Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds

The name Escherichia vulneris sp. nov. (formerly called Alma group 1 and Enteric group 1 by the Centers for Disease Control and API group 2 by Analytab Products, Inc.) is proposed for a group of isolates from the United States and Canada, 74% of which were from human wounds. E. vulneris is a gram-negative, oxidase-negative, fermentative, motile rod with the characteristics of the family Enterobacteriaceae. Biochemical reactions characteristic of 61 E. vulneris strains were positive tests for methyl red, malonate, and lysine decarboxylase; a delayed positive test for arginine dihydrolase; acid production from d-mannitol, l-arabinose, raffinose, l-rhamnose, d-xylose, trehalose, cellobiose, and melibiose; negative tests for Voges-Proskauer, indole, urea, H(2)S, citrate, ornithine decarboxylase, phenylalanine deaminase, and DNase; and no acid from dulcitol, adonitol, myo-inositol, and d-sorbitol. Two-thirds of the strains produced yellow pigment. Most strains gave negative or delayed positive reactions in tests for lactose, sucrose, and KCN. The E. vulneris strains tested were resistant to penicillin and clindamycin, were resistant or showed intermediate zones of inhibition to carbenicillin and erythromycin, and were susceptible to 14 other antibiotics. DNA relatedness of 15 E. vulneris strains to the type strain averaged 75% in reactions at 60 degrees C and 69% in reactions at 75 degrees C, indicating that they comprise a separate species. DNA relatedness to other species in the family Enterobacteriaceae was 6 to 39%, an indication that this new species belongs in the family. E. vulneris showed the highest relatedness to species of Escherichia (25 to 39%) and Enterobacter (24 to 35%). On the basis of biochemical similarity, the new species was placed in the genus Escherichia. The type strain of E. vulneris is ATCC 33821 (CDC 875-72).

Moderate dietary protein restriction alters the composition of gut microbiota and improves ileal barrier function in adult pig model

This study was conducted to investigate impacts of dietary protein levels on gut bacterial community and gut barrier. The intestinal microbiota of finishing pigs, fed with 16%, 13% and 10% crude protein (CP) in diets, respectively, were investigated using Illumina MiSeq sequencing. The ileal bacterial richness tended to decrease when the dietary protein concentration reduced from 16% to 10%. The proportion of Clostridium_sensu_stricto_1 in ileum significantly decreased, whereas Escherichia-Shigella increased with reduction of protein concentration. In colon, the proportion of Clostridium_sensu_stricto_1 and Turicibacter increased, while the proportion of RC9_gut_group significantly decreased with the dietary protein reduction. Notably, the proportion of Peptostreptococcaceae was higher in both ileum and colon of 13% CP group. As for metabolites, the intestinal concentrations of SCFAs and biogenic amines decreased with the dietary protein reduction. The 10% CP dietary treatment damaged ileal mucosal morphology, and decreased the expression of biomarks of intestinal cells (Lgr5 and Bmi1), whereas the expression of tight junction proteins (occludin and claudin) in 13% CP group were higher than the other two groups. In conclusion, moderate dietary protein restriction (13% CP) could alter the bacterial community and metabolites, promote colonization of beneficial bacteria in both ileum and colon, and improve gut barrier function.

The gastrointestinal epithelium and its autochthonous bacterial flora

Colonization of the gastrointestinal tract by bacteria of the normal flora was followed by bacteriological and special histological techniques in mice from several colonies. These histological techniques were designed to preserve the intimate associations that become established between particular strains of microorganisms and the epithelium of the mucosa of certain areas of the gut. The findings were as follows: 1. The various strains of bacteria of the normal flora became established in the different areas of the guts of infant mice according to a definite time sequence. 2. The first types of bacteria that could be cultured from the gut were lactobacilli and Group N streptococci. Within the first day after birth, these bacteria colonized the entire digestive tract and formed layers on the stratified squamous epithelium of the nonsecreting portion of the stomach and of the distal esophagus. 3. The bacterial types that appeared next were coliforms and enterococci. From about the 9th to the 18th day after birth, these bacteria could be cultured in extremely high numbers from the cecum and the colon. Histological sections of those organs taken during the first 2 or 3 days of that interval revealed microcolonies of Gram-positive cocci in pairs and tiny Gram-negative rods embedded in the mucous layer of the epithelium. The microcolonies were well separated from the mixture of digesta and bacteria that occupied the center of the lumen; they may have consisted of the coliforms and enterococci mentioned above; but this possibility remains to be proved. 4. Histological sections also revealed that, at about the 12th day after birth, long, thin Gram-variable rods with tapering ends were present, side by side, with the small Gram-negative rods and Gram-positive cocci in the mucous layer. By the 15th day after birth, the fusiform bacteria formed thick layers in the mucus, and seemed to be the only bacteria remaining in that location. It has not yet been possible to enumerate these tapered rods by culture methods, but as judged by visual appearances in the histological sections, they seemed to outnumber all other bacteria in the cecum and the colon by a factor of as much as 1000. It must be stressed that these bacterial layers are readily disrupted and even washed away by conventional histological techniques; their discovery was largely due to the use of the special histological techniques described in the text. The bacteriological and histological findings described here constitute further evidence for the hypothesis that symbiotic associations exist between microorganisms and animals, and that a very large percentage of the bacteria in the gastrointestinal tract constitutes a true autochthonous flora. The constant occurrence of several distinct associations of bacteria with the special histological structures of the animal host renders obsolete the notion that the intestine constitutes a chemostat in which the bacterial populations are randomly mixed. For a full understanding of the ecology of the normal microflora, it is necessary to think of body surfaces as distinct microenvironments in which virtually pure cultures of a few species of microorganisms interact with their host and the adjacent microbial populations. Experiments based on this hypothesis are admittedly difficult to design, but on the other hand studies based on the assumption that microorganisms exist as mixtures in the gastrointestinal tract will be only of limited value and may often be misleading.

Characteristics of fecal and mucosa-associated microbiota in Chinese patients with inflammatory bowel disease

The intestinal microbiota plays an important role in the pathogenesis of inflammatory bowel disease (IBD), and geographical and genetic backgrounds impact the composition of the intestinal microbiota. However, there is a lack of evidence regarding the overall changes and characteristics of fecal-associated microbiota (FAM) and mucosa-associated microbiota (MAM) in Chinese patients with IBD. We recruited 26 patients with Crohn's disease (CD), 46 patients with ulcerative colitis (UC), and 21 healthy individuals; we collected matched fresh fecal and mucosal samples from the same subjects. The microbial communities were studied by 454-pyrosequencing. Community-wide changes in FAM and MAM were observed in patients with IBD. The proportion of several butyrate-producing bacteria, such as of the genera Roseburia, Coprococcus, and Ruminococcus were significantly reduced, whereas the pathogens Escherichia-Shigella and Enterococcus were prevalent in patients with IBD. FAM and MAM were similar between CD and UC. FAM differed from MAM in healthy individuals and patients with UC. In conclusion, the compositions of FAM and MAM were altered in patients with IBD. The reduction of butyrate-producing bacteria and the increase in opportunistic pathogens might be associated with the pathogenesis of IBD.

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes

BACKGROUND

Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.

RESULTS

The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.

CONCLUSIONS

We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.

Escherichia albertii sp. nov., a diarrhoeagenic species isolated from stool specimens of Bangladeshi children

The taxonomic position of a group of five D-sorbitol- and lactose-negative enterobacterial isolates recovered from diarrhoeal stools of children at the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), was investigated by DNA-DNA hybridization, phenotypic characterization and 16S rDNA sequencing. These strains were originally identified as 'Hafnia alvei-like' with the API 20E system but, in fact, show more phenotypic and genotypic resemblance to members of the genus Escherichia. By 16S rDNA sequencing, one representative strain of the ICDDR,B group was shown to be closely affiliated to the genera Escherichia and Shigella. Using the fluorimetric microplate hybridization method, the diarrhoeagenic ICDDR,B isolates were found to constitute a homogeneous taxon (> or = 82% internal DNA relatedness), with the closest affiliation to the type strains of Escherichia coli (55-64%) and Shigella flexneri (54-60%). The DNA-DNA hybridization levels were much lower with members of other described Escherichia species (16-45%) and with the type strain of H. alvei (9-17%). The G + C content of the ICDDR,B strains ranged from 50.5 to 50.7 mol%. Together with the diagnostic characteristics reported previously, including the presence of the eaeA gene of enteropathogenic E. coli and of the E. coli and Shigella-specific phoE gene, it is concluded that the ICDDR,B strains represent a novel taxon in the genus Escherichia, for which the name Escherichia albertii sp. nov. is proposed. Its type strain is Albert 19982(T) (= LMG 20976(T) = CCUG 46494(T)).

Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii and related Shigella boydii strains

A bacterium originally described as Hafnia alvei induces diarrhea in rabbits and causes epithelial damage similar to the attachment and effacement associated with enteropathogenic Escherichia coli. Subsequent studies identified similar H. alvei-like strains that are positive for an intimin gene (eae) probe and, based on DNA relatedness, are classified as a distinct Escherichia species, Escherichia albertii. We determined sequences for multiple housekeeping genes in five E. albertii strains and compared these sequences to those of strains representing the major groups of pathogenic E. coli and Shigella. A comparison of 2,484 codon positions in 14 genes revealed that E. albertii strains differ, on average, at approximately 7.4% of the nucleotide sites from pathogenic E. coli strains and at 15.7% from Salmonella enterica serotype Typhimurium. Interestingly, E. albertii strains were found to be closely related to strains of Shigella boydii serotype 13 (Shigella B13), a distant relative of E. coli representing a divergent lineage in the genus Escherichia. Analysis of homologues of intimin (eae) revealed that the central conserved domains are similar in E. albertii and Shigella B13 and distinct from those of eae variants found in pathogenic E. coli. Sequence analysis of the cytolethal distending toxin gene cluster (cdt) also disclosed three allelic groups corresponding to E. albertii, Shigella B13, and a nontypeable isolate serologically related to S. boydii serotype 7. Based on the synonymous substitution rate, the E. albertii-Shigella B13 lineage is estimated to have split from an E. coli-like ancestor approximately 28 million years ago and formed a distinct evolutionary branch of enteric pathogens that has radiated into groups with distinct virulence properties.

Isolation and Characterization of Arsenate-Reducing Bacteria from Arsenic-Contaminated Sites in New Zealand

Two environmental sites in New Zealand were sampled (e.g., water and sediment) for bacterial isolates that could use either arsenite as an electron donor or arsenate as an electron acceptor under aerobic and anaerobic growth conditions, respectively. These two sites were subjected to widespread arsenic contamination from mine tailings generated from historic gold mining activities or from geothermal effluent. No bacteria were isolated from these sites that could utilize arsenite or arsenate under the respective growth conditions tested, but a number of chemoheterotrophic bacteria were isolated that could grow in the presence of high concentrations of arsenic species. In total, 17 morphologically distinct arsenic-resistant heterotrophic bacteria isolates were enriched from the sediment samples, and analysis of the 16S rRNA gene sequence of these bacteria revealed them to be members of the genera Exiguobacterium, Aeromonas, Bacillus, Pseudomonas, Escherichia, and Acinetobacter. Two isolates, Exiguobacterium sp. WK6 and Aeromonas sp. CA1, were of particular interest because they appeared to gain metabolic energy from arsenate under aerobic growth conditions, as demonstrated by an increase in cellular growth yield and growth rate in the presence of arsenate. Both bacteria were capable of reducing arsenate to arsenite via a non-respiratory mechanism. Strain WK6 was positive for arsB, but the pathway of arsenate reduction for isolate CA1 was via a hitherto unknown mechanism. These isolates were not gaining an energetic advantage from arsenate or arsenite utilization, but were instead detoxifying arsenate to arsenite. As a subsidiary process to arsenate reduction, the external pH of the growth medium increased (i.e., became more alkaline), allowing these bacteria to grow for extended periods of time.

Direct selection for P1-sensitive mutants of enteric bacteria

A method has been developed to isolate mutants sensitive to coliphage P1 from bacterial genera normally not sensitive to this phage. P1clr100KM was used. This phage is heat inducible and confers kanamycin resistance when present as a prophage (in lysogens). P1-sensitive mutants of Klebsiella, Enterobacter, Citrobacter, and Erwinia have been found. This technique provides a well-known genetic system for the study of many bacterial genera that previously had either no such system or only a marginally useful means of genetic manipulation. It also extends the range of possible intergeneric hybrids that may be constructed and studied.

Metal accumulation and vanadium-induced multidrug resistance by environmental isolates of Escherichia hermannii and Enterobacter cloacae

Contaminated soils from an oil refinery were screened for the presence of microorganisms capable of accumulating either nickel, vanadium, or both metals. Three strains of bacteria that belonged to the family Enterobacteriaceae were selected. Two of them were Escherichia hermannii strains, and outer membrane profile (OMP) analysis showed that they were similar to a strain of clinical origin; the other one was an Enterobacter cloacae strain that differed from clinical isolates. The selected bacteria accumulated both nickel and vanadium. Growth in the presence of vanadium induced multidrug resistance phenotypes in E. hermannii and E. cloacae. Incubation with this metal changed the OMP profile of E. hermannii but did not produce variations in the expression of the major OMPs of E. cloacae.

Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis

Methods are described for the isolation and identification of aerobic bacteria occurring naturally in the hind-gut of the cockroach Blatta orientalis captured from a number of wild sources, to establish whether or not human pathogens occurred naturally within the gut. During the investigation an organism was frequently found which could not be classified in any described species, and for which we propose the name Escherichia blattae.

Oligonucleotide probe for the visualization of Escherichia coli/Escherichia fergusonii cells by in situ hybridization: specificity and potential applications

There are several occasions when enumeration of Escherichia coli cells is needed. These include examination of urine specimens and water or food samples. Present methods rely on growth in more or less selective media (colony-forming units on agar or the most probable number method using liquid media). Unfortunately, no really selective medium with 100% efficiency of plating is available for E. coli. A 24-mer oligonucleotide probe (Colinsitu), complementary to a piece of 16S ribosomal ribonucleic acid, has been tested for specifically visualizing E. coli cells by in situ hybridization and epifluorescence microscopy. The fluorescent dye-labeled probe was able to stain cells of E. coli, Shigella spp. and E. fergusonii. Shigella spp. are known to belong to the E. coli genomospecies and E. fergusonii is the nomenspecies closest to E. coli by DNA-DNA hybridization. The probe did not stain any strain of 169 other genomospecies of the family Enterobacteriaceae or of a few other species frequently encountered in the environment. Revivification without cell division allowed the visualization of E. coli cells in contaminated water. In situ hybridization using the Colinsitu probe is a potential tool for the confirmation of (atypical) E. coli in reference centers and the rapid (3-6 h) detection and enumeration of E. coli in urine specimens, contaminated water and food. More work is needed to include in situ hybridization in laboratory routine.

Evaluation of a fluorogenic assay for detection of Escherichia coli in foods

A fluorogenic assay procedure with 4-methylumbelliferyl-beta-D-glucuronide incorporated into lauryl sulfate broth was evaluated to detect and confirm the presence of Escherichia coli in foods. Fluorescence is indicative of the presence of E. coli; extensive biochemical confirmation is unnecessary with this assay. The 4-methylumbelliferyl-beta-D-glucuronide assay was tested concurrently with our present methodology for detection of E. coli on 270 samples of raw ingredients and powdered food products. Total agreement between the two methods was 94.8%; there was a false-positive rate of 4.8% and no false-negatives. We found the 4-methylumbelliferyl-beta-D-glucuronide assay to be rapid, accurate, simple to perform, and inexpensive.

Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease

AIM

To analyze the alterations of fecal microbiota in Chinese patients with inflammatory bowel disease (IBD).

METHODS

Fecal samples from 15 patients with Crohn’s disease (CD) (11 active CD, 4 inactive CD), 14 patients with active ulcerative colitis (UC) and 13 healthy individuals were collected and subjected to 16S ribosomal DNA (rDNA) gene sequencing. The V4 hypervariable regions of 16S rDNA gene were amplified from all samples and sequenced by the Illumina MiSeq platform. Quality control and operational taxonomic units classification of reads were calculated with QIIME software. Alpha diversity and beta diversity were displayed with R software.

RESULTS

Community richness (chao) and microbial structure in both CD and UC were significantly different from those in normal controls. At the phyla level, analysis of the microbial compositions revealed a significantly greater abundance of Proteobacteria in IBD as compared to that in controls. At the genera level, 8 genera in CD and 23 genera in UC (in particular, the Escherichia genus) showed significantly greater abundance as compared to that in normal controls. The relative abundance of Bacteroidetes in the active CD group was markedly lower than that in the inactive CD group. The abundance of Proteobacteria in patients with active CD was nominally higher than that in patients with inactive CD; however, the difference was not statistically significant after correction. Furthermore, the relative abundance of Bacteroidetes showed a negative correlation with the CD activity index scores.

CONCLUSION

Our study profiles specific characteristics and microbial dysbiosis in the gut of Chinese patients with IBD. Bacteroidetes may have a negative impact on inflammatory development.

Assay for beta-glucuronidase in species of the genus Escherichia and its applications for drinking-water analysis

Recently, Escherichia species other than Escherichia coli have been isolated from potable water. Environmental isolates as well as clinical isolates of E. adecarboxylata, E. blattae, E. fergusonii, E. hermannii, and E. vulneris were assayed for the enzyme beta-glucuronidase by using EC MUG medium and the Colilert system. None of the isolates were positive for the enzyme by either method.

The "Cryptic" Escherichia

In 2009, five monophyletic Escherichia clades were described and referred to as "cryptic" based on the inability to distinguish them from representative E. coli isolates using diagnostic biochemical reactions. Since this original publication, a number of studies have explored the genomic, transcriptomic, and phenotypic diversity of cryptic clade isolates to better understand their phylogenetic, physiological, and ecological distinctiveness with respect to previously named Escherichia species. This chapter reviews the original discovery of the cryptic clades, discusses available evidence that some are environmentally adapted, and evaluates current support for taxonomic designations of these microorganisms. The importance of these clades to clinical research, epidemiology, population genetics, and microbial speciation is also discussed.

Feeding human milk to rats increases Bifidobacterium in the cecum and colon which correlates with enhanced folate status

The purpose of this investigation was to determine if feeding diets containing human milk resulted in increased numbers of microorganisms implicated in increased folate production and the effect on folate availability. Following a folate-depletion period (5 wk), 30 rats were fed folate-repletion diets (4 wk) with or without 20% milk solids (human, cow or goat) and containing either 906 or 4530 nmol folic acid/kg. At the end of the test period, the cecum and colon were removed in an anaerobic chamber, homogenized, diluted (10(-2) -10(-8)), and the contents of each plated on selective and nonselective media. In addition to enumeration of the total anaerobic load, five genera of bacteria were counted (Bacteroides, Bifidobacterium, Clostridium, Escherichia and Streptococcus). Rats fed human milk solids had at least a seven- and onefold mean increase in the Bifidobacterium concentration in the cecum (P < 0.006) and colon (P < 0.04), respectively, compared with rats fed other diets. The total anaerobic bacterial concentration in the cecum and the colon of rats fed human milk solids was also greater than that of rats fed the other diets (P < 0.05). The single exception was the total anaerobic count in the cecum of rats consuming goat milk solids, which did not differ from that of rats consuming human milk solids. Further, rats fed human milk solids had at least a 42 and 48% higher mean plasma folate concentration and total cecal material folate content, respectively, than rats in other dietary treatments containing 906 nmol/kg folic acid. Therefore, the improved folate status of rats fed human milk-containing diets appears to be due, at least in part, to increased folate synthesis by Bifidobacteria and other folate-synthesizing microbes in the cecum and colon.

Klebsiella biotypes among coliforms isolated from forest environments and farm produce

Samples of water, soil, needles, and bark were collected from three different forest environments and from a pulp and paper mill. In addition, samples of fresh produce were obtained from a local supermarket. All samples were examined for total and fecal coliforms. The counts obtained from the forestrelated samples did not correlate with sample type or location. When 123 isolates were identified biochemically, 71% were Klebsiella, 19% Enterobacter, 8% Citrobacter, and 2% Escherichia. All the Citrobacter, 75% of the Enterobacter, and 65% of the Klebsiella were negative for growth in elevated coliform (EC) broth. All the Escherichia were EC positive. The counts obtained from the fresh produce were generally higher than the forest counts, but the distribution of biotypes was similar. Of the 146 isolates examined 64% were Klebsiella, 14% were Escherichia, 14% were Enterobacter, and 8% were Citrobacter. All the Enterobacter and Citrobacter were EC negative, whereas 25% of the Klebesiella and 80% of the Escherichia were EC positive.

Natural antibiotic susceptibility of Escherichia coli, Shigella, E. vulneris, and E. hermannii strains

The natural antibiotic susceptibility of 139 Escherichia coli strains (including 18 enterohemorrhagic E. coli), 73 Shigella strains (S. sonnei (n = 37), S. flexneri (n = 29), S. boydii (n = 6), S. dysenteriae (n = 1)), 23 E. vulneris, and 20 E. hermannii strains toward 71 antibiotics was examined. MICs were determined using a microdilution procedure. All examined taxa were naturally sensitive/intermediate toward tetracyclines, aminoglycosides, some penicillins (amoxycillin/clavulanate, ampicillin/sulbactam, piperacillin [with and without tazobactam], mezlocillin, azlocillin), cephalosporins, carbapenems, monobactams, quinolones, trimethoprim, cotrimoxazole, and chloramphenicol and were naturally resistant/intermediate toward benzylpenicillin, oxacillin, macrolides, lincosamides, glycopeptides, rifampicin, and fusidic acid. No differences in natural antibiotic susceptibility were seen between enterohemorrhagic and other E. coli strains. Likewise, with one exception, no significant differences in natural antibiotic susceptibility were seen either among the Shigella subgroups or between Shigella and E. coli. The natural population of S. flexneri was slightly more susceptible to chloramphenicol than the natural populations of other taxa within the Shigella-E. coli complex. E. vulneris and E. hermannii showed susceptibility patterns to many antibiotics similar to Shigella and E. coli, but there were other antibiotics toward which there were significant differences in natural susceptibility. E. vulneris and E. hermannii were less susceptible to nitrofurantoin and slightly more susceptible to several aminoglycosides than E. coli and Shigella. E. hermannii was the only species that was naturally resistant/intermediate to ticarcillin and amoxycillin (DIN standard). The addition of clavulanic acid to the latter resulted in a decrease of seven twofold dilution steps (E. vulneris: four twofold dilution steps, E. coli/Shigella: two twofold dilution steps) of the MICs of the natural population. With the exception of cefoperazone and cefepime, E. hermannii was more susceptible to cephalosporins than strains of the other species. E. vulneris was the species most susceptible to ticarcillin and the only species that was highly resistant to fosfomycin (MIC > 256 micrograms/mL). The antibiotic susceptibility to fosfomycin was also unique for E. hermannii (MIC 32-128 micrograms/mL), whereas the natural populations of E. coli and Shigella showed lower MIC values. The data of this study represent an assessment of the natural susceptibility of strains of Escherichia spp. and Shigella subgroups to a wide range of antibiotics. These databases can be used for the validation of antibiotic susceptibility test results of Escherichia spp. and shigellae. The conformity of the natural antibiotic susceptibility test results not only among the Shigella subgroups but also between Shigella and E. coli support the status of Shigella as a subgroup of the species E. coli.

Genomic diversity of Escherichia isolates from diverse habitats

Our understanding of the Escherichia genus is heavily biased toward pathogenic or commensal isolates from human or animal hosts. Recent studies have recovered Escherichia isolates that persist, and even grow, outside these hosts. Although the environmental isolates are typically phylogenetically distinct, they are highly related to and phenotypically indistinguishable from their human counterparts, including for the coliform test. To gain insights into the genomic diversity of Escherichia isolates from diverse habitats, including freshwater, soil, animal, and human sources, we carried out comparative DNA-DNA hybridizations using a multi-genome E. coli DNA microarray. The microarray was validated based on hybridizations with selected strains whose genome sequences were available and used to assess the frequency of microarray false positive and negative signals. Our results showed that human fecal isolates share two sets of genes (n>90) that are rarely found among environmental isolates, including genes presumably important for evading host immune mechanisms (e.g., a multi-drug transporter for acids and antimicrobials) and adhering to epithelial cells (e.g., hemolysin E and fimbrial-like adhesin protein). These results imply that environmental isolates are characterized by decreased ability to colonize host cells relative to human isolates. Our study also provides gene markers that can distinguish human isolates from those of warm-blooded animal and environmental origins, and thus can be used to more reliably assess fecal contamination in natural ecosystems.

Genotypic characterization of bacteria cultured from duck faeces

AIMS

To characterize the bacterial composition of mallard duck faeces and determine if novel bacterial species are present that could be utilized as potential indicators of avian faecal contamination.

METHODS AND RESULTS

Combined samples of fresh faeces from four ducks were serially diluted and plated onto six different media selected to allow the growth of a range of organisms at 42 degrees C under three atmospheric conditions: aerobic, microaerophilic and anaerobic. Forty-seven morphologically dissimilar isolates were purified and partial sequencing of the16S rRNA indicated at least 31 bacterial species. Twenty of these could be identified to the species level including pathogenic species of Bacillus, Campylobacter, Clostridium and Streptococcus. Other species identified included: Enterococcus, Escherichia, Megamonas, Cellulosimicrobium, Neisseria, Staphylococcus and Veillonella. Potentially novel species, which could represent bacteria specific to avian fauna included Bacillus, Corynebacterium, Macrococcus and Peptostreptococcus, while four isolates had <97% similarity to known bacterial species in the available databases.

CONCLUSION

A survey of the natural microflora of the mallard duck and its hybrid with the grey duck identified both bacteria that are potentially human pathogenic and putative novel bacteria species as determined by 16S rRNA sequencing.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides further evidence that duck faeces is a potential human health hazard, and has identified bacteria potentially useful for distinguishing duck faeces from other faecal sources.