Thesis
Reference
Diagnostic Challenges in Acute Central Nervous System Infections in the 2020s
SCHIBLER, Manuel
Abstract
Acute central nervous system (CNS) infection can manifest as various distinct entities, according to the affected anatomic structures, hence the terms encephalitis, meningitis, meningoencephalitis, myelitis, encephalomyelitis, amongst others. Most of these syndromes are caused by viruses and bacteria, and less frequently by fungi and parasites. Some CNS diseases are caused by an aberrant immune response to microorganisms. Noninfectious CNS inflammation causes mimicking CNS infection include autoimmunity, as well as drug- related reactions. Given the numerous etiologies, which most often cannot be identified based on clinical manifestations, diagnosing CNS infections is challenging and requires broad knowledge in the field and sharp clinical sense, in order to appropriately tailor diagnostic and therapeutic strategies. This thesis comprises four original publications illustrating two aspects regarding the implication of routine and emerging diagnostic tools that can be used for viral CNS infection diagnosis. The first two deal with the use of high throughput sequencing (HTS) in cases of CNS inflammation of undetermined [...]
SCHIBLER, Manuel. Diagnostic Challenges in Acute Central Nervous System Infections in the 2020s. Thèse de privat-docent : Univ. Genève, 2021
DOI : 10.13097/archive-ouverte/unige:155980
Available at:
http://archive-ouverte.unige.ch/unige:155980
Disclaimer: layout of this document may differ from the published version.
1
2
3 4
Clinical Medicine Section 5
Department of Medicine 6
7 8 9 10 11
DIAGNOSTIC CHALLENGES IN ACUTE CENTRAL NERVOUS SYSTEM 12
INFECTIONS IN THE 2020s 13
14 15 16
Thesis submitted to the Faculty of Medicine of 17
the University of Geneva 18
19
for the degree of Privat-Docent 20
by 21
22 23 24
Manuel SCHIBLER 25
26 27 28 29 30
Geneva 31
32 33
2020 34
35 36 37 38
TABLE OF CONTENT 39 40
SUMMARY ... 3 41
INTRODUCTION ... 4 42
Infectious and noninfectious causes of CNS inflammation ... 5 43
Diagnostic approaches... 14 44
STUDY 1 SUMMARY : Viral Sequences Detection by High-Throughput Sequencing in 45
Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease . 18 46
STUDY 2 SUMMARY : Astrovirus MLB2, a New Gastroenteric Virus Associated with 47
Meningitis and Disseminated Infection ... 19 48
STUDY 3 SUMMARY : Compartmentalization of a Multidrug-Resistant Cytomegalovirus 49
UL54 Mutant in a Stem Cell Transplant Recipient with Encephalitis ... 20 50
STUDY 4 SUMMARY : Cerebrospinal fluid features in SARS-CoV-2 RT-PCR positive 51
patients ... 21 52
CONCLUSION ... 22 53
REFERENCES ... 29 54
PUBLISHED STUDIES ... 33 55
56 57 58 59 60 61 62 63 64 65 66 67 68 69 70
SUMMARY 71
Acute central nervous system (CNS) infection can manifest as various distinct entities, 72
according to the affected anatomic structures, hence the terms encephalitis, meningitis, 73
meningoencephalitis, myelitis, encephalomyelitis, amongst others. Most of these syndromes 74
are caused by viruses and bacteria, and less frequently by fungi and parasites. Some CNS 75
diseases are caused by an aberrant immune response to microorganisms. Noninfectious 76
CNS inflammation causes mimicking CNS infection include autoimmunity, as well as drug- 77
related reactions. Given the numerous etiologies, which most often cannot be identified 78
based on clinical manifestations, diagnosing CNS infections is challenging and requires 79
broad knowledge in the field and sharp clinical sense, in order to appropriately tailor 80
diagnostic and therapeutic strategies. 81
This thesis comprises four original publications illustrating two aspects regarding the 82
implication of routine and emerging diagnostic tools that can be used for viral CNS infection 83
diagnosis. The first two deal with the use of high throughput sequencing (HTS) in cases of 84
CNS inflammation of undetermined cause, and the last two exemplify how the judicious 85
application of routine microbiological diagnostic means can help to decipher a complex 86
CMV encephalitis case, as well as to extend the understanding of CNS disease caused by 87
an emerging viral disease, such as COVID-19. This selected work is put into perspective 88
with a more global approach aimed at improving and optimizing CNS infection diagnosis. 89
90 91 92 93 94 95 96 97 98 99 100 101
INTRODUCTION 102
The central nervous system (CNS) can be considered to be composed of two parenchymal 103
structures, the brain and the spinal cord, and of their surrounding structures, the meninges. 104
Any of these compartments can become acutely inflamed, and in various combinations, 105
hence the syndromes encephalitis, meningitis, meningoenephalitis, myelitis, 106
encephalomyeltis, meningomyelitis and meningoencephalomyelitis. Encephalopathy is a 107
distinct physiopathological process and refers to impaired CNS function without evidence of 108
inflamed tissues. 109
Although infections constitute the predominant causes of CNS inflammation, other 110
phsysiopathological mechanisms, such as dysimmunity, neoplasia and drug-related 111
reaction, must be kept in mind when confronted to one of these syndromes. 112
Clinical pictures can vary from mild syndromes, e.g. enterovirus meningitis to life- 113
threatening presentations, such as Streptococcus pneumoniae or tuberculous meningitis, or 114
viral encephalitis, e.g. HSV-1. Regarding these examples, management improvements 115
including prompt and appropriate antimicrobial treatment have drastically reduced mortality 116
and neurological sequelae related to these diseases. Nevertheless, severe neurological 117
complications are still relatively frequent, especially in non-curable encephalitis causes. 118
This thesis focuses on the various infectious agents currently responsible for CNS 119
infections, and the diagnostic tools available to identify them, with an attempt to propose a 120
rational use of the various available tests. Non microbiological investigations, such as CNS 121
imaging studies and serological tests to identify auto-immune encephalitis causes are also 122
briefly mentioned. The four original articles presented in this thesis illustrate selected 123
aspects of clinical virology tools applied to CNS infection diagnosis. 124
When suspecting CNS infection, the first diagnostic step remains, as in medicine in general, 125
medical history and clinical examination. Travel history, outdoor activities, animal exposure, 126
sexual activity, immunity status, medical status particularities, such as a skin rash, provide 127
important clues that help the clinician to choose the most relevant diagnostic tests to use at 128
an initial stage. Microbiological testing for CNS infections can be categorized as direct- 129
detecting, including direct microscopic examination, culture, antigenic and nucleic acid 130
detection, and as indirect, involving serological assays designed to identify pathogen- 131
specific antibodies. The most commonly used direct-detecting test type in CNS infection 132
diagnosis is real-time (reverse-transcription) PCR (r(RT-)PCR), which is mainly applied to 133
using peripheral blood samples. Serologic tests can be used in serum and/or CSF, 135
depending on the suspected pathogen (1). CNS imaging using computed tomography and 136
particularly magnetic resonance imaging is useful non microbiological diagnostic tool (2). 137
Before elaborating further on diagnostic strategies, the main causes of CNS infections and 138
noninfectious causes of CNS inflammation will be reviewed, according to distinct clinical 139
syndromes. 140
141
Infectious and noninfectious causes of CNS inflammation 142
Meningitis 143
This syndrome is caused by inflammation of the meninges and subarachnoid space, and 144
clinically characterized by fever, non-habitual and intense headache, photo- and phono- 145
phobia, and nuchal rigidity. More than 2 million meningitis cases are reported annually 146
around the world. Most of these are bacterial meningitis cases occurring in low-income 147
countries (3). The far most common meningitis-causing bacteria worldwide are by order of 148
frequency Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae 149
(https://www.who.int/health-topics/meningitis). H. influenza meningitis nowadays occurs 150
mainly in children in areas of insufficient vaccination against H. influenza type b. N. 151
meningitidis currently comprises 13 identified serogroups, among which 6 (A, B, C, W, X 152
and Y) cause epidemics. An extended sub-Saharan African region, named the meningitis 153
belt, experiences large N. meningitidis meningitis outbreaks (4). 154
The clinical picture is often quite obvious, with patients typically displaying a severe illness 155
with high grade fever, signs of sepsis confusion, lethargy and sometimes even septic shock. 156
CSF analysis reveals high neutrophil counts and hypoglycorachia, and microbiological 157
diagnosis is usually straightforward, since blood cultures are often positive, CSF Gram 158
stains shows Gram-positive or Gram-negative diplococci, suggesting the presence of S. 159
pneumoniae and N. meningitidis (or H. influenza), respectively. CSF culture readily 160
identifies the causative agent, except if antibiotics have been administered long before 161
lumbar puncture, and subsequent antibiotic susceptibility testing allows for tailored 162
antimicrobial therapy. These pathogens are also targeted in commercial 163
meningitis/encephalitis multiplex PCR panels (1). 164
Mycobacterium tuberculosis and Listeria monocytogenes are other important causes of 165
bacterial meningitis. Albeit being completely different microorganisms, they display similar 166
diagnostic challenges. Both organisms are fastidious to grow, and by causing paucibacillary 167
infections, they do not always yield positive cultures. Real-time PCR (rPCR) assay are 168
available for both bacteria, and are slightly less sensitive than culture, but more sensitive 169
than direct examination (Ziehl-Niessen stain for M. tuberculosis and Gram stain for L. 170
monocytogenes) (2). L. monocytogenes should be considered for patients above 50 years 171
of age, in case of underlying co-morbidities, such as alcohol abuse, diabetes, or 172
immunosuppression. Of note, both infectious agents are also significant causes of 173
encephalitis (5, 6). 174
Escherichia coli and Streptococcus agalactiae are significant meningitis causes in 175
neonates. 176
Spirochetes, such as Borrelia burdorferi species, and Treponema pallidum, can cause 177
lymphocytic meningitis, and microbiological diagnosis mainly relies on CSF and serum 178
serological tests (2). Sensitivity of PCR-based assays in CSF samples is poor for both 179
pathogens. Quantitative detection of CXCL13, a B-lymphocyte-attracting chemokine, is an 180
interesting adjunctive laboratory test in neuroborreliosis diagnosis, since it tends to be 181
elevated early in the course of the disease (7, 8). 182
Nosocomial meningitis, e.g. post neurosurgery, is caused by distinct types of bacteria, such 183
as enterobacteria, Pseumonomas aeruginosa, and Staphylococcus spp, and is beyond the 184
scope of this thesis. 185
Viruses are also important meningitis agents, typically causing less leucorachia than 186
bacterial meningitis, with a monocyte-lymphocyte predominance. The most frequent 187
worldwide are enteroviruses, usually causing benign meningitis in both children and adults 188
(9). Of note, neutrophils can predominate in enterovirus meningitis, especially if lumbar 189
puncture is performed early after onset of symptoms. Parechoviruses, another genus within 190
the Picornaviridae family, cause meningitis mainly in neonates. These viruses are detected 191
in CSF by real-time RT-PCR (rRT-PCR) assays. 192
Meningitis can be one of the manifestations of HIV primoinfection, and HIV screening 193
should be part of the initial work-up of all CNS infections in sexually active individuals (2). 194
Diagnosis is confirmed by rRT-PCR in a CSF sample. 195
Certain herpesviruses, especially herpes simplex virus type 2 (HSV-2), and varicella-zoster 196
virus (VZV), are relatively frequent meningitis causes. HSV-2 meningitis is often cause by 197
viral reactivation and tends to be recurrent, a particularity known as Mollaret meningitis (10). 198
VZV reactivation can cause various forms of CNS disease, including lymphocytic 199
meningitis, encephalitis, CNS vasculitis and myelitis (11). These forms of meningitis are 200
a positive intrathecal specific IgG antibody index (AI) in a later course of the disease, when 202
viral DNA is no longer detectable. 203
Tick-borne encephalitis virus (TBEV), a flavivirus transmitted to humans via Ixodes ticks, 204
and can cause meningitis, encephalitis, myelitis, or a combination of these entities. The 205
neurological complications of TBEV infections are most likely immune-mediated, and viral 206
RNA is usually not detectable in CSF. Hence, diagnosis relies on positive serum IgM and 207
IgG, documented seroconversion, or by positive CSF IgM (2). 208
Many arboviruses displaying complex geographical distributions, known to cause 209
encephalitis, can also lead to meningitis (figure 2). 210
The following viruses are rarer causes of meningitis. Lymphocytic choriomeningitis virus 211
(LCMV), an arenavirus transmitted to humans by contact with urine or feces of various 212
rodents, as well as by research laboratory incidents involving experiments with rodents (12). 213
Mumps meningitis is rarely seen since the advent of widespread vaccination programs 214
undertaken against this virus. (13). Astroviruses are relatively recently discovered enteric 215
viruses, occasionally causing CNS infections, including meningitis (14). A case of astrovirus 216
MLB2 meningitis, diagnosed by high throughput sequencing (HTS), is described in the 217
second original paper of this thesis. 218
Fungal meningitis is mainly represented by the yeast Cryptococcus neoformans, 219
predominantly in immunosuppressed patients, and has become frequent with the 220
emergence of the HIV pandemic. In contrast, Cryptococcus gattii seems to cause CNS 221
infection irrespective of the host’s immunity status. While the former has a worldwide 222
distribution, the latter has been described in Oceania and more recently in the USA (15). Of 223
note, both yeasts can also cause meningoencephalitis. Classic diagnostic means include 224
direct examination using India ink stain and culture, performed on CSF samples, but 225
capsular antigen detection in CSF and/or serum, including by point-of-care lateral flow 226
assays, made cryptococcal meningitis more straightforward (16, 17). Nucleic acid detection 227
methods are now available, but their diagnostic performance remain incompletely validated. 228
Candida albicans and other Candida spp can cause chronic meningitis, mainly secondary to 229
iatrogenic events. 230
Parasitic meningitis is very rare and mainly occur in tropical countries. It should be 231
suspected especially when eosinophils represent more than 10% of CSF cell counts. 232
Angiostrongylus cantonensis, Gnathostoma spinigerum, and cysticercosis (Taenia solium) 233
are the main causes. Microbiologic diagnosis relies on specific serological tests (18). 234
Non-infectious causes of meningitis are briefly reviewed here. Drug-induced aseptic 235
meningitis is due to an immunologic hypersensitivity reaction to a drug administered 236
systemically, and is an exclusion diagnosis. The most common pharmacological compound 237
classes involved are IVIG, NSAIDs, antibiotics, monoclonal antibodies, analgesics, 238
anesthetics, and vaccines (19). Neoplasias, such as hematologic malignancies, particularly 239
large cell lymphomas and acute leukemias, and metatstatic solid tumors (breast cancer, 240
lung cancer, melanoma), can cause meningeal inflammation. Lastly, systemic diseases, 241
including Sjögren's syndrome, Behçet's disease, sarcoidosis, systemic lupus erythematosus 242
and granulomatosis with polyangiitis, can lead to meningeal involvement (20). 243
244
Encephalitis 245
Encephalitis refers to inflammation of brain parenchyma causing CNS dysfunction. This 246
syndrome is clinically identified using criteria shown in table1. 247
When meningeal inflammation is concurrently present, usually assessed by increased CSF 248
leucocyte counts, the term meningoencephalitis is used. Since the underlying causes are 249
virtually the same, these two entities will be considered as a single one in this thesis, and 250
referred to as encephalitis. The main physiopathological processes leading to encephalitis 251
are infection and dysimmunity. Among infectious causes, viruses are the most frequent 252
(21). 253
Hepresviruses are ubiquitous and can lead to severe encephalitis across the world. The 254
most feared type of encephalitis remains herpes simplex encephalitis (HSE) caused by 255
herpes simplex virus type 1 (HSV-1), which can causing devastating to fatal brain injury, 256
especially if not treated promptly with high-dose intravenous acyclovir. In children, HSE 257
usually results from HSV-1 primo infection, often in the setting of genetic predisposition 258
related to mutations in genes involved in Toll-like receptor 3 pathways (22). In contrast, 259
HSV is often secondary to viral reactivation in adults. Brain MRI is particularly useful in the 260
diagnosis of HSE, characteristically showing temporal lobe(s) inflammation, as exemplified 261
in figure 1. HSV-1 DNA detection in CSF by PCR confirms HSE diagnosis. Early in the 262
course of the disease, HSV-1 DNA might not yet be detected in CSF. Hence, repeating 263
lumbar puncture with a second HSV-1 PCR is warranted in case of suspected HSE with 264
negative HSV-1 PCR in a CSF sample drawn less than three days after symptom onset. 265
HSV-2 typically causes meningitis as mentioned above, and rarely cause encephalitis, 266
Table 1. Encephalitis diagnostic criteria. Adapted from Schibler et al. (2), and Venkatesan et al. (23). 268
Major Criterion (required)
Altered mental status (decreased or altered level of consciousness, lethargy or personality change) lasting ≥24 h with no alternative cause identified
Minor Criteria (in addition to the major criteria if 2= possible; if ≥3 = probable)
Documented fever ≥ 38° C (100.4°F) within the 72 h before or after presentation
CSF WBC count ≥5/cubic mm
Generalized or partial seizures not fully attributable to a preexisting seizure disorder
Abnormality of brain parenchyma on neuroimaging suggestive of encephalitis
New onset of focal neurologic findings Abnormality on electroencephalography that is consistent with encephalitis and not attributable to another cause
Possible encephalitis: major criterion and 2 minor criteria
Probable encephalitis: major criterion and ≥ 3 minor criteria
Confirmed encephalitis: probable encephalitis and 1 one of the following:
- Pathologic confirmation of brain inflammation consistent with encephalitis
- Pathologic, microbiologic, or serologic evidence of acute infection with a microorganism strongly associated with encephalitis from an appropriate clinical specimen
- Laboratory evidence of an autoimmune condition strongly associated with encephalitis
269
VZV, as described in the meningitis section above, is a major encephalitis etiology. 270
For the three above-mentioned viruses, measuring intrathecal specific IgG antibody index 271
can be useful for diagnosis, when viral DNA is cannot be or is no longer detected in CSF. 272
Epstein-Barr virus (EBV), the cause of infectious mononucleosis, has rarely be described in 273
case reports as being responsible for meningitis or encephalitis. In immunocompetent 274
individuals, this can infrequently occur during primo-infection (24), and in 275
immunocompromised patients, EBV encephalitis can result from viral reactivation. However, 276
in the latter population EBV DNA detection in CSF is mostly associated with EBV-linked 277
CNS lymphoma. Furthermore, positive CSF EBV PCR can simply reflect detection of latent 278
episomal DNA, which is found in memory B cell nuclei, without indicating an EBV-related 279
pathological process. 280
281
282
283
Figure 1. Upper panel: MRI illustrating typical HSE findings: high signal intensity of the mesial-temporal region 284
(left hippocampus, indicated by black asterisk) and insula (indicated by white asterisk) on T2 and FLAIR 285
sequences, without contrast enhancement on T1 sequence (c). Lower panel: same patient at follow-up; FLAIR 286
sequence showing temporal region destruction. Adapted from Schibler et al (2). 287
288
Cytomegalovirus and human herpesvirus 6 (HHV-6) belong to the same subfamily 289
Betaherpesvirinae, and both cause life-threatening encephalitis in highly 290
immunocompromised patients, via viral reactivation. Both are diagnosed by rPCR in CSF 291
under antiviral treatment. CMV encephalitis is discussed in the third article presented in this 293
thesis. HHV-6 has a unique latency pattern among human herpes viruses, namely 294
chromosomal integration of its genome in infected cells. When occurring in germinal cells, 295
subsequent inherited chromosomally integrated HHV-6 (iciHHV-6) can ensue (25). As a 296
consequence, all nucleated cells in an individual having iciHHV-6 will harbor an HHV-6 297
genome copy, which has important diagnostic consequences when interpreting a positive 298
HHV-6 PCR result in CSF (or elsewhere). This phenomenon is present among 299
approximately in 1% of the population, and is more and more frequently identified with the 300
increasing use of multiplex PCR panels which include an HHV-6 target. Diagnostic 301
confirmation of iciHHV-6 relies on positive HHV-6 PCR performed on nail or hair follicle 302
samples. Alternatively, high HHV-6 DNA values, typically above 5.5 log10 copies/ml, 303
obtained by HHV-6 qPCR performed on whole blood samples are highly suggestive of 304
iciHHV-6 (26). To further complicate things, there is increasing emerging evidence 305
supporting HHV-6 reactivation from iciHHV-6 (27). 306
JC virus a polyomavirus, which like herpesviruses is capable of latency, is distributed 307
worldwide, can cause disease by reactivating in immunosuppressed hosts. The disease 308
associated with this virus is a particular form of encephalitis, called progressive multifocal 309
leukoencephalopathy (PML), predominantly described in AIDS patients (28). 310
Importantly, in contrast to virtually all other encephalitis causes, CSF leucocyte counts are 311
typically normal in CMV, HHV-6 and JCV encephalitis. 312
Other ubiquitous viruses associated to CNS disease are listed in table 2. Enteroviral 313
encephalitis is mainly caused by enterovirus-A71 in children in South-East Asia (29). Of 314
note, enterovirus RNA is rarely detected by rRT-PCR in CSF, and stool samples should be 315
tested when suspecting enterovirus encephalitis. 316
Table 2 also lists zoonotic viruses causing encephalitis in Europe, each displaying specific 317
geographical distributions. WNV, like TBEV, is a flavivirus, initially described in Africa prior 318
to emergence in other areas, such as North America in 1999, and more recently in several 319
European areas (https://www.who.int/news-room/fact-sheets/detail/west-nile-virus) 320
Serologic assays and viral RNA detection by rRT-PCR are complementary to diagnose 321
WNV encephalitis. 322
323 324
Table 2. Ubiquitous and zoonotic viruses causing encephalitis in immunocompetent adults in Europe, 325
adapted from Schibler et al. (2). 326
Ubiquitous viruses Zoonotic viruses
HSV TBEV
VZV WNV
Enteroviruses Sandfly fever Naples viruses Adenoviruses Usutu virus
Measles virus Rabies virus
HIV-1 VSBV-1
327
HSV: Herpes simplex virus; TBEV : Tick-borne encephalitis virus; VZV: varicella zoster virus; WNV: West Nile 328
virus; VSBV-1: Variegated squirrel bornavirus 1 329
330
While allowing for definite diagnosis in the early phase of disease, rRT-PCR often fails to 331
detect viral RNA in CSF or plasma because of relatively weak and fugacious viral 332
replication. WNV RNA shedding in urine is slightly more long-lived. Positive serum IgM, 333
preferably with concomitant positive IgG allows to raise the diagnostic probability, and 334
documented seroconversion allows to confirm diagnosis. Flavivirus serology results are 335
tricky to interpret because of frequent cross-reactions among antibodies produced in 336
response to different flavivirus members. Pan-flavivirus immunofluorescence assays can 337
help detecting such cross-reactions (2). 338
Of note, encephalitis caused by enteroviruses, adenoviruses, measles virus, HIV, Sandfly 339
fever Naples viruses, Usutu virus, Rabies virus and VSBV-1 is extremely rare. 340
Many other arboviruses are known to cause encephalitis across the world, as shown in 341
figure 2. The diagnostic means available to diagnose them are reviewed in (16). 342
343
344 345
Figure 2. Worldwide distribution of selected encephalitis pathogens. Ubiquitous neuropathogens mentioned 346
earlier in the text are not shown. 347
Legends: 1. Viruses, 2. Bacteria, 3. Parasites, 4. Fungi. 348
Abbreviations: 349
ABLV: Australian Bat Lyssavirus; CHIKV: Chikungunya virus; CTFV: Colorado tick fever virus; DENV: Dengue 350
virus; EEEV: Eastern equine encephalitis virus; EV71: Enterovirus A71; HeV: Hendra virus; JEV: Japanese 351
encephalitis virus; LACV: La Crosse encephalitis virus; MVEV: Murray Valley encephalitis virus; NiV : Nipah 352
virus; POWV: Powassan virus; RABV: Rabies virus; RVFV: Rift Valley fever virus; SLEV: Saint-Louis 353
encephalitis virus; TBEV: Tick-borne encephalitis virus; VEEV: Venezuelan equine encephalitis virus; WEEV: 354
Western Equine Encephalitis virus; WNV: West Nile virus; YFV: Yellow fever virus; ZIKV: Zika virus. Adapted 355
from Kenfak et al (16). 356
357 358
Some bacteria, in addition to cause meningitis, are also important encephalitis agents, such 359
as M. tuberculosis and L. monocytogenes, and need to be considered in the differentia 360
diagnosis (5, 6). The diagnostic means used to identify them are discussed in the meningitis 361
section. Among spirochaetal neuropathogens, it is worth mentioning T. pallidum and B. 362
Burgdorferi spp. While neurosyphilis is a well-known disease and challenging diagnosis to 363
make, neuroborreliosis infrequently manifests as encephalitis. 364
Encephalitis due to exotic bacteria, fungi and parasites is rare, and reviewed in (16). 365
Exceptions include cryptococcal meningoencephalitis, discussed in the meningitis section, 366
as well as CNS toxoplasmosis in immunocompromised patients. The latter is diagnosed by 367
combining brain MRI displaying characteristic ring enhancing lesions, positive serology, and 368
rPCR performed in a CSF specimen. 369
Various infections can trigger immune-mediated pathological processes, in turn leading to 370
encephalitis (30). Acute disseminated encephalomyelitis (ADEM), caused by post-infectious 371
demyelination, predominantly occurs in children, and is characterized by encephalopathy 372
and frequently motor deficits, as well as by often spectacular multiple poorly defined lesions 373
in the white matter, suggestive of demyelination. In this type of conditions, the microbial 374
culprit is usually no longer detectable. 375
Autoimmune encephalitis is an increasingly recognized entity, which is difficult to distinguish 376
from infectious encephalitis on a clinical basis. A well experienced neurologist’s clinical 377
skills, combined with brain imaging and a broad CSF and serum serology work-up are 378
necessary to optimize the diagnostic strategy (31, 32). 379
380
Myelitis 381
Virtually all microbial pathogens discussed above have been associated with various forms 382
of spinal cord inflammation (33). It is worthwhile noting that compared to encephalitis, the 383
causative pathogens are less frequently identified by direct-detecting tests. Similarly to 384
encephalitis, post-infectious immune-mediated processes account for a significant 385
proportion of acute myelitis cases. 386
Human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus causing slowly progressive 387
myelopathy, called HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/ TSP) 388
in specific geographic areas, and is diagnosed by serology and sometimes CSF proviral 389
DNA quantification by rPCR (34). 390
391
Diagnostic approaches 392
The previous sections illustrate how abundant infectious (and noninfectious) causes of CNS 393
infections are, often making them overwhelmingly challenging to diagnose. Since pathogens 394
responsible for meningitis, encephalitis and myelitis largely overlap, it seems reasonable to 395
consider them together when diagnosing CNS infections. 396
After case history evaluation and clinical examination, routine laboratory testing and CSF 397
analysis often allow to orient the underlying cause to either bacterial or viral. For instance, 398
highly elevated CSF leucocytes, above 1000 M/L, mainly consisting of neutrophils, 399
combined with marked hypoglycorachia, strongly argues in favor of bacterial meningitis. In 400
contrast, less elevated leucorachia with a lymphocytic predominance typically suggests viral 401
meningitis or meningoencephalitis, except for tuberculous and Listeria CNS infections. 402
Classical bacterial meningitis is relatively straightforward to diagnose, and the following 403
considerations concern lymphocytic meningitis and encephalitis. Microbiological testing 404
should prioritize the identification of frequent and/or treatable causes, such as HSV-1, HSV- 405
2, VZV, EV and HIV-1, in immunocompetent hosts. These targets, except HIV-1, are 406
included in commercial meningitis/meningoencephalitis panels. 407
408
Table 3. Pathogens to be screened in all patients presenting with lymphocytic meningitis or encephalitis. 409
Adapted from Schibler et al. (2). 410
Pathogen Serology r(RT-)PCR
HSV-1 Yes (CSF)
HSV-2 Yes (CSF)
VZV AI (IgG) Yes (CSF)
EV Yes (CSF)
HIV-1
4th or 5th generation test (serum)
Yes, if screening test positive (CSF)
HSV-1 : Herpes Simplex Virus 1 ; HSV-2 : Herpes Simplex Virus 2 ; VZV : Varicella Zoster Virus ; EV : 411
Enteroviruses ; HIV-1: Human Immunodeficiency Virus 1 412
AI: antibody index 413
414
In highly immunocompromised patients, such as hematopoietic stem cell transplant 415
recipients and AIDS patients, the following additional microorganisms should be searched 416
for: CMV, HHV-6, JCV, T. gondii, and C. neoformans. 417
Additional testing to be considered in Europe according to the patient’s exposure history, 418
clinical presentation or epidemiology is proposed in table 4. 419
Table 4. Meningitis and encephalitis pathogens to consider either initially or in a second step, depending on 420
the clinical and epidemiological context, in Europe. Adapted from Schibler et al. (2). 421
Pathogen Serology r(RT-)PCR Other
M. tuberculosis Yes (CSF)
Acid fast stain (or auramin), culture (CSF) IGRA assay (peripheral blood)
L. monocytogenes Yes (CSF)
Gram stain (or orange acridin), culture (CSF)
TBEV IgM/IgG (serum) (Yes, CSF)
WNV IgM/IgG (serum)
Yes (CSF, plasma and/or urine) Sandfly fever Naples
viruses IgM/IgG (serum)
Yes (CSF or plasma)
B. burgdorferi
IgM/IgG with IB
confirmation (serum) CXCL13 (CSF)
T. pallidum
RPR, VDRL or ELISA Ig (serum)
422
IB: immunoblot 423
424
Regarding direct-detecting microbiogical tools, targeted singleplex and duplex rPCR assays 425
tend to become increasingly replaced by commercial multiplex PCR panels in recent years. 426
While exhibiting obvious practical advantages, such panels also have several limitations 427
that must be taken into account, and are listed in table 5. 428
429 430 431 432 433
Table 5. Advantages and limitations of multiplex PCR assays, such as the FilmArray® ME panel. Adapted from 434
Vetter et al (1). 435
436
Advantages Limitations
Easy to use Not fully comprehensive : does not exclude an
infection
Sealed format Specific epidemiology not considered
Low turnaround time Not adapted for nosocomial infections or immunocompromised patients
Multiple targets tested simultaneously Too extensive for most clinical situations
(i.e., meningoencephalitis in non-traveler immunocompetent individuals)
Potential decreased length of stay Lower sensitivity than conventional singleplex assays for most targets
Decreased health costs by rapid HSV and EV results
Lack of clinical validation for most targets
Decreased antimicrobial use (mainly acyclovir) Need for confirmation test for some targets
437 438
The nucleic acid detections methods currently used in clinical microbiology, i.e. mainly 439
PCR-based assays, are biased. In other words, only what is specifically searched for can be 440
found, leading to the potential for missed diagnoses. HTS (also called deep-sequencing, or 441
next-generation sequencing) is a promising non-biased direct-detecting method, which has 442
emerged in the early 2010’s. It allows to sequence whatever RNA and/or DNA that is 443
present in a given sample, irrespective of the a priori clinical suspicion. HTS has already 444
been applied to many microbiology research areas, including CNS infections (35). Its 445
application to the identification of viral causes of CNS infections will be discussed in the first 446
two original articles of this thesis. 447
Non microbiological tests that are useful in diagnosing CNS infections include CNS imaging 448
and electroencephalography (EEG). MRI is the imaging tool of choice in the setting of 449
meningoencephalitis, and specific findings can help guiding the diagnosis (2). EEG findings 450
are not specific, but can be of prognostic value in the context of encephalitis (2). 451
452 453
STUDY 1 SUMMARY 454
Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of 455
Individuals with and without Central Nervous System Disease 456
Genes (Basel). 2019 Aug 19;10(8). pii: E625 457
458
This study aimed at identifying viral genome sequences using high-throughput sequencing, 459
in cerebrospinal fluid (CSF) samples collected from 26 patients diagnosed with meningitis, 460
encephalitis, myelitis or a combination of these entities, of unknown origin. 10 additional 461
patients had defined causes of CNS diseases, and 30 CSF obtained from patients 462
undergoing elective spinal anesthesia samples were used as negative controls. 463
All patients with CNS disease had an extensive microbiological work-up, and CNS imaging 464
(CT and/or MRI) and/or electroencephalogram was performed on a case by case basis. 465
HTS was performed on both RNA and DNA libraries prepared for all CSF samples, using 466
HiSeq 2500 or 4000 sequencing systems. The sequencing data was analyzed using a 467
locally designed bioinformatics pipeline based on a comprehensive viral sequences data 468
base, called ezVIR. Additionally, a de novo analysis was performed on nonhuman 469
sequence reads. 470
Among the 26 patients with CNS inflammation of unspecified cause, one had a sequence 471
identified by HTS, belonging to astrovirus (HAstV)-MLB2, which was presumably 472
responsible for the patient’s meningitis. This case is comprehensively described in the 473
second paper of this thesis. 474
Other viral sequences were detected by HTS in CSF, in all three patient groups, and were 475
confirmed or infirmed by specific rRT-PCR assays whenever possible. After a careful 476
analysis and interpretation, these sequences were classified as 1) nonsignificant viral 477
sequences and reagent contamination, 2) sequence cross-contamination and 3) viral 478
sequences assigned to commensal viruses. 479
These results show that while HTS applied to CSF of patients presenting acute CNS 480
inflammation of unknown etiology has the power to identify viruses previously unknown to 481
be neuropathogens, the overall yield of this technology remains low in this context. 482
Furthermore, this study underscores the need for careful interpretation of positive viral 483
sequences findings obtained with HTS in clinical specimens. 484
STUDY 2 SUMMARY 485
Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and 486
Disseminated Infection 487
Emerg Infect Dis. 2016 May;22(5):846-53 488
489
This case report describes a case of astrovirus MLB2 disseminated infection with meningitis 490
in a young immunocompetent female patient, identified by HTS. The specimen in which the 491
sequencing coverage was the highest was an anal swab, followed, by CSF, and plasma 492
and urine. Following these findings a specific rRT-PCR assay was designed and used for 493
astrovirus MLB2 RNA detection in 943 stool and 424 CSF samples collected from 494
hospitalized patients. Five stool samples proved to be positive; one from an infant suffering 495
from acute diarrhea, and four from pediatric transplant patients. One CSF sample from a 496
patient with meningitis was astrovirus MLB2-positive. Like in the case described above, 497
feces and plasma samples from the same patient were also positive. These results suggest 498
that astrovirus MLB2 is an enteric virus, relatively frequently replicating in human guts, and 499
which is occasionally able to disseminate and cause acute meningitis. 500
501
502 503 504 505 506 507 508 509 510 511 512 513 514
STUDY 3 SUMMARY 515
Compartmentalization of a Multidrug-Resistant Cytomegalovirus UL54 Mutant in a 516
Stem Cell Transplant Recipient with Encephalitis 517
J Infect Dis. 2019 Sep 13;220(8):1302-1306 518
519
This report comprehensively describes a CMV reactivation in a hematopoietic stem cell 520
transplant recipient, leading to encephalitis, allowing for the characterization of a new 521
mutation associated with antiviral resistance. 522
The neurological picture was dominated by absence epilepsy. Brain MRI showed bifrontal 523
leptomeningeal enhancement and bilateral precuneus lesions, and CSF analysis revealed 524
normal leucocyte counts, and a CMV DNA load of 13’000 IU/ml. While already receiving 525
anti-CMV treatment at the time encephalitis developed, antiviral therapy was switched to 526
double dose intravenous ganciclovir when the CSF viral load was available, pending 527
sequencing results. 528
Sanger sequencing revealed a viral population harboring a previously unrecognized 529
mutation (V787E) in the CMV gene coding for the viral polymerase, UL54, in CSF, but not in 530
plasma. 531
In order to phenotypically assess the function of this mutation, it was introduced into the 532
backbone genome of a laboratory CMV strain. The known mutations V787A was also 533
introduced in separate clones. In vitro viral replication in presence of the antivirals 534
ganciclovir, foscarnet and cidofovir was assessed in parallel for the wildtype virus, 2 V787E 535
clones, 2 V787A clones and a V756K UL54 mutant, known to be multiresistant. The V787E 536
clones displayed significant resistance to all 3 ploymerase inhibitors. 537
This translational study highlights the possible compartmentalization of CMV resistance, 538
possibly due to low antiviral concentration in CSF, and thus the need for CSF sequencing in 539
case of herpesvirus-related encephalitis in highly immunosuppressed patients. 540
541 542 543 544 545
STUDY 4 SUMMARY 547
Cerebrospinal fluid features in SARS-CoV-2 RT-PCR positive patients 548
Clin Infect Dis. 2020 Aug 8:ciaa1165 549
550
In this study, CSF features of 31 COVID-19 patients presenting neurological manifestations 551
were analyzed using standard clinical virology and other laboratory medicine tools. Most 552
patients were hospitalized (29/31), and 18 were admitted to ICU. 553
Encephalopathy was the main neurological manifestation (19/31 patients, 61%), and was 554
particularly frequent among ICU patients (83%). Other clinical pictures included isolated 555
headache (3/31 patients, 10%) meningitis (4/31 patients, 13%), epilepsy (1 patient, 3%), 556
Guillain-Barré syndrome (3/31 patients, 10%), and critical illness polyneuropathy (1 patient, 557
3%). 558
SARS-CoV-2 rRT-PCR was negative in all samples, and no intrathecal production of 559
specific anti-SARS-CoV-2 IgG was observed. 560
Most patients (58%) had an altered blood-brain barrier (BBB), as assessed by elevated 561
CSF/plasma albumin ratio. Another interesting finding was the abnormal presence of 562
macrophages in 60% of the CSF samples, suggesting microglial activation, leading to 563
expression and release of potentially neurotoxic cytokines. This hypothesis could explain 564
the nature of SARS-CoV-2-related encephalopathy, resembling septic encephalopathy and 565
perhaps influenza-associated encephalopathy. These clues might serve as a basis for 566
further investigations exploring the mechanisms underlying COVID-19-associated 567
neurologic disorders. 568
569 570 571 572 573 574 575 576 577
CONCLUSION 578
Diagnosing CNS infections remains challenging. The causes are numerous and vary 579
according to geographical distribution, exposure types and host status. Furthermore, they 580
can be mimicked by noninfectious physiopathological processes, such as dysimmunity, 581
neoplasia and drug-related reactions. Despite intensive investigation in the field and past 582
years’ developments, circa 50% of encephalitis diagnoses remain of unknown origin. As in 583
medicine in general, finding the correct diagnosis is key to adapt therapeutic strategies. 584
The four original articles presented in this thesis illustrate selected aspects of viral CNS 585
infections diagnosis. The first two focused on the use of a locally developed viral genome 586
HTS pipeline in CSF to fill the gap left by routine microbiological diagnostic tools. However, 587
as shown in the first study, the diagnostic yield was rather low. This may either be due to 588
the type of sample tested, CSF, which does not necessarily contain genomic material from 589
viruses replicating in deep brain parenchyma. Brain biopsy would potentially represent the 590
optimal sample. However, due to its invasive nature, this procedure is rarely performed, and 591
HTS data deriving from such specimens is currently lacking. Alternatively, bacterial, fungal 592
or parasitic genomes would have been missed by the virus-oriented HTS pipeline used. The 593
first investigation also highlighted the need for careful interpretation of viral sequences 594
results obtained with HTS. Indeed, in addition to the identification of a viral neuropathogen, 595
such sequences could be attributed to reagent contamination, sequence cross- 596
contamination or to the presence of nonpathogenic viruses. 597
The third article is a comprehensively documented case report exemplifying how the 598
judicious use of routine quantitative PCR and standard sequencing methods, can help 599
understanding and dealing with puzzling clinical situations. Furthermore, this translational 600
research example illustrates how the phenotype of a previously uncharacterized viral 601
mutation can be assessed by using complementary genetic engineering research tools. 602
Lastly, this report highlights the challenges related to the management of life-threatening 603
encephalitis caused by a herpesvirus such as CMV in highly immunosuppressed patients. 604
The fourth study describes CSF features of patients infected by SARS-CoV-2 suffering from 605
neurological complications. A reproducible CSF pattern could be identified, consisting of 606
normal leucocyte count, the presence of macrophages, altered BBB integrity, the absence 607
of SARS-CoV-2 RNA detection, and the absence of intrathecal production of specific anti- 608
SARS-CoV-2 antibodies. Together, these findings suggest that COVID-19-related 609
Rather, they might be secondary to a more indirect mechanism, such as neurotoxic effects 611
of cytokines produced within or reaching the CNS parenchyma. This hypothesis contrasts 612
the neuroinvasive theory regarding SARS-CoV-2, which is postulated in several publications 613
(36, 37). Overall, this work shows how the combined use of standard microbiology 614
diagnostic tools and other routine biomedical analyses applied to an emerging infectious 615
disease, such as COVID-19, can provide hints regarding underlying physiopathological 616
processes. 617
Future potentially interesting and useful research and development projects aimed at 618
improving diagnosis and clinical management of CNS infections are numerous and some 619
are proposed below. 620
Smarter testing approaches exploring ways to optimize the use of abundantly available 621
clinical microbiology assays may lead to substantial cost and laboratory labor reduction, 622
possibly without affecting diagnostic yields. Indeed, extensive microbiologic testing is often 623
launched for each lumbar puncture, sometimes before the initial biological CSF analysis 624
results are available. A rational step-by-step testing approach has been proposed by Vetter 625
et al. (1), and is depicted in figure 3. In this algorithm, microbiologic testing would be 626
restricted to patients showing signs of CSF inflammation, as indicated by elevated leucocyte 627
counts and/or elevated CSF protein, provided that patients are over two years of age and 628
presumably immunocompetent. These criteria, known as Reller criteria, have initially been 629
established regarding HSV-1 PCR testing in CSF (38), and potentially might be applied for 630
CNS infections in general. The first testing bundle would include mainly frequent and/or 631
treatable neuropathogens. Additional testing would be performed according to the initial 632
workup results, particular exposures, and immunity status. 633
As a first step, retrospective studies could be performed to ensure that important 634
microbiological diagnosis would not be missed by applying this restrictive algorithm. In a 635
second step, a prospective studies could allow to assess the practical feasibility of this step- 636
by-step testing strategy. In parallel, further cost/benefit analyses regarding the use of 637
multiplex PCR panels versus selected singleplex or duplex PCR assays are still needed. In 638
particular, careful clinical validation of new multiplex nucleic acid detection panels appearing 639
on the market will remain key to ensure quality clinical microbiology results. 640
641
642
Figure 3. Proposed step-by step testing algorithm for CNS infections. Adapted from Vetter et al. (1) 643
644
This approach also includes the rationale for using restricted testing panels in a step by step 645
manner, rather than using an extended molecular panel, such as the Filmarray® 646
Meningitis/Encephalitis panel (Biofire®), including targets that are not necessarily 647
appropriate according to the clinical situation. For instance, testing for HSV-1, HSV-2, VZV 648
and enteroviruses in every case of suspected case of meningitis or encephalitis based on 649
the clinical and CSF features makes sense because these viral pathogens can affect people 650
of all ages, all over the world, and irrespective of the immune status. In other words, the 651
pre-test probability for these pathogens is unneglectable. In contrast, testing for E. coli or S. 652
agalctiae, which can cause meningitis in neonates, in adult patients, is not useful. Worse, a 653
positive result for a pathogen for which the pre-test probability is infinitesimal is most likely a 654
false-positive. Such false-positive results are known to misguide the clinicians in patient 655
management. Therefore, it seems more rational to use restricted testing panels that 656
specific antimicrobial treatment should also guide the selection of pathogens to be included 658
in the initial screening. For instance, the identification of either HSV-1, HSV-2 or VZV in the 659
CSF warrants continuation of acyclovir treatment initiated empirically, whereas the negative 660
PCR results for the three viruses allows for discontinuation of the antiviral treatment. 661
One could imagine to apply the “ubiquitous” meningitis/encephalitis panel mentioned above 662
in all cases of clinical and biological suspicion of acute CNS infection, to which a “neonate 663
meningitis” panel (including E. coli and S. agalctiae) or an “immunosuppressed 664
meningoencephalitis” panel (including CMV, HHV-6, JC virus, Cryptococcus neoformans, 665
Listeria monocytogenes, and Toxoplasma gondii) could be added if appropriate. Regarding 666
the Listeria monocytogenes PCR, it should also be possible to prescribe it individually for 667
patients who are not highly immunosuppressed, but who are either over 50, or who display 668
other risk factors for neurolisteriosis, such as diabetes or chronic alcohol abuse. 669
Another issue to consider when using a commercial multiplex PCR panel, is the fact that the 670
results they generate nowadays are only qualitative (i.e. positive or negative) and lack the 671
quantitative information provided by r(RT-)PCR. Indeed, while a high microbial genome load 672
indicates an active infection in most cases, a low microbial genome quantity is more 673
suggestive of either past infection with residual nucleic acid fragments, or detection of a 674
latent state (e.g. latent episomal EBV DNA detection present in memory B cells sometimes 675
present in CSF), or PCR contamination. However, it is important to keep in mind that some 676
CNS infection are caracterized by a low number of pathogens present in CSF, such as M. 677
tuberculosis, Listeria monocytogenes, and JCV. 678
Concerning returning travelers, the possible neuropathogens are numerous and their 679
distribution is often restricted to specific areas. Therefore, the additional microbiological 680
tests to perform in these patients should be assessed on a case by case basis, with the 681
help of an infectious diseases specialist and/or a tropical medicine specialist. Regarding 682
TBE, it should be screened for in every area where TBE cases are known to occur. More 683
specifically, in Switzerland, the geographic areas in which TBE cases have been identified 684
have substantially extended over the last years. Therefore, TBE serology should now 685
probably be performed in all cases of suspected acute CNS infection in this country. This 686
would allow for an improved surveillance of TBEV distribution. 687
While parsimonious testing approaches as proposed above are certainly welcomed, many 688
yet unknown causes of CNS infection probably remain to be discovered. In this respect, the 689
use of exploratory diagnostic means, such as HTS, have the potential to further fill existing 690
etiologic gaps. However, many aspects with respect to HTS need to be improved. First, 691
HTS methodology varies a lot between different groups. RNA and DNA libraries preparation 692
techniques, the type of sequencer used, database choice, and bioinformatics analysis can 693
all affect final sequencing results. Efforts of inter-institutional HTS pipelines comparisons 694
have started and need to be pursued, in order to standardize methodologies (39). Second, 695
HTS pipelines are often designed to detect sequences belonging to a single group of 696
microorganisms. Further developing HTS pipelines able to detect pan-microbial sequences 697
will most likely enhance CNS infection diagnostic yield (35). For this purpose, 698
comprehensive and relevant databases should be developed regarding not only viruses, but 699
also bacteria, fungi and parasites. In addition, concerning bacteria and fungi, DNA libraries 700
preparation should include PCR amplification of conserved regions, such as the regions 701
coding for ribosomal RNA, in order to optimize both sensitivity and specificity. In parallel, 702
optimizing de novo sequence assembly protocols might further improve the identification of 703
all types of pathogenic microorganisms. On the other hand, careful interpretation of 704
sequence results is of utmost importance since HTS reagents tend to be contaminated by 705
environmental microorganisms. Third, HTS encompasses a highly complex process, which 706
is multidisciplinary, labor intensive, costly, and associated with turnaround times, which are 707
not yet compatible with rapid diagnosis. Hence, identifying means to simplify the whole 708
process and render it faster and more affordable will be necessary for HTS to be optimally 709
implementable in routine clinical practice. Fourth, testing alternative samples, such as 710
plasma, stool or respiratory swabs, in addition to CSF, might further increase HTS 711
diagnostic yields in the context of CNS infections. 712
Notwithstanding the remaining challenges related to HTS applied to central nervous system 713
diagnosis, this technology has already shown its ability to identify various microbial 714
pathogens in meningitis and encephalitis cases (35, 40-42). With the shortening of 715
turnaround time and lowering of the costs, HTS is already more and more used in real-life 716
clinical situations to investigate CNS inflammation of undetermined origin, with a current 717
turnaround time varying from 48 hours to 7 days (35). 718
In addition to improve positive CNS infection diagnosis, negative CSF HTS results might 719
also be used in the future to exclude active CNS infection in suspected autoimmune CNS 720
inflammation, prior to the administration of immunosuppressive drugs. 721
In parallel to improving direct-detecting diagnostic methods, developing more specific 722
723
response to related viruses. Specific neutralization assays are in fact available, but are 724
fastidious and limited to highly specialized laboratories. Easy-to-use, ELISA-based 725
surrogate virus neutralization tests have recently been developed for neutralizing anti- 726
SARS-CoV-2 antibodies (43). Evaluating similar assays applied to other viruses, such as 727
flaviviruses, which are particularly prone to elicit cross-reactive antibodies, would certainly 728
be useful. 729
Yet another potentially interesting laboratory medicine field to explore is the screening of 730
CSF cytokines and other mediators, which may be associated with specific neuropathogens 731
or types of CNS infections, as exemplified with the CXCL13 chemokine in neuroborreliosis 732
diagnosis. 733
Lastly, a more global approach to improve acute CNS inflammation diagnosis and 734
management may reside in the constitution of a multidisciplinary “acute CNS inflammation 735
team”, as has been described for infective endocarditis (44). Indeed, the possible infectious 736
and noninfectious etiologies are numerous, and distinguishing infectious from autoimmune 737
CNS inflammation based on clinical features is unrealistic. Therefore, combining the 738
knowledge and clinical skills of an infectious diseases (ID) specialist, a neurologist, and a 739
neuroradiologist, might help to promptly coordinate diagnostic and therapeutic strategies 740
whenever a new patient with suspected CNS infection/inflammation is hospitalized. Since 741
prompt and appropriate treatment of various CNS infections has shown to significantly 742
reduce mortality and neurologic sequelae, empiric antimicrobial treatment is started 743
immediately after CNS infection is suspected in the emergency room. Initial treatment 744
generally includes an antibiotic such as intravenous (IV) high-dose ceftriaxone to cover for 745
S. pneumoniae and N. meningitidis, and IV high-dose acyclovir, which is active against 746
HSV-1, HSV-2 and VZV. If L. monocytogenes is suspected based on clinical presentation 747
and/or on the presence of risk factors, IV high-dose amoxicillin is added to the regimen. On 748
the other hand, quickly stopping unnecessary broad spectrum treatment upon exclusion of 749
the concerned pathogens to avoid side effects and selection of resistant microbes is equally 750
important. A step-by-step diagnostic approach quickly confirming or excluding these major 751
infectious causes while rapidly consider and testing for autoimmune causes of CNS 752
inflammation in more tricky situations, is crucial to optimize patient management and 753
outcome. Indeed, whatever the cause of CNS inflammation, prompt and appropriate 754
treatment is key to reduce mortality and neurologic morbidity, hence the motto “time is 755
brain”. Thus, a multidisciplinary coordinated step-by-step approach combining clinical 756
evaluation, targeted versus broad microbiological testing, CNS imaging, EEG and 757
autoimmune antibodies screening, together with a consensual interpretation of findings, 758
seems to be the way to go in order to fine-tune antimicrobial therapy or stop unnecessary 759
antibiotics and antivirals, while searching for an alternative infectious or noninfectious 760
cause. Indeed, rapidly distinguishing between infection requiring prompt and appropriate 761
microbial therapy, and dysimmunity, for which immunosuppressive therapy is indicated, is of 762
utmost importance (45). 763
764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783
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