Search

Purpose: To determine and compare the reliability and efficiency of various methods of leg-length measurement. Methods: A total of 88 leg-lengths were measured among 50 subjects (79%–84% female, mean age = 30–33 years). Leg-lengths were measured in both supine and standing positions using multiple devices, including a tape measure, a LASER distance meter, and diagnostic ultrasound. Results: All methods of leg-length measurement using the middle of the femoral head as a reference point, identified via ultrasound, demonstrated excellent reliability (intraclass correlation coefficient = 0.95–1.00). Measurements performed in supine, using the anterior superior iliac spine as a reference point, with a tape measure, demonstrated good-to-excellent reliability (intraclass correlation coefficient = 0.86–0.95, standard error of the measurement = 16.1–19.9 cm). Standing measurements using the anterior superior iliac spine as a reference point, using a tape measure, demonstrated fair-to-excellent reliability (intraclass correlation coefficient = 0.71–0.95). Conclusion: Ultrasound-guided landmark identification appear to be a more reliable method compared to palpation of the anterior superior iliac spine for measurement of leg-length using clinical tools. When coupled with ultrasound guidance, a hand-held LASER distance meter/pitch locator apparatus or a retractable tape measure appears to be acceptable alternatives to a fixed LASER distance meter on a linear actuator for leg-length measurement. [ABSTRACT FROM AUTHOR]

Hard ticks (Acari: Ixodidae) have been historically identified by morphological methods which require highly specialized expertise and more recently by DNA-based molecular assays that involve high costs. Although both approaches provide complementary data for tick identification, each method has limitations which restrict their use on large-scale settings such as regional or national tick surveillance programs. To overcome those obstacles, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced as a cost-efficient method for the identification of various organisms, as it balances performance, speed, and high data output. Here we describe the use of this technology to validate the distinction of two closely related Dermacentor tick species based on the development of the first nationwide MALDI-TOF MS reference database described to date. The dataset obtained from this protein-based approach confirms that tick specimens collected from United States regions west of the Rocky Mountains and identified previously as Dermacentor variabilis are the recently described species, Dermacentor similis. Therefore, we propose that this integrative taxonomic tool can facilitate vector and vector-borne pathogen surveillance programs in the United States and elsewhere., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Haematospirillum jordaniae is a gram-negative bacterium that has been identified in the blood of septic patients. The environmental source or potential zoonotic host of this bacterium, recently described as a human bacterial pathogen is unknown. An increasing number of H. jordaniae clinical infections identified by our laboratory suggested the need for an assay to detect this organism in order to aid clinical teams and practitioners with faster identification and treatment thus improving patient prognosis. Described here is a real-time qualitative PCR assay designed using gene targets identified from the analysis of 14 H. jordaniae genomes sequenced by the Center for Disease Control and Prevention's (CDC) Special Bacterial Reference Laboratory (SBRL) culture collection. The assay was validated on clinical EDTA whole blood samples as well as on plasma and determined to be effective at detecting as few as 10 copies per microliter (10,000 copies per mL, 4 log/mL) for whole blood samples and 1 copy per microliter (1,000 copies per mL, 3 log mL) for plasma samples., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Inc.)

The Gram-negative Elizabethkingia express multiple antibiotic resistance and cause severe opportunistic infections. Vancomycin is commonly used to treat Gram-positive infections and has also been used to treat Elizabethkingia infections, even though Gram-negative organisms possess a vancomycin permeability barrier. Elizabethkingia anophelis appeared relatively vancomycin-susceptible and challenge with this drug led to morphological changes indicating cell lysis. In stark contrast, vancomycin growth challenge revealed that E. anophelis populations refractory to vancomycin emerged. In addition, E. anophelis vancomycin-selected mutants arose at high frequencies and demonstrated elevated vancomycin resistance and reduced susceptibility to other antimicrobials. All mutants possessed a SNP in a gene ( vsr1 = vancomycin-susceptibility regulator 1) encoding a PadR family transcriptional regulator located in the putative operon vsr1-ORF551 , which is conserved in other Elizabethkingia spp as well. This is the first report linking a padR homologue ( vsr1 ) to antimicrobial resistance in a Gram-negative organism. We provide evidence to support that vsr1 acts as a negative regulator of vsr1-ORF551 and that vsr1-ORF551 upregulation is observed in vancomycin-selected mutants. Vancomycin-selected mutants also demonstrated reduced cell length indicating that cell wall synthesis is affected. ORF551 is a membrane-spanning protein with a small phage shock protein conserved domain. We hypothesize that since vancomycin-resistance is a function of membrane permeability in Gram-negative organisms, it is likely that the antimicrobial resistance mechanism in the vancomycin-selected mutants involves altered drug permeability.

Limited data significantly hinders our capability of biothreat assessment of novel bacterial strains. Integration of data from additional sources that can provide context about the strain can address this challenge. Datasets from different sources, however, are generated with a specific objective and which makes integration challenging. Here, we developed a deep learning-based approach called the neural network embedding model (NNEM) that integrates data from conventional assays designed to classify species with new assays that interrogate hallmarks of pathogenicity for biothreat assessment. We used a dataset of metabolic characteristics from a de-identified set of known bacterial strains that the Special Bacteriology Reference Laboratory (SBRL) of the Centers for Disease Control and Prevention (CDC) has curated for use in species identification. The NNEM transformed results from SBRL assays into vectors to supplement unrelated pathogenicity assays from de-identified microbes. The enrichment resulted in a significant improvement in accuracy of 9% for biothreat. Importantly, the dataset used in our analysis is large, but noisy. Therefore, the performance of our system is expected to improve as additional types of pathogenicity assays are developed and deployed. The proposed NNEM strategy thus provides a generalizable framework for enrichment of datasets with previously collected assays indicative of species., (© 2023. The Author(s).)

This review serves as an update to the previous Nocardia review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.

Rat bite fever and Haverhill fever are often difficult to diagnose in a clinical setting. This difficulty results in part from clinicians and laboratory professionals not being able to reliably recover the causative agent Streptobacillus moniliformis using culture-based methods. After utilizing an automated continuous-monitoring blood culture bottle system, we showed that the organism can be reliably cultured when a blood volume inoculum of 10 mL is used. Further, we showed that when the above recommendation is followed, sodium polyanethole sulfonate (up to a concentration of 0.05% w/v) in commercially purchased blood culture bottle formulations seems to be inactivated, allowing for the growth and detection of S. moniliformis. Herein, we offer data and methods used to overcome these clinical limitations. This is a comprehensive study of the historical collection of S. moniliformis isolates maintained by our facility and believed to be the largest of its kind to date., (Published by Oxford University Press on behalf of American Society for Clinical Pathology 2021.)

Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Rhodococcus sp. strain W8901 is a Gram-positive, aerobic, mycolic acid-containing coccobacillus obtained from a patient with acute lymphocytic leukemia. Here, we report on the complete, circular genome sequence obtained using Illumina MiSeq and Oxford Nanopore Technologies MinION reads in order to better resolve the phylogeny of a rare pathogen.

Rat bite fever (RBF) caused by Streptobacillus moniliformis has been described as a diagnostic challenge. While it has a favorable prognosis with treatment, timely diagnosis is hindered by the lack of culture-free identification methods. Here we present a multiplex real-time PCR assay that detects the zoonotic Streptobacillus spp. as well as differentiate the primary causative agent of RBF, Streptobacillus moniliformis. The performance of this assay was evaluated using mock clinical specimens for blood, serum, and urine. Analytical sensitivity was determined to be 3-4 genome equivalents (GE)/µl for the zoonotic Streptobacillus spp. target, and 1-2 GE/µl for the S. moniliformis specific target. The assay correctly detected only the intended targets with no cross-reactivity identified. The pathogen was detected in all spiked matrices and not detected in the negative non-spiked specimens. This rapid diagnostic assay may permit quicker diagnosis of RBF patients., Competing Interests: Conflict of interests No reported conflicts of interest. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention., (Published by Elsevier Inc.)

Gordonia sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with Gordonia araii NBRC 100433 T as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.75 Mbp with 3,601 predicted coding sequences.

Kroppenstedtia eburnea DSM 45196 T and Kroppenstedtia pulmonis W9323 T are aerobic, Gram-positive, filamentous, chemoorganotrophic thermoactinomycetes. Here, we report on the complete and circular genome assemblies generated using Illumina MiSeq and Oxford Nanopore Technologies MinION reads. Putative gene clusters predicted to be involved in the production of secondary metabolites were also identified.

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 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.

Background: Rat-bite fever is a rare disease associated with rat bites or direct/indirect rodent contact., Methods: We examined rat-bite fever and rat-bite injury diagnoses in the United States during 2001-2015. We analyzed national, state, and Indian Health Service healthcare encounter datasets for rat-bite fever and rat-bite injury diagnoses. We calculated average-annual encounter rates per 1 000 000 persons., Results: Nationally, the rat-bite fever Emergency Department visit rate was 0.33 (95% confidence interval [CI], 0.19-0.47) and the hospitalization rate was 0.20 (95% CI, 0.17-0.24). The rat-bite injury Emergency Department visit rate was 10.51 (95% CI, 10.13-10.88) and the hospitalization rate was 0.27 (95% CI, 0.23-0.30). The Indian Health Service Emergency Department/outpatient visit rate was 3.00 for rat-bite fever and 18.89 for rat-bite injury. The majority of rat-bite fever encounters were among individuals 0-19 years of age., Conclusions: Our results support the literature that rat-bite fever is rare and affects children and young adults. Targeted education could benefit specific risk groups., (Published by Oxford University Press on behalf of Infectious Diseases Society of America 2020.)

Salmonella is a leading cause of foodborne illness worldwide, and foods containing Salmonella (except raw meat and poultry products) are considered adulterated. Serotyping of Salmonella is an essential part of surveillance and investigation of outbreaks. This study evaluated a bead-based Salmonella molecular serotyping (SMS) method, which included the O-group 1, H-antigen, alternate target, and O-group 2 assays, compared with traditional serotyping. Salmonella was isolated from food, pet food, and environmental samples or were reference strains. A total of 572 isolates were analyzed by using two formats of the SMS method in comparison with traditional methods: 485 were analyzed by using Radix SMS (a custom user-mixed format), 218 were analyzed by using Luminex SMS (a commercial kit format), and 131 of the total isolates were analyzed by both formats for comparison. The SMS method was evaluated on the basis of the successful identification of antigens by the probes included in the method. The method identified 550 (96.2%) isolates as expected, 6 (1.0%) isolates were not identified as initially expected but were shown to be correctly identified by SMS after reanalysis by traditional serotyping, and 16 (2.8%) isolates not identified as expected possessed an antigen that should have been detected by the method but was not. Among the isolates considered correctly identified, 255 (44.6%) were identified to a single serovar, 44 (7.7%) required additional biochemical testing to differentiate variants or subspecies, and 251 (43.9%) were partially serotyped because probes for some antigens were not in the assay or had allelic variation for known serovars. Whole genome sequencing, SeqSero, and the Salmonella In Silico Typing Resource gave added confirmation for three isolates. Addition of the O-group 2 assay enabled the identification of 55 (9.6%) of 572 isolates. The SMS method could fully or partially serotype most isolates within a day. The SMS method should be a valuable tool when faster screening methods are needed, such as outbreaks and screening large numbers of environmental isolates.

Kroppenstedtia sanguinis X0209 T , a thermoactinomycete, was isolated from the blood of a patient in Sweden. We report on the draft genome sequence obtained with an Illumina MiSeq instrument. The assembled genome totaled 3.73 Mb and encoded 3,583 proteins. Putative genes for virulence, transposons, and biosynthetic gene clusters have been identified.

The taxonomic position of strain 15-057A T , an acidophilic actinobacterium isolated from the bronchial lavage of an 80-year-old male, was determined using a polyphasic approach incorporating morphological, phenotypic, chemotaxonomic and genomic analyses. Pairwise 16S rRNA gene sequence similarities calculated using the GGDC web server between strain 15-057A T and its closest phylogenetic neighbours, Streptomyces griseoplanus NBRC 12779 T and Streptacidiphilus oryzae TH49 T , were 99.7 and 97.6 %, respectively. The G+C content of isolate 15-057A T was determined to be 72.6 mol%. DNA-DNA relatedness and average nucleotide identity between isolate 15-057A T and Streptomyces griseoplanus DSM 40009 T were 29.2±2.5 % and 85.97 %, respectively. Chemotaxonomic features of isolate 15-057A T were consistent with its assignment within the genus Streptacidiphilus: the whole-cell hydrolysate contained ll-diaminopimelic acid as the diagnostic diamino acid and glucose, mannose and ribose as cell-wall sugars; the major menaquinone was MK9(H8); the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycophospholipid, aminoglycophospholipid and an unknown lipid; the major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phenotypic and morphological traits distinguished isolate 15-057A T from its closest phylogenetic neighbours. The results of our taxonomic analyses showed that strain 15-057A T represents a novel species within the evolutionary radiation of the genus Streptacidiphilus, for which the name Streptacidiphilus bronchialis sp. nov. is proposed. The type strain is 15-057A T (=DSM 106435 T =ATCC BAA-2934 T ).

Nosocomial infections of Elizabethkingia species can have fatal outcomes if not identified and treated properly. The current diagnostic tools available require culture and isolation, which can extend the reporting time and delay treatment. Using comparative genomics, we developed an efficient multiplex real-time PCR for the simultaneous detection of all known species of Elizabethkingia , as well as differentiating the two most commonly reported species, Elizabethkingia anophelis and Elizabethkingia meningoseptica ., (This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.)

The complete genome sequence of the Nocardia farcinica type strain was obtained by combining Illumina HiSeq and PacBio reads, producing a single 6.29-Mb chromosome and 2 circular plasmids. Bioinformatic analysis identified 5,991 coding sequences, including putative genes for virulence, microbial resistance, transposons, and biosynthesis gene clusters.

Background: Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation., Methods: We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions., Results: The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses., Conclusions: This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.).

Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 ± 0.36% completeness). The number of protein-coding DNA sequences (2,174 ± 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis' pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ''metabolism" and ''information storage/processing." However, most genes were classified as ''function unknown" or "unclassified". Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system., Competing Interests: The authors have declared that no competing interests exist.

Streptacidiphilus sp. strain 15-057A was isolated from a bronchial lavage sample and represents the only member of the genus not isolated from acidic soils. A single circular chromosome of 7.01 Mb was obtained by combining Illumina and PacBio sequencing data. Bioinformatic analysis detected 63 putative secondary biosynthetic gene clusters and recognized 43 transposons.

We report the isolation and characterization of two Elizabethkingia anophelis strains (OSUVM-1 and OSUVM-2) isolated from sources associated with horses in Oklahoma. Both strains appeared susceptible to fluoroquinolones and demonstrated high MICs to all cell wall active antimicrobials including vancomycin, along with aminoglycosides, fusidic acid, chloramphenicol, and tetracycline. Typical of the Elizabethkingia, both draft genomes contained multiple copies of β-lactamase genes as well as genes predicted to function in antimicrobial efflux. Phylogenetic analysis of the draft genomes revealed that OSUVM-1 and OSUVM-2 differ by only 6 SNPs and are in a clade with 3 strains of Elizabethkingia anophelis that were responsible for human infections. These findings therefore raise the possibility that Elizabethkingia might have the potential to move between humans and animals in a manner similar to known zoonotic pathogens., Competing Interests: The authors have declared that no competing interests exist.

Chromobacterium violaceum is a rare, potentially serious pathogen. Most clinicians have no experience with its clinical appearance or treatment. We describe a case of a child presenting with necrotizing pneumonia caused by C. violaceum . We describe case complexities, including the need for a multidisciplinary approach to diagnosis and treatment.

We report here a nearly complete draft genome sequence for a Corynebacterium mastitidis isolate from a mouse. The total read coverage is 198×, and the genome size is 2,264,319 bp with a 69.04% GC content. This genome complements the only other genome available for C. mastitidis , which was obtained from a sheep., (Copyright © 2018 Cheleuitte-Nieves et al.)

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 T  = DSM 2975 T  = CCUG 69503 T  = CIP 111191 T ) and Elizabethkingia ursingii sp. nov. (type strain, G4122 T  = DSM 2974 T  = CCUG 69496 T  = CIP 111192 T ), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070 T  = DSM 2976 T  = CCUG 69505 T  = CIP 111193 T ), is proposed.

We provide complete circularized genome sequences of two mosquito-derived Elizabethkingia anophelis strains with draft sequences currently in the public domain (R26 and Ag1), and two novel E. anophelis strains derived from a different mosquito species, Anopheles sinensis (AR4-6 and AR6-8). The genetic similarity of all four mosquito-derived strains is remarkable.

We report here 1 near-complete genome sequence and 12 complete genome sequences for clinical Capnocytophaga isolates. Total read coverages ranged from 211× to 737×, and genome sizes ranged from 2.41 Mb to 3.10 Mb. These genomes will enable a more comprehensive taxonomic evaluation of the Capnocytophaga genus.

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 inclusion of molecular methods in the characterization of the novel species Enterococcus horridus necessitated the sequencing and assembly of the genomes of the closely related Enterococcus rotai and Enterococcus silesiacus Sequencing using Illumina technology in combination with optical mapping led to the generation of closed genomes for both isolates., (Copyright © 2016 Lauer et al.)

Eight Gram-stain-negative bacteria (B4199T, C6819, C6918, D2441, D3318, E1086, E1148 and E5571) were identified during a retrospective study of unidentified strains from a historical collection held in the Special Bacteriology Reference Laboratory at the Centers for Disease Control and Prevention. The strains were isolated from eight patients: five female, two male and one not specified. No ages were indicated for the patients. The sources were urine (3), leg tissue (2), foot wound, lung tissue and deep liver. The strains originated from seven different states across the USA [Colorado, Connecticut (2), Indiana, North Carolina, Oregon and Pennsylvania]. The strains grew at 10-42 °C, were non-motile, alkalitolerant, slightly halophilic, microaerophilic, and catalase- and oxidase-positive. The DNA G+C content was 47.3-47.6 mol%. The major cellular fatty acids were tetradecanoic acid (C14 : 0), hexadecanoic acid (C16 : 0) and 11-octadecenoic acid (C18 : 1ω7c). Polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unknown phospholipids; the only respiratory quinone detected was the ubiquinone Q-9 (100 %). 16S rRNA gene sequence analysis produced results with 95.6 % similarity to Pseudomonas caeni DSM 24390T and 95.2 % similarity to Thiopseudomonas denitrificans X2T. The results of the biochemical, chemotaxonomic and phylogenetic analyses between the study strains and some related type strains indicated that these strains represent a novel species of a new genus within the family Pseudomonadaceae, for which the name Oblitimonas alkaliphila gen. nov., sp. nov. is proposed. The type strain is B4199T (=DSM 100830T=CCUG 67636T).

Gram-stain-positive, partially acid-fast, non-spore-forming, anaerobic, catalase-positive, pleomorphic bacteria were isolated from human abscesses. Strains X1036T, X1698 and NML 120705, were recovered from a spinal abscess, a peritoneal abscess and a breast abscess respectively. A phylogenetic analysis of the 16S rRNA gene sequences showed that the strains shared 100 % similarity, and the nearest phylogenetic neighbour was Dietzia timorensis DSM 45568T (95%). Chemotaxonomic characteristics of the strains were consistent with those described for members of the suborder Corynebacterineae. Mycolic acids were detected using HPLC and one-dimensional TLC; whole-cell hydrolysates yielded meso-diaminopimelic acid with arabinose and galactose as the predominant sugars; the muramic acid acyl type was acetylated; the major menaquinone was MK-9 (96.3%); polar lipids detected were phosphatidylglycerol, phosphatidylinositol and an unknown glycophospholipid. Cellular fatty acids were hexadecanoic acid (C16 : 0), octadecenoic acid (C18 : 1ω9c) and decanoic acid (C10 : 0). Tuberculostearic acid was not detected. Based on the results of this polyphasic study, we conclude that these strains represent a novel genus and species within the suborder Corynebacterineae for which we propose the name Lawsonella clevelandensis gen. nov., sp. nov., with the type strain X1036T (=DSM 45743T=CCUG 66657T).

The complete circularized genome sequences of selected specimens from the largest known Elizabethkingia anophelis outbreak to date are described here. Genomic rearrangements observed among the outbreak strains are discussed., (Copyright © 2016 Nicholson et al.)

A Gram-negative, aerobic, motile, spiral-shaped bacterium, strain H5569(T), was isolated from a human blood sample. Phenotypic and molecular characteristics of the isolate were investigated. Optimal growth was found to occur at 35 °C under aerobic conditions on Heart Infusion Agar supplemented with 5 % rabbit blood. The major fatty acids present in the cells were identified as C16:0, C16:1ω7c and C18:1ω7c. The predominant respiratory quinone was found to be ubiquinone-Q10. The G+C content of genomic DNA for strain H5569(T) was found to be 49.9 %. Based on 16S rRNA gene sequence analysis results, 13 additional isolates were also analysed in this study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism, represented by strain H5569(T), forms a distinct lineage within the family Rhodospirillaceae, closely related to two Novispirillum itersonii subspecies (93.9-94.1 %) and two Caenispirillum sp. (91.2-91.6 %). Based on these results, the isolate H5569(T) is concluded to represent a new genus and species for which the name Haematospirillum jordaniae gen. nov., sp. nov. is proposed. The type strain is H5569(T) (=DSM(T) 28903 = CCUG 66838(T)).

Draft genome sequences of Elizabethkingia meningoseptica and representatives of each of its four historically described genomospecies were sequenced here. Preliminary analysis suggests that Elizabethkingia miricola belongs to genomospecies 2, and both Elizabethkingia anophelis and Elizabethkingia endophytica are most similar to genomospecies 1., (Copyright © 2016 Nicholson et al.)

Results obtained through 16S rRNA gene sequencing and phenotypic testing of eight related, but unidentified, isolates located in a historical collection at the Centers for Disease Control and Prevention suggested that these isolates belong to a novel genera of bacteria. The genomes of the bacteria, to be named Oblitimonas alkaphilia gen. nov. sp. nov., were sequenced using Illumina technology. Closed genomes were produced for all eight isolates., (Copyright © 2015 Lauer et al.)

Here we report the complete genome sequences of two strains of the novel fastidious, partially acid-fast, Gram-positive bacillus "Lawsonella clevelandensis" (proposed). Their clinical relevance and unusual growth characteristics make them intriguing candidates for whole-genome sequencing., (Copyright © 2015 Nicholson et al.)

The CDC Special Bacteriology Reference Laboratory (SBRL) collection of human clinical pathogens contains several strains from the genus Devosia, usually found environmentally. We provide here the complete genome of strain H5989, which was isolated from a human cerebrospinal fluid (CSF) specimen and represents a putative novel species in the genus Devosia., (Copyright © 2015 Nicholson et al.)

Corynebacterium minutissimum was first isolated in 1961 from infection sites of patients presenting with erythrasma, a common cutaneous infection characterized by a rash. Since its discovery, C. minutissimum has been identified as an opportunistic pathogen in immunosuppressed cancer and HIV patients. Here, we report the whole-genome sequence of C. minutissimum., (Copyright © 2015 Penton et al.)

We report a novel anaerobe causing abscess in four patients at three hospitals. In the clinical specimen, bacilli were branching, Gram positive, and acid fast. The organism grew slowly and was not identified by 16S rRNA sequencing. Our findings support the description of a new genus and species of the suborder Corynebacterineae.

Serotyping of Salmonella has been an invaluable subtyping method for epidemiologic studies for more than 70 years. The technical difficulties of serotyping, primarily in antiserum production and quality control, can be overcome with modern molecular methods. We developed a DNA-based assay targeting the genes encoding the flagellar antigens (fliC and fljB) of the Kauffmann-White serotyping scheme. Fifteen H antigens (H:a, -b, -c, -d, -d/j, -e,h, -i, -k, -r, -y, -z, -z(10), -z(29), -z(35), and -z(6)), 5 complex major antigens (H:G, -EN, -Z4, -1, and -L) and 16 complex secondary antigens (H:2, -5, -6, -7, -f, -m/g,m, -m/m,t, -p, -s, -t/m,t, -v, -x, -z(15), -z(24), -z(28), and -z(51)) were targeted in the assay. DNA probes targeting these antigens were designed and evaluated on 500 isolates tested in parallel with traditional serotyping methods. The assay correctly identified 461 (92.2%) isolates based on the 36 antigens detected in the assay. Among the isolates considered correctly identified, 47 (9.4%) were partially serotyped because probes corresponding to some antigens in the strains were not in the assay, and 13 (2.6%) were monophasic or nonmotile strains that possessed flagellar antigen genes that were not expressed but were detected in the assay. The 39 (7.8%) strains that were not correctly identified possessed an antigen that should have been detected by the assay but was not. Apparent false-negative results may be attributed to allelic divergence. The molecular assay provided results that paralleled traditional methods with a much greater throughput, while maintaining the integrity of the Kauffmann-White serotyping scheme, thus providing backwards-compatible epidemiologic data. This assay should greatly enhance the ability of clinical and public health laboratories to serotype Salmonella.

In 2006, Salmonella enterica serovar I 9,12:l,v:- emerged in Bulgaria. The aim of this study was to characterize Salmonella serovar I 9,12:l,v:- isolates from Bulgaria, Denmark, and the United States. We compared isolates of Salmonella I 9,12:l,v:- and diphasic serovars with similar antigenic formulas by pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility. The phase 2 flagellin gene (fljB) was also sequenced for selected isolates. By PFGE, the Salmonella I 9,12:l,v:- isolates from Bulgaria were indistinguishable from the isolate from the United States and distinct from isolates from Denmark; furthermore, several Salmonella I 9,12:l,v:- were indistinguishable from an isolate of Salmonella serovar Goettingen. Sequence analysis showed 100% sequence identity with known H:e,n,z15 sequences of Salmonella Goettingen, which has the antigenic formula I 9,12:l,v:e,n,z15. The study indicated that Salmonella I 9,12:l,v:- is a monophasic variant of Salmonella Goettingen and is present in different countries and on different continents.

The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.

Salmonellae are enterobacteria that have the unique ability to change their flagellar composition by switching expression among two loci that encode the major flagellin protein. This property is not available to all Salmonella, but is species, subspecies and serotype specific. Curiously, the subsequent loss of the second locus in some lineages of Salmonella has apparently been tolerated and, indeed, has led to considerable success for some lineages. We discuss here an evolutionary model for maintenance of this unique function and the possible evolutionary advantages of loss or preservation of this mechanism. We hypothesize that the second flagellin locus is a genetic 'spare tyre' used in particular environmental circumstances.

A DNA-based microarray designed to detect somatic (O) and flagellar (H) antigens present in the five most commonly isolated Salmonella serovars within Canada was developed as an alternative to the traditional Kauffmann-White serotyping scheme currently used to serotype salmonellae. Short oligonucleotide probes were designed based on publicly available sequence data of selected genes responsible for O and H antigen biosynthesis. These targets included: antigen-specific sequences within the flagella (H) antigen phase 1 (fliC) and phase 2 (fljB) genes and somatic (O) antigen biosynthesis genes within the rfb cluster (Groups B--rfbJ, C1--wbaA, C2--rfbJ, D1--rfbS). A prototype microarray with 117 O and H antigen-specific probes and controls was used to assess probe performance against two pools of gene target PCR amplicons. A set of 31 of these antigen-specific probes (8 O and 23 H) with high specific signal and low non-specific signal were selected based on t-test (p-value <0.01) and log(2) ratio distribution analysis to create a prototype microarray. The microarray was tested against 16 Salmonella strains of known serotype. Based on the strains tested in this study, these probes successfully identified and differentiated 11 of the 12 antigens targeted. The prototype DNA-based typing microarray described here has the potential to be an automated alternative to the traditional antigen-antibody serotyping scheme currently used for Salmonella.