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J J Farmer

Publications and source records attributed to J J Farmer.

At least 19 recordsLinked to original sources
PubMed2000

Outbreak of nosocomial infections due to extended-spectrum beta-lactamase-producing strains of enteric group 137, a new member of the family Enterobacteriaceae closely related to Citrobacter farmeri and Citrobacter amalonaticus.

A member of the Enterobacteriaceae initially identified as Kluyvera cryocrescens by the MicroScan Gram-Negative Combo 13 panel caused an outbreak of nosocomial infections in four patients (pneumonia, n = 2; urinary tract infection, n = 1; wound infection, n = 1) and urinary tract colonization in one patient. When the strains were tested by the Enteric Reference Laboratory of the Centers for Disease Control and Prevention, biochemical results were most compatible with Yersinia intermedia, Kluyvera cryocrescens, and Citrobacter farmeri but identification scores were low and test results were discrepant. However, when the biochemical test profile was placed in the computer database as a new organism, all strains were identified as the organism with high identification scores (0. 999968 to 0.999997) and no discrepant test results. By 16S rRNA sequence analysis the organism clustered most closely with, but was distinct from, Citrobacter farmeri and Citrobacter amalonaticus. Based on its unique biochemical profile and rRNA sequence, this organism is designated Enteric Group 137. Restriction endonuclease analysis and taxonomic antibiograms of strains causing the outbreak demonstrated a single clone of Enteric Group 137, and antibiotic susceptibility testing revealed the presence of extended-spectrum beta-lactamase (ESBL) resistance. Enteric Group 137 appears to be a new opportunistic pathogen that can serve as a source of ESBL resistance in the hospital.

Aged↗
PubMed1999

Clinical, epidemiological, and microbiological features of Vibrio vulnificus biogroup 3 causing outbreaks of wound infection and bacteraemia in Israel. Israel Vibrio Study Group.

BACKGROUND: Vibrio vulnificus is a gram-negative bacterium that causes septicaemia and wound infection. Cases occur sporadically, and no previous outbreaks due to a common source or a clonal strain have been reported. In the summer and autumn of 1996 and 1997, an outbreak of invasive V. vulnificus infection occurred in Israel in people who had recently handled fresh, whole fish purchased from artificial fish-ponds. METHODS: We reviewed clinical and epidemiological information, and undertook an environmental investigation to assess disease characteristics, modes of transmission, phenotypic characteristics of the bacterium, and fish-marketing policy. The clonal nature of 19 isolates was studied by biotyping, pulsed-field gel electrophoresis, and restriction-fragment length polymorphism (RFLP) analysis of a PCR fragment. FINDINGS: During 1996-97, 62 cases of wound infection and bacteraemia occurred. 57 patients developed cellulitis, four had necrotising fasciitis, and one developed osteomyelitis. In all cases, the fish were cultivated in inland fish-ponds. In the summer of 1996, fish-pond managers initiated a new marketing policy, in which fish were sold alive instead of being packed in ice. Phenotypically, the isolates had five atypical biochemical test results. The isolates were non-typeable by pulsed-field gel electrophoresis, and all had the same PCR-RFLP pattern which had not been seen previously. INTERPRETATION: The cause of the outbreak was a new strain of V. vulnificus, classified as biogroup 3. A new fish-marketing policy that began in 1996 may have exposed susceptible people to the organism.

Adolescent↗
PubMed1998

Polyazamacrolides from ladybird beetles: ring-size selective oligomerization.

The pupal defensive secretion of the 24-pointed ladybird beetle, Subcoccinella vigintiquatuorpunctata, consists of a mixture of macrocyclic polyamines, dominated by the three dimeric, 30-membered macrocycles 11-13, derived from the two building blocks 11-(2-hydoxyethylamino)-5-tetradecenoic acid (9) and 11-(2-hydoxyethylamino)-5,8-tetradecadienoic acid (10). Smaller amounts of the four possible cyclic trimers of 9 and 10 were also detected, corresponding to 45-membered macrocycles. Structural assignments were based on NMR-spectroscopic investigations and HPLC-MS analyses. In addition, the all-S absolute configuration of the S. vigintiquatuorpunctata macrocycles was determined by comparison of derivatives of the natural material with enantiomerically pure synthetic samples. Comparing this alkaloid mixture with that of the pupal defensive secretion in related ladybird beetle species indicates that the degree of oligomerization of the 2-hydroxyethylamino carboxylic acid building blocks can be carefully controlled by the insects.

Alkaloids↗
PubMed1998

Combinatorial chemistry in insects: a library of defensive macrocyclic polyamines.

The pupal defensive secretion of the coccinellid beetle Epilachna borealis is composed principally of a combinatorial library of macrocyclic polyamines. These compounds constitute a previously unrecognized family of natural products, characterized by extremely large-ring lactonic structures derived from a small set of (2-hydroxyethylamino)alkanoic acids. The combinatorial assembly of these simple building blocks generates a high degree of structural diversity, which is further increased by slow, spontaneous intramolecular rearrangement of the macrocycles.

Amino Acids↗
PubMed1995

Molecular subtyping of toxigenic Vibrio cholerae O139 causing epidemic cholera in India and Bangladesh, 1992-1993.

Since October 1992, > 150,000 cases of cholera have been reported from India and Bangladesh; the great majority of Vibrio cholerae isolates belong to the newly established serogroup O139. To better understand the interaction of genetic and epidemiologic factors responsible for their sudden appearance and rapid spread, representative toxigenic V. cholerae O139 isolates were molecularly characterized and compared with a set of toxigenic V. cholerae O1 and non-O1/non-O139 strains. DNA sequences of the cholera toxin B subunit gene and multilocus enzyme electrophoresis markers of V. cholerae O139 strains were identical to those of V. cholerae O1 isolates of the seventh pandemic. Two distinct ribotypes and four pulsed-field gel electrophoretic patterns were observed for O139 strains. V. cholerae O139 strains were very similar to V. cholerae O1 strains of the seventh pandemic but clearly different from the toxigenic V. cholerae strains of serogroups other than O1 and O139.

Bacterial Typing Techniques↗
PubMed1994

Differentiation of Salmonella enteritidis phage type 8 strains: evaluation of three additional phage typing systems, plasmid profiles, antibiotic susceptibility patterns, and biotyping.

Three additional phage typing systems for Salmonella enteritidis, plasmid analysis, biochemical tests, and antimicrobial susceptibility tests, were used in an attempt to subdivide 30 phage type 8 (phage typing system used by the WHO International Center for Enteric Phage Typing, London, England) isolates. These isolates represented 18 different egg-related outbreaks (21 strains) and 9 reference strains or strains that were not egg-associated. Only 7 of the 30 strains (28%) were subdivided by one or more of the methods used; this included 3 of the 21 strains from egg-related outbreaks. Twenty-seven strains contained a 55-kb plasmid that is associated with S. enteritidis. Of 65 additional phages tested, 2 from the phage typing system obtained from the Pasteur Institute, Paris, France, were useful in differentiating the three strains that lacked the 55-kb plasmid. Although the results obtained for the 21 strains from egg-related outbreaks showed that the strains had minor phenotypic differences, the overall results suggested that the strains may represent a single clone. Studies are planned to test additional phages and other typing methods to see whether strains of phage type 8 can be further differentiated.

Bacterial Typing Techniques↗
PubMed1992

Pyrazinamidase, CR-MOX agar, salicin fermentation-esculin hydrolysis, and D-xylose fermentation for identifying pathogenic serotypes of Yersinia enterocolitica.

We evaluated several simple laboratory tests that have been used to identify pathogenic serotypes of Yersinia enterocolitica or to indicate the pathogenic potential of individual strains. A total of 100 strains of Y. enterocolitica were studied, including 25 isolated during five outbreak investigations, 63 from sporadic cases, and 12 from stock cultures. The pyrazinamidase test, which does not depend on the Yersinia virulence plasmid, correctly identified 60 of 63 (95% sensitivity) strains of pathogenic serotypes and 34 of 37 (92% specificity) strains of nonpathogenic serotypes. Salicin fermentation-esculin hydrolysis (25 degrees C, 48 h) correctly identified all 63 (100% sensitivity) strains of the pathogenic serotypes and 34 of 37 (92% specificity) strains of the nonpathogenic serotypes. The results of the pyrazinamidase and salicin-esculin tests disagreed for only 7 of the 100 strains of Y. enterocolitica, and these would require additional testing. Congo red-magnesium oxalate (CR-MOX) agar determines Congo red dye uptake and calcium-dependent growth at 36 degrees C, and small red colonies are present only if the strain contains the Yersinia virulence plasmid. This test has proven to be extremely useful for freshly isolated cultures, but only 15 of 62 strains of pathogenic serotypes that had been stored for 1 to 10 years were CR-MOX positive. None of the 16 strains of Y. enterocolitica serotype O3 fermented D-xylose, so this test easily differentiated strains of this serotype, which now appears to be the most common in the United States. Although antisera that can actually be used to serotype strains of Y. enterocolitica are not readily available, the four simple tests described above can be used to screen for pathogenic serotypes.

Agar↗
PubMed1991

Yersinia enterocolitica O:3: an emerging cause of pediatric gastroenteritis in the United States. The Yersinia enterocolitica Collaborative Study Group.

After an outbreak of Yersinia enterocolitica infections among black children in Atlanta, a seven-hospital study was conducted to determine the importance of this pathogen in other communities with large black populations. Of 4841 stool specimens from patients with gastroenteritis examined between November 1989 and January 1990, Y. enterocolitica, Shigella, Campylobacter, and Salmonella were identified in 38, 49, 60, and 98 specimens, respectively; 34 (92%) of 37 Y. enterocolitica isolates were serotype O:3. Of the 38 patients with yersiniosis, 37 (97%) were children. Illnesses were clustered around the holidays, and 20 (62%) of 32 patients had been exposed to raw pork intestines in the 2 weeks before onset. Exposure was significantly associated with illness in a case-control study of eight patients identified at one hospital (P = .004). Infants less than or equal to 6 months old with yersiniosis were more likely to have immature-to-total neutrophil ratios greater than 0.50 than were infants of comparable age with salmonellosis (P = .02). Infrequently isolated in the past, Y. enterocolitica O:3 is emerging as an important enteric pathogen in this country, particularly among black children.

Adolescent↗
PubMed1991

Phage typing of Salmonella enteritidis in the United States.

The number of reported isolates of Salmonella enteritidis has increased dramatically in the last 10 years. For many years phage typing has been a useful epidemiologic tool for studying outbreaks of S. typhi and S. typhimurium. In 1987, Ward et al. (L. R. Ward, J. De Sa, and B. Rowe, Epidemiol. Infect. 99:291-294, 1987) described a phage typing scheme for S. enteritidis. This system differentiated 27 phage types by use of 10 typing phages. With these phages, we typed 573 strains of S. enteritidis from humans (42 outbreaks), animals, food, and the environment. Ninety-six percent of the strains were typeable. The most common phage types were 8 (48.2%), 13a (20.1%), 13 (7.8%), and 14b (7.8%). Most of the strains were specifically collected from egg-related outbreaks in the northeastern United States in 1988 and 1989, probably accounting for the distribution of the four most common types in this sample. This system was particularly useful for differentiating a group of animal strains that had a number of diverse phage types. For 49 animal strains typed, 16 different patterns were obtained. Phage type 8 represented 32% of these strains, but no other phage type represented more than 8% of these strains. One-half of the 16 animal strains that were phage type 8 were from poultry. This phage typing system will be useful for comparing phage types found in the United States with those types encountered worldwide and for determining whether virulent strains of phage type 4 are entering the United States. Additional phage typing systems as well as molecular techniques are being studied to determine whether they can differentiate strains of phage types 8 and 13a.

Animals↗
PubMed1991

Trabulsiella guamensis, a new genus and species of the family Enterobacteriaceae that resembles Salmonella subgroups 4 and 5.

In 1985 the vernacular name Enteric Group 90 was coined for a small group of strains that had been referred to our laboratory as probable strains of Salmonella but did not agglutinate in Salmonella typing antisera. By DNA-DNA hybridization (hydroxyapatite method, 32P), seven strains of Enteric Group 90 were found to be closely related (98 to 100% at 60 degrees C and 94 to 100% at 75 degrees C) to the first strain received (0370-85). The relatedness of Enteric Group 90 to 62 strains of other species of the family Enterobacteriaceae was only 6 to 41%, with the highest values obtained with strains of Salmonella, Kluyvera, Shigella, Klebsiella, Enterobacter, and Citrobacter. We propose a new genus, Trabulsiella, with a single new species, Trabulsiella guamensis, for the highly related group of eight strains formerly known as Enteric Group 90. The type strain is designated ATCC 49490 (CDC 0370-85). T. guamensis strains grew well at 36 degrees C and had positive reactions in the following tests: methyl red, citrate utilization (Simmons) (38% positive at day 1, 88% positive at 2 days), H2S production, lysine decarboxylase, arginine dihydrolase (50% positive at 2 days, 100% positive at 7 days), ornithine decarboxylase, motility, growth in KCN medium, mucate fermentation, acetate utilization, nitrate reduction to nitrite, weak tyrosine hydrolysis (88% positive at 2 days, 100% positive at 7 days), and ONPG (o-nitrophenyl-beta-D-galactopyranoside) test. The strains fermented D-glucose with gas production and fermented L-arabinose, cellobiose, D-galactose, D-galacturonate, maltose, D-mannitol, D-mannose, L-rhamnose, D-sorbitol, trehalose, and D-xylose. T. guamensis strains had negative reactions in the following tests: indole production (13% positive), Voges-Proskauer, urea hydrolysis, phenylalanine deaminase, malonate utilization, lipase (corn oil), DNase, oxidase, pigment production, and acid production from adonitol, D-arabitol, dulcitol, erythritol, myo-inositol, melibiose, alpha-methyl-D-glucoside, raffinose, and sucrose. There were delayed positive reactions for gelatin liquefaction (22 degrees C), which was positive at 12 to 23 days, esculin hydrolysis (13% positive at day 1, 50% positive at 7 days), lactose fermentation (13% positive at 3 to 7 days, 100% positive at 8 to 10 days), glycerol fermentation (88% positive at 7 days), and salicin fermentation (13% positive at day 1, 88% positive at 7 days). All strains were susceptible by the disk diffusion method to colistin, nalidixic acid, gentamicin, streptomycin, kanamycin, chloramphenicol, and trimethoprim-sulfamethoxazole, and most strains were susceptible to sulfadiazine (75% susceptible), tetracycline (88%), and carbenicillin (75%). The strains were resistant to penicillin, cephalothin, and ampicillin. The strains were isolated from vacuum cleaner dust (five strains), soil (one strain), and human feces (two strains). Although T. guamensis can occur in human diarrheal stools, there is no evidence that it actually causes diarrhea. Its main interest to clinical microbiologists may be its possible misidentification as a strain Salmonella.

DNA, Bacterial↗
PubMed1990

Comparison of a latex agglutination assay and an enzyme-linked immunosorbent assay for detecting cholera toxin.

To determine the pandemic potential of Vibrio cholerae, one must demonstrate both the presence of O1 antigen and the production of enterotoxin (CT). Tissue culture or enzyme-linked immunosorbent assays (ELISAs) for CT have been limited to research and reference laboratories. A kit for detecting CT by reversed passive latex agglutination is now commercially available and was used to test 168 strains of V. cholerae O1 and non-O1. When compared with the routine ELISA, the latex test was 98% accurate (86 of 88) for serogroup O1 strains and 100% accurate (80 of 80) for non-O1 strains. For both O1 and non-O1 study strains, the sensitivity of the latex agglutination test was 0.97 and the specificity was 1.00 when results were compared with ELISA results. The latex test is commercially available and has the advantages of being less complicated and less time-consuming than the ELISA.

Cholera Toxin↗
PubMed1989

Ribosomal RNA gene restriction patterns provide increased sensitivity for typing Salmonella typhi strains.

To date, epidemiologic associations among strains of Salmonella typhi are based exclusively on phage typing, which may be of limited value if a common phage type is involved. Analysis of ribosomal RNA gene restriction patterns allows separation of most independently isolated strains of identical phage types. The sensitivity of the method is dependent on the restriction enzymes used to digest chromosomal DNA. It was highest for PstI, which separated 16 of 20 strains that belonged to 8 phage types including 3 untypable strains. Three strains differed in their phage types but had identical ribosomal RNA gene restriction patterns. Also, two pairs of strains indistinguishable by phage typing exhibited identical patterns; however, two of these strains were expected to be identical because they were isolated from two patients who were likely exposed to the same source. Ribosomal RNA gene restriction patterns appear to be stable. Thus, the method may complement phage typing and aid in further differentiation of strains.

Bacteriophage Typing↗
PubMed1989

The ail locus is found uniquely in Yersinia enterocolitica serotypes commonly associated with disease.

Yersinia enterocolitica is a heterogeneous group of organisms with more than 50 serotypes and several biotypes. Only a few of these serotypes cause gastrointestinal disease in otherwise healthy hosts; these serotypes are the pathogenic serotypes. Although Y. enterocolitica requires a high-molecular-weight plasmid to cause disease, chromosome-encoded determinants are required for the full expression of virulence. The ability of Yersinia spp. to invade eucaryotic cells is thought to be a virulence factor, because nonpathogenic serotypes are noninvasive in animals and in tissue culture cell models. Current evidence indicates that invasion ability is chromosome encoded. We recently reported cloning two loci, inv and ail, from Y. enterocolitica O8 strain 8081c that allow Escherichia coli to invade tissue culture cells. We investigated the link between invasion in an in vitro tissue culture invasion (TCI) model and hybridization to probes derived from the two invasion loci, inv and ail. We examined 177 Yersinia strains. Strains of serotypes and species associated with disease were TCI+, whereas strains of serotypes and species not associated with disease were TCI-. Only TCI+ strains had DNA homologous to probes derived from ail. All strains (TCI+ and TCI-) had DNA homologous to probes derived from inv, but there were certain restriction fragment-linked polymorphisms that were associated primarily with TCI+ strains. These observations held true for strains epidemiologically associated with disease. Both the inv and ail loci were found to be clearly located on the chromosome. No other genera, including other invasive organisms, had DNA homologous to inv or ail. These data support the hypothesis that the ail locus encodes a Y. enterocolitica invasion factor that may be involved in pathogenesis.

Bacteriological Techniques↗
PubMed1989

Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov.

Crude cell extracts of 26 isolates of Salmonella serotype typhi (S. typhi) and 48 other Salmonella isolates representing 28 serotypes and seven DNA hybridization subgroups were analyzed for electrophoretic variants of 24 metabolic enzymes by starch gel electrophoresis. All strains of S. typhi had identical isoenzyme patterns, indicating that they were a single clone. All of the enzymes detected in the remaining strains were polymorphic, and the degree of genetic variation was quite high. The average number of alleles per enzyme locus was 4.7, and the mean genetic diversity per locus was 0.556. Thirty-two distinct allele profiles, or electrophoretic types (ETs), were found in these 48 strains of Salmonella serotypes other than S. typhi. Analysis of the genetic relationships of the ETs to each other showed that, with one exception, the ETs formed subgroups that were consistent with the subgroupings based on DNA hybridization studies. ET profiles were not always linked to specific serologic patterns. These data show that multilocus enzyme electrophoresis has a potential application in epidemiologic and taxonomic studies of salmonellae, although it is not differential for S. typhi. We also propose a new species, Salmonella bongori comb. nov., a new combination base on the elevation of Salmonella choleraesuis subsp. bongori to the level of species.

Chromosome Mapping↗
PubMed1989

Xenorhabdus luminescens (DNA hybridization group 5) from human clinical specimens.

An unusual isolate from a human leg wound was identified as Xenorhabdus luminescens. This finding led to the discovery or isolation of four additional strains, two from blood and two from wounds. Three of the five strains were from patients in San Antonio, Tex. Three strains were studied by DNA-DNA hybridization (S1 nuclease-trichloroacetic acid method) and were 77 to 100% related to each other, 34% related to the type strain of X. luminescens, 35 to 40% related to three of Grimont's other DNA hybridization groups of X. luminescens, and 9% related to the type strain of Xenorhabdus nematophilus. The new group of five strains was designated X. luminescens DNA hybridization group 5. All five strains were very inactive biochemically and fermented only D-glucose and D-mannose. The key reactions for recognizing this new organism are yellow pigment production, negative test for nitrate reduction to nitrite, weak bioluminescence (10 to 15 min of dark adaptation is required to see the weak light produced), and a unique hemolytic reaction on sheep blood agar plates incubated at 25 degrees C. Two case histories of strains from wounds are given; these suggest that X. luminescens DNA hybridization group 5 may be a new bacterial agent that causes wound infections. The two cases of wound infection, along with the two blood isolates, suggest that the new organism is clinically significant.

Aged↗
PubMed1989

Enterobacter hormaechei, a new species of the family Enterobacteriaceae formerly known as enteric group 75.

The name Enterobacter hormaechei is proposed for a new species of the family Enterobacteriaceae, formerly called Enteric Group 75, which consists of 23 strains, 22 of which were isolated from humans. DNAs from 12 E. hormaechei strains tested were highly related to the type strain (ATCC 49162) by DNA hybridization, using the hydroxyapatite method (80 to 97% in 60 degrees C reactions; 80 to 90% in 75 degrees C reactions). The strains were most closely related (50 to 63%) to Enterobacter cloacae, Enterobacter dissolvens, Enterobacter taylorae, and Enterobacter nimipressuralis. E. hormaechei strains were positive within 48 h for the following: Voges-Proskauer test; citrate utilization (Simmons and Christensen); urea hydrolysis (87%); ornithine decarboxylase; growth in potassium cyanide (KCN); malonate utilization; production of acid from D-glucose, L-arabinose, cellobiose, dulcitol (87%), D-galactose, maltose, D-mannitol, D-mannose, L-rhamnose, sucrose, trehalose, and D-xylose; acid production from mucate; nitrate reduction; and o-nitrophenyl-beta-D-galactopyranoside. Delayed positive reactions were seen in tests for arginine dihydrolase, gas from D-glucose, acid from alpha-methyl-D-glucoside, and acetate utilization. E. hormaechei was negative in tests for indole production; H2S production; phenylalanine deaminase; lysine decarboxylase; gelatin hydrolysis; acid production from D-adonitol, D-arabitol, erythritol, glycerol, i(myo)-inositol, melibiose, raffinose, and D-sorbitol; esculin hydrolysis; DNase; lipase; and tyrosine clearing. Variable reactions occurred in tests for methyl red, motility, and tartrate. All strains tested were susceptible or moderately susceptible to amikacin, azlocillin, cefotaxime, ceftazidime, ceftriaxone, chloramphenicol, gentamicin, mezlocillin, moxalactam, piperacillin, trimethoprim-sulfamethoxazole, sulfisoxazole, thienamycin, tobramycin, and trimethoprim. All strains tested were resistant to nitrofurantoin; the majority were resistant to ampicillin, cefoxitin, and cephalothin. Four isolates were from blood; most other isolates were from wounds or sputum.

Adolescent↗