An isothermal CRISPR- based lateral flow assay for detection of Neisseria meningitidis.

BACKGROUND: Neisseria meningitidis can cause life-threatening meningococcal meningitis and meningococcemia. Old standard microbiological results from CSF/blood cultures are time consuming. This study aimed to combine the sensitivity of loop-mediated isothermal nucleic acid amplification (LAMP) with the specificity of CRISPR/Cas12a cleavage to demonstrate a reliable diagnostic assay for rapid detection of N. meningitidis. METHODS: A total of n = 139 samples were collected from patients with suspected meningococcal disease and were used for evaluation. The extracted DNA was subjected to qualitative real-time PCR, targeting capsular transporter gene (ctrA) of N. meningitidis. LAMP-specific primer pairs, also targeting the ctrA, were designed and the LAMP products were subjected to CRISPR/Cas12 cleavage reaction. the readout was on a lateral flow strip. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of LAMP-CRISPR/Cas was compared with real-time PCR assays. The limit of detection (LOD) was established with serial dilutions of the target N. meningitidis DNA and calculated by Probit regression analysis. RESULTS: Six LAMP assay-specific primers were developed targeting the ctrA gene of N. meningitidis, which is conserved in all meningococcal serogroups. The LAMP primers did not amplify DNA from other bacterial DNA tested, showing 100% specificity. The use of 0.4 M betaine increased the sensitivity and stability of the reaction. LAMP-CRISPR/Cas detected meningococcal serogroups (B, C, W). The assay showed no cross-reactivity and was specific for N. meningitidis. The LOD was 74 (95% CI: 47-311) N. meningitidis copies. The LAMP-CRISPR/Cas performed well compared to the gold standard. In the 139 samples from suspected patients, the sensitivity and specificity of the test were 91% and 99% respectively. CONCLUSION: This developed and optimized method can complement for the available gold standard for the timely diagnosis of meningococcal meningitis and meningococcemia.

Predictive signs and symptoms of bacterial meningitis isolates in Northern Ghana.

Cerebrospinal meningitis (CSM) is a public health burden in Ghana that causes up to 10% mortality in confirmed cases annually. About 20% of those who survive the infection suffer permanent sequelae. The study sought to understand the predictive signs and symptoms of bacterial meningitis implicated in its outcomes. Retrospective data from the Public Health Division, Ghana Health Service on bacterial meningitis from 2015 to 2019 was used for this study. A pre-tested data extraction form was used to collect patients' information from case-based forms kept at the Disease Control Unit from 2015 to 2019. Data were transcribed from the case-based forms into a pre-designed Microsoft Excel template. The data was cleaned and imported into SPSS version 26 for analysis. Between 2015 and 2019, a total of 2446 suspected bacterial meningitis cases were included in the study. Out of these, 842 (34.4%) were confirmed. Among the confirmed cases, males constituted majority with 55.3% of the cases. Children below 14 years of age were most affected (51.4%). The pathogens commonly responsible for bacterial meningitis were Neisseria meningitidis (43.7%) and Streptococcus pneumoniae (53.0%) with their respective strains Nm W135 (36.7%), Nm X (5.1%), Spn St. 1 (26.2%), and Spn St. 12F/12A/12B/44/4 (5.3%) accounting for more than 70.0% of the confirmed cases. The presence of neck stiffness (AOR = 1.244; C.I 1.026-1.508), convulsion (AOR = 1.338; C.I 1.083-1.652), altered consciousness (AOR = 1.516; C.I 1.225-1.876), and abdominal pains (AOR = 1.404; C.I 1.011-1.949) or any of these signs and symptoms poses a higher risk for testing positive for bacterial meningitis adjusting for age. Patients presenting one and/or more of these signs and symptoms (neck stiffness, convulsion, altered consciousness, and abdominal pain) have a higher risk of testing positive for bacterial meningitis after statistically adjusting for age.

Skin biopsy in adult patients with meningococcal purpura fulminans: a multicenter retrospective cohort study.

BACKGROUND: Neisseria meningitidis is the leading responsible bacterium of Purpura Fulminans (PF) accounting for two thirds of PF. Skin biopsy is a simple and minimally invasive exam allowing to perform skin culture and polymerase chain reaction (PCR) to detect Neisseria meningitidis. We aimed to assess the sensitivity of skin biopsy in adult patients with meningococcal PF. METHODS: A 17-year multicenter retrospective cohort study including adult patients admitted to the ICU for a meningococcal PF in whom a skin biopsy with conventional and/or meningococcal PCR was performed. RESULTS: Among 306 patients admitted for PF, 195 had a meningococcal PF (64%) with a skin biopsy being performed in 68 (35%) of them. Skin biopsy was performed in median 1 day after the initiation of antibiotic therapy. Standard culture of skin biopsy was performed in 61/68 (90%) patients and grew Neisseria meningitidis in 28 (46%) of them. Neisseria meningitidis PCR on skin biopsy was performed in 51/68 (75%) patients and was positive in 50 (98%) of them. Among these 50 positive meningococcal PCR, five were performed 3 days or more after initiation of antibiotic therapy. Finally, skin biopsy was considered as contributive in 60/68 (88%) patients. Identification of the meningococcal serogroup was obtained with skin biopsy in 48/68 (71%) patients. CONCLUSIONS: Skin biopsy with conventional culture and meningococcal PCR has a global sensitivity of 88% and should be systematically considered in case of suspected meningococcal PF even after the initiation of antimicrobial treatment.

Epidemiología de la enfermedad meningocócica en República Dominicana 2012-2022: bases para su prevención / Epidemiology of meningococcal disease in Dominican Republic 2012-2022: strategies for its prevention

Objetivo: La Enfermedad Meningocócica Invasiva es una causa frecuente de morbimortalidad mundial. El objetivo de este estudioes describir la epidemiología de la enfermedad meningocócica en República Dominicana desde 2012 a 2022 y proponer las basespara su prevención.Método: En el análisis se calcularon incidencias, tasas de hospitalización por cada 100.000 habitantes, tasas de letalidad y se hizouna comparación entre grupos de edad de los 325 casos de meningococcemia reportados en el Sistema Nacional de VigilanciaEpidemiológica Dominicano durante estos 10 años.Resultados principales: El 33% de los casos (103) tenía menos de 5 años. Este grupo de edad fue el que tuvo la tasa de hospitalizaciónmás alta, la mayor tasa de mortalidad en edad pediátrica la mayor letalidad.Conclusiones: Si la República Dominicana vacunara a su población, debería comenzar con los menores de 5 años, y así se reduciríanlas hospitalizaciones, muertes, complicaciones y secuelas producidas por el meningococo. (AU)

Objective: Invasive meningococcal disease is a frequent cause of morbidity and mortality worldwide. The aim of this study is todescribe the epidemiology of meningococcal disease in the Dominican Republic from 2012 to 2022 and to propose the basis for itsprevention.Methods: Incidences, hospitalization rates per 100,000 population, case fatality rates and a comparison between age groups ofthe 325 cases of meningococcemia reported in the Dominican National Epidemiological Surveillance System during these 10 yearswere calculated in the analysis.Main results: 33% of the cases (103) were less than 5 years old. This age group had the highest hospitalization rate, the highestmortality rate in pediatric age and the highest case fatality rate.Conclusions: If the Dominican Republic were to vaccinate its population, it should start with those under 5 years of age, and thiswould reduce hospitalizations, deaths, complications and sequelae caused by meningococcus. (AU)

Transtentorial herniation syndrome from meningococcal meningitis in a young woman: the case for neurocritical care.

We report a case of a previously healthy early adolescent female who presented with meningococcal meningitis. While in hospital, she had marked neurologic deterioration with clinical herniation from malignant cerebral oedema. She was transferred to a neurocritical care centre where she underwent invasive intracranial pressure (ICP) and brain tissue oxygen (PbtO2) monitoring. Early in her course, she demonstrated a compete absence of autoregulation, with pressure passive cerebral blood flow. As a result, maintaining a mean arterial pressure between 50 mm Hg and 60 mm Hg, which ensured adequate cerebral oxygenation, while avoiding increases in ICP. Although her course was initially complicated by bilateral optic neuropathy, she has subsequently made a full neurologic recovery and is now undertaking postsecondary education. This case highlights that access to specialist neurocritical care, guided by neurophysiologic monitoring of ICP and PbtO2, may help improve outcomes, even among those patients with catastrophic cerebral oedema from bacterial meningitis.

[Recurrent meningococcal infection in a young woman witha mutation in the C8B gene].

This is a case report of recurrent meningococcal infection in a young woman. She had no positive microbiological findings but was serologically diagnosed with the meningococcal antibody test. Investigation of the complement system showed no function of the terminal pathway. Further genetical analysis revealed a pathogen mutation in the C8B gene in the patient and her sister. They were both immunised with meningococcal vaccines. Complement deficiencies are rare but potentially fatal. Workup for complement deficiency is important for correct acute and prophylactic treatment.

Clinical Conundrum: Neisseria meningitidis Septic Abortion.

Septic shock after abortion is an important cause of global maternal mortality but is rarely encountered in developed countries. We describe a case of septic abortion with a novel associated pathogen: Neisseria meningitidis. A 30-year-old multiparous woman presented in septic shock after an incomplete spontaneous abortion. She received empiric antibiotics and vasopressors, underwent an urgent dilatation and curettage, and was admitted to the intensive care unit. Her blood cultures and endometrial tissue were positive for N. meningitidis. Antibiotics were adjusted based on culture, and the patient recovered. Septic shock requires prompt identification, antibiotic administration, and source control. Here, we identify an uncommon pathogen associated with septic abortion and highlight the importance of broad empiric and subsequent culture-guided antibiotic choice to ensure coverage.

Clinical implications of C6 complement component deficiency.

Background: Terminal complement component deficiencies are risk factors for neisserial infections. Objective: To review the clinical characteristics, the diagnosis and the management of patients with a terminal complement component deficiency. Methods: Pertinent articles were selected and reviewed in relation to a case presentation of C6 deficiency. Results: A case of a 56-year old patient with a history of meningitis, chronic rash, and C6 deficiency was presented, followed by discussion of clinical characteristics, diagnosis, and management of terminal complement component deficiencies. Clinical pearls and pitfalls were reviewed for the practicing allergist/immunologist and fellow-in-training. Conclusion: C6 deficiency is the most common terminal complement component deficiency and can present later in age with N. meningitidis infections. Patients can be screened for terminal complement component deficiency by checking CH50.

A pooled analysis of the LAMP assay for the detection of Neisseria meningitidis.

BACKGROUND: Neisseria meningitidis is a major cause of bacterial meningitis, and these infections are associated with a high mortality rate. Rapid and reliable diagnosis of bacterial meningitis is critical in clinical practice. However, this disease often occurs in economically depressed areas, so an inexpensive, easy to use, and accurate technology is needed. We performed a pooled-analysis to assess the potential of the recently developed loop-mediated isothermal amplification (LAMP) assay for detection of meningococcus. METHODS: Pubmed, Embase, and Web of Science were searched to identify original studies that used the LAMP assay to detect meningococcus. After pooling of data, the sensitivity and specificity were calculated, a summary receiver operating characteristic (SROC) curve was determined, and the area under the SROC curve was computed to determine diagnostic accuracy. Publication bias was assessed using Deek's funnel plot. RESULTS: We examined 14 studies within 6 publications. The LAMP assay had high sensitivity (94%) and specificity (100%) in the detection of meningococcus in all studies. The area under the SROC curve (0.980) indicated high overall accuracy of the LAMP assay. There was no evidence of publication bias. DISCUSSION: The LAMP assay has accuracy comparable to bacterial culture and PCR for detection of meningococcus, but is less expensive and easier to use. We suggest the adoption of the LAMP assay to detect meningococcus, especially in economically depressed areas.

Recurrent meningococcal meningitis with complement 6 (C6) deficiency: A case report.

RATIONALE: Late complement deficiency increases susceptibility to meningococcal disease and recurrent infections. In Korea, 5 case reports have described meningococcal disease with complement deficiency. However, C6 deficiency has not been described previously. PATIENT CONCERNS: A 21-year-old police trainee presented with recurrent meningococcal meningitis. He was housed in communal living quarters until 20 days before the initial symptom onset. DIAGNOSIS: He was diagnosed with meningococcal meningitis with C6 deficiency. INTERVENTIONS: He was treated with intravenous ceftriaxone. An additional dose of quadrivalent meningococcal conjugate vaccine was administered after discharge. OUTCOMES: He was discharged without complications. LESSONS: Screening for complement deficiency is necessary in patients with a history of recurrent meningococcal infections to provide appropriate care and prevent recurrent infections.

Loop-Primer Endonuclease Cleavage-Loop-Mediated Isothermal Amplification Technology for Multiplex Pathogen Detection and Single-Nucleotide Polymorphism Identification.

Loop-mediated isothermal amplification (LAMP) provides effective diagnostic technology for infectious disease pathogen identification and is compatible with inexpensive instrumentation for use in disease-prevalent developing regions. However, simultaneous multiple-target detection and single-nucleotide polymorphism (SNP) identification, essential properties of nucleic acid diagnostics, are difficult to achieve using LAMP. This study introduces loop-primer endonuclease cleavage (LEC)-LAMP, a singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification. We developed a singleplex LEC-LAMP Neisseria meningitidis assay that demonstrated complete analytical specificity and a limit of detection of 3.1 genome copies per reaction. Small-scale clinical testing of this assay demonstrated 100% diagnostic specificity and sensitivity when assessed with anonymized DNA extracts from confirmed cases of bacterial meningitis infection. The single-base specificity of this assay indicated effective SNP identification properties when challenged with DNA templates containing SNPs located within a specific six-base region. This assay was modified to generate an allele-specific LEC-LAMP N. meningitidis assay that successfully demonstrated single-tube differentiation of wild-type and mutant allele templates. The singleplex assay was further modified to generate a multiplex LEC-LAMP assay that successfully demonstrated simultaneous multiple-target detection of three bacterial targets, N. meningitidis, Streptococcus pneumonia, and Hemophilus influenzae. LEC-LAMP is the first report of single-tube, real-time, singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification.

Validation of a New Rapid Detection Test for Detection of Neisseria meningitidis A/C/W/X/Y Antigens in Cerebrospinal Fluid.

Meningococcal meningitis remains a life-threatening disease worldwide, with high prevalence in the sub-Saharan meningitis belt. A rapid diagnosis is crucial for implementing adapted antimicrobial treatment. We describe the performances of a new immunochromatographic test (MeningoSpeed, BioSpeedia, France) for detecting and grouping Neisseria meningitidis Cerebrospinal fluids (CSFs) were collected from 5 African countries and France. For the rapid diagnostic test (RDT), the CSF sample was deposited on each of the 3 cassettes for a total volume of 90 µl. The results of the RDT were compared to those of a reference multiplex PCR assay detecting the major serogroups of N. meningitidis on 560 CSF specimens. Five specimens were found uninterpretable by RDT (0.9%). The results of interpretable specimens were as follows: 305 positive and 212 negative samples by both techniques, 14 positive by PCR only, and 24 positive by RDT only (sensitivity, specificity, and positive and negative predictive values of 92.7%, 93.8%, 95.6%, and 89.8%, respectively, with an accuracy of 93.2% and a kappa test of 0.89; P < 0.05). From 319 samples positive by PCR for serogroups A, C, W, X, or Y, the grouping results were concordant for 299 specimens (sensitivity of 93.0%, 74.4%, 98.1%, 100%, and 83.3% for serogroups A, C, W, X, and Y, respectively). The MeningoSpeed RDT exhibited excellent performances for the rapid detection of N. meningitidis antigens. It can be stored at room temperature, requires a minimal amount of CSF, is performed in 15 minutes or less, and is easy to use at bedside.

[Meningococcal sepsis without cerebrospinal fluid abnormalities under treatment with eculizumab]. / Meningokokkensepsis ohne Liquorpathologie unter Eculizumabtherapie.

Infections with Neisseriameningitidis are life-threatening conditions, generally presenting as meningitis. This case of a young woman who had a history of paroxysmal nocturnal hemoglobinuria under treatment with the complement inhibitor eculizumab had been presented with septic shock. While blood cultures were positive for Neisseria meningitidis, she showed no evidence for bacterial meningitis in the cerebrospinal fluid. This case shows that meningococcal sepsis without signs for bacterial meningitis despite repetitive vaccinations is possible in adults under eculizumab.

A New Sequence Type of Neisseria meningitidis Serogroup C Associated With a 2016 Meningitis Outbreak in Mali.

In 2016, Mali reported a bacterial meningitis outbreak consisting of 39 suspected cases between epidemiologic weeks 9 and 17 with 15% case fatality ratio in the health district of Ouéléssebougou, 80 kilometers from the capital Bamako. Cerebrospinal fluid specimens from 29 cases were tested by culture and real-time polymerase chain reaction; 22 (76%) were positive for bacterial meningitis pathogens, 16 (73%) of which were Neisseria meningitidis (Nm). Of the Nm-positive specimens, 14 (88%) were N meningitidis serogroup C (NmC), 1 was NmW, and 1 was nongroupable. Eight NmC isolates recovered by culture from the outbreak were characterized using whole genome sequencing. Genomics analysis revealed that all 8 isolates belonged to a new sequence type (ST) 12446 of clonal complex 10217 that formed a distinct clade genetically similar to ST-10217, a NmC strain that recently caused large epidemics of meningitis in Niger and Nigeria. The emergence of a new ST of NmC associated with an outbreak in the African meningitis belt further highlights the need for continued molecular surveillance in the region.

Estimation of the real burden of invasive meningococcal disease in Argentina.

Among the different existing types of bacterial meningitis, the one caused by Neisseria meningitidis is the main presentation of invasive meningococcal disease (IMD). IMD is a significant public health concern and has a reported incidence rate in Argentina of 0.44 cases per 100 000 inhabitants in 2015. However, the actual incidence is thought to be higher as passive surveillance systems neither report nor identify 100% of all cases. The aim of this study is to develop an estimation of the burden of IMD in Argentina closer to reality by adjusting/correcting several limitations observed in the surveillance data available. A retrospective observational study has been performed using four Argentinean national databases recording the number of IMD cases and deaths, serogroups of N. meningitidis and ages, between 2007 to 2016. The reported data were adjusted to account for underreporting and to also integrate the cases missed due to well-known limitations associated with the diagnosis of N. meningitidis detection methods. Data were further analysed by serogroups of N. meningitidis and by age groups. After these adjustments, the potential numbers of IMD cases and IMD-related deaths are estimated to be 3.1 and 1.9 higher than reported, respectively. The study corrects the previous underestimation of the disease burden and provides expectedly more robust estimates aligned with international evidence and highlights the importance of active surveillance, with high-quality methods, for a better definition of preventive strategies against IMD in Argentina.

Bacterial meningitis in Sudanese children; critical evaluation of the clinical decision using clinical prediction rules.

BACKGROUND: Sudan falls in the meningitis belt where most global cases of bacterial meningitis are reported. Highly accurate decision support tools have been developed by international specialized societies to guide the diagnosis and limit unnecessary hospital admissions and prolonged antibiotic use that have been frequently reported from countries around the world. The goals of this study are to critically evaluate the clinical decision of bacterial meningitis in children in Sudan using clinical prediction rules and to identify the current bacterial aetiology. METHODS: This cross-sectional hospital-based study was conducted in October to July of 2010 in a major referral pediatric hospital in Khartoum, Sudan. Febrile children age 1 day to 15 years who were provisionally diagnosed as having meningitis on admission were included (n = 503). Cerebrospinal fluid (CSF) specimens were obtained from all patients while clinical and demographic data were available for only 404. Conventional laboratory investigations were performed. The clinical decision was evaluated by the International Classification of Diseases-Clinical Modification code 320.9 and the Bacterial Meningitis Score. Ethical clearance and permissions were obtained. RESULTS: Out of 503 provisionally diagnosed bacterial meningitis patients, the final clinical confirmation was assigned to 55.9%. When codes were applied; 5.7% (23/404) with CSF pleocytosis were re-classified as High Risk for bacterial meningitis and 1.5% (6/404) with confirmed bacterial aetiology as Proven Bacterial Meningitis. Neisseria meningitidis was identified in 0.7% (3/404) and Streptococcus pneumoniae in another 0.7%. Typical laboratory findings (i.e. CSF pleocytosis and/or low glucose and high protein concentrations, Gram positive or Gram negative diplococcic, positive bacterial culture) were seen in 5 (83%). Clinically, patients showed fever, seizures, chills, headache, vomiting, stiff neck and bulging fontanelle. All confirmed cases were less than 5 years old and were admitted in summer. All patients were prescribed with antibiotics; they were all recovered and discharged. CONCLUSIONS: Bacterial meningitis is over-diagnosed in hospitals in Khartoum therefore clinical prediction rules must be adopted and applied to guide the clinical decision. The sole bacterial aetiology in this selected group of Sudanese children remain N. meningitidis and S. pneumoniae, but with significant decrease in prevalence. Some cases showed atypical clinical and laboratory findings.

Culture and Real-time Polymerase Chain reaction sensitivity in the diagnosis of invasive meningococcal disease: Does culture miss less severe cases?

BACKGROUND: Invasive meningococcal disease (IMD) is a highly lethal disease. Diagnosis is commonly performed by culture or Realtime-PCR (qPCR). AIMS: Our aim was to evaluate, retrospectively, whether culture positivity correlates with higher bacterial load and fatal outcome. Our secondary aim was to compare culture and qPCR sensitivity. METHODS: The National Register for Molecular Surveillance was used as data source. Cycle threshold (CT), known to be inversely correlated with bacterial load, was used to compare bacterial load in different samples. RESULTS: Three-hundred-thirteen patients were found positive for Neisseria meningitidis by qPCR, or culture, or both; 41 died (case fatality rate 13.1%); 128/143 (89.5%) blood samples and 138/144 (95.8%) CSF were positive by qPCR, 37/143 (25.9%) blood samples and 45/144 (31.2%) CSF were also positive in culture. qPCR was 3.5 times (blood) or 3.1 times (CSF) more sensitive than culture in achieving a laboratory diagnosis of IMD (OR 24.4; 95% CI 12.2-49.8; p < .10-4; Cohen's κ 0.08 for blood and OR 49.0; 95% CI 19.1-133.4; p<10-4; Cohen's κ 0.02; for CSF). Positivity of culture did not correlate with higher bacterial loads in blood (mean CT 27.7±5.71, and CT 28.1±6.03, p = 0.739 respectively in culture positive or negative samples) or in CSF (mean CT 23.1±4.9 and 24.7±5.4 respectively in positive or negative CSF samples, p = 0.11).CT values in blood from patients who died were significantly lower than in patients who survived (respectively mean 18.0, range 14-23 and mean 29.6, range 16-39; p<10-17). No deaths occurred in patients with CT in blood over 23. Positive blood cultures were found in 10/25 (40%) patients who died and in 32/163 (19.6%) patients who survived, p = 0.036, OR 2.73; 95% CL 1.025-7.215), however 60% of deaths would have remained undiagnosed with the use of culture only. CONCLUSIONS: In conclusion our study demonstrated that qPCR is significantly (at least 3 times) more sensitive than culture in the laboratory confirmation of IMD. The study also demonstrated that culture negativity is not associated with lower bacterial loads and with less severe cases. On the other side, in patients with sepsis, qPCR can predict fatal outcome since higher bacterial load, evaluated by qPCR, appears strictly associated with most severe cases and fatal outcome. The study also showed that molecular techniques such as qPCR can provide a valuable addition to the proportion of diagnosed and serotyped cases of IMD.

Phylogenetic relationships and regional spread of meningococcal strains in the meningitis belt, 2011-2016.

BACKGROUND: Historically, the major cause of meningococcal epidemics in the meningitis belt of sub-Saharan Africa has been Neisseria meningitidis serogroup A (NmA), but the incidence has been substantially reduced since the introduction of a serogroup A conjugate vaccine starting in 2010. We performed whole-genome sequencing on isolates collected post-2010 to assess their phylogenetic relationships and inter-country transmission. METHODS: A total of 716 invasive meningococcal isolates collected between 2011 and 2016 from 11 meningitis belt countries were whole-genome sequenced for molecular characterization by the three WHO Collaborating Centers for Meningitis. FINDINGS: We identified three previously-reported clonal complexes (CC): CC11 (n = 434), CC181 (n = 62) and CC5 (n = 90) primarily associated with NmW, NmX, and NmA, respectively, and an emerging CC10217 (n = 126) associated with NmC. CC11 expanded throughout the meningitis belt independent of the 2000 Hajj outbreak strain, with isolates from Central African countries forming a distinct sub-lineage within this expansion. Two major sub-lineages were identified for CC181 isolates, one mainly expanding in West African countries and the other found in Chad. CC10217 isolates from the large outbreaks in Nigeria and Niger were more closely related than those from the few cases in Mali and Burkina Faso. INTERPRETATIONS: Whole-genome based phylogenies revealed geographically distinct strain circulation as well as inter-country transmission events. Our results stress the importance of continued meningococcal molecular surveillance in the region, as well as the development of an affordable vaccine targeting these strains. FUND: Meningitis Research Foundation; CDC's Office of Advanced Molecular Detection; GAVI, the Vaccine Alliance.