic acid decarboxylase (GAD) encephalitis, acute disseminated encephalomyelitis (ADEM) and Bickerstaf encephalitis. Results from the Oxford Neuroimmunology laboratory identifed additional 3 cases with NMDAR encephalitis. Figure 2A,B show the absolute counts and percentages of patients with meningitis, encephalitis or meningoen- cephalitis stratifed by etiology. Bacterial and TB infections caused both meningitis and meningoencephalitis; fungal infections caused only meningitis. Interestingly, viral infections and the unknown etiology group had similar proportions of all 3 syndromes. Te counts and percentages of good or poor outcomes (as measured by the modifed Rankin Scale (mRS) score ≤ 2 or ≥ 3, respectively) at two weeks and six months, stratifed by etiology, are shown in Fig. 2C–F. At 2 weeks, fungal infections caused greatest morbidity, with poor outcomes in more than 75% of cases, followed by autoimmune etiology, TB and bacterial infections. Similarly, viral infections and the unknown etiology group had similar proportions of good and poor outcomes. Scientifc Reports | (2020) 10:18219 | https://doi.org/10.1038/s41598-020-75088-4