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Zhao J, Pu D, Li Z, Zhang Y, Liu X, Zhuo X, Lu B, Cao B. Loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing K1-ST23 hypervirulent Klebsiella pneumoniae. Virulence 2024; 15:2348251. [PMID: 38697754 PMCID: PMC11067985 DOI: 10.1080/21505594.2024.2348251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVES This study aimed at revealing the underlying mechanisms of the loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing hypervirulent Klebsiella pneumoniae (hvKp). METHODS Here we longitudinally recovered 3 non-carbapenemase-producing K1-ST23 hvKp strains at a one-month interval (KP29105, KP29499 and KP30086) from an elderly male. Antimicrobial susceptibility testing, whole genome sequencing, transcriptomic sequencing, gene cloning, plasmid conjugation, quantitative real-time PCR (qRT-PCR), and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) were conducted. RESULTS Among the 3 hvKp strains, KP29105 was resistant to the third- and fourth-generation cephalosporins, KP29499 acquired resistance to both ceftazidime-avibactam and carbapenems, while KP30086 restored its susceptibility to ceftazidime-avibactam, imipenem and meropenem but retained low-level resistance to ertapenem. KP29105 and KP29499 carried plasmid-encoded genes blaCTX-M-15 and blaCTX-M-71, respectively, but KP30086 lost both. Cloning of gene blaCTX-M-71 and conjugation experiment of blaCTX-M-71-carrying plasmid showed that the transformant and transconjugant were susceptible to ceftazidime-avibactam but had a more than 8-fold increase in MICs. Supplementation with an outer membrane permeabilizer could reduce the MIC of ceftazidime-avibactam by 32 folds, indicating that porins play a key role in ceftazidime-avibactam resistance. The OmpK35 of the 3 isolates was not expressed, and the OmpK36 of KP29499 and KP30086 had a novel amino acid substitution (L359R). SDS-PAGE and qRT-PCR showed that the expression of porin OmpK36 of KP29499 and KP30086 was significantly down-regulated compared with KP29105. CONCLUSIONS In summary, we reported the rare ceftazidime-avibactam resistance in a non-carbapenemase-producing hvKp strain. Resistance plasmid carrying blaCTX-M-71 and mutated OmpK36 had a synergetic effect on the resistance.
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Affiliation(s)
- Jiankang Zhao
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Danni Pu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ziyao Li
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Yulin Zhang
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xinmeng Liu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xianxia Zhuo
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Department of Respiratory Medicine, Capital Medical University, Beijing, China
| | - Binghuai Lu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Cao
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Department of Respiratory Medicine, Capital Medical University, Beijing, China
- Tsinghua University-Peaking University Joint Center for Life Sciences, Beijing, China
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Allander L, Vickberg K, Fermér E, Söderhäll T, Sandegren L, Lagerbäck P, Tängdén T. Impact of porin deficiency on the synergistic potential of colistin in combination with β-lactam/β-lactamase inhibitors against ESBL- and carbapenemase-producing Klebsiella pneumoniae. Antimicrob Agents Chemother 2024:e0076224. [PMID: 39365067 DOI: 10.1128/aac.00762-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 08/25/2024] [Indexed: 10/05/2024] Open
Abstract
Combinations of colistin and β-lactam/β-lactamase inhibitors (BLBLIs) have shown in vitro synergy against β-lactamase-producing strains. However, data are limited and conflicting, potentially attributed to variations among the examined strains. This study investigated whether loss of porins OmpK35 and OmpK36 impacts the synergistic potential of colistin in combination with ceftazidime-avibactam or meropenem-avibactam against β-lactamase-producing Klebsiella pneumoniae. Genetically modified strains were constructed by introducing blaCTX-M-15, blaKPC-2, and blaOXA-48 chromosomally into K. pneumoniae ATCC 35657, in which the major porin-encoding genes (ompK35, ompK36) were either intact or knocked out. The in vitro activity of colistin in combination with ceftazidime-avibactam or meropenem-avibactam was evaluated by time-lapse microscopy screening and in static time-kill experiments. The deletion of porins in the β-lactamase-producing strains resulted in 2- to 128-fold increases in MICs for the β-lactams and BLBLIs. The activity of avibactam was concentration-dependent, and 4- to 16-fold higher concentrations were required to achieve similar inhibition of the β-lactamases in strains with porin loss. In the screening, synergy was observed for colistin and ceftazidime-avibactam against the CTX-M-15-producing strains and colistin and meropenem-avibactam against the KPC-2- and OXA-48-producing strains. The combination effects were less pronounced in the time-kill experiments, where synergy was rarely detected. No apparent associations were found between the loss of OmpK35 and OmpK36 and combination effects with colistin and BLBLIs, indicating that additional factors determine the synergistic potential of such combinations.
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Affiliation(s)
- Lisa Allander
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Karin Vickberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Elin Fermér
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Thomas Söderhäll
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Uppsala Antibiotic Center, Uppsala University, Uppsala, Sweden
| | | | - Thomas Tängdén
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Kawang K, Thongsuk P, Cholsaktrakool P, Anuntakarun S, Kunadirek P, Chuaypen N, Nilgate S, Chatsuwan T, Nookaew I, Sangpiromapichai N, Nilaratanakul V. Sensitivity and specificity of Nanopore sequencing for detecting carbapenem and 3rd-generation cephalosporin-resistant Enterobacteriaceae in urine samples: Real-time simulation with public antimicrobial resistance gene database. Heliyon 2024; 10:e35816. [PMID: 39253247 PMCID: PMC11382077 DOI: 10.1016/j.heliyon.2024.e35816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024] Open
Abstract
Objectives To evaluate the accuracy of beta-lactamase gene detection directly from urine samples by Nanopore sequencing. Methods DNA was extracted from bacterial pellets in spun urine. The purified DNA was then sequenced in native form by a Nanopore sequencer (MinION) to identify the organisms and beta-lactamase genes. Results were compared to routine urine cultures and standard antimicrobial susceptibility tests (AST). Results We processed 60 urine samples of which routine cultures grew Enterobacteriaceae, including 28 carbapenem-resistant (CRE), 17 extended-spectrum beta-lactamase (ESBL) or AmpC producing, and 15 non-ESBL/AmpC phenotypes. We excluded 7 samples with extremely low DNA amounts (<1 ng/μl) for a final case of 53 in total. The sensitivity of antimicrobial resistance gene detection within 6 h, the optimal duration from real-time simulation, of Nanopore sequencing for the diagnosis of carbapenem-resistant and ceftriaxone-resistant phenotypes was 73.9 % (95%CI 56.0-91.9 %) and 81.1 % (95%CI 68.5-93.7 %), while the specificity was 96.7 % (95%CI 90.2-100.0 %) and 56.3 % (95%CI 31.9-80.6 %), respectively. The median times for MinION to generate DNA reads containing carbapenemase and ESBL/AmpC genes were 93 min (IQR 17-245.5) and 99 min (IQR 31.25-269.75) after sequencing commencement, respectively. Conclusions Nanopore sequencing can identify bacterial genotypic resistance in urine and may enable clinicians to adjust antimicrobial therapy earlier than routine AST.
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Affiliation(s)
- Kornthara Kawang
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
- Excellence Center for Infectious Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Pannaporn Thongsuk
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Pornsawan Cholsaktrakool
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Songtham Anuntakarun
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pattapon Kunadirek
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Bumrungrad International Hospital, Bangkok, 10110, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Metabolic Disease in Gastrointestinal and Urinary System Research Unit, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sumanee Nilgate
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences (UAMS), Arkansas, 72205, United States
| | - Nicha Sangpiromapichai
- Master of Science Program in Medical Sciences, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Voraphoj Nilaratanakul
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research), Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Infectious Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
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Liao Q, Zhang W, Deng J, Wu S, Liu Y, Xiao Y, Kang M. Relationship between virulence and carbapenem resistance phenotype of Klebsiella pneumoniae from blood infection: identification of a carbapenem-resistant and hypervirulent strain. Zhejiang Da Xue Xue Bao Yi Xue Ban 2024; 53:490-497. [PMID: 39183061 PMCID: PMC11375489 DOI: 10.3724/zdxbyxb-2024-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
OBJECTIVES To investigate the relationship between the virulence and the carbapenem resistance phenotype of Klebsiella pneumoniae from blood infection, and to identify carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-HVKP)strains. METHODS A total of 192 Klebsiella pneumoniae strains were isolated from blood culture of patients with bloodstream infections from 2016 to 2019, of which 96 isolates were carbapenem-resistant Klebsiella pneumoniae (CRKP) and 96 were carbapenem-sensitive Klebsiella pneumoniae (CSKP). The drug susceptibility was detected by VITEK-2 automatic microbial analyzer; carbapenemase genes, virulence genes and capsule typing were detected by polymerase chain reaction; the high viscosity phenotype of strains was detected by string test, and the genome characteristics of CR-HVKP were detected by whole genome sequencing. Serum killing and biofilm formation test were used to further verify the virulence of CR-HVKP. RESULTS There were significant differences in drug resistance to common antibiotics, except for minocycline between CSKP and CRKP isolates (all P<0.05). 92 out of 96 CRKP isolates carried carbapenemase genes, mainly blaKPC-2. The string tests were positive in 4 isolates of CRKP and 36 isolates of CSKP (P<0.05). The detection rates of virulence genes Kfu, aerobictin, iutA, ybtS, rmpA, magA, allS, and capsule antigen K1 and K2 in CSKP group were significantly higher than those in CRKP group (all P<0.05). One HVKP strain was detected in the CRKP group (CR-HVKP) and 36 HVKP was detected in the CSKP group (P<0.05). The CR-HVKP strain belonged to the MLST412, serotype K57, expressed iutA, entB, mrkD, fimH, and rmpA virulence genes, and showed strong biofilm formation and significantly increased serum resistance. Whole genome sequencing results showed that this CR-HVKP isolate carried blaSHV-145, blaTEM-1, blaCTX-M-3, fosA6, oqxA5, oqxB26, and aac(3)-IId resistance genes, accompanied by abnormalities in outer membrane protein K (OmpK) 35 and OmpK36. CONCLUSIONS The drug resistance of CRKP is significantly higher than that of CSKP, while CRKP carrying fewer virulence genes in both number and types compared to CSKP. A new MLST type of carbapenem-resistant and hypervirulent Klebsiella pneumoniae strain has been detected, which requires clinical awareness and epidemiological monitoring.
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Affiliation(s)
- Quanfeng Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Weili Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jin Deng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Siying Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ya Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuling Xiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
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Ikhimiukor OO, Zac Soligno NI, Akintayo IJ, Marcovici MM, Souza SSR, Workman A, Martin IW, Andam CP. Clonal background and routes of plasmid transmission underlie antimicrobial resistance features of bloodstream Klebsiella pneumoniae. Nat Commun 2024; 15:6969. [PMID: 39138200 PMCID: PMC11322185 DOI: 10.1038/s41467-024-51374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Bloodstream infections caused by the opportunistic pathogen Klebsiella pneumoniae are associated with adverse health complications and high mortality rates. Antimicrobial resistance (AMR) limits available treatment options, thus exacerbating its public health and clinical burden. Here, we aim to elucidate the population structure of K. pneumoniae in bloodstream infections from a single medical center and the drivers that facilitate the dissemination of AMR. Analysis of 136 short-read genome sequences complemented with 12 long-read sequences shows the population consisting of 94 sequence types (STs) and 99 clonal groups, including globally distributed multidrug resistant and hypervirulent clones. In vitro antimicrobial susceptibility testing and in silico identification of AMR determinants reveal high concordance (90.44-100%) for aminoglycosides, beta-lactams, carbapenems, cephalosporins, quinolones, and sulfonamides. IncF plasmids mediate the clonal (within the same lineage) and horizontal (between lineages) transmission of the extended-spectrum beta-lactamase gene blaCTX-M-15. Nearly identical plasmids are recovered from isolates over a span of two years indicating long-term persistence. The genetic determinants for hypervirulence are carried on plasmids exhibiting genomic rearrangement, loss, and/or truncation. Our findings highlight the importance of considering both the genetic background of host strains and the routes of plasmid transmission in understanding the spread of AMR in bloodstream infections.
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Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| | - Nicole I Zac Soligno
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Ifeoluwa J Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M Marcovici
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
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Weston G, Giri A, Komarow L, Ge L, Baum KR, Abbenante E, Gallagher JC, Jacob JT, Kaye KS, Kim AC, Huskins WC, Zervos M, Herc E, Patel R, Van Duin D, Doi Y. Clinical outcomes in patients infected with ertapenem-only-resistant Enterobacterales versus multi-carbapenem-resistant Enterobacterales. J Antimicrob Chemother 2024; 79:1929-1937. [PMID: 38863337 PMCID: PMC11290877 DOI: 10.1093/jac/dkae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/20/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Use of anti-carbapenem-resistant Enterobacterales (anti-CRE) agents such as ceftazidime/avibactam has been associated with improved clinical outcome in cohorts that primarily include patients infected with CRE that are resistant to meropenem (MCRE). OBJECTIVES To clarify whether patients with CRE resistant to ertapenem but susceptible to meropenem (ertapenem-only-resistant Enterobacterales; EORE) benefit from therapy with anti-CRE agents. METHODS Patients treated for CRE infection in hospitals in the USA between 2016 and 2019 and enrolled in the CRACKLE-2 study were included. The primary outcome was the desirability of outcome ranking (DOOR) assessed at 30 days after index cultures. RESULTS The EORE group included 213 patients and the MCRE group included 643. The demographics were similar between the groups except for the patients' race and origin before admission. The MCRE group received anti-CRE agents for definitive therapy significantly more frequently compared with the EORE group (30% versus 5% for ceftazidime/avibactam). We did not observe a significant difference between the groups in the adjusted DOOR probability of a more desirable outcome for a randomly selected patient in the EORE group compared with the MCRE group (52.5%; 95% CI, 48.3%-56.7%). The MCRE group had a similar proportion of patients who died at 30 days (26% versus 21%) and who were discharged to home (29% versus 40%), compared with the EORE group. CONCLUSIONS Patients with clinical EORE infection rarely received anti-CRE agents, but attained similar outcomes compared with patients with MCRE infection. The findings support current IDSA treatment guidance for meropenem- or imipenem-based therapy for treatment of EORE infections.
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Affiliation(s)
- Gregory Weston
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Abhigya Giri
- The Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Lauren Komarow
- The Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Lizhao Ge
- The Biostatistics Center, George Washington University, Rockville, MD, USA
| | - Keri R Baum
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Erin Abbenante
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jason C Gallagher
- Department of Pharmacy Practice, Temple University School of Pharmacy, Philadelphia, PA, USA
| | - Jesse T Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Keith S Kaye
- Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Angela C Kim
- Division of Infectious Diseases, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - W Charles Huskins
- Division of Pediatric Infectious Diseases, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Marcus Zervos
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, MI, USA
| | - Erica Herc
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, MI, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - David Van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
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7
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Santerre Henriksen A, Arena F, Attwood M, Canton R, Gatermann S, Naas T, Morrissey I, Longshaw C. In vitro activity of cefiderocol against European Enterobacterales, including isolates resistant to meropenem and recentβ-lactam/β-lactamase inhibitor combinations. Microbiol Spectr 2024; 12:e0418123. [PMID: 38904361 PMCID: PMC11302063 DOI: 10.1128/spectrum.04181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/19/2024] [Indexed: 06/22/2024] Open
Abstract
Carbapenem-resistant Enterobacterales represent a major health threat and have few approved therapeutic options. Enterobacterales isolates were collected from hospitalized inpatients from 49 sites in six European countries (1 January-31 December 2020) and underwent susceptibility testing to cefiderocol and β-lactam/β-lactamase inhibitor combinations. Meropenem-resistant (MIC >8 mg/L) and cefiderocol-susceptible isolates were analyzed by PCR, and cefiderocol-resistant isolates by whole-genome sequencing, to identify resistance mechanisms. Overall, 1,909 isolates (including 970 Klebsiella spp., 382 Escherichia coli, and 244 Enterobacter spp.) were collected, commonly from bloodstream infections (43.6%). Cefiderocol susceptibility was higher than approved β-lactam/β-lactamase inhibitor combinations and largely comparable to cefepime-taniborbactam and aztreonam-avibactam against all Enterobacterales (98.1% vs 78.1%-97.4% and 98.7%-99.1%, respectively) and Enterobacterales resistant to meropenem (n = 148, including 125 Klebsiella spp.; 87.8% vs 0%-71.6% and 93.2%-98.6%, respectively), β-lactam/β-lactamase inhibitor combinations (66.7%-92.1% vs 0%-88.1% and 66.7%-97.9%, respectively), and to both meropenem and β-lactam/β-lactamase inhibitor combinations (61.9%-65.9% vs 0%-20.5% and 76.2%-97.7%, respectively). Susceptibilities to approved and developmental β-lactam/β-lactamase inhibitor combinations against cefiderocol-resistant Enterobacterales (n = 37) were 10.8%-56.8% and 78.4%-94.6%, respectively. Most meropenem-resistant Enterobacterales harbored Klebsiella pneumoniae carbapenemase (110/148) genes, although metallo-β-lactamase (35/148) and oxacillinase (OXA) carbapenemase (6/148) genes were less common; cefiderocol susceptibility was retained in β-lactamase producers, other than NDM, AmpC, and non-carbapenemase OXA producers. Most cefiderocol-resistant Enterobacterales had multiple resistance mechanisms, including ≥1 iron uptake-related mutation (37/37), carbapenemase gene (33/37), and ftsI mutation (24/37). The susceptibility to cefiderocol was higher than approved β-lactam/β-lactamase inhibitor combinations against European Enterobacterales, including meropenem- and β-lactam/β-lactamase inhibitor combination-resistant isolates. IMPORTANCE This study collected a notably large number of Enterobacterales isolates from Europe, including meropenem- and β-lactam/β-lactamase inhibitor combination-resistant isolates against which the in vitro activities of cefiderocol and developmental β-lactam/β-lactamase inhibitor combinations were directly compared for the first time. The MIC breakpoint for high-dose meropenem was used to define meropenem resistance, so isolates that would remain meropenem resistant with doses clinically available to patients were included in the data. Susceptibility to cefiderocol, as a single active compound, was high against Enterobacterales and was higher than or comparable to available β-lactam/β-lactamase inhibitor combinations. These results provide insights into the treatment options for infections due to Enterobacterales with resistant phenotypes. Early susceptibility testing of cefiderocol in parallel with β-lactam/β-lactamase inhibitor combinations will allow patients to receive the most appropriate treatment option(s) available in a timely manner. This is particularly important when options are more limited, such as against metallo-β-lactamase-producing Enterobacterales.
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Affiliation(s)
| | - Fabio Arena
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Marie Attwood
- PK/PD Laboratory, North Bristol NHS Trust, Bristol, United Kingdom
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Sören Gatermann
- Department for Medical Microbiology, Ruhr University, Bochum, Germany
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Hôpital Bicêtre, AP-HP Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Ian Morrissey
- Antimicrobial Focus Ltd., Sawbridgeworth, United Kingdom
| | | | - ARTEMIS Study InvestigatorsWillingerBirgitLeysseneDavidCattoenChristianAlauzetCorentineBoyerPierreDuboisVéroniqueJeannotKatyCorvecStephanePantelAlixGuillardThomasGontierAudrey MerensNaasThierryRohdeHolgerZiesingStefanImirzaliogluCanHunfeldKlaus-PeterJungJetteGatermannSörenPletzMathiasBiancoGabrieleGiammancoAnnaCarcioneDavideRaponiGiammarcoMatinatoCaterinaDomenicoEnea Gino DiGaibaniPaoloMarcheseAnnaArenaFabioNiccolaiClaudiaStefaniStefaniaPitartCristinaBarriosJose LuisCercenadoEmiliaBouGermanLopezAlicia BetetaCantonRafaelHontangasJose LopezGracia-AhufingerIreneOliverAntonioLopez-CereroLorenaLarrosaNievesWarehamDavidPerryJohnCaseyAnnaNahlJasvirHughesDanielCoyneMichaelListerMichelleAttwoodMarie
- Medical Affairs, Shionogi B.V., London, United Kingdom
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
- PK/PD Laboratory, North Bristol NHS Trust, Bristol, United Kingdom
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department for Medical Microbiology, Ruhr University, Bochum, Germany
- Department of Bacteriology-Hygiene, Hôpital Bicêtre, AP-HP Paris-Saclay, Le Kremlin-Bicêtre, France
- Antimicrobial Focus Ltd., Sawbridgeworth, United Kingdom
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8
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Pustam A, Jayaraman J, Ramsubhag A. Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies. J Glob Antimicrob Resist 2024; 37:141-149. [PMID: 38608934 DOI: 10.1016/j.jgar.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
OBJECTIVES Antibiotic-resistant Klebsiella pneumoniae is a human pathogen of major global concern due to its ability to cause multiple severe diseases that are often difficult to treat therapeutically. This study aimed to investigate the resistome of local clinical K. pneumoniae isolates. METHODS Herein, we used a whole genome sequencing approach and bioinformatics tools to reconstruct the resistome of 10 clinical K. pneumoniae isolates and one clinical isolate of the closely related Klebsiella quasipneumoniae obtained from patients from three major hospitals in Trinidad, West Indies. RESULTS The results of the study revealed the presence of a complex antibiotic-resistant armoury among the local isolates with multiple resistance mechanisms involving (i) inactivation of antibiotics, (ii) efflux pumps, (iii) antibiotic target alteration, protection, and replacement against antibiotics, and (iv) altered porin protein that reduced the permeability to antibiotics. Several resistance genes such as blaCTX-M-15, blaTEM-1B, blaSHV-28, blaKPC-2, oqxA, sul1, tetD, aac(6')-Ib-cr5, aph(6)-Id, and fosA6, which are known to confer resistance to antibiotics used to treat K. pneumoniae infections. In most cases, the resistance genes were flanked by mobile elements, including insertion sequences and transposons, which facilitate the spread of these genetic features among related organisms. CONCLUSION This is the first comprehensive study to thoroughly investigate the resistome of clinical K. pneumoniae isolates and K. quasipneumoniae from Trinidad, West Indies. These findings suggest that monitoring K. pneumoniae and its genome-wide antibiotic resistance features in clinical strains would be of critical importance for guiding antibiotic stewardship programs and improving regional disease management systems for this pathogen.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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9
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Rahmat Ullah S, Irum S, Mahnoor I, Ismatullah H, Mumtaz M, Andleeb S, Rahman A, Jamal M. Exploring the resistome, virulome, and mobilome of multidrug-resistant Klebsiella pneumoniae isolates: deciphering the molecular basis of carbapenem resistance. BMC Genomics 2024; 25:408. [PMID: 38664636 PMCID: PMC11044325 DOI: 10.1186/s12864-024-10139-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 02/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has become highly resistant to antibiotics due to the widespread acquisition of genes encoding a variety of enzymes such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases. We collected Klebsiella pneumoniae isolates from a local tertiary care hospital from February 2019-February 2021. To gain molecular insight into the resistome, virulome, and genetic environment of significant genes of multidrug-resistant K. pneumoniae isolates, we performed the short-read whole-genome sequencing of 10 K. pneumoniae isolates recovered from adult patients, neonates, and hospital tap water samples. RESULTS The draft genomes of the isolates varied in size, ranging from 5.48 to 5.96 Mbp suggesting the genome plasticity of this pathogen. Various genes conferring resistance to different classes of antibiotics e.g., aminoglycosides, quinolones, sulfonamides, tetracycline, and trimethoprim were identified in all sequenced isolates. The highest resistance was observed towards carbapenems, which has been putatively linked to the presence of both class B and class D carbapenemases, blaNDM, and blaOXA, respectively. Moreover, the biocide resistance gene qacEdelta1 was found in 6/10 of the sequenced strains. The sequenced isolates exhibited a broad range of sequence types and capsular types. The significant antibiotic resistance genes (ARGs) were bracketed by a variety of mobile genetic elements (MGEs). Various spontaneous mutations in genes other than the acquired antibiotic-resistance genes were observed, which play an indirect role in making these bugs resistant to antibiotics. Loss or deficiency of outer membrane porins, combined with ESBL production, played a significant role in carbapenem resistance in our sequenced isolates. Phylogenetic analysis revealed that the study isolates exhibited evolutionary relationships with strains from China, India, and the USA suggesting a shared evolutionary history and potential dissemination of similar genes amongst the isolates of different origins. CONCLUSIONS This study provides valuable insight into the presence of multiple mechanisms of carbapenem resistance in K. pneumoniae strains including the acquisition of multiple antibiotic-resistance genes through mobile genetic elements. Identification of rich mobilome yielded insightful information regarding the crucial role of insertion sequences, transposons, and integrons in shaping the genome of bacteria for the transmission of various resistance-associated genes. Multi-drug resistant isolates that had the fewest resistance genes exhibited a significant number of mutations. K. pneumoniae isolate from water source displayed comparable antibiotic resistance determinants to clinical isolates and the highest number of virulence-associated genes suggesting the possible interplay of ARGs amongst bacteria from different sources.
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Affiliation(s)
- Sidra Rahmat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Sidra Irum
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Iqra Mahnoor
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Humaira Ismatullah
- Research Centre for Modelling & Simulation (RCMS), National University of Sciences and Technology, Islamabad, Pakistan
| | - Mariam Mumtaz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan.
| | - Abdur Rahman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
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10
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Singh R, Ryu J, Park SS, Kim S, Kim K. Monitoring viruses and beta-lactam resistance genes through wastewater surveillance during a COVID-19 surge in Suwon, South Korea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171223. [PMID: 38417514 DOI: 10.1016/j.scitotenv.2024.171223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
The present study reports data on a long-term campaign for monitoring SARS-CoV-2, norovirus, hepatitis A virus, and beta-lactam resistance genes in wastewater samples from a wastewater treatment plant during COVID-19 surge in Suwon, South Korea. Real-time digital PCR (RT-dPCR) assays indicated 100 % occurrence of all but hepatitis A virus and blaNDM gene in influent wastewater samples. CDC-N1 assay detected SARS-CoV-2 in all influent samples with an average log-transformed concentration of 5.1 ± 0.39 and the highest level at 6.02 gene copies/L. All samples were also positive for norovirus throughout the study with a mean concentration 5.67 ± 0.65 log10 gene copies/L. On the contrary, all treated wastewater (effluent) tested negative for both viruses' genetic materials. Furthermore, plasmid-mediated AmpC β-lactamases (PABLs) genes blaDHA, blaACC, and blaFOX, extended-spectrum β-lactamases (ESBLs) genes blaTEM and blaCTX, and Klebsiella pneumoniae carbapenemase (blaKPC) gene were measured at average concentrations of 7.05 ± 0.26, 5.60 ± 0.35, 7.82 ± 0.43, 8.38 ± 0.20, 7.64 ± 0.29, and 7.62 ± 0.41 log10 gene copies/L wastewater, respectively. Beta-lactam resistance genes showed strong correlations (r), the highest being 0.86 for blaKPC - blaFOX, followed by 0.82 for blaTEM - blaCTX and 0.79 for blaTEM - blaDHA. SARS-CoV-2 RNA occurrence in the wastewater was strongly associated (r = 0.796) with COVID-19 cases in the catchment during the initial study period of six months. A positive association of the SARS-CoV-2 RNA with the prevalence of COVID-19 cases showed a promising role of community-scale monitoring of pathogens to provide considerable early signals of infection dynamics. High concentrations of beta-lactam resistance genes in wastewater indicated a high concern for one of the biggest global health threats in South Korea and the need to find control measures. Moreover, antibiotic-resistance genes in treated wastewater flowing through water bodies and agricultural environments indicate further dissemination of antibiotic resistance traits and increasing microbial antibiotic resistance.
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Affiliation(s)
- Rajendra Singh
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea
| | - Jaewon Ryu
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea
| | - Sung Soo Park
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea
| | - Sungpyo Kim
- Department of Environmental Systems Engineering, Korea University, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Keugtae Kim
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea.
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11
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Lin CK, Page A, Lohsen S, Haider AA, Waggoner J, Smith G, Babiker A, Jacob JT, Howard-Anderson J, Satola SW. Rates of resistance and heteroresistance to newer β-lactam/β-lactamase inhibitors for carbapenem-resistant Enterobacterales. JAC Antimicrob Resist 2024; 6:dlae048. [PMID: 38515868 PMCID: PMC10957161 DOI: 10.1093/jacamr/dlae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
Background Heteroresistance (HR), the presence of antibiotic-resistant subpopulations within a primary isogenic population, may be a potentially overlooked contributor to newer β-lactam/β-lactamase inhibitor (BL/BLI) treatment failure in carbapenem-resistant Enterobacterales (CRE) infections. Objectives To determine rates of susceptibility and HR to BL/BLIs ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam in clinical CRE isolates. Methods The first CRE isolate per patient per year from two >500 bed academic hospitals from 1 January 2016 to 31 December 2021, were included. Reference broth microdilution (BMD) was used to determine antibiotic susceptibility, and population analysis profiling (PAP) to determine HR. Carbapenemase production (CP) was determined using the Carba NP assay. Results Among 327 CRE isolates, 46% were Enterobacter cloacae, 38% Klebsiella pneumoniae and 16% Escherichia coli. By BMD, 87% to 98% of CRE were susceptible to the three antibiotics tested. From 2016 to 2021, there were incremental decreases in the rates of susceptibility to each of the three BL/BLIs. HR was detected in each species-antibiotic combination, with the highest rates of HR (26%) found in K. pneumoniae isolates with imipenem/relebactam. HR or resistance to at least one BL/BLI by PAP was found in 24% of CRE isolates and 65% of these had detectable CP. Conclusion Twenty-four percent of CRE isolates tested were either resistant or heteroresistant (HR) to newer BL/BLIs, with an overall decrease of ∼10% susceptibility over 6 years. While newer BL/BLIs remain active against most CRE, these findings support the need for ongoing antibiotic stewardship and a better understanding of the clinical implications of HR in CRE.
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Affiliation(s)
- Christina K Lin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Alex Page
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Lohsen
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali A Haider
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jesse Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Gillian Smith
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Georgia Emerging Infections Program, Atlanta, GA, USA
- Atlanta Veterans Affairs Medical Center, Decatur, GA, USA
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jesse T Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Georgia Emerging Infections Program, Atlanta, GA, USA
| | - Jessica Howard-Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Georgia Emerging Infections Program, Atlanta, GA, USA
| | - Sarah W Satola
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Georgia Emerging Infections Program, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
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12
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Fan F, Chen G, Deng S, Wei L. Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae. Microbiol Spectr 2024; 12:e0291723. [PMID: 38236023 PMCID: PMC10846168 DOI: 10.1128/spectrum.02917-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an important multidrug resistance (MDR) pathogen that threatens human health and is the main source of hospital-acquired infection. Outer membrane vesicles (OMVs) are extracellular vesicles derived from Gram-negative bacteria and contain materials involved in bacterial survival and pathogenesis. They also contribute to cellular communication to nearby or distant recipient cells and influence their functions and phenotypes. In this study, we sought to understand the mechanism of bacterial response to meropenem pressure and explore the relationship between pathogenic proteins and the high pathogenicity of bacteria. We performed whole-genome PacBio sequencing on a clinical CRKP strain, and its OMVs were characterized using nanoparticle tracking analysis, transmission electron microscopy, and proteomic analysis. Thousands of vesicle proteins have been identified in mass spectrometry-based high-throughput proteomics analyses of K. pneumoniae OMVs. Protein functionality analysis showed that the OMVs were predominantly involved in metabolic, intracellular compartments, nucleic acid binding, survival, defense, and antibiotic resistance, such as Chromosome partition protein MukB, 3-methyl-2-oxobutanoate hydroxymethyltransferase, methionine-tRNA ligase, Heat shock protein 60 family chaperone GroEL, and Gamma-glutamyl phosphate reductase. Additionally, a protein-protein interaction network demonstrated that OMVs from meropenem-treated K. pneumoniae showed the highest connectivity in DNA polymerase I, phenylalanine-tRNA ligase beta subunit, DNA-directed RNA polymerase subunit beta, methionine-tRNA ligase, DNA-directed RNA polymerase subunit beta, and DNA-directed RNA polymerase subunit alpha. The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-treated K. pneumoniae, which provides clues for revealing the biogenesis and pathophysiological functions of Gram-negative bacteria OMVs. The significant differentially expressed proteins identified in this study are of great significance for exploring effective control strategies for CRKP infection.IMPORTANCEMeropenem is one of the main antibiotics used in the clinical treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP). This study demonstrated that some important metabolic changes occurred in meropenem-induced CRKP-outer membrane vesicles (OMVs), The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-induced Klebsiella pneumoniae. Furthermore, this is the first study to discuss the protein-protein interaction network of the OMVs released by CRKP, especially under antibiotic stress.
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Affiliation(s)
- Fangfang Fan
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Guangzhang Chen
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Siqian Deng
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Li Wei
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
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13
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Di Pilato V, Pollini S, Miriagou V, Rossolini GM, D'Andrea MM. Carbapenem-resistant Klebsiella pneumoniae: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge. Expert Rev Anti Infect Ther 2024; 22:25-43. [PMID: 38236906 DOI: 10.1080/14787210.2024.2305854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Klebsiella pneumoniae is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in K. pneumoniae has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant K. pneumoniae (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids. AREAS COVERED Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in K. pneumoniae. EXPERT OPINION CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.
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Affiliation(s)
- Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Vivi Miriagou
- Laboratory of Bacteriology, Hellenic Pasteur Institute, Athens, Greece
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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14
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Kyung SM, Lee JH, Lee ES, Hwang CY, Yoo HS. Whole genome structure and resistance genes in carbapenemase-producing multidrug resistant ST378 Klebsiella pneumoniae. BMC Microbiol 2023; 23:323. [PMID: 37924028 PMCID: PMC10623767 DOI: 10.1186/s12866-023-03074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Carbapenemase-producing Klebsiella pneumoniae (CPKP) is one of the most dangerous multidrug-resistant (MDR) pathogens in human health due to its widespread circulation in the nosocomial environment. CPKP carried by companion dogs, which are close to human beings, should be considered a common threat to public health. However, CPKP dissemination through companion animals is still under consideration of major diagnosis and surveillance systems. METHODS Two CPKP isolates which were genotyped to harbor bla NDM-5-encoding IncX3 plasmids, were subjected to the whole-genome study. Whole bacterial DNA was isolated, sequenced, and assembled with Oxford Nanopore long reads and corrected with short reads from the Illumina NovaSeq 6000 platform. The whole-genome structure and positions of antimicrobial resistance (AMR) genes were identified and visualized using CGView. Worldwide datasets were downloaded from the NCBI GenBank database for whole-genome comparative analysis. The whole-genome phylogenetic analysis was constructed using the identified whole-chromosome SNP sites from K. pneumoniae HS11286. RESULTS As a result of the whole-genome identification, 4 heterogenous plasmids and a single chromosome were identified, each carrying various AMR genes. Multiple novel structures were identified from the AMR genes, coupled with mobile gene elements (MGE). The comparative whole-genome epidemiology revealed that ST378 K. pneumoniae is a novel type of CPKP, carrying a higher prevalence of AMR genes. CONCLUSIONS The characterized whole-genome analysis of this study shows the emergence of a novel type of CPKP strain carrying various AMR genes with variated genomic structures. The presented data in this study show the necessity to develop additional surveillance programs and control measures for a novel type of CPKP strain.
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Affiliation(s)
- Su Min Kyung
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Seo Lee
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Cheol-Yong Hwang
- Department of Veterinary Dermatology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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15
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Qi Y, Xue JZ, Li SS, Elken EM, Haqmal MA, Li XS, Xu GY, Kong LC, Ma HX. Analysis of an IncR plasmid carried by carbapenem-resistant Klebsiella pneumoniae: A survey of swine Klebsiella pneumoniae in Jilin Province. J Glob Antimicrob Resist 2023; 34:83-90. [PMID: 37210003 DOI: 10.1016/j.jgar.2023.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023] Open
Abstract
OBJECTIVES This study was conducted in Jilin Province to investigate the mechanism involved in the antibiotic resistance and pathogenicity of Klebsiella pneumoniae. METHODS Lung samples were collected from large-scale pig farms in Jilin Province. Antimicrobial susceptibility and mouse lethality assays were carried out. K. pneumoniae isolate JP20, with high virulence and antibiotic resistance, was chosen for whole-genome sequencing. The complete sequence of its genome was annotated, and the virulence and antibiotic resistance mechanism were analysed. RESULTS A total of 32 K. pneumoniae strains were isolated and tested for antibiotic resistance and pathogenicity. Among them, the JP20 strain showed high levels of resistance to all tested antimicrobial agents and strong pathogenicity in mice (lethal dose of 1.35 × 1011 CFU/mL). Sequencing of the multidrug-resistant and highly virulent K. pneumoniae JP20 strain revealed that the antibiotic resistance genes were mainly carried by an IncR plasmid. We speculate that extended-spectrum β-lactamases and loss of outer membrane porin OmpK36 play an important role in carbapenem antibiotic resistance. This plasmid contains a mosaic structure consisting of a large number of mobile elements. CONCLUSION Through genome-wide analysis, we found that an lncR plasmid carried by the JP20 strain may have evolved in pig farms, possibly leading to multidrug resistance in the JP20 strain. It is speculated that the antibiotic resistance of K. pneumoniae in pig farms is mainly mediated by mobile elements (insertion sequences, transposons, and plasmids). These data provide a basis for monitoring the antibiotic resistance of K. pneumoniae and lay a foundation for an improved understanding of the genomic characteristics and antibiotic resistance mechanism of K. pneumoniae.
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Affiliation(s)
- Yu Qi
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jun-Ze Xue
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Shuang-Shuang Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Emad Mohammed Elken
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China; Department of Animal Production, Faculty of Agriculture, Al-Azhar University, Nasr City, Cairo, Egypt
| | - M Aman Haqmal
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xue-Song Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Guan-Yi Xu
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Ling-Cong Kong
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China.
| | - Hong-Xia Ma
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China; The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Changchun, China.
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16
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Cornacchia A, Janowicz A, Centorotola G, Saletti MA, Ranieri SC, Ancora M, Ripà P, Cammà C, Pomilio F, Chiaverini A. Multi-approach methods to predict cryptic carbapenem resistance mechanisms in Klebsiella pneumoniae detected in Central Italy. Front Microbiol 2023; 14:1242693. [PMID: 37700864 PMCID: PMC10493390 DOI: 10.3389/fmicb.2023.1242693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023] Open
Abstract
The rapid emergence of carbapenem-resistant Klebsiella pneumoniae (Kp) strains in diverse environmental niches, even outside of the clinical setting, poses a challenge for the detection and the real-time monitoring of novel antimicrobial resistance trends using molecular and whole genome sequencing-based methods. The aim of our study was to understand cryptic resistance determinants responsible for the phenotypic carbapenem resistance observed in strains circulating in Italy by using a combined approach involving whole genome sequencing (WGS) and genome-wide association study (GWAS). In this study, we collected 303 Kp strains from inside and outside clinical settings between 2018-2022 in the Abruzzo region of Italy. The antimicrobial resistance profile of all isolates was assessed using both phenotypic and bioinformatic methods. We identified 11 strains resistant to carbapenems, which did not carry any known genetic determinants explaining their phenotype. The GWAS results showed that incongruent carbapenem-resistant phenotype was associated specifically with strains with two capsular types, KL13 and KL116 including genes involved in the capsule synthesis, encoding proteins involved in the assembly of the capsule biosynthesis apparatus, capsule-specific sugar synthesis, processing and export, polysaccharide pyruvyl transferase, and lipopolysaccharide biosynthesis protein. These preliminary results confirmed the potential of GWAS in identifying genetic variants present in KL13 and KL116 that could be associated with carbapenem resistance traits in Kp. The implementation of advanced methods, such as GWAS with increased antimicrobial resistance surveillance will potentially improve Kp infection treatment and patient outcomes.
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Affiliation(s)
- Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Anna Janowicz
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Maria Antonietta Saletti
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Sofia Chiatamone Ranieri
- Operative Unit of Clinical Pathology and Microbiology, Department of Services, ASL of Teramo, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Paola Ripà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
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17
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Hazen TH, Adediran T, Hitchcock S, O’Hara LM, Pineles L, Michalski JM, Johnson JK, Nguyen MH, Calfee DP, Miller LG, Harris AD, Rasko DA. Clinical and Bacterial Characteristics Associated with Glove and Gown Contamination by Carbapenem-Resistant Klebsiella pneumoniae in the Health Care Setting. Microbiol Spectr 2023; 11:e0177523. [PMID: 37289087 PMCID: PMC10434059 DOI: 10.1128/spectrum.01775-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a pathogen of significant concern to public health, as it has become increasingly associated with difficult-to-treat community-acquired and hospital-associated infections. Transmission of K. pneumoniae between patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings. However, it is not known whether specific lineages or isolates of K. pneumoniae are associated with increased transmission. Thus, we used whole-genome sequencing to analyze the genetic diversity of 166 carbapenem-resistant K. pneumoniae isolates from five U.S. hospitals in four states as part of a multicenter study examining risk factors for glove and gown contamination by carbapenem-resistant Enterobacterales (CRE). The CRKp isolates exhibited considerable genomic diversity with 58 multilocus sequence types (STs), including four newly designated STs. ST258 was the most prevalent ST, representing 31% (52/166) of the CRKp isolates, but was similarly prevalent among patients who had high, intermediate, and low CRKp transmission. Increased transmission was associated with clinical characteristics including a nasogastric (NG) tube or an endotracheal tube or tracheostomy (ETT/Trach). Overall, our findings provide important insight into the diversity of CRKp associated with transmission from patients to the gloves and gowns of HCP. These findings suggest that certain clinical characteristics and the presence of CRKp in the respiratory tract, rather than specific lineages or genetic content, are more often associated with increased transmission of CRKp from patients to HCP. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a significant public health concern that has contributed to the spread of carbapenem resistance and has been linked to high morbidity and mortality. Transmission of K. pneumoniae among patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings; however, it remains unknown whether particular bacterial characteristics are associated with increased CRKp transmission. Using comparative genomics, we demonstrate that CRKp isolates associated with high or intermediate transmission exhibit considerable genomic diversity, and there were no K. pneumoniae lineages or genes that were universally predictive of increased transmission. Our findings suggest that certain clinical characteristics and the presence of CRKp, rather than specific lineages or genetic content of CRKp, are more often associated with increased transmission of CRKp from patients to HCP.
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Affiliation(s)
- Tracy H. Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Timileyin Adediran
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Stephanie Hitchcock
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lyndsay M. O’Hara
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lisa Pineles
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jane M. Michalski
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - J. Kristie Johnson
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - M. Hong Nguyen
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David P. Calfee
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Loren G. Miller
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Anthony D. Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - David A. Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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18
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Alonso-García I, Vázquez-Ucha JC, Martínez-Guitián M, Lasarte-Monterrubio C, Rodríguez-Pallares S, Camacho-Zamora P, Rumbo-Feal S, Aja-Macaya P, González-Pinto L, Outeda-García M, Maceiras R, Guijarro-Sánchez P, Muíño-Andrade MJ, Fernández-González A, Oviaño M, González-Bello C, Arca-Suárez J, Beceiro A, Bou G. Interplay between OXA-10 β-Lactamase Production and Low Outer-Membrane Permeability in Carbapenem Resistance in Enterobacterales. Antibiotics (Basel) 2023; 12:999. [PMID: 37370318 DOI: 10.3390/antibiotics12060999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The OXA-10 class D β-lactamase has been reported to contribute to carbapenem resistance in non-fermenting Gram-negative bacilli; however, its contribution to carbapenem resistance in Enterobacterales is unknown. In this work, minimum inhibitory concentrations (MICs), whole genome sequencing (WGS), cloning experiments, kinetic assays, molecular modelling studies, and biochemical assays for carbapenemase detection were performed to determine the impact of OXA-10 production on carbapenem resistance in two XDR clinical isolates of Escherichia coli with the carbapenem resistance phenotype (ertapenem resistance). WGS identified the two clinical isolates as belonging to ST57 in close genomic proximity to each other. Additionally, the presence of the blaOXA-10 gene was identified in both isolates, as well as relevant mutations in the genes coding for the OmpC and OmpF porins. Cloning of blaOXA-10 in an E. coli HB4 (OmpC and OmpF-deficient) demonstrated the important contribution of OXA-10 to increased carbapenem MICs when associated with porin deficiency. Kinetic analysis showed that OXA-10 has low carbapenem-hydrolysing activity, but molecular models revealed interactions of this β-lactamase with the carbapenems. OXA-10 was not detected with biochemical tests used in clinical laboratories. In conclusion, the β-lactamase OXA-10 limits the activity of carbapenems in Enterobacterales when combined with low permeability and should be monitored in the future.
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Affiliation(s)
- Isaac Alonso-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Martínez-Guitián
- NANOBIOFAR, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Campus Vida Avenida Barcelona s/n, 15782 Santiago de Compostela, Spain
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, Universidade da Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Salud Rodríguez-Pallares
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Camacho-Zamora
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Soraya Rumbo-Feal
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Aja-Macaya
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Lucía González-Pinto
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Michelle Outeda-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Romina Maceiras
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - María José Muíño-Andrade
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Ana Fernández-González
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Marina Oviaño
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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19
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Xie Z, Huang J, Zhang S, Xu B, Zhang Q, Li B. Genomic and functional characterization of carbapenem-resistant Klebsiella pneumoniae from hospital wastewater. BMC Microbiol 2023; 23:115. [PMID: 37095431 PMCID: PMC10124015 DOI: 10.1186/s12866-023-02862-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/15/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) attracted extensive attention. Information on CRKP from hospital wastewater (HWW) is limited. The aims of this study were to investigate the genomic characteristics and to evaluate the survivability characteristics of 11 CRKP from HWW in a Chinese teaching hospital in Fujian province. RESULTS A total of 11 CRKP from HWW were recovered in this study. All CRKP from HWW were resistant to most antibiotics. Comparative genetic analysis demonstrated that all CRKP isolates were clustered into the three distinct phylogenetic clades and clade 2 and clade 3 were mixtures of samples collected from both HWW and clinical settings. Varieties of resistance genes, virulence genes and plasmid replicon types were detected in CRKP from HWW. In vitro transfer of blaKPC-2 was successful for 3 blaKPC-2-positive CRKP from HWW with high conjugation frequency. Our study demonstrated that the genetic environments of blaKPC-2 shared core structure with ISKpn27-blaKPC-2-ISKpn6. Group analysis showed that CRKP from HWW had a lower survivability in serum compared to clinical CRKP (p < 005); and CRKP from HWW had no significant difference in survivability in HWW compared to clinical CRKP (p > 005). CONCLUSIONS We analyzed the genomic and survivability characteristics of CRKP from HWW in a Chinese teaching hospital. These genomes represent a significant addition of genomic data from the genus and could serve as a valuable resource for future genomic studies about CRKP from HWW.
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Affiliation(s)
- Zhiqiang Xie
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - BinBin Xu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Qianwen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, 29 Xinquan Rd, Fuzhou, 350001, Fujian, China.
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20
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Venne DM, Hartley DM, Malchione MD, Koch M, Britto AY, Goodman JL. Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa. Antimicrob Resist Infect Control 2023; 12:29. [PMID: 37013626 PMCID: PMC10071777 DOI: 10.1186/s13756-023-01220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/18/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa. METHODS Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped. RESULTS Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations. CONCLUSIONS While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.
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Affiliation(s)
- Danielle M Venne
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - David M Hartley
- James M. Anderson Center for Health Systems Excellence, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Marissa D Malchione
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
- Sabin Vaccine Institute, Influenza Vaccine Innovation, 2175 K St NW, Washington, DC, 20037, USA
| | - Michala Koch
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - Anjali Y Britto
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - Jesse L Goodman
- Center on Medical Product Access, Safety and Stewardship, Georgetown University, 3900 Reservoir Road, Washington, DC, 20057, USA.
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21
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Li S, Feng X, Li M, Shen Z. In vivo adaptive antimicrobial resistance in Klebsiella pneumoniae during antibiotic therapy. Front Microbiol 2023; 14:1159912. [PMID: 37007508 PMCID: PMC10061107 DOI: 10.3389/fmicb.2023.1159912] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Klebsiella pneumoniae is one of the leading pathogens contributing to antimicrobial resistance. The emergence of carbapenem-resistant K. pneumoniae (CRKP) has put the use of clinical antimicrobial agents in a dilemma. In particular, CRKP exhibiting resistance to ceftazidime/avibactam, tigecycline and colistin have raised great clinical concern, as these are the last-resort antibiotics for the treatment of CRKP infections. Within-host evolution is a survival strategy closely related to the emergence of antimicrobial resistance, while little attention has been paid to the in vivo genetic process of conversion from antibiotic-susceptible to resistant K. pneumoniae. Here we have a literature review regarding the in vivo evolution of resistance to carbapenems, ceftazidime/avibactam, tigecycline, and colistin in K. pneumoniae during antibacterial therapy, and summarized the detailed resistance mechanisms. In general, acquiring bla KPC and bla NDM harboring-plasmid, specific mutations in bla KPC, and porin genes, such as ompK35 and ompK36, upregulation of bla KPC, contribute to the development of carbapenem and ceftazidime/avibactam resistance in vivo. Overexpression of efflux pumps, acquiring plasmid-carrying tet (A) variants, and ribosomal protein change can lead to the adaptive evolution of tigecycline resistance. Specific mutations in chromosomes result in the cationic substitution of the phosphate groups of lipid A, thus contributing to colistin resistance. The resistant plasmid might be acquired from the co-infecting or co-colonizing strains, and the internal environment and antibiotic selection pressure contribute to the emergence of resistant mutants. The internal environment within the human host could serve as an important source of resistant K. pneumoniae strains.
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Affiliation(s)
- Shuangshuang Li
- Department of Laboratory Medicine, Ningbo Hospital, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Ningbo, China
| | - Xudong Feng
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Shen
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective. Diagnostics (Basel) 2023; 13:1014. [PMID: 36980322 PMCID: PMC10047325 DOI: 10.3390/diagnostics13061014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | | | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA
| | - Amrutha Lakshmi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
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23
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Wen LL, Kuo PY, Thuy TTD, Duong TTT, Huang YT, Hsueh PR, Chen YC, Kao CY. Genome-based characterization of conjugative IncHI1B plasmid carrying carbapenemase genes bla VIM-1, bla IMP-23, and truncated bla OXA-256in Klebsiella pneumoniae NTU107224. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105420. [PMID: 36868443 DOI: 10.1016/j.meegid.2023.105420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/17/2023] [Accepted: 02/25/2023] [Indexed: 03/05/2023]
Abstract
The wide dissemination of plasmids carrying antibiotic resistance determinants among bacteria is a severe threat to global public health. Here, we characterized an extensively drug-resistant (XDR) Klebsiella pneumoniae NTU107224 by whole genome sequencing (WGS) in combination with phenotypic tests. Broth dilution method was used to determine the minimal inhibitory concentrations (MICs) of NTU107224 to 24 antibiotics. The whole genome sequence of NTU107224 was determined by Nanopore/Illumina hybrid genome sequencing. Conjugation assay was performed to determine the transferability of plasmids in NTU107224 to recipient K. pneumoniae 1706. Larvae infection model was used to determine the effect(s) of conjugative plasmid pNTU107224-1 on bacterial virulence. Among the 24 antibiotics tested, XDR K. pneumoniae NTU107224 had low MICs only for amikacin (≤1 μg/mL), polymyxin B (0.25 μg/mL), colistin (0.25 μg/mL), eravacycline (0.25 μg/mL), cefepime/zidebactam (1 μg/mL), omadacycline (4 μg/mL), and tigecycline (0.5 μg/mL). Whole genome sequencing showed that the closed NTU107224 genome comprises a 5,076,795-bp chromosome, a 301,404-bp plasmid named pNTU107224-1, and a 78,479-bp plasmid named pNTU107224-2. IncHI1B plasmid pNTU107224-1 contained three class 1 integrons accumulated various antimicrobial resistance genes (including carbapenemase genes blaVIM-1, blaIMP-23, and truncated blaOXA-256) and the blast results suggested the dissemination of IncHI1B plasmids in China. By day 7 after infection, larvae infected with K. pneumoniae 1706 and transconjugant had 70% and 15% survival rates, respectively. We found that the conjugative plasmid pNTU107224-1 is closely related to IncHI1B plasmids disseminated in China and contributes to the virulence and antibiotic resistance of pathogens.
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Affiliation(s)
- Li-Li Wen
- Graduate Institute of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu City, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tran Thi Dieu Thuy
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tran Thi Thuy Duong
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Ph.D. Program for Aging, School of Medicine, China Medical University, Taichung, Taiwan; Department of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Chen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Li T, Wang Z, Guo J, de la Fuente-Nunez C, Wang J, Han B, Tao H, Liu J, Wang X. Bacterial resistance to antibacterial agents: Mechanisms, control strategies, and implications for global health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160461. [PMID: 36435256 DOI: 10.1016/j.scitotenv.2022.160461] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
The spread of bacterial drug resistance has posed a severe threat to public health globally. Here, we cover bacterial resistance to current antibacterial drugs, including traditional herbal medicines, conventional antibiotics, and antimicrobial peptides. We summarize the influence of bacterial drug resistance on global health and its economic burden while highlighting the resistance mechanisms developed by bacteria. Based on the One Health concept, we propose 4A strategies to combat bacterial resistance, including prudent Application of antibacterial agents, Administration, Assays, and Alternatives to antibiotics. Finally, we identify several opportunities and unsolved questions warranting future exploration for combating bacterial resistance, such as predicting genetic bacterial resistance through the use of more effective techniques, surveying both genetic determinants of bacterial resistance and the transmission dynamics of antibiotic resistance genes (ARGs).
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Affiliation(s)
- Ting Li
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing 100071, PR China
| | - Zhenlong Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America.
| | - Jinquan Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Bing Han
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Hui Tao
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Jie Liu
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Xiumin Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China.
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Yu M, Wei Q, Song W, Yuan J. Phenotypic and Genetic Analysis of KPC-49, a KPC-2 Variant Conferring Resistance to Ceftazidime-Avibactam and Maintaining Resistance to Imipenem and Meropenem. Infect Drug Resist 2023; 16:2477-2485. [PMID: 37138840 PMCID: PMC10150759 DOI: 10.2147/idr.s406319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Purpose Klebsiella pneumoniae, a gram-negative bacterium, poses a severe hazard to public health, with many bacterial hosts having developed resistance to most antibiotics in clinical use. The goal of this study was to look into the development of resistance to both ceftazidime-avibactam and carbapenems, including imipenem and meropenem, in a K. pneumonia strain expressing a novel K. pneumoniae carbapenemase-2 (KPC-2) variant, referred to as KPC-49. Methods After 1 day of incubation of K1 on agar containing ceftazidime-avibactam (MIC = 16/4 mg/L), a second KPC-producing K. pneumoniae strain (K2) was recovered. Antimicrobial susceptibility assays, cloning assays, and whole genome sequencing were performed to analyse and evaluate antibiotic resistance phenotypes and genotypes. Results K. pneumoniae strain (K1), that produced KPC-2, was susceptible to ceftazidime-avibactam but resistant to carbapenems. The K2 isolate harboured a novel bla KPC-49 variant, which differs from bla KPC-2 by a single nucleotide (C487A), and results in an arginine-serine substitution at amino acid position 163 (R163S). The mutant K2 strain was resistant to both ceftazidime-avibactam and carbapenems. We demonstrated the ability of KPC-49 to hydrolyse carbapenems, which may be attributed to high KPC-49 expression or presence of an efflux pump and/or absence of membrane pore proteins in K2. Furthermore, blaKPC-like was carried on an IncFII (pHN7A8)/IncR-type plasmid within a TnAs1-orf-orf-orf-orf-orf-orf-ISKpn6-bla KPC-ISKpn27 structure. The bla KPC-like gene was flanked by various insertion sequences and transposon elements, including the Tn3 family transposon, such as TnAs1, TnAs3, IS26, and IS481-ISKpn27. Conclusion New KPC variants are emerging owing to sustained exposure to antimicrobials and modifications in their amino acid sequences. We demonstrated the drug resistance mechanisms of the new mutant strains through experimental whole genome sequencing combined with bioinformatics analysis. Enhanced understanding of laboratory and clinical features of infections due to K. pneumoniae of the new KPC subtype is key to early and accurate anti-infective therapy.
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Affiliation(s)
- Meng Yu
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
| | - Qingzheng Wei
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
| | - Weiqing Song
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
| | - Jiangshui Yuan
- Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China
- Correspondence: Jiangshui Yuan; Weiqing Song, Clinical Laboratory, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, People’s Republic of China, Tel +86-0532-6602-7876, Email ;
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Interruption of Capsular Polysaccharide Biosynthesis Gene wbaZ by Insertion Sequence IS 903B Mediates Resistance to a Lytic Phage against ST11 K64 Carbapenem-Resistant Klebsiella pneumoniae. mSphere 2022; 7:e0051822. [PMID: 36377881 PMCID: PMC9769513 DOI: 10.1128/msphere.00518-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major challenge for clinical management worldwide with limited antimicrobial options. Phages are considered an alternative option. Here, we isolated and identified a phage able to lyse ST11-K64 CRKP, the major type in China. This phage has a narrow host range, only lysing ST11-K64 CRKP, and inhibits the growth of host strains for 3 h forming large clear plaques (3.0 to 6.0 mm in diameter) with a surrounding halo. This phage exhibited excellent stability in different temperatures and pH and did not contain any virulence, lysogenic, antimicrobial resistance genes nor tRNA, meeting the criteria for phage therapy. Genomic analysis revealed that it represents a novel species of the Przondovirus genus according to ICTV standards. However, phage-resistant bacterial mutants emerged after 4-h exposure. Compared to the parental strain, phage-resistant mutants showed nonmucoid appearance and exhibited significantly reduced virulence for Galleria mellonella larva. Three randomly selected phage-resistant mutants were genome sequenced. Interruption of capsular polysaccharide biosynthesis-associated gene wcaJ or wbaZ by IS903B alone or an IS903-formed composite transposon was identified. Interruption of wcaJ is a known phage resistant mechanism, while that of wbaZ is not. By complementing the intact wbaZ, the phage susceptibility was restored, confirming the role of wbaZ interruption in phage resistance. This highlights that alteration in the capsular polysaccharide biosynthesis gene cluster, which could be due to transposable elements, is a major mechanism for resistance to Przondovirus phages in CRKP. Noncapsule-targeting phages may be combined for improving phage therapy against CRKP. IMPORTANCE Phage therapy is an alternative approach against multidrug resistant microorganisms such as carbapenem-resistant Klebsiella pneumoniae (CRKP), which represents a major challenge for treatment due to very limited options of antimicrobial agents. For optimizing phage therapy, more new lytic phages are needed. Here, we isolated and characterized a phage of a novel species able to rapidly lyse a major type of CRKP without carrying any virulence, lysogenic, antimicrobial resistance genes. This phage is therefore suitable for clinical treatment. However, phage-resistant mutants of CRKP strains were observed after exposure. We found a new mechanism, i.e., interruption of a capsular polysaccharide biosynthesis gene wbaZ by an insertion sequence-formed composite transposon. Our study demonstrates the capsular polysaccharide biosynthesis gene cluster as a major source of resistance to certain lytic phages in CRKP. This requires more studies to counter phage resistance. Our studies also highlight the critical role of insertion sequences in phage resistance.
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Competitive Transmission of Carbapenem-Resistant Klebsiella pneumoniae in a Newly Opened Intensive Care Unit. mSystems 2022; 7:e0079922. [PMID: 36445111 PMCID: PMC9764986 DOI: 10.1128/msystems.00799-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We conducted a 6-month prospective study in a newly opened ICU for high-resolution tracking of carbapenem-resistant Klebsiella pneumoniae (CRKP) through environmental surveillance, patient screening, and genome sequencing. Among all ICU patients (n = 348) screened, 3.5% carried CRKP on admission and 16.3% acquired CRKP thereafter. CRKP was not detected in the environment until 10 weeks and was then isolated from 98 of 2,989 environmental samples (3.3%). The first CRKP isolate from rectal swabs (n = 37) and the first clinical isolate (n = 8) of each patient as well as the 98 isolates from environmental were subjected to whole-genome sequencing. The 143 CRKP isolates from patients and environment samples were assigned to four sequence types, with ST11 dominating (95.8%) and further divided into 14 clones, suggesting introduction of multiple clones. Subsequent CRKP transmission was complex and dynamic with 10 clones found in multiple patients and seven also detected in the environment. Two particular ST11 clones caused extensive (≥5 rooms) and persistent (≥10 weeks) environmental contamination. Both clones were associated with patients who carried CRKP throughout their prolonged ICU stay. Such "super-contaminators" are a priority for isolation and environmental surveillance. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global challenge for human health. In health care settings, patients have frequent interactions with other patients and the environment, rendering challenges for untangling the introduction and transmission of CRKP. We conducted a prospective surveillance study in a newly opened ICU for high-resolution tracking of CRKP. Our study demonstrated the dynamic, complicated transmission of CRKP and has important findings that may help to curb its spread in health care settings. First, compliance with basic measures such as routine environment cleaning and postdischarge terminal cleaning is needed to minimize the environmental contamination-driven spread. Second, active screening could demonstrate the scale of the problem, and room transfer of patients with CRKP should be prohibited whenever possible. Third, the priority for single-room isolation should be given to patients with prolonged carriage of CRKP, especially in resource-limited settings. Good infection control practice lays a foundation for tackling multidrug-resistant organisms like CRKP.
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Characterisation of Non-Carbapenemase-Producing Carbapenem-Resistant Klebsiella pneumoniae Based on Their Clinical and Molecular Profile in Malaysia. Antibiotics (Basel) 2022; 11:antibiotics11111670. [PMID: 36421313 PMCID: PMC9686620 DOI: 10.3390/antibiotics11111670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae (NC-CRKP) confers carbapenem resistance through a combination of chromosomal mutations and acquired non-carbapenemase resistance mechanisms. In this study, we aimed to evaluate the clinical and molecular profiles of NC-CRKP isolated from patients in a tertiary teaching hospital in Malaysia from January 2013 to October 2019. During the study period, 54 NC-CRKP-infected/colonised patients’ isolates were obtained. Clinical parameters were assessed in 52 patients. The all-cause in-hospital mortality rate among NC-CRKP patients was 46.2% (24/52). Twenty-three (44.2%) patients were infected, while others were colonised. Based on the Charlson Comorbidity Index (CCI) score, 92.3% (48/52) of the infected/colonised patients had a score of ≥ 1. Resistance genes found among the 54 NC-CRKP isolates were blaTEM, blaSHV, blaCTX-M, blaOXA, and blaDHA. Porin loss was detected in 25/54 (46.3%) strains. None of the isolated strains conferred carbapenem resistance through the efflux pumps system. In conclusion, only 25/54 (46.3%) NC-CRKP conferred carbapenem resistance through a combination of porin loss and the acquisition of non-carbapenemase resistance mechanisms. The carbapenem resistance mechanisms for the remaining strains (53.7%) should be further investigated as rapid identification and distinction of the NC-CRKP mechanisms enable optimal treatment and infection control efforts.
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Saki M, Amin M, Savari M, Hashemzadeh M, Seyedian SS. Beta-lactamase determinants and molecular typing of carbapenem-resistant classic and hypervirulent Klebsiella pneumoniae clinical isolates from southwest of Iran. Front Microbiol 2022; 13:1029686. [PMID: 36406386 PMCID: PMC9669656 DOI: 10.3389/fmicb.2022.1029686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/26/2022] [Indexed: 08/27/2023] Open
Abstract
This study investigated the molecular epidemiology of carbapenem-resistant classic Klebsiella pneumoniae (CR-cKp) and carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) isolates in southwestern Iran. From 2019 to 2021, 136 (88.9%) cKp and 17 (11.1%) hvKp isolates were identified using biochemical tests and polymerase chain reaction (PCR). Antibiotic resistance, beta-lactamases, and clonal relatedness of carbapenem-resistant isolates were investigated using disk diffusion, PCR, and enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), respectively. The different markers of hvKp isolates were as follows: string test (35.3%, n = 6/17), magA (11.8%, n = 2/17), rmpA (11.8%, n = 2/17), rmpA2 (52.9%, n = 9/17), iucA (52.9%, n = 9/17), and peg344 (35.3%, n = 6/17). Also, 55.1% (n = 75/136) of cKp and 47.1% (n = 8/17) of hvKp isolates were CR-cKp and CR-hvKp, respectively. All CR-hvKp (100.0%, n = 8) isolates were MDR. Colistin, tetracycline, and tigecycline were the most effective antibiotics. The occurrence of beta-lactamase genes in 75 CR-cKp and 8 CR-hvKp isolates was as follows: bla NDM (41.3, 25.0%), bla IMP (4.0, 0.0%), bla VIM (8.0, 0.0%), bla GES (14.7, 25.0%), bla OXA-48-like (20.0, 0.0%), bla CTX-M (26.7, 12.5%), bla SHV (24.0, 12.5%), bla TEM (10.7, 0.0%), bla FOX (6.7, 0.0%), bla DHA (6.7, 0.0%), bla CMY (5.3, 0.0%), bla LAT (12.0, 0.0%), and bla ACT (8.0, 0.0%). ERIC-PCR showed a high diversity among isolates. In this study, the occurrence of MDR CR-hvKp isolates harboring bla NDM and bla GES was detected for the first time in southwestern Iran. To prevent the spread of CR-hvKp and reduce selection pressure, long-term surveillance and more effective treatment strategies should be implemented.
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Affiliation(s)
- Morteza Saki
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mansour Amin
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Saeid Seyedian
- Alimentary Tract Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Mmatli M, Leshaba TMS, Skosana LB, Mbelle NM, Osei Sekyere J. Molecular Screening of Clinical Multidrug-Resistant Gram-Negative Bacteria Shows Endemicity of Carbapenemases, Coexistence of Multiple Carbapenemases, and Rarity of mcr in South Africa. Microb Drug Resist 2022; 28:1028-1036. [PMID: 36251876 DOI: 10.1089/mdr.2022.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: Extensive use of carbapenems to treat multidrug-resistant (MDR) Gram-negative bacteria (GNB) facilitates the wide dissemination of carbapenemase-producing carbapenem-resistant GNB. Colistin was reintroduced into clinical settings to manage these GNB infections. However, there is currently an increase in the dissemination of mobile colistin resistance (mcr)-producing colistin-resistant GNB isolates in clinical settings. The epidemiology of carbapenemases and mcr in Pretoria was evaluated. Methods: Clinical MDR GNB were collected and screened for carbapenemases and mcr using polymerase chain reaction (PCR); their antibiotic susceptibility profiles were elucidated using the Vitek® 2 automated system (Biomerieux, France) and microbroth dilution (for colistin). Results and Discussion: A total of 306 isolates were collected; a majority of these were Klebsiella pneumoniae (n = 208) and were collected from males (n = 158). The isolates were retrieved from a variety of infection sites, including urine, blood cultures, and rectal swabs. The Vitek 2 system found that these isolates were largely resistant to β-lactams, where 217 (70.9%) had reduced susceptibility to at least one carbapenem (ertapenem, meropenem, or imipenem), and 81 isolates (26.5%) were resistant to colistin. PCR screening identified 201 (65.7%) isolates harboring carbapenemase genes consisting of blaOXA-48 (170, 84.2%), blaNDM (31, 15.4%), blaIMP (5, 2%), blaKPC (4, 1%), and blaVIM (5, 2%). Furthermore, 14 blaOXA-48-producing isolates were coharboring blaVIM (2), blaNDM (9), blaKPC (1), and blaIMP (2) genes. Only one isolate harbored the mobile colistin resistance (mcr)-1 gene, and this is the first report of an mcr-1-producing Acinetobacter baumannii isolate in South Africa. Conclusion: There is high endemicity of carbapenemase genes and a low prevalence of mcr genes in GNB, particularly in K. pneumoniae, in health care facilities in Pretoria and surrounding regions of South Africa. Significance: Health care facilities in Pretoria are becoming breeding grounds for MDR infections that threaten public health. Careful use of carbapenems and other antibiotics is necessary to prevent further escalation and outbreak of these MDR strains that can claim several lives.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | | | - Lebogang B Skosana
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa.,Tshwane Academic Division, Department of Medical Microbiology, National Health Laboratory Service, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa.,Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
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Dixon B, Ahmed WM, Felton T, Fowler SJ. Molecular phenotyping approaches for the detection and monitoring of carbapenem-resistant Enterobacteriaceae by mass spectrometry. J Mass Spectrom Adv Clin Lab 2022; 26:9-19. [PMID: 36105942 PMCID: PMC9464899 DOI: 10.1016/j.jmsacl.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Breanna Dixon
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, United Kingdom
| | - Waqar M Ahmed
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, United Kingdom
| | - Tim Felton
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Stephen J Fowler
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Corresponding author at: Education and Research Centre, Wythenshawe Hospital, Manchester M23 9LT, United Kingdom.
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Ma J, Song X, Li M, Yu Z, Cheng W, Yu Z, Zhang W, Zhang Y, Shen A, Sun H, Li L. Global Spread of Carbapenem-Resistant Enterobacteriaceae: Epidemiological Features, Resistance Mechanisms, Detection and Therapy. Microbiol Res 2022; 266:127249. [DOI: 10.1016/j.micres.2022.127249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
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Cephalosporin translocation across enterobacterial OmpF and OmpC channels, a filter across the outer membrane. Commun Biol 2022; 5:1059. [PMID: 36198902 PMCID: PMC9534850 DOI: 10.1038/s42003-022-04035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
Gram-negative porins are the main entry for small hydrophilic molecules. We studied translocation of structurally related cephalosporins, ceftazidime (CAZ), cefotaxime (CTX) and cefepime (FEP). CAZ is highly active on E. coli producing OmpF (Outer membrane protein F) but less efficient on cells expressing OmpC (Outer membrane protein C), whereas FEP and CTX kill bacteria regardless of the porin expressed. This matches with the different capacity of CAZ and FEP to accumulate into bacterial cells as quantified by LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometry). Furthermore, porin reconstitution into planar lipid bilayer and zero current assays suggest permeation of ≈1,000 molecules of CAZ per sec and per channel through OmpF versus ≈500 through OmpC. Here, the instant killing is directly correlated to internal drug concentration. We propose that the net negative charge of CAZ represents a key advantage for permeation through OmpF porins that are less cation-selective than OmpC. These data could explain the decreased susceptibility to some cephalosporins of enterobacteria that exclusively express OmpC porins. The translocation of cephalosporins across enterobacterial OmpF and OmpC channels is monitored in real-time, demonstrating differential permeation of some cephalosporins through OmpF and OmpC.
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Dixon B, Ahmed WM, Mohamed AA, Felton T, Fowler SJ. Metabolic phenotyping of acquired ampicillin resistance using microbial volatiles from Escherichia coli cultures. J Appl Microbiol 2022; 133:2445-2456. [PMID: 35835588 PMCID: PMC9804386 DOI: 10.1111/jam.15716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 01/05/2023]
Abstract
AIMS This study sought to assess the volatile organic compound (VOC) profiles of ampicillin-resistant and -susceptible Escherichia coli to evaluate whether VOC analysis may be utilized to identify resistant phenotypes. METHODS AND RESULTS An E. coli BL21 (DE3) strain and its pET16b plasmid transformed ampicillin-resistant counterpart were cultured for 6 h in drug-free, low- and high-concentrations of ampicillin. Headspace analysis was undertaken using thermal desorption-gas chromatography-mass spectrometry. Results revealed distinct VOC profiles with ampicillin-resistant bacteria distinguishable from their susceptible counterparts using as few as six compounds. A minimum of 30 compounds (fold change >2, p ≤ 0.05) were differentially expressed between the strains across all set-ups. Furthermore, three compounds (indole, acetoin and 3-methyl-1-butanol) were observed to be significantly more abundant (fold change >2, p ≤ 0.05) in the resistant strain compared to the susceptible strain both in the presence and in the absence of drug stress. CONCLUSIONS Results indicate that E. coli with acquired ampicillin resistance exhibit an altered VOC profile compared to their susceptible counterpart both in the presence and in the absence of antibiotic stress. This suggests that there are fundamental differences between the metabolisms of ampicillin-resistant and -susceptible E. coli which may be detected by means of VOC analysis. SIGNIFICANCE AND IMPACT OF THE STUDY Our findings suggest that VOC profiles may be utilized to differentiate between resistant and susceptible bacteria using just six compounds. Consequently, the development of machine-learning models using VOC signatures shows considerable diagnostic applicability for the rapid and accurate detection of antimicrobial resistance.
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Affiliation(s)
- Breanna Dixon
- Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, School of Biological SciencesUniversity of ManchesterManchesterUK,Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK
| | - Waqar M. Ahmed
- Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, School of Biological SciencesUniversity of ManchesterManchesterUK,Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK
| | - Abubaker A. Mohamed
- Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK,Department of Materials, Faculty of Science and EngineeringUniversity of ManchesterManchesterUK
| | - Tim Felton
- Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, School of Biological SciencesUniversity of ManchesterManchesterUK,NIHR Manchester Biomedical Research CentreManchester University Hospitals NHS Foundation TrustManchesterUK
| | - Stephen J. Fowler
- Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, School of Biological SciencesUniversity of ManchesterManchesterUK,NIHR Manchester Biomedical Research CentreManchester University Hospitals NHS Foundation TrustManchesterUK
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Molecular Characteristics and Quantitative Proteomic Analysis of Klebsiella pneumoniae Strains with Carbapenem and Colistin Resistance. Antibiotics (Basel) 2022; 11:antibiotics11101341. [PMID: 36289999 PMCID: PMC9598126 DOI: 10.3390/antibiotics11101341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/05/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) are usually multidrug resistant (MDR) and cause serious therapeutic problems. Colistin is a critical last-resort therapeutic option for MDR bacterial infections. However, increasing colistin use has led to the emergence of extensively drug-resistant (XDR) strains, raising a significant challenge for healthcare. In order to gain insight into the antibiotic resistance mechanisms of CRKP and identify potential drug targets, we compared the molecular characteristics and the proteomes among drug-sensitive (DS), MDR, and XDR K. pneumoniae strains. All drug-resistant isolates belonged to ST11, harboring blaKPC and hypervirulent genes. None of the plasmid-encoded mcr genes were detected in the colistin-resistant XDR strains. Through a tandem mass tag (TMT)-labeled proteomic technique, a total of 3531 proteins were identified in the current study. Compared to the DS strains, there were 247 differentially expressed proteins (DEPs) in the MDR strains and 346 DEPs in the XDR strains, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that a majority of the DEPs were involved in various metabolic pathways, which were beneficial to the evolution of drug resistance in K. pneumoniae. In addition, a total of 67 DEPs were identified between the MDR and XDR strains. KEGG enrichment and protein-protein interaction network analysis showed their participation in cationic antimicrobial peptide resistance and two-component systems. In conclusion, our results highlight the emergence of colistin-resistant and hypervirulent CRKP, which is a noticeable superbug. The DEPs identified in our study are of great significance for the exploration of effective control strategies against infections of CRKP.
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Shortridge D, Deshpande LM, Streit JM, Castanheira M. Activity of meropenem/vaborbactam and comparators against non-carbapenemase-producing carbapenem-resistant Enterobacterales isolates from Europe. JAC Antimicrob Resist 2022; 4:dlac097. [PMID: 36196439 PMCID: PMC9524562 DOI: 10.1093/jacamr/dlac097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/20/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Carbapenem-resistant Enterobacterales (CRE) isolates have disseminated worldwide. CREs usually produce a carbapenemase; however, some isolates are negative for known carbapenemases. In this study, we evaluated the activity of meropenem/vaborbactam and comparators against CREs without a carbapenemase (nonCP CREs) collected from European hospitals from 2016 to 2019.
Materials and methods
23 043 Enterobacterales clinical isolates were collected in 41 hospitals located in 20 countries. Susceptibility (S) testing was performed using the broth microdilution method. CLSI/EUCAST (2021) interpretive criteria were used. 978 CREs were identified with MICs >2 mg/L to meropenem or imipenem. Whole-genome sequencing was performed on each CRE isolate. 125 isolates were negative for carbapenemase genes, including blaKPC, blaNDM, blaIMP, blaVIM and blaOXA-48-like. NonCP CRE isolates were analysed for the presence of other β-lactamases, multilocus sequence types (ST) and mutations in outer membrane protein (OMP) sequences.
Results
Most nonCP CRE were Klebsiella pneumoniae (KPN; n = 97/125). 84.0% of nonCP CRE (n = 105) were from Poland, including 88 KPN. The most common β-lactamase was blaCTX-M-15 in 92/125 isolates. OMP disruptions or alterations were noted among 76 KPN. Among KPN isolates that had MLST typing, 30 belonged to ST11, 18 to ST152 and 17 to ST147, while 13 other STs were observed. Susceptibility to meropenem/vaborbactam was 96.0/97.6% (CLSI/EUCAST) while meropenem was 2.4/8.0%S.
Conclusions
Meropenem/vaborbactam had potent in vitro activity against CRE isolates that lacked known carbapenemases. Resistance mechanisms observed among nonCP CREs included acquired β-lactamases and OMP alterations. These results indicate that meropenem/vaborbactam may be a useful treatment for infections caused by nonCP CREs.
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Chen H, Li N, Wang F, Wang L, Liang W. Carbapenem antibiotic stress increases bla KPC -2 gene relative copy number and bacterial resistance levels of Klebsiella pneumoniae. J Clin Lab Anal 2022; 36:e24519. [PMID: 35718993 PMCID: PMC9280016 DOI: 10.1002/jcla.24519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/03/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Background The clinical isolation rates of carbapenem‐resistant Klebsiella pneumoniae (CR‐KP) continue to increase. In China, clinical CR‐KP isolates are mainly attributed to the blaKPC‐2 gene carried on plasmids, and the blaKPC‐2 copy number correlates with the expression of KPC enzymes, which can cause elevated carbapenem MICs. Methods Thirty‐seven CR‐KP isolates were collected at the Second People’s Hospital of Lianyungang City between January 2020 and March 2021, with no duplicate isolates, and were screened for the blaKPC‐2 gene with PCR. Analysis of current CRKP resistance to clinically relevant antimicrobials using the bioMérieux VITEK® 2 bacterial identification card. The multilocus sequence types of the strains were confirmed with PCR and DNA sequencing. Recombinant plasmids pET20b‐blaKPC‐2 and pET20b‐CpsG were constructed, and the copy numbers of the recombinant plasmids per unit volume was calculated based on the molecular weight of the plasmids. After the genomes DNA of clinical isolates of K. pneumoniae carrying the blaKPC‐2 gene were purified, the blaKPC‐2 gene relative copy number in individual K. pneumoniae strains was indicated by the double standard curve method. Detection of MIC values changes of K. pneumoniae under imipenem selection pressure by broth microdilution method. Results Among the 37 CR‐KP strains isolated, only the blaKPC‐2 gene was detected in 30 strains, three strains were positive for the blaNDM‐1 gene, two strains carried both the blaKPC‐2 and blaNDM‐1 genes, and two strains without detectable carbapenem resistance genes. The ST11 clone was predominant among the 37 carbapenem‐resistant K. pneumoniae isolates. Drug sensitivity testing showed that except for polymyxins (100% susceptible) and tigecycline (75.7% intermediate), the 37 CR‐KP strains were resistant to almost all antimicrobial drugs. The blaKPC‐2 relative copy number in nine ST11 clinical isolates of K. pneumoniae was 7.64 ± 2.51 when grown on LB plates but 27.67 ± 13.04 when grown on LB plates containing imipenem. Among these nine isolates, five CRKP strains exhibited elevated MICs to imipenem, while the remaining four strains showed unchanged MIC values to imipenem. Conclusion Carbapenem‐resistant Klebsiella pneumoniae isolates may have multiple pathways to achieve high levels of carbapenem resistance, and moderate carbapenem pressure can increase the copy number of KPC enzyme genes in CRKP strains and enhance the degree of carbapenem resistance in the strains.
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Affiliation(s)
- Huimin Chen
- Lianyungang Second People's Hospital affiliated to Jiangsu University, Lianyungang, China
| | - Na Li
- Lianyungang Second People's Hospital Affiliated to Bengbu Medical College, Lianyungang, China
| | - Fang Wang
- Lianyungang Second People Hospital, Lianyungang, China
| | - Lei Wang
- Jiangsu University of Science and Technology, Zhenjiang, China
| | - Wei Liang
- Lianyungang Second People's Hospital affiliated to Jiangsu University, Lianyungang, China
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Phenotypic and molecular characterization of extended-spectrum β-lactamase/AmpC- and carbapenemase-producing Klebsiella pneumoniae in Iran. Mol Biol Rep 2022; 49:4769-4776. [PMID: 35657452 DOI: 10.1007/s11033-022-07328-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The objective of the current study is to evaluate the phenotypic and molecular characterization of ESBL/AmpC- and carbapenemase-producing K. pneumoniae isolates in Iran. METHODS From October 2018 until the end of April 2020, different clinical samples were collected and K. pneumoniae isolates were identified using conventional biochemical tests and PCR assay. Antibiotic susceptibility pattern was determined using the Kirby-Bauer disk diffusion method. Modified Hedge Test (MHT) was applied to the identification of carbapenemase-producing K. pneumoniae. ESBL and AmpC-producing K. pneumoniae were detected using Double Disc Test (DDT) and Disc Potentiation Test (DPT), respectively. The presence of carbapenemase, ESBL, and AmpC encoding genes was screened by Polymerase Chain Reaction (PCR) assay. RESULTS A total of 100 K. pneumoniae isolates were collected. K. pneumoniae isolates had the highest resistance rate to cefazolin (66%) and cefotaxime (66%). Meropenem and amikacin with sensitivity rates of 76% and 69% were the most effective antimicrobial agents on K. pneumoniae isolates. It was found that 12 (12%), 27 (27%), and 9 (9%) K. pneumoniae isolates were positive in MHT, DDT, and DPT tests, respectively. Among the carbapenemase-encoding genes, blaOXA-48 (24%) and blaIMP (13%) genes had the highest frequency, while blaKPC and blaGIM genes were not detected among K. pneumoniae isolates. blaTEM (48%) and blaCMY (8%) genes had the highest frequency among ESBL and AmpC β-lactamase-encoding genes, respectively. CONCLUSIONS It is vital to adopt effective control strategies for K. pneumoniae infections and ensure rapid identification of antibiotic resistance profile.
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Liao Q, Deng J, Feng Y, Zhang W, Wu S, Liu Y, Che H, Xie Y. Emergence of Ceftazidime-Avibactam Resistance Due to A Novel blaKPC-2 Mutation during Treatment of Carbapenem-Resistant Klebsiella pneumoniae Infections. J Infect Public Health 2022; 15:545-549. [DOI: 10.1016/j.jiph.2022.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022] Open
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Wang H, Li J, Min C, Xia F, Tang M, Li J, Hu Y, Zou M. Characterization of Silver Resistance and Coexistence of sil Operon with Antibiotic Resistance Genes Among Gram-Negative Pathogens Isolated from Wound Samples by Using Whole-Genome Sequencing. Infect Drug Resist 2022; 15:1425-1437. [PMID: 35392367 PMCID: PMC8982571 DOI: 10.2147/idr.s358730] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/12/2022] [Indexed: 12/18/2022] Open
Abstract
Purpose Methods Results Conclusion
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Affiliation(s)
- Haichen Wang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Jia Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Changhang Min
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Fengjun Xia
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Mengli Tang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Jun Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Yongmei Hu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Mingxiang Zou
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
- Correspondence: Mingxiang Zou, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 41008, People’s Republic of China, Tel/Fax +86 7384327440, Email
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Chen X, Tian J, Luo C, Wang X, Li X, Wang M. Cell Membrane Remodeling Mediates Polymyxin B Resistance in Klebsiella pneumoniae: An Integrated Proteomics and Metabolomics Study. Front Microbiol 2022; 13:810403. [PMID: 35222333 PMCID: PMC8866958 DOI: 10.3389/fmicb.2022.810403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022] Open
Abstract
Polymyxin B (PB) is introduced into the clinic as the last-line therapy against carbapenem-resistant Klebsiella pneumoniae (CRKP). Unfortunately, increased resistance to PB in Klebsiella pneumoniae (K. pneumoniae) has threatened global health. Resistance of K. pneumoniae to PB was induced by passaging in serial concentrations of PB and determined by microbroth dilution method. Growth characteristics of induced strains including growth curve, reversibility of resistance, and biofilm formation (crystal violet staining method) were measured. This study employed TMT-labeled quantitative proteomics and LC-MS/MS metabolomics analysis to investigate the key biological processes associated with PB resistance in K. pneumoniae. A total of 315 differentially expressed proteins (DEPs) were identified, of which 133 were upregulated and 182 were downregulated in the PB-resistant K. pneumoniae. KEGG enrichment analysis revealed that the DEPs were mainly involved in ATP-binding cassette (ABC) transporters and cationic antimicrobial peptide (CAMP) resistance. Proteins related to central carbon metabolism were inhibited in the PB-resistant K. pneumoniae, but proteins mediating LPS modification were activated. Transcriptional levels of CAMP resistance-related proteins were significantly different between PB-susceptible and -resistant K. pneumoniae. PB treatment led to an increase in reactive oxygen species (ROS) levels of K. pneumoniae. Metabolomics data demonstrated that 23 metabolites were significantly upregulated in PB-resistant K. pneumoniae and 5 were downregulated. The differential metabolites were mainly lipids, including glycerophospholipids, sphingolipids, and fatty acids. Exposure to PB resulted in increased level of phospholipid transport gene mlaF in K. pneumoniae. Our study suggested that membrane remodeling and inhibited central carbon metabolism are conducive to the development of PB resistance in K. pneumoniae.
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Affiliation(s)
| | | | | | | | | | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
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Ejaz H. Analysis of diverse β-lactamases presenting high-level resistance in association with OmpK35 and OmpK36 porins in ESBL-producing Klebsiella pneumoniae. Saudi J Biol Sci 2022; 29:3440-3447. [PMID: 35844436 PMCID: PMC9280233 DOI: 10.1016/j.sjbs.2022.02.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/20/2022] [Indexed: 11/18/2022] Open
Abstract
Emerging extensively drug-resistant (XDR) Klebsiella pneumoniae due to the production of β-lactamases and porin loss is a substantial worldwide concern. This study aimed to elucidate the role of outer membrane porin (OMP) loss, AmpC, and carbapenemases among extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae strains with XDR phenotype. This study analyzed 79 K. pneumoniae from several clinical sources and detected ESBLs in 29 strains co-harbored with other β-lactamases using standard microbiological practices and phenotypic procedures. Minimum inhibitory concentrations (MICs) were determined against several antibiotics using Microscan WalkAway plus. OMP analysis was carried out using sodium dodecyl sulfate–polyacrylamide gel electrophoresis. ESBL, AmpC, and carbapenemase genes were detected using molecular methods. The microbiological analysis discovered 29 (36.7%) ESBL strains of K. pneumoniae, which showed the co-existence of 7 (24.1%) AmpC β-lactamases and 22 (75.9%) carbapenemases. Porin loss of OmpK35 was observed in 13 (44.8%) and OmpK36 in 8 (27.5%) K. pneumoniae strains. The strains were significantly associated with the intensive care unit (ICU) (p = 0.006) and urinary sources (p = 0.004). The most commonly detected gene variants in each β-lactamase class included 16 (55.2%) blaCTX-M−1, 7 (100%) blaCYM-2, 11 (50%) blaNDM-1, and integron-1 was detected in 21/29 (72.4%) strains. MICs of cephalosporin, fluoroquinolone, carbapenem, aminoglycoside, and β-lactam combinations demonstrated a high number of XDR strains. Tigecycline (2 µg/mL MIC50 and >32 µg/mL MIC90) and colistin (1 µg/mL MIC50 and 8 µg/mL MIC90) presented lower resistance. ESBL K. pneumoniae strains with OmpK35 and OmpK36 porin loss demonstrate conglomerate resistance mechanisms with AmpC and carbapenemases, leading to emerging XDR and pan drug resistance.
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Xiong Y, Han Y, Zhao Z, Gao W, Ma Y, Jiang S, Wang M, Zhang Q, Zhou Y, Chen Y. Impact of Carbapenem Heteroresistance Among Multidrug-Resistant ESBL/AmpC-Producing Klebsiella pneumoniae Clinical Isolates on Antibiotic Treatment in Experimentally Infected Mice. Infect Drug Resist 2022; 14:5639-5650. [PMID: 34992390 PMCID: PMC8711563 DOI: 10.2147/idr.s340652] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose Antibiotic resistance is a growing health crisis that is further complicated by treatment failures caused by bacteria that exhibit heterogeneous susceptibility to antibiotics. The aim of this study was to describe imipenem (IPM)-heteroresistant strains among multidrug-resistant (MDR) ESBL/AmpC-producing Klebsiella pneumoniae clinical isolates, investigate their molecular phenotypic characteristics, and elucidate the outcome of antibiotic treatment in mice infected with the heteroresistant isolates. Materials and Methods Antimicrobial susceptibility of K. pneumoniae isolates was determined by the disk diffusion and E-test methods. Heteroresistance to IPM was confirmed by population analysis profile (PAP) assays. PCR and sequencing were employed to detect MDR determinants. Molecular differences between the susceptible and resistant subpopulations were evaluated by sequencing and quantitative real-time reverse transcription PCR (qRT-PCR) analysis. The effect of the carbapenem-heteroresistant strains on antibiotic treatment was assessed using a mouse model of peritonitis with heteroresistant K. pneumoniae and subsequent treatment with IPM. Results In total, 37 MDR ESBL/AmpC-producing clinical isolates of K. pneumoniae were identified between September 2018 and December 2019. These strains were notably resistant to conventional antimicrobials other than carbapenems. Among the isolates, three strains exhibited heteroresistance to IPM and carried several ESBL and/or AmpC genes. Mice infected with a lethal dose of any of the three heteroresistant isolates were unable to survive in the presence of IPM treatment, as the percentage of the IPM-resistant subpopulation of each strain was increased in the peritoneum of these mice at 24 h after infection. The resistant subpopulation of the strains presented pulsed-field gel electrophoresis (PFGE) profiles that were identical to those of the susceptible subpopulation, but ompK36 porin showed a reduction in gene expression (0.09- to 0.50-fold) in the resistant subpopulation. Conclusion Carbapenem-heteroresistant strains were present among the MDR K. pneumoniae isolates producing ESBL/AmpC β-lactamases, and these heteroresistant strains failed IPM therapy in experimentally infected mice.
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Affiliation(s)
- Yilin Xiong
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, People's Republic of China
| | - Yuqiao Han
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, People's Republic of China
| | - Zinan Zhao
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, People's Republic of China
| | - Wenting Gao
- Institute of Genome Engineered Animal Models for Human Disease, Dalian Medical University, Dalian, People's Republic of China
| | - Yong Ma
- Institute of Genome Engineered Animal Models for Human Disease, Dalian Medical University, Dalian, People's Republic of China
| | - Shiyu Jiang
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, People's Republic of China
| | - Mengyao Wang
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, People's Republic of China
| | - Qingqing Zhang
- Laboratory of Pathogenic Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, People's Republic of China
| | - Yun Zhou
- Department of Clinical Nutrition, Second Affiliated Hospital of Dalian Medical University, Dalian, People's Republic of China
| | - Yang Chen
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, People's Republic of China
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Flannery DD, Chiotos K, Gerber JS, Puopolo KM. Neonatal multidrug-resistant gram-negative infection: epidemiology, mechanisms of resistance, and management. Pediatr Res 2022; 91:380-391. [PMID: 34599280 PMCID: PMC8819496 DOI: 10.1038/s41390-021-01745-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/31/2021] [Indexed: 02/08/2023]
Abstract
Infants admitted to the neonatal intensive care unit, particularly those born preterm, are at high risk for infection due to the combination of an immature immune system, prolonged hospitalization, and frequent use of invasive devices. Emerging evidence suggests that multidrug-resistant gram-negative (MDR-GN) infections are increasing in neonatal settings, which directly threatens recent and ongoing advances in contemporary neonatal care. A rising prevalence of antibiotic resistance among common neonatal pathogens compounds the challenge of optimal management of suspected and confirmed neonatal infection. We review the epidemiology of MDR-GN infections in neonates in the United States and internationally, with a focus on extended-spectrum β-lactamase (ESBL)-producing Enterobacterales and carbapenem-resistant Enterobacterales (CRE). We include published single-center studies, neonatal collaborative reports, and national surveillance data. Risk factors for and mechanisms of resistance are discussed. In addition, we discuss current recommendations for empiric antibiotic therapy for suspected infections, as well as definitive treatment options for key MDR organisms. Finally, we review best practices for prevention and identify current knowledge gaps and areas for future research. IMPACT: Surveillance and prevention of MDR-GN infections is a pediatric research priority. A rising prevalence of MDR-GN neonatal infections, specifically ESBL-producing Enterobacterales and CRE, compounds the challenge of optimal management of suspected and confirmed neonatal infection. Future studies are needed to understand the impacts of MDR-GN infection on neonatal morbidity and mortality, and studies of current and novel antibiotic therapies should include a focus on the pharmacokinetics of such agents among neonates.
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Affiliation(s)
- Dustin D Flannery
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Kathleen Chiotos
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Critical Care Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Anesthesia and Critical Care, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jeffrey S Gerber
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karen M Puopolo
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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Onishi R, Shigemura K, Osawa K, Yang YM, Maeda K, Fang SB, Sung SY, Onuma K, Uda A, Miyara T, Fujisawa M. The Antimicrobial Resistance Characteristics of Imipenem-Non-Susceptible, Imipenemase-6-Producing Escherichia coli. Antibiotics (Basel) 2021; 11:antibiotics11010032. [PMID: 35052909 PMCID: PMC8772982 DOI: 10.3390/antibiotics11010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Imipenemase-6 (IMP-6) type carbapenemase-producing Enterobacteriaceae is regarded as dangerous due to its unique lack of antimicrobial susceptibility. It is resistant to meropenem (MEPM) but susceptible to imipenem (IPM). In addition to carbapenemase, outer membrane porins and efflux pumps also play roles in carbapenem resistance by reducing the antimicrobial concentration inside cells. Extended-spectrum β-lactamase (ESBL) is transmitted with IMP-6 by the plasmid and broadens the spectrum of antimicrobial resistance. We collected 42 strains of IMP-6-producing Escherichia coli and conducted a molecular analysis of carbapenemase, ESBL, porin, efflux, and epidemiological characteristics using plasmid replicon typing. Among the 42 isolates, 21 strains were susceptible to IPM (50.0%) and 1 (2.4%) to MEPM. Seventeen strains (40.5%) co-produced CTX-M-2 type ESBL. We found that the relative expression of ompC and ompF significantly correlated with the MIC of IPM (p = 0.01 and p = 0.03, respectively). Sixty-eight% of CTX-M-2-non-producing strains had IncI1, which was significantly different from CTX-M-2-producing strains (p < 0.001). In conclusion, 50.0% of our IMP-6-producing strains were non-susceptible to IPM, which is different from the typical pattern and can be attributed to decreased porin expression. Further studies investigating other types of carbapenemase are warranted.
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Affiliation(s)
- Reo Onishi
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan;
| | - Katsumi Shigemura
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan;
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
- Correspondence: ; Tel.: +81-78-382-6155
| | - Kayo Osawa
- Department of Medical Technology, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe 653-0838, Japan;
| | - Young-Min Yang
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
| | - Koki Maeda
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
| | - Shiuh-Bin Fang
- Department of Pediatrics, Division of Pediatric Gastroenterology and Hepatology, Shuang Ho Hospital, Taipei Medical University, 291 Jhong Jheng Road, Jhong Ho District, New Taipei City 23561, Taiwan;
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Shian-Ying Sung
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Kenichiro Onuma
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (K.O.); (A.U.); (T.M.)
| | - Atsushi Uda
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (K.O.); (A.U.); (T.M.)
| | - Takayuki Miyara
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (K.O.); (A.U.); (T.M.)
| | - Masato Fujisawa
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
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46
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Chang D, Sharma L, Dela Cruz CS, Zhang D. Clinical Epidemiology, Risk Factors, and Control Strategies of Klebsiella pneumoniae Infection. Front Microbiol 2021; 12:750662. [PMID: 34992583 PMCID: PMC8724557 DOI: 10.3389/fmicb.2021.750662] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Klebsiella species cause infections at multiple sites, including lung, urinary tract, bloodstream, wound or surgical site, and brain. These infections are more likely to occur in people with preexisting health conditions. Klebsiella pneumoniae (K. pneumoniae) has emerged as a major pathogen of international concern due to the increasing incidences of hypervirulent and carbapenem-resistant strains. It is imperative to understand risk factors, prevention strategies, and therapeutic avenues to treat multidrug-resistant Klebsiella infections. Here, we highlight the epidemiology, risk factors, and control strategies against K. pneumoniae infections to highlight the grave risk posed by this pathogen and currently available options to treat Klebsiella-associated diseases.
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Affiliation(s)
- De Chang
- Department of Pulmonary and Critical Care Medicine, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Lokesh Sharma
- Section of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Charles S. Dela Cruz
- Section of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Dong Zhang
- Department of Oncology, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
- College of Tuberculosis Medicine, Chinese PLA General Hospital, Beijing, China
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47
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Singkham-in U, Muhummudaree N, Chatsuwan T. In Vitro Synergism of Azithromycin Combination with Antibiotics against OXA-48-Producing Klebsiella pneumoniae Clinical Isolates. Antibiotics (Basel) 2021; 10:1551. [PMID: 34943763 PMCID: PMC8698995 DOI: 10.3390/antibiotics10121551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae has globally emerged as an urgent threat leading to the limitation for treatment. K. pneumoniae carrying blaOXA-48, which plays a broad magnitude of carbapenem susceptibility, is widely concerned. This study aimed to characterize related carbapenem resistance mechanisms and forage for new antibiotic combinations to combat blaOXA-48-carrying K. pneumoniae. Among nine isolates, there were two major clones and a singleton identified by ERIC-PCR. Most isolates were resistant to ertapenem (MIC range: 2->256 mg/L), but two isolates were susceptible to imipenem and meropenem (MIC range: 0.5-1 mg/L). All blaOXA-48-carrying plasmids conferred carbapenem resistance in Escherichia coli transformants. Two ertapenem-susceptible isolates carried both outer membrane proteins (OMPs), OmpK35 and OmpK36. Lack of at least an OMP was present in imipenem-resistant isolates. We evaluated the in vitro activity of an overlooked antibiotic, azithromycin, in combination with other antibiotics. Remarkably, azithromycin exhibited synergism with colistin and fosfomycin by 88.89% and 77.78%, respectively. Bacterial regrowth occurred after exposure to colistin or azithromycin alone. Interestingly, most isolates were killed, reaching synergism by this combination. In conclusion, the combination of azithromycin and colistin may be an alternative strategy in dealing with blaOXA-48-carrying K. pneumoniae infection during a recent shortage of newly effective antibiotic development.
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Affiliation(s)
- Uthaibhorn Singkham-in
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Netchanok Muhummudaree
- Interdisciplinary Program of Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
- Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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48
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Schultze TG, Ferstl PG, Villinger D, Hogardt M, Bechstein WO, Göttig S, Wichelhaus TA, Zeuzem S, Trebicka J, Waidmann O, Welker MW, Kempf VAJ. Molecular Surveillance of Carbapenem-Resistant Gram-Negative Bacteria in Liver Transplant Candidates. Front Microbiol 2021; 12:791574. [PMID: 34880850 PMCID: PMC8645865 DOI: 10.3389/fmicb.2021.791574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Carbapenem-resistant Gram-negative bacteria (CRGN) cause life-threatening infections due to limited antimicrobial treatment options. The occurrence of CRGN is often linked to hospitalization and antimicrobial treatment but remains incompletely understood. CRGN are common in patients with severe illness (e.g., liver transplantation patients). Using whole-genome sequencing (WGS), we aimed to elucidate the evolution of CRGN in this vulnerable cohort and to reconstruct potential transmission routes. Methods: From 351 patients evaluated for liver transplantation, 18 CRGN isolates (from 17 patients) were analyzed. Using WGS and bioinformatic analysis, genotypes and phylogenetic relationships were explored. Potential epidemiological links were assessed by analysis of patient charts. Results: Carbapenem-resistant (CR) Klebsiella pneumoniae (n=9) and CR Pseudomonas aeruginosa (n=7) were the predominating pathogens. In silico analysis revealed that 14/18 CRGN did not harbor carbapenemase-coding genes, whereas in 4/18 CRGN, carbapenemases (VIM-1, VIM-2, OXA-232, and OXA-72) were detected. Among all isolates, there was no evidence of plasmid transfer-mediated carbapenem resistance. A close phylogenetic relatedness was found for three K. pneumoniae isolates. Although no epidemiological context was comprehensible for the CRGN isolates, evidence was found that the isolates resulted of a transmission of a carbapenem-susceptible ancestor before individual radiation into CRGN. Conclusion: The integrative epidemiological study reveals a high diversity of CRGN in liver cirrhosis patients. Mutation of carbapenem-susceptible ancestors appears to be the dominant way of CR acquisition rather than in-hospital transmission of CRGN or carbapenemase-encoding genetic elements. This study underlines the need to avoid transmission of carbapenem-susceptible ancestors in vulnerable patient cohorts.
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Affiliation(s)
- Tilman G Schultze
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt, Germany.,University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,University Center of Competence for Infection Control of the State of Hesse, Frankfurt, Germany
| | - Philip G Ferstl
- University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,Division of Gastroenterology and Hepatology, Department for Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - David Villinger
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt, Germany.,University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,University Center of Competence for Infection Control of the State of Hesse, Frankfurt, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt, Germany.,University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,University Center of Competence for Infection Control of the State of Hesse, Frankfurt, Germany
| | - Wolf O Bechstein
- Department of General and Visceral Surgery, Goethe University Frankfurt, Frankfurt, Germany
| | - Stephan Göttig
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt, Germany.,University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,University Center of Competence for Infection Control of the State of Hesse, Frankfurt, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt, Germany.,University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,University Center of Competence for Infection Control of the State of Hesse, Frankfurt, Germany
| | - Stefan Zeuzem
- University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,Division of Gastroenterology and Hepatology, Department for Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Jonel Trebicka
- University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,Division of Gastroenterology and Hepatology, Department for Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Oliver Waidmann
- University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,Division of Gastroenterology and Hepatology, Department for Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Martin-Walter Welker
- University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,Division of Gastroenterology and Hepatology, Department for Internal Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Volkhard A J Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt, Germany.,University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany.,University Center of Competence for Infection Control of the State of Hesse, Frankfurt, Germany
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49
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Mashaly MES, Mashaly GES. Activity of imipenem/relebactam on Klebsiella pneumoniae with different mechanisms of imipenem non-susceptibility. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 13:785-792. [PMID: 35222856 PMCID: PMC8816701 DOI: 10.18502/ijm.v13i6.8080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Background and Objectives: Imipenem/relebactam (IMP/R) is a newly FDA approved β-lactam/β-lactamase inhibitor combination. Relebactam ability to restore IMP activity could differ according to the cause of imipenem non-susceptibility. Therefore, we investigated the in-vitro activity of IMP/R against Klebsiella pneumoniae with different mechanisms of imipenem non-susceptibility. Materials and Methods: Imipenem-nonsusceptible (IMP-NS) K. pneumoniae isolates were collected and characterized for β-lactamase encoding genes by multiplex PCR. For IMP-NS carbapenemase-negative isolates, study of Ompk35 & Ompk36 gene expression was performed by reverse transcription-PCR while efflux pump activity was studied by minimum inhibitory concentration (MIC) reduction assay using efflux pump inhibitor. Susceptibility testing of K. pneumoniae to IMP and IMP/R were achieved by broth microdilution (BMD) method. Results: During the study period, 140 isolates of IMP-NS K. pneumoniae were collected. BMD method showed that relebactam restored IMP susceptibility in 100%, 60% and 49% of isolates that only harbor AmpC, extended spectrum beta lactamase (ESBL) and carbapenemases, respectively. IMP/R was most potent against all bla
KPC
and 50% of bla
OXA-48
_producing isolates. No demonstrable activity of IMP/R against K. pneumoniae harboring metallo-β-lactamases (MBLs). Out of 18 isolates with IMP non-suceptibility due to porins loss with overproduction of ESBL and/or AmpC, 14 (77.7%) isolates were IMP/R susceptible. IMP/R showed no activity against isolates with only efflux pump hyperactivity. Conclusion: Relebactam could restore IPM activity in KPC or AmpC-producing IMP/NS K. pneumoniae but with no activity against MBL− producing isolates. Relebactam activity against isolates harbouring-bla
OXA-48
or with altered Ompk35 & Ompk36 gene expression and efflux pump hyperactivity need further studies. Therefore, using IMP/R antibiotic in the treatment of infections caused by IMP/NS K. pneumoniae should be based on its molecular profile of IMP resistance to optimize the utility of IMP/R.
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Affiliation(s)
- Mervat El-Sayed Mashaly
- Department of Clinical Pathology, Clinical Microbiology Unit, School of Medicine, Mansoura University, Mansoura, Egypt
| | - Ghada El-Saeed Mashaly
- Department of Medical Microbiology and Immunology, School of Medicine, Mansoura University, Mansoura, Egypt
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50
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Benlabidi S, Raddaoui A, Achour W, Hassen B, Torres C, Abbassi MS, Ghrairi T. Genetic characterization of ESBL/pAmpC-producing Escherichia coli isolated from forest, urban park and cereal culture soils. FEMS Microbiol Ecol 2021; 97:6425737. [PMID: 34788430 DOI: 10.1093/femsec/fiab146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 11/09/2021] [Indexed: 01/26/2023] Open
Abstract
Little is known about the role of forestland and non-fertilized agriculture soils as reservoirs of extended-spectrum beta-lactamase (ESBL) and plasmid-borne AmpC (pAmpC)-producing Escherichia coli isolates. Thus, in the present study, 210 soil samples from various origins (forest of Oued Zen (Ain Drahem), non-agriculture soils from different park gardens in Tunis City, cereal culture soils and home gardens) were investigated to characterize cefotaxime-resistant E. coli isolates. A total of 22 ESBL/pAmpC-producing E. coli were collected, and all harbored variants of the blaCTX-M gene (15 blaCTX-M-1, 5 blaCTX-M-55 and 2 blaCTX-M-15). A total of seven and two isolates harbored also blaEBC and blaDHA-like genes, respectively. Resistances to tetracycline, sulfonamides and fluoroquinolones were encoded by tetA (n = 4)/tetB (n = 12), sul1 (n = 17)/sul2 (n = 19) and aac(6')-Ib-cr (n = 2)/qnrA (n = 1)/qnrS (n = 1) genes, respectively. A total of seven isolates were able to transfer by conjugation cefotaxime-resistance in association or not with other resistance markers. PFGE showed that ten and two isolates were clonally related (pulsotypes P1 and P2). The 10 P1 isolates had been collected from forestland, cereal culture soils and an urban park garden in Tunis City, arguing for a large spread of clonal strains. Our findings highlight the occurrence of ESBL/pAmpC-E. coli isolates in soils under limited anthropogenic activities and the predominance of CTX-M enzymes that are largely disseminated in E. coli from humans and animals in Tunisia.
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Affiliation(s)
- Saloua Benlabidi
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, 20 Street Jebel Lakhdhar, Bab Saadoun, 1006 Tunis, Tunisia
| | - Anis Raddaoui
- Faculty of Medicine of Tunis, Laboratory Ward, National Bone Marrow Transplant Center, University of Tunis El Manar, LR18ES39, 1006 Tunis, Tunisia
| | - Wafa Achour
- Faculty of Medicine of Tunis, Laboratory Ward, National Bone Marrow Transplant Center, University of Tunis El Manar, LR18ES39, 1006 Tunis, Tunisia
| | - Bilel Hassen
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, 20 Street Jebel Lakhdhar, Bab Saadoun, 1006 Tunis, Tunisia
| | - Carmen Torres
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Mohamed Salah Abbassi
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, 20 Street Jebel Lakhdhar, Bab Saadoun, 1006 Tunis, Tunisia.,Faculty of Medicine of Tunis, Laboratory of Antibiotic Resistance LR99ES09, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Taoufik Ghrairi
- Faculty of Sciences of Tunis, Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation, University Tunis El Manar, LR18ES03, Tunis, Tunisia
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