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Coccidioides immitis and C. posadasii, the etiologic agents of coccidioidomycosis, also known as Valley fever, are environmental filamentous fungi with distinct geographic ranges in the western United States, northern Mexico, [...]

Onchocerca lupi is a species of zoonotic, filarial nematode that causes onchocerciasis in dogs, cats, and humans. It was first described in 1967 in Georgia, then part of the USSR, [...]

Mucormycosis is a debilitating fungal infection; the mortality rate among persons with predisposing factors such as skin trauma (e.g., surgery), diabetes mellitus, or organ transplant is high. The fungus can [...]

Coccidioides immitis is a rare but emerging fungal pathogen in Washington, USA; Only the south-central region of Washington has been established as an area to which Coccidioides spp. are endemic; [...]

Coccidioidomycosis, also known as Valley fever, is a disease of growing public health concern and is caused by 2 closely related fungal species, Coccidioides immitis and C. posadasii. Coccidioides spp. [...]

Each year, 9.4 million episodes of foodborne illness occur in the United States (1). According to the Centers for Disease Control and Prevention, -95% of these infections are sporadic, nonoutbreak [...]

Background The incidence of multidrug-resistant tuberculosis (MDR-TB) remains critically high in countries of the former Soviet Union, where >20% of new cases and >50% of previously treated cases have resistance to rifampin and isoniazid. Transmission of resistant strains, as opposed to resistance selected through inadequate treatment of drug-susceptible tuberculosis (TB), is the main driver of incident MDR-TB in these countries. Methods and findings We conducted a prospective, genomic analysis of all culture-positive TB cases diagnosed in 2018 and 2019 in the Republic of Moldova. We used phylogenetic methods to identify putative transmission clusters; spatial and demographic data were analyzed to further describe local transmission of Mycobacterium tuberculosis. Of 2,236 participants, 779 (36%) had MDR-TB, of whom 386 (50%) had never been treated previously for TB. Moreover, 92% of multidrug-resistant M. tuberculosis strains belonged to putative transmission clusters. Phylogenetic reconstruction identified 3 large clades that were comprised nearly uniformly of MDR-TB: 2 of these clades were of Beijing lineage, and 1 of Ural lineage, and each had additional distinct clade-specific second-line drug resistance mutations and geographic distributions. Spatial and temporal proximity between pairs of cases within a cluster was associated with greater genomic similarity. Our study lasted for only 2 years, a relatively short duration compared with the natural history of TB, and, thus, the ability to infer the full extent of transmission is limited. Conclusions The MDR-TB epidemic in Moldova is associated with the local transmission of multiple M. tuberculosis strains, including distinct clades of highly drug-resistant M. tuberculosis with varying geographic distributions and drug resistance profiles. This study demonstrates the role of comprehensive genomic surveillance for understanding the transmission of M. tuberculosis and highlights the urgency of interventions to interrupt transmission of highly drug-resistant M. tuberculosis., Author(s): Chongguang Yang 1,2, Benjamin Sobkowiak 3, Vijay Naidu 3, Alexandru Codreanu 4, Nelly Ciobanu 4, Kenneth S. Gunasekera 2, Melanie H. Chitwood 2, Sofia Alexandru 4, Stela Bivol 5, [...]

Francisella tularensis, a Tier 1 select agent (7), has 3 subspecies: tularensis (type A), holarctica (type B), and mediasiatica (Appendix 1 Figure, https://wwwnc. cdc.gov/EID/article/25/5/18-0363-App1.pdf). In humans, disease is caused by [...]

The pathogenic fungus Cryptococcus gattii, recently designated as a separate species from Cryptococcus neoformans, is now recognized as a separate species complex (1-3). In the United States, C. gattii was [...]

Despite modem advances in technology to control fungal contamination in clinical settings, fungi are continuously implicated in clusters or outbreaks of infections, particularly among immunosuppressed patients (1). The sources of [...]

Background Accurate, comprehensive, and timely detection of drug-resistant tuberculosis (TB) is essential to inform patient treatment and enable public health surveillance. This is crucial for effective control of TB globally. Whole-genome sequencing (WGS) and targeted next-generation sequencing (NGS) approaches have potential as rapid in vitro diagnostics (IVDs), but the complexity of workflows, interpretation of results, high costs, and vulnerability of instrumentation have been barriers to broad uptake outside of reference laboratories, especially in low- and middle-income countries. A new, solid-state, tabletop sequencing instrument, Illumina iSeq100, has the potential to decentralize NGS for individual patient care. Methods and findings In this study, we evaluated WGS and targeted NGS for TB on both the new iSeq100 and the widely used MiSeq (both manufactured by Illumina) and compared sequencing performance, costs, and usability. We utilized DNA libraries produced from Mycobacterium tuberculosis clinical isolates for the evaluation. We conducted WGS on three strains and observed equivalent uniform genome coverage with both platforms and found the depth of coverage obtained was consistent with the expected data output. Utilizing the standardized, cloud-based ReSeqTB bioinformatics pipeline for variant analysis, we found the two platforms to have 94.0% (CI 93.1%-94.8%) agreement, in comparison to 97.6% (CI 97%-98.1%) agreement for the same libraries on two MiSeq instruments. For the targeted NGS approach, 46 M. tuberculosis-specific amplicon libraries had 99.6% (CI 98.0%-99.9%) agreement between the iSeq100 and MiSeq data sets in drug resistance-associated SNPs. The upfront capital costs are almost 5-fold lower for the iSeq100 ($19,900 USD) platform in comparison to the MiSeq ($99,000 USD); however, because of difference in the batching capabilities, the price per sample for WGS was higher on the iSeq100. For WGS of M. tuberculosis at the minimum depth of coverage of 30x, the cost per sample on the iSeq100 was $69.44 USD versus $28.21 USD on the MiSeq, assuming a 2 x 150 bp run on a v3 kit. In terms of ease of use, the sequencing workflow of iSeq100 has been optimized to only require 27 minutes total of hands-on time pre- and post-run, and the maintenance is simplified by a single-use cartridge-based fluidic system. As these are the first sequencing attempts on the iSeq100 for M. tuberculosis, the sequencing pool loading concentration still needs optimization, which will affect sequencing error and depth of coverage. Additionally, the costs are based on current equipment and reagent costs, which are subject to change. Conclusions The iSeq100 instrument is capable of running existing TB WGS and targeted NGS library preparations with comparable accuracy to the MiSeq. The iSeq100 has reduced sequencing workflow hands-on time and is able to deliver sequencing results in, Author(s): Rebecca E. Colman 1,2,*, Aurélien Mace 1, Marva Seifert 2, Jonathan Hetzel 3, Haifa Mshaiel 2, Anita Suresh 1, Darrin Lemmer 4, David M. Engelthaler 4, Donald G. Catanzaro [...]

Genotyping of microorganisms typically relies on comparison of genomic features (e.g., fragment size, repeats, single-nucleotide polymorphisms [SNPs]) between strains and/or against a database of feature profiles (e.g., PulseNET and mlst.net) [...]

Francisella tularensis contains several highly pathogenic subspecies, including Francisella tularensis subsp. holarctica, whose distribution is circumpolar in the northern hemisphere. The phylogeography of these subspecies and their subclades was examined using whole-genome single nucleotide polymorphism (SNP) analysis, high-density microarray SNP genotyping, and real-time-PCR-based canonical SNP (canSNP) assays. Almost 30,000 SNPs were identified among 13 whole genomes for phylogenetic analysis. We selected 1,655 SNPs to genotype 95 isolates on a high-density microarray platform. Finally, 23 clade- and subclade-specific canSNPs were identified and used to genotype 496 isolates to establish global geographic genetic patterns. We confirm previous findings concerning the four subspecies and two Francisella tularensis subsp. tularensis subpopulations and identify additional structure within these groups. We identify 11 subclades within F. tularensis subsp. holarctica, including a new, genetically distinct subclade that appears intermediate between Japanese F. tularensis subsp. holarctica isolates and the common F. tularensis subsp. holarctica isolates associated with the radiation event (the B radiation) wherein this subspecies spread throughout the northern hemisphere. Phylogenetic analyses suggest a North American origin for this B-radiation clade and multiple dispersal events between North America and Eurasia. These findings indicate a complex transmission history for F. tularensis subsp. holarctica.

Coccidioidomycosis is a common cause of community-acquired pneumonia (CAP) in disease-endemic areas. Because testing rates influence interpretation of reportable-disease data and quality of CAP patient care, we determined the proportion [...]

Burkholderia pseudomallei is endemic to Southeast Asia and northern Australia; the organism has also been identified on other continents and islands but not North America (1). B. pseudomallei is present [...]

To investigate climatic, spatial, temporal, and environmental patterns associated with hantavirus pulmonary syndrome (HPS) cases in the Four Corners region, we collected exposure site data for HPS cases that occurred [...]