Hazenella coriacea gen. nov., sp nov., isolated from clinical specimens

A Gram-staining-positive, endospore-forming rod was isolated independently from clinical specimens in New York State, USA, once in 2009 and twice in 2011. The three isolates had identical 16S rRNA gene sequences and, based on their 16S rRNA gene sequence, are most closely related to the type strains of Laceyella sediminis and L. sacchari (94.6% similarity). The partial 23S rRNA gene sequences of the three strains were also 100% identical. Maximumlikelihood phylogenetic analysis suggests that the new isolates belong to the family Thermoactinomycetaceae. Additional biochemical and phenotypic characteristics of the strains support the family designation and suggest that the three isolates represent a single species. In each of the strains, the predominant menaquinone is MK-7, the diagnostic diamino acid is mesodiaminopimelic acid and the major cellular fatty acids are iso-C15 : 0, anteiso-C15 : 0 and iso-C13 : 0. The polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids, four unknown aminophospholipids and an unknown lipid. It is proposed that the novel isolates represent a single novel species within a new genus, for which the name Hazenella coriacea gen. nov., sp. nov. is proposed. The type strain of Hazenella coriacea is strain 23436T (5DSM 45707T5LMG 27204T)

Biodiversity of Clostridium botulinum Type E Associated with a Large Outbreak of Botulism in Wildlife from Lake Erie and Lake Ontario ▿

The genetic relatedness of Clostridium botulinum type E isolates associated with an outbreak of wildlife botulism was studied using random amplification of polymorphic DNA (RAPD). Specimens were collected from November 2000 to December 2008 during a large outbreak of botulism affecting birds and fish living in and around Lake Erie and Lake Ontario. In our present study, a total of 355 wildlife samples were tested for the presence of botulinum toxin and/or organisms. Type E botulinum toxin was detected in 110 samples from birds, 12 samples from fish, and 2 samples from mammals. Sediment samples from Lake Erie were also examined for the presence of C. botulinum. Fifteen of 17 sediment samples were positive for the presence of C. botulinum type E. Eighty-one C. botulinum isolates were obtained from plants, animals, and sediments; of these isolates, 44 C. botulinum isolates produced type E toxin, as determined by mouse bioassay, while the remaining 37 isolates were not toxic for mice. All toxin-producing isolates were typed by RAPD; that analysis showed 12 different RAPD types and multiple subtypes. Our study thus demonstrates that multiple genetically distinct strains of C. botulinum were involved in the present outbreak of wildlife botulism. We found that C. botulinum type E is present in the sediments of Lake Erie and that a large range of bird and fish species is affected

Use of the National Committee for Clinical Laboratory Standards Guidelines for Disk Diffusion Susceptibility Testing in New York State Laboratories

Accurate antimicrobial susceptibility testing is vital for patient care and surveillance of emerging antimicrobial resistance. The National Committee for Clinical Laboratory Standards (NCCLS) outlines generally agreed upon guidelines for reliable and reproducible results. In January 1997 we surveyed 320 laboratories participating in the New York State Clinical Evaluation Program for General Bacteriology proficiency testing. Our survey addressed compliance with NCCLS susceptibility testing guidelines for bacterial species designated a problem (Staphylococcus aureus and Enterococcus species) or fastidious (Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria gonorrhoeae) organism. Specifically, we assessed compliance with guidelines for inoculum preparation, medium choice, number of disks per plate, and incubation conditions for disk diffusion tests. We also included length of incubation for S. aureus and Enterococcus species. We found overall compliance with the five characteristics listed above in 80 of 153 responding laboratories (50.6%) for S. aureus and 72 of 151 (47.7%) laboratories for Enterococcus species. The most common problem was an incubation time shortened to less than 24 h. Overall compliance with the first four characteristics was reported by 92 of 221 (41.6%) laboratories for S. pneumoniae, 49 of 163 (30.1%) laboratories for H. influenzae, and 11 of 77 (14.3%) laboratories for N. gonorrhoeae. Laboratories varied from NCCLS guidelines by placing an excess number of disks per plate. Laboratories also reported using alternative media for Enterococcus species, N. gonorrhoeae, and H. influenzae. This study demonstrates a need for education among clinical laboratories to increase compliance with NCCLS guidelines

Implementing the Bruker MALDI Biotyper in the Public Health Laboratory for C. botulinum Neurotoxin Detection

Currently, the gold standard method for active botulinum neurotoxin (BoNT) detection is the mouse bioassay (MBA). A Centers for Disease Control and Prevention-developed mass spectrometry (MS)-based assay that detects active BoNT was successfully validated and implemented in a public health laboratory in clinical matrices using the Bruker MALDI-TOF MS (Matrix-assisted laser desorption ionization–time of flight mass spectrometry) Biotyper. For the first time, a direct comparison with the MBA was performed to determine MS-based assay sensitivity using the Bruker MALDI Biotyper. Mice were injected with BoNT/A, /B, /E, and /F at concentrations surrounding the established MS assay limit of detection (LOD) and analyzed simultaneously. For BoNT/B, /E, and /F, MS assay sensitivity was equivalent or better than the MBA at 25, 0.3, and 8.8 mLD50, respectively. BoNT/A was detected by the MBA between 1.8 and 18 mLD50, somewhat more sensitive than the MS method of 18 mLD50. Studies were performed to compare assay performance in clinical specimens. For all tested specimens, the MS method rapidly detected BoNT activity and serotype in agreement with, or in the absence of, results from the MBA. We demonstrate that the MS assay can generate reliable, rapid results while eliminating the need for animal testing

Rapid Molecular Characterization of Clostridium difficile and Assessment of Populations of C. difficile in Stool Specimens▿

Our laboratory has developed testing methods that use real-time PCR and pyrosequencing analysis to enable the rapid identification of potential hypervirulent Clostridium difficile strains. We describe a real-time PCR assay that detects four C. difficile genes encoding toxins A (tcdA) and B (tcdB) and the binary toxin genes (cdtA and cdtB), as well as a pyrosequencing assay that detects common deletions in the tcdC gene in less than 4 h. A subset of historical and recent C. difficile isolates (n = 31) was also analyzed by pulsed-field gel electrophoresis to determine the circulating North American pulsed-field (NAP) types that have been isolated in New York State. Thirteen different NAP types were found among the 31 isolates tested, 13 of which were NAP type 1 strains. To further assess the best approach to utilizing our conventional and molecular methods, we studied the populations of C. difficile in patient stool specimens (n = 23). Our results indicated that 13% of individual stool specimens had heterogeneous populations of C. difficile when we compared the molecular characterization results for multiple bacterial isolates (n = 10). Direct molecular analysis of stool specimens gave results that correlated well with the results obtained with cultured stool specimens; the direct molecular analysis was rapid, informative, and less costly than the testing of multiple patient stool isolates

Sporosarcina newyorkensis sp. nov. from clinical specimens and raw cow's milk

Twelve independent isolates of a Gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, U.S.A and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13% similarity). DNA-DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbors. The partial sequence of the 23S rRNA gene for the new strains and their nearest neighbors also provide support for the new species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α L-Lys-Gly-D-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The predominant fatty acids are iso-C(14:0), iso-C(15:0), and anteiso-C(15:0). In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062(T) =DSM 23544(T) =CCUG 59649(T) =LMG 26022(T)) is proposed

Clostridium difficile Strains from Community-Associated Infections ▿

Clostridium difficile isolates from presumed community-associated infections (n = 92) were characterized by toxinotyping, pulsed-field gel electrophoresis, tcdC and cdtB PCR, and antimicrobial susceptibility. Nine toxinotypes (TOX) and 31 PFGE patterns were identified. TOX 0 (48, 52%), TOX III (18, 20%), and TOX V (9, 10%) were the most common; three isolates were nontoxigenic