Although Campylobacter jejuni is the pathogen responsible for the most common foodborne illness, tracing of the infection source remains challenging due to its highly variable genome. Therefore, one of the aim of the study was to compare three genotyping methods (MLST, PFGE, and mP-BIT) to determine the most effective genotyping tool. C. jejuni strains were divided into 4 clusters based on strain similarity in the cgMLST dendrogram. Subsequently, the dendrograms of the 3 tested methods were compared to determine the accuracy of each method compared to the reference cgMLST method. Moreover, a cost-benefit analysis has showed that MLST had the highest inverse discrimination index (97%) and required less workflow, time, fewer consumables, and low bacterial sample quantity. PFGE was shown to be obsolete both because of its low discriminatory power and the complexity of the procedure. Similarly, mP‐BIT showed low separation results, which was compensated by its high availability. Therefore, our data showed that MLST is the optimal tool for genotyping C. jejuni. Another aim was to compare the antimicrobial resistance to ciprofloxacin, erythromycin, and tetracycline in C. jejuni strains isolated from human, water, air, food, and animal samples by two gene sequence-based prediction methods and to compare them with the actual susceptibility of C. jejuni strains using the disc diffusion method. Both tools, ResFinder and RGI, synchronously predict the antimicrobial susceptibility of C. jejuni and either can be used.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- Campylobacter jejuni * genetika MeSH
- genotyp MeSH
- kampylobakterové infekce * mikrobiologie MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- multilokusová sekvenční typizace MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Despite numerous studies on Escherichia coli (E. coli) from sheep, there have been few reports on the characterization of E. coli isolates from various organs of individual sheep until now. The present study conducted molecular typing, antibiotics resistance, biofilm formation, and virulence genes on E. coli isolated from 57 freshly slaughtered apparently healthy sheep carcasses, gallbladders, fecal samples, and mesenteric lymph nodes (MLNs). The results demonstrated that the detection rate of R1 LPS core type in E. coli isolated from fecal samples (70.83%) was higher than that from other organs, but the detection rate of antibiotic resistance genes was lower (P < 0.05). The predominant phylogenetic group of E. coli isolated from the carcasses was group B1 (93.33%), and the detection rate of multidrug-resistance phenotype (80%) and the resistance rate of E. coli was higher than that from other organs (P < 0.05). Interestingly, the intensity of biofilm formation of E. coli isolated from MLNs was higher than that from other organs (P < 0.05). However, except for ibeB, the detection rates of virulence genes did not differ in E.coli isolated from different organs. In conclusion, differences were noted in these parameters of E. coli isolated from different organs of individual sheep. Therefore, the data may contain considerable mistakes concerning the actual situation in the host if we only analyze the data of E. coli isolated from feces or carcasses.
- MeSH
- antibakteriální látky * farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- biofilmy * růst a vývoj účinky léků MeSH
- Escherichia coli * genetika účinky léků izolace a purifikace klasifikace fyziologie MeSH
- faktory virulence * genetika MeSH
- feces mikrobiologie MeSH
- fylogeneze MeSH
- infekce vyvolané Escherichia coli mikrobiologie veterinární MeSH
- molekulární typizace MeSH
- nemoci ovcí mikrobiologie MeSH
- ovce MeSH
- virulence genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Antimicrobial resistance is well-known to be a global health and development threat. Due to the decrease of effective antimicrobials, re-evaluation in clinical practice of old antibiotics, as fosfomycin (FOS), have been necessary. FOS is a phosphonic acid derivate that regained interest in clinical practice for the treatment of complicated infection by multi-drug resistant (MDR) bacteria. Globally, FOS resistant Gram-negative pathogens are raising, affecting the public health, and compromising the use of the antibiotic. In particular, the increased prevalence of FOS resistance (FOSR) profiles among Enterobacterales family is concerning. Decrease in FOS effectiveness can be caused by i) alteration of FOS influx inside bacterial cell or ii) acquiring antimicrobial resistance genes. In this review, we investigate the main components implicated in FOS flow and report specific mutations that affect FOS influx inside bacterial cell and, thus, its effectiveness. FosA enzymes were identified in 1980 from Serratia marcescens but only in recent years the scientific community has started studying their spread. We summarize the global epidemiology of FosA/C2/L1-2 enzymes among Enterobacterales family. To date, 11 different variants of FosA have been reported globally. Among acquired mechanisms, FosA3 is the most spread variant in Enterobacterales, followed by FosA7 and FosA5. Based on recently published studies, we clarify and represent the molecular and genetic composition of fosA/C2 genes enviroment, analyzing the mechanisms by which such genes are slowly transmitting in emerging and high-risk clones, such as E. coli ST69 and ST131, and K. pneumoniae ST11. FOS is indicated as first line option against uncomplicated urinary tract infections and shows remarkable qualities in combination with other antibiotics. A rapid and accurate identification of FOSR type in Enterobacterales is difficult to achieve due to the lack of commercial phenotypic susceptibility tests and of rapid systems for MIC detection.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- Escherichia coli genetika MeSH
- fosfomycin * farmakologie MeSH
- Klebsiella pneumoniae genetika MeSH
- proteiny z Escherichia coli * genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Fosfomycin (FOS) has been recently reintroduced into clinical practice, but its effectiveness against multidrug-resistant (MDR) Enterobacterales is reduced due to the emergence of FOS resistance. The copresence of carbapenemases and FOS resistance could drastically limit antibiotic treatment. The aims of this study were (i) to investigate fosfomycin susceptibility profiles among carbapenem-resistant Enterobacterales (CRE) in the Czech Republic, (ii) to characterize the genetic environment of fosA genes among the collection, and (iii) to evaluate the presence of amino acid mutations in proteins involved in FOS resistance mechanisms. During the period from December 2018 to February 2022, 293 CRE isolates were collected from different hospitals in the Czech Republic. FOS MICs were assessed by the agar dilution method (ADM), FosA and FosC2 production was detected by the sodium phosphonoformate (PPF) test, and the presence of fosA-like genes was confirmed by PCR. Whole-genome sequencing was conducted with an Illumina NovaSeq 6000 system on selected strains, and the effect of point mutations in the FOS pathway was predicted using PROVEAN. Of these strains, 29% showed low susceptibility to fosfomycin (MIC, ≥16 μg/mL) by ADM. An NDM-producing Escherichia coli sequence type 648 (ST648) strain harbored a fosA10 gene on an IncK plasmid, while a VIM-producing Citrobacter freundii ST673 strain harbored a new fosA7 variant, designated fosA7.9. Analysis of mutations in the FOS pathway revealed several deleterious mutations occurring in GlpT, UhpT, UhpC, CyaA, and GlpR. Results regarding single substitutions in amino acid sequences highlighted a relationship between ST and specific mutations and an enhanced predisposition for certain STs to develop resistance. This study highlights the occurrence of several FOS resistance mechanisms in different clones spreading in the Czech Republic. IMPORTANCE Antimicrobial resistance (AMR) currently represents a concern for human health, and the reintroduction of antibiotics such as fosfomycin into clinical practice can provide further option in treatment of multidrug-resistant (MDR) bacterial infections. However, there is a global increase of fosfomycin-resistant bacteria, reducing its effectiveness. Considering this increase, it is crucial to monitor the spread of fosfomycin resistance in MDR bacteria in clinical settings and to investigate the resistance mechanism at the molecular level. Our study reports a large variety of fosfomycin resistance mechanisms among carbapenemase-producing Enterobacterales (CRE) in the Czech Republic. Our study summarizes the main achievements of our research on the use of molecular technologies, such as next-generation sequencing (NGS), to describe the heterogeneous mechanisms that reduce fosfomycin effectiveness in CRE. The results suggest that a program for widespread monitoring of fosfomycin resistance and epidemiology fosfomycin-resistant organisms can aide timely implementation of countermeasures to maintain the effectiveness of fosfomycin.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- beta-laktamasy genetika MeSH
- Escherichia coli MeSH
- fosfomycin * farmakologie MeSH
- karbapenemy farmakologie MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
Klebsiella pneumoniae is an important cause of nosocomial infections and displays increasing resistance to fluoroquinolones (FQ). This study surveyed the mechanisms of FQ resistance and molecular typing of K. pneumoniae isolates from intensive care units patients in Tehran, Iran. A total of 48 ciprofloxacin (CIP) resistant K. pneumoniae isolates from urine samples were included in this study. Broth microdilution assays revealed high-level CIP resistance (MIC > 32 μg/mL) in 31.25% of the isolates. Plasmid-mediated quinolone resistance genes were detected in 41 (85.4%) isolates. Among which, qnrS (41.67%) was the most prevalent followed by qnrD (35.42%), qnrB (27.1%), qnrA (25%), qepA (22.9%), aac(6')-Ib-cr (20.83%), and qnrC (6.25%). Target site mutations (gyrA and parC) were assessed using PCR and sequencing on all isolates. A single mutation in gyrA (S83I) was found in 13 (27.1%) isolates and two isolates harbored six simultaneous mutations. Fourteen isolates (29.2%) had mutations in parC and S129A and A141V mutations were the most prevalent. Real time PCR showed an increase in the expression level of acrB and oqxB efflux genes in 68.75 and 29.16% isolates, respectively. Enterobacterial repetitive intergenic consensus (ERIC)-PCR revealed 14 genotypes and 11 of them were classified by multilocus sequence typing (MLST) into 11 different sequence types belonging to seven clonal complexes and two singletons, most of them have not been reported in Iran yet. We are concerned about the spread of these clones throughout our country. Most FQ resistance mechanisms were detected among our isolates. However, target site mutation had the greatest effect on CIP resistance among our isolates.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- ciprofloxacin * farmakologie MeSH
- DNA gyráza genetika MeSH
- fluorochinolony * farmakologie MeSH
- Klebsiella pneumoniae genetika MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- molekulární epidemiologie MeSH
- multilokusová sekvenční typizace MeSH
- plazmidy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Írán MeSH
Globally, 94% of Treponema pallidum subsp. pallidum (TPA) clinical strains belong to the SS14-like group and 6% to the Nichols-like group, with a prevalence of macrolide resistance of 90%. Our goal was to determine whether local TPA strain distribution and macrolide resistance frequency have changed significantly since our last report, which revealed that Buenos Aires had a high frequency of Nichols-like strains (27%) and low levels of macrolide resistance (14%). Swab samples from patients with suspected syphilis were collected during 2015-2019 and loci TP0136, TP0548, TP0705 were sequenced in order to perform multilocus sequence typing. Strains were classified as Nichols-like or SS14-like. The presence of macrolide resistance-associated mutations was determined by examination of the 23S rDNA gene sequence. Of 46 typeable samples, 37% were classified as Nichols-like and 63% as SS14-like. Macrolide resistance prevalence was 45.7%. Seven allelic profiles were found, five were SS14-like and two were Nichols-like. The frequency of Nichols-like strains increased between studies (26.8% vs. 37%, p = 0.36). A dramatic increase was found in the frequency of macrolide resistant strains between studies (14.3% vs. 45.7%, p = 0.005). Our results are in agreement with international trends and underscore the need to pursue further TPA molecular typing studies in South America.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- infekce bakteriemi rodu Treponema * MeSH
- lidé MeSH
- makrolidy farmakologie MeSH
- multilokusová sekvenční typizace MeSH
- ribozomální DNA MeSH
- Treponema pallidum * genetika MeSH
- Treponema MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Argentina MeSH
BACKGROUND: Colistin belongs to the last-resort antibiotics. The discovery of plasmid-bound colistin resistance mediated by the mcr-gene(s) is of great concern because, given its biological potential, there is a risk of its rapid spread. OBJECTIVES: To discuss the current literature on the methods for the screening for mcr-mediated resistance to colistin. SOURCES: Literature was drawn from a search of PubMed from 1 January 2016 to 26 April 2021. CONTENT: The selective culture-based or culture-independent approach can be used for the screening of mcr-mediated resistance to colistin in clinical samples. Rapid Polymyxin NP, Colistin Drop or Colistin Agar Spot tests are applicable for the selection of isolates with a suspected resistance to colistin that has to be confirmed by broth microdilution. The mcr-mediated resistance to colistin can be confirmed by the detection of the causal gene(s) or by phenotype using EDTA-colistin broth disc elution; production of the MCR-1 enzyme can be confirmed with lateral flow immunoassay, using matrix-assisted laser desorption/ionization time-of flight or liquid chromatography-based mass spectrometry. Whole-genome sequencing (WGS) is the ultimate typing method. When a WGS platform is not available at a healthcare facility, a WGS-outsourced service, in combination with freely available bioinformatics tools, allows for the characterization of the mcr-gene(s) carrying isolates. IMPLICATIONS: mcr-mediated colistin resistance should be monitored through active targeted screening. The broth microdilution method is required for colistin susceptibility testing but as only a selected number of clinical isolates are tested, colistin resistance, including mcr-mediated, may remain undetected. In mcr-1-positive Escherichia coli isolates, the MIC to colistin can range from 2 to 8 mg/L, so it is proposed that Enterobacterales with a colistin MIC of 2 mg/L should also be included in the mcr-mediated colistin resistance screening and those with a confirmed mcr-genotype and/or MCR-phenotype should be considered to be colistin-resistant.
The present study was conducted to investigate the virulence gene profile and antimicrobial resistance of non-typeable Streptococcus suis isolates circulating in pigs of North East India. Fifty-two non-typeable S. suis isolates from clinically healthy and diseased pigs were screened by using PCR for the presence of the muramidase-released protein (mrp), extracellular factor (epf), hemolysin suilysin (sly), arginine deiminase (arcA), and glutamate dehydrogenase (gdh) genes. Five different virulence gene profiles were observed and the most predominant virulence gene profile found in healthy pigs was mrp- + sly- + arcA- + gdh + + epf- whereas the most predominant virulence gene profile recorded in diseased pigs was mrp+ + sly- + arcA+ + gdh+ + epf-. Significantly lower carrier rate of mrp+ + sly- + arcA+ + gdh+ + epf- virulence gene profile was observed among the isolates from healthy pigs compared to those from diseased pigs (P < 0.05). Antimicrobial resistance patterns of the S. suis isolates revealed fourteen resistance groups (R1 to R14) where 88.46% isolates showed multi-drug resistance. The most predominant resistance pattern observed was CD-COT-E-TE. This is perhaps the first study reporting virulence gene profile and antimicrobial resistance of non-typeable S. suis isolates from pigs in North East India. The occurrence of relatively high levels of resistance of S. suis to some antimicrobials (e.g. macrolides, tetracyclines, and sulphonamides) as observed in the present study may represent a human health concern.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- lidé MeSH
- nemoci prasat * epidemiologie MeSH
- prasata MeSH
- Streptococcus suis * genetika MeSH
- streptokokové infekce * veterinární MeSH
- virulence genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Indie MeSH
INTRODUCTION: Clostridioides difficile is a major pathogen responsible for hospital-associated diarrhoea. This study investigated the molecular epidemiology and antibiotic resistance of C. difficile isolates in five Algerian hospitals. METHODOLOGY: Between 2016 and 2019, faecal specimens were collected from in-patients and were cultured for C. difficile. Isolates were characterised by toxin genes detection, Polymerase Chain Reaction (PCR)-ribotyping, Multilocus Sequence Typing (MLST), antimicrobial susceptibility testing against a panel of antibiotics, and screened for antimicrobial resistance genes. RESULTS: Out of 300 patient stools tested, 18 (6%) were positive for C. difficile by culture, and were found to belong to 11 different ribotypes (RT) and 12 sequence types (ST): RT 085/ST39, FR 248/ST259, FR 111/ST48, RT 017/ST37, RT 014/ST2, RT 014/ST14, FR 247/new ST, RT 005/ST6, RT 029/ST16, RT 039/ST26, RT 056/ST34 and RT 446/ST58. MLST analysis assigned the isolates to two clades, 1 and 4. Clade 4 was more homogeneous, as it mainly included non-toxigenic isolates. Three toxin gene profiles were detected, two toxigenic, A+B+CDT- (33.3%) and A-B+CDT- (11%); and one non-toxigenic, A-B-CDT- (55.5%). All C. difficile isolates were susceptible to metronidazole, vancomycin and moxifloxacin. CONCLUSIONS: Overall prevalence of C. difficile in our healthcare settings was 6%. Antibiotic resistance rates ranged from 72.2% (clindamycin) to 16.6% (tetracycline). This study highlighted a relatively high genetic diversity in term of ribotypes, sequence types, toxin and antibiotic resistance patterns, in the C. difficile isolates. Further larger studies are needed to assess the true extent of C. difficile infections in Algeria.
- MeSH
- antibakteriální látky farmakologie terapeutické užití MeSH
- bakteriální léková rezistence genetika MeSH
- Clostridioides difficile * genetika MeSH
- Clostridioides MeSH
- klostridiové infekce * farmakoterapie epidemiologie MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- molekulární epidemiologie MeSH
- multilokusová sekvenční typizace MeSH
- nemocnice MeSH
- ribotypizace MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Alžírsko MeSH
