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Journal of Industrial Microbiology &... Feb 2014The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining... (Review)
Review
The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining bacterial secondary metabolism in the framework of its ecological niche, insights into the upregulation of orphan biosynthetic pathways and the enhancement of the enzyme substrate supply can be obtained, leading to the discovery of new secondary metabolic pathways that would otherwise be silent or undetected under typical laboratory cultivation conditions. Access to these new natural products (i.e., the chemotypes) facilitates experimental genotype-to-phenotype linkages. Here, we describe certain functional natural products produced by Xenorhabdus and Photorhabdus bacteria with experimentally linked biosynthetic gene clusters as illustrative examples of the synergy between chemical ecology and bacterial genome mining in connecting genotypes to phenotypes through chemotype characterization. These Gammaproteobacteria share a mutualistic relationship with nematodes and a pathogenic relationship with insects and, in select cases, humans. The natural products encoded by these bacteria distinguish their interactions with their animal hosts and other microorganisms in their multipartite symbiotic lifestyles. Though both genera have similar lifestyles, their genetic, chemical, and physiological attributes are distinct. Both undergo phenotypic variation and produce a profuse number of bioactive secondary metabolites. We provide further detail in the context of regulation, production, processing, and function for these genetically encoded small molecules with respect to their roles in mutualism and pathogenicity. These collective insights more widely promote the discovery of atypical orphan biosynthetic pathways encoding novel small molecules in symbiotic systems, which could open up new avenues for investigating and exploiting microbial chemical signaling in host-bacteria interactions.
Topics: Biological Products; Biosynthetic Pathways; Ecological and Environmental Phenomena; Enterobacteriaceae; Genome, Bacterial; Photorhabdus; Secondary Metabolism; Symbiosis
PubMed: 24127069
DOI: 10.1007/s10295-013-1356-5 -
The American Journal of Case Reports Mar 2021BACKGROUND Leclercia adecarboxylata is a gram-negative rod, which is normally found in water and food. It is an emerging pathogen that affects immunocompromised...
BACKGROUND Leclercia adecarboxylata is a gram-negative rod, which is normally found in water and food. It is an emerging pathogen that affects immunocompromised patients, including patients with hematological malignancies or those receiving chemotherapy. Generally, L. adecarboxylata is considered a low-virulence pathogen with an excellent susceptibility profile, but some strains may be resistant to multiple antibiotics, such as b-lactams. Moreover, L. adecarboxylata is usually isolated as a part of polymicrobial cultures in immunocompetent individuals, but there have been cases where it was the only isolate. CASE REPORT A 74-year-old woman who was non-immunosuppressed and had multiple comorbidities was admitted with acute decompensated heart failure due to pneumonia. She was treated with multiple courses of antibiotics including amoxicillin-clavulanate and ciprofloxacin for pneumonia, but her infection worsened, and she had cardiopulmonary arrest. After resuscitation, she was stable for several days but suddenly became confused and hypotensive. The septic screen showed L. adecarboxylata bacteremia without a clear source, which was treated successfully with meropenem for 14 days. After the meropenem course, the patient developed diarrhea and was found to have severe Clostridium difficile infection. She did not respond to oral vancomycin and intravenous metronidazole and died. CONCLUSIONS This case illustrated an infection in a non-immunosuppressed individual by an organism that is considered an opportunistic pathogen, mainly affecting immunocompromised patients. The patient's blood culture grew L. adecarboxylata, which was sensitive to all antibiotics but resolved with meropenem treatment. Owing to increasing L. adecarboxylata infections, we recommend further studies to understand the organism's pathogenesis, risk factors, and resistance pattern.
Topics: Aged; Anti-Bacterial Agents; Bacteremia; Enterobacteriaceae; Enterobacteriaceae Infections; Female; Humans; Immunocompromised Host
PubMed: 33782375
DOI: 10.12659/AJCR.929537 -
Diagnostic Microbiology and Infectious... Nov 2013In the past 2 decades, we have observed a rapid increase of infections due to multidrug-resistant Enterobacteriaceae. Regrettably, these isolates possess genes encoding... (Review)
Review
In the past 2 decades, we have observed a rapid increase of infections due to multidrug-resistant Enterobacteriaceae. Regrettably, these isolates possess genes encoding for extended-spectrum β-lactamases (e.g., blaCTX-M, blaTEM, blaSHV) or plasmid-mediated AmpCs (e.g., blaCMY) that confer resistance to last-generation cephalosporins. Furthermore, other resistance traits against quinolones (e.g., mutations in gyrA and parC, qnr elements) and aminoglycosides (e.g., aminoglycosides modifying enzymes and 16S rRNA methylases) are also frequently co-associated. Even more concerning is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (e.g., blaKPC, blaNDM). Therefore, the spread of these pathogens puts in peril our antibiotic options. Unfortunately, standard microbiological procedures require several days to isolate the responsible pathogen and to provide correct antimicrobial susceptibility test results. This delay impacts the rapid implementation of adequate antimicrobial treatment and infection control countermeasures. Thus, there is emerging interest in the early and more sensitive detection of resistance mechanisms. Modern non-phenotypic tests are promising in this respect, and hence, can influence both clinical outcome and healthcare costs. In this review, we present a summary of the most advanced methods (e.g., next-generation DNA sequencing, multiplex PCRs, real-time PCRs, microarrays, MALDI-TOF MS, and PCR/ESI MS) presently available for the rapid detection of antibiotic resistance genes in Enterobacteriaceae. Taking into account speed, manageability, accuracy, versatility, and costs, the possible settings of application (research, clinic, and epidemiology) of these methods and their superiority against standard phenotypic methods are discussed.
Topics: Enterobacteriaceae; Enterobacteriaceae Infections; Humans; Mass Spectrometry; Microbial Sensitivity Tests; Molecular Diagnostic Techniques
PubMed: 24091103
DOI: 10.1016/j.diagmicrobio.2013.06.001 -
PloS One 2021We studied the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in dairy calves as part of a routine health check protocol. In...
We studied the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in dairy calves as part of a routine health check protocol. In addition, data regarding antimicrobial use (AMU), farm hygiene, and farm management were collected in order to identify possible risks for ESBL occurrence. Ten farms participated in the study with a median of 781 milking cows (319-1701). All calves investigated were younger than two weeks with an average age of 6.8 (±3.9) days. The farms were visited and samples were collected twice at an interval of 7-11 months. Faecal samples diluted 1:10, were plated onto BrillianceTM ESBL agar in duplicates. After 24 hours at 37°C, colonies were counted and total colony forming units (cfu)/ml calculated. Bacteria species were identified biochemically. ESBL-production was phenotypically confirmed using the MICRONAUT-S β-Lactamases system. Additionally, antimicrobial susceptibility was tested using VITEK® 2 technology. Phylotyping of E. coli isolates and screening for bla genes was performed by PCR. ESBL-producing enterobacteria were detected on all farms and 96.5% of calves investigated shed ESBL-positive bacteria. Of all ESBL-producing isolates, the majority were E. coli (92.9%), followed by Enterobacter cloacae (5.1%) and Klebsiella pneumoniae subsp. pneumoniae (2.0%). The majority of E. coli isolates was clearly assigned to phylogroup C (25.0%), followed by phylogroups A (15.2%) and E (14.1%). CTX-M group 1 was most frequently detected (80.4%). E. cloacae contained blaCTX-M and blaTEM or blaSHV. K. pneumoniae harboured blaSHV only. Besides resistance to penicillins and cephalosporins, the majority of isolates was also resistant to one or more antibiotic classes, with a high proportion being resistant against fluoroqinolones. 52.5% of isolates were further characterised as threefold multidrug resistant gram-negative bacteria (3MDR-GNB) according to the German Commission for Hospital Hygiene and Infection Prevention. None of the isolates were 4MDR-GNB, i.e. none revealed carbapenem-resistance. Penicillins were the most frequently administered antibiotics to calves on most farms and were the predominant substance class at herd level on all farms. Overall, the number of calves treated prior to sampling was rather low (11.7%). Analyses of data regarding the farm management identified weaknesses in biosecurity and cleaning and disinfection. Besides beta-lactam antibiotics being the most commonly used antibiotics no other risk factors could be identified. In summary, the prevalence of ESBL-carriers in dairy calves was exceptionally high and should be motivation to develop strategies for the reduction of multidrug-resistant bacteria in farm animals.
Topics: Animals; Animals, Newborn; Cattle; Drug Resistance, Multiple, Bacterial; Enterobacteriaceae; Female
PubMed: 33711073
DOI: 10.1371/journal.pone.0248291 -
Microbiology (Reading, England) Apr 2024is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted as an emerging pathogen harbouring virulence and...
is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted as an emerging pathogen harbouring virulence and resistance determinants. Little information exists on virulence and resistance determinants in strains isolated from environmental, food, and clinical samples. To determine the presence of resistance and virulence determinants and plasmid features in strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship. All strains tested showed resistance to β-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of , the resistance phenotype was only observed in 50 % of the strains; was the most prevalent BLEE gene (70 %), while the quinolone gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains. is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.
Topics: Anti-Bacterial Agents; Plasmids; Virulence; Microbial Sensitivity Tests; Enterobacteriaceae; Phylogeny; Virulence Factors; Humans; Enterobacteriaceae Infections; Phenotype; Drug Resistance, Bacterial; Quinolones; beta-Lactams; Drug Resistance, Multiple, Bacterial; Food Microbiology
PubMed: 38661713
DOI: 10.1099/mic.0.001457 -
International Journal of Infectious... Nov 2020Members of the bacterial genus Cedecea cause acute infections worldwide in compromised hosts with serious underlying medical conditions. While global reports of Cedecea... (Review)
Review
Members of the bacterial genus Cedecea cause acute infections worldwide in compromised hosts with serious underlying medical conditions. While global reports of Cedecea infections remain sporadic in the medical literature, cases of multidrug-resistant clinical isolates have been documented each year over the past decade, warranting a comprehensive update on this emerging opportunistic pathogen. Here, we review the clinical manifestations, pathogenesis, natural distribution, epidemiology, and antimicrobial resistance of Cedecea species. Acute infection commonly manifests as bacteremia and pneumonia; however, the spectrum of infectious pathologies associated with Cedecea has expanded to include oral and cutaneous ulcers, orbital cellulitis, and peritonitis. The frequency of resistance among reported clinical isolates was highest to ampicillin, cephalothin, cefoxitin, cefazolin, and ceftazidime. Cedecea isolates harboring metallo-β-lactamases exhibited resistance to carbapenems and fourth-generation cephalosporins. Further research is needed to understand the pathogenicity and multidrug resistance of Cedecea species. Appropriate therapeutic management of Cedecea infections depends on antibiotic susceptibility testing because of variable resistance patterns and the enhanced infection risk in vulnerable populations.
Topics: Animals; Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Enterobacteriaceae; Enterobacteriaceae Infections; Humans
PubMed: 32950733
DOI: 10.1016/j.ijid.2020.09.036 -
Applied Microbiology Nov 1970A medium designed for detection of motility, indole, and ornithine decarboxylase production in one tube was devised and evaluated. Results, using 182 strains of...
A medium designed for detection of motility, indole, and ornithine decarboxylase production in one tube was devised and evaluated. Results, using 182 strains of Enterobacteriaceae, were the same as obtained with commonly used standard methods, although 11 of 87 positive indole tests were weak with the new medium.
Topics: Bacteriological Techniques; Carboxy-Lyases; Culture Media; Enterobacteriaceae; Indoles; Ornithine
PubMed: 4922086
DOI: 10.1128/am.20.5.849-850.1970 -
Annals of the Academy of Medicine,... Aug 2021
Topics: Anti-Bacterial Agents; Bacteremia; Enterobacteriaceae; Hospitals; Humans; Singapore
PubMed: 34472560
DOI: 10.47102/annals-acadmedsg.202195 -
The Journal of Antimicrobial... Aug 2017International data on the molecular epidemiology of Enterobacteriaceae with VIM carbapenemases are limited.
BACKGROUND
International data on the molecular epidemiology of Enterobacteriaceae with VIM carbapenemases are limited.
METHODS
We performed short read (Illumina) WGS on a global collection of 89 VIM-producing clinical Enterobacteriaceae (2008-14).
RESULTS
VIM-producing (11 varieties within 21 different integrons) isolates were mostly obtained from Europe. Certain integrons with bla VIM were specific to a country in different species and clonal complexes (CCs) (In 87 , In 624 , In 916 and In 1323 ), while others had spread globally among various Enterobacteriaceae species (In 110 and In 1209 ). Klebsiella pneumoniae was the most common species ( n = 45); CC147 from Greece was the most prevalent clone and contained In 590 -like integrons with four different bla VIM s. Enterobacter cloacae complex was the second most common species and mainly consisted of Enterobacter hormaechei ( Enterobacter xiangfangensis , subsp. steigerwaltii and Hoffmann cluster III). CC200 (from Croatia and Turkey), CC114 (Croatia, Greece, Italy and the USA) and CC78 (from Greece, Italy and Spain) containing bla VIM-1 were the most common clones among the E. cloacae complex.
CONCLUSIONS
This study highlights the importance of surveillance programmes using the latest molecular techniques in providing insight into the characteristics and global distribution of Enterobacteriaceae with bla VIM s.
Topics: Bacterial Proteins; Enterobacteriaceae; Enterobacteriaceae Infections; Epidemiological Monitoring; Global Health; Humans; Molecular Epidemiology; beta-Lactamases
PubMed: 28520983
DOI: 10.1093/jac/dkx148 -
BMC Infectious Diseases Feb 2021This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in...
BACKGROUND
This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN).
METHODS
For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase-encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary.
RESULTS
All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for bla, bla, and bla genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The bla gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains.
CONCLUSION
We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.
Topics: Anti-Bacterial Agents; Bacteremia; Carbapenem-Resistant Enterobacteriaceae; Child; Disease Outbreaks; Enterobacteriaceae; Enterobacteriaceae Infections; Genome, Bacterial; Hospitals; Humans; Mexico; Microbial Sensitivity Tests; Multilocus Sequence Typing; Parenteral Nutrition, Total; Phylogeny; beta-Lactamases
PubMed: 33639886
DOI: 10.1186/s12879-021-05923-0