Burkholderia pseudomallei strain Bp1651, a human isolate, is resistant to all clinically relevant antibiotics. We report here on the finished genome sequence assembly and annotation of the two chromosomes of this strain. This genome sequence may assist in understanding the mechanisms of antimicrobial resistance for this pathogenic species.

Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer membrane proteins (pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the pmps and T3SS genes that may partially explain differences noted in C. psittaci host infection and disease.

Exserohilum rostratum was the cause of most cases of fungal meningitis and other infections associated with the injection of contaminated methylprednisolone acetate produced by the New England Compounding Center (NECC). Until this outbreak, very few human cases of Exserohilum had been reported and very little was known about this dematiaceous fungus, which usually infects plants. Here we report using whole genome sequencing (WGS) for detection of single nucleotide polymorphisms (SNP) and phylogenetic analysis to investigate molecular origin of the outbreak using 22 isolates of E. rostratum isolated from 19 case-patients with meningitis or epidural/spinal abscesses, six isolates isolated from contaminated NECC vials, and seven isolates that are unrelated to the outbreak. Our analysis indicates that all 28 isolates associated with the outbreak had nearly identical genomes of 33.8 Mb. A total of eight SNPs were detected among the outbreak genomes, with no more than two SNPs separating any two of the 28 genomes. The outbreak genomes were separated from the next most closely related control strain by approximately 136,000 SNPs. We also observed significant genomic variability among strains unrelated to the outbreak, which may suggest a possibility of cryptic speciation in E. rostratum.

Microorganisms may colonize needleless connectors (NCs) on intravascular catheters, forming biofilms and predisposing patients to catheter- associated infection (CAI). Standard and silver-coated NCs were collected from catheterized intensive care unit patients to characterize biofilm formation using culture-dependent and culture-independent methods and to investigate association between NC usage and biofilm characteristics. Viable microorganisms were detected by plate count (PC) from 46% of standard and 59% of silver-coated NCs (p=0.11). There were no significant associations (p>0.05, chi-squared test) between catheter type, side of catheter placement, number of catheter lumens, site of catheter placement, or NC duration, and positive NC. There was an association (p=0.04, chi-squared test) between infusion type and positive standard NCs. Viable microorganisms exhibiting intracellular esterase activity were detected on >90% of both NC types (p=0.751), suggesting that a large percentage of organisms were not culturable using the conditions provided in this study. Amplification of the 16S ribosomal RNA gene from selected NCs provided a substantially larger number of operational taxonomic units per NC than PC (26-43 vs 1-4), suggesting that culture-dependent methods may substantially underestimate microbial diversity on NCs. NC bacterial communities were clustered by patient and venous access type and may reflect the composition of the patient's local microbiome but may also contain organisms from the healthcare environment. NCs provide a portal of entry for a wide diversity of opportunistic pathogens to colonize the catheter lumen, forming a biofilm and increasing the potential for CAI, highlighting the importance of catheter maintenance practices to reduce microbial contamination.

Zoonotic and vector-borne pathogens have comprised a significant component of emerging human infections in recent decades, and bats are increasingly recognized as reservoirs for many of these disease agents. To identify novel pathogens associated with bats, we screened tissues of bats collected in Kenya. Virus isolates were identified by next generation sequencing of viral nucleic acid preparations from the infected cell culture supernatant and characterized. Here we report the identification of Fikirini rhabdovirus, a novel rhabdovirus isolated from a bat, Hipposideros vittatus, captured along the Kenyan coast.

Bordetella holmesii, a human pathogen, can confound the diagnosis of respiratory illness caused by Bordetella pertussis. We present the draft genome sequences of two B. holmesii isolates, one from blood, F627, and one from the nasopharynx, H558. Interestingly, important virulence genes that are present in B. pertussis are not found in B. holmesii.

BACKGROUND: Cowpox virus is an Orthopoxvirus that can cause infections in humans and a variety of animals. Infections occur in Eurasia; human nor animal infection has been reported in the United States. This report describes the occurrence of the first known human case of laboratory-acquired cowpox virus infection in the United States and ensuing investigation. METHODS: The patient and laboratory personnel were interviewed, and laboratory activities were reviewed. Real-time PCR and serologic assays were used to test the patient's specimens. PCR assays were used to test specimens obtained during the investigation. RESULTS: The patient's lesion tested positive for cowpox virus DNA. Genome sequencing revealed a recombinant region consistent with a strain of cowpox virus stored in the research laboratory's freezer. Cowpox virus contamination was detected in six additional laboratory stocks of viruses. Orthopoxvirus DNA was present in three of twenty environmental swabs taken from laboratory surfaces. CONCLUSIONS: The handling of contaminated reagents or contact with contaminated surfaces was likely the mode of transmission. Delays in recognition and diagnosis of this infection in a laboratory researcher underscore the importance of a thorough patient history--including occupational information--and laboratory testing to facilitate a prompt investigation and application of control and remediation measures.

Influenza A virus reservoirs in animals have provided novel genetic elements leading to the emergence of global pandemics in humans. Most influenza A viruses circulate in waterfowl, but those that infect mammalian hosts are thought to pose the greatest risk for zoonotic spread to humans and the generation of pandemic or panzootic viruses. We have identified an influenza A virus from little yellow-shouldered bats captured at two locations in Guatemala. It is significantly divergent from known influenza A viruses. The HA of the bat virus was estimated to have diverged at roughly the same time as the known subtypes of HA and was designated as H17. The neuraminidase (NA) gene is highly divergent from all known influenza NAs, and the internal genes from the bat virus diverged from those of known influenza A viruses before the estimated divergence of the known influenza A internal gene lineages. Attempts to propagate this virus in cell cultures and chicken embryos were unsuccessful, suggesting distinct requirements compared with known influenza viruses. Despite its divergence from known influenza A viruses, the bat virus is compatible for genetic exchange with human influenza viruses in human cells, suggesting the potential capability for reassortment and contributions to new pandemic or panzootic influenza A viruses.