An atypically large outbreak of Elizabethkingia anophelis infections occurred in Wisconsin. Here we show that it was caused by a single strain with thirteen characteristic genomic regions. Strikingly, the outbreak isolates show an accelerated evolutionary rate and an atypical mutational spectrum. Six phylogenetic sub-clusters with distinctive temporal and geographic dynamics are revealed, and their last common ancestor existed approximately one year before the first recognized human infection. Unlike other E. anophelis, the outbreak strain had a disrupted DNA repair mutY gene caused by insertion of an integrative and conjugative element. This genomic change probably contributed to the high evolutionary rate of the outbreak strain and may have increased its adaptability, as many mutations in protein-coding genes occurred during the outbreak. This unique discovery of an outbreak caused by a naturally occurring mutator bacterial pathogen provides a dramatic example of the potential impact of pathogen evolutionary dynamics on infectious disease epidemiology.

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species ( Chryseobacterium arachidiradicis , Chryseobacterium bovis , Chryseobacterium caeni , Chryseobacterium hispanicum , Chryseobacterium hominis , Chryseobacterium hungaricum , Chryseobacterium molle , Chryseobacterium pallidum and Chryseobacterium zeae ) to the genus Epilithonimonas and eleven ( Chryseobacterium anthropi , Chryseobacterium antarcticum , Chryseobacterium carnis , Chryseobacterium chaponense , Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum , Chryseobacterium palustre , Chryseobacterium solincola , Chryseobacterium treverense and Chryseobacterium yonginense ) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146 = DSM 2975 = CCUG 69503 = CIP 111191) and Elizabethkingia ursingii sp. nov. (type strain, G4122 = DSM 2974 = CCUG 69496 = CIP 111192), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070 = DSM 2976 = CCUG 69505 = CIP 111193), is proposed.

dPCR detecting the protein D (hpd) and fuculose kinase (fucK) genes showed high sensitivity and specificity for identifying Haemophilus influenzae and differentiating it from H. haemolyticus. Phylogenetic analysis using the 16S rRNA gene demonstrated two distinct groups for H. influenzae and H. haemolyticus. Haemophilus species account for approximately 10% of the bacterial flora in the human respiratory tract (9). At least 8 different Haemophilus species are found to colonize the pharyngeal cavity of humans (13) Discrimination between the two organisms can be challenging due to similarities in colony and cell morphology, biochemical characteristics, and genetic background. Hemolytic H. haemolyticus can be differentiated from H. influenzae by production of clear (beta) hemolysis on horse blood agar. The hemolysis activity may be lost after subculture, however, and nonhemolytic H. haemolyticus strains are often misidentified as H. influenzae (10,13,15,16,18).DNA-DNA hybridization is the gold standard for identifying bacterial species (2-4). Because of the complexity of DNA-DNA hybridization, 16S rRNA gene sequence similarity is widely used as a tool to identify bacteria at the species level and assist with differentiating between closely related bacterial species (8). Several molecular tools have been assessed for differentiation of H. haemolyticus from H. influenzae, such as the fuculose kinase gene fucK, the H. influenzae adherence and penetration protein gene hap, the [Cu, Zn]-superoxide dismutase gene sodC, the immunoglobulin A protease gene iga, the lipopolysaccharide (LPS) gene lgtC, and the outer membrane protein P6 (1, 16-18, 24, 26). fucK has been proposed as a reliable marker gene for discrimination of H. influenzae from other Haemophilus species (17). A real-time PCR assay targeting the Haemophilus protein D gene (hpd) has been developed to identify H. influenzae (28). The hpd assay is highly specific for H. influenzae and provides a potential tool to differentiate H. influenzae from H. haemolyticus, including nonhemolytic H. haemolyticus. In this study, both hpd and fucK PCR assays were evaluated against 16S rRNA gene phylogeny for distinguishing H. influenzae from H. haemolyticus by the use of Haemophilus isolates identified during a carriage study in Minnesota (12,22 All isolates were further characterized using the hpd and fucK PCR assays with crude DNA as the template (28). All of the 31 hemolytic H. haemolyticus and 128 other Haemophilus species isolates were negative by both hpd and fucK PCR assays. Of the 245 presumed H. influenzae isolates, 121 (49.4%) were positive for both the hpd and fucK genes, which is the expected genotype for H. influenzae, and 98 (40.0%) were negative for both hpd and fucK,

One-centimeter cubes of the semimembranosus and adductor muscles of beef were inoculated with 5.2 × 106 of Salmonella typhimurium, Shigella sonnei, Yersinia enterocolitica, Escherichia coli, Pseudomonas aeruginosa or Streptococcus faecalis. Exposure of the meat by dipping in 1.2% acetic acid for 10 s reduced averge numbers recoverable of these bacteria by 65%. E. coli was the most resistant, losing 46% of its viable cells. One-half of the acetic acid was replaced with 0.046% formic acid without loss in effectiveness. The rate of increase in antimicrobial effects of the treatment declined with time. Discoloration of the meat occurred after dipping in both 1.2% acetic acid, and 0.6% acetic plus 0.046% formic acids for 10 s. In triangle tests of flavor, panelists failed to differentiate samples of baked ground beef treated (before grinding) with 0.6% acetic acid and 0.046% formic acid from controls dipped in water (P<0.05). However, the same type of test showed a significant flavor difference between meat dipped in 1.2% acetic acid or distilled water.