A strain defined as a novel species in the Acinetobacter genus co-harboring chromosomal associated tet(X3) and plasmid associated bla (NDM-1) from a beef cattle farm in Hebei, China. - Related Documents




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199101.0000A strain defined as a novel species in the Acinetobacter genus co-harboring chromosomal associated tet(X3) and plasmid associated bla (NDM-1) from a beef cattle farm in Hebei, China. INTRODUCTION: The co-existence phenomenon of antibiotic resistance genes (ARGs), particularly of last-resort antibiotics in multi-drug resistant (MDR) bacteria, is of particular concern in the least studied bacterial species. METHODS: In 2023, strain M2 was isolated from the sludge sample at a commercial bovine farm in Hebei province, China, using a MacConkey plate containing meropenem. PCR amplification and Sanger sequencing verified it co-carrying bla (NDM) and tet(X) genes. It was classified within the Acinetobacter genus by MALDI-TOF-MS and 16S rDNA analyses. Whole-genome sequencing (WGS) was performed on the Oxford Nanopore platform, with species-level identification via ANI and dDDH. Antimicrobial susceptibility testing was performed against 20 antibiotics. Conjugation assays employed the filter-mating method using E. coli J53 and Salmonella LGJ2 as recipients. RESULTS: This strain was confirmed as a novel species of Acinetobacter genus, showing resistance to meropenem, ampicillin, ceftazidime, cefepime, gentamicin, kanamycin, fosfomycin, imipenem, ertapenem, and tetracycline. Despite carrying tet(X3), it remained susceptible to tigecycline, omadacycline, and doxycycline. The genome carried 11 ARG types, multiple metal resistance genes (MRGs), and virulence factor (VF) genes. The bla (NDM-1) was located in a skeleton, ISAba125-bla (NDM-1)-ble (MBL)-trpF, which was carried by an ISAba14-mediated rolling-circle-like structure in pM2-2-NDM-1 (rep_cluster_481). Integrative and conjugative element (ICE) and multiple pdif modules (driven by the XerCD site-specific recombination (XerCD SSR) system), which were associated with the mobilization of resistance determinants, were identified in this plasmid. Chromosomal tet(X3) was mediated by ISVsa3, forming a skeleton, ISVsa3-XerD-tet (X3)-res-ISVsa3. DISCUSSION: The co-occurrence of bla (NDM) and tet(X) in a novel species of the Acinetobacter genus hints that substantial undiscovered bacteria co-carrying high-risk ARGs are concealing in the agroecological system, which should cause particular concern.202540673007
88810.9996Identification of New Delhi metallo-β-lactamase 1 in Acinetobacter lwoffii of food animal origin. BACKGROUND: To investigate the presence of metallo-β-lactamase (MBL) genes and the genetic environment of the New Delhi metallo-β-lactamase gene bla(NDM-1) in bacteria of food animal origin. METHODOLOGY/PRINCIPAL FINDINGS: Gram-negative bacteria with low susceptibility to imipenem (MIC>8 µg/mL) were isolated from swab samples collected from 15 animal farms and one slaughterhouse in eastern China. These bacteria were selected for phenotypic and molecular detection of known MBL genes and antimicrobial susceptibility testing. For the bla(NDM-1) positive isolate, conjugation and transformation experiments were carried out to assess plasmid transfer. Southern blotting was conducted to localize the bla(NDM-1) genes, and DNA sequencing was performed to determine the sequences of bla(NDM-1) and the flanking genes. In total, nine gram-negative bacteria of four different species presented a MBL phenotype. bla(NDM-1) was identified on a mobile plasmid named pAL-01 in an Acinetobacter lwoffii isolate of chicken origin. Transfer of pAL-01 from this isolate to E. coli J53 and JM109 resulted in resistance to multiple β-lactams. Sequence analysis revealed that the bla(NDM-1) gene is attached to an intact insertion element ISAba125, whose right inverted repeat (IR-R) overlaps with the promoter sequence of bla(NDM-1). Thus, insertion of ISAba125 likely enhances the expression of bla(NDM-1). CONCLUSION: The identification of a bla(NDM-1)- carrying strain of A. lwoffii in chickens suggests the potential for zoonotic transmission of bla(NDM-1) and has important implications for food safety.201222629360
152220.9995Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-β-lactamase, in an urban river in South Korea. OBJECTIVES: To examine the presence of pathogenic bacteria carrying New Delhi metallo-β-lactamase in the environment and to characterize the genome structures of these strains. METHODS: Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated from an urban river. RESULTS: Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess bla NDM-9 genes. Antimicrobial susceptibility testing indicated resistance of these strains to aminoglycosides, carbapenems, cephems, folate pathway inhibitors, fosfomycin and penicillins, but susceptibility to fluoroquinolones, phenicols, tetracyclines and miscellaneous agents. WGS revealed that the 108 kb IncFII(Y)-like plasmids carry bla NDM-9 sandwiched between IS 15 for the GJ1 strain, IS 26 for the GJ2 strain, IS 15D1 for the GJ3 strain and IS Vsa3 , and further bracketed by IS 26 and Tn AS3 along with the mercury resistance operon upstream and the class 1 integron composed of gene cassettes of aadA2 , dfrA12 and sul1 downstream. An aph(3')-Ia gene conferring resistance to aminoglycosides is located after the integrons. Chromosomally encoded bla LEN-13 , fosA , aqxA and oqxB genes, as well as plasmid-mediated bla TEM-1B and bla CTX-M-65 encoding ESBL, ant(3')-Ia and mph (A) genes, were also identified. CONCLUSIONS: The findings of the present study provide us with the information that NDM-9 has been spreading into the environment. Dissemination of NDM-9 in the environment has raised a health risk alarm as this variant of NDM carries MDR genes with highly transferable mobile genetic elements, increasing the possibility of resistance gene transfer among microorganisms in the environment.201728087584
119130.9995IncFII plasmid carrying antimicrobial resistance genes in Shigella flexneri: Vehicle for dissemination. OBJECTIVES: Plasmids harbouring antimicrobial resistance determinants in clinical strains are a significant public-health concern worldwide. The present study investigated such plasmids in clinical isolates of Shigella flexneri. METHODS: A total of 162 Shigella isolates were obtained from stool specimens in the year 2015. Among the 70 multidrug-resistant (MDR) Shigella spp., 27 S. flexneri isolates were randomly selected for further characterisation. Antimicrobial resistance genes (ARGs) and plasmid incompatibility (Inc) types were analysed. RESULTS: IncFII plasmids were found in 63% (17/27) of the studied S. flexneri isolates. ARGs such as dhfr1a (81%), sulII (74%), bla(OXA) (74%), bla(TEM) (33%), bla(AmpC) (30%), qnrS (15%) and qnrB (4%) were identified by PCR, whereas bla(CTX-M) was not detected. Next-generation sequencing of a representative S. flexneri IncFII-type plasmid (pSF470) revealed the presence of bla(TEM1-B), bla(DHA-1), qnrB10, mphA, sulI, sulII, strA, strB and tetR ARGs along with the intI1 integrase gene. In addition, pMLST analysis showed that the replicon belonged to F2:A-:B- type. CONCLUSIONS: This study helps to know the prevalent plasmid types in MDR Shigella isolates and will improve our understanding of resistance dissemination among enteric bacteria. ARGs in plasmids further highlight the importance of such studies in enteric bacteria.201930342929
151340.9995Occurrence and Characterization of NDM-1-Producing Shewanella spp. and Acinetobacter portensis Co-Harboring tet(X3) in a Chinese Dairy Farm. Bacteria with carbapenem or tigecycline resistance have been spreading widely among humans, animals and the environment globally, being great threats to public health. However, bacteria co-carrying drug resistance genes of carbapenem and tigecycline in Shewanella and Acinetobacter species remain to be investigated. Here, we detected nine bla(NDM-1)-carrying Shewanella spp. isolates as well as three A. portensis isolates co-harboring tet(X3) and bla(NDM-1) from seventy-two samples collected from a dairy farm in China. To explore their genomic characteristic and transmission mechanism, we utilized various methods, including PCR, antimicrobial susceptibility testing, conjugation experiment, whole-genome sequencing, circular intermediate identification and bioinformatics analysis. Clonal dissemination was found among three A. portensis, of which tet(X3) and bla(NDM-1) were located on a novel non-conjugative plasmid pJNE5-X3_NDM-1 (333,311 bp), and the circular intermediate ΔISCR2-tet(X3)-bla(NDM-1) was identified. Moreover, there was another copy of tet(X3) on the chromosome of A. portensis. It was verified that bla(NDM-1) could be transferred to Escherichia coli C600 from Shewanella spp. by conjugation, and self-transmissible IncA/C(2) plasmids mediated the transmission of bla(NDM-1) in Shewanella spp. strains. Stringent surveillance was warranted to curb the transmission of such vital resistance genes.202236290080
189950.9995Characteristics of plasmids in multi-drug-resistant Enterobacteriaceae isolated during prospective surveillance of a newly opened hospital in Iraq. BACKGROUND: Gram-negative multidrug-resistant (MDR) bacteria are major causes of nosocomial infections, and antibiotic resistance in these organisms is often plasmid mediated. Data are scarce pertaining to molecular mechanisms of antibiotic resistance in resource constrained areas such as Iraq. METHODOLOGY/PRINCIPAL FINDINGS: In this study, all MDR Enterobacteriaceae (n = 38) and randomly selected non-MDR counterparts (n = 41) isolated from patients, healthcare workers and environmental surfaces in a newly opened hospital in Iraq were investigated to characterize plasmids found in these isolates and determine their contribution to antibiotic resistance. Our results demonstrated that MDR E. coli and K. pneumoniae isolates harbored significantly more (≥ 3) plasmids compared to their non-MDR counterparts, which carried ≤ 2 plasmids (p<0.01). Various large plasmids (~52 to 100 kb) from representative isolates were confirmed to contain multiple resistance genes by DNA microarray analysis. Aminoglycoside (acc, aadA, aph, strA/B, and ksgA), β-lactam (bla(TEM1), bla(AMPC), bla(CTX-M-15), bla(OXA-1), bla(VIM-2) and bla(SHV)), sulfamethoxazole/trimethoprim (sul/dfr), tetracycline (tet) and chloramphenicol (cat) resistance genes were detected on these plasmids. Additionally, multiple plasmids carrying multiple antibiotic resistance genes were found in the same host strain. Genetic transfer-associated genes were identified on the plasmids from both MDR and non-MDR isolates. Seven plasmid replicon types (FII, FIA, FIB, B/O, K, I1 and N) were detected in the isolates, while globally disseminated IncA/C and IncHI1 plasmids were not detected in these isolates. CONCLUSIONS/SIGNIFICANCE: This is the first report of the characteristics of the plasmids found in Enterobacteriaceae isolated following the opening of a new hospital in Iraq. The information provided here furthers our understanding of the mechanisms of drug resistance in this specific region and their evolutionary relationship with other parts of world. The large plasmids, carrying resistance genes and transfer-associated genes, may be potential factors for regional dissemination of antibiotic resistance.201222808141
164560.9995Epidemiological investigation and β-lactam antibiotic resistance of Riemerella anatipestifer isolates with waterfowl origination in Anhui Province, China. Riemerella anatipestifer (R. anatipestifer) is a highly pathogenic and complex serotypes waterfowl pathogen with inherent resistance to multiple antibiotics. This study was aimed to investigate the antibiotic resistance characteristics and genomic features of R. anatipestifer isolates in Anhui Province, China in 2023. A total of 287 cases were analysed from duck farms and goose farms, and the R. anatipestifer isolates were subjected to drug resistance tests for 30 antimicrobials. Whole genome sequencing (WGS) and bioinformatics analysis were performed on the bacterial genomes, targeting the β-lactam resistance genes. The results showed that a total of 74 isolates of R. anatipestifer were isolated from 287 cases, with a prevalence of 25.8%. The antimicrobial susceptibility testing (AST) revealed that all the 74 isolates were resistant to multiple drugs, ranging from 13 to 26 kinds of drugs. Notably, these isolates showed significant resistance to aminoglycosides and macrolides, which are also commonly used in clinical practices. Data revealed the presence of several β-lactamase-related genes among the isolates, including a novel bla(RASA-1) variant (16.2%), the class A extended-spectrum β-lactamase bla(RAA-1) (12.2%), and a bla(OXA-209) variant (98.6%). Functional analysis of the variants bla(RASA-1) and bla(OXA-209) showed that the bla(RASA-1) variant exhibited activity against various β-lactam antibiotics while their occurrence in R. anatipestifer were not common. The bla(OXA-209) variant, on the other hand, did not perform any β-lactam antibiotic resistance. Furthermore, we observed that bla(RAA-1) could undergo horizontal transmission among different bacteria via the insertion sequence IS982. In conclusion, this study delves into the high prevalence of R. anatipestifer infection in waterfowl in Anhui, China. The isolated strains exhibit severe drug resistance issues, closely associated with the prevalence of antibiotic resistance genes (ARG). Additionally, our research investigates the β-lactam antibiotic resistance mechanism in R. anatipestifer.202438387287
88170.9995Genetic analysis of multidrug-resistant and AmpC-producing Citrobacter freundii. OBJECTIVE: During the last decade, antimicrobial resistance within pet animals has received worldwide concern owing to their close contact with humans and the possibility of animal-human co-transmission of multidrug-resistant bacteria. This study examined phenotypic as well as molecular mechanisms associated with antimicrobial resistance in a multidrug-resistant, and AmpC-producing Citrobacter freundii recovered from a dog suffering from kennel cough in. MATERIALS AND METHODS: The isolate was recovered from a two-year-old dog suffering from severe respiratory manifestations. Phenotypically, the isolate was resistant to a wide range of antimicrobial agents including, aztreonam, ciprofloxacin, levofloxacin, gentamicin, minocycline, piperacillin, sulfamethoxazole-trimethoprim, and tobramycin. PCR and sequencing confirmed that the isolate harbors multiple antibiotic resistance genes, such as blaCMY-48 and blaTEM-1B which mediate resistance to B-lactams, and qnrB6 which mediate resistance to quinolone antibiotics. RESULTS: Multilocus sequence typing confirmed that the isolate belongs to ST163. Due to the unique characteristics of this pathogen, the whole genome sequencing was performed. In addition to the previously confirmed antibiotic resistance genes by PCR, the isolate was also confirmed to harbor other resistance genes which mediate resistance to aminoglycoside (aac(3)-IId, aac(6')-Ib-cr, aadA16, aph(3'')-Ib, and aph(6)-Id), macrolides [mph(A)), phenicols (floR), rifampicin (ARR-3), sulphonamides (sul1 and sul2), trimethoprim (dfrA27), and tetracycline (tet(A) and tet(B)]. CONCLUSIONS: The results presented in this study confirm that pets are possible sources of highly pathogenic multidrug-resistant microbes with unique genetic characteristics taking into consideration the high potential for their dissemination to humans, which can undoubtedly develop of severe infections in these hosts.202336808363
164780.9995Genomic 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
202890.9995Short communication: Whole-genome sequence analysis of 4 fecal bla(CMY-2)-producing Escherichia coli isolates from Holstein dairy calves. This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 4 fecal bla(CMY-2)-producing Escherichia coli isolated from Holstein dairy calves on the same farm using whole-genome sequencing. Genomic analysis revealed that 3 of the 4 isolates shared similar genetic features, including sequence type (ST), serotype, plasmid characteristics, insertion ST, and virulence genes. In addition to genes encoding for complex multidrug resistance efflux systems, all 4 isolates were carriers of genes conferring resistance to β-lactams (bla(CMY-2), bla(TEM-1B)), tetracyclines (tetA, tetB, tetD), aminoglycosides [aadA1, aph(3")-lb, aph(6)-ld], sulfonamides (sul2), and trimethoprim (dfrA1). We also detected 4 incompatibility plasmid groups: Inc.F, Inc.N, Inc.I, and Inc.Q. A novel ST showing a new purA and mdh allelic combination was found. The 4 isolates were likely enterotoxigenic pathotypes of E. coli, based on serotype and presence of the plasmid Inc.FII(pCoo). This study provides information for comparative genomic analysis of AMR genes and mobile genetic elements. This analysis could give some explanation to the multidrug resistance characteristics of bacteria colonizing the intestinal tract of dairy calves in the first few weeks of life.202031733866
884100.9995Fecal carriage and molecular epidemiology of mcr-1-harboring Escherichia coli from children in southern China. BACKGROUND: The increase of multidrug-resistant Enterobacteriaceae bacteria has led to the reintroduction of colistin for clinical treatments, and colistin has become a last resort for infections caused by multidrug-resistant bacteria. Enterobacteriaceae bacteria carrying the mcr-1 gene are majorly related to colistin resistance, which may be the main reason for the continued increase in the colistin resistance rate of Enterobacteriaceae. The study aimed to investigate the sequence type and prevalence of Escherichia coli (E. coli) harboring the mcr-1 gene in the gut flora of children in southern China. METHODS: Fecal samples (n = 2632) of children from three medical centers in Guangzhou were cultured for E. coli. The mcr-1-harboring isolates were screened via polymerase chain reaction (PCR). The colistin resistance transfer frequency was studied by conjugation experiments. DNA sequencing data of seven housekeeping genes were used for multi-locus sequence typing analysis (MLST). RESULTS: PCR indicated that 21 of the 2632 E. coli (0.80%) isolates were positive for mcr-1; these strains were resistant to colistin. Conjugation experiments indicated that 18 mcr-1-harboring isolates could transfer colistin resistance phenotypes to E. coli J53. MLST analysis revealed that the 21 isolates were divided into 18 sequence types (STs); E. coli ST69 was the most common (14.3%), followed by E. coli ST58 (9.5%). CONCLUSION: These results demonstrate the colonization dynamics and molecular epidemiology of E. coli harboring mcr-1 in the gut flora of children in southern China. The mcr-1 gene can be horizontally transmitted within species; hence, it is necessary to monitor bacteria that harbor mcr-1 in children.202337196369
887110.9995Characterization of fosfomycin resistance and molecular epidemiology among carbapenem-resistant Klebsiella pneumoniae strains from two tertiary hospitals in China. BACKGROUND: Fosfomycin has been proven to be a vital choice to treat infection caused by multidrug resistance bacteria, especially carbapenem-resistant Klebsiella pneumoniae (CRKP). However, fosfomycin resistant cases has been reported gradually. In this study, we reported the fosfomycin-resistant rate in CRKP strains and further revealed the molecular mechanisms in resistance gene dissemination. RESULTS: A total of 294 non-duplicated CRKP strains were collected. And 55 fosfomyin-resistant strains were detected, 94.5% of which were clustered to sequence type (ST) 11 by PCR followed up sequencing. PFGE further revealed two major groups and four singletons. The positive rates of genes responsible to fosfomycin and carbapenem resistance were 81.8% (fosA3), 12.7% (fosA5) and 94.5% (bla(KPC-2)), respectively. Genomic analysis confirmed insertion sequence (IS) 26 was the predominant structure surrounding fosA3. The fosA3 genes in six isolates were located on plasmids which were able to transfer to E. coli J53 recipient cells by means of conjugation. CONCLUSIONS: Although the resistant rate of CRKP to fosfomycin is relatively low in our area, considering its gene is located on transferrable plasmid and inserted in IS structure, continuous monitoring is still needed.202133838639
1525120.9995Genetic Characterization of Enterobacter hormaechei Co-Harboring bla (NDM-1) and mcr-9 Causing Upper Respiratory Tract Infection. PURPOSE: With the spread of multiple drug-resistant bacteria, bla (NDM-1) and mcr-9 have been detected in various bacteria worldwide. However, the simultaneous detection of bla (NDM-1) and mcr-9 in Enterobacter hormaechei has been rarely reported. This study identified an E. hormaechei strain carrying both bla (NDM-1) and mcr-9. We investigated the genetic characteristics of these two resistance genes in detail, elucidating various potential mechanisms by which they may be transmitted. METHODS: Bacterial genomic features and possible origins were assessed by whole-genome sequencing (WGS) with Illumina and PacBio platforms and phylogenetic analysis. Subsequent investigations were performed, including antimicrobial susceptibility testing and multilocus sequence typing (MLST). RESULTS: We isolated an E. hormaechei strain DY1901 carrying both bla (NDM-1) and mcr-9 from the sputum sample. Susceptibility testing showed that the isolate was multidrug-resistant. Multiple antibiotic resistance genes and virulence genes are widely distributed in DY1901. S1-PFGE, Southern blotting, and plasmid replicon typing showed that DY1901 carried four plasmids. The plasmid carrying mcr-9 was 259Kb in size and belonged to IncHI2, while the plasmid carrying bla (NDM-1) was 45Kb in length and belonged to IncX3. CONCLUSION: The E. hormaechei strain isolated in this study has a broad antibiotic resistance spectrum, posing a challenge to clinical treatment. Plasmids carrying mcr-9 are fusion plasmids, and those taking NDM are widely disseminated in China, suggesting that we should conduct routine genomic surveillance on such plasmids to curb the spread of drug-resistant bacteria in the region.202236068833
894130.9995Molecular characterisations of integrons in clinical isolates of Klebsiella pneumoniae in a Chinese tertiary hospital. BACKGROUND: Integrons are mobile genetic elements that play an important role in the distribution of antibiotic-resistance genes among bacteria. This study aimed to investigate the distribution of integrons in clinical isolates of Klebsiella pneumoniae and explore the molecular mechanism of integron-mediated multiple-drug resistance in K. pneumoniae. METHODS: Class 1, 2, and 3 integrases were identified by polymerase chain reaction (PCR) among 178 K. pneumoniae clinical isolates. Antibiotic susceptibility was examined by disk-diffusion method. Conjugation experiments were conducted to evaluate the horizontal-transfer capability, and multilocus sequence typing (MLST) assays were conducted to explore the genetic relationships among the isolates. Highly virulent serotypes were identified by PCR from the 44 integron-positive isolates with variable regions. RESULTS: Class1 and 2 integrons were detected in 60.1% and 1.7% of isolates, respectively. One isolate carried both class 1 and 2 integrons. Class 3 integrons were not detected in all 178 isolates. Among the 44 integrons containing variable regions, 39 were located in conjugative plasmids. Dihydrofolate reductase (dfrA) and aminoglycoside adenyltransferase (aad) were found to be the most common in class 1 and 2 integrons. These gene cassettes encoded resistance to trimethoprim and aminoglycosides. Moreover, the association between integron carriage and antibiotic resistance was most significant for aminoglycosides, phenicols, and fluoroquinolones. Among the 44 integron-positive isolates with variable regions, 9 were classified as highly virulent serotypes (k1, k2, k20, and k54). In addition, MLST analysis detected 13 sequence types (STs), with the predominant ones being ST11 and ST15. The eBURST analysis revalued the existence of 11 singleton STs and one group, which is comprised of ST11 and ST437. CONCLUSIONS: The wide diversity of detected integrons suggested that the horizontal transfer by mobile genetic elements played a major role in the distribution of antimicrobial resistance genes, thereby indicating the urgent need to use effective means of avoiding the spread of drug-resistant bacteria.201728111326
843140.9995Whole Genome Sequencing Reveals Presence of High-Risk Global Clones of Klebsiella pneumoniae Harboring Multiple Antibiotic Resistance Genes in Multiple Plasmids in Mwanza, Tanzania. BACKGROUND: Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen, causing both community- and healthcare-associated infections. The resistance is due to the continuous accumulation of multiple antibiotic-resistance-genes (ARGs) through spontaneous genomic mutations and the acquisition of conjugative plasmids. This study presents antibiotics resistance genes, plasmids replicons, and virulence genes of K. pneumoniae isolates from clinical specimens in a tertiary hospital, Mwanza, Tanzania. METHODS: Whole genome sequencing (WGS) of 34 K. pneumoniae was performed, using an Illumina NextSeq 500, followed by in silco analysis. RESULTS: A total of 34 extended-spectrum beta-lactamase-producing K. pneumoniae, isolated from blood samples from neonatal units were whole-genome sequenced. Of these, 28 (82.4%) had an identified sequence type (ST), with ST14 (39.3%, n = 11) being frequently identified. Moreover, 18 (52.9%) of the bacteria harbored at least one plasmid, from which a total of 25 plasmid replicons were identified with a predominance of IncFIB(K) 48.0% (n = 12). Out of 34 sequenced K. pneumoniae, 32 (94.1%) were harboring acquired antibiotic/biocides-resistance-genes (ARGs) with a predominance of bla(CTX-M-15) (90.6%), followed by oqxB (87.5%), oqxA (84.4%), bla(TEM-1B) (84.4%) and sul2 (84.4%). Interestingly, we observed the ColRNAI plasmid-replicon (n = 1) and qacE gene (n = 4) for the first time in this setting. CONCLUSION: Global high-risk clones of K. pneumoniae isolates carry multiple ARGs in multiple plasmid-replicons. Findings from this study warrant genomic-based surveillance to monitor high-risk global clones, epidemic plasmids and ARGs in low- and middle-income countries.202236557648
1205150.9995Prevalence and Genomic Investigation of Multidrug-Resistant Salmonella Isolates from Companion Animals in Hangzhou, China. Salmonella is a group of bacteria that constitutes the leading cause of diarrheal diseases, posing a great disease burden worldwide. There are numerous pathways for zoonotic Salmonella transmission to humans; however, the role of companion animals in spreading these bacteria is largely underestimated in China. We aimed to investigate the prevalence of Salmonella in pet dogs and cats in Hangzhou, China, and characterize the antimicrobial resistance profile and genetic features of these pet-derived pathogens. In total, 137 fecal samples of pets were collected from an animal hospital in Hangzhou in 2018. The prevalence of Salmonella was 5.8% (8/137) in pets, with 9.3% (5/54) of cats and 3.6% (3/83) of dogs being Salmonella positive. By whole-genome sequencing (WGS), in silico serotyping, and multilocus sequence typing (MLST), 26 pet-derived Salmonella isolates were identified as Salmonella Dublin (ST10, n = 22) and Salmonella Typhimurium (ST19, n = 4). All of the isolates were identified as being multidrug-resistant (MDR), by conducting antimicrobial susceptibility testing under both aerobic and anaerobic conditions. The antibiotics of the most prevalent resistance were streptomycin (100%), cotrimoxazole (100%), tetracycline (96.20%), and ceftriaxone (92.30%). Versatile antimicrobial-resistant genes were identified, including floR (phenicol-resistant gene), blaCTX-M-15, and blaCTX-M-55 (extended-spectrum beta-lactamase genes). A total of 11 incompatible (Inc) plasmids were identified, with IncA/C2, IncFII(S), and IncX1 being the most predominant among Salmonella Dublin, and IncFIB(S), IncFII(S), IncI1, and IncQ1 being the most prevailing among Salmonella Typhimurium. Our study applied WGS to characterize pet-derived Salmonella in China, showing the presence of MDR Salmonella in pet dogs and cats with a high diversity of ARGs and plasmids. These data indicate a necessity for the regular surveillance of pet-derived pathogens to mitigate zoonotic diseases.202235625269
910160.9995Analysis of Antimicrobial Resistance Genes (ARGs) in Enterobacterales and A. baumannii Clinical Strains Colonizing a Single Italian Patient. The dramatic increase in infections caused by critically multidrug-resistant bacteria is a global health concern. In this study, we characterized the antimicrobial resistance genes (ARGs) of K. pneumoniae, P. mirabilis, E. cloacae and A. baumannii isolated from both surgical wound and rectal swab of a single Italian patient. Bacterial identification was performed by MALDI-TOF MS and the antimicrobial susceptibility was carried out by Vitek 2 system. The characterization of ARGs was performed using next-generation sequencing (NGS) methodology (MiSeq Illumina apparatus). K. pneumoniae, P. mirabilis and E. cloacae were resistant to most β-lactams and β-lactam/β-lactamases inhibitor combinations. A. baumannii strain was susceptible only to colistin. The presence of plasmids (IncN, IncR, IncFIB, ColRNAI and Col (MGD2)) was detected in all Enterobacterales but not in A. baumannii strain. The IncN plasmid and bla(NDM-1) gene were found in K. pneumoniae, P. mirabilis and E. cloacae, suggesting a possible transfer of this gene among the three clinical species. Conjugation experiments were performed using K. pneumoniae (1 isolate), P. mirabilis (2 isolates) and E. cloacae (2 isolates) as donors and E. coli J53 as a recipient. The bla(NDM-1) gene was identified by PCR analysis in all transconjugants obtained. The presence of four different bacterial species harboring resistance genes to different classes of antibiotics in a single patient substantially reduced the therapeutic options.202336978306
1143170.9995Antimicrobial Resistance and Virulence Profiles of mcr-1-Positive Escherichia coli Isolated from Swine Farms in Heilongjiang Province of China. ABSTRACT: The emergence and global distribution of the mcr-1 gene for colistin resistance have become a public concern because of threats to the role of colistin as the last line of defense against some bacteria. Because of the prevalence of mcr-1-positive Escherichia coli isolates in food animals, production of these animals has been regarded as one of the major sources of amplification and spread of mcr-1. In this study, 249 E. coli isolates were recovered from 300 fecal samples collected from swine farms in Heilongjiang Province, People's Republic of China. Susceptibility testing revealed that 186 (74.70%) of these isolates were colistin resistant, and 86 were positive for mcr-1. The mcr-1-positive isolates had extensive antimicrobial resistance profiles and additional resistance genes, including blaTEM, blaCTX-M, aac3-IV, tet(A), floR, sul1, sul2, sul3, and oqxAB. No mutations in genes pmrAB and mgrB were associated with colistin resistance. Phylogenetic group analysis revealed that the mcr-1-positive E. coli isolates belonged to groups A (52.33% of isolates), B1 (33.72%), B2 (5.81%), and D (8.14%). The prevalence of the virulence-associated genes iutA, iroN, fimH, vat, ompA, and traT was moderate. Seven mcr-1-positive isolates were identified as extraintestinal pathogenic. Among 20 mcr-1-positive E. coli isolates, multilocus sequence typing revealed that sequence type 10 was the most common (five isolates). The conjugation assays revealed that the majority of mcr-1 genes were transferable at frequencies of 7.05 × 10-7 to 7.57 × 10-4. The results of this study indicate the need for monitoring and minimizing the further dissemination of mcr-1 among E. coli isolates in food animals, particularly swine.202032730609
1994180.9995Antibiotic resistance genes, mobile elements, virulence genes, and phages in cultivated ESBL-producing Escherichia coli of poultry origin in Kwara State, North Central Nigeria. The paucity of information on the genomic diversity of drug-resistant bacteria in most food-producing animals, including poultry in Nigeria, has led to poor hazard characterization and the lack of critical control points to safeguard public health. Hence, this study used whole genome sequencing (WGS) to assess the presence and the diversity of antibiotic resistance genes, mobile genetic elements, virulence genes, and phages in Extended Spectrum Beta Lactamase producing Escherichia coli (ESBL - E. coli) isolates obtained from poultry via the EURL guideline of 2017 in Ilorin, Nigeria. The prevalence of ESBL - E. coli in poultry was 10.5 % (n = 37/354). The phenotypic antibiotic susceptibility testing showed that all the ESBL- E. coli isolates were multi-drug resistant (MDR). The in-silico analysis of the WGS raw-read data from 11 purposively selected isolates showed that the isolates had a wide array of ARGs that conferred resistance to beta-lactam antibiotics, and 8 other classes of antibiotics (fluoroquinolones, foliate pathway antagonists, aminoglycoside, phenicol, tetracycline, epoxide, macrolides, and rifamycin). All the ARGs were in the bacterial chromosome except in two isolates where plasmid-mediated quinolone resistance (PMQR) was detected. Two isolates carried the gyrAp.S83L mutation which confers resistance to certain fluoroquinolones. The mobilome consisted of several Col-plasmids and the predominant IncF plasmids belonged to the IncF64:A-:B27 sequence type. The virulome consisted of genes that function as adhesins, iron acquisition genes, toxins, and protectins. Intact phages were found in 8 of the 11 isolates and the phageome consisted of representatives of four families of viruses: Myoviridae (62.5 %, n = 5/8), Siphoviridae (37.5 %, n = 3/8), Inoviridae (12.5 %, n = 1), and Podoviridae (12.5 %, n = 1/8). ESBL - E. coli isolates harboured 1-5 intact phages and no ARGs were identified on any of the phages. Although five of the isolates belonged to phylogroup A, the isolates were diverse as they belonged to different serotype and sequence types. Our findings demonstrate the high genomic diversity of ESBL - E. coli of poultry origin in Ilorin, Nigeria. These diverse isolates harbor clinically relevant ARGs, mobile elements, virulence genes, and phages that may have detrimental zoonotic potentials on human health.202336738714
1526190.9995Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon. BACKGROUND: The occurrence of carbapenem-resistant bacterial infections has increased significantly over the years with Gram-negative bacteria exhibiting the broadest resistance range. In this study we aimed to investigate the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE). METHODS: Seventeen representative multi-drug resistant (MDR) isolates from a hospital setting showing high level of resistance to carbapenems (ertapenem, meropenem and imipenem) were chosen for further characterization through whole-genome sequencing. Resistance mechanisms and transferability of plasmids carrying carbapenemase-encoding genes were also determined in silico and through conjugative mating assays. RESULTS: We detected 18 different β-lactamases, including four carbapenemases (bla(NDM-1), bla(NDM-5), bla(NDM-7), bla(OXA-48)) on plasmids with different Inc groups. The combined results from PBRT and in silico replicon typing revealed 20 different replicons linked to plasmids ranging in size between 80 and 200 kb. The most prevalent Inc groups were IncFIB(K) and IncM. OXA-48, detected on 76-kb IncM1 conjugable plasmid, was the most common carbapenemase. We also detected other conjugative plasmids with different carbapenemases confirming the role of horizontal gene transfer in the dissemination of antimicrobial resistance genes. CONCLUSION: Our findings verified the continuing spread of carbapenemases in Enterobacterales and revealed the types of mobile elements circulating in a hospital setting and contributing to the spread of resistance determinants. The occurrence and transmission of plasmids carrying carbapenemase-encoding genes call for strengthening active surveillance and prevention efforts to control antimicrobial resistance dissemination in healthcare settings.202337871361