Antibiotic Resistance Analysis Research Articles

Genomic analysis of <i>Klebsiella pneumoniae</i> strains virulence and antibiotic resistance

Recently, Klebsiella pneumoniae strains have become widespread both in community-acquired infectious processes and in nosocomial infections. There are two pathotypes of K. pneumoniae: classical (cKp) and hypervirulent (hvKp). Representatives of any pathotype are prone to acquire and further transmit genetic factors of antibiotic resistance and virulence. This combination accounts for severity of the infectious process. Therefore, information about whether the strain belongs to either pathotype can help in prescribing proper therapy. Since there is no consensus upon hypervirulence marker, we attempted to find the most significant combinations of genetic markers of virulence and antibiotic resistance in K. pneumoniae strains. The study was aimed to conduct a genomic analysis of virulence and antibiotic resistance of K. pneumoniae clinical isolates. Materials and methods. There were examined 85 strains of K. pneumoniae isolated from diverse clinical material samples from patients in large St. Petersburg hospitals. In our work, we used classical bacteriological methods, including determination of the hypermucoviscous type using the “string test”, the mass spectrometric method (MALDI-ToF MS) for identifying bacteria, molecular methods for studying markers of virulence and antibiotic resistance (multilocus sequence typing, genome sequencing of K. pneumoniae strains). Results. Among the studied K. pneumoniae strains, the most common carbapenemase genes were OXA-48 (18.7%) and NDM-1 genes — 17.3% of strains; in 6.7% of strains, NDM-1 and OXA-48 genes were found simultaneously. The percentage of strains with β-lactamase genes CTX-M-15 was 54.7%, OXA-1 — 17.3%, TEM-1D — 13.3%, and in 17.3% of cases the OXA-1 and TEM-1D genes were simultaneously present in bacterial strains. Quinolone resistance genes were found in 68.4% of strains. The most common genes were qnrS1 (40% of strains) and qnrB1 (22.7%). Phenotypic antimicrobial susceptibility testing showed that 23.5% and 64.7% strains were resistant to colistin and carbapenems, respectively. 32.9% K. pneumoniae strains, isolated in patients with phlegmon, pneumonia, sepsis, and peritonitis, had a hypermucoid phenotype. The most common sequence types were: ST395 (24.3%), ST23 (17.6%) and ST512 (9.5%). 8% and 25.3% of strains belonged to capsule types K1 and K2, respectively. The polyketide synthesis locus ybt, which characterizes virulent strains, was detected in 69.3% isolates, and the clb locus was present in 10.7% of strains. In 73.3% and 14.7% strains, the plasmid-associated virulence loci iuc and iro were identified, which encode the biosynthesis of the siderophores aerobactin and salmochelin. We described 44 cases (58.7% of strains) of genotypic convergence of virulence and antibiotic resistance, as shown by simultaneously detected the aerobactin (iuc) locus and β-lactamase or carbapenemase genes. Thus, identification of hypervirulence may provide valuable information for the clinical management of patients with hvKp infections. Therefore, it is is obviously necessary to develop comprehensive diagnostic test for simultaneous screening of multidrug-resistant hypervirulent K. pneumoniae strains.

Metabolic Labeling and Digital Microfluidic Single-Cell Sequencing for Single Bacterial Genotypic-Phenotypic Analysis.

Accurate assessment of phenotypic and genotypic characteristics of bacteria can facilitate comprehensive cataloguing of all the resistance factors for better understanding of antibiotic resistance. However, current methods primarily focus on individual phenotypic or genotypic profiles across different colonies. Here, a Digital microfluidic-based automated assay for whole-genome sequencing of single-antibiotic-resistant bacteria is reported, enabling Genotypic and Phenotypic Analysis of antibiotic-resistant strains (Digital-GPA). Digital-GPA can efficiently isolate and sequence antibiotic-resistant bacteria illuminated by fluorescent D-amino acid (FDAA)-labeling, producing high-quality single-cell amplified genomes (SAGs). This enables identifications of both minor and major mutations, pinpointing substrains with distinctive resistance mechanisms. Digital-GPA can directly process clinical samples to detect and sequence resistant pathogens without bacterial culture, subsequently provide genetic profiles of antibiotic susceptibility, promising to expedite the analysis of hard-to-culture or slow-growing bacteria. Overall, Digital-GPA opens a new avenue for antibiotic resistance analysis by providing accurate and comprehensive molecular profiles of antibiotic resistance at single-cell resolution.

Antibiotic Resistance and Genomic Analysis of Shiga Toxin-Producing Escherichia coli from Dairy Cattle, Raw Milk, and Farm Environment in Shaanxi Province, China.

To investigate the epidemiology of Shiga toxin-producing Escherichia coli (STEC) in dairy cattle, 975 samples (185 feces, 34 silage, 36 cattle drinking water, 360 raw milk, and 360 teat skin swabs) were collected from two dairy farms in Baoji and Yangling, Shaanxi Province, China, and were screened for STEC. Whole-genome sequencing was used to analyze the genomic characteristics and potential transmission of STEC isolates. A total of 32 samples were contaminated with STEC, including 4.0% (19/479) in Farm A and 2.6% (13/496) in Farm B. Compared with adult cows (4.5%), nonadult cows had a higher rate (21.3%) of STEC colonization. A total of 14 serotypes and 11 multilocus sequence typing were identified in 32 STEC isolates, among which O55:H12 (25.0%) and ST101 (31.3%) were the most predominant, respectively. Six stx subtypes/combinations were identified, including stx1a (53.1%), stx2g (15.6%), stx2d, stx2a+stx2d, stx1a+stx2a (6.3%, for each), and stx2a (3.1%). Of 32 STEC isolates, 159 virulence genes and 27 antibiotic resistance genes were detected. Overall, STEC isolates showed low levels of resistance to the 16 antibiotics tested (0-40.6%), with most common resistance to ampicillin (40.6%). The phylogenetic analysis confirmed that STEC in the gut of cattle can be transmitted through feces. The results of this study help to improve our understanding of the epidemiological aspects of STEC in dairy cattle and provide early warning and control of the prevalence and spread of the bacterium.

Analysis of antibiotic resistance in Gram-negative bacilli in wild and exotic healthy birds in Brazil: A warning sign

Bacterial antibiotic resistance is a public health problem affecting humans and animals. This study focuses on identifying Gram-negative bacilli (GNB) (MALDI-TOF MS and Klebsiella MALDI TypeR) resistant to antimicrobials in freshly emitted feces of healthy captive and rescued wild birds from a zoo in Brazil. Birds from the zoo and rescued from sixteen different orders were investigated. Resistant bacteria from feces were selected (MacConkey agar with 2 μg/mL cefotaxime). Genomic similarity and plasmid were investigated by Pulsed-Field Gel Electrophoresis of XbaI fragments (XbaI-PFGE) and S1-PFGE. Polymerase Chain Reaction (PCR) was performed to search for beta-lactamase genes. From 80 birds included, 26 from the zoo (50 %) and 18 rescued wild birds (64 %) presented cefotaxime-resistant GNB. E. coli and Klebsiella spp were the most prevalent species. Among 65 isolates from the zoo and rescued wild birds, 75 % were considered multidrug-resistant (MDR). The majority of the isolates were extended-spectrum beta-lactamases (ESBL) producing and resistant to enrofloxacin. blaCTX-M-GROUP-1, blaTEM, and blaSHV were the most detected genes, and blaKPC was detected in K. pneumoniae complex. According to genomic similarity results, some identical profiles were found in birds with no known contact among the zoo or rescued birds. Several isolates carried one to three plasmids (15–350 kb). The presence of multidrug-resistant (MDR) isolates from healthy captive and wild birds brings novel data on the dissemination of these elements to the environment.

A secure visualization platform for pathogenic genome analysis with accurate reference database

Investigating the genetic and developmental characteristics, infection transmission attributes, and epidemiological trends of pathogens using genomic data represents the foundation for pathogen surveillance and is a crucial prerequisite for guaranteeing global health security. To meet the analytical demands of research relating to pathogen prevention and control, we designed a secure visualization system capable of pathogen genome assembly, annotation, species identification, sequence typing, antibiotic resistance and virulence analysis, genomic mobile element and transferable resistance gene annotation, and phylogenetic tree reconstruction. For highly pathogenic organisms requiring complete data protection, we have developed a secure computing tool that utilizes a trusted execution environment, is combined with blockchain and privacy computing technologies, and is specifically designed for nucleotidebasiclocalalignmentsearchtool(BLASTn) comparison analysis. This technological advancement offers scientific support for in-depth investigations into pathogen transmission and epidemiological mechanisms, environmental adaptability, evolutionary trends, and immune evasion mechanisms, as well as the identification of new or emerging pathogen strains. This, in turn, aids efforts in infectious disease prevention, treatment, and research.

Whole-Genome Sequence Analysis of Antibiotic Resistance, Virulence, and Plasmid Dynamics in Multidrug-Resistant E. coli Isolates from Imported Shrimp.

We analyzed antimicrobial resistance and virulence traits in multidrug-resistant (MDR) E. coli isolates obtained from imported shrimp using whole-genome sequences (WGSs). Antibiotic resistance profiles were determined phenotypically. WGSs identified key characteristics, including their multilocus sequence type (MLST), serotype, virulence factors, antibiotic resistance genes, and mobile elements. Most of the isolates exhibited resistance to gentamicin, streptomycin, ampicillin, chloramphenicol, nalidixic acid, ciprofloxacin, tetracycline, and trimethoprim/sulfamethoxazole. Multilocus sequence type (MLST), serotype, average nucleotide identity (ANI), and pangenome analysis showed high genomic similarity among isolates, except for EC15 and ECV01. The EC119 plasmid contained a variety of efflux pump genes, including those encoding the acid resistance transcriptional activators (gadE, gadW, and gadX), resistance-nodulation-division-type efflux pumps (mdtE and mdtF), and a metabolite, H1 symporter (MHS) family major facilitator superfamily transporter (MNZ41_23075). Virulence genes displayed diversity, particularly EC15, whose plasmids carried genes for adherence (faeA and faeC-I), invasion (ipaH and virB), and capsule (caf1A and caf1M). This comprehensive analysis illuminates antimicrobial resistance, virulence, and plasmid dynamics in E. coli from imported shrimp and has profound implications for public health, emphasizing the need for continued surveillance and research into the evolution of these important bacterial pathogens.

Antimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou, China.

Salmonella enteritidis is a main pathogen responsible for sporadic outbreaks of gastroenteritis, and therefore is an important public health problem. This study investigated the drug resistance and genomic characteristics of S. enteritidis isolated from clinical and food sources in Huzhou, Zhejiang Province, China, from February 1, 2021, to December 30, 2023. In total, 43 S. enteritidis strains isolated during the study period were subjected to virulence gene, drug resistance gene, genetic correlation, antibiotic resistance, and multilocus sequence typing analyses. All 43 isolates were identified as ST11, and contained 108 virulence-related genes. Drug sensitivity analysis of the 43 isolates showed resistance rates of 100% to nalidixic acid and 90.70% to ampicillin and ampicillin/sulbactam. Multidrug resistance is a serious issue, with 81.40% of strains resistant to three or more antibacterial drugs. Genome sequencing indicated that S. enteritidis possessed 23 drug resistance genes, of which 14 were common to all 43 isolates. Phylogenetic analysis based on core genome single-nucleotide polymorphisms divided the 43 S. enteritidis strains into three clusters, with the 10 samples from an outbreak forming an independent branch located in cluster 3.

Ecological Characteristics of Culturable Myxobacteria in the Rhizosphere Soil of Saline-Tolerant Plants in the Ebinur Saline Wetlands

T his study investigated the ecological distribution of myxobacteria in the saline environment of the Ebinur Lake Wetland, in China, which provides a unique microecological environment for their survival. Culturable myxobacteria were isolated using traditional methods including Escherichia coli DH5α, rabbit feces, and filter paper flakes as food sources. Molecular identification along with physiological, biochemical assays and morphological characterization was carried out for the classification and identification of myxobacteria. Associations between soil environmental factors and myxobacterial diversity were analyzed using redundancy analysis. This study involved collecting rhizosphere soil from 15 species of salt-tolerant plants, ultimately yielding 15 strains of myxobacteria from eight of these species. Fifteen strains of myxobacteria were taxonomically placed by analyzing 16S rRNA homology, seven strains were closely related to Myxococcus virescens, six strains were closely related to Myxococcus fulvus and two strains were closely related to Myxococcus xanthus. Myxococcus virescens, the dominant cultivable species of myxobacteria in the Ebinur Lake Wetland, was isolated from various sampling sites using traditional methods. Analysis of antibiotic resistance revealed that myxobacterial strains M2, M6, M9, M13, and M15 are resistant to gentamicin. Furthermore, predation assays demonstrated that myxobacterial strain M14 exhibits the broadest spectrum of predation against both bacterial and fungal prey. The limited culturable myxobacterial diversity observed in the Ebinur Lake Wetland could potentially result from variations in soil physicochemical properties, vegetation type, and employed isolation methods. These findings enhance our comprehension of the myxobacterial resources within this specific salt desert ecosystem.

The characteristics of the novel bacterial strain Pseudomonas mendocina isolated from freshwater aquaculture farm.

Plastic contamination can cause damage to the water quality of fish farm ponds, and also affect the quality of the final product. Pseudomonas mendocina was found to biodegrade plastics. Our study aimed to investigate the physicochemical properties and drug resistance of P. mendocina isolated from local freshwater aquaculture farms. Firstly, the strain was isolated from aquaculture water and then identified by matrix-assisted flight mass spectrometry and 16S rDNA sequencing. Then, biochemical and antibiotic resistance analyses were performed, and a microbial high-throughput growth detector was used to assess the growth of the strain. Finally, PCR and proteomics analyses were conducted to determine drug-resistance-related genes/proteins. According to the results of the spectrum diagram and sequencing, the isolated bacteria were identified as P. mendocina, and were positive for reactions of ADH, MTE, LAC, MNE, FRU, CIT, MLT, ONPG, and ACE. P. mendocina was sensitive to most of the antibiotics, and its resistance to CHL, MIN, and TIC/CLA was intermediate. Additionally, gyrB was the resistance gene, and mdtA2, mdtA3, mdaB, and emrK1 were closely related to the drug resistance of P. mendocina. Our results show the biochemical properties of P. mendocina in isolated aquaculture water, and provide a new perspective for P. mendocina involved in the biological removal of plastics or microplastics in freshwater aquaculture farms.

Metagenomic and Antibiotic Resistance Analysis of the Gut Microbiota in Larus relictus and Anatidae Species Inhabiting the Honghaizi Wetland of Ordos, Inner Mongolia, from 2021 to 2023.

Gut microbes thrive by utilising host energy and, in return, provide valuable benefits, akin to a symbiotic relationship. Here, metagenomic sequencing was performed to characterise and compare the community composition, diversity and antibiotic resistance of the gut microbiota of Relict gull (Larus relictus) and Anatidae species. Alpha diversity analysis revealed that the intestinal microbial richness of L. relictus was significantly lower than that of Anatidae, with distinct differences observed in microbial composition. Notably, the intestines of L. relictus harboured more pathogenic bacteria such as clostridium, which may contribute to the decline in their population and endangered status. A total of 117 strains of Escherichia coli were isolated, with 90.60% exhibiting full susceptibility to 21 antibiotics, while 25.3% exhibited significant biofilm formation. Comprehensive Antibiotic Resistance Database data indicated that glycopeptide resistance genes were the most prevalent type carried by migratory birds, alongside quinolone, tetracycline and lincosamide resistance genes. The abundance of resistance genes carried by migratory birds decreased over time. This metagenomic analysis provides valuable insights into the intestinal microbial composition of these wild bird species, offering important guidance for their conservation efforts, particularly for L. relictus, and contributing to our understanding of pathogen spread and antibiotic-resistant bacteria.

Epidemiological, Virulence, and Antibiotic Resistance Analysis of Klebsiella pneumoniae, a Major Source of Threat to Livestock and Poultry in Some Regions of Xinjiang, China.

Klebsiella pneumoniae (K. pneumoniae) is recognized as a zoonotic pathogen with an increasing threat to livestock and poultry. However, research on K. pneumoniae of animal origin remains limited. To address the gap, a comprehensive investigation was carried out by collecting a total of 311 samples from the farms of four animal species (dairy cow, chicken, sheep, and pig) in selected areas of Xinjiang, China. Isolates were identified by khe gene amplification and 16S rRNA gene sequencing. Genotyping of K. pneumonia isolates was performed using wzi typing and multilocus sequence typing (MLST). PCR was employed to identify virulence and resistance genes. An antibiotic susceptibility test was conducted using the Kirby-Bauer method. The findings revealed an isolation of 62 K. pneumoniae strains, with an average isolation rate of 19.94%, with the highest proportion originating from cattle sources (33.33%). Over 85.00% of these isolates harbored six virulence genes (wabG, uge, fimH, markD, entB, and ureA); while more than 75.00% of isolates possessed four resistance genes (blaTEM, blaSHV, oqxA, and gyrA). All isolates exhibited complete resistance to ampicillin and demonstrated substantial resistance to sulfisoxazole, amoxicillin/clavulanic acid, and enrofloxacin, with an antibiotic resistance rate of more than 50%. Furthermore, 48.39% (30/62) of isolates were classified as multidrug-resistant (MDR) strains, with a significantly higher isolation rate observed in the swine farms (66.67%) compared to other farms. Genetic characterization revealed the classification of the 62 isolates into 30 distinct wzi allele types or 35 different sequence types (STs). Notably, we identified K. pneumoniae strains of dairy and swine origin belonging to the same ST42 and wzi33-KL64 types, as well as strains of dairy and chicken origin belonging to the same wzi31-KL31-K31 type. These findings emphasize the widespread occurrence of drug-resistant K. pneumoniae across diverse animal sources in Xinjiang, underscoring the high prevalence of multidrug resistance. Additionally, our results suggest the potential for animal-to-animal transmission of K. pneumoniae and there was a correlation between virulence genes and antibiotic resistance genes. Moreover, the current study provides valuable data on the prevalence, antibiotic resistance, and genetic diversity of K. pneumoniae originating from diverse animal sources in Xinjiang, China.

Postoperative prophylactic antibiotic therapy after pancreaticoduodenectomy in bile duct-stented patients reduces postoperative major complications

BackgroundPancreaticoduodenectomy can entail a high complication rate, especially in patients who underwent preoperative bile duct drainage through bile duct stenting. Pancreaticoduodenectomy bile duct stenting patients frequently receive prophylactic antibiotic therapy in the postoperative period. However, the exact value and the benefit of prophylactic antibiotic therapy in pancreaticoduodenectomy bile duct stenting patients remains under-investigated and thus unclear. MethodWe conducted a retrospective single-center study of pancreaticoduodenectomy bile duct stenting patients between January 2007 and December 2022. Demographic, clinical, laboratory, and pathology data of 370 patients were collected, and intraoperative swab cultures of the bile were obtained from all patients upon transection of the common bile duct. The groups to be investigated were formed on the basis of postoperative antibiotic prophylaxis. Postoperative complications and antibiotic resistance analysis were recorded. ResultsPostoperative antibiotic prophylaxis in stented patients after pancreaticoduodenectomy significantly reduced major complications (odds ratio: 0.547 [95% confidence interval 0.327–0.915]; P = .02) such as reoperation (P = .041) and readmission to the intensive care unit (P = .037). Patients with Enterococcus faecalis (odds ratio: 1.699 [95% confidence interval 0.978–2.950];P = .048), Enterococcus faecium (odds ratio: 1.808 [95% confidence interval 1.001–3.264]; P = .050), or Citrobacter (odds ratio: 2.211 [95% confidence interval 1.087–4.497]; P = .029) in their bile had a higher probability of developing wound infections. Appropriate antibiotic prophylaxis, according to the bile duct microbiome, significantly reduced the risk of wound infection (odds ratio: 2.239 [95% confidence interval 1.167–4.298]; P = .015). ConclusionPostoperative antibiotic prophylaxis in pancreaticoduodenectomy bile duct stenting patients significantly reduced major complications such as intensive care stay and reoperation. Targeted antibiotic treatment according to the biliary microbiome reduced the incidence of wound infections.

Comparative Analysis of Antibiotic Resistance and Biofilm Characteristics of Two Major Enterococcus Species from Poultry Slaughterhouses in South Korea.

The spread of antibiotic-resistant Enterococcus in the poultry industry poses significant public health challenges due to multidrug resistance and biofilm formation. We investigated the antibiotic resistance profiles and biofilm characteristics of E. faecalis and E. faecium isolates from chicken meat in poultry slaughterhouses in South Korea. Ninety-six isolates (forty-eight each of E. faecalis and E. faecium) were collected between March and September 2022. Both species were analyzed using MALDI-TOF, PCR, antibiotic susceptibility testing, and biofilm assays. A high level of multidrug resistance was observed in E. faecalis (95.8%) and E. faecium (93.8%), with E. faecium exhibiting a broader range of resistance, particularly to linezolid (52.1%) and rifampicin (47.9%). All E. faecalis isolates formed biofilm in vitro, showing stronger biofilm formation than E. faecium with a significant difference (p < 0.001) in biofilm strength. Specific genes (cob, ccf, and sprE) were found to be correlated with biofilm strength. In E. faecium isolates, biofilm strength was correlated with resistance to linezolid and rifampicin, while a general correlation between antibiotic resistance and biofilm strength was not established. Through analysis, correlations were noted between antibiotics within the same class, while no general trends were evident in other analyzed factors. This study highlights the public health risks posed by multidrug-resistant enterococci collected from poultry slaughterhouses, emphasizing the complexity of the biofilm-resistance relationship and the need for enhanced control measures.

Complete genome sequences and multidrug resistance genotypes of nontuberculous mycobacteria isolates from the Central Tuberculosis Reference Laboratory Muhimbili Tanzania

Background: Nontuberculous mycobacteria (NTM) usually comprise a group of environmental bacteria, with emerging but elusive coinfection with tuberculous mycobacteria, causing pulmonary tuberculosis. Whole genome sequencing may give insight into potential antimicrobial resistance genotypes, giving clinicians and policymakers proper directions in clinical applications and management regimens. Methods: WGS was performed on twenty-four gDNA isolates from archival samples at the Central Tuberculosis Reference Laboratory using the MinION Oxford Nanopore Sequencing approach. Out of twenty-four, two were confirmed to belong to the NTM group. Further analysis was done to resolve the complete genomes of two nontuberculous mycobacteria strains isolated from tuberculosis patients. We then combined phylogenomics, reference-based scaffolding and average nucleotide identity (ANI) analysis to delineate each strain's taxonomic position and corresponding features. Results: Our findings reveal that the two strains fit into the genus Mycolicibacterium, and the closest relative is Mycolicibacterium novocastrense. Coupling BacAnt and CARD-based antibiotic resistance analyses revealed multidrug-resistant genotypes of diverse spectra and mechanisms. While the BC02 strain is genetically resistant to beta-lactams, macrolides and rifamycins, the BC05 strain portrays an extended drug resistance genotype encompassing beta-lactams, macrolides, polyamines, and aminoglycosides. Both strains possess a single nucleotide polymorphism (SNP) of the RNA polymerase beta-subunit (rpoB), representing resistance to the first-line rifampicin. Additionally, the BC05 strain genetically portrays resistance to ethambutol, isoniazid and fosfomycin through mechanisms involving target alteration through SNPs, drug inactivation and efflux. Conclusion: Our findings strongly suggest the potential implication of multidrug-resistant NTM clinical isolates in the pathogenesis of pulmonary tuberculosis.

Comprehensive analysis of Salmonella in poultry meat and products in Türkiye: Prevalence, antibiotic susceptibility and genomic characterisation

SummaryThe study aimed to determine the prevalence and characteristics of Salmonella isolated from raw chicken meat and products. For this purpose, a total of 293 samples were collected, including chicken breast (n = 90), skinned drumstick (n = 80), skinned chicken chop (n = 42), wing (n = 32), chicken offal (n = 27) and chicken patty (n = 22). The samples were subjected to Salmonella enterica. detection and the obtained suspicious isolates were confirmed by conventional PCR. Their phenotypical antibiotic resistance profiles were subsequently determined. The prevalence of Salmonella Enteritidis and Typhimurium serovars among S. enterica isolates were investigated using TaqMan probe Real‐Time PCR (qPCR) analysis, and the detected serovars were evaluated with whole genome sequencing. In the study, 112 (38.22%) of the 293 chicken samples contained S. enterica, with five (4.46%) and one (0.89%) of the isolates identified as Salmonella Enteritidis and Typhimurium, respectively. Antibiotic resistance analysis revealed that all isolates were sensitive to Meropenem and Aztreonam, while the most resistant antibiotics were Doxycycline (96.42%) and Trimethoprim‐sulfamethoxazole (71.42%). Whole genome sequencing, specifically SNP‐based phylogenetic analyses, indicated that Salmonella Enteritidis and Typhimurium isolates were distinct clones. All Salmonella Enteritidis isolates shared the same antigenic profiles (9: g, m:‐) and cgMLST types of 11, while the Salmonella Typhimurium isolate had cgMLST type 19 and a 4:i:1,2 antigenic profile. It was observed that the phenotypic resistance profiles of the isolates were consistent with the whole genome characterisation. The data obtained in the study reveal the continued importance of Salmonella monitoring for the poultry industry across different regions of Türkiye to maintain food safety. Chicken meat and products are indispensable to public health in providing healthy nutrition and access to animal protein. The microbiological and epidemiological risks observed in mass production can be minimised, particularly by integrating epidemiological and molecular findings with an effective strategy.

Quality, safety, and microbiological assessment of loose market milk and antibiotic resistance analysis of Escherichia coli isolates in different areas of Faisalabad, Pakistan

Unpacked milk consumption is common in developing countries like Pakistan, raising concerns regarding adulteration and pathogen contamination. This study analyzed market-sold unpacked milk samples (n = 40) from Faisalabad for qualitative, adulteration, and microbiological parameters and antimicrobial resistance of Escherichia coli. The mean ± standard deviation for each component was determined: Fat% (4.22 ± 0.78), Solid-Not-Fat (SNF)% (7.98 ± 1.19), Protein% (2.96 ± 0.50), Lactose% (4.49 ± 0.70), Density (25.59 ± 3.81 g mL−1), Salts% (0.66 ± 0.08), Added water% (8.56 ± 9.72), Temperature (28.00 ± 1.67), and Freezing point (−0.52 ± 0.72). Adulterants such as sodium chloride, detergent, formalin, urea, carbonate, and hydro-peroxide, along with high heterotrophic bacterial load, were detected. Antibiotic resistance profiling of E. coli strains exhibited resistance, including Multidrug-Resistant (MDR) strains. These findings highlight compromised microbiological and hygiene standards in locally sold unpacked milk in Faisalabad, necessitating urgent attention to ensure public health safety.

Whole Genome Sequencing Highlights the Pathogenic Profile in Nocardia Keratitis.

Nocardia keratitis is a serious and sight-threatening condition. This study aims to reveal the virulence and antimicrobial resistance gene profile of Nocardia strains using whole genome sequencing. Whole-genome sequencing was performed on 23 cornea-derived Nocardia strains. Together with genomic data from the respiratory tract and the environment, 141 genomes were then utilized for phylogenetic and pan-genome analyses, followed by virulence and antibiotic resistance analysis. The correlations between virulence genes and pathogenicity were experimentally validated, including the characteristics of Nocardia colonies and clinical and histopathological evaluations of Nocardia keratitis mice models. Whole-genome sequencing of 141 Nocardia strains revealed a mean of 220 virulence genes contributed to bacterial pathogenesis. The mce gene family analysis led to the categorization of strains from the cornea into groups A, B, and C. The colonies of groupC had the largest diameter, height, and fastest growth rate. The size of corneal ulcers and the clinical scores showed a significant increase in mouse models induced by groupC. The relative expression levels of pro-inflammatory cytokines (CD4, IFN-γ, IL-6Rα, and TNF-α) in the lesion area exhibited an increasing trend from groupA to groupC. Antibiotic resistance genes (ARGs) spanned nine distinct drug classes, four resistance mechanisms, and seven primary antimicrobial resistance gene families. Whole genome sequencing highlights the pathogenic role of mce gene family in Nocardia keratitis. Its distribution pattern may contribute to the distinct characteristics of the growth of Nocardia colonies and the clinical severity of the mice models.

Antibiotic resistance of ESKAPE group-microorganisms in health institutions from Hermosillo and Ciudad Obregón, Sonora, México.

Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. are microorganisms referred as the ESKAPE group pathogens. These microorganisms have generated great concern in health institutions around the world since most of them have resistance to multiple antibiotics and cause most infections associated with healthcare, as well as community infections. The aim of this study was the analysis of antibiotic resistance in microorganisms of the ESKAPE group, recovered from clinical samples in 11 health institutions from Hermosillo and Ciudad Obregón in the State of Sonora, México, during the period from 2019 to 2020. A cross-sectional, descriptive, observational, and temporality epidemiological study was carried out. A comparative and statistical analysis of antibiotic resistance was carried out using the chi-square test, and small values were analyzed using Fisher's exact test p ≤ 0.05. All the ESKAPE group microorganisms showed significant differences in antibiotic resistance percentages between both cities. High resistance percentages for some antibiotics, like cephalosporins and ciprofloxacin were detected for Klebsiella pneumoniae and Acinetobacter baumannii.

Distribution characteristics of antibiotic resistance in direct-eating food and analysis of Citrobacter freundii genome and pathogenicity

Purpose This study aims to study the distribution characteristics of antibiotic resistance in direct-eating food and analysis of Citrobacter freundii genome and pathogenicity. Residual antibiotics and antibiotic resistance genes (ARGs) in the environment severely threaten human health and the ecological environment. The diseases caused by foodborne pathogenic bacteria are increasing daily, and the enhancement of antibiotic resistance of pathogenic bacteria poses many difficulties in the treatment of disease. Design/methodology/approach In this study, six fresh fruits and vegetable samples were selected for isolation and identification of culturable bacteria and analysis of antibiotic resistance. The whole genome of Citrobacter freundii isolated from cucumber was sequenced and analyzed by Oxford Nanopore sequencing. Findings The results show that 270 strains of bacteria were identified in 6 samples. From 12 samples of direct food, 2 kinds of probiotics and 10 kinds of opportunistic pathogens were screened. The proportion of Citrobacter freundii screened from cucumber was significantly higher than that from other samples, and it showed resistance to a variety of antibiotics. Whole genome sequencing showed that Citrobacter freundii was composed of a circular chromosome containing signal peptides, transmembrane proteins and transporters that could induce antibiotic efflux, indicating that Citrobacter freundii had strong adaptability to the environment. The detection of genes encoding carbohydrate active enzymes is more beneficial to the growth and reproduction of Citrobacter freundii in crops. A total of 29 kinds of ARGs were detected in Citrobacter freundii, mainly conferring resistance to fluoroquinolones, aminoglycosides, carbapenem, cephalosporins and macrolides. The main mechanisms are the change in antibiotic targets and efflux pumps, the change in cell permeability and the inactivation of antibiotics and the detection of virulence factors and ARGs, further indicating the serious risk to human health. Originality/value The detection of genomic islands and prophages increases the risk of horizontal transfer of virulence factors and ARGs, which spreads the drug resistance of bacteria and pathogenic bacteria more widely.

Genomic insights and antimicrobial resistance profiles of CRKP and non-CRKP isolates in a Beijing geriatric medical center: emphasizing the blaKPC-2 carrying high-risk clones and their spread.

The escalating resistance of Klebsiella pneumoniae, a prevalent pathogen in healthcare settings, especially its carbapenem-resistant K. pneumoniae (CRKP), to a wide array of antibiotics, notably β-lactams, constitutes a formidable challenge for healthcare and global public health management. This research compared the resistance phenotypes and genomic profiles of CRKP and Non-CRKP isolates in a Beijing hospital, focusing on high-risk blaKPC-2 gene-bearing CRKP clones and the structure of mobile genetic elements facilitating their spread across hospital departments. Forty K. pneumoniae isolates were collected from various departments of the hospital and subjected to antimicrobial susceptibility testing and whole-genome sequencing to analyze their resistance phenotypes and genomic features. The study revealed that among the 31 CRKP isolates, ST11 is the most common sequence type, with K47 and OL101 being the dominant capsule types, primarily observed in the respiratory department. In terms of antimicrobial susceptibility: 87.5% of the isolates exhibited multidrug resistance (MDR), with a high resistance rate of 30% against tigecycline. All CRKP isolates demonstrated resistance to multiple drug classes (≥5 CLSI classes). Non-CRKP isolates also showed high resistance rates to minocycline and doxycycline (77.8%). the ST11-KL47-OL101 type emerged as the predominant clone among the CRKP isolates carrying the blaKPC-2 gene. This dominance appears to be mediated by the pKpnR03_2 plasmid, which harbors not only blaKPC-2 and rmtb but also gene clusters pertinent to iron transport and arsenic resistance. These isolates, clustering in the C3 clade of the phylogenetic tree, exhibited minor genetic variations and close evolutionary relationships, suggesting a plasmid-driven spread across various hospital departments. In summary, our study highlights the extensive spread of antibiotic-resistant K. pneumoniae across various departments in our hospital, with a particular emphasis on the dominant clonal proliferation of the ST11-KL47-OL101 CRKP strain. This finding underscores the significant role of plasmid-mediated gene transfer in the evolution and dissemination of resistant strains within hospital environments. The study emphasizes the necessity for ongoing surveillance of antibiotic resistance and genomic analysis in hospital settings to effectively monitor and manage these challenges.