Characterization of a Novel mcr-8.2-Bearing Plasmid in ST395 Klebsiella pneumoniae of Chicken Origin. - Related Documents




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152401.0000Characterization of a Novel mcr-8.2-Bearing Plasmid in ST395 Klebsiella pneumoniae of Chicken Origin. The emergence of mobile colistin resistance mcr genes undermines the efficacy of colistin as the last-resort drug for multi-drug resistance infections and constitutes a great public health concern. Plasmids play a critical role in the transmission of mcr genes among bacteria. One colistin-resistant Klebsiella pneumoniae strain of chicken origin was collected and analyzed by antimicrobial susceptibility testing, PCR, conjugation assay and S1-PFGE. Whole-genome sequencing (WGS) approach combining Illumina and MinION platforms was utilized to decipher the underlying colistin resistance mechanism and genetic context. A novel mcr-8.2-bearing plasmid p2019036D-mcr8-345kb with 345 655 bp in size encoding various resistance genes including floR, sul1, aadA16, aadA2, bla (CTX-M-27), bla (DHA-1), tet(D), dfrA12 and qnrB4 was identified responsible for the colistin resistance phenotype. Plasmid comparison has shown that the mcr-8.2-bearing plasmid differed from other reported plasmids positive for mcr-8.2 but shared the same core mcr-8.2-bearing conserved region. This study demonstrates the emergence of mcr-8.2-bearing K. pneumoniae of animal origin is a potential risk to humans.202032606828
152510.9998Genetic 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
152720.9998Emergence of an Escherichia coli strain co-harbouring mcr-1 and bla(NDM-9) from a urinary tract infection in Taiwan. OBJECTIVES: Multidrug-resistant bacteria have become a serious threat worldwide. In particular, the coexistence of carbapenemase genes and mcr-1 leaves few available treatment options. Here we report a multidrug-resistant Escherichia coli isolate harbouring both mcr-1 and bla(NDM-9) from a patient with a urinary tract infection. METHODS: Antimicrobial susceptibility and resistance genes of the E. coli isolate were characterised. Furthermore, the assembled genome sequences of mcr-1- and bla(NDM-9)-carrying plasmids were determined and comparative genetic analysis with closely related plasmids was carried out. RESULTS: Three contigs were assembled comprising the E. coli chromosome and two plasmids harbouring mcr-1 (p5CRE51-MCR-1) and bla(NDM-9) (p5CRE51-NDM-9), respectively. Whole-genome sequencing revealed that the two antimicrobial resistance genes are located on individual plasmids. CONCLUSIONS: The emergence of coexistence of carbapenemase genes and mcr-1 in Enterobacteriaceae highlights a serious threat to antimicrobial therapy.201930312830
152630.9998Carbapenem 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
89140.9998Identification of mobile colistin resistance genes (mcr-1.1, mcr-5 and mcr-8.1) in Enterobacteriaceae and Alcaligenes faecalis of human and animal origin, Nigeria. Colistin is a last-resort drug used to treat infections caused by multidrug-resistant Gram-negative bacteria that have developed carbapenem resistance. Emergence and rapid dissemination of the nine plasmid-mediated mobile colistin resistance genes (mcr-1 to mcr-9) has led to fear of pandrug-resistant infections worldwide. To date, there is only limited information on colistin resistance in African countries where the drug is widely used in agriculture. In this Nigerian study, 583 non-duplicate bacterial strains were isolated from 1119 samples from humans, camels, cattle, dogs, pigs and poultry using colistin-supplemented MacConkey agar, among which 17.0% (99/583) were colistin-resistant. PCR (mcr-1 to mcr-9) and whole-genome sequencing (WGS) identified mcr in 21.2% (21/99) of colistin-resistant isolates: mcr-1.1 (n = 13), mcr-8.1 (n = 5), mcr-1.1 and mcr-8.1 (n = 2), and mcr-1.1 and mcr-5 (n = 1). Of the 21 mcr-positive strains, 9 were isolated from human samples, with 8 being Klebsiella pneumoniae, and 6 of these human K. pneumoniae had a high colistin MIC (>64 μg/mL). In contrast, 9 of the 12 mcr-positive animal isolates were Escherichia coli, of which only 2 had a colistin MIC of >64 μg/mL. This study is the first to report mcr-1 in Alcaligenes faecalis and the emergence of mcr-5 and mcr-8 in Nigeria. WGS determined that mcr-1 was localised on an IncX4 plasmid and that 95.2% of mcr-1 harbouring isolates (20/21) transferred colistin resistance successfully by conjugation. These findings highlight the global spread of colistin resistance and emphasise the urgent need for co-ordinated global action to combat resistant bacteria.202032721596
150750.9997Characterization of Five Escherichia coli Isolates Co-expressing ESBL and MCR-1 Resistance Mechanisms From Different Origins in China. Present study characterized five Escherichia coli co-expressing ESBL and MCR-1 recovered from food, food-producing animals, and companion animals in China. Antimicrobial susceptibility tests, conjugation experiments, and plasmid typing were performed. Whole genome sequencing (WGS) was undertaken for all five isolates using either PacBio RS II or Illumina HiSeq 2500 platforms. The cefotaxime and colistin resistance encoded by bla (CTX-M) and mcr-1 genes, respectively, was transferable by conjugation either together or separately for all five strains. Interestingly, the ESBL and mcr-1 genes could be co-selected by cefotaxime, while the colistin only selected the mcr-1-carrying plasmids during the conjugation experiments. Five E. coli sequence types (ST88, ST93, ST602, ST162, and ST457) were detected. Although diverse plasmid profiles were identified, IncI2, IncFIB, and IncFII plasmid types were predominant. These five clonally unrelated isolates harbored the mcr-1 gene located on similar plasmid backbones, which showed high nucleotide similarity to plasmid pHNSHP45. The mcr-1 gene can be co-transmitted with bla (CTX-M) genes through IncI2 plasmids with or without ISApl1 in our study. Characterization of these co-existence ESBL and mcr-1 isolates extends our understanding on the dissemination of these resistance markers among bacteria of diverse origins.201931555232
173160.9997Prevalence of Colistin Resistance in Escherichia coli in Eastern Turkey and Genomic Characterization of an mcr-1 Positive Strain from Retail Chicken Meat. Colistin is one of the most effective antibiotics against multidrug resistant Gram-negative bacteria. However, the recent emergence of plasmid-borne mobilized colistin resistance (mcr) genes is considered a serious antimicrobial resistance challenge worldwide. In this study, we report detection of an mcr-1 carrying Escherichia coli isolate (named ATAVET mcr-1 Turkey) from retail raw chicken meat in Turkey. Of the 11 (from 500 total tested) phenotypically colistin-resistant isolates, 1 was shown to carry the mcr-1 gene by PCR. Whole-genome sequencing indicated that mcr-1 was located on a ∼13 kb-long contig that was almost identical to the corresponding part in pZJ1635, an IncI2 plasmid encoding mcr-1 in the same genetic context in another E. coli strain. In addition, ATAVET mcr-1 Turkey harbored bla(CTX-M-8), qnrB19, mdf(A), tet(A), sul2, aph(3″)-Ib, aph(6)-Id, and floR resistance genes. Phylogenetic analysis based on whole genome and multilocus sequence typing indicated that ATAVET mcr-1 Turkey was more closely related to mcr-1 carrying E. coli isolates from food and human clinical samples previously reported from different parts of the world than to those from Turkey. These findings further emphasize the worldwide emergence and spread of mcr meditated colistin resistance in bacteria with zoonotic potential within animals and the food chain.202132721263
150670.9997Detection of Five mcr-9-Carrying Enterobacterales Isolates in Four Czech Hospitals. The aim of this study was to report the characterization of the first mcr-positive Enterobacterales isolated from Czech hospitals. In 2019, one Citrobacter freundii and four Enterobacter isolates were recovered from Czech hospitals. The production of carbapenemases was examined by a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) imipenem hydrolysis assay. Additionally, bacteria were screened for the presence of carbapenemase-encoding genes and plasmid-mediated colistin resistance genes by PCR. To define the genetic units carrying mcr genes, the genomic DNAs of mcr-carrying clinical isolates were sequenced on the PacBio Sequel I platform. Results showed that all isolates carried bla(VIM)- and mcr-like genes. Analysis of whole-genome sequencing (WGS) data revealed that all isolates carried mcr-9-like alleles. Furthermore, the three sequence type 106 (ST106) Enterobacter hormaechei isolates harbored the bla(VIM-1) gene, while the ST764 E. hormaechei and ST95 C. freundii included bla(VIM-4) Analysis of plasmid sequences showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. Additionally, at least one multidrug resistance (MDR) region was identified in each mcr-9-carrying IncHI2 plasmid. The bla(VIM-4) gene was found in the MDR regions of p48880_MCR_VIM and p51929_MCR_VIM. In the three remaining isolates, bla(VIM-1) was localized on plasmids (∼55 kb) exhibiting repA-like sequences 99% identical to the respective gene of pKPC-CAV1193. In conclusion, to the best of our knowledge, these 5 isolates were the first mcr-9-positive bacteria of clinical origin identified in the Czech Republic. Additionally, the carriage of the bla(VIM-1) on pKPC-CAV1193-like plasmids is described for the first time. Thus, our findings underline the ongoing evolution of mobile elements implicated in the dissemination of clinically important resistance determinants.IMPORTANCE Infections caused by carbapenemase-producing bacteria have led to the revival of polymyxins as the "last-resort" antibiotic. Since 2016, several reports describing the presence of plasmid-mediated colistin resistance genes, mcr, in different host species and geographic areas were published. Here, we report the first detection of Enterobacterales carrying mcr-9-like alleles isolated from Czech hospitals in 2019. Furthermore, the three ST106 Enterobacter hormaechei isolates harbored bla(VIM-1), while the ST764 E. hormaechei and ST95 Citrobacter freundii isolates included bla(VIM-4) Analysis of WGS data showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. bla(VIM-4) was found in the MDR regions of IncHI2 plasmids, while bla(VIM-1) was localized on pKPC-CAV1193-like plasmids, described here for the first time. These findings underline the ongoing evolution of mobile elements implicated in dissemination of clinically important resistance determinants. Thus, WGS characterization of MDR bacteria is crucial to unravel the mechanisms involved in dissemination of resistance mechanisms.202033298573
88780.9997Characterization 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
151790.9997Co-occurrence of blaNDM-1, rmtC, and mcr-9 in multidrug-resistant Enterobacter kobei strain isolated from an infant with urinary tract infection. OBJECTIVES: The co-emergence of mcr and carbapenem resistance genes in Gram-negative bacteria is a serious problem. This study aims to clarify the genetic characteristic of one novel multidrug-resistant Enterobacter kobei EC1382 with mcr-9 causing urinary tract inflammation in an infant. METHODS: Antimicrobial drug susceptibility testing was performed for this isolate using the broth microdilution method. Whole-genome sequencing was performed using the Illumina PacBio RS II platform and HiSeq platform, and the antimicrobial resistance genes, mobile elements, and plasmid replicon types were identified. Conjugation analysis was performed using Escherichia coli C600 as recipients. RESULTS: Enterobacter kobei EC1382 was resistant to carbapenem, aminoglycoside, and cephalosporin. Twenty-five antimicrobial resistance genes were identified, including genes conferring resistance to carbapenem (blaNDM-1), colistin (mcr-9), and aminoglycosides (rmtC). The blaNDM-1 gene, accompanied by bleMBL and rmtC located downstream of an ISCR14 element, was detected in the IncFII(Yp) type plasmid pEC1382-2. Interestingly, although E. kobei EC1382 was susceptible to colistin, it had three identical mcr-9 genes (two in the chromosome and one in the IncHI2-type plasmid pEC1382-1). The backbone (∼12.2-kb genetic fragment) of these mcr-9 (flanked by IS903B and IS481-IS26) regions were conserved in this strain, and they were found to be present in various bacteria as three types, implying a silent distribution. CONCLUSIONS: To the best of our knowledge, this is the first study to demonstrate the coexistence of blaNDM-1, rmtC, and mcr-9 in E. kobei. The silent prevalence of mcr-9 in bacteria may be a threat to public health.202337062506
1732100.9997High Carriage Rate of the Multiple Resistant Plasmids Harboring Quinolone Resistance Genes in Enterobacter spp. Isolated from Healthy Individuals. Antimicrobial-resistant bacteria causing intractable and even fatal infections are a major health concern. Resistant bacteria residing in the intestinal tract of healthy individuals present a silent threat because of frequent transmission via conjugation and transposition. Plasmids harboring quinolone resistance genes are increasingly detected in clinical isolates worldwide. Here, we investigated the molecular epidemiology of plasmid-mediated quinolone resistance (PMQR) in Gram-negative bacteria from healthy service trade workers. From 157 rectal swab samples, 125 ciprofloxacin-resistant strains, including 112 Escherichia coli, 10 Klebsiella pneumoniae, two Proteus mirabilis, and one Citrobacter braakii, were isolated. Multiplex PCR screening identified 39 strains harboring the PMQR genes (including 17 qnr,19 aac(6')-Ib-cr, and 22 oqxA/oqxB). The genome and plasmid sequences of 39 and 31 strains, respectively, were obtained by short- and long-read sequencing. PMQR genes mainly resided in the IncFIB, IncFII, and IncR plasmids, and coexisted with 3-11 other resistance genes. The high PMQR gene carriage rate among Gram-negative bacteria isolated from healthy individuals suggests the high-frequency transmission of these genes via plasmids, along with other resistance genes. Thus, healthy individuals may spread antibiotic-resistant bacterial, highlighting the need for improved monitoring and control of the spread of antibiotic-resistant bacteria and genes in healthy individuals.202135052892
1858110.9997Molecular Characteristics of Antimicrobial Resistance and Virulence in Klebsiella pneumoniae Strains Isolated from Goose Farms in Hainan, China. We retrospectively investigated 326 samples that were collected from goose farms in Hainan Province, China, in 2017. A total of 33 carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates were identified from 326 samples, and the 33 CRKP isolates were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. All of these 33 CRKP isolates possessed bla(NDM-5), and a single isolate coharbored mcr-1 and bla(NDM-5), while 4 isolates carried multiple virulence and metal tolerance gene clusters. One CRKP strain (CMG-35-2) was selected for long sequence reading. A hybrid plasmid carrying the virulence, resistance, and metal resistance gene in the strain was found. It possessed 2 backbones [IncFIB(K)-IncFII(K)] within a single plasmid that were closely related to K. pneumoniae plasmids from a human-associated habitat in the United States and from a human isolate in Hong Kong. A mouse abdominal infection model indicated that that strain was of the moderate virulence phenotype. This study revealed that K. pneumoniae on goose farms is an important reservoir for bla(NDM-5) and these bacteria are represented by a diversity of sequence types. The heterozygous multiple drug resistance genes carried on plasmids highlighted the genetic complexity of CRKP and the urgent need for continued active surveillance. IMPORTANCE CRKP is one of the most important pathogens, which can cause infection not only in humans but also in waterfowl. The discovery of bla(NDM-5)-producing K. pneumoniae in waterfowl farms in recent years suggests that waterfowl are an important reservoir for bla(NDM-5)-producing Enterobacteriaceae. However, there are few studies on the spread of bla(NDM-5)-producing bacteria in waterfowl farms. Our study showed that the IncX3 plasmid carrying bla(NDM-5) in goose farms is widely present in K. pneumoniae isolates and a large number of resistance genes are accumulated in it. We found a transferable IncFIB-FII hybrid plasmid that combines virulence, resistance, and metal resistance genes, which allow transfer of these traits between bacteria in different regions. The results of this study contribute to a better understanding of the prevalence and transmission of carbapenem-resistant K. pneumoniae in goose farms.202235389252
1523120.9997The characterization of an IncN-IncR fusion plasmid co-harboring bla(TEM-40), bla(KPC-2), and bla(IMP-4) derived from ST1393 Klebsiella pneumoniae. Plasmids, as important genetic elements apart from chromosomes, often carry multiple resistance genes and various mobile genetic elements, enabling them to acquire more exogenous genes and confer additional resistance phenotypes to bacteria. Various carbapenem resistance genes are often located on IncN plasmids, and several reports have linked fusion plasmids to IncN plasmids. Therefore, this study aims to explore the emergence, molecular structure characteristics, and resistance features mediated by IncN fusion plasmids carrying multiple carbapenem resistance genes. In this study, species identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Polymerase chain reaction (PCR) was employed to detect the presence of carbapenem resistance genes in the strains. PCR-based replicon typing (PBRT) was used to identify IncN plasmids. Plasmids were analyzed through S1-nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blotting, conjugation experiments, and stability tests. Whole-genome sequencing (WGS) and antimicrobial susceptibility testing (AST) were conducted to characterize the target strains. Four strains containing IncN plasmids were identified: two Klebsiella pneumoniae, one Escherichia coli, and one Enterobacter cloacae, all harboring carbapenem resistance genes. Among them, two IncN plasmids (pFAHZZU7605-KPC-IMP and pFAHZZU7865-IMP) contained blaIMP-4 and exhibited similar molecular structure characteristics. Notably, the pFAHZZU7605-KPC-IMP plasmid harbored both IncN and IncR replicons. We hypothesize that the pFAHZZU7605-KPC-IMP fusion plasmid resulted from the recombination of a pFAHZZU7865-IMP-like plasmid and an IncR-like plasmid. Further analysis of the plasmid's genetic elements revealed that insertion sequences ISKpn19 and ISKpn27 played crucial roles in the plasmid recombination and fusion process. In clinical settings, plasmids carrying different resistance genes can undergo fusion, mediated by genetic elements, thereby expanding the resistance spectrum of host bacteria. Hence, it is essential to enhance the monitoring and research of transposable elements to control the spread of multidrug-resistant bacteria.202439496788
1721130.9997Convergence of MCR-8.2 and Chromosome-Mediated Resistance to Colistin and Tigecycline in an NDM-5-Producing ST656 Klebsiella pneumoniae Isolate From a Lung Transplant Patient in China. We characterized the first NDM-5 and MCR-8.2 co-harboring ST656 Klebsiella pneumoniae clinical isolate, combining with chromosomal gene-mediated resistance to colistin and tigecycline. The K. pneumoniae KP32558 was isolated from the bronchoalveolar lavage fluid from a lung transplant patient. Complete genome sequences were obtained through Illumina HiSeq sequencing and nanopore sequencing. The acquired resistance genes and mutations in chromosome-encoded genes associated with colistin and tigecycline resistance were analyzed. Comparative genomic analysis was conducted between mcr-8.2-carrying plasmids. The K. pneumoniae KP32558 was identified as a pan-drug resistant bacteria, belonging to ST656, and harbored plasmid-encoded bla(NDM-5) and mcr-8.2 genes. The bla(NDM-5) gene was located on an IncX3 type plasmid. The mcr-8.2 gene was located on a conjugative plasmid pKP32558-2-mcr8, which had a common ancestor with another two mcr-8.2-carrying plasmids pMCR8_020135 and pMCR8_095845. The MIC of KP32558 for colistin was 256 mg/L. The mcr-8.2 gene and mutations in the two-component system, pmrA and crrB, and the regulator mgrB, had a synergistic effect on the high-level colistin resistance. The truncation in the acrR gene, related to tigecycline resistance, was also identified. K. pneumoniae has evolved a variety of complex resistance mechanisms to the last-resort antimicrobials, close surveillance is urgently needed to monitor the prevalence of this clone.202235899054
1686140.9997Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates. The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The blaNDM-1 and blaOXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A blaOXA-48-carrying IncL/M-type plasmid was found in all blaOXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.201829883490
1522150.9997Emergence 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
1853160.9997Dissemination dynamics of colistin resistance genes mcr-9 and mcr-10 across diverse Inc plasmid backbones. BACKGROUND: The polymyxin antibiotic colistin is used as a final line of treatment for life threatening infections caused by multidrug resistant and carbapenem-resistant Gram-negative bacteria. Mobile colistin resistance genes mcr-9 and mcr-10 are increasingly detected in Enterobacteriaceae but their epidemiology is poorly understood. METHODS: The genetic characteristics of mcr-9 and mcr-10, being the only mobile colistin resistance genes detected in a local population of Enterobacter species isolated from bloodstream infections in Dartmouth Hitchcock Medical Center, USA, were elucidated and contextualized against a global dataset of mcr-9/10-bearing plasmids using genomic and phylogenetic tools. RESULTS: Seven out of 59 Enterobacter isolates carry either an mcr-9 or mcr-10 on a plasmid with distinct single and multiple replicon configurations, including IncFIB(pECLA), IncFIB(K), IncFIA(HI1)-IncFIB(K), IncFIB(pECLA)--IncFII(pECLA) and IncFIB(K)--IncFII(pECLA), whereas two genomes harbor mcr-9 on their chromosome. Global contextualization reveals that allelic variants of mcr-9 and mcr-10 are widely disseminated across diverse Inc-type plasmids, transcending geographic and taxonomic boundaries. Plasmid-borne genes conferring resistance to other antimicrobial agents, such as aminoglycoside, tetracycline and trimethoprim, tend to co-occur with mcr-9.1 and mcr-9.2 alleles. CONCLUSIONS: Findings from this study enhance our understanding of the plasmid backgrounds of mcr-9 and mcr-10, their associated antimicrobial resistance gene carriage and co-occurrence. This knowledge may be critical to inform scalable and effective public health interventions aimed at preserving the efficacy of colistin.202540999001
1725170.9997Letter to the Editor: Escherichia fergusonii Harboring IncHI2 Plasmid Containing mcr-1 Gene-A Novel Reservoir for Colistin Resistance in Brazil. Emergence of colistin-resistant bacteria harboring mobile colistin resistance genes (mcr genes) pose a threat for food-producing animals and humans. In this article, we aim to highlight the emergence of Escherichia fergusonii as an important new reservoir to mcr-1-harboring plasmid in poultry production. Three strains closely related were isolated from cloacal swabs. Their genome contains four plasmids, including a 182,869 bp IncHI2 plasmid harboring the colistin resistance gene mcr-1. These results will contribute to our understanding of plasmid-mediated mcr-1 gene presence and transmission in E. fergusonii.202133001761
1667180.9997Colistin Resistance Gene mcr-8 in a High-Risk Sequence Type 15 Klebsiella pneumoniae Isolate from Kenya. The emergence and rise of mobile colistin resistance genes are of great global concern due to the ease of transfer of resistance to other bacteria. This report describes the genome of a colistin- and multidrug-resistant Klebsiella pneumoniae isolate bearing mcr-8, obtained from a hospitalized patient in Kenya.202032972937
1514190.9997Widespread prevalence and molecular epidemiology of tet(X4) and mcr-1 harboring Escherichia coli isolated from chickens in Pakistan. The emergence and spread of plasmid-mediated tigecycline resistance gene tet(X4) and colistin resistance gene mcr-1 in Escherichia coli (E. coli) pose a potential threat to public health, due to the importance of colistin and tigecycline for treating serious clinical infections. However, the characterization of bacteria coharboring both genes was few reported. Here, we described the molecular epidemiology of tet(X4) and mcr-1 harboring E. coli strains of chicken origin in Pakistan, with methods including PCR, antimicrobial susceptibility testing, DNA transfer assays, plasmid replicon typing, whole-genome sequencing and bioinformatics analysis. The tet(X4) gene was identified in 36 isolates exhibiting high levels of tigecycline resistance (MICs, 16-128 mg/L). Worryingly, 24 of the 36 tet(X4)-bearing isolates were confirmed as colistin resistance, positive for plasmid-borne mcr-1. We observed the prevalence of tet(X4)-bearing IncFII plasmid with mcr-1-bearing IncI2 plasmid in 12 E. coli isolates, with a high co-transfer frequency except for one strain PK8233, in which tet(X4)- and mcr-1-bearing plasmids were non-transferable. Coexistence of tet(X4)-bearing IncFII plasmid with mcr-1-carrying multidrug-resistant (MDR) IncHI2 plasmid was also identified in 10 E. coli isolates, and a relatively low co-transfer frequency was obtained except PK8575, in which mcr-1 was non-transferable. The transferability of pPK8275-tetX in PK8275 and pPK8233-tetX in PK8233, that could transfer from E. coli J53 to C600 by conjugation, was interfered by certain factors in PK8275 and PK8233. This may provide new insights to prevent and control the spread of antibiotic resistance genes. Two strains were reported to co-carry tet(X4)-positive IncQ1 plasmid and mcr-1-positive IncI2 plasmid. Convergence of tet(X4) and mcr-1 genes in E. coli by conjugative or mobilizable plasmids may lead to potentially widespread transmission of such resistance genes, which may incur antibiotic-resistance crisis globally.202234599956