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PubMed1998

The incidence of Weeksella- and Bergeyella-like bacteria in the food environment.

Eighty-five catalase- and oxidase-positive Gram-negative rods and cocci susceptible to penicillin G were isolated from a variety of food sources. The phenotypic relationships of these isolates with reference cultures of Bergeyella-like, Chryseobacterium, Empedobacter, Myroides, Moraxella, Sphingobacterium and Weeksella-like strains were examined by numerical taxonomy. Seventy-three isolates were recovered in five groups; 80% of the isolates clustered in groups 1, 2 and 3 and produced indole, bearing a strong resemblance to Weeksella and Bergeyella. They could not, however, be regarded as belonging to the known species of W. virosa and B. zoohelcum. It is suggested that three species may be necessary to accommodate the environmental Weeksella- or Bergeyella-like bacteria. The isolates in groups 4 and 5 had white colonies and were unable to produce indole, in this way resembling the Moraxella genus.

Bacterial Typing Techniques↗

PubMed2003

Occurrence and antimicrobial resistance of Gram-negative bacteria isolated in haemodialysis water and dialysate of renal units: results of a Greek multicentre study.

AIMS: To evaluate the occurrence, identity and antimicrobial resistance of Gram-negative bacteria isolated from municipal water supplies, treated water, and dialysate of all 85 Greek haemodialysis centres. METHODS AND RESULTS: A total of 141 Gram-negative bacterial isolates (98 non-fermentative and 43 enterobacteria) were recovered from 255 water samples. Twenty-four of them were isolated from tap water, 31 from treated water, and 86 from dialysate samples. The mean concentrations (CFU per 100 ml +/- s.d.) of the positive Gram-negative bacteria samples were 69.2 +/- 43.9, 31.2 +/- 28.7 and 3552.3 +/- 4485.0, respectively. The most common isolates, in order of frequency were Pseudomonas aeruginosa (22.7%), Chryseobacterium meningosepticum (14.9%), Stenotrophomonas maltophilia (13.5%), Escherichia coli (12.8%) and Enterobacter cloacae (7.8%), representing 71.6% of all isolates. Ps. aeruginosa was the most prevalent isolate in all types of water sample followed by C. meningosepticum in tap and treated water and by E. coli in dialysate. Nineteen per cent of the enterobacteria and 35% of the non-fermenters were resistant against three or more of the nine antibiotics tested. CONCLUSIONS: These data suggest that dialysate and treated water could be a source of infection for several non-fermentative and enterobacterial species. IMPACT OF THE STUDY: Microbiological monitoring of such samples is needed in order to know the identity and antibiotic resistance profiles of their potentially pathogenic bacterial population.

Anti-Bacterial Agents↗

PubMed2002

Substrate-activated zinc binding of metallo-beta -lactamases: physiological importance of mononuclear enzymes.

We have investigated the influence of substrate binding on the zinc ion affinity of representatives from the three metallo-beta-lactamase subclasses, B1 (BcII from Bacillus cereus and BlaB from Chryseobacterium meningosepticum), B2 (CphA from Aeromonas hydrophila), and B3 (L1 from Stenotrophomonas maltophilia). By competition experiments with metal-free apoenzymes and chromophoric zinc chelators or EDTA, we determined the dissociation constants in the absence and presence of substrates. For the formation of the monozinc enzymes we determined constants of 1.8, 5.1, 0.007, and 2.6 nm in the absence and 13.6, 1.8, 1.2, and 5.7 pm in the presence of substrates for BcII, BlaB, CphA, and L1, respectively. A second zinc ion binds in the absence (presence) of substrates with considerably higher dissociation constants, namely 1.8 (0.8), 0.007 (0.025), 50 (1.9), and 0.006 (0.12) microm for BcII, BlaB, CphA, and L1, respectively. We have concluded that the apo form might be the prevailing state of most of the metallo-beta-lactamases under physiological conditions in the absence of substrates. Substrate availability induces a spontaneous self-activation due to a drastic decrease of the dissociation constants, resulting in the formation of active mononuclear enzymes already at picomolar free zinc ion concentrations. In the presence of substrates, the binuclear state of the enzymes only exists at unphysiologic high zinc concentrations and might be of no biological relevance. From the competition experiments with EDTA it is further concluded that the reactivation rate does not depend on the pool of free zinc ions but proceeds via the EDTA-Zn(II)-enzyme ternary complexes.

Aeromonas↗

PubMed2005

Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic.

Two yellow-pigmented, Gram-negative and aerobic bacterial strains, designated AT1013T and AT1047T, were isolated from terrestrial samples of the Antarctic. On the basis of 16S rRNA gene sequence analyses, the two Antarctic strains shared 97.7 % sequence similarity and showed moderate relationships to the genera Chryseobacterium (92.5-95.3 %), Riemerella (92.3-93.5 %), Bergeyella (92.5-92.6 %) and Kaistella (92.5-93.3 %). In phylogenetic analyses, the two isolates formed a robust monophyletic clade and represented a distinct phyletic line that equated to novel generic status. Cells were non-motile, non-gliding and psychrotolerant with an optimum growth temperature of about 20 degrees C. Flexirubins were absent. The major isoprenoid quinone was MK-6. The predominant cellular fatty acids were 15 : 0 iso, 15 : 0 anteiso and 17 : 1 iso omega9c. DNA G+C contents were 34-36 mol%. The two isolates shared low genomic relatedness (27 %) and were differentiated from each other by several phenotypic characteristics. The polyphasic data presented in this study indicated that these isolates should be recognized as two separate novel species in a novel genus within the family Flavobacteriaceae. The name Sejongia gen. nov. is therefore proposed for the Antarctic isolates, with the type species Sejongia antarctica sp. nov. (type strain AT1013T=IMSNU 14040T=KCTC 12225T=JCM 12381T) and Sejongia jeonii sp. nov. (type strain AT1047T=IMSNU 14049T=KCTC 12226T=JCM 12382T).

Antarctic Regions↗

PubMed2006

Cloacibacterium normanense gen. nov., sp. nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater.

Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G+C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4 x 10(5) cells ml(-1), and untreated wastewater from a second plant yielded an estimated count of 1.4 x 10(4) cells ml(-1). Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1(T) (=CCUG 46293(T) = CIP 108613(T) = ATCC BAA-825(T) = DSM 15886(T)).

Base Composition↗

PubMed2003

Characterization of a soil-derived bacterial consortium degrading 4-chloroaniline.

A bacterial consortium comprising four different species was isolated from an Indonesian agricultural soil using a mixture of aniline and 4-chloroaniline (4CA) as principal carbon sources. The four species were identified as Chryseobacterium indologenes SB1, Comamonas testosteroni SB2, Pseudomonas corrugata SB4 and Stenotrophomonas maltophilia SB5. Growth studies on aniline and 4CA as single and mixed substrates demonstrated that the bacteria preferred to grow on and utilize aniline rather than 4CA, although both compounds were eventually depleted from the culture supernatant. However, despite 100 % disappearance of the parent substrates, the degradation of 4CA was always characterized by incomplete dechlorination and 4-chlorocatechol accumulation. This result suggests that further degradation of 4-chlorocatechol may be the rate-limiting step in the metabolism of 4CA by the bacterial consortium. HPLC-UV analysis showed that 4-chlorocatechol was further degraded via an ortho-cleavage pathway by the bacterial consortium. This hypothesis was supported by the results from enzyme assays of the crude cell extract of the consortium revealing catechol 1,2-dioxygenase activity which converted catechol and 4-chlorocatechol to cis,cis-muconic acid and 3-chloro-cis,cis-muconic acid respectively. However, the enzyme had a much higher conversion rate for catechol [156 U (g protein)(-1)] than for 4-chlorocatechol [17.2 U (g protein)(-1)], indicating preference for non-chlorinated substrates. Members of the bacterial consortium were also characterized individually. All isolates were able to assimilate aniline. P. corrugata SB4 was able to grow on 4CA solely, while S. maltophilia SB5 was able to grow on 4-chlorocatechol. These results suggest that the degradation of 4CA in the presence of aniline by the bacterial consortium was a result of interspecies interactions.

Aniline Compounds↗

PubMed2004

Proposal to transfer 'Aegyptianella ranarum', an intracellular bacterium of frog red blood cells, to the family Flavobacteriaceae as 'Candidatus Hemobacterium ranarum' comb. nov.

'Aegyptianella ranarum' (order Rickettsiales), an ultrastructurally defined small, Gram-negative rod, is known to replicate in the red blood cells of frogs. Heretofore, this bacterium has not been characterized genetically. We cloned and sequenced the 16S rRNA (1310 bp) and gyrB (718 bp) genes of 'A. ranarum' from a Canadian frog blood specimen. In situ hybridization (with an 'A. ranarum' 16S rRNA gene polymerase chain reaction product as probe) and electron microscopy confirmed that 'A. ranarum' forms cytoplasmic inclusions in frog erythrocytes. blast comparisons with GenBank 16S rRNA and gyrB sequences showed that both 'A. ranarum' genes were most similar (91% and 67% identity) to those of Chryseobacterium meningosepticum, a bacterium in the family Flavobacteriaceae. In contrast, 'A. ranarum' 16S rRNA shared only 61% identity with Aegyptianella pullorum. Phylogenetic analyses of these genes using phylip supported 'A. ranarum' as a member of Flavobacteriaceae, but suggested that its cladistic sibling may be Bergeyella zoohelcum or Weeksella virosa, rather than C. meningosepticum. We propose to classify 'Aegyptianella ranarum' as 'Candidatus Hemobacterium ranarum' in the family Flavobacteriaceae. Our results provide a starting point for studies of related intraerythrocytic bacterial infections in frogs.

Anaplasmataceae↗

PubMed1999

Cloning and characterization of blaVIM, a new integron-borne metallo-beta-lactamase gene from a Pseudomonas aeruginosa clinical isolate.

Production of a metallo-beta-lactamase activity was detected in a carbapenem-resistant Pseudomonas aeruginosa clinical isolate (isolate VR-143/97) from an Italian inpatient at the Verona University Hospital (northern Italy). The metallo-beta-lactamase determinant was isolated from a genomic library of VR-143/97, constructed in an Escherichia coli plasmid vector, by screening for clones with reduced susceptibility to imipenem. Sequencing of the cloned gene revealed that it encoded a new class B beta-lactamase that was named VIM-1. At the sequence level VIM-1 was rather divergent from the other class B enzymes (16.4 to 38.7% identity), overall being more similar to members of subclass B1 including the beta-lactamase II of Bacillus cereus (Bc-II), the Bacteroides fragilis CcrA, the Chryseobacterium meningosepticum BlaB, and the cassette-encoded IMP-1 enzymes. Among these, VIM-1 showed the highest degree of similarity to Bc-II. Similarly to blaIMP, blaVIM was also found to be carried on a gene cassette inserted into a class 1 integron. The blaVIM-containing integron was located on the chromosome of P. aeruginosa VR-143/97, and the metallo-beta-lactamase-encoding determinant was not transferable to E. coli by conjugation. Expression of the integron-borne blaVIM gene in E. coli resulted in a significant decrease in susceptibility to a broad array of beta-lactams (ampicillin, carbenicillin, piperacillin, mezlocillin, cefotaxime, cefoxitin, ceftazidime, cefoperazone, cefepime, and carbapenems), revealing a very broad substrate specificity of the VIM-1 enzyme.

Amino Acid Sequence↗

PubMed2000

TLA-1: a new plasmid-mediated extended-spectrum beta-lactamase from Escherichia coli.

Escherichia coli R170, isolated from the urine of an infected patient, was resistant to expanded-spectrum cephalosporins, aztreonam, ciprofloxacin, and ofloxacin but was susceptible to amikacin, cefotetan, and imipenem. This particular strain contained three different plasmids that encoded two beta-lactamases with pIs of 7.0 and 9.0. Resistance to cefotaxime, ceftazidime, aztreonam, trimethoprim, and sulfamethoxazole was transferred by conjugation from E. coli R170 to E. coli J53-2. The transferred plasmid, RZA92, which encoded a single beta-lactamase, was 150 kb in length. The cefotaxime resistance gene that encodes the TLA-1 beta-lactamase (pI 9.0) was cloned from the transconjugant by transformation to E. coli DH5alpha. Sequencing of the bla(TLA-1) gene revealed an open reading frame of 906 bp, which corresponded to 301 amino acid residues, including motifs common to class A beta-lactamases: (70)SXXK, (130)SDN, and (234)KTG. The amino acid sequence of TLA-1 shared 50% identity with the CME-1 chromosomal class A beta-lactamase from Chryseobacterium (Flavobacterium) meningosepticum; 48.8% identity with the VEB-1 class A beta-lactamase from E. coli; 40 to 42% identity with CblA of Bacteroides uniformis, PER-1 of Pseudomonas aeruginosa, and PER-2 of Salmonella typhimurium; and 39% identity with CepA of Bacteroides fragilis. The partially purified TLA-1 beta-lactamase had a molecular mass of 31.4 kDa and a pI of 9.0 and preferentially hydrolyzed cephaloridine, cefotaxime, cephalothin, benzylpenicillin, and ceftazidime. The enzyme was markedly inhibited by sulbactam, tazobactam, and clavulanic acid. TLA-1 is a new extended-spectrum beta-lactamase of Ambler class A.

Amino Acid Sequence↗

PubMed2002

Chromosome-encoded beta-lactamases TUS-1 and MUS-1 from Myroides odoratus and Myroides odoratimimus (formerly Flavobacterium odoratum), new members of the lineage of molecular subclass B1 metalloenzymes.

Myroides odoratus and Myroides odoratimimus (formerly designated in a single species as Flavobacterium odoratum) are gram-negative aerobes and sources of nosocomial infections in humans. They have variable susceptibility to beta-lactams and a decreased susceptibility to carbapenems. Using genomic DNAs of M. odoratus CIP 103105 and M. odoratimimus CIP 103073 reference strains, shotgun cloning of beta-lactamase genes was performed, followed by protein expression in Escherichia coli. The deduced amino acid sequences of these beta-lactamase genes revealed that TUS-1 and MUS-1 from M. odoratus CIP 103105 and M. odoratimimus CIP 103073, respectively, shared 73% amino acid identity. Mature proteins TUS-1 and MUS-1, with pI values of 7.8 and 5.2, respectively, had relative molecular masses of ca. 26 kDa. These beta-lactamases are members of the subclass B1 of metallo-beta-lactamases and are distantly related to other metalloenzymes, being most closely related to IND-1 from Chryseobacterium indologenes (42% amino acid identity). However, phylogenic analysis showed that TUS-1 and MUS-1 belong to the same phylogenic lineage of subclass B1 enzymes that groups the subclass B1 beta-lactamases of Flavobacterium species. Kinetic parameters of purified beta-lactamases TUS-1 and MUS-1 detailed their hydrolysis spectra, which encompass most beta-lactams except aztreonam. beta-Lactamases TUS-1 and MUS-1 were classified in functional subgroup 3a of metalloenzymes. This work further characterizes chromosome-encoded metalloenzymes from Flavobacteriaceae species that explain at least part of their intrinsic resistance to beta-lactams.

Amino Acid Sequence↗

PubMed2005

TLA-2, a novel Ambler class A expanded-spectrum beta-lactamase.

Beta-lactamase TLA-2 is encoded by a 47-kb plasmid isolated from an unidentified bacterial strain from a wastewater treatment plant. TLA-2 is an Ambler class A beta-lactamase that shares 52% amino acid identity with CGA-1 from Chryseobacterium gleum and 51% with TLA-1 from Escherichia coli. The enzyme hydrolyzes mostly cephalosporins.

Amino Acid Sequence↗

PubMed2006

Succession of bacterial communities during early plant development: transition from seed to root and effect of compost amendment.

Compost amendments to soils and potting mixes are routinely applied to improve soil fertility and plant growth and health. These amendments, which contain high levels of organic matter and microbial cells, can influence microbial communities associated with plants grown in such soils. The purpose of this study was to follow the bacterial community compositions of seed and subsequent root surfaces in the presence and absence of compost in the potting mix. The bacterial community compositions of potting mixes, seed, and root surfaces sampled at three stages of plant growth were analyzed via general and newly developed Bacteroidetes-specific, PCR-denaturing gradient gel electrophoresis methodologies. These analyses revealed that seed surfaces were colonized primarily by populations detected in the initial potting mixes, many of which were not detected in subsequent root analyses. The most persistent bacterial populations detected in this study belonged to the genus Chryseobacterium (Bacteroidetes) and the family Oxalobacteraceae (Betaproteobacteria). The patterns of colonization by populations within these taxa differed significantly and may reflect differences in the physiology of these organisms. Overall, analyses of bacterial community composition revealed a surprising prevalence and diversity of Bacteroidetes in all treatments.

Bacteria↗

PubMed2003

Use of a packed-column bioreactor for isolation of diverse protease-producing bacteria from antarctic soil.

Seventy-five aerobic heterotrophs have been isolated from a packed-column bioreactor inoculated with soil from Antarctica. The column was maintained at 10 degrees C and continuously fed with a casein-containing medium to enrich protease producers. Twenty-eight isolates were selected for further characterization on the basis of morphology and production of clearing zones on skim milk plates. Phenotypic tests indicated that the strains were mainly psychrotrophs and presented a high morphological and metabolical diversity. The extracellular protease activities tested were optimal at neutral pH and between 30 and 45 degrees C. 16S ribosomal DNA sequence analyses showed that the bioreactor was colonized by a wide variety of taxons, belonging to various bacterial divisions: alpha-, beta-, and gamma-Proteobacteria; the Flexibacter-Cytophaga-Bacteroides group; and high G+C gram-positive bacteria and low G+C gram-positive bacteria. Some strains represent candidates for new species of the genera Chryseobacterium and Massilia. This diversity demonstrates that the bioreactor is an efficient enrichment tool compared to traditional isolation strategies.

Antarctic Regions↗

PubMed2006

Freeze-thaw tolerance and clues to the winter survival of a soil community.

Although efforts have been made to sample microorganisms from polar regions and to investigate a few of the properties that facilitate survival at freezing or subzero temperatures, soil communities that overwinter in areas exposed to alternate freezing and thawing caused by Foehn or Chinook winds have been largely overlooked. We designed and constructed a cryocycler to automatically subject soil cultures to alternating freeze-thaw cycles. After 48 freeze-thaw cycles, control Escherichia coli and Pseudomonas chlororaphis isolates were no longer viable. Mixed cultures derived from soil samples collected from a Chinook zone showed that the population complexity and viability were reduced after 48 cycles. However, when bacteria that were still viable after the freeze-thaw treatments were used to obtain selected cultures, these cultures proved to be >1,000-fold more freeze-thaw tolerant than the original consortium. Single-colony isolates obtained from survivors after an additional 48 freeze-thaw cycles were putatively identified by 16S RNA gene fragment sequencing. Five different genera were recognized, and one of the cultures, Chryseobacterium sp. strain C14, inhibited ice recrystallization, a property characteristic of antifreeze proteins that prevents the growth of large, potentially damaging ice crystals at temperatures close to the melting temperature. This strain was also notable since cell-free medium derived from cultures of it appeared to enhance the multiple freeze-thaw survival of another isolate, Enterococcus sp. strain C8. The results of this study and the development of a cryocycler should allow further investigations into the biochemical and soil community adaptations to the rigors of a Chinook environment.

Adaptation, Physiological↗

PubMed2000

Evaluation of autoSCAN-W/A and the Vitek GNI+ AutoMicrobic system for identification of non-glucose-fermenting gram-negative bacilli.

The autoSCAN-W/A (W/A; Dade Behring Microscan Inc., West Sacramento, Calif.) and Vitek AutoMicrobic System (Vitek AMS; bioMérieux Vitek Systems, Inc., Hazelwood, Mo.) are both fully automated microbiology systems. We evaluated the accuracy of these two systems in identifying nonglucose-fermenting gram-negative bacilli. We used the W/A with conventional-panel Neg Combo type 12 and Vitek GNI+ identification systems. A total of 301 isolates from 25 different species were tested. Of these, 299 isolates were identified in the databases of both systems. The conventional biochemical methods were used for reference. The W/A correctly identified 215 isolates (71. 4%) to the species level at initial testing with a high probability of >/=85%. The Vitek GNI+ correctly identified 216 isolates (71.8%) to the species level at initial testing with a high probability of >/=90%. After additional testing that was recommended by the manufacturer's protocol, the correct identifications of the W/A and Vitek GNI+ improved to 96.0 and 92.3%, respectively. The major misidentified species were Sphingomonas paucimobilis and Agrobacterium radiobacter in the W/A system and Acinetobacter lwoffii, Chryseobacterium indologenes, and Comamonas acidovorans in the Vitek GNI+ system. The error rates were 4.0 and 7.6%, respectively. The overall accuracy for both systems was above 90% if the supplemental tests were applied. There was no significant difference in accuracy (P > 0.05) between the two systems.

Automation↗

PubMed2002

Characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of Inquilinus limosus gen. nov., sp. nov.

Using a polyphasic approach (including cellular protein and fatty acid analysis, biochemical characterization, 16S ribosomal DNA sequencing, and DNA-DNA hybridizations), we characterized 51 bacterial isolates recovered from respiratory secretions of cystic fibrosis (CF) patients. Our analyses showed that 24 isolates belong to taxa that have so far not (or only rarely) been reported from CF patients. These taxa include Acinetobacter sp., Bordetella hinzii, Burkholderia fungorum, Comamonas testosteroni, Chryseobacterium sp., Herbaspirillum sp., Moraxella osloensis, Pandoraea genomospecies 4, Ralstonia gilardii, Ralstonia mannitolilytica, Rhizobium radiobacter, and Xanthomonas sp. In addition, one isolate most likely represents a novel Ralstonia species, whereas nine isolates belong to novel taxa within the alpha-PROTEOBACTERIA: Eight of these latter isolates are classified into the novel genus Inquilinus gen. nov. as Inquilinus limosus gen. nov., sp. nov., or as Inquilinus sp. The remaining 17 isolates are characterized as members of the family ENTEROBACTERIACEAE: The recovery of these species suggests that the CF lung is an ecological niche capable of supporting the growth of a wide variety of bacteria rarely seen in clinical samples. Elucidation of the factors that account for the association between these unusual species and the respiratory tract of CF patients may provide important insights into the pathophysiology of CF infection. Because accurate identification of these organisms in the clinical microbiology laboratory may be problematic, the present study highlights the utility of reference laboratories capable of identifying unusual species recovered from CF sputum.

Alphaproteobacteria↗

PubMed2002

Evaluation of a new Etest for detecting metallo-beta-lactamases in routine clinical testing.

Several Etest (AB BIODISK, Solna, Sweden) gradient formats were developed for detection of metallo-beta-lactamases based on the reduction of imipenem (IP) or ceftazidime (TZ) MICs in the presence of EDTA or 2-mercaptopropionic acid (MPA). The Etest metallo-beta-lactamase (Etest MBL) strips consisted of a double-sided seven-dilution range of IP or TZ (4 to 256 microg/ml) and IP or TZ (1 to 64 microg/ml) overlaid with a constant concentration of EDTA or MPA. The prototype strips were evaluated on several agar media (brain heart infusion agar, Isosensitest agar, nutrient agar, and Mueller-Hinton agar for aerobes and brucella blood agar for anaerobes) with 138 challenge strains: Acinetobacter spp. (n = 9), Aeromonas spp. (n = 8), Chryseobacterium spp. (n = 28), Escherichia coli (n = 1), Klebsiella pneumoniae (n = 4), Pseudomonas aeruginosa (n = 14), Proteus mirabilis (n = 3), Serratia spp. (n = 10), Stenotrophomonas maltophilia (n = 43), Sphingobacterium spp. (n = 3), and Bacteroides fragilis group (n = 15). PCR analysis using specific primers for IMP-1, L1, CcrA, and bla(B/C) confirmed the presence of the metallo-beta-lactamase genes. Enzyme assays were also performed with IP as an indicator substrate followed by EDTA inhibition profiles. EDTA was found to be a better inhibitor of metallo-beta-lactamases, especially for anaerobes. IP was a better than TZ. Mueller-Hinton agar was the preferred medium, particularly when compared to Isosensitest agar, which frequently produced falsely low MICs for IP. Etest IP plus IP-EDTA with Mueller-Hinton agar had a sensitivity of 94% (79 of 84) and specificity of 95% (124 of 130). The Etest MBL strip appears to be an acceptable diagnostic reagent to detect metallo-beta-lactamase phenotypes in the clinical microbiology laboratory.

Anti-Bacterial Agents↗

PubMed2024

Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.

UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields. IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.

Saccharum↗