Species Of Enterobacteriaceae Research Articles

Antibiotic resistance profiles of sentinel bacteria isolated from aquaculture in Cambodia

ABSTRACT The misuse of antibiotics and the emergence of antimicrobial resistance (AMR) is a concern in the aquaculture industry because it contributes to global health risks and impacts the environment. This study analyzed the AMR of sentinel bacteria associated with striped catfish (Pangasianodon hypophthalmus) and giant snakehead (Channa micropeltes), the two main fish species reared in the pond culture in Cambodia. Phenotypic and genotypic characterization of the recovered isolates from fish, water, and sediment revealed the presence of bacteria, such as 22 species belonging to families Aeromonadaceae, Enterobacteriaceae, and Pseudomonadaceae. Among 48 isolates, Aeromonas caviae (n = 2), Aeromonas hydrophila (n = 2), Aeromonas ichthiosmia (n = 1), and Aeromonas salmonicida (n = 4) were detected. Both A. salmonicida and A. hydrophila are known as fish pathogens that occur worldwide in both fresh and marine water aquaculture. Antibiotic susceptibility testing for Enterobacteriaceae and Pseudomonadaceae species and six antibiotics for Aeromonadaceae species revealed antibiotic resistance patterns of 24 (50%) isolates among the 48 isolates with higher multiple antibiotic resistance index scores (>0.2). All the isolates of Enterobacteriaceae were susceptible to ciprofloxacin. Ciprofloxacin is a frontline antibiotic that is not recommended for use in aquaculture. This study expands our knowledge of the AMR status in aquaculture farms, which is very limited in Cambodia.

Evaluation of epiphytic microbiota in red clover and alfalfa on silage fermentation products, bacterial community diversity and functionality of oat

Abstract The purpose of this experiment was to evaluate the contribution of epiphytic microbiota on alfalfa (AL), oat (OT), and red clover (RC) to ensiling characteristics and bacterial community diversity of oat. With the irradiation of γ-ray, sterile OT (~233 g/kg dry matter (DM)) was inoculated by sterile water (STOT), epiphytic microbiota from OT (OTOT), AL (OTAL) and RC (OTRC), respectively. Triplicate silage-bags for each treatment were sampled after different days (1, 3, 7, 15, 30 and 60) of fermentation, respectively. Similar chemical compositions were found between fresh oat and STOT. Lower (P < 0.05) contents of ammonia nitrogen (NH3-N) and higher (P < 0.05) accumulation of lactic acid were found in OTAL compared with OTRC and OTOT on day 3. The greatest (P < 0.05) NH3-N, acetic acid concentrations and pH and the lowest (P < 0.05) concentration of lactic acid were found in OTRC on day 60. After 3 days of ensiling, Lactobacillus accounted for a big proportion in OTAL and OTOT, and Hafnia-Obesumbacterium was predominant in OTRC. The bacterial communities in OTAL and OTOT had lower (P < 0.05) abundances of ‘Genetic Information Processing’ than OTRC after 3 days. Overall, the composition, diversity, and activity of epiphytic microbiota can notably influence the ensiling characteristics of forage oat. The lactic acid bacteria (hetero-fermentative type) and Enterobacteriaceae species played an important role in producing ethanol contents during the ensiling of forage oat.

Phenotypic and Genotyping Identification of Extended Spectrum Beta-Lactamase (ESBL) Producing Enterobacteriaceae Obtained from Animal Fecal Samples within Owerri Metropolis

Background: One of the major means for the spread or distribution of antibiotic resistance is through animal, either by consumption or as companions. Most of the antibiotic resistant bacteria investigated have been reported to exhibit multidrug resistance which can either be acquired or natural. The present study was targeted at investigating the epidemiology of extended spectrum beta-lactamase-producing Enterobacteriaceae. Using stratified randomized sample design, three hundred (n = 300) fecal samples [of cattle, and goats (n = 150 for each)] were collected from various abattoir in Owerri metropolis. The isolation, purification, and antibiotic sensitivity were carried out using standard procedures. The resistant genes were investigated using forward and reverse primers specific for the following genes blaTEM, blaCTX-M, and blaSHV.
 Results: The result showed 97.67 % growth of Enterobacteriaceae. The highest Enterobacteriaceae isolated was in cattle fecal sample (61.00 %), while 2.33 % of the total samples did not show any growth for Enterobacteriaceae. Only three Enterobacteriaceae species were identified: Escherichia coli, Proteus vulgaris, and Klebsiella pneumonia. Escherichia coli was the most abundant Enterobacteriaceae (42.32 %) and P. vulgaris was the least abundant (23.89 %). The isolates showed multiple resistances to most of the antibiotics tested. All the isolates were susceptible to Imipenem (IPM). The molecular characterization showed the presence of the three genes (blaTEM, blaCTX-M, and blaSHV) investigated. The blaCTX gene-band was the most prevalent (72.22 %) while the blaSHV gene-band was the lowest prevalent resistant gene (61.11 %).
 Conclusion: It was concluded that the genes: blaTEM, blaCTX-M, and blaSHV were present in Enterobacteriaceae species (K. pneumoniae, P. vulgaris, and E. coli) isolated from abattoir in Owerri metropolis, Imo State.

A15 LEVERAGING CULTURE-DEPENDENT AND -INDEPENDENT METAGENOMICS TO IDENTIFY ENTEROBACTERIACEAE GENES ASSOCIATED WITH ACTIVE ULCERATIVE COLITIS

Abstract Background Ulcerative colitis (UC) is a type of inflammatory bowel disease (IBD) that is restricted to the large intestine and is characterized by mucosal inflammation. There is evidence that pathogenic bacteria contribute to UC pathogenesis in at least some patients and the bacterial family Enterobacteriaceae are prime suspects. Some strains of Enterobacteriaceae carry virulence genes important for colonizing the gut (e.g. fimH) and disrupting the intestinal epithelium (e.g. hemolysins). We hypothesize that key virulence genes carried by strains of many Enterobacteriaceae species contribute to disease activity in some UC patients. As we predict virulence genes are strain-specific, the detection of the species alone (e.g. Escherichia coli) is insufficient to predict pathogenic potential and this has confounded previous studies to identify infectious agents in UC. Aims We aim to use culture-dependent and -independent sequencing approaches to identify Enterobacteriaceae genes in the UC gut microbiome associated with active disease. Methods UC patient stool samples collected throughout enrolment in randomized control trials of fecal microbiota transplantation (FMT) for adult UC (n=10) and microbiome studies in early-onset pediatric UC (n=25) were cultured on MacConkey (MAC) agar to enrich for Enterobacteriaceae. Strains were isolated from baseline stool samples cultured on MAC agar for whole genome sequencing and virulence gene characterization. Baseline and post-treatment stool samples cultured on MAC agar were sent for metagenomic sequencing. Using a subset of 11 pediatric patients, I developed a metagenomic pipeline to identify Enterobacteriaceae genes enriched during active UC compared to periods of remission or milder disease. Results Known virulence genes, including fimH and hemolysins, were present in some strains across multiple Enterobacteriaceae species. Using an unbiased metagenomic approach with the pediatric cohort, we identified 42 genes enriched at baseline with the criteria they must be elevated in at least three of the 11 patients. The majority of the 42 genes were distributed into six gene clusters, including a small plasmid. Conclusions Our approach allows us to identify genes enriched in active UC that have not been previously described in the literature and our analysis will be repeated with our adult cohort. Genes that are enriched in active UC in the pediatric and/or adult cohort will be validated in publicly available metagenomic datasets that consist of both IBD patients and healthy controls. Furthermore, culture-dependent approaches allow us to test mechanisms in vivo that are informed by our bioinformatics. Leveraging microbiome and clinical data provides a unique window to guide future diagnostics and treatments to improve outcomes for UC patients. Funding Agencies CIHROGS

A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital

Reports of nosocomial infections typically describe recognised microorganisms. In this study, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterised. Determined to be a possible Enterobacterales, whole genome sequencing and phylogenetic analysis confirmed identification as Pseudocitrobacter, a relatively new genus (2013) with three known species. This isolate was found to be distinct from these, with 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacteriaceae, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobacter corydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P. corydidari is stated to not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, β-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistances were confirmed. In addition to evident variations in ARG profiles, human colonisation and origin in a clinically-relevant niche that is geographically, physically and chemically disparate, lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonised only and did not require antimicrobial treatment.

Identification of bacteria species among Enterobacteriaceae found in confectionery cakes

The goal of this research was to identify which Enterobacteriaceae species are present in cakes from confectionery establishments and whether these are species that can be considered pathogenic for humans and what their harmful impact on human health could be. The sampling of confectionery cakes was carried out in the area of the City of Zagreb, and the samples were analysed for the presence of Enterobacteriaceae in accordance with the HRN ISO 21528-2:2017 standard. In cases where the samples contained the number of Enterobacteriaceae greater than 102 CFU/g, the MALDI-TOF method was used to identify individual species of enterobacteria. The results of the analyses determined the presence of 10 Enterobacteriaceae species: Enterobacter kobei, Enterobacter cloacae, Pantoea agglomerans, Serratia liquefaciens, Enterobacter asburiae, Klebsiella oxytoca, Buttiauxella gaviniae, Buttiauxella warmboldiae, Raoultella and Cedecea neteri. All species of Enterobacteriaceae determined in this research, according to the literature, were previously isolated from food or water, and all species except Buttiauxella warmboldiae were isolated from humans and the environment. However, for none of the species of Enterobacteriaceae determined in this research a literature reference to support food as a vehicle in case of human illness was found.

Agtrevirus phage AV101 recognizes four different O-antigens infecting diverse E. coli.

Bacteriophages in the Agtrevirus genus are known for expressing multiple tail spike proteins (TSPs), but little is known about their genetic diversity and host recognition apart from their ability to infect diverse Enterobacteriaceae species. Here, we aim to determine the genetic differences that may account for the diverse host ranges of Agrevirus phages. We performed comparative genomics of 14 Agtrevirus and identified only a few genetic differences including genes involved in nucleotide metabolism. Most notably was the diversity of the tsp gene cluster, specifically in the receptor-binding domains that were unique among most of the phages. We further characterized agtrevirus AV101 infecting nine diverse Extended Spectrum β-lactamase (ESBL) Escherichia coli and demonstrated that this phage encoded four unique TSPs among Agtrevirus. Purified TSPs formed translucent zones and inhibited AV101 infection of specific hosts, demonstrating that TSP1, TSP2, TSP3, and TSP4 recognize O8, O82, O153, and O159 O-antigens of E. coli, respectively. BLASTp analysis showed that the receptor-binding domain of TSP1, TSP2, TSP3, and TSP4 are similar to TSPs encoded by E. coli prophages and distant related virulent phages. Thus, Agtrevirus may have gained their receptor-binding domains by recombining with prophages or virulent phages. Overall, combining bioinformatic and biological data expands the understanding of TSP host recognition of Agtrevirus and give new insight into the origin and acquisition of receptor-binding domains of Ackermannviridae phages.

Potential Pathogenicity of Escherichia coli Isolated from the Stools of Healthy Children Suffering from Diarrhea Admitted to Hospitals in Southern Benin

Aims: Infant mortality linked to infectious diseases remains a major public health concern, especially in the context of antibiotic resistance. This work aimed to study the potential pathogenicity of Escherichia coli strains isolated from the stools of children suffering from diarrhea and healthy from 0 to 15 years old admitted to hospitals in southern Benin.
 Methodology: The isolation and characterization of the strains were carried out according to standard microbiology methods. Molecular characterization was carried out by searching for eight virulence factors (Stx1, Stx2, eaeA, bfpB, LT, InVE, IpaH, AggR) and three antibiotic resistance genes (blaTEM, blaSHV, blaCTX -M) by the PCR technique.
 Results: This study shows that 47.06% of the children sampled suffered from diarrhea, against 52.94% who were healthy. A total of 9 species of Enterobacteriaceae were identified in different proportions: Escherichia coli (66.66%), Klebsiella ornithinolytica (13.72%), Klebsiella pneumonia (5.88%), Enterobacter aerogenes (3.92%), Escherichia vulneris (1.96%), Salmonella arizonae (1.96%), Salmonella spp (1.96%), Enterobacter sakazakii (1.96%), Serratia fonticola (1.96%). All E. coli showed total resistance to amoxicillin, ceftazidime, and cefotaxime. In addition, they showed variable resistance to norfloxacin (95.33%), trimethoprim (83.33%), and sulfamethoxazole (95.24%). 70.83% of E. coli strains isolated from apparently healthy children carry resistance genes blaTEM (12.5%), blaSHV (25%), and blaCTX-M (33.33%). While 66.67% of strains of E. coli isolated from children with diarrhea carry resistance genes blaTEM (12.5%), blaSHV (37.5%), and blaCTX-M (16.67%). Only EPEC was isolated and only in diarrheal children, with a frequency of 20.83%.
 Conclusion: The relatively high prevalence of ECD in this study is remarkable, and it highlights the fact that E. coli is an important agent of infectious diarrhea and could be the leading cause of gastroenteritis in Benin.

Hygienic indicator bacteria in the 2 species of wild-caught Japanese cicadas, large brown cicadas and robust cicadas

Abstract Entomophagy is considered a potent dietary practice to replace animal protein due to its highly nutritious and environmentally sustainable features. While entomophagy has many advantages, safety and security concerns still remain, especially for wild-caught insects, not farm-reared insects. This study aimed to clarify the potential microbiological hazards of eating wild-caught cicadas. Large brown cicadas and robust cicadas, which were commonly inhabited in Japan, were caught and examined the hygienic indicator bacteria, standard plate counts (SPC) and Enterobacteriaceae. Then, representative colonies of Enterobacteriaceae were identified. Also, the distribution of bacteria, i.e. the surface or inside the body of the cicadas, and the changes in the bacterial number during the storage of the dead cicadas were examined. SPC was in the range of 3.0 to 9.0 log CFU/g and Enterobacteriaceae was detected in the most of cicadas. Most of the Enterobacteriaceae species identified were biosafety level 2 pathogens or opportunistic pathogens. SPC and Enterobacteriaceae were distributed both on the surface and in the body of the cicadas. SPC and Enterobacteriaceae rapidly increased in the dead cicadas during the storage (at 25 °C). In this study, it is concluded that sufficient heat cooking and proper cold storage should be necessary for the safe consumption of cicadas as food.

Draft genome sequence of an Atlantibacter hermannii clinical strain isolated from human muscle tissue.

Atlantibacter hermannii is a species of the family Enterobacteriaceae and a rare opportunistic pathogen. The draft genome sequence of an Atlantibacter hermannii clinical strain that had been isolated from infected muscle tissue was obtained. The genome contains about 4.4 million bases and has no known plasmid replicons.

Bacteremia due to Serratia rubidaea in intensive care unit: a case series

IntroductionBacteremia caused by Serratia rubidaea is seldom mentioned in comparison with other Enterobacteriaceae species. It primarily affects immunocompromised patients undergoing invasive procedures. Furthermore, the incidence, clinical features, and microbiological profile of this pathogen in the intensive care unit are rarely described.Case presentationWe present four North African case studies of bacteremia in four young female patients admitted to the intensive care unit for ketoacidosis with a history of diabetes mellitus. All four patients developed catheter-related infections complicated by deep vein thrombosis. The catheter site was femoral in all cases, and the main clinical manifestation was poorly tolerated fever. The pathogen was isolated in multiple peripheral blood cultures (> 4) for each patient, showing a similar profile in all cases: resistance to third-generation cephalosporins and sensitivity to aminoglycosides, piperacillin, fluoroquinolones, and folate-pathway inhibitors. Targeted treatment consisted of a combination of ciprofloxacin 400 mg twice per day and trimethoprim/sulfamethoxazole 400/80 mg thrice per day for all four cases. However, in one case, this regimen was switched to amikacin due to adverse effects. The outcomes were favorable in the majority of cases. The patients described in this study were 21, 66, 22, and 27-year-old North African women.ConclusionMost of the reported cases shared common risk factors and clinical aspects. Notably, a case of thrombosis complicating a catheter infection caused by Serratia rubidaea has not been previously reported in the literature. Furthermore, this bloodstream infection typically affects deeply immunocompromised patients. However, our four cases, admitted to the intensive care unit for ketoacidosis, only had a history of diabetes mellitus.

Genomic characterization of extended spectrum beta lactamases producing multidrug-resistant Escherichia coli clinically isolated harboring chromosomally mediated CTX-M-15 from Alkharj, KSA

Extended Spectrum Beta Lactamases (ESBLs) are the most prevalent enzymes conferring resistance to beta-lactams encoded on plasmids and rarely in chromosomes. This genomic study aims to characterize Escherichia coli to identify antimicrobial resistance genes (ARG), virulence factors, and phylogenetic relationships among ESBL-positive and negative isolates of E. coli obtained from Al-Kharj, Riyadh region, Saudi Arabia. Three clinical isolates from urine and vaginal swabs were obtained and subjected to whole genome sequencing, minimum inhibitory concentration, and antibiotic sensitivity tests. The pathogenicity and ARG were discovered, and the raw genomic sequences were assembled and annotated. Two isolates (E5 and E15) were MDR and ESBLs producers; the sequence type (ST) for E5 was 58, while those for E15 and E21 were 106. Most of the virulence genes were detected as plasmid-mediated; E21 was identified with a hyper-virulent plasmid (pH 2332–166) carrying different virulence factors (TraJ, traT, iss, etsC, hlyF, and iron acquisition associated proteins), plasmids (IncFII, IncFIB, and IncFIA), and insertion sequences (ISEc31). While most of the antimicrobial resistance genes were chromosomally mediated, a rare chromosome insertion of qnrS1 and blaCTX−M−15 with co-occurrence of Tn2 and ISKpn19 was identified in the E5 isolate. The consistent preservation of these genetic elements on bacterial chromosomes and plasmids could enhance the spread of Multidrug-Resistant (MDR) strains across various Enterobacteriaceae Species. This poses a significant threat to the effectiveness of existing antimicrobial treatments.

Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes.

Plasmids play important roles in bacterial genome diversification. In the Serratia marcescens complex (SMC), a notable contribution of plasmids to genome diversification was also suggested by our recent analysis of >600 draft genomes. As accurate analyses of plasmids in draft genomes are difficult, in this study we analysed 142 closed genomes covering the entire complex, 67 of which were obtained in this study, and identified 132 plasmids (1.9-244.4 kb in length) in 77 strains. While the average numbers of plasmids in clinical and non-clinical strains showed no significant difference, strains belonging to clade 2 (one of the two hospital-adapted lineages) contained more plasmids than the others. Pangenome analysis revealed that of the 28 954 genes identified, 12.8 % were plasmid-specific, and 1.4 % were present in plasmids or chromosomes depending on the strain. In the latter group, while transposon-related genes were most prevalent (31.4 % of the function-predicted genes), genes related to antimicrobial resistance and heavy metal resistance accounted for a notable proportion (22.7 %). Mash distance-based clustering separated the 132 plasmids into 23 clusters and 50 singletons. Most clusters/singletons showed notably different GC contents compared to those of host chromosomes, suggesting their recent or relatively recent appearance in the SMC. Among the 23 clusters, 17 were found in only clinical or only non-clinical strains, suggesting the possible preference of their distribution on the environmental niches of host strains. Regarding the host strain phylogeny, 16 clusters were distributed in two or more clades, suggesting their interclade transmission. Moreover, for many plasmids, highly homologous plasmids were found in other species, indicating the broadness of their potential host ranges, beyond the genus, family, order, class or even phylum level. Importantly, highly homologous plasmids were most frequently found in Klebsiella pneumoniae and other species in the family Enterobacteriaceae, suggesting that this family, particularly K. pneumoniae, is the main source for plasmid exchanges with the SMC. These results highlight the power of closed genome-based analysis in the investigation of plasmids and provide important insights into the nature of plasmids distributed in the SMC.

The F pilus serves as a conduit for the DNA during conjugation between physically distant bacteria.

Horizontal transfer of F-like plasmids by bacterial conjugation is responsible for disseminating antibiotic resistance and virulence determinants among pathogenic Enterobacteriaceae species, a growing health concern worldwide. Central to this process is the conjugative F pilus, a long extracellular filamentous polymer that extends from the surface of plasmid donor cells, allowing it to probe the environment and make contact with the recipient cell. It is well established that the F pilus can retract to bring mating pair cells in tight contact before DNA transfer. However, whether DNA transfer can occur through the extended pilus has been a subject of active debate. In this study, we use live-cell microscopy to show that while most transfer events occur between cells in direct contact, the F pilus can indeed serve as a conduit for the DNA during transfer between physically distant cells. Our findings enable us to propose a unique model for conjugation that revises our understanding of the DNA transfer mechanism and the dissemination of drug resistance and virulence genes within complex bacterial communities.

Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model.

Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.

Detection of Enterobacteriaceae in cerebrospinal fluid fluid of neonates with meningitis from tertiary care hospitals.

This study aimed to determine the bacteriological profile of childhood acute bacterial meningitis in Pakistan. The study included a total of 100 children aged between 1 month and 5 years, who were admitted with a diagnosis of meningitis based on clinical findings and positive cerebrospinal fluid (CSF) tests. Out of the 100 CSF samples collected, 21 isolates were confirmed to contain Enterobacteriaceae. The most prevalent Enterobacteriaceae species were Pseudomonas (n=8, 38.09%), Klebsiella (n=4, 19.04%), E. coli (n=4, 19.04%), and Acinetobacter (n=4, 19.04%), while Citrobacter (n=1, 4.76%) was less common. Antibiotic susceptibility patterns were analyzed for these isolates. Pseudomonas (n=8) exhibited 25% resistance to cefepime and 38% resistance to imipenem. Klebsiella (n=4) showed 75% resistance to imipenem. Acinetobacter (n=4) demonstrated 50% resistance to imipenem, along with varying resistance to cefepime, amikacin, ciprofloxacin, and gentamicin. E. coli (n=4) showed 0% resistance to imipenem and amikacin. However, Citrobacter (n=1) showed 0% resistance to ciprofloxacin, aztreonam, gentamicin, amikacin, levofloxacin, and cefepime. Acute bacterial meningitis primarily affects children under 1 year of age. CSF culture revealed that Gram-negative bacteria, specifically Pseudomonas spp., were the predominant pathogens in this family based on Pakistani data.

Genomic characterization of New Delhi metallo-beta-lactamase-producing species of Morganellaceae, Yersiniaceae, and Enterobacteriaceae (other than Klebsiella) from Brazil over 2013-2022.

Over the last decade, New Delhi metallo-beta-lactamase (NDM) carbapenemase has silently spread in Brazil. In this study, we analyzed a large collection of Enterobacterales other than Klebsiella spp. received in our reference laboratory between 2013 and 2022. A total of 32 clinical isolates displaying different pulsed-field gel electrophoresis profiles, and represented by 11 species in the families Enterobacteriaceae (Citrobacter freundii, Citrobacter portucalensis, Enterobacter hormaechei, and Escherichia coli), Morganellaceae (Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, and Raoultella ornithinolytica), and Yersiniaceae (Serratia marcescens) had their whole genomes sequenced and further analyzed. Antimicrobial susceptibility was determined by disk diffusion, except for polymyxin B, assessed by broth microdilution. The blaNDM-1 allele was predominant (n = 29), but blaNDM-5 was identified in an E. coli specimen with a novel ST, and the blaNDM-7 allele was found in E. hormaechei ST45 and E. coli ST1049. Polymyxin was active against all but one Enterobacteriaceae isolate: an mcr-1-producing E. coli presenting minimal inhibitory concentration (4 mg/L). Isolates producing extended-spectrum β-lactamases were common: cefotaximase from Munich (CTX-M)-15 (n = 10), CTX-M-2 (n = 4), and CTX-M-8 (n = 3) were detected, and the mcr-1-producing E. coli was found to co-produce both CTX-M-8 and CTX-M-55 β-lactamases. The mcr-9 gene was found in 5/8 E. hormaechei isolates, distributed in four different sequence types, all of them presenting susceptibility to polymyxin. This study showed that NDM-producing Enterobacterales other than Klebsiella are already spread in Brazil, in diversified species, and cocarrying important resistance genes. Prompt detection and effective implementation of measures to prevent further spread are mandatory for mitigating the dissemination of NDM carbapenemase in hospital settings and preserving the already limited antimicrobial therapy options.

Isolation and Identification of Bacterial Soft-Rot-Causing Isolates from Cassava, Homa-Bay County, Kenya

Cassava bacterial soft rot is of great importance to economically valuable crop varieties. Commonly, bacterial soft rot strains cause destructive vegetable and potato diseases worldwide. The strain act similar to other species of the family Enterobacteriaceae that cause soft rot in plants. However, the disease has spread in a wide range of environment with its prevalence and causative strains less known to most agroecological zones of Kenya. Generally, aim of this study was to isolate, characterize and identify bacterial soft rot causative strains in cassava, Homa-Bay County. At the Sub County level, 104 farms were identified through a simple random method and symptomatic cassava plants sampled along laid transect in each farm. Rotten cassava tubers were then randomly sampled, packed and taken to the laboratory for pathogen identification. The bacterial strains were isolated in Nutrient Agar at 37˚c for 24 hours to obtain pure cultures. Identification was done using morphological, biochemical and 16S rRNA analysis method. The study identified: two Pectobacterium carotovorum, three Bacillus species: Bacillus amyloliquefaciens, Bacillus subtilis, and Bacillus tropicus, and three Achromobacter species: Achromobacter marplatensis, Verticiella sediminum, and Achromobacter xylosoxidans, pathogenic strains causing cassava bacterial soft rot. In this study, characterization and identification of cassava bacterial soft rot in Homa Bay County was done for the first time. The results can not only be used in the characterization enzymes produced by cassava bacterial soft rot strains but also in the development of effective control strategy.

Comparative analysis of intestinal microbiota distribution characteristics based on metagenomics in patients with hepatitis B cirrhosis with or without ascites

Objective: To use metagenomic sequencing to compare the differences in intestinal microbiota species and metabolic pathways in patients with hepatitis B cirrhosis with or without ascites and further explore the correlation between the differential microbiota and clinical indicators and metabolic pathways. Methods: 20 hepatitis B cirrhosis cases [10 without ascites (HBLC-WOA), 10 with ascites (HBLC-WA), and 5 healthy controls (HC)] were selected from the previously studied 16S rRNA samples. Metagenome sequencing was performed on the intestinal microbiota samples. The Kruskal-Wallis rank sum test and Spearman test were used to identify and analyse differential intestinal microbiota populations, metabolic pathways, and their correlations. Results: (1) The overall structure of the intestinal microbiota differed significantly among the three groups (R = 0.19, P = 0.018). The HC group had the largest abundance of Firmicutes and the lowest abundance of Proteobacteria at the genus level. Firmicutes abundance was significantly decreased (P(fdr) < 0.01), while Proteobacteria abundance was significantly increased (P(fdr) < 0.01) in patients with cirrhosis accompanied by ascites; (2) LEfSe analysis revealed that 29 intestinal microbiota (18 in the HBLC-WA group and 11 in the HBLC-WOA group) played a significant role in the disease group. The unclassified Enterobacteriaceae and Klebsiella species in the HBLC-WA group and Enterobacteriaceae in the HBLC-WOA group were positively correlated with the Child-Turcotte-Pugh (CTP) score, prothrombin time, and international normalized ratio score and negatively correlated with albumin and hemoglobin levels (P < 0.05). Escherichia and Shigella in the HBLC-WA group were positively correlated with CTP scores (P < 0.05); (3) The correlation analysis results between the KEGG pathway and 29 specific intestinal microbiota revealed that Enterobacteriaceae and arachidonic acid, α-linolenic acid, glycerolipid metabolism, and fatty acid degradation were positively correlated in the lipid metabolism pathway, while most Enterobacteriaceae were positively correlated with branched-chain amino acid degradation and negatively correlated with aromatic amino acid biosynthesis in the amino acid metabolic pathway. Conclusion: A significant increment of Enterobacteriaceae in the intestines of HBLC-WA patients influenced hepatic reserve function and was associated with amino acid and lipid metabolic pathways. Therefore, attention should be paid to controlling the intestinal microbiota to prevent complications and improve the prognosis in patients with hepatitis B cirrhosis, especially in those with ascites.

High-throughput sequencing analysis of the characteristics of the gut microbiota in aged patients with sarcopenia

BackgroundThe gut microbiota is a complex microbial community that changes in response to various intestinal diseases, including aging-related diseases such as sarcopenia. Several studies have shown that the metabolites of the gut microbiota affect the dynamic balance of the skeletal muscle. However, the effect of gut microbiota imbalance on sarcopenia is still largely unknown. MethodsWe collected the baseline characteristics and fecal samples of 14 patients with sarcopenia and 21 patients without sarcopenia, and used the 16S rRNA sequencing technology to analyze the differences in the gut microbiota in the two groups. α-diversity and β-diversity were employed to assess the abundance and diversity of species and variations in microflora composition, respectively. Moreover, Tax4Fun was employed to predict the functional capacities of the microbial communities. ResultsIn the sarcopenia group, the abundances of beneficial bacteria such as Bacteroides, Faecalibacterium, Fusobacterium, and Prevotella were reduced, whereas those of pathogenic bacteria, such as Escherichia-Shigella and Klebsiella, were increased. The genera and species of the family Enterobacteriaceae were the main pathogenic bacteria in patients with sarcopenia, and Escherichia-Shigella and Klebsiella could be used as key biomarkers of sarcopenia. The defective protein processing and amino acid synthesis pathways in patients with sarcopenia indicated that protein synthesis and nutrient transport may be damaged. Moreover, the abundances of Escherichia-Shigella and Enterobacteriaceae have been found to have a negative correlation with muscle mass and were the main parameters predicting the change in muscle mass. ConclusionsIn this study, we have identified changes in the gut microbiota of sarcopenic individuals, which were linked to the loss of muscle mass and function. Escherichia-Shigella is a conditional pathogen of sarcopenic patients, and its levels are found to have a significant negative correlation with muscle mass.