Characterization of florfenicol resistance genes in the coagulase-negative Staphylococcus (CoNS) isolates and genomic features of a multidrug-resistant Staphylococcus lentus strain H29. - Related Documents




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540501.0000Characterization of florfenicol resistance genes in the coagulase-negative Staphylococcus (CoNS) isolates and genomic features of a multidrug-resistant Staphylococcus lentus strain H29. BACKGROUND: With the wide use of florfenicol to prevent and treat the bacterial infection of domestic animals, the emergence of the florfenicol resistance bacteria is increasingly serious. It is very important to elucidate the molecular mechanism of the bacteria's resistance to florfenicol. METHODS: The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method, and polymerase chain reaction was conducted to analyze the distribution of florfenicol resistance genes in 39 CoNS strains isolated from poultry and livestock animals and seafood. The whole genome sequence of one multidrug resistant strain, Staphylococcus lentus H29, was characterized, and comparative genomics analysis of the resistance gene-related sequences was also performed. RESULTS: As a result, the isolates from the animals showed a higher resistance rate (23/28, 82.1%) and much higher MIC levels to florfenicol than those from seafood. Twenty-seven animal isolates carried 37 florfenicol resistance genes (including 26 fexA, 6 cfr and 5 fexB genes) with one carrying a cfr gene, 16 each harboring a fexA gene, 5 with both a fexA gene and a fexB gene and the other 5 with both a fexA gene and a cfr gene. On the other hand, all 11 isolates from seafood were sensitive to florfenicol, and only 3 carried a fexA gene each. The whole genome sequence of S. lentus H29 was composed of a chromosome and two plasmids (pH29-46, pH29-26) and harbored 11 resistance genes, including 6 genes [cfr, fexA, ant(6)-Ia, aacA-aphD, mecA and mph(C)] encoded on the chromosome, 4 genes [cfr, fexA, aacA-aphD and tcaA] on pH29-46 and 1 gene (fosD) on pH29-26. We found that the S. lentus H29 genome carried two identical copies of the gene arrays of radC-tnpABC-hp-fexA (5671 bp) and IS256-cfr (2690 bp), of which one copy of the two gene arrays was encoded on plasmid pH29-46, while the other was encoded on the chromosome. CONCLUSIONS: The current study revealed the wide distribution of florfenicol resistance genes (cfr, fexA and fexB) in animal bacteria, and to the best of our knowledge, this is the first report that one S. lentus strain carried two identical copies of florfenicol resistance-related gene arrays.202133413633
542010.9995A high incidence and coexistence of multiresistance genes cfr and optrA among linezolid-resistant enterococci isolated from a teaching hospital in Wenzhou, China. Linezolid is considered as a last-resort antimicrobial agent, the resistance of which is of great concern. The aim of this study was to investigate the mechanisms and transferability of linezolid resistance and molecular epidemiology of linezolid-resistant enterococcal isolates in Wenzhou, China. A collection of 1623 enterococcal strains, including 789 Enterococcus faecalis and 834 Enterococcus faecium, were isolated from our hospital during 2011-2016. Antimicrobial susceptibility testing and clinical data analysis were performed. Molecular mechanisms of linezolid resistance, including the existence of resistance genes cfr and optrA, as well as the mutations in 23S rRNA and ribosomal proteins L3, L4, and L22, were investigated by PCR and sequencing. Conjugation experiments were conducted, and epidemiological characteristics were analyzed by PFGE and MLST. In our study, 31 (3.93%) E. faecalis and 2 (0.24%) E. faecium exhibited resistance to linezolid. Risk factors correlated with linezolid-resistant enterococcal infections included gastrointestinal surgery hospitalization, urogenital disorders, tumor, diabetes, and polymicrobial infections. Among these isolates, 6 (18.18%) harbored cfr, 9 (27.27%) harbored optrA, and 18 (54.55%) co-harbored cfr and optrA. However, mutational mechanisms were not found in this study. Conjugation experiments demonstrated the transferability of cfr and optrA between Gram-positive and Gram-negative bacteria. The clone of these isolates was diverse and scattered. It is noteworthy that cfr and optrA were the main mechanisms of linezolid resistance in this study, posing a potential risk of spread of linezolid resistance. Strikingly, it reported firstly that the two transferable resistance genes cfr and optrA coexisted in the same E. faecalis isolates.201829909468
541720.9994Molecular characteristics of oxazolidinone resistance in enterococci from a multicenter study in China. BACKGROUND: Linezolid-resistant enterococci pose great challenges in clinical practice. The aim of this study is to study the mechanisms underlying the resistance and genetic environment of antimicrobial resistance gene of linezolid-resistant enterococci. RESULTS: The linezolid MICs of 16 enterococci were 4 mg/L to 16 mg/L. Four strains belonged to multi-drug resistant (MDR) bacteria. The sequence types (STs) of 13 enterococci strains performed WGS were diverse: 3 ST476, 1 ST86, ST116, ST480, ST59, ST416, ST21, ST67, ST16, ST585 and ST18. None of them carried multi-drug resistance gene cfr. Only one strain had the G2658 T mutation of target 23S rRNA gene. Thirteen (13/16, 81.3%) strains harbored the novel oxazolidinone resistance gene optrA. WGS analysis showed that the optrA gene was flanked by sequence IS1216E insertion in 13 strains, and optrA was adjacent to transposons Tn558 in two strains and Tn554 in one strain. The optrA gene was identified to be co-localized with fexA, the resistance genes mediated florfenicol resistance in 13 strains, and ermA1, the resistance genes mediated erythromycin resistance in 9 strains, indicating that linezolid-resistant strains may be selected due to non-oxazolidinone antibiotics (i.e. macrolides and florfenicol) usage. CONCLUSION: Our findings demonstrate the high diversity of optrA-carrying genetic platforms. The mobile genetic elements (MGEs) may play an important role in the dissemination of optrA into the enterococci isolates of human origin. The genetic evidence of transferable feature and co-selection of optrA should be gave more attention in clinical practice.201931299904
541830.9994Detection of optrA in the African continent (Tunisia) within a mosaic Enterococcus faecalis plasmid from urban wastewaters. OBJECTIVES: Oxazolidinone resistance is a serious limitation in the treatment of MDR Enterococcus infections. Plasmid-mediated oxazolidinone resistance has been strongly linked to animals where the use of phenicols might co-select resistance to both antibiotic families. Our goal was to assess the diversity of genes conferring phenicol/oxazolidinone resistance among diverse enterococci and to characterize the optrA genetic environment. METHODS: Chloramphenicol-resistant isolates (>16 mg/L, n = 245) from different sources (hospitals/healthy humans/wastewaters/animals) in Portugal, Angola and Tunisia (1996-2016) were selected. Phenicol (eight cat variants, fexA, fexB) or phenicol + oxazolidinone [cfr, cfr(B), optrA] resistance genes were searched for by PCR. Susceptibility (disc diffusion/microdilution), filter mating, stability of antibiotic resistance (500 bacterial generations), plasmid typing (S1-PFGE/hybridization), MLST and WGS (Illumina-HiSeq) were performed for optrA-positive isolates. RESULTS: Resistance to phenicols (n = 181, 74%) and phenicols + oxazolidinones (n = 2, 1%) was associated with the presence of cat(A-8) (40%, predominant in hospitals and swine), cat(A-7) (29%, predominant in poultry and healthy humans), cat(A-9) (2%), fexB (2%) and fexA + optrA (1%). fexA and optrA genes were co-located in a transferable plasmid (pAF379, 72 918 bp) of two ST86 MDR Tunisian Enterococcus faecalis (wastewaters) carrying several putative virulence genes. MICs of chloramphenicol, linezolid and tedizolid were stably maintained at 64, 4 and 1 mg/L, respectively. The chimeric pAF379 comprised relics of genetic elements from different Gram-positive bacteria and origins (human/porcine). CONCLUSIONS: To the best of our knowledge, we report the first detection of optrA in an African country (Tunisia) within a transferable mosaic plasmid of different origins. Its identification in isolates from environmental sources is worrisome and alerts for the need of a concerted global surveillance on the occurrence and spread of optrA.201729029072
96440.9993Distribution of plasmid-mediated quinolone resistance in Gram-negative bacteria from a tertiary hospital in Nigeria. BACKGROUND: Until recently, mechanisms of resistance to quinolones in Gram-negative bacteria were believed to be only chromosome encoded. However, emergence of plasmid-mediated quinolone resistance (PMQR) has been reported worldwide. AIM: This study investigated distribution of PMQR in Gram-negative bacteria from a tertiary hospital in eastern part of Nigeria. MATERIALS AND METHODS: Seventy-one nonduplicate Gram-negative bacterial isolates of eight species were analyzed for antimicrobial susceptibility, genotypic detection of various PMQRs, typed by random amplified polymorphic DNA (RAPD) and analysis of plasmids present, including replicon typing. RESULTS: The minimum inhibitory concentrations showed MIC90values as high as 256 μg/ml for fluoroquinolones. Carriage of PMQR was found to be 35.2%. Twenty (28.2%) isolates carried various qnr genes, of which seven (9.9%) qnrA1; four (5.6%) qnrB1; eight (11.3%) qnrS1 while one (1.4%) encoded qnrD1. Eighteen (25.4%) isolates were positive for aac(6')-Ib-cr while carriage of multiple genes exists in some strains. Similarly, 13 isolates (18.7%) were found to carry PMQR efflux pump gene, qepA. Conjugation experiments revealed that the plasmids once transferred coded for fluoroquinolone resistance. The transconjugant strains carried a common plasmid estimated to be 65 kb. These plasmids were untypable for replicon/incompatibility. Typing revealed high diversity among all species tested with no identical RAPD pattern seen. CONCLUSION: This study further confirms high level resistance to many antimicrobials in different species of Gram-negative bacteria including fluoroquinolones and spread of PMQR genes in Southern Nigeria.201627510669
540650.9993Detection of poxtA- and optrA-carrying E. faecium isolates in air samples of a Spanish swine farm. OBJECTIVE: Two linezolid-resistant Enterococcus faecium isolates, C10004 and C10009, were recovered from air samples of a Spanish swine farm and comprehensively characterized. METHODS: Detection of linezolid resistance mechanisms (mutations and acquisition of resistance genes) was performed by PCR/sequencing. Isolates were characterized by multilocus sequence typing (MLST), antimicrobial susceptibility testing, detection of antimicrobial resistance and virulence genes, and analysis of the genetic environment of the linezolid resistance genes. The characterization of isolate C10009 was performed by Whole-Genome-Sequencing and of isolate C10004 by PCR and amplicon sequencing, where applicable. Conjugation experiments to assess the transferability of the optrA and poxtA genes implicated in linezolid resistance were performed. RESULTS: The linezolid-resistant E. faecium isolates C10004 and C10009, assigned to ST128 and ST437, respectively, harbored the optrA and poxtA genes. Neither mutations in the 23S rRNA nor in the genes for the ribosomal proteins L3, L4 and L22 were detected. C10004 and C10009 carried fourteen and thirteen antimicrobial resistance genes, respectively. The sequence alignment indicated that the genetic environment of the poxtA gene was identical in both isolates, with a downstream-located fexB gene. The poxtA gene was transferred by conjugation together with the fexB gene, and also with tet(M) and tet(L) in the case of isolate C10004. The optrA gene could not be transferred. CONCLUSIONS: This is the first report of the poxtA gene in Spain. The presence of poxtA- and optrA-carrying E. faecium isolates in air samples represents a public health concern, indicating an involvement of swine farms in the spread of linezolid-resistant bacteria.202031884049
541960.9993Detection of the optrA Gene Among Polyclonal Linezolid-Susceptible Isolates of Enterococcus faecalis Recovered from Community Patients. Dispersion of transferable oxazolidinone resistance genes among enterococci poses a serious problem to human health. Prompt detection of bacteria carrying these genes is crucial to avoid their spread to multidrug-resistant bacteria. The aim of the study was to describe the presence of optrA-positive isolates among enterococci in a Spanish hospital, and to determine their genetic context and location through whole genome sequencing. All enterococci recovered in a Spanish hospital (Hospital El Bierzo; HEB) from February to December 2018 (n = 443), with minimal inhibitory concentrations (MICs) to linezolid (LZD) ≥4 mg/L, were tested by polymerase chain reaction for the presence of cfr, optrA, and poxtA transferable genes. Only four Enterococcus faecalis isolates (0.9%) had LZD MICs ≥4 mg/L and none of them was positive for cfr or poxtA genes. However, the optrA gene was detected in three isolates collected from urine samples of community patients, whose genomes were sequenced and subjected to bioinformatics analysis. These isolates belonged to different clones: ST7, ST480, and ST585. In these three isolates, the optrA gene was located on plasmids, associated with IS1216 in different arrays. In one isolate, the optrA plasmid coexists with a second plasmid, which carried multiple resistance genes for different classes of antibiotics. Detection of optrA-positive E. faecalis isolates in the community is a matter of concern. The spread of these bacteria into hospital settings, particularly in those, such as the HEB, where vancomycin-resistant enterococci are endemic, should be avoided, to preserve the efficacy of the last-resort oxazolidinones.202235727074
545570.9993Two novel plasmids harbouring the multiresistance gene cfr in porcine Staphylococcus equorum. BACKGROUND: The emergence and transmission of the multidrug resistance gene cfr have raised public health concerns worldwide. OBJECTIVES: Multidrug-resistant Staphylococcus equorum isolates can pose a threat to public health. In this study, we have characterised the whole-genome of one Staphylococcus equorum isolate harbouring two distinct cfr-carrying plasmids. METHODS: Antimicrobial susceptibility testing was performed by broth microdilution. Genomic DNA was sequenced using both the Illumina HiSeq X Ten and Nanopore MinION platforms. De novo hybrid assembly was performed by Unicycler. Genomic data were assessed by in silico prediction and bioinformatic tools. RESULTS: Staphylococcus equorum isolate SN42 exhibited resistance or high MICs to linezolid, erythromycin, tetracycline, oxacillin, clindamycin, virginiamycin, tiamulin, chloramphenicol and florfenicol. It carried two cfr-harbouring plasmids: the RepA N-family plasmid pSN42-51 K and the Inc18-family plasmid pSN42-50 K. These two plasmids exhibited low structural similarities to the so far reported cfr-carrying plasmids. Both plasmids harboured an arsenic resistance operon, copper and cadmium resistance genes as well as the lincosamide-pleuromutilin-streptogramin A resistance gene lsa(B). In addition, plasmid pSN42-51 K carried two erm(B) genes for macrolide-lincosamide-streptogramin B resistance, the streptomycin resistance gene ant(6)-Ia as well as mercury resistance genes while pSN42-50 K was associated with the heavy metal translocating P-type ATPase gene hmtp. The co-carriage and co-existence of these antimicrobial resistance and heavy metal resistance genes increases the likelihood of co-selection of the cfr-carrying plasmids. CONCLUSION: This is the first report of S. equorum carrying two distinct cfr-carrying plasmids, underscoring the need for ongoing surveillance to address the potential dissemination of multi-drug resistance in bacteria from food-producing animals to ensure food safety and public health.202439362467
540780.9993Resistance mechanisms and tedizolid susceptibility in clinical isolates of linezolid-resistant bacteria in Japan. OBJECTIVES: Studies combining linezolid resistance mechanisms and tedizolid susceptibility in linezolid-resistant clinical isolates are scarce. This study investigated the linezolid resistance mechanisms and tedizolid susceptibility of linezolid-resistant strains isolated clinically in Japan. METHODS: We analysed 25 linezolid-resistant strains of Enterococcus faecium and Enterococcus faecalis isolated from Japanese hospitals between 2015 and 2021. MICs of linezolid and tedizolid were determined using the agar plate dilution method. Each 23S rRNA copy was amplified by PCR, sequenced and analysed for mutations. The linezolid resistance genes cfr, poxtA, optrA, fexA and fexB were also detected by PCR. RESULTS: Drug susceptibility tests revealed that five linezolid-resistant E. faecium isolates had low (≤1 mg/L) tedizolid MICs. Resistance mechanisms included the G2576T mutation in 23S rRNA, the T2504A mutation and the resistance genes optrA, fexA and fexB. The T2504A mutation was identified in one E. faecium isolate, which exhibited linezolid and tedizolid MICs of 64 and 32 mg/L, respectively. CONCLUSIONS: Some linezolid-resistant isolates demonstrated low (≤1 mg/L) tedizolid MICs. To determine whether tedizolid susceptibility testing should be performed on linezolid-resistant isolates, more linezolid-resistant isolates should be collected and tested for tedizolid MICs. Tedizolid MICs were 2-3 doubling dilutions lower than linezolid MICs. The results of this study suggest that future research should investigate whether the T2504A mutation contributes to tedizolid resistance. To our knowledge, this is the first study to report tedizolid susceptibility in E. faecium with the T2504A mutation and in isolate harbouring this mutation.202540463587
242090.9993Distribution of erm(F) and tet(Q) genes in 4 oral bacterial species and genotypic variation between resistant and susceptible isolates. BACKGROUND: Bacteroides forsythus, Porphyromonas gingivalis and Prevotella intermedia are Gram-negative anaerobic bacteria that are currently considered potential periopathogens. Prevotella nigrescens has recently been separated from P. intermedia and its rôle in periodontitis is unknown. The erm(F) gene codes for an rRNA methylase, conferring resistance to macrolides, lincosamides and streptogramin B (MLSB), and the tet(Q) gene for a ribosomal protection protein, conferring resistance to tetracycline. The presence of these resistance genes could impair the use of antibiotics for therapy. PURPOSE: The aim of this study was to determine the carriage of erm(F) and tet(Q), and genetic variability of 12 Porphyromonas gingivalis, 10 Prevotella intermedia, 25 Prevotella nigrescens and 17 Bacteroides forsythus isolates from 9 different patient samples. METHODS: We used polymerase chain reaction (PCR) for detecting antibiotic resistance genes, and pulsed-field gel electrophoresis (PFGE) for detecting genetic variability among the isolates. RESULTS: Thirty-one (48%) isolates were resistant to both erythromycin and tetracycline and carried the erm(F) and tet(Q) genes, eight (13%) were tetracycline resistant and carried the tet(Q) gene, 9 (14%) were erythromycin resistant and carried the erm(F) gene, and 12 (19%) isolates did not carry antibiotic resistance genes. PFGE was used to compare isolates from the same patient and isolates from different patient samples digested with XbaI. No association was found between antibiotic resistance gene carriage and PFGE patterns in any species examined. All isolates of the same species from the same patient had highly related or identical PFGE patterns. Isolates of same species from different patients had unique PFGE pattern for each species tested. CONCLUSION: All isolates of the same species from any one patient were genetically related to each other but distinct from isolates from other patients, and 66% of the patients carried antibiotic resistant isolates, which could impair antibiotic therapy.200211895543
5421100.9993Florfenicol Resistance in Enterobacteriaceae and Whole-Genome Sequence Analysis of Florfenicol-Resistant Leclercia adecarboxylata Strain R25. Due to inappropriate use, florfenicol resistance is becoming increasingly serious among animal respiratory tract and gut bacteria. To detect the florfenicol resistance mechanism among Enterobacteriaceae bacteria, 292 isolates from animal feces were examined. The agar dilution method was conducted to determine the minimum inhibitory concentration (MIC) for florfenicol, and polymerase chain reaction (PCR) was performed to detect florfenicol resistance genes. To further explore the molecular mechanism of florfenicol resistance, the whole-genome Leclercia adecarboxylata R25 was sequenced. Of the strains tested, 61.6% (180/292) were resistant to florfenicol, 64.4% (188/292) were positive for floR, and 1.0% (3/292) for cfr. The whole-genome sequence analysis of L. adecarboxylata R25 revealed that the floR gene is carried by a transposon and located on a plasmid (pLA-64). Seven other resistance genes are also encoded on pLA-64, all of which were found to be related to mobile genetic elements. The sequences sharing the greatest similarities to pLA-64 are the plasmids p02085-tetA of Citrobacter freundii and p234 and p388, both from Enterobacter cloacae. The resistance gene-related mobile genetic elements also share homologous sequences from different species or genera of bacteria. These findings indicate that floR mainly contributes to the high rate of florfenicol resistance among Enterobacteriaceae. The resistance gene-related mobile genetic elements encoded by pLA-64 may be transferred among bacteria of different species or genera, resulting in resistance dissemination.201931662959
5457110.9993Persistence of transferable oxazolidinone resistance genes in enterococcal isolates from a swine farm in China. The appearance of transferable oxazolidinone resistance genes poses a major challenge to public health and environmental safety. These genes not only lead pathogenic bacteria to become resistant to linezolid but also reduce sensitivity to florfenicol, which is widely used in the veterinary field. To verify the dissemination of oxazolidinone resistance genes in enterococcal isolates from pigs at different production stages in a swine farm in China, we collected 355 enterococcal isolates that were resistant to florfenicol from 600 (150 per stage) fresh fecal swabs collected from a swine farm. Through initial PCR screening and whole-genome sequencing, 175 isolates harboring different oxazolidinone resistance genes were identified. All isolates carried the optrA gene. A total of 161 (92%, 161/175) isolates carried only the optrA gene. Three (1.71%, 3/175) isolates carried both the optrA and poxtA genes, and 11 (3.1%, 11/175) isolates contained the optrA gene and poxtA2 and cfr(D) variants. A total of 175 isolates that harbored oxazolidinone resistance genes included 161 E. faecalis, 6 E. faecium, and 8 E. hirae. By sequencing the whole genomes, we found that the 161 isolates of E. faecalis belonged to 28 different STs, including 8 new STs, and the 6 isolates of E. faecium belonged to four different STs, including one new ST. The phylogenetic tree based on SNPs of the core genome showed that both clonal spread and horizontal transfer mediated the diffusion of oxazolidone resistance genes in enterococcal isolates at specific stages in pig farms. Moreover, enterococcal isolates carrying oxazolidone resistance genes could spread from breeding pigs to fattening pigs, while transferable oxazolidone resistance genes in enterococcal isolates could persist on a pig farm throughout all production stages. Representative enterococcal isolates with different oxazolidinone resistance genes were further studied through Nanopore sequencing. We identified a novel plasmid, pM4-80 L4 (15,008 bp), carrying the poxtA2 and cfr(D) genes in enterococcal isolates at different stages. We also found three different plasmids harboring the poxtA gene with high genetic variation, and all poxtA genes were flanked by two copies of IS1216E elements. In addition, four genetically distinct plasmids carrying the optrA gene were identified, and Tn554 was found to mediate chromosome-localized optrA gene transfer. Our study highlighted that transferable oxazolidinone resistance genes in enterococcal isolates could persist throughout all production stages on a pig farm, and the prevalence and dissemination of oxazolidinone resistance genes in enterococcal isolates from animal farms should be continually monitored.202236299730
5941120.9993Characterization of macrolide resistance genes in Haemophilus influenzae isolated from children with cystic fibrosis. OBJECTIVES: to determine the mechanism(s) of macrolide resistance in Haemophilus influenzae isolated from cystic fibrosis (CF) patients participating in a randomized placebo-controlled trial of azithromycin. METHODS: macrolide susceptibility, mutations and carriage of the macrolide resistance genes erm(A), erm(B), erm(C), erm(F) and mef(A) were determined using PCR assays and sequencing or hybridization of the PCR products. H. influenzae isolates were used as donors in conjugation studies with H. influenzae and Enterococcus faecalis recipients. Transconjugant susceptibility and the macrolide resistance genes carried were determined. RESULTS: of the 106 H. influenzae isolates, 27 were resistant and 78 intermediate resistant to azithromycin and/or erythromycin. All isolates carried one or more macrolide resistance gene(s), with the mef(A), erm(B) and erm(F) genes found in 74%, 31% and 29% of the isolates, respectively. None of the selected isolates had L4 or L22 mutations. Twenty-five donors, with various macrolide MICs, transferred macrolide resistance genes to H. influenzae Rd (3.5 × 10(-7)-1 × 10(-10)) and/or E. faecalis (1 × 10(-7)-1 × 10(-8)) recipients. The H. influenzae transconjugants were phenotypically resistant or intermediate to both macrolides while E. faecalis transconjugants were erythromycin resistant. CONCLUSIONS: this is the first identification of erm(A), erm(C) and erm(F) genes in H. influenzae or bacteria from CF patients and the first characterization of macrolide gene transfer from H. influenzae donors. The high level of H. influenzae macrolide gene carriage suggests that the use of azithromycin in the CF population may ultimately reduce the effectiveness of continued or repeated macrolide therapy.201121081549
2670130.9993Molecular characterisation and antimicrobial resistance of Streptococcus agalactiae isolates from dairy farms in China. INTRODUCTION: Streptococcus agalactiae (S. agalactiae) is a pathogen causing bovine mastitis that results in considerable economic losses in the livestock sector. To understand the distribution and drug resistance characteristics of S. agalactiae from dairy cow mastitis cases in China, multilocus sequence typing (MLST) was carried out and the serotypes and drug resistance characteristics of the bacteria in the region were analysed. MATERIAL AND METHODS: A total of 21 strains of bovine S. agalactiae were characterised based on MLST, molecular serotyping, antimicrobial susceptibility testing, and the presence of drug resistance genes. RESULTS: The serotypes were mainly Ia and II, accounting for 47.6% and 42.9% of all serotypes, respectively. Five sequence types (STs) were identified through MLST. The ST103 and ST1878 strains were predominant, with rates of 52.4% and 28.6%, respectively. The latter is a novel, previously uncharacterised sequence type. More than 90% of S. agalactiae strains were susceptible to penicillin, oxacillin, cephalothin, ceftiofur, gentamicin, florfenicol and sulfamethoxazole. The bacteria showed high resistance to tetracycline (85.7%), clindamycin (52.1%) and erythromycin (47.6%). Resistant genes were detected by PCR, the result of which showed that 47.6%, 33.3% and 38.1% of isolates carried the tet(M), tet(O) and erm(B) genes, respectively. CONCLUSION: The results of this study indicate that S. agalactiae show a high level of antimicrobial resistance. It is necessary to monitor the pathogens of mastitis to prevent the transmission of these bacteria.202338143824
5459140.9993Transferable linezolid resistance genes (optrA and poxtA) in enterococci derived from livestock compost at Japanese farms. OBJECTIVES: Linezolid is a last-resort antimicrobial in human clinical settings to treat multidrug-resistant Gram-positive bacterial infections. Mobile linezolid resistance genes (optrA, poxtA, and cfr) have been detected in various sources worldwide. However, the presence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in Japan remains uncertain. Therefore, we clarified the existence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in farm environments in Japan. METHODS: Enterococci isolates from faeces compost collected from 10 pig and 11 cattle farms in Japan in 2021 were tested for antimicrobial susceptibility and possession of mobile linezolid resistance genes. Whole-genome sequencing of optrA and/or poxtA genes positive-enterococci was performed. RESULTS: Of 103 enterococci isolates, 12 from pig farm compost were not-susceptible (2 resistant and 10 intermediate) to linezolid. These 12 isolates carried mobile linezolid resistance genes on plasmids or chromosomes (5 optrA-positive Enterococcus faecalis, 6 poxtA-positive E. hirae or E. thailandicus, and 1 optrA- and poxtA-positive E. faecium). The genetic structures of optrA- and poxA-carrying plasmids were almost identical to those reported in other countries. These plasmids were capable of transferring among E. faecium and E. faecalis strains. The optrA- and poxtA-positive E. faecium belonged to ST324 (clade A2), a high-risk multidrug-resistant clone. The E. faecalis carrying optrA gene on its chromosome was identified as ST593. CONCLUSIONS: Although linezolid is not used in livestock, linezolid-not-susceptible enterococci could be indirectly selected by frequently used antimicrobials, such as phenicols. Moreover, various enterococci species derived from livestock compost may serve as reservoirs of linezolid resistance genes carried on globally disseminated plasmids and multidrug-resistant high-risk clones.202438336229
2954150.9993Prevalence and genetic characterization of linezolid resistance gene reservoirs in hospital sewage from Zhejiang Province, China. Hospital sewage represented important hotspots for the aggregation and dissemination of clinically relevant pathogens and antimicrobial resistance genes. To investigate the prevalence and molecular epidemiology of linezolid resistance genes in hospital sewage, both influent and effluent samples from 11 hospitals in Zhejiang Province, China, were collected and analyzed for linezolid resistance gene carriers. Thirty colonies of putative isolates that grew on the selective media with 10 mg/L florfenicol were randomly picked per sample. A total of 420 Gram-positive isolates, including 330 from 11 influent samples and 90 from three effluent samples, were obtained. Each isolate carried at least one of the linezolid resistance genes, including optrA, poxtA, cfr, and cfr(D), and the optrA gene was highly dominant (388/420). Enterococci displayed predominance among the linezolid resistance gene carriers in the hospital sewage, exhibiting a resistance rate to linezolid of 77.8 %. The wild-type OptrA and OptrA variants KLDP, RDK, and KLDK, all associated with high linezolid MICs, were most frequently detected. Phylogenetic analysis revealed the multispecies and polyclonal distribution of linezolid-resistant bacteria in hospital sewage, while Enterococcus faecalis sequence types (STs) 16 and 179 demonstrated the widest dissemination across different hospitals. Despite generally high genetic diversity, phylogenetic analysis showed that 87 isolates, assigned to ten STs from both sewage and other sources, were genetically related. Moreover, the genetic environment of linezolid resistance genes in isolates from sewage was similar to that from animals, humans, or the environment, with "Tn554-fexA-optrA" as the most common structure. These findings revealed the potential risk of the transmission of linezolid resistance genes through hospital sewage to other environments.202439461535
5463160.9993Antibiotic Susceptibility Profiling of Human Pathogenic Staphylococcus aureus Strains Using Whole Genome Sequencing and Genome-Scale Annotation Approaches. Staphylococcus species are major pathogens with increasing importance due to the rise in antibiotic resistance. Whole genome sequencing and genome-scale annotation are promising approaches to study the pathogenicity and dissemination of virulence factors in nosocomial methicillin-resistant and multidrug-resistant bacteria in intensive care units. Draft genome sequences of eight clinical S. aureus strains were assembled and annotated for the prediction of antimicrobial resistance genes, virulence factors, and phylogenetic analysis. Most of the studied S. aureus strains displayed multi-resistance toward the tested drugs, reaching more than seven drugs up to 12 in isolate S22. The mecA gene was detected in three isolates (S14, S21, and S23), mecC was identified in S8 and S9, and blaZ was commonly identified in all isolates except strain S23. Additionally, two complete mobile genomic islands coding for methicillin resistance SCCmec Iva (2B) were identified in strains S21 and S23. Numerous antimicrobial resistance genes (norA, norC, MgrA, tet(45), APH(3')-IIIa, and AAC(6')-APH(2″)) were identified in chromosomes of different strains. Plasmid analysis revealed the presence of blaZ, tetK, and ermC in different plasmid types, located in gene cassettes containing plasmid replicons (rep) and insertion sequences (IS). Additionally, the aminoglycoside-resistant determinants were identified in S1 (APH(3')-IIIa), while AAC(6)-APH(2″) was detected in strains S8 and S14. The trimethoprim (dfrC) resistance gene was detected in S. aureus S21, and the fosfomycin (fosB) resistance gene was detected only in S. aureus S14. We also noted that S. aureus S1 belongs to ST1-t127, which has been reported as one of the most frequent human pathogen types. Additionally, we noted the presence of rare plasmid-mediated mecC-MRSA in some of our isolates.202337317098
892170.9993Sequencing analysis of tigecycline resistance among tigecycline non-susceptible in three species of G-ve bacteria isolated from clinical specimens in Baghdad. BACKGROUND: Recent emergence of high-level tigecycline resistance is mediated by tet(X) genes in Gram-negative bacteria, which undoubtedly constitutes a serious threat for public health worldwide. This study aims to identify tigecycline non-susceptible isolates and detect the presence of genes that are responsible for tigecycline resistance among local isolates in Iraq for the first time. METHODS: Thirteen clinical isolates of Klebsiella pneumonia, Acinetobacter baumannii and Pseudomonas aeruginosa tigecycline non-susceptible were investigated from blood, sputum and burns specimens. The susceptibility of different antibiotics was tested by the VITEK-2 system. To detect tigecycline resistance genes, PCR was employed. RESULTS: Strains studied in this work were extremely drug-resistant and they were resistant to most antibiotic classes that were studied. The plasmid-encoded tet(X), tet(X1), tet(X2), tet(X3), tet(X4), tet(X5), tet(M) and tet(O) genes were not detected in the 13 isolates. The results showed that there is a clear presence of tet(A) and tet(B) genes in tigecycline non-susceptible isolates. All 13 (100%) tigecycline non-susceptible K. pneumoniae, A. baumannii and P. aeruginosa isolates harbored the tet(B) gene. In contrast, 4 (30.77%) tigecycline non-susceptible P. aeruginosa isolates harbored the tet(A) gene and there was no tigecycline non-susceptible A. baumannii isolate harboring the tet(A) gene (0%), but one (7.69%) tigecycline non-susceptible K. pneumoniae isolate harbored the tet(A) gene. A phylogenetic tree, which is based on the nucleotide sequences of the tet(A) gene, showed that the sequence of the local isolate was 87% similar to the nucleotide sequences for all the isolates used for comparison from GenBank and the local isolate displayed genetic diversity. CONCLUSIONS: According to this study, tet(B) and tet(A) play an important role in the appearance of tigecycline non-susceptible Gram-negative isolates.202236207501
1213180.9992Fosfomycin resistance determinants in Escherichia coli isolates of human and animal origin from Iran. BACKGROUND: Fosfomycin has regained clinical interest over the last years due to its superior activity against multidrug-resistant bacterial pathogens. In the current study we aimed to characterize genotypic and phenotypic features of fosfomycin resistant (FosR) Escherichia coli isolates originating from human and animal. METHODS AND RESULTS: Five FosR bacteria were selected from a population of 150 E. coli isolates of human and broiler chickens. The sequence types of isolates were determined by multi-locus sequencing typing. Fosfomycin MICs were determined by agar dilution and gradient diffusion methods. Molecular detection of plasmid encoded fosfomycin resistance genes, fosA, fosA3, fosA4, fosA5 and fosC2 was performed by PCR. The modifications of fosfomycin target (MurA), transporters (GlpT, UhpT), and transporter regulator (PtsI) were investigated by gene sequencing. The MICs of fosfomycin were found to be ≥ 128 mg/L according to agar dilution and > 1024 mg/L according to gradient diffusion method. FosR isolates belonged to sequence types ST10 (n = 2), ST361, ST209 and ST1158 (n = 1). While all FosR isolates carried fos genes (fosA3 (n = 2), fosA5 (n = 2) and fosA4(n = 1)), only three isolates revealed amino acid substations in MurA, PtsI and GlpT with MurA P99S change being predicted to have deleterious impact on the function of protein. CONCLUSIONS: Emergence of fosfomycin resistance among studied isolates was mainly attributed to plasmid genes coding for fosfomycin modifying enzymes. The similarity in fosfomycin resistance determinants among clonally diverse E. coli isolates of human and animals indicates a possible cross-sectoral dissemination of fos genes by epidemic plasmids between bacterial isolates of clinical settings and those from animals.202540465084
1647190.9992Genomic and antimicrobial resistance genes diversity in multidrug-resistant CTX-M-positive isolates of Escherichia coli at a health care facility in Jeddah. BACKGROUND: Whole genome sequencing has revolutionized epidemiological investigations of multidrug-resistant pathogenic bacteria worldwide. Aim of this study was to perform comprehensive characterization of ESBL-positive isolates of Escherichia coli obtained from clinical samples at the King Abdulaziz University Hospital utilizing whole genome sequencing. METHODS: Isolates were identified by MALDI-TOF mass spectrometry. Genome sequencing was performed using a paired-end strategy on the MiSeq platform. RESULTS: Nineteen isolates were clustered into different clades in a phylogenetic tree based on single nucleotide polymorphisms in core genomes. Seventeen sequence types were identified in the extended-spectrum β-lactamase (ESBL)-positive isolates, and 11 subtypes were identified based on distinct types of fimH alleles. Forty-one acquired resistance genes were found in the 19 genomes. The bla(CTX-M-15) gene, which encodes ESBL, was found in 15 isolates and was the most predominant resistance gene. Other antimicrobial resistance genes (ARGs) found in the isolates were associated with resistance to tetracycline (tetA), aminoglycoside [aph(3″)-Ib, and aph(6)-Id], and sulfonamide (sul1, and sul2). Nonsynonymous chromosomal mutations in the housekeeping genes parC and gyrA were commonly found in several genomes. CONCLUSION: Several other ARGs were found in CTX-M-positive E. coli isolates confer resistance to clinically important antibiotics used to treat infections caused by Gram-negative bacteria.202031279801