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Effective laboratory-based surveillance and public health response to bacterial meningitis depends on timely characterization of bacterial meningitis pathogens. Traditionally, characterizing bacterial meningitis pathogens such as Neisseria meningitidis (Nm) and Haemophilus influenzae (Hi) required several biochemical and molecular tests. Whole genome sequencing (WGS) has enabled the development of pipelines capable of characterizing the given pathogen with equivalent results to many of the traditional tests. Here, we present the Bacterial Meningitis Genomic Analysis Platform (BMGAP): a secure, web-accessible informatics platform that facilitates automated analysis of WGS data in public health laboratories. BMGAP is a pipeline comprised of several components, including both widely used, open-source third-party software and customized analysis modules for the specific target pathogens. BMGAP performs de novo draft genome assembly and identifies the bacterial species by whole-genome comparisons against a curated reference collection of 17 focal species including Nm, Hi, and other closely related species. Genomes identified as Nm or Hi undergo multi-locus sequence typing (MLST) and capsule characterization. Further typing information is captured from Nm genomes, such as peptides for the vaccine antigens FHbp, NadA, and NhbA. Assembled genomes are retained in the BMGAP database, serving as a repository for genomic comparisons. BMGAP's species identification and capsule characterization modules were validated using PCR and slide agglutination from 446 bacterial invasive isolates (273 Nm from nine different serogroups, 150 Hi from seven different serotypes, and 23 from nine other species) collected from 2017 to 2019 through surveillance programs. Among the validation isolates, BMGAP correctly identified the species for all 440 isolates (100% sensitivity and specificity) and accurately characterized all Nm serogroups (99% sensitivity and 98% specificity) and Hi serotypes (100% sensitivity and specificity). BMGAP provides an automated, multi-species analysis pipeline that can be extended to include additional analysis modules as needed. This provides easy-to-interpret and validated Nm and Hi genome analysis capacity to public health laboratories and collaborators. As the BMGAP database accumulates more genomic data, it grows as a valuable resource for rapid comparative genomic analyses during outbreak investigations., Competing Interests: RK, HS, ER, and GD were employed by General Dynamics Information Technology. FH was employed by IHRC Inc. DM was employed by Weems Design Studio, Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Buono, Kelly, Topaz, Retchless, Silva, Chen, Ramos, Doho, Khan, Okomo-Adhiambo, Hu, Marasini and Wang.)

The epidemiology, symptomology, and viral aetiology of endemic influenza remain largely uncharacterized in Cambodia. In December 2006, we established passive hospital-based surveillance to identify the causes of acute undifferentiated fever in patients seeking healthcare. Fever was defined as tympanic membrane temperature >38 degrees C. From December 2006 to December 2008, 4233 patients were screened for influenza virus by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR). Of these patients, 1151 (27.2%) were positive for influenza. Cough (68.8% vs. 50.5%, P < 0.0001) and sore throat (55.0% vs. 41.9%, P < 0.0001) were more often associated with laboratory-confirmed influenza-infected patients compared to influenza-negative enrollees. A clear influenza season was evident between July and December with a peak during the rainy season. Influenza A and B viruses were identified in 768 (66.3%) and 388 (33.7%) of the influenza-positive population (n = 1153), respectively. In December 2008, passive surveillance identified infection of the avian influenza virus H5N1 in a 19-year-old farmer from Kandal province who subsequently recovered. From a subset of diagnostic samples submitted in 2007, 15 A(H1N1), seven A(H3N2) and seven B viruses were isolated. The predominant subtype tested was influenza A(H1N1), with the majority antigenically related to the A/Solomon Island/03/2006 vaccine strain. The influenza A(H3N2) isolates and influenza B viruses analysed were closely related to A/Brisbane/10/2007 or B/Ohio/01/2005 (B/Victoria/2/87-lineage) vaccine strains, respectively. Phylogenetic analysis of the HA1 region of the HA gene of influenza A(H1N1) viruses demonstrated that the Cambodian isolates belonged to clade 2C along with representative H1N1 viruses circulating in SE Asia at the time. These viruses remained sensitive to oseltamivir. In total, our data suggest that viral influenza infections contribute to nearly one-fifth of acute febrile illnesses and demonstrate the importance of influenza surveillance in Cambodia.