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Microbial Genomics Mar 2024spp. are associated with a number of infectious syndromes in humans including gastroenteritis and dysentery. Our understanding of the genetic diversity, population...
spp. are associated with a number of infectious syndromes in humans including gastroenteritis and dysentery. Our understanding of the genetic diversity, population structure, virulence determinants and antimicrobial resistance of the genus has been limited by a lack of sequenced genomes linked to metadata. We performed a comprehensive analysis of the whole genome sequences of 447 isolates from children in Karachi, Pakistan, with moderate-to-severe diarrhoea (MSD) and from matched controls without diarrhoea that were collected as part of the Global Enteric Multicenter Study (GEMS). Human-associated isolates exhibited high species diversity and extensive antimicrobial and virulence gene content. , , and were all significantly associated with MSD in at least one cohort group. The and genes that encode components of polar and lateral flagella, respectively, exhibited a weak association with isolates originating from cases of gastroenteritis.
Topics: Child; Humans; Aeromonas; Genomics; Diarrhea; Gastroenteritis; Anti-Infective Agents; Genetic Variation
PubMed: 38451244
DOI: 10.1099/mgen.0.001211 -
Antibiotics (Basel, Switzerland) Feb 2024spp. are environmental bacteria able to infect animals and humans. Here, we aim to evaluate the role of biofilms in persistence in freshwater. were isolated from...
spp. are environmental bacteria able to infect animals and humans. Here, we aim to evaluate the role of biofilms in persistence in freshwater. were isolated from water and biofilm samples and identified by Vitek-MS and sequencing. Antibiotic susceptibility profiles were determined according to EUCAST, and a crystal violet assay was used to assess biofilm assembly. MTT and the enumeration of colony-forming units were used to evaluate biofilm and planktonic susceptibility to chlorination, respectively. Identification at the species level was challenging, suggesting the need to improve the used methodologies. Five different species (, , , and ) were identified from water, and one species was identified from biofilms (). and presented resistance to different antibiotics, whith the highest resistance rate observed for (multiple antibiotic resistance index of 0.25). Of the 21 isolates, 11 were biofilm producers, and 10 of them were strong biofilm producers (SBPs). The SBPs presented increased tolerance to chlorine disinfection when compared with their planktonic counterparts. In order to elucidate the mechanisms underlying biofilm tolerance to chlorine and support the importance of preventing biofilm assembly in water reservoirs, further research is required.
PubMed: 38391552
DOI: 10.3390/antibiotics13020166 -
Cureus Jan 2024-associated ulcerative colitis flare is sparsely reported in the literature but is a treatable condition with antibiotics including trimethoprim/sulfamethoxazole...
-associated ulcerative colitis flare is sparsely reported in the literature but is a treatable condition with antibiotics including trimethoprim/sulfamethoxazole (TMP-SMX), fluoroquinolones, and second/third-generation cephalosporins. We report a case of a patient with long-standing ulcerative colitis (UC), who presented with bloody stools, fatigue, and oliguria that did not respond to standard regimen including steroids. The lab finding was significant for leukocytosis and anemia. was cultured in the stool specimens. The patient was started on ciprofloxacin with marked improvement of symptoms on the second day of initiation of the antibiotic. Although rare, a possible Aeromonas infection should be suspected in patients presenting with a flare of ulcerative colitis. A prompt initiation of treatment can provide rapid improvement in clinical status of these patients.
PubMed: 38344629
DOI: 10.7759/cureus.52010 -
BMC Genomics Feb 2024DNA N6-methyladenosine (6mA), as an important epigenetic modification, widely exists in bacterial genomes and participates in the regulation of toxicity, antibiotic...
BACKGROUND
DNA N6-methyladenosine (6mA), as an important epigenetic modification, widely exists in bacterial genomes and participates in the regulation of toxicity, antibiotic resistance, and antioxidant. With the continuous development of sequencing technology, more 6mA sites have been identified in bacterial genomes, but few studies have focused on the distribution characteristics of 6mA at the whole-genome level and its association with gene expression and function.
RESULTS
This study conducted an in-depth analysis of the 6mA in the genomes of two pathogenic bacteria, Aeromonas veronii and Helicobacter pylori. The results showed that the 6mA was widely distributed in both strains. In A. veronii, 6mA sites were enriched at 3' end of protein-coding genes, exhibiting a certain inhibitory effect on gene expression. Genes with low 6mA density were associated with cell motility. While in H. pylori, 6mA sites were enriched at 5' end of protein-coding genes, potentially enhancing gene expression. Genes with low 6mA density were closely related to defense mechanism.
CONCLUSIONS
This study elucidated the distribution characteristics of 6mA in A. veronii and H. pylori, highlighting the effects of 6mA on gene expression and function. These findings provide valuable insights into the epigenetic regulation and functional characteristics of A. veronii and H. pylori.
Topics: Helicobacter pylori; Epigenesis, Genetic; Aeromonas veronii; DNA; Adenosine; DNA Methylation
PubMed: 38331763
DOI: 10.1186/s12864-024-10074-y -
Microorganisms Jan 2024This study aimed to characterize 300 spp. strains isolated from 123 ornamental fish of 32 different species presenting with septicemia, skin lesions, and/or eye...
This study aimed to characterize 300 spp. strains isolated from 123 ornamental fish of 32 different species presenting with septicemia, skin lesions, and/or eye lesions. Within the 300 strains, 53.0% were identified as , 41.3% as , and 5.7% as . Among the six virulence genes investigated, the most frequent were (90.3%) and (79.3%). More than 50% of strains were positive for all the studied genes. A total of 30 virulence profiles were identified, with the five main profiles identified comprising 75% of strains. Only five strains were negative for all genes and were identified as and . The antimicrobial susceptibility profile was performed for 234 strains, with sulfonamides presenting more than 50% of the resistance rates. Susceptibility was observed mainly for cephalosporins, aminoglycosides, chloramphenicol and piperacillin-tazobactam. Multidrug resistance was detected in 82.5% of the studied strains, including with 100% multidrug resistance, and with 90.9% multidrug resistance. The SE-AFLP analysis resulted in 66 genotypes of , 118 genotypes of , and 14 genotypes of , demonstrating the greater heterogeneity of and A. . However, no direct correlation was observed between the genotypes and the strains' origins or virulence and resistance profiles.
PubMed: 38258002
DOI: 10.3390/microorganisms12010176 -
Animals : An Open Access Journal From... Jan 2024The ubiquitous Gram-negative bacterial pathogen () can easily cause inflammatory reactions in aquatic organisms, resulting in high mortality and huge economic losses....
The ubiquitous Gram-negative bacterial pathogen () can easily cause inflammatory reactions in aquatic organisms, resulting in high mortality and huge economic losses. MicroRNAs (miRNAs) participate in immune regulation and have certain conserved properties. MiRNAs are involved in the immune responses of a variety of teleost fish infected with bacteria, whereas there is no related report in silver carp (). Therefore, we identified the expression profiles of miRNA in silver carp stimulated by and LPS. Among them, the quantity of differentially expressed miRNAs (DEmiRNAs) obtained in the silver carp challenge group was 73 () and 90 (LPS). The GO enrichment and analysis of KEGG pathways have shown that the predicted target genes are mainly associated with lipid metabolism and the immune response in silver carp. This indicates the possibility that miRNAs play a role in regulating immune-related pathways. In addition, a total of eight DEmiRNAs validated the accuracy of the sequencing result via quantitative real-time PCR (qRT-PCR). Finally, we selected the silver carp head kidney macrophage cells (HKCs) as model cells and proved that miR-30b-5p can regulate the inflammatory response in silver carp HKCs. This study lays the foundation for exploring miRNA regulation in silver carp during pathogenic bacterial infection. In addition, it provides a reference for the future development of non-coding RNA antibacterial drugs.
PubMed: 38254454
DOI: 10.3390/ani14020285 -
BMC Veterinary Research Jan 2024Aeromonas species are one of the most important etiologies of diseases in fish farms, leading to clinical manifestation and mortality and are associated with public...
BACKGROUND
Aeromonas species are one of the most important etiologies of diseases in fish farms, leading to clinical manifestation and mortality and are associated with public health risks. This study aimed to investigate the prevalence, phenotypic and molecular characteristics of Aeromonas species isolated from farmed Clarias gariepinus using 16 S rRNA sequencing. Additionally, their antibiogram and multiple antibiotic resistance index were determined using a disc diffusion test.
RESULTS
A total of 230 Aeromonas strains were isolated from Clarias gariepinus with 40.9% obtained from diseased fish, and 25% isolated from apparently healthy ones. Five different species including Aeromonas caviae, Aeromonas veronii, Aeromonas hydrophila, Aeromonas dhakensis and Aeromonas enteropelogenes were fully identified and genetically characterized. Based on the available literature, this is the first report of Aeromonas enteropelogenes from the study area. The phylogenetic analysis showed genetic heterogeneity and distance within the species and the reference strains. The multiple resistant Aeromonas species were susceptible to ciprofloxacin, gentamycin, and florfenicol. The Aeromonas species' multiple antibiotic resistance index values varied between 0.20 and 0.80 and were isolated from the farms where antibiotics were intensively used.
CONCLUSIONS
The diversity of multidrug-resistant Aeromonas species isolated from fish farms is a major threat to fish production giving us more understanding of epidemiology and the multidrug Aeromonas species with a MAR index of greater than 0.2 were isolated from farms where antibiotic use was widespread. As a result, a considerably increased danger of multiple antibiotic resistance spreading to the fish culture environment may impact aquaculture production. Hence there is a need for appropriate and monitored drug usage.
Topics: Animals; Catfishes; Phylogeny; Aeromonas; Drug Resistance, Microbial; Anti-Bacterial Agents
PubMed: 38184574
DOI: 10.1186/s12917-023-03860-5 -
PloS One 2024The presence of carbapenem-resistant bacteria and carbapenem resistance genes (CRGs) in livestock is increasing. To evaluate the presence of carbapenemase-producing...
The presence of carbapenem-resistant bacteria and carbapenem resistance genes (CRGs) in livestock is increasing. To evaluate the presence of carbapenemase-producing Enterobacteriaceae (CPE) and the main CRGs along swine food chains of the Marche Region (Central Italy), samples of faeces, feed, and animal-food derived products were collected from seven small/medium, medium, and large-scale pig farms. A total of 191 samples were analysed using a culture-dependent method, with the aim of isolating CPE. Isolates were analysed for their resistance to carbapenems using a modified Hodge test and the microdilution method for the minimum inhibitory concentration (MIC) determination. Moreover, the extraction of microbial DNA from each sample was performed to directly detect selected CRGs via qPCR. Among the 164 presumptive resistant isolates, only one strain from a liver sample, identified as Aeromonas veronii, had an ertapenem MIC of 256 μg/mL and carried a carbapenemase- (cphA) and a β-lactamase- (blaOXA-12) encoding genes. A low incidence of CRGs was found; only nine and four faecal samples tested positive for blaNDM-1 and blaOXA-48, respectively. Overall, the importance of monitoring CPE and CRGs in livestock and their food chains should be stressed to control all potential non-human CPE and CRGs reservoirs and to determine safety levels for human health.
Topics: Animals; Swine; Food Chain; Bacteria; Carbapenem-Resistant Enterobacteriaceae; Carbapenems; Italy; Livestock
PubMed: 38181018
DOI: 10.1371/journal.pone.0296098 -
MBio Feb 2024Many pathogenic Gram-negative bacteria use repeats-in-toxin adhesins for colonization and biofilm formation. In the cholera agent , flagellar-regulated hemagglutinin A...
Many pathogenic Gram-negative bacteria use repeats-in-toxin adhesins for colonization and biofilm formation. In the cholera agent , flagellar-regulated hemagglutinin A (FrhA) enables these functions. Using bioinformatic analysis, a sugar-binding domain was identified in FrhA adjacent to a domain of unknown function. AlphaFold2 indicated the boundaries of both domains to be slightly shorter than previously predicted and assisted in the recognition of the unknown domain as a split immunoglobulin-like fold that can assist in projecting the sugar-binding domain toward its target. The AlphaFold2-predicted structure is in excellent agreement with the molecular envelope obtained from small-angle X-ray scattering analysis of a recombinant construct spanning the sugar-binding and unknown domains. This two-domain construct was probed by glycan micro-array screening and showed binding to mammalian fucosylated glycans, some of which are characteristic erythrocyte markers and intestinal cell epitopes. Isothermal titration calorimetry further showed the construct-bound l-fucose with a of 21 µM. Strikingly, this recombinant protein construct bound and lysed erythrocytes in a concentration-dependent manner, and its hemolytic activity was blocked by the addition of l-fucose. A protein ortholog construct from was also produced and showed a similar glycan-binding pattern, binding affinity, erythrocyte-binding, and hemolytic activities. As demonstrated here with Hep-2 cells, fucose-based inhibitors of this sugar-binding domain can potentially be developed to block colonization by and other pathogenic bacteria that share this adhesin domain.IMPORTANCEThe bacterium, , which causes cholera, uses an adhesion protein to stick to human cells and begin the infection process. One part of this adhesin protein binds to a particular sugar, fucose, on the surface of the target cells. This binding can lead to colonization and killing of the cells by the bacteria. Adding l-fucose to the bacteria before they bind to the human cells can prevent attachment and has promise as a preventative drug to protect against cholera.
Topics: Animals; Humans; Vibrio cholerae; Cholera; Aeromonas veronii; Fucose; Adhesins, Bacterial; Polysaccharides; Toxins, Biological; Sugars; Mammals
PubMed: 38171003
DOI: 10.1128/mbio.02291-23 -
Open Forum Infectious Diseases Dec 2023The genus is increasingly implicated in human infections, but knowledge of its clinical characteristics and antimicrobial resistance profiles has been limited owing to...
BACKGROUND
The genus is increasingly implicated in human infections, but knowledge of its clinical characteristics and antimicrobial resistance profiles has been limited owing to its complex taxonomy.
METHODS
We conducted a multicenter prospective cohort study of patients with infections at hospitals across Japan. Patients were eligible for inclusion if they had an spp. strain in a clinical culture and were considered infected at the culture site. Clinical data were collected, and isolates underwent susceptibility testing and whole-genome sequencing.
RESULTS
A total of 144 patients were included. Hepatobiliary infection accounted for a majority of infections (73% [105 of 144]), which mostly occurred in elderly patients with comorbid conditions, including hepatobiliary complications. The all-cause 30-day mortality rate was 10.0% (95% confidence interval, 4.9%-14.8%). By whole-genome sequencing, 141 strains (98%) belonged to 4 species, , , and with significant intraspecies diversity. was predominant in all infection sites except skin and soft tissue, for which was the prevailing species. The genes encoding chromosomally mediated class B, C, and D β-lactamases were harbored by 92%-100% of the isolates in a species-specific manner, but they often lacked association with resistance phenotypes. The activity of cefepime was reliable. All isolates of and carried an like colistin resistance gene and showed reduced susceptibility to colistin.
CONCLUSIONS
Hepatobiliary tract was the most common infection site of spp., with being the dominant causative species. The resistance genotype and phenotype were often incongruent for β-lactam agents.
PubMed: 38156048
DOI: 10.1093/ofid/ofad587