Journal of global antimicrobial resistance最新文献

{"title":"The prevalent dynamic and genetic characterization of mcr-1 encoding multidrug resistant Escherichia coli strains recovered from poultry in Hebei, China","authors":"","doi":"10.1016/j.jgar.2024.04.001","DOIUrl":"10.1016/j.jgar.2024.04.001","url":null,"abstract":"<div><h3>Objectives</h3><p>Colistin is known as the last resort antibiotic to treat the infections caused by multidrug resistant foodborne pathogens. The emergence and widespread dissemination of plasmid-mediated colistin resistance gene <em>mcr-1</em> in the <em>Escherichia coli</em> (<em>E. coli</em>) incurs potential threat to public health. Here, we investigated the epidemiology, transmission dynamics, and genetic characterization of <em>mcr-1</em> harbouring <em>E. coli</em> isolates from poultry originated in Hebei Province, China.</p></div><div><h3>Methods</h3><p>A total of 297 faecal samples were collected from the two large poultry farms in Hebei Province, China. The samples were processed for <em>E. coli</em> identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S rDNA sequencing. Then, the <em>mcr-1</em> gene harbouring <em>E. coli</em> strains were identified by polymerase chain reaction and subjected to antimicrobial susceptibility testing by broth microdilution assay. The genomic characterization of the isolates was done by whole genome sequencing using the various bioinformatics tools, and multi-locus sequence typing was done by sequence analysis of the seven housekeeping genes. The conjugation experiment was done to check the transferability of <em>mcr-1</em> along with the plasmid stability testing.</p></div><div><h3>Results</h3><p>A total of six <em>mcr-1 E. coli</em> isolates with minimum inhibitory concentration of 4 μg/mL were identified from 297 samples (2.02%). The <em>mcr-1</em> harbouring <em>E. coli</em> were identified as multidrug resistant and belonged to ST101 (<em>n</em> = 4) and ST410 (<em>n</em> = 2). The genetic environment of <em>mcr-1</em> presented its position on IncHI2 plasmid in 4 isolates and p0111 in 2 isolates, which is a rarely reported plasmid type for <em>mcr-1</em>. Moreover, both type of plasmids was transferable to recipient J53, and <em>mcr-1</em> was flanked by 3 mobile elements <em>ISApl1</em>, Tn3, and IS26 forming a novel backbone <em>Tn3–IS26-mcr-1– pap2-ISApl1</em> on the p0111 plasmid. The phylogenetic analysis shared a common lineage with <em>mcr-1</em> harbouring isolates from the environment, humans, and animals, which indicate its horizontal spread among the diverse sources, species, and hosts.</p></div><div><h3>Conclusion</h3><p>This study recommends the one health approach for future surveillance across multiple sources and bacterial species to adopt relevant measures and reduce global resistance crises.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 354-362"},"PeriodicalIF":3.7,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000717/pdfft?md5=72df3281fa9ca548cffee5394952fab4&pid=1-s2.0-S2213716524000717-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141142057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome sequence of a sequence type 1 NDM-5-producing carbapenem-resistant Klebsiella pneumoniae in China","authors":"","doi":"10.1016/j.jgar.2024.05.001","DOIUrl":"10.1016/j.jgar.2024.05.001","url":null,"abstract":"<div><h3>Objectives</h3><p>The emergence of carbapenem-resistant <em>Klebsiella pneumoniae</em> presents significant health challenges. Here, we present the structural genome sequence of an NDM-5–producing <em>K. pneumoniae</em> (HZKP2) in China.</p></div><div><h3>Methods</h3><p>Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing was performed for genomic analysis. Wzi and capsular polysaccharide (KL) were analysed using Kaptive. Resistance genes, virulence factors, and comparative genomics analyses were also conducted. Multilocus sequence typing (MLST), replicons type, and core genome MLST analysis were further conducted using BacWGSTdb server.</p></div><div><h3>Results</h3><p>HZKP2 was resistant to cefepime, ceftazidime, ciprofloxacin, ciprofloxacin, meropenem, and ertapenem. It harboured <em>fosA, bla</em>_SHV-187, <em>oqxA, oqxB, sul1, dfrA1, tet(A), floR, aph(6)-Id, aph(3′')-Ib, sul2, bla</em>_CTX-M-55, and <em>bla</em>_NDM-5. Based on the RAST results, 5563 genes that belonged to 398 subsystems were annotated. The complete genome sequence of HZKP2 was characterized as ST1, <em>wzi</em> 19, and KL19, 5 five contigs totalling 5 654 446 bp, including one chromosome and four plasmids. Further analysis found that <em>bla</em>_NDM-5 was located in a 46 161 bp IncX3 plasmid (pHZKP2-3). The genetic structure of <em>bla</em>_NDM-5 gene was IS<em>Kox3</em>-IS<em>26</em>-<em>ble</em>_MBL-<em>bla</em>_NDM-5-IS<em>5</em>-IS<em>Ab125</em>-IS<em>3000</em>. Further analysis revealed that insertion sequences mediated the dissemination of <em>bla</em>_NDM-5 from other species of <em>Enterobacterales</em>. Phylogenetic analysis showed that the closest relative was from a human stool specimen in China, which differed by 53 core genome MLST alleles.</p></div><div><h3>Conclusions</h3><p>Our study provides the first structural perspective of the ST1 <em>K. pneumoniae</em> isolate producing NDM-5 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant <em>K. pneumoniae</em> in clinical settings.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 271-274"},"PeriodicalIF":3.7,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000833/pdfft?md5=a6a41cda4d6df31b523c42f62d8363e9&pid=1-s2.0-S2213716524000833-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141093466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efflux pump gene single-nucleotide variants associated with resistance in Mycobacterium tuberculosis isolates with discrepant drug genotypes","authors":"Zahra Hasan ,&nbsp;Safina Abdul Razzak ,&nbsp;Akbar Kanji,&nbsp;Sadia Shakoor,&nbsp;Rumina Hasan","doi":"10.1016/j.jgar.2024.05.006","DOIUrl":"10.1016/j.jgar.2024.05.006","url":null,"abstract":"<div><h3>Introduction</h3><p>Single-nucleotide variants (SNVs) in <em>Mycobacterium tuberculosis</em> (<em>M. tuberculosis</em>) genomes can predict multidrug resistance (MDR) but not all phenotype-genotype correlations can be explained. We investigated SNVs in efflux pumps (EPs) in the context of <em>M. tuberculosis</em> drug resistance.</p></div><div><h3>Methods</h3><p>We analysed 2221 <em>M. tuberculosis</em> genomes from 1432 susceptible and 200 MDR, 172 pre-extensively drug resistant (XDR) and 417 XDR isolates. Analysis of 47 EP genes was conducted using MTB-VCF, an in-house bioinformatics pipeline. SNVs were categorized according to their SIFT/Polyphen scores. Resistance genotypes were also called using the TB-Profiler tool.</p></div><div><h3>Results</h3><p>Genome comparisons between susceptible and drug resistant (DR) isolates identified 418 unique SNVs in EP of which; 53.5% were in MDR, 68.9% in pre-XDR and 61.3% in XDR isolates. Twenty EPs had unique SNVs with a high SIFT/PolyPhen score, comprising 38 unique SNVs. Sixteen SNVs across 12 EP genes were significantly associated with drug resistance and enriched in pre-XDR and XDR strains. These comprised 12 previously reported SNVs (in <em>Rv0191, Rv0507, Rv0676, Rv1217, Rv1218, Rv1273, Rv1458, Rv1819</em>, and <em>Rv2688</em>) and 4 novel SNVs (in <em>Rv1877</em> and <em>Rv2333</em>). We investigated their presence in genomes of 52 MDR isolates with phenotype-genotype discrepancies to rifampicin (RIF), isoniazid (INH), or fluoroquinolones. SNVs associated with RIF and INH (<em>Rv1217_1218, Rv1819, Rv0450, Rv1458, Rv3827, Rv0507, Rv0676, Rv1273</em>, and <em>Rv2333</em>), and with fluoroquinolone (<em>Rv2688</em>) resistance were present in these discrepant strains.</p></div><div><h3>Conclusions</h3><p>Considering SNVs in EPs as part of <em>M. tuberculosis</em> genome-based resistance interpretation may add value, especially in evaluation of XDR resistance in strains with phenotype-genotype discrepancies.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 128-139"},"PeriodicalIF":3.7,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S221371652400095X/pdfft?md5=4cfcc6226dfa8778d8742911efb2beb8&pid=1-s2.0-S221371652400095X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141093464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro activity of cefiderocol against carbapenemase-producing and meropenem-non-susceptible Gram-negative bacteria collected in the Japan Antimicrobial Resistant Bacterial Surveillance","authors":"Shizuo Kayama,&nbsp;Sayoko Kawakami,&nbsp;Kohei Kondo,&nbsp;Norikazu Kitamura,&nbsp;Liansheng Yu,&nbsp;Wataru Hayashi,&nbsp;Koji Yahara,&nbsp;Yo Sugawara,&nbsp;Motoyuki Sugai","doi":"10.1016/j.jgar.2024.05.009","DOIUrl":"10.1016/j.jgar.2024.05.009","url":null,"abstract":"<div><h3>Objectives</h3><p>The treatment options available for infections caused by multidrug-resistant Gram-negative pathogens are often limited. Cefiderocol (CFDC) is a novel siderophore cephalosporin that exhibits activity against these pathogens. Several studies have reported the in vitro activity of CFDC against isolates from Europe, the United States, and China, but the activity against carbapenem-resistant bacteria with IMP-type carbapenemase has not been extensively studied. We, therefore, studied the in vitro activities of CFDC against carbapenem-resistant bacteria with available genomic backgrounds based on whole-genome sequencing (WGS) in Japan, where the IMP-type is the predominant carbapenemase produced by Gram-negative rods.</p></div><div><h3>Methods</h3><p>We selected 603 isolates (528 Enterobacterales, 18 <em>Pseudomonas aeruginosa</em>, and 57 <em>Acinetobacter</em> spp.) from a collection of Gram-negative clinical isolates collected during a Japan Antimicrobial Resistance Bacterial Surveillance program and evaluated the antimicrobial activities of CFDC, ceftolozane/tazobactam (CTLZ/TAZ), imipenem-relebactam (IPM/REL), and ceftazidime/avibactam (CAZ/AVI) against carbapenemase-producing Enterobacterales, carbapenemase-non-producing meropenem-non-susceptible Enterobacterales, and carbapenemase-producing nonfermentative bacteria.</p></div><div><h3>Results</h3><p>Among these, 97.7% of carbapenemase-producing Enterobacterales (99.2% of IMP-type carbapenemase-producing Enterobacterales), 100% of carbapenemase-producing <em>P. aeruginosa</em>, and 91.2% of carbapenemase-producing <em>Acinetobacter</em> spp. were susceptible to CFDC, showing better antimicrobial activity than the other antimicrobial agents evaluated in this study. CFDC was highly effective against class A-, B-, and D β-lactamase-harbouring isolates when compared to the other antimicrobial agents. In addition, the relationship between CFDC resistance and three genetic factors involved in resistance was discussed.</p></div><div><h3>Conclusions</h3><p>This is the first large-scale study to systematically demonstrate the efficacy of CFDC against IMP-type carbapenemase-producing strains with known genomic backgrounds.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 12-20"},"PeriodicalIF":4.6,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000985/pdfft?md5=a6fb2a443fb0a6760c769d1d31ff0168&pid=1-s2.0-S2213716524000985-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141093469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into in-ICU emergence of last-resort antimicrobial resistance in a rare, carbapenem resistant, ST16 Klebsiella pneumoniae strain from Jodhpur, India","authors":"Ardhendu Chakrabortty ,&nbsp;Aastha Kapoor ,&nbsp;Tamal Dey ,&nbsp;Sharvika Subodh Khochare ,&nbsp;Lavanya Arora ,&nbsp;Vibhor Tak ,&nbsp;Vijaya Lakshmi Nag ,&nbsp;Pradeep Kumar Bhatia ,&nbsp;Manoharan Shankar","doi":"10.1016/j.jgar.2024.05.008","DOIUrl":"10.1016/j.jgar.2024.05.008","url":null,"abstract":"<div><h3>Objectives</h3><p>To investigate the genomic differences between two extensively drug resistant, ST16 strains of <em>Klebsiella pneumoniae</em> recovered from patients in the same ICU, one of which was colistin resistant.</p></div><div><h3>Methods</h3><p>Antimicrobial susceptibilities of the isolates were determined using VITEK-2. Hybrid assemblies for both strains were generated using Oxford Nanopore and Illumina technologies. The sequence type, capsule type, O-locus type, antimicrobial resistance determinants and plasmids carried by the isolates were inferred from the genome sequence. The phylogenetic placement, antimicrobial resistance, and virulence determinants of the isolates relative to a collection (<em>n</em> = 871) of ST16 isolates were assessed.</p></div><div><h3>Results</h3><p>Both BC16, a colistin-resistant blood stream isolate and U23, a colistin-sensitive urinary isolate displayed near-identical antimicrobial resistance profiles and genome sequences with varying plasmid profiles. The BC16 genome only had 21 SNPs relative to U23 and belonged to the same capsule, O-antigen locus and multi-locus sequence types. The <em>mgrB</em> locus in BC16 was disrupted by an IS<em>5</em> element. Phylogenetically, U23 and BC16 were placed on a clade with 4 strains belonging to K-type K48 and O-type O2a as opposed to majority (<em>n</em> = 807) of the strains (K-type K51 and O-type O3b).</p></div><div><h3>Conclusions</h3><p>BC16 was a colistin resistant derivative of U23, which evolved colistin resistance by an IS<em>5</em>-mediated disruption of the <em>mgrB</em> locus, likely during treatment of the index patient with colistin in the ICU. The strains belong to a rare subtype of ST16 with unique capsular and O-antigen types underscoring the utility of genomic surveillance networks and open-access genomic surveillance data in tracking problem clones.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 90-97"},"PeriodicalIF":3.7,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000961/pdfft?md5=1c22b3fbc46382da8c730977c5969533&pid=1-s2.0-S2213716524000961-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sepsis and pneumonia caused by Enterococcus faecium following liver transplantation treated with contezolid as the first-line therapy","authors":"Xiangyan Liu,&nbsp;Zhuoyi Wang,&nbsp;Weilin Wu,&nbsp;Shusen Zheng","doi":"10.1016/j.jgar.2024.05.005","DOIUrl":"10.1016/j.jgar.2024.05.005","url":null,"abstract":"<div><h3>Background</h3><p><em>Enterococcus faecium (E. faecium)</em> stands as a prominent pathogen contributing to Gram-positive bacterial infections in individuals who have undergone liver transplantation.</p></div><div><h3>Case presentation</h3><p>A 66-year-old male with a three-year history of treated anxiety disorder was admitted to our hospital due to recurrent abdominal distension and oliguria. He was diagnosed with hepatic veno-occlusive disease (HVOD), hepatic failure, pneumonia, renal insufficiency and abdominal ascites. A liver transplantation procedure was performed, but the patient's infection index increased on the first day after surgery. Empirical antibiotic therapy with ceftriaxone and meropenem and preventive antifungal therapy were applied. Sputum culture, blood culture, ascites culture and bronchoalveolar lavage fluid (BALF) next-generation sequencing (NGS), revealed the presence of <em>E. faecium</em>. Given the application of various nephrotoxic immunosuppressive agents after liver transplantation, pre-existing renal insufficiency, severe bone marrow suppression, and a history of anxiety disorder treated with sertraline, contezolid was added for the treatment of the Gram-positive bacterial infection. Sixteen days after surgery, cultures from ascites and sputum yielded negative results for fungi and bacteria. Contezolid was subsequently discontinued without any reported adverse events during follow-up.</p></div><div><h3>Conclusion</h3><p>Treatment with contezolid as the first-line therapy for sepsis and pneumonia caused by <em>E. faecium</em> following liver transplantation has shown satisfactory efficacy and safety. Therefore, contezolid may hold great promise for managing this life-threatening condition.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 1-5"},"PeriodicalIF":4.6,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000936/pdfft?md5=cdd2e3d990ea732099ca734ef8d26c89&pid=1-s2.0-S2213716524000936-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The correlation between intestinal colonization and infection of carbapenem-resistant Klebsiella pneumoniae: A systematic review","authors":"","doi":"10.1016/j.jgar.2024.04.013","DOIUrl":"10.1016/j.jgar.2024.04.013","url":null,"abstract":"<div><p>As a widely spread Gram-negative bacteria, <em>Klebsiella pneumoniae</em> (KP) mainly causes acquired infections in hospitals, such as lung infections, urinary tract infections, and bloodstream infections. In recent years, the number of multidrug-resistant KP strains has increased dramatically, posing a great threat to human health. Carbapenem-resistant KP (CRKP) can be colonized in human body, especially in gastrointestinal tract, and some colonized patients can be infected during hospitalization, among which invasive operation, underlying disease, admission to intensive care unit, antibiotic use, severity of the primary disease, advanced age, operation, coma, and renal failure are common risk factors for secondary infection. Active screening and preventive measures can effectively prevent the occurrence of CRKP infection. Based on the epidemiological status, this study aims to discuss the correlation between colonization and secondary infection induced by CRKP and risk factors for their happening and provide some reference for nosocomial infection prevention and control.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 187-193"},"PeriodicalIF":3.7,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000894/pdfft?md5=7fb4b12a1383ab7dd56ffaeb8544766a&pid=1-s2.0-S2213716524000894-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic characterization of plasmid-borne blaOXA-58 and blaOXA-72 in Acinetobacter pittii in Shaanxi, China","authors":"","doi":"10.1016/j.jgar.2024.05.007","DOIUrl":"10.1016/j.jgar.2024.05.007","url":null,"abstract":"<div><h3>Objectives</h3><p><em>Acinetobacter pittii</em> has emerged as an opportunistic nosocomial pathogen associated with hospital-acquired infections. The purpose of this study was to investigate the genetic structures of plasmids carrying carbapenemase genes <em>bla</em>_OXA-58 and <em>bla</em>_OXA-72 in <em>A. pittii</em> strains AR3676 and AR3651 isolated from patients.</p></div><div><h3>Methods</h3><p>Antimicrobial susceptibility testing was performed using broth microdilution. Whole-genome sequencing and bioinformatics analysis were performed to characterize the genome of <em>A. pittii</em> AR3676 and AR3651. Conjugation experiments were conducted to evaluate plasmid transferability. Phylogenetic and comparative genomic analysis were performed to explore the characteristics of carbapenem-resistant <em>A. pittii</em> isolates worldwide.</p></div><div><h3>Results</h3><p>The AR3676 strain showed resistance to imipenem. The 19 700-bp plasmid pAR3676-OXA-58 harboured <em>bla</em>_OXA-58 with genetic contexts consisting of a truncated IS<em>Aba3</em>-like-<em>bla</em>_OXA58-IS<em>Aba3</em>. Additionally, the AR3651 strain showed resistance to imipenem and meropenem. The AR3651 genome comprised one 9,837-bp RepA_AB plasmid pAR3651-OXA-72 harbouring <em>bla</em>_OXA-72. This <em>bla</em>_OXA-72 was flanked by <em>XerC/XerD</em> recombination sites. The conjugation of plasmids pAR3676-OXA-58 and pAR3651-OXA-72 from <em>A. pittii</em> to <em>Acinetobacter baumannii</em> ATCC 17978RIF^R failed three independent times. Phylogenetic analysis of <em>A. pittii</em> strains AR3676, AR3651, and a further 504 <em>A. pittii</em> strains collected between 1966 and 2022 from various geographic localities revealed genetic diversity with a heterogeneous distribution of carbapenemase genes.</p></div><div><h3>Conclusions</h3><p><em>A. pittii</em> strains with a plasmid carrying <em>bla</em>_OXA-58 or <em>bla</em>_OXA-72 may serve as an important reservoir of carbapenemase genes. Carbapenemase genes on a single plasmid may facilitate their dissemination and persistence. Additionally, pdif sites and mobile elements play an important role in the mobilization of resistance genes and plasmid evolution.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 167-172"},"PeriodicalIF":3.7,"publicationDate":"2024-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000948/pdfft?md5=3c8c183cb6b6a2d20e073b01c6429a9c&pid=1-s2.0-S2213716524000948-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Occurrence and characteristics of blaOXA-181-carrying Klebsiella aerogenes from swine in China","authors":"Lin Sun ,&nbsp;Nan Meng ,&nbsp;Hanyun Wang ,&nbsp;Zhenyu Wang ,&nbsp;Xinan Jiao ,&nbsp;Jing Wang","doi":"10.1016/j.jgar.2024.04.009","DOIUrl":"10.1016/j.jgar.2024.04.009","url":null,"abstract":"<div><h3>Objectives</h3><p><em>Klebsiella aerogenes</em> is a largely understudied opportunistic pathogen that can cause sepsis and lead to high mortality rates. In this study, we reported the occurrence of carbapenem-resistant <em>bla</em>_OXA-181-carrying <em>Klebsiella aerogenes</em> from swine in China and elucidate their genomic characteristics.</p></div><div><h3>Methods</h3><p>A total of 126 samples, including 109 swine fecal swabs, 14 environmental samples, and three feed samples were collected from a pig farm in China. The samples were enriched with LB broth culture and then inoculated into MacConkey agar plates for bacterial isolation. After PCR detection of carbapenemases genes, the <em>bla</em>_OXA-181-carrying isolates were subjected to antimicrobial susceptibility testing, and whole-genome sequence analysis.</p></div><div><h3>Results</h3><p>Four <em>Klebsiella aerogenes</em> isolates carrying the <em>bla</em>_OXA-181 gene were obtained from swine faecal samples. All the 4 strains were belonged to ST438. The <em>bla</em>_OXA-181 genes were located in IncX3-ColKP3 hybrid plasmids with the core genetic structure of IS<em>26</em>-ΔIS<em>3000</em>-ΔIS<em>Ecp1</em>-<em>bla</em>_OXA-181-Δ<em>lysR</em>-Δ<em>ereA</em>-Δ<em>repA</em>-IS<em>Kpn19</em>-<em>tinR</em>-<em>qnrS1</em>-ΔIS<em>2</em>-IS<em>26</em>, which suggests the potential for horizontal transfer and further dissemination of this resistance gene among <em>Enterobacteriaceae</em> and other sources.</p></div><div><h3>Conclusions</h3><p>This study represents the first instance of OXA-181-producing <em>K. aerogenes</em> being identified from swine faeces in China. It is crucial to maintain continuous monitoring and ongoing attention to the detection of <em>K. aerogenes</em> carrying <em>bla</em>_OXA-181 and other resistance genes in pigs.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 35-41"},"PeriodicalIF":4.6,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000870/pdfft?md5=2b5df5485220a5c025bdb93034a6c1b8&pid=1-s2.0-S2213716524000870-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141033657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome sequence of Porphyromonas pogonae PP01-1, a human strain harbouring blaOXA-347 and tet(Q)with chromosomal location","authors":"Junwei Huang ,&nbsp;Yijun Zhu ,&nbsp;Daojun Gong ,&nbsp;Shanshan Ma ,&nbsp;Yongjun Ma ,&nbsp;Cong Wu","doi":"10.1016/j.jgar.2024.04.015","DOIUrl":"10.1016/j.jgar.2024.04.015","url":null,"abstract":"<div><h3>Objectives</h3><p>The aim of this study was to characterise the first complete genome of <em>Porphyromonas pogonae</em> strain PP01-1 of human origin in China.</p></div><div><h3>Methods</h3><p>The Illumina NovaSeq 6000 (200X coverage) and Nanopore MinION platforms (100× coverage) were used for genome sequencing. A de novo hybrid assembly of short Illumina reads and long MinION reads was performed using Unicycler (v.0.5.0). Genome annotation of PP01-1 was performed using the prokaryotic gene-prediction tool Prokka1.14.6. The genome was further analysed using several bioinformatics tools, including ResFinder, VFDB, VirulenceFinder, Type Strain Genome Server, AntiSMASH, PathogenFinder, MobileElementfinder, CRISPRFinder, and IslandViewer.</p></div><div><h3>Results</h3><p>The assembled circular genome of <em>P. pogonae</em> strain PP01-1 was 2 916 423 bp in length, with a GC content of 41.0%, and no plasmid sequence was detected. A total of 2399 coding sequences were predicted by Prokka. PP01-1 harbours antimicrobial resistance genes <em>bla</em>_OXA-347 (β-lactamase resistance), <em>tet(Q)</em> (tetracycline resistance), and <em>floR</em> (chloramphenicol and florfenicol resistance).</p></div><div><h3>Conclusions</h3><p>Here, we are the first to report the complete genome of <em>P. pogonae</em> strain PP01-1 of human origin. In this strain, we first identified <em>bla</em>_OXA-347 and <em>tet(Q)</em> in <em>P. pogonae</em>, which will pave the way for further analysis that could identify the potential mechanism of antibiotic resistance and virulence factors in <em>P. pogonae</em>.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"38 ","pages":"Pages 103-105"},"PeriodicalIF":3.7,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000882/pdfft?md5=1956e05687e025681577cbb5229ab18b&pid=1-s2.0-S2213716524000882-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140944980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}