Fusobacteria behaving badly: Masquerading strains of strictly anaerobic Escherichiacoli misidentified due to the deletion of the hemB gene.

Three strictly anaerobic strains of Escherichia coli were misidentified as Fusobacterium mortiferum, due to a deletion of the hemB gene which is involved in anaerobic respiration. An unusual antimicrobial susceptibility pattern sparked the further diagnostic strategies that eventually identified these strains as true anaerobic E. coli This phenomenon is more common than appreciated and can have an impact on clinical practice including persistent and relapsing infections.

Comparative In Vitro Activity of Omadacycline against Dog and Cat Bite Wound Isolates.

Omadacycline was tested against 125 isolates recovered from infected cat and dog bites in humans. Its activity was similar to that of other compounds in the tetracycline class, and it was active against strains exhibiting tetracycline resistance. Against anaerobic isolates, resistance to tetracyclines was more prominent and omadacycline was the most active of the group. All isolates had omadacycline MICs of <1 µg/ml, with the exception of Eikenella corrodens, which showed reduced susceptibility to the entire tetracycline group.

Comparative In Vitro Activities of Relebactam, Imipenem, the Combination of the Two, and Six Comparator Antimicrobial Agents against 432 Strains of Anaerobic Organisms, Including Imipenem-Resistant Strains.

Relebactam is an important beta-lactamase inhibitor for certain aerobic organisms, but alone it has no antianaerobic activity, with most anaerobes having MICs of ≥32 µg/ml with the exception of a very few strains. There was no enhancement or antagonism of imipenem activity with the addition of relebactam, including activity against imipenem-resistant strains. The relebactam-imipenem combination had excellent overall activity against the anaerobes tested.

In vitro activity of eravacycline and comparator antimicrobials against 143 recent strains of Bacteroides and Parabacteroides species.

Eravacycline, a novel fluorocycline antibiotic, has been evaluated against complicated mixed aerobic/anaerobic intra-abdominal infections but scant supporting in vitro data against anaerobes has been published. We found that eravacycline had good anaerobic in vitro activity with MICs of 4 µg/ml or less against all Bacteroides and Parabacteroides strains tested, except for two B. ovatus strains that had MICs of 8 µg/ml and one strain that had an MIC of 16 µg/ml. Eravacycline was four-to-eight fold more active than tigecycline.

In vitro stability of three oral vancomycin preparations stored at 2- 5 °C and ambient room temperature for up to 60 days against 100 Clostridioides (Clostridium) difficile and 51Staphylococcus aureus strains.

Oral vancomycin is used to treat Clostridioides (Clostridium) difficile infection. Several different preparations are available including reconstituted IV solutions, vancomycin capsules, and grape flavored vancomycin oral solution kit (CutisPharma). The shelf life for IV after reconstitution varies between 7 and 14 days under refrigeration, and a standard 30 days for vancomycin oral solution kit (CutisPharma). The impact of storage on the in vitro potency was determined in 3 different vancomycin preparations by measuring MICs for 100 strains of C. difficile and 25 strains of Staphylococcus aureus, at T0, 14, 30, and 60 days, stored at ambient (RT) and refrigerated (2-5 °C) temperatures. All vancomycin preparations showed potency over a period of 60 days regardless of storage conditions. However, the capsule preparation showed mold after 60 days at room temperature, but unlike vancomycin oral solution kit, which retained a clear appearance, the IV and capsule preps showed evidence of crystallization.

In Vitro Activities of Pexiganan and 10 Comparator Antimicrobials against 502 Anaerobic Isolates Recovered from Skin and Skin Structure Infections.

Pexiganan, a cationic peptide, exhibited a broad range of anti-anaerobic antimicrobial activity. The MIC90s of studied isolates were as follows: Bacteroides fragilis, 16 µg/ml; other B. fragilis group spp., 4 µg/ml; Prevotella and Fusobacterium spp., 32 µg/ml; Porphyromonas spp., 64 µg/ml; Propionibacterium acnes, 4 µg/ml; Eggerthella lenta and Peptostreptococcus anaerobius, 32 µg/ml; other Gram-positive rods and cocci, 4 µg/ml; Clostridium perfringens, 128 µg/ml; and other clostridia, 256 µg/ml. Pexiganan cream shows potential as adjunctive therapy for skin and skin structure infections (SSSIs) involving anaerobes.

In Vitro Activity of Pexiganan and 10 Comparator Antimicrobials against 234 Isolates, Including 93 Pasteurella Species and 50 Anaerobic Bacterial Isolates Recovered from Animal Bite Wounds.

Animal bite wounds affect more than 5 million Americans annually, resulting in 300,000 emergency department visits, 10,000 hospitalizations, and an untold number of physician office visits. Various forms of topical therapy are empirically self-employed by many patients prior to seeking medical attention. Pexiganan, a 22-amino-acid synthetic cationic analogue of the peptide magainin II, acts by selectively damaging bacterial cell membranes. We determined the MICs for pexiganan and other antimicrobial agents often used for treatment of bite wounds. Most isolates were from U.S. patients, and ∼10% were from European and Canadian patients. The comparator antimicrobials studied were penicillin, amoxicillin-clavulanate, piperacillin-tazobactam, meropenem, clindamycin, doxycycline, moxifloxacin, ceftriaxone, linezolid, and metronidazole. The MIC90s of pexiganan were 32 µg/ml (against Pasteurella multocida subsp. multocida), 16 µg/ml (P. multocida subsp. septica, Pasteurella canis, and Pasteurella dagmatis), 8 µg/ml (Pasteurella stomatis), 8 µg/ml (Eikenella corrodens), 2 µg/ml (Neisseria weaveri, Neisseria zoodegmatis, and Moraxella canis-Moraxella lacunata group), 16 µg/ml (Bergeyella zoohelcum), 64 µg/ml (Bacteroides pyogenes), 4 µg/ml (Fusobacterium russii), 32 µg/ml (Fusobacterium canifelinum), and 64 µg/ml (Prevotella heparinolytica). The concentration of pexiganan in the cream used was 8,000 µg/ml, more than 60 to 100 times the highest MIC obtained. Pexiganan exhibited a broad range of antimicrobial activity, showing potential for treating animal bite infections. A clinical trial seems warranted.

Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibaculum rodentium.

To better characterize murine intestinal microbiota, a large number (187) of Gram-positive-staining, rod- and coccoid-shaped, and facultatively or strictly anaerobic bacteria were isolated from small and large intestinal contents from mice. Based on 16S rRNA gene sequencing, a total 115 isolates formed three phylogenetically distinct clusters located within the family Erysipelotrichaceae. Group 1, as represented by strain NYU-BL-A3T, was most closely related to Allobaculum stercoricanis, with 16S rRNA gene sequence similarity values of 87.7 %. A second group, represented by NYU-BL-A4T, was most closely related to Faecalibaculum rodentium, with 86.6 % 16S rRNA gene sequence similarity. A third group had a nearly identical 16S rRNA gene sequence (99.9 %) compared with the recently described Faecalibaculum rodentium, also recovered from a laboratory mouse; however, this strain had a few differences in biochemical characteristics, which are detailed in an emended description. The predominant (>10 %) cellular fatty acids of strain NYU-BL-A3T were C16 : 0 and C18 : 0, and those of strain NYU-BL-A4T were C10 : 0, C16 : 0, C18 : 0 and C18 : 1ω9c. The two groups could also be distinguished by multiple biochemical reactions, with the group represented by NYU-BL-A4T being considerably more active. Based on phylogenetic, biochemical and chemotaxonomic criteria, two novel genera are proposed, Ileibacterium valens gen. nov., sp. nov. with NYU-BL-A3T (=ATCC TSD-63T=DSM 103668T) as the type strain and Dubosiella newyorkensis gen. nov., sp. nov. with NYU-BL-A4T (=ATCC TSD-64T=DSM 103457T) as the type strain.

The underappreciated in vitro activity of tedizolid against Bacteroides fragilis species, including strains resistant to metronidazole and carbapenems.

Because Bacteroides fragilis has the ability to develop mechanisms of resistance to almost all antibiotics, we studied the comparative in vitro activity of tedizolid against 124 Bacteroides group species clinical isolates, including carbapenem, metronidazole and piperacillin-tazobactam resistant strains. Tedizolid had an MIC90 of 2 µg/ml (range, 0.5-4 µg/ml) and was 1-4 times more active than linezolid that had an MIC90 of 8 µg/ml (range, 2-16 µg/ml). It was also active (MICs 0.5-2 µg/ml) against the 27 ertapenem, 2 metronidazole and 12 piperacillin-tazobactam resistant strains tested. This suggests that tedizolid may be useful treating infections, including bacteremias, due to resistant B. fragilis group species, as well as, mixed skin and soft tissue infections such as diabetic foot infections caused by Gram-positive aerobes and B. fragilis group species.

Impact of Surotomycin on the Gut Microbiota of Healthy Volunteers in a Phase 1 Clinical Trial.

Clostridium difficile-associated diarrhea has been associated with disruption of the normal intestinal microbiota, particularly theBacteroides fragilisgroup andPrevotellaspecies. Surotomycin is a bactericidal cyclic lipopeptide in development for treatment ofClostridium difficile-associated diarrhea that has selective and potent activity againstC. difficileand other Gram-positive bacteria and a minimal impact on intestinal Gram-negative organisms. The impacts of ascending doses of surotomycin on major organism groups in the gut microbiota of healthy volunteers were evaluated during a randomized, double-blind, placebo-controlled, multiple-dose phase 1 study. Thirty volunteers were randomized into 3 cohorts, using a 4:1 ratio, to receive 250 mg, 500 mg, or 1,000 mg of surotomycin, or placebo, twice daily for 14 days. Stool samples collected at baseline (days 0 and 1) and at the end of treatment (days 13 to 15) were cultured quantitatively. TheB. fragilisgroup, theBacteroides/Prevotellagroup, andEnterobacteriaceaewere also quantified by quantitative real-time PCR. Baseline and end-of-treatment stool samples showed 1- to 2-log10CFU/g reductions in total bacterial counts for most volunteers. Various decreases in clostridial,Lactobacillus-Bifidobacteriumgroup, and enterococcus-streptococcus group counts occurred while patients were receiving surotomycin, whereas the enterobacteria and theB. fragilisgroup persisted at the end of treatment. There was no change in enterococcus MICs of surotomycin, nor was vancomycin-resistantEnterococcusdetected after exposure. Surotomycin at doses of up to 1,000 mg twice daily had only modest disruptive effects on the gut microbiota. The potential sparing of the gut microbiota by surotomycin may decrease the risk of disease recurrence.

Comparison of the Copan eSwab System with an Agar Swab Transport System for Maintenance of Fastidious Anaerobic Bacterium Viability.

We compared the eSwab system to a swab with an anaerobic transport semisolid agar system for their capacities to maintain the viability of 20 species of fastidious anaerobes inoculated on the bench and held at ambient or refrigerator temperature for 24 or 48 h. On average, both systems maintained similar viabilities among analogous groups of organisms at both temperatures, although there were quantitative differences among some species.

Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O'Toole 1935) Prévot 1938.

The recent proposal by Lawson and Rainey (2015) to restrict the genus Clostridium to Clostridium butyricum and related species has ramifications for the members of the genera that fall outside this clade that should not be considered as Clostridium sensu stricto. One such organism of profound medical importance is Clostridioides difficile that is a major cause of hospital-acquired diarrhea and mortality in individuals. Based on 16S rRNA gene sequence analysis, the closest relative of Clostridium difficile is Clostridium mangenotii with a 94.7% similarity value and both are located within the family Peptostreptococcaceae that is phylogenetically far removed from C. butyricum and other members of Clostridium sensu stricto. Clostridium difficile is Clostridium mangenotii each produce abundant H2 gas when grown in PYG broth and also produce a range of straight and branched chain saturated and unsaturated fatty acids with C16:0 as a major product. The cell wall peptidoglycan contains meso-DAP as the diagnostic diamino acid. Based on phenotypic, chemotaxonomic and phylogenetic analyses, novel genus Clostridioides gen. nov. is proposed for Clostridium difficile as Clostridioides difficile gen. nov. comb. nov. and that Clostridium mangenotii be transferred to this genus as Clostridioides mangenotii comb. nov. The type species of Clostridioides is Clostridioides difficile.

Lactobacillus species: taxonomic complexity and controversial susceptibilities.

The genus Lactobacillus is a taxonomically complex and is composed of over 170 species that cannot be easily differentiated phenotypically and often require molecular identification. Although they are part of the normal human gastrointestinal and vaginal flora, they can also be occasional human pathogens. They are extensively used in a variety of commercial products including probiotics. Their antimicrobial susceptibilities are poorly defined in part because of their taxonomic complexity and are compounded by the different methods recommended by Clinical Laboratory Standards Institute and International Dairy Foundation. Their use as probiotics for prevention of Clostridium difficile infection is prevalent among consumers worldwide but raises the question of will the use of any concurrent antibiotic effect their ability to survive. Lactobacillus species are generally acid resistant and are able to survive ingestion. They are generally resistant to metronidazole, aminoglycosides and ciprofloxacin with L. acidophilus being susceptible to penicillin and vancomycin, whereas L. rhamnosus and L. casei are resistant to metronidazole and vancomycin.

Comparative in vitro activities of SMT19969, a new antimicrobial agent, against 162 strains from 35 less frequently recovered intestinal Clostridium species: implications for Clostridium difficile recurrence.

We determined the comparative activity of SMT19969 (SMT) against 162 strains representing 35 well-characterized Clostridium species in clusters I to XIX and 13 Clostridium species that had no 16S rRNA match. SMT MICs ranged from 0.06 to >512 µg/ml and were not species related. SMT might have less impact on normal gut microbiota than other Clostridium difficile infection (CDI) antimicrobials.

Bacterial counts from five over-the-counter probiotics: are you getting what you paid for?

There is concern that the bacterial colony counts present at the time of manufacture and listed on the probiotic package may not be reflective of the numbers viable colonies at the time of purchase and patient consumption thereby diminishing efficacy. We performed a colony count study of three separate samples of five different probiotics purchased from three different stores: Bifidobacterium infantis (Align(®)); Lactobacillus acidophilus CL1285(®) and Lactobacillus casei LBC80R(®) (Bio-K+(®)); Lactobacillus rhamnosus GG (Culturelle(®)); Saccharomyces boulardii (Florastor(®)) and "L. acidophilus" and "Lactobacillus helveticus" (Lactinex(®)). Approximately 1 g of powder of each (Lactinex(®) tablets were crushed before testing) was reconstituted in sterile distilled water, serial 10-fold dilutions were prepared and plated in duplicate onto blood agar plates, with incubation for 48 h in an anaerobic chamber (except the Saccharomyces which was incubated aerobically) after which colony counts were performed. The Florastor(®) packaging did not state an expected concentration and was found to have 9.2 × 10(9)-1.3 × 10(10) CFU/g. Lactinex(®), Align(®), Bio-K+(®), and Culturelle(®) had viable colony counts that were similar to those stated on the package.

Comparative in vitro activities of GSK2251052, a novel boron-containing leucyl-tRNA synthetase inhibitor, against 916 anaerobic organisms.

We studied the comparative in vitro activity of GSK2251052, a novel boron leucyl-tRNA synthetase inhibitor, against 916 clinical anaerobic isolates using CLSI methods. The GSK MIC50/MIC90 for all isolates tested were 2 and 4 µg/ml, and the MIC90s against 302 Bacteroides fragilis and Bacteroides thetaiotaomicron strains were 4 and 8 µg/ml, respectively. All Clostridium perfringens strains had GSK2251052 MICs of >32 µg/ml. There was no relationship between increased MICs for any other antibiotics and that of GSK2251052.

In vitro activity of Biapenem plus RPX7009, a carbapenem combined with a serine ß-lactamase inhibitor, against anaerobic bacteria.

Biapenem is a carbapenem being developed in combination with RPX7009, a new inhibitor of serine ß-lactamases. Biapenem was tested alone and in combination with fixed concentrations of RPX7009 by agar dilution against 377 recent isolates of anaerobes. A separate panel of 27 isolates of Bacteroides spp. with decreased susceptibility or resistance to imipenem was also tested. Comparator drugs included meropenem, piperacillin-tazobactam, ampicillin-sulbactam, cefoxitin, ceftazidime, metronidazole, clindamycin, and tigecycline plus imipenem, doripenem, and ertapenem for the 27 selected strains. For recent consecutive strains of Bacteroides species, the MIC(90) for biapenem-RPX7009 was 1 µg/ml, with a MIC(90) of 4 µg/ml for meropenem. Other Bacteroides fragilis group species showed a MIC90 of 0.5 µg/ml for both agents. The MIC(90)s for biapenem-RPX7009 were 0.25 µg/ml for Prevotella spp., 0.125 µg/ml for Fusobacterium nucleatum and Fusobacterium necrophorum, 2 µg/ml for Fusobacterium mortiferum, 0.5 µg/ml for Fusobacterium varium, ≤ 0.5 µg/ml for Gram-positive cocci and rods, and 0.03 to 8 µg/ml for clostridia. Against 5 B. fragilis strains harboring a known metallo-beta-lactamase, biapenem-RPX7009 MICs were comparable to those of other carbapenems (≥ 32 µg/ml). Against Bacteroides strains with an imipenem MIC of 2 µg/ml, biapenem-RPX7009 had MICs of 0.5 to 2 µg/ml, with MICs of 0.5 to 32 µg/ml for meropenem, doripenem, and ertapenem. For strains with an imipenem MIC of 4 µg/ml, the MICs for biapenem-RPX7009 were 4 to 16 µg/ml, with MICs of 8 to >32 µg/ml for meropenem, doripenem, and ertapenem. The inhibitor RPX7009 had no antimicrobial activity when tested alone, and it showed little or no potentiation of biapenem versus anaerobes. Biapenem-RPX7009 showed activity comparable to that of imipenem and was superior to meropenem, doripenem, and ertapenem against imipenem-nonsusceptible Bacteroides spp.

Comparative in vitro activities of SMT19969, a new antimicrobial agent, against Clostridium difficile and 350 gram-positive and gram-negative aerobic and anaerobic intestinal flora isolates.

The comparative in vitro activity of SMT19969, a novel, narrow-spectrum, nonabsorbable agent, was studied against 50 ribotype-defined Clostridium difficile strains, 174 Gram-positive and 136 Gram-negative intestinal anaerobes, and 40 Gram-positive aerobes. SMT19969 was one dilution more active against C. difficile isolates (MIC range, 0.125 to 0.5 µg/ml; MIC90, 0.25 µg/ml), including ribotype 027 strains, than fidaxomicin (range, 0.06 to 1 µg/ml; MIC90, 0.5 µg/ml) and two to six dilutions lower than either vancomycin or metronidazole. SMT19969 and fidaxomicin were generally less active against Gram-negative anaerobes, especially the Bacteroides fragilis group species, than vancomycin and metronidazole, suggesting that SMT19969 has a lesser impact on the normal intestinal microbiota that maintain colonization resistance. SMT19969 showed limited activity against other Gram-positive anaerobes, including Bifidobacteria species, Eggerthella lenta, Finegoldia magna, and Peptostreptococcus anaerobius, with MIC90s of >512, >512, 64, and 64 µg/ml, respectively. Clostridium species showed various levels of susceptibility, with C. innocuum being susceptible (MIC90, 1 µg/ml) and C. ramosum and C. perfringens being nonsusceptible (MIC90, >512 µg/ml). Activity against Lactobacillus spp. (range, 0.06 to >512 µg/ml; MIC90, >512 µg/ml) was comparable to that of fidaxomicin and varied by species and strain. Gram-positive aerobic cocci (Staphylococcus aureus, Enterococcus faecalis, E. faecium, and streptococci) showed high SMT19969 MIC90 values (128 to >512 µg/ml).

Evaluation of cycloserine-cefoxitin fructose agar (CCFA), CCFA with horse blood and taurocholate, and cycloserine-cefoxitin mannitol broth with taurocholate and lysozyme for recovery of Clostridium difficile isolates from fecal samples.

Cycloserine-cefoxitin fructose agar (CCFA), CCFA with horse blood and taurocholate (CCFA-HT), and cycloserine-cefoxitin mannitol broth with taurocholate and lysozyme (CCMB-TAL) were compared for recovery of Clostridium difficile from 120 stool specimens. Compared to CCFA, CCFA-HT enhanced C. difficile growth and improved recovery by 4%. In a separate study, 9% (8/91) of stool samples previously C. difficile negative on plate medium were C. difficile positive when cultured in CCMB-TAL.

Anaerobic and aerobic bacteriology of the saliva and gingiva from 16 captive Komodo dragons (Varanus komodoensis): new implications for the "bacteria as venom" model.

It has been speculated that the oral flora of the Komodo dragon (Varanus komodoensis) exerts a lethal effect on its prey; yet, scant information about their specific oral flora bacteriology, especially anaerobes, exists. Consequently, the aerobic and anaerobic oral bacteriology of 16 captive Komodo dragons (10 adults and six neonates), aged 2-17 yr for adults and 7-10 days for neonates, from three U.S. zoos were studied. Saliva and gingival samples were collected by zoo personnel, inoculated into anaerobic transport media, and delivered by courier to a reference laboratory. Samples were cultured for aerobes and anaerobes. Strains were identified by standard methods and 16S rRNA gene sequencing when required. The oral flora consisted of 39 aerobic and 21 anaerobic species, with some variation by zoo. Adult dragons grew 128 isolates, including 37 aerobic gram-negative rods (one to eight per specimen), especially Enterobacteriaceae; 50 aerobic gram-positive bacteria (two to nine per specimen), especially Staphylococcus sciuri and Enterococcusfaecalis, present in eight of 10 and nine of 10 dragons, respectively; and 41 anaerobes (one to six per specimen), especially clostridia. All hatchlings grew aerobes but none grew anaerobes. No virulent species were isolated. As with other carnivores, captive Komodo oral flora is simply reflective of the gut and skin flora of their recent meals and environment and is unlikely to cause rapid fatal infection.