Antibiotic Resistance Determinants Research Articles

Mobilizable multidrug resistance plasmid identified in Staphylococcus xylosus isolated from fermented soybean food.

We identified two Staphylococcus xylosus strains that were isolated from the same Korean fermented soybean food with different antibiotic resistance profiles. Strain 14BME10 showed multidrug resistance to erythromycin and tetracycline, whereas strain 14BME18 was resistant to tetracycline only. We sought to elucidate the genetic background of the antibiotic resistance in these strains. A comparative genomic analysis with three other antibiotic-sensitive S. xylosus strains revealed antibiotic resistance determinants located on two mobilizable plasmids in the isolates. The 73.7kb plasmid p14BME10-1, encoding the ABC-F type ribosomal protection protein gene msr(A) and the Mph(C) family macrolide 2'-phosphotransferase gene mph(C), might have contributed to erythromycin resistance. The 4.4kb plasmid harboring the tetracycline efflux MFS transporter gene tet(K) conferred tetracycline resistance and showed 100% DNA sequence identity with the prototype tetracycline resistance plasmid pT181, widely identified in staphylococci. We discovered that the MOBP relaxase gene cluster in p14BME10-1 consists of four genes and an oriT, which might be involved in plasmid mobilization and was also found in many staphylococcal plasmids. The plasmid p14BME10-1 harbors multiple genes for replication, mobilization, transposition, recombination, and resistance to erythromycin, streptomycin, and bacitracin, indicating several occurrences of recombination and integration events, but lacks the genes necessary for conjugal transfer.

Bacteriological analysis of the sanitary pads available in the local markets of Surat, Gujarat, India

Sanitary pads are widely used menstrual hygiene products that come into direct contact with the skin and mucosal surfaces for extended periods, making their microbial safety a critical public health concern. This study focuses on the bacteriological analysis of commercially available sanitary pads to assess their bacterial contamination levels and ensure user safety. Samples from various brands, including those sold as loose pickings, were subjected to standard bacteriological procedures, including the isolation and identification of probable contaminants, as well as the determination of antibiotic resistance in the isolates. The results indicated that Staphylococcus aureus, Escherichia coli, Enterobacter spp., Klebsiella spp., Pseudomonas aeruginosa, and Bacillus spp. were the probable bacterial isolated from different sanitary pads. The probable isolates exhibited antibiotic resistance; 3 strains of S. aureus were found to be resistant to tetracycline, penicillin and combine resistant to penicillin and streptomycin, 2 strains of E.coli one resistant to ampicillin another resistant to both tetracycline and chloramphenicol, Enterobacter spp. strain was found resistant to both tetracycline and Penicillin G, while one strain each of B. cereus and Klebsiella spp. were resistant to ampicillin. The present study provides insight into which types of sanitary pads should be purchased, as well as recommendations for their storage at home. The presence of antibiotic-resistant bacterial isolates in sanitary pads raises concerns about their prolonged use. Keywords: Sanitary pads, bacterial contaminants, antibiotic resistant isolates, menstruation, microbial quality control, sterility

Large-scale global molecular epidemiology of antibiotic resistance determinants in Streptococcus pneumoniae.

Streptococcus pneumoniae is a leading pathogen in terms of deaths attributable to or associated with antimicrobial resistance globally. Thus, monitoring antibiotic resistance determinants constitutes a key aspect of surveillance efforts for this microbe. Leveraging publicly available whole-genome sequencing (WGS) data, we aimed to investigate the presence and distribution patterns of antibiotic resistance determinants in S. pneumoniae with a focus on multidrug resistance (MDR) and serotype distribution. Metadata and genomes were obtained from the National Center for Biotechnology Information Pathogen Detection database. Curation and harmonization were performed in R and SPSS. Data on resistance patterns were defined according to AMRFinderPlus, and a combination of prediction tools was employed for in silico serotyping. Analyses involved 75,161 genomes totalling 122,673 gene/allele counts from 14 antibiotic classes. MDR was observed in 16.7% of isolates, with the highest increasing rates in Asia and South America. Within antibiotic classes, an increase in macrolide resistance genes was highlighted, particularly in the proportion of genomes presenting mef(A)/msr(D). Over a third of isolates with serotypes 19F, 23F, 15A, 6B and 19A showed MDR. We further observed the highest significant increases in the presence of resistance in 33F, 22F, 10A and 23A. Serotype 13, not included in any vaccine formulation, presented high MDR rates with a strong increasing trend. The findings of this study highlight variations in resistance determinants globally and across serotypes over time. Collectively, these data underscore the added value of utilizing public WGS data to investigate the effectiveness and repercussions of treatment and vaccination strategies on managing antibiotic resistance.

Сombat wounds microflora in modern warfare

The purpose. Analysis of the clonal characteristics and antibiotic resistance of the most prevalent wound pathogens among individuals injured in the Russian-Ukrainian war to support microbiota surveillance of combat wounds and optimize treatment strategies. Materials and Methods. A bacteriological examination was conducted on wound specimens from 171 injured individuals who received treatment in three healthcare facilities located in the central region of Ukraine between 2022 and 2023. Results from bacteriological studies of 151 wounded individuals treated in the same hospitals during the period from 2017 to 2020 were used for comparative analysis. Antibiotic susceptibility testing was performed using the disk diffusion method in accordance with the recommendations of EUCAST (European Committee on Antimicrobial Susceptibility Testing). To determine antibiotic resistance determinants and phylogenetic relationships between strains, whole-genome sequencing (WGS) of the isolated cultures was carried out using next-generation sequencing (NGS) technology on the Applied Biosystems/Life Technologies SOLiD platform, followed by core genome multilocus sequence typing (cgMLST). Identification of resistance genes was conducted by comparing the obtained nucleotide sequences against the GenBank® database of the National Center for Biotechnology Information (NCBI) using the BLAST (Basic Local Alignment Search Tool) algorithm. Data analysis was performed using descriptive statistics with assessment of statistical significance of differences between alternative indicators (case proportions) by Student’s t-test, utilizing the STATISTICA 13.3 software package (license AXA905I924220FAACD‐N). Results. The composition of predominant wound pathogens in the most recent observation period changed insignificantly compared to the 2017–2020 period. Throughout the entire observation period, the dominant species among wound infection pathogens were A. baumannii, P. aeruginosa, and K. pneumoniae. Among the isolated strains, a high frequency of high-risk global clonal lineages was observed, namely K. pneumoniae ST395, ST147; A. baumannii ST2, ST78; P. aeruginosa ST773 and ST1047. Over 90% of isolates, regardless of species, were multidrug-resistant. A high prevalence of genes responsible for the production of beta-lactamases (blaOXA-23, blaOXA-72) and metallo-beta-lactamases (blaNDM-1, blaIMP-1) was identified among the isolated strains. Conclusion. A bacteriological study of combat wound content was conducted among injured individuals receiving treatment at three healthcare institutions located in the central region of Ukraine during the periods of 2017–2020 and 2022–2023. The results indicate a shift in the etiological structure of purulent-inflammatory complications of combat wounds, with a predominance of Gram-negative microorganisms, primarily non-fermenting bacteria and members of the Enterobacteriaceae family. It was found that, following the onset of the full-scale invasion, the total proportion of these microorganisms among all isolated strains significantly increased to 93.5%, compared to 80.2% prior to 2021 (p<0.001). Notably, the frequency of Enterobacteriaceae isolation from wounds showed an upward trend: Escherichia coli was isolated in 9.1% of cases versus 5.0% before 2021, while the proportion of Klebsiella pneumoniae significantly increased to 20.7% compared to 8.6% prior to the full-scale war (p<0.001). High-risk globally distributed clonal lineages, such as K. pneumoniae ST395 and ST147; A. baumannii ST2 and ST78; and P. aeruginosa ST773 and ST1047 were the most frequently identified among the isolates. More than 90% of all isolates, regardless of species, were multidrug-resistant. Molecular genetic analysis revealed a high prevalence of international clones of A. baumannii associated with increased antibiotic resistance. Specifically, 17.6% of A. baumannii isolates belonged to the high-risk, globally distributed ST2 lineage (IC II), which harbored genes encoding carbapenemases blaOXA-23 and blaOXA-72, as well as 16S rRNA methyltransferase (armA), conferring resistance to aminoglycosides and fluoroquinolones. Furthermore, 33.8% of isolates were identified as belonging to another high-risk international clone, IC VI (ST78, ST1077). The high concentration of injured individuals in both domestic and foreign healthcare facilities created a vast reservoir of multidrug-resistant microorganisms with a significant potential for global dissemination. This situation necessitates close surveillance and continuous microbiological monitoring, as well as the development and implementation of a comprehensive set of multimodal infection prevention and control measures.

Unveiling the probiotic potential ofEnterococcusspp.: Mechanisms and roles in animal and human health, A comprehensive review.

Enterococci, a subset of lactic acid bacteria, are ubiquitous in a variety of ecosystems, including the gastrointestinal tracts of mammalian and avian species. Due to their extreme adaptability, enterococci thrive in exceptionally unfavorable conditions characterized by high salinity levels, exposure to bile salts, a wide range of pH variations and high-temperature thresholds. Investigation into enterococcal strains as potential probiotics has encompassed the fields of human health, animal husbandry and companion animal welfare. In the context of human applications, the objectives are related to increasing immune responses, reducing cholesterol levels and providing anti-inflammatory and antioxidant attributes. Similarly, the livestock sector has recognized the potential of enterococci to stimulate growth, inhibit pathogen proliferation and amplify immune reactivity. Pet health interventions using enterococci aim to balance the microbiota, boost immune function and improve the animal's general well-being. The mechanisms of probiotic effects mediated by enterococci are manifold, including the production of enterocins, improvement of cholesterol levels, immunomodulation, antioxidant activities, attenuation of inflammatory cascades and the support of liver functions. While enterococcal probiotics hold great promises for optimizing human and animal health, safety considerations must be taken into account. Given the pathogenic character of enterococci and their capacity to carry antibiotic resistance determinants, rigorous evaluation of safety profiles is an imperative prelude to their judicious use as probiotics.

Staphylococcus aureus and methicillin-resistant Staphylococcus aureus in juvenile green turtle (Chelonia mydas) carcasses, rearing seawater, feed and their antibiotic resistances.

Staphylococcus aureus is an opportunistic bacterium that can infect humans and animals. We previously reported that Staphylococcus aureus as one of the most frequent Gram-positive bacteria found in the infection in juvenile green turtles (Chelonia mydas) from the Sea Turtle Conservation Center of Thailand (STCCT), Sattahip, Chonburi Province. It was also the most detected Gram-positive bacteria in rearing seawater. In this study, we investigated the presence of S. aureus in coastal seawater used as supply water to rearing containers, rearing water, fish fillet used as feed, and juvenile green turtle carcasses at STCCT. From the results, S. aureus can be isolated from rearing water, fish fillet, and juvenile turtle carcasses but not from incoming coastal seawater. The determination of antibiotic resistance against 11 drugs demonstrated that more S. aureus from juvenile turtles were antibiotic resistant than the isolates from rearing water and fish fillet. Furthermore, a higher isolate number of methicillin-resistant S. aureus (MRSA) was found in juvenile turtle carcasses. We also detected penicillin-susceptible MRSA and mecA-positive methicillin-susceptible S. aureus from juvenile turtles and fish fillet, respectively. Differences in the antibiotic resistance profiles were observed in this study compared with our previous observation. A change in the antibiotic resistance properties possibly continued in S. aureus. This finding suggests that the status of animal health is at high risk and emphasizes the need for a surveillance plan and treatment strategies to confront this serious threat.

Antibiotic Resistance and Genetic Determinants of Helicobacter pylori in Oman: Insights from Phenotypic and Whole-Genome Analysis

Helicobacter pylori antibiotic resistance data in Oman are limited yet crucial for effective treatment selection. The genetic diversity within H. pylori influences its pathogenicity and clinical outcomes. This study evaluates resistance patterns and genetic determinants to guide treatment strategies. This study assessed antibiotic susceptibility in 15 H. pylori isolates (from 169 clinical samples) from naïve and treatment-failed patients. Resistance to clarithromycin (CLA), amoxicillin (AMX), metronidazole (MTZ), tetracycline, rifampicin (RIF), and levofloxacin (LEV) was tested alongside genetic analysis of virulence and resistance-associated mutations by whole-genome sequencing (WGS). Among the 15 resistant isolates, 20% were resistant to one antibiotic, 33.3% to two, 20% to three, and 26.6% to four antibiotics. MTZ resistance was universal among single-drug resistant isolates (100%). AMX-MTZ dual resistance was present in 60%, while triple resistance (CLA-AMX-MTZ) was present in 66.7%. Quadruple resistance (CLA-AMX-MTZ-RIF) was present in 75%. WGS revealed 23S rRNA mutations in 33.3% of CLA-resistant strains and pbp-1 mutations in 66.6% of AMX-resistant strains. MTZ resistance was linked to rdxA/frxA mutations, while RIF and LEV resistance correlated with rpoB (65.7%) and gyrA (20%) mutations, respectively. The genotype–phenotype agreement was insignificant (p = 1). High mutation heterogeneity, virulence factors, and environmental influences contribute to resistance. Further studies on host–pathogen interactions are needed to understand resistance mechanisms.

Comparative genomics of Acinetobacter baumannii from Egyptian healthcare settings reveals high-risk clones and resistance gene mobilization

BackgroundAcinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classification. This pilot study aimed to characterize 18 A. baumannii isolates from Egyptian healthcare settings, focusing on clonal lineages, antibiotic resistance determinants, horizontal gene transfer potential, and the presence of virulence factors and chromosomal mutations.MethodsAntimicrobial susceptibility testing was performed to determine resistance profiles using minimum inhibitory concentrations. Whole-genome sequencing was used to identify β-lactamase, carbapenemase, and other antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs). Clonal relationships among isolates were assessed via core genome multilocus sequence typing (cgMLST).ResultsPhenotypic analysis revealed that 72% of the isolates were extensively drug-resistant (XDR), exhibiting resistance to all tested antibiotics except colistin. Clonal diversity analysis identified 11 Oxford sequence types (STs), including two novel STs (ST3309OXF and ST3321OXF), and six international clonal (IC) groups, with IC2 being the most prevalent. Additionally, eight Pasteur STs were detected, with ST570PAS being the most frequent. The cgMLST analysis showed that two Egyptian ST570PAS isolates clustered with a strain from Saudi Arabia, suggesting potential regional transmission. Genomic analysis revealed the widespread dissemination of ARGs via MGEs, particularly rep plasmids and insertion sequence elements, which contributed significantly to genomic diversity and antibiotic resistance.ConclusionsThis pilot study highlights the clonal diversity of A. baumannii in Egypt and underscores the critical role of MGEs in the spread of resistance genes. Targeted genomic surveillance and infection control are essential to curb the spread of high-risk resistant A. baumannii clones in Egyptian clinical settings.

First detection of resistance genes and virulence factors in Escherichia coli and Salmonella spp in Togo: the case of imported chicken and frozen by-products

BackgroundThe increasing importation of frozen poultry into Togo raises concerns about the microbiological safety and antimicrobial resistance of associated pathogens. Despite the public health risks posed by resistant foodborne bacteria, data on resistance profiles, resistance genes, and virulence factors in imported frozen chickens in Togo remain limited. This study aims to address this gap by characterizing these factors in pathogenic strains isolated from imported poultry.MethodsA cross-sectional prospective study was undertaken to assess the microbiological quality and resistance profiles of imported poultry products. Samples were collected from seven cold storage facilities located within the Golfe prefecture of the Greater Lomé metropolitan area. In total, 285 poultry meat and cut samples were analyzed following standardized AFNOR microbiological protocols. Isolated Salmonella spp. and Escherichia coli strains underwent antibiotic susceptibility testing using the disk diffusion method, adhering to the guidelines established by the Comité de l’Antibiogramme de la Société Française de Microbiologie (CA-SFM). Furthermore, polymerase chain reaction (PCR) assays were employed to identify genetic determinants of antibiotic resistance and virulence factors in the bacterial isolates.ResultsMicrobiological analysis revealed a prevalence of Escherichia coli of 32.98%, while Salmonella spp. were detected in 2.46% of the samples. Antibiotic susceptibility testing demonstrated resistance among isolates to several beta-lactams and quinolones. Specifically, resistance to cefoxitin was observed in 14.28% of strains, whereas resistance to cefalexin, cefuroxime, ceftazidime, ceftriaxone, and nalidixic acid was uniformly detected at a prevalence of 28.57%. Among the E. coli isolates, 9.44% exhibited multidrug resistance to both beta-lactams and quinolones. Molecular characterization identified class 1 integrons in 17.6% of isolates, with gene cassettes predominantly harboring aadA1 and dfr1, which encode resistance to streptomycin, spectinomycin, and trimethoprim. Notably, class 2 and class 3 integrons were absent. Additionally, the plasmid-mediated qnrB gene was detected in 5.9% of isolates. The study also documented the emergence of resistance to third-generation cephalosporins (C3G), primarily associated with extended-spectrum beta-lactamase (ESBL) production, as evidenced by the presence of blaCTX (35.3%) and blaTEM (58.8%) genes among ESBL-producing strains.ConclusionsThis study reveals a notable presence of antimicrobial-resistant Escherichia coli and Salmonella in imported frozen poultry in Togo, highlighting significant public health risks. The findings call for improved surveillance and stricter control measures to prevent the spread of resistant pathogens via the food supply.Clinical trial numberNot applicable.

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.

Phenotypic and molecular determination of biofilm formation and antibiotic resistance of coagulase negative staphylococci isolated from food samples of animal origin in Turkey

Aim: This study aimed to investigate the antibiotic resistance and biofilm formation characteristics of the coagulase-negative Staphylococcus (CNS) isolated from various animal food samples (raw milk, cheese, chicken, meat). Methods: A total of 60 Staphylococcus isolates collected from various animal food samples (raw milk, cheese, chicken, meat) were obtained from the frozen culture collection of the Microbiology Laboratory of the Gazi University. The isolates were assessed regarding antibiotic resistance, biofilm and s-layer formation, and biofilm-associated genes. Results: In total, 22 CNS isolates were identified. The CNS isolates were highly resistant to fosfomycin (68.2%; 15/22), fusidic acid (63.6%, n=14/22), and tetracycline (59.1%, n=13/22). There was an intermediate resistance to other antibiotics as well. There was very strong slime production (54.5%, n=12/22) and S-layer production (40.9%, n=9/22). The biofilm formation of CNS isolates was better at 24 hours. Regarding the biofilm-producing genes, 10 (45%) of 22 CNS isolates were positive for the icaA gene, and 4 (18%) isolates were positive for the icaD gene, while all of the isolates were negative for the bap gene. Conclusion: The CNS existing in foods from animals may lead to public health problems with clinical implications as a result of being one of the important factors associated with antibiotic resistance. The bacteria that can gain antibiotic resistance and biofilm formation capabilities in the stages of production and consumption may be a critical healthcare issue for humans and animals.

Genomic characteristics of the multiresistant Acinetobacter baumannii global clone 1 reference strain A297/RUH875

ObjectivesAcinetobacter baumannii ST1, also known as global clone 1 (GC1), is a globally distributed lineage associated with antimicrobial resistance (AMR). The multiresistant isolate A297/RUH8751, recovered from a urinary tract infection in the Netherlands in 1984, has served as a reference strain for ST1. We aimed to generate and analyse the complete genome sequence of A297/RUH8751 to provide insights into its genomic features, antibiotic resistance determinants and phylogenetic placement.MethodsWGS was performed using Oxford Nanopore GridION and Illumina HiSeq platforms. Assembly was conducted with Autocycler v0.2.1. Genomic features, including antibiotic resistance genes, insertion sequences and restriction-modification systems, were characterized using ResFinder, ISFinder and REBASE. Comparative analyses were conducted with the draft genome of NIPH 527, which also represents RUH875, to assess sequence variations. Phylogenetic analysis was performed to determine the evolutionary placement of A297/RUH875 within GC1.ResultsThe complete genome of RUH875 (A297) consists of a 3 965 450 bp chromosome and three plasmids: pA297-1 (pRAY*; 6078 bp), pA297-2 (8731 bp) and pA297-3 (a 200 kb conjugative plasmid). The chromosome harbours the AbaR21 genomic resistance island, carrying seven antibiotic resistance genes and six prophage regions. Notably, bap1 and bap2, biofilm-associated genes, were fully resolved, with bap1 identical to that of A. baumannii A1—the earliest GC1 isolate. Comparative analysis with A1 revealed 122 SNPs, with clustered variations suggesting potential recombination events. Phylogenetic analysis confirmed A297/RUH875 as a distinct lineage within GC1. The completed genome sequence provides a reference, in addition to strain A1, for studying AMR evolution in GC1 and enhances comparative genomic analyses.

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.

Genomic characterization of group B Streptococcus from Argentina: insights into prophage diversity, virulence factors and antibiotic resistance genes

Group B Streptococcus (GBS) is a commensal bacterium that can cause severe infections in infants and adults with comorbidities. Resistance and reduced susceptibility to antibiotics are continually on the rise, and vaccines remain in development. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on prophage contribution to the epidemiology of GBS isolates from humans in South America. In the context of an Argentinian multicentric study, we had previously phenotypically characterized 365 human GBS isolates from invasive disease, urinary infections and maternal colonization. These isolates had been whole-genome sequenced, and their prophage presence was bioinformatically determined. In this study, we genomically characterized the isolates and analysed the prophage content in the context of the epidemiological data. The phylogenetic analysis of the 365 genomes with 103 GBS from public databases revealed that Argentinian GBS were related to isolates from around the world. The most prevalent lineages, independent of the isolated source, were CC23/Ia and CC12/Ib. Genes encoding virulence factors involved in immune response evasion, tissue damage and adherence to host tissues, and invasion were found in all of the genomes in accordance with previously described lineage distribution. According to the prevalent capsular types and the distribution of specific virulence factors in Argentinian GBS, over 95% coverage would be expected from the vaccines currently under development. Antibiotic resistance determinants (ARDs) to at least one antibiotic class were found in 90% of the genomes, including novel mutations in pbp2x, while more than 15% carried ARDs to three or more classes. GBS collected from urinary infections carried a significantly higher proportion of ARDs to multiple antibiotic classes than the rest of the isolates. A total of 454 prophages were found among the 468 genomes analysed, which were classified into 23 prophage types. Prophage presence exhibited variations based on GBS clonal complex and capsular type. A possible association between an increased GBS pathogenicity and the carriage of prophages with integrase type GBSInt8 and/or the presence of genes that encode the Phox Homology domain has been observed. The highest prevalence of prophages per genome was found in lineages CC17/III and CC19/III, while the lowest amount was observed in CC12/Ib. Overall, the highest density of prophages, virulence factors and ARDs determinants was found in CC19 isolates, mostly of capsular type III, independent of the isolates’ source. This is the first analysis of the human-associated GBS population in South America based on whole-genome sequencing data, which will make a significant contribution to future studies on the global GBS population structure.