Antibiotic Resistance Determinants Research Articles

Prevalence, antibiotic resistance, resistance and virulence determinants of Campylobacter jejuni in China: A systematic review and meta-analysis.

Prevalence, antibiotic resistance, resistance and virulence determinants of Campylobacter jejuni in China: A systematic review and meta-analysis.

Evolutionary relationships and genetic diversity in the BlaTEM gene among selected gram-negative bacteria.

Evolutionary relationships and genetic diversity in the BlaTEM gene among selected gram-negative bacteria.

Upflow anaerobic sludge blanket based full-scale wastewater treatment plant, its performance evaluation and role as a breeding ground of antibiotic resistance determinants

Upflow anaerobic sludge blanket based full-scale wastewater treatment plant, its performance evaluation and role as a breeding ground of antibiotic resistance determinants

Broadly reactive monoclonal antibodies against beta-lactamases for immunodetection of bacterial resistance to antibiotics

With antibiotic resistance reaching alarming levels globally, rapid detection of resistance determinants is crucial for administering appropriate antimicrobial therapies. This study aimed to develop monoclonal antibodies (MAbs) against bacterial β-lactamases, which are key enzymes in antibiotic resistance, for potential diagnostic use. To generate MAbs capable of recognising a broad range of β-lactamases in bacterial isolates, the bacteriophage vB_EcoS_NBD2 tail tube protein gp39-derived nanotubes, as a scaffold displaying a highly conserved 17-amino acid peptide of AmpC β-lactamases, were produced in yeast and used as an immunogen for generation of MAbs by hybridoma technology. Thirteen hybridoma clones producing peptide-specific MAbs were developed. To assess MAb reactivity with AmpC enzymes, recombinant DHA-1, PDC-195, ACT-14, CMY-34, and ADC-144 β-lactamases were generated. Eleven of thirteen MAbs demonstrated cross-reactivity with all tested β-lactamases in ELISA and Western blot. Immunoprecipitation and Western blot analyses confirmed MAb reactivity with natural CMY-34 in the Citrobacter portucalensis isolate. Epitope analysis revealed that most MAbs recognise a highly conserved epitope of 11 amino acids. The MAbs were comprehensively characterised using different immunoassays, total internal reflection ellipsometry and computational modelling. These novel MAbs, which recognise a wide range of AmpC enzymes, represent a promising tool for immunodetection of antibiotic resistance determinants.

No Genomic Signatures Were Found in Escherichia coli Isolates from Camels With or Without Clinical Endometritis.

Clinical endometritis is a leading cause of infertility in she-camels. We commonly isolate E. coli from camel uteri with and without endometritis during our routine diagnosis of conception failure. From an epidemiological standpoint, it is critical to know if certain E. coli genotypes and virulence factors are specifically associated with endometritis. Thus, we aimed to compare the abundance of virulence elements and genotypes in uterine E. coli from camels with and without endometritis and understand their evolution. For this investigation, we retrieved data from the genomes of 28 E. coli isolates from humans, cats, dogs, horses, cows, and birds and 14 sequenced genomes of camel uterine E. coli isolates. We found no specific E. coli genotype or virulence factor associated with endometritis. Instead, multiple genotypes and high genomic diversity were observed. Moreover, horizontal gene transfer driven by genomic islands and plasmids contributed to the genetic diversity of the isolates, resulting in the acquisition of virulence genes, metabolic characteristics, and antibiotic resistance determinants to trimethoprim, sulfonamide, streptomycin, and tetracycline. Additionally, the phylogenetic position of the E. coli isolates from camel uteri suggests that they originated from intestinal strains. In conclusion, there was no evidence of E. coli specialization, and E. coli alone may not be able to develop endometritis, as other factors are required. Also, we elucidated the mechanism behind the diversity of the gene repertoire of E. coli isolated from camel uteri. These findings provide insight into the evolutionary origins of E. coli isolates from camel uteri.

Coagulase-Negative Staphylococci Determined as Blood Culture Contamination Have High Virulence Characteristic Including Transfer of Antibiotic Resistance Determinants to Staphylococcus aureus and Escherichia coli.

This study aimed to evaluate the virulence of 36 clinical isolates estimated as blood culture contaminants (BCCs). MALDI-TOF MS classified all isolates as coagulase-negative staphylococci (CoNS) with the highest percentage of S. epidermidis (77.78%). All tested strains formed biofilms with greater ability at room temperature than 37 °C. CoNS were sensitive to vancomycin (0% resistance) and had relatively low resistance to linezolid and rifampicin (8.33 and 22.22% resistance). The highest resistance was observed for penicillin (94.44%). Moreover, we observed the transfer of antibiotic resistance genes from the tested CoNS to S. aureus and even to E. coli, although with lower efficiency. CoNS in planktonic form were completely combated by antiseptics after 10 and 60 s exposition, and activity against biofilms was time-dependent. The complete elimination of biofilms was observed after a 180 s exposure to Kodan and CITROclorex, and this exposure to Rivanol and Octenidyne showed still viable cells (>0.9 log CFU/mL). Our findings showed that a careful selection of antiseptics and extending the exposure time before blood collection can reduce the occurrence of blood culture contamination. However, our most important finding is the indication that CoNS naturally occurring on human skin and mucous membranes exhibit antibiotic resistance, and what is more, determinants of antibiotic resistance are transferred to both closely related Gram-positive bacteria and phylogenetically distant Gram-negative bacteria. Thus, our findings shed new light on CoNS-they indicate the necessity of their control due to the effective transfer of mobile genetic elements harboring antibiotic resistance genes, which may contribute to the spread of resistance genes and deepening the antibiotic crisis.

Effects of Short-Term Feeding with Diets Containing Insect Meal on the Gut Microbiota of African Catfish Hybrids.

The impact of short-term feeding of three distinct diets containing insect meals on the intestinal microbiota of African catfish hybrid (Clarias gariepinus × Heterobranchus longifilis) juveniles was examined. The animals received experimental diets containing 30% insect meals derived from black soldier-fly larvae (BSL) (Hermetia illucens), yellow mealworm (Tenebrio molitor) or blue bottle-fly larvae (Calliphora vicina) for 18 days. The relative abundance of the Bacillaceae, the Planococcaceae and other bacteria significantly increased (p < 0.05) in the intestinal microbiota of the BSL group and also in the pooled group of the three catfish groups that received insect meals. Several strains of the Bacillales cultured from BSL feed had higher (p < 0.05) abundance in the intestinal microbiota of the BSL group compared to those of the control group. Among these Bacillales strains, a single fosB antibiotic resistance gene was identified. In the gut resistomes of both the BSL and the control catfish groups, the tetA(P), tetB(P) and lnu(C) antibiotic-resistance determinants were detected, while fosB was detected only in the BSL group. Overall, the study showed that a short-term shift to diets containing insect meals can induce significant (q < 0.05) changes in the gut microbiota of the African catfish without the development of reduced α-diversity and without the overgrowth of bacteria pathogenic to fish.

Identification of genetic determinants of antibiotic resistance in Helicobacter pylori isolates in Vietnam by high-throughput sequencing

The aim of this study was to identify genetic factors responsible for antibiotic resistance in Helicobacter pylori, a bacterium that can cause long-term gastroduodenal disease. The primary resistance of H. pylori to commonly used antibiotics was studied, and high-throughput next-generation sequencing (NGS) was employed to discover genetic determinants of resistance using a reference-based approach. A total of 123 H. pylori strains were cultured and tested for antibiotic susceptibility using an E test. Genotypic analysis was performed using NGS data with ARIBA v2.14.7 and PlasmidSeeker v1.3 for plasmid detection. Statistical correlations between resistant genotypes and phenotypes were evaluated. In addition, a genome-wide association study (GWAS) and linear mixed model were used to identify genetic variants associated with antimicrobial resistance phenotypes while adjusting for covariates such as population structure. Our results showed that 78.2% of the strains were resistant to metronidazole (MTZ), 22.5% to levofloxacin (LVX), 43.5% to clarithromycin (CLR) and 13.7% to amoxicillin (AMX). Resistance to tetracycline was not detected. Multi-drug resistance was detected in 48.8% of the strains. While plasmids were not detected, chromosomal genetic determinants of resistance to CLR, LVX, and AMX were identified, including mutations in 23S rRNA (A2142G and A2143G), gyrA (N87K/Y and D91Y/N/G), and pbp1 A (F366L, S414R, F473V, G595_V596insE, as well as the mutations T558S and T593A/G/P/S). Additionally, missense, frameshift, and nonsense mutations in rdxA were identified as genetic determinants of resistance to MTZ. No genetic determinants associated with tetracycline resistance were detected. A strong correlation was observed between resistance genotypes and phenotypes for CLR, LVX, AMX, and MTZ. In addition, we found that missense, frameshift and nonsense mutations in rdxA were genetic determinants of resistance to MTZ. We did not detect any genetic determinants associated with tetracycline resistance. There was a strong correlation between resistance genotypes and phenotypes for CLR, LVX, AMX, and MTZ. Furthermore, unitig-based GWAS revealed that AMX, LVX, and CLR resistance in H. pylori was mainly caused by chromosomal mutations that affected the targets of these antibiotics (pbp1 A, gyrA, and 23S rRNA, respectively). Our results highlight the need for regular evaluation and alternative therapies in Vietnam, given the high rates of H. pylori resistance to CLR, MTZ, and LVX. Our study also demonstrated the high capacity of NGS to detect genetic resistance determinants and its potential for implementation in local treatment policies.

Safety Assessment of Lactiplantibacillus plantarum GUANKE Based on Whole-Genome Sequencing, Phenotypic, and Anti-Inflammatory Capacity Analysis.

Lactiplantibacillus plantarum GUANKE (L. plantarum GUANKE) is a Gram-positive bacterium isolated from the feces of healthy volunteers. Whole-genome sequencing analysis (WGS) revealed that the genome of L. plantarum GUANKE consists of one chromosome and two plasmids, with the chromosome harbors 2955 CDS, 66 tRNAs, and 5 rRNAs. The genome is devoid of virulence factors and Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems. It contains three intact prophage regions and bacteriocin biosynthesis genes (plantaricins K, F, and E), as well as seventeen genomic islands lacking antibiotic resistance or pathogenicity determinants. Functional prediction outcomes identified that the genome of L. plantarum GUANKE is closely related to transcription, carbohydrate transport and metabolism, and amino acid transport and metabolism. Carbohydrate-active enzymes (CAZymes) analysis and GutSMASH analysis revealed that the genome of L. plantarum GUANKE contained 100 carbohydrate-active enzyme genes and two specialized metabolic gene clusters. Safety assessments confirmed that L. plantarum GUANKE neither exhibited β-hemolytic activity nor harbored detectable transferable drug resistance genes. The strain exhibited remarkable acid tolerance and bile salt resistance. Cellular adhesion assays demonstrated moderate binding capacity to Caco-2 intestinal epithelium (4.3 ± 0.007)%. In vitro analyses using lipopolysaccharide (LPS)-stimulated macrophage models demonstrated that L. plantarum GUANKE significantly suppressed the secretion of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β), exhibiting dose-dependent anti-inflammatory activity. In vivo experiments showed that L. plantarum GUANKE was involved in the regulation of the apical junction pathway and interferon pathway in colon tissue of normal mice.

Plasmid-driven strategies for clone success in Escherichia coli

Escherichia coli is the most widely studied microbe in history, but the population structure and evolutionary trends of its extrachromosomal elements known as plasmids remain poorly delineated. Here we used long-read technology to high-resolution sequence the entire plasmidome and the corresponding host chromosomes from an unbiased longitudinal survey covering two decades and over 2000 E. coli isolates. We find that some plasmids have persisted in lineages even for centuries, demonstrating strong plasmid-lineage associations. Our analysis provides a detailed map of recent vertical and horizontal evolutionary events involving plasmids with key antibiotic resistance, competition and virulence determinants. We present genomic evidence of both chromosomal and plasmid-driven success strategies adopted by distant lineages by independently inheriting the same genomic elements. Further, we use in vitro experiments to verify the importance of key bacteriocin-producing plasmids for clone success. Our study has general implications for understanding plasmid biology and bacterial evolutionary strategies.

Molecular characterization of putative antibiotic resistance determinant and virulence factors genes of Acinetobacter baumannii strains isolated from intensive care unit patients in Riyadh, Saudi Arabia.

Molecular characterization of putative antibiotic resistance determinant and virulence factors genes of Acinetobacter baumannii strains isolated from intensive care unit patients in Riyadh, Saudi Arabia.

Comparative genomic analysis of clinical isolates of &lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; isolated from newborns with different outcomes of the infectious process in the neonatal period

Introduction. Some progress has been made in the study of the molecular mechanisms of antibiotic resistance, namely, genes and their variants have been identified that ensure the inactivation of beta-lactam antibiotics. Nevertheless, there is still a necessity for further studies of genetic diversity of nosocomial strains, prevalence of genetic determinants of resistance to other groups of antibiotics, virulence factors and realization of pathogenic potential by opportunistic microorganisms. Aim of the study was to compare the genetic profile of clinical isolates of Klebsiella pneumoniae isolated from newborns with different outcomes of the infectious process in the neonatal period. Materials and methods. Using whole-genome sequencing and bioinformatic analysis to search for determinants of resistance and virulence, 3 strains of K. pneumoniae were studied, 2 of which were isolated from the blood of a generalized form of infection, 1 from the feces of a newborn child. Results. K. pneumoniae strains belonged to sequence types (ST) ST23, ST14 and ST3559, and differed in genetic determinants of antibiotic resistance and virulence factors. At the same time, they all had the genetic determinants fimH, mrkA and iutA, which are associated with an increased ability to attach to substrates and transport aerobactin. Strain 222 of ST3559, which has the largest number of antibiotic resistance genes, contained the smallest number of virulence factor genes, and vice versa, strain 144 of ST23, in which the smallest number of antibacterial drug resistance genes was detected, contained the most virulence factor genes. Conclusions. Identification of K. pneumoniae strains that differ in the genetic profile of antibiotic resistance and virulence in neonatal hospital patients indicates a complex interaction between bacteria and the macroorganism, in which isolates with low pathogenic potential can cause serious infectious complications, and vice versa, when a highly virulent strain does not realize its pathogenic potential, as demonstrated in case of K. pneumoniae strains ST14, ST3559 and ST23, respectively. This highlights the difficulty of effectively predicting and managing infection risks in hospital operations.

Antibiotic Resistance and Virulence Determinants of Pseudomonas aeruginosa Isolates Cultured from Hydrocarbon-Contaminated Environmental Samples.

Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a P. aeruginosa isolate cultured from a hydrocarbon-contaminated soil sample from Ogoniland, Nigeria, and to compare its characteristics with P. aeruginosa isolates cultured worldwide from hydrocarbon-contaminated environments or from clinical samples. Using the ResFinder reference database, a catB7 chloramphenicol acetyltransferase gene, an ampC-type PDC β-lactamase gene, and an OXA-50 type β-lactamase gene were identified in all P. aeruginosa strains analyzed in this study. In some of these P. aeruginosa strains, loss-of-function mutations were detected in the regulatory genes mexR, nalC, or nalD, predicting an efflux-mediated acquired antibiotic-resistance mechanism. Several P. aeruginosa sequence types that were associated with oil-contaminated environments have also been cultured from human clinical samples worldwide, including sequence types ST532, ST267, ST244, and ST1503. Our findings also indicate that environmental P. aeruginosa may serve as the source of human infections, warranting further studies from a One Health perspective about the application of P. aeruginosa for the in situ bioremediation of hydrocarbon-contaminated sites.

Analysis of co-occurrence of type II toxin-antitoxin systems and antibiotic resistance determinants in Staphylococcus aureus.

Toxin-antitoxin (TA) systems are entities unique to bacteria. They are involved in the maintenance of mobile genetic elements (MGEs), regulation of gene expression and bacterial virulence. Staphylococcus aureus is a dangerous human pathogen with increasing antibiotic resistance (AR). The maintenance and dissemination of AR determinants is often driven by MGEs, which link AR and TA systems. Our study identified a negative correlation between TA systems and AR determinants in S. aureus. Furthermore, we have shown that the expression of a toxic component of an exemplary TA system negatively affects antibiotic resistance. We argue that in particular strains, a selective pressure maintains either the TA system or AR determinant. Alternatively, TA systems are inactivated by mutations when present together with AR determinants to maintain the functionality of the latter. Our observations uncover an important factor shaping the spread and evolution of both TA systems and AR determinants in bacteria, which is especially relevant to pathogenic species.

Progression of antibiotic resistance in Neisseria meningitidis.

SUMMARYThe human pathogen Neisseria meningitidis (Nm) is the causative agent of invasive meningococcal disease (IMD), usually presenting as meningitis, bacteremia, or sepsis. Unlike Neisseria gonorrhoeae, antibiotic resistance in Nm has developed slowly. However, in the last two decades and with the reemergence of IMD following the COVID-19 pandemic, antibiotic-resistant Nm isolates, especially to penicillin and fluoroquinolones, have progressively increased. Recent worldwide studies of penicillin intermediate and resistant Nm isolates and the PubMLST global database reveal a notable increase in fully penicillin-resistant isolates since 2016, mediated by mosaic penA alleles or the β-lactamase genes blaROB-1 and blaTEM-1. Fluoroquinolone-resistant isolates, mediated by gyrA mutations, have increased since 2005. Also, while still exceptionally rare, four Nm isolates have been identified with third-generation cephalosporin-resistance since 2011. We review the emergence of antibiotic resistance determinants and lineages in Nm, the resistance to agents previously or currently used in treatment or chemoprophylaxis, and summarize updated treatment and prevention guidelines for IMD. Special populations (e.g., individuals on complement inhibitors) and antibiotic resistance in Nm urethritis isolates are also reviewed. The increasing number of resistant Nm isolates worldwide affects chemoprophylaxis and treatment options for IMD and emphasizes the need for enhanced global surveillance of antibiotic resistance in Nm.

Genome sequence of prodigiosin-producing and tetracycline-resistant Serratia marcescens (IFSMLMEK1), identified from a freshwater bivalve Lamellidens marginalis.

We report the genome sequence of a tetracycline-resistant Serratia marcescens, IFSMLMEK1, isolated from the freshwater bivalve Lamellidens marginalis. The genome (5,185,668 bp, G+C% 59.65) reveals antibiotic resistance determinants, including tetracycline efflux genes, providing valuable insights into prodigiosin production and tetracycline resistance in environmental isolates.

Co-occurrence of mcr-9 and blaNDM-5 in Multidrug-ResistantEnterobacter hormaechei Strain Isolated from a Patient with Bloodstream Infection.

Enterobacter hormaechei (E. hormaechei), a member of the Enterobacter cloacae complex, has emerged as an important pathogen in healthcare-associated infections. In this study, a multidrug-resistant E. hormaechei EH001 co-carrying mcr-9 and blaNDM-5 was isolated from a patient with bloodstream infection in China. To investigate the genomic characteristics of a multidrug-resistant E. hormaechei EH001 co-carrying mcr-9 and blaNDM-5, whole-genome sequencing was employed and conjugation experiment was performed by using the recipient E. coli EC600. The antimicrobial susceptibility profiles of E. hormaechei EH001 revealed resistance to the most commonly used antimicrobial agents, with the exception of polymyxin B, polymyxin E, and minocycline. E. hormaechei EH001 was classified as sequence type 78 (ST78) and harbored multiple resistance genes, especially co-carried mcr-9 and blaNDM-5 located on an IncHI2 plasmid (pMCR9_EH001) and an IncX3 plasmid (pNDM5_EH001), respectively. Both plasmids were successfully co-transferred to E. coli EC600 by conjugation. Analysis of the genetic environment of mcr-9 and blaNDM-5 revealed the multiple mobile genetic elements, such as insertion sequences (IS) and transposon (Tn). ∆Tn3-IS3000-∆ISAba125-5'-IS5-∆ISAba125-3' were situated upstream of blaNDM-5, while bleMBL-trpF-dsbD-CutA-IS26 were situated downstream of it. In addition, rcnR, rcnA, pcoE, pcoS, and IS5 family transposase (IS903B) were situated upstream of mcr-9, while IS3000 was situated downstream of it, followed by blaCTX-M-3 and IS26. The majority of the plasmid-mediated resistance genes reside within or adjacent to diverse mobile genetic elements, which may potentially promote the horizontal transfer of antibiotic resistance determinants. This study represents the initial investigation providing the detailed genomic characteristics associated with co-occurrence of mcr-9 and blaNDM-5 in E. hormaechei. The findings advocate for heightened clinical vigilance toward such strains, particularly to prevent nosocomial transmission.

Is our winter experience safe? Micropollutant risks for artificial snowing.

Is our winter experience safe? Micropollutant risks for artificial snowing.

Phenotypic antibiotic resistance prediction using antibiotic resistance genes and machine learning models in Mannheimia haemolytica.

Phenotypic antibiotic resistance prediction using antibiotic resistance genes and machine learning models in Mannheimia haemolytica.

Enterococcus: Understanding Their Resistance Mechanisms, Therapeutic Challenges, and Emerging Threats.

The Enterococcus species originates as non-harmful bacteria indigenous to human intestines but has transformed into severe hospital-acquired pathogens due to antimicrobial resistance (AMR). The clinical speciesEnterococcus faecalisandEnterococcus faeciumcreate the most relevant infections because they appear in urinary tract infections, bloodstream infections, endocarditis, and wound infections.Enterococcusspecies demonstrate multiple antibiotic class resistance and resistance determinant acquisition properties that make treatment difficult for medical professionals. Vancomycin-resistant enterococci (VRE) together with high-level aminoglycoside-resistant strains and resistance to both linezolid and daptomycin have exhausted available treatment options. The review investigates the development process ofEnterococcusinfections by examining virulence characteristics, which involve biofilm production and defense mechanisms against the immune response and transmission of resistance genes. A thorough investigation of medical publications used Google Scholar along with PubMed and ScienceDirect and Medical Subject Headings (MeSH) as appropriate search terms. The traditional classification ofEnterococcusspecies from historical context to modern epidemiology and pathogenesis and available treatment and test approaches are explained in this review. This section examines two categories of resistance together with their mechanisms of action with a specific focus on vancomycin resistance produced by van gene clusters as well as its prevalence trends. An examination of how horizontal gene transfer functions in transferring resistance throughout healthcare facilities is included. The paper investigates the different symptoms of enterococcal infections together with diagnostic obstacles and treatment modalities. Drug-resistantEnterococcusinfections continue to increase internationally, so healthcare professionals need new therapeutic methods, better antimicrobial policies, and stronger infection prevention measures. The examination surveysEnterococcusinfections through an extensive evaluation of developing resistance patterns combined with emerging intervention requirements.