1
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Mushtaq S, Vickers A, Woodford N, Livermore DM. Activity of aztreonam/avibactam and ceftazidime/avibactam against Enterobacterales with carbapenemase-independent carbapenem resistance. Int J Antimicrob Agents 2024; 63:107081. [PMID: 38176458 DOI: 10.1016/j.ijantimicag.2023.107081] [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: 09/18/2023] [Revised: 12/01/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
Enterobacterales with carbapenemase-independent resistance to carbapenems are sometimes selected during therapy and, on rare occasions, cause outbreaks. Most have extended-spectrum or AmpC β-lactamases, together with changes to permeability or penicillin-binding proteins (PBPs). Newer β-lactam-β-lactamase inhibitor combinations may present useful options for infections due to these organisms. Accordingly, Clinical and Laboratory Standards Institute/European Committee on Antimicrobial Susceptibility Testing broth-microdilution was used to measure the minimum inhibitory concentrations (MICs) of ceftazidime/avibactam and aztreonam/avibactam for 51 carbapenemase-negative Enterobacterales with resistance or reduced susceptibility to carbapenems: genomic sequencing of the least-susceptible organisms was also undertaken. MICs of the two avibactam combinations cross-correlated closely, but with fewer MICs (2/51 vs. 10/51) exceeding 8+4 mg/L in the case of ceftazidime/avibactam. Raised MICs for Escherichia coli were associated with PBP3 inserts together with CMY-42 β-lactamase; correlates among Enterobacter cloacae complex isolates remain elusive, with AmpC and PBP3 sequences found to be species specific. In the case of Klebsiella spp., no MICs exceeding 2 mg/L were seen for either combination. It appears that these avibactam combinations have potential against Enterobacterales with carbapenemase-independent carbapenem resistance or reduced susceptibility, with ceftazidime/avibactam being more reliably active than aztreonam/avibactam.
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Affiliation(s)
- Shazad Mushtaq
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Anna Vickers
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
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2
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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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3
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Souza PMS, Ribeiro ACOA, Pena EPN, Silva FAC, Calsa Júnior T, Morais MMC, Almeida ACS. Distinct carbapenems susceptibility profiles in isogenic isolates of Klebsiella pneumoniae presenting Ompk36 disruption and expression of down-regulated blaKPC-2. BRAZ J BIOL 2023; 83:e269946. [PMID: 37283335 DOI: 10.1590/1519-6984.269946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/27/2023] [Indexed: 06/08/2023] Open
Abstract
The isolation of multidrug-resistant Klebsiella pneumoniae in hospitals is a major public health threat, increasing patient hospitalization costs, morbidity and mortality. Therefore, this work investigated the resistance mechanisms that produced different carbapenems susceptibility profiles in two isogenic strains of K. pneumoniae isolated from the same patient in a public hospital in Recife, Pernambuco. The genes that encode the main porins in K. pneumoniae, ompK35 and ompK36, and several beta-lactamase genes were analyzed. The expression of these genes was evaluated by quantitative real time PCR (polymerase chain reaction) with reverse transcriptase (RT-qPCR). SDS-PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis) was performed to analyze the outer membrane proteins. The analysis of the ompK36 genetic environment disclosed an IS903 insertion sequence disrupting this gene in the ertapenem resistant isolate (KPN133). The blaKPC-2 gene showed down-regulated expression in both isolates. Our findings show that changes in porins, especially OmpK36, are more determinant to carbapenems susceptibility profile of bacterial isolates than variations in blaKPC gene expression.
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Affiliation(s)
- P M S Souza
- Universidade de Pernambuco - UPE, Instituto de Ciências Biológicas, Laboratório de Resistência Microbiana, Recife, PE, Brasil
| | - A C O A Ribeiro
- Universidade de Pernambuco - UPE, Instituto de Ciências Biológicas, Laboratório de Resistência Microbiana, Recife, PE, Brasil
| | - E P N Pena
- Universidade Federal de Pernambuco - UFPE, Departamento de Genética, Laboratório de Genômica e Proteômica de Plantas, Recife, PE, Brasil
| | - F A C Silva
- Universidade Federal de Pernambuco - UFPE, Departamento de Genética, Laboratório de Genômica e Proteômica de Plantas, Recife, PE, Brasil
| | - T Calsa Júnior
- Universidade Federal de Pernambuco - UFPE, Departamento de Genética, Laboratório de Genômica e Proteômica de Plantas, Recife, PE, Brasil
| | - M M C Morais
- Universidade de Pernambuco - UPE, Instituto de Ciências Biológicas, Laboratório de Resistência Microbiana, Recife, PE, Brasil
| | - A C S Almeida
- Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Biologia, Laboratório de Genética, Bioquímica e Sequenciamento de DNA, Recife, PE, Brasil
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4
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Martin MJ, Stribling W, Ong AC, Maybank R, Kwak YI, Rosado-Mendez JA, Preston LN, Lane KF, Julius M, Jones AR, Hinkle M, Waterman PE, Lesho EP, Lebreton F, Bennett JW, Mc Gann PT. A panel of diverse Klebsiella pneumoniae clinical isolates for research and development. Microb Genom 2023; 9. [PMID: 37141116 DOI: 10.1099/mgen.0.000967] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Klebsiella pneumoniae are a leading cause of healthcare-associated infections worldwide. In particular, strains expressing extended-spectrum β-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, leading the World Health Organization (WHO) to designate ESBL and carbapenem-resistant Enterobacteriaceae as 'critical' threats to human health. Research efforts to combat these pathogens can be supported by accessibility to diverse and clinically relevant isolates for testing novel therapeutics. Here, we describe a panel of 100 diverse K. pneumoniae isolates that are publicly available to assist the research community in this endeavour. Whole-genome sequencing (WGS) was performed on 3878 K. pneumoniae clinical isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. The isolates were cultured from 63 facilities in 19 countries between 2001 and 2020. Core-genome multilocus sequence typing and high-resolution single-nucleotide polymorphism-based phylogenetic analyses captured the genetic diversity of the collection and were used to select the final panel of 100 isolates. In addition to known multidrug-resistant (MDR) pandemic lineages, the final panel includes hypervirulent lineages and isolates with specific and diverse resistance genes and virulence biomarkers. A broad range of antibiotic susceptibilities, ranging from pan-sensitive to extensively drug-resistant isolates, are described. The panel collection, and all associated metadata and genome sequences, are available at no additional cost and will be an important resource for the research community and for the design and development of novel antimicrobial agents and diagnostics against this important pathogen.
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Affiliation(s)
- Melissa J Martin
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - William Stribling
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ana C Ong
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Joshua A Rosado-Mendez
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lan N Preston
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Katharine F Lane
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Michael Julius
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Anthony R Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mary Hinkle
- Infectious Diseases Unit, Rochester General Hospital, Rochester, New York, USA
| | - Paige E Waterman
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Emil P Lesho
- Infectious Diseases Unit, Rochester General Hospital, Rochester, New York, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Patrick T Mc Gann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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5
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Lustri WR, Lazarini SC, Simei Aquaroni NA, Resende FA, Aleixo NA, Pereira DH, Lustri BC, Moreira CG, Ribeiro CM, Pavan FR, Nakahata DH, Gonçalves AM, Nascimento-Júnior NM, Corbi PP. A new complex of silver(I) with probenecid: Synthesis, characterization, and studies of antibacterial and extended spectrum β-lactamases (ESBL) inhibition activities. J Inorg Biochem 2023; 243:112201. [PMID: 37003189 DOI: 10.1016/j.jinorgbio.2023.112201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
This article describes the in vitro antibacterial and β-lactamase inhibition of a novel silver(I) complex with the sulfonamide probenecid (Ag-PROB). The formula Ag2C26H36N2O8S2·2H2O for the Ag-PROB complex was proposed based on elemental analysis. High-resolution mass spectrometric studies revealed the existence of the complex in its dimeric form. Infrared, nuclear magnetic resonance spectroscopies and Density Functional Theory calculations indicated a bidentate coordination of probenecid to the silver ions by the oxygen atoms of the carboxylate. In vitro antibacterial activities of Ag-PROB showed significant growth inhibitory activity over Mycobacterium tuberculosis, S. aureus, and P. aeruginosa PA01biofilm-producers, B. cereus, and E. coli. The Ag-PROB complex was active over multi-drug resistant of uropathogenic E. coli extended spectrum β-lactamases (ESBL) producing (EC958 and BR43), enterohemorrhagic E. coli (O157:H7) and enteroaggregative E. coli (O104:H4). Ag-PROB was able to inhibit CTX-M-15 and TEM-1B ESBL classes, at concentrations below the minimum inhibitory concentration for Ag-PROB, in the presence of ampicillin (AMP) concentration in which EC958 and BR43 bacteria were resistant in the absence of Ag-PROB. These results indicate that, in addition to ESBL inhibition, there is a synergistic antibacterial effect between AMP and the Ag-PROB. Molecular docking results revealed potential key residues involved in interactions between Ag-PROB, CTX-M-15 and TEM1B, suggesting the molecular mechanism of the ESBL inhibition. The obtained results added to the absence of mutagenic activity and low cytotoxic activity over non-tumor cell of the Ag-PROB complex open a new perspective for future in vivo tests demonstrating its potential of use as an antibacterial agent.
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6
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Li Y, Yan M, Xue F, Zhong W, Liu X, Chen X, Wu Y, Zhang J, Wang Q, Zheng B, Lv Y. In vitro and in vivo activities of a novel β-lactamase inhibitor combination imipenem/XNW4107 against recent clinical Gram-negative bacilli from China. J Glob Antimicrob Resist 2022; 31:1-9. [PMID: 35820591 DOI: 10.1016/j.jgar.2022.07.006] [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: 01/03/2022] [Revised: 03/22/2022] [Accepted: 07/05/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES XNW4107 is a novel β-lactamase inhibitor that possesses broad activity against serine-β-lactamases. XNW4107 in combination with imipenem exhibited potent in vitro activity against carbapenem-resistant bacteria and particularly against carbapenem-resistant Acinetobacter baumannii. This study aimed to evaluate the in vitro and in vivo antibacterial activities of imipenem/XNW4107. METHODS The minimum inhibitory concentrations, minimum bactericidal concentrations, time-kill curves, post-antibiotic effects, and spontaneous frequency of resistance were used to investigate the imipenem/XNW4107 in vitro activity. A mouse systemic infection model was used to evaluate the imipenem/XNW4107 in vivo efficacy. RESULTS MIC90 of imipenem/XNW4107 against imipenem-nonsusceptible A. baumannii (n = 106) was 8 mg/L, which was 16-fold lower than the MIC90 of imipenem; the resistance rate decreased from 90% to 20% applying the CLSI imipenem breakpoint. MIC90 of imipenem/XNW4107 against imipenem-resistant Klebsiella pneumoniae (n = 54) was 2 mg/L, which was 128-fold lower than the MIC90 of imipenem; 80% imipenem-nonsusceptible Pseudomonas aeruginosa (n = 101) exhibited MICs of imipenem/XNW4107 from 2 to 8 mg/L, which were 4- to 8-fold lower than the MICs of imipenem. Imipenem/XNW4107 was bactericidal against A. baumannii, K. pneumoniae, and Escherichia coli. The time-kill curves showed that increasing concentrations did not result in progressively increased killing at concentrations >4 × MIC. Imipenem/XNW4107 has a low potential for resistance development in tested strains except for K. pneumoniae. Imipenem/XNW4107 provided good protection against imipenem-resistant A. baumannii and K. pneumoniae in vivo. CONCLUSIONS The broad-spectrum profile and potent in vitro and in vivo antibacterial activities support imipenem/XNW4107 as a promising investigational candidate.
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Affiliation(s)
- Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Mengyao Yan
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Wei Zhong
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Xiao Liu
- Suzhou Sinovent Pharmaceuticals Co., Ltd., Beijing, China
| | - Xi Chen
- Suzhou Sinovent Pharmaceuticals Co., Ltd., Beijing, China
| | - Yuchuan Wu
- Suzhou Sinovent Pharmaceuticals Co., Ltd., Beijing, China
| | - Jia Zhang
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Qing Wang
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Bo Zheng
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
| | - Yuan Lv
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
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7
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Molecular patterns of clinically important fluoroquinolone resistance in multidrug-resistant Klebsiella pneumoniae isolates during nosocomial outbreaks in Shanghai, PR China. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Introduction. The soaring resistance of
Klebsiella pneumoniae
to fluoroquinolones in PR China has substantially limited the application of these antimicrobials, especially in those clinical settings that were threatened by persistent carbapenem-resistant
K. pneumoniae
(CRKP), necessitating strict implementation of antimicrobial stewardship and active enhanced surveillance of infection control.
Hypothesis. There is interplay between plasmid-mediated quinolone resistance (PMQR) determinants and quinolone resistance-determining region (QRDR) mutations during the acquisition of a clinically important fluoroquinolone resistance (CI-FR) profile in multidrug-resistant
K. pneumoniae
(MDR-KP) isolates.
Aim. To investigate the high-risk CRKP clones responsible for nosocomial spread and analyse the molecular patterns of CI-FR in MDR-KP isolates in a tertiary hospital in Shanghai, PR China.
Methodology. A total of 34 isolates, including 30 CRKPs, were molecularly characterized. Investigations included antimicrobial susceptibility tests, multilocus sequence typing (MLST) and wzi genotyping, PCR sequencing and phylogenetic analysis for resistance-associated genes, and clinical information retrieval from medical records.
Results. Two high-risk CRKP clones, ST11-wzi64 and ST15-wzi19/wzi24, were identified as being responsible for nosocomial outbreaks in the intensive care unit (ICU) and the neurosurgery department, potentially by the respiratory route. QRDR mutations of both gyrA and parC were detected in isolates of ST15 (S83F/D87A/S80I), ST11 (S83I/D87G/S80I) and ST218 (D87A/S80I), respectively. The PMQR genes, qnrS1, aac(6′)-Ib-cr and oqxAB, were present in 32 (94.1 %) of the isolates alone or in combination, co-occurring with genes (bla) encoding β-lactamases, 16S rRNA methylases and putrescine ABC permeases. AcrR, an AcrAB transcriptional repressor, was insertion-inactivated by the IS5-like element in ST11 isolates. The encoding sequences of OmpK35 and OmpK36 genes were associated with specific STs and wzi alleles. ST11, ST15-wzi19 and ST218 isolates had frameshift disruptions in OmpK35 and specific GD insertions at position 134–135 in OmpK36. The 27 isolates with clinically important ciprofloxacin resistance (MICs ≥2 mg l−1) included 25 isolates (ST15, ST11, ST218) with multiple QRDR mutations, plus 1 with only 2 PMQR determinants (ST290-wzi21) and another with an unknown resistance mechanism (ST65-wzi72). Ciprofloxacin-susceptible isolates maintained intact ompK36 genes, including two CRKPs each with ST13-wzi74 (KPC-2 and NDM-1 coproducers) and ST65-wzi72, plus carbapenem-susceptible isolates (ST15-wzi24, ST65-wzi72, ST107-wzi173).
Conclusions. Under selective pressures, the accumulation of mutations of three types (QRDR, acrR, ompK36) and the acquisition of resistance-conferring genes have continuously contributed to CI-FR in MDR-KP isolates.
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8
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Yuan Y, Wang D, Cai H, Li D, Xu X, Guo Q, He T, Wang M. High-level ertapenem resistance in Klebsiella pneumoniae is due to RamA downregulation of ompK35 through micF. Int J Antimicrob Agents 2022; 60:106653. [PMID: 35952849 DOI: 10.1016/j.ijantimicag.2022.106653] [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: 12/08/2021] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
Abstract
An ertapenem-resistant Klebsiella pneumoniae clinical isolate (KP20) without carbapenemase and negative for the efflux pump inhibition test was resistant to ertapenem at a high level [minimum inhibitory concentration (MIC) = 64 mg/L] but susceptible to meropenem and imipenem. Second-generation sequencing was performed and a termination mutation was found in ramR. Complementation of ramR in KP20 reduced the ertapenem MIC by 128 times (from 64 mg/L to 0.5 mg/L). Overexpression of ramA and loss of OmpK35 were discovered in strain KP20 by quantitative reverse transcription PCR (RT-qPCR) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), respectively. Furthermore, ramA deletion in strain KP20 resulted in a 128-fold decrease in the MIC of ertapenem (from 64 mg/L to 0.5 mg/L), and expression of OmpK35 was observed in KP20ΔramA by SDS-PAGE. Complementation of ramA in KP20ΔramA led to a 45.45-fold downregulation of ompK35. Complementation of ompK35 in KP20 could restore susceptibility to ertapenem (MIC reduced from 64 mg/L to 0.25 mg/L). Furthermore, results of the electrophoretic mobility shift assay showed that RamA could bind to the promoter of micF. These results showed that the termination mutation in ramR resulted in overexpression of ramA causing loss of OmpK35 expression through upregulation of micF, revealing the mechanism of ertapenem resistance only in K. pneumoniae.
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Affiliation(s)
- Yuan Yuan
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou 730000, Gansu Province, China
| | - Dongliang Wang
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou 730000, Gansu Province, China
| | - Hui Cai
- Department of General Surgery, Gansu Provincial Hospital, Lanzhou 730000, Gansu Province, China
| | - Dan Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Tianpeng He
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou 730000, Gansu Province, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China.
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9
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David S, Wong JLC, Sanchez-Garrido J, Kwong HS, Low WW, Morecchiato F, Giani T, Rossolini GM, Brett SJ, Clements A, Beis K, Aanensen DM, Frankel G. Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae. PLoS Pathog 2022; 18:e1010334. [PMID: 35816554 PMCID: PMC9302836 DOI: 10.1371/journal.ppat.1010334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/21/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies.
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Affiliation(s)
- Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Joshua L C Wong
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Hok-Sau Kwong
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, United Kingdom
- Department of Life Sciences, Imperial College London; London, United Kingdom
| | - Wen Wen Low
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Fabio Morecchiato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Stephen J Brett
- Department of Surgery and Cancer, Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London, London, United Kingdom
| | - Abigail Clements
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Konstantinos Beis
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, United Kingdom
- Department of Life Sciences, Imperial College London; London, United Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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10
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Bonardi S, Cabassi CS, Manfreda G, Parisi A, Fiaccadori E, Sabatino A, Cavirani S, Bacci C, Rega M, Spadini C, Iannarelli M, Crippa C, Ruocco F, Pasquali F. Survey on Carbapenem-Resistant Bacteria in Pigs at Slaughter and Comparison with Human Clinical Isolates in Italy. Antibiotics (Basel) 2022; 11:777. [PMID: 35740183 PMCID: PMC9219774 DOI: 10.3390/antibiotics11060777] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022] Open
Abstract
This study is focused on resistance to carbapenems and third-generation cephalosporins in Gram-negative microorganisms isolated from swine, whose transmission to humans via pork consumption cannot be excluded. In addition, the common carriage of carbapenem-resistant (CR) bacteria between humans and pigs was evaluated. Sampling involved 300 faecal samples collected from slaughtered pigs and 300 urine samples collected from 187 hospitalised patients in Parma Province (Italy). In swine, MIC testing confirmed resistance to meropenem for isolates of Pseudomonas aeruginosa and Pseudomonas oryzihabitans and resistance to cefotaxime and ceftazidime for Escherichia coli, Ewingella americana, Enterobacter agglomerans, and Citrobacter freundii. For Acinetobacter lwoffii, Aeromonas hydrofila, Burkolderia cepacia, Corynebacterium indologenes, Flavobacterium odoratum, and Stenotrophomonas maltophilia, no EUCAST MIC breakpoints were available. However, ESBL genes (blaCTXM-1, blaCTX-M-2, blaTEM-1, and blaSHV) and AmpC genes (blaCIT, blaACC, and blaEBC) were found in 38 and 16 isolates, respectively. P. aeruginosa was the only CR species shared by pigs (4/300 pigs; 1.3%) and patients (2/187; 1.1%). P. aeruginosa ST938 carrying blaPAO and blaOXA396 was detected in one pig as well as an 83-year-old patient. Although no direct epidemiological link was demonstrable, SNP calling and cgMLST showed a genetic relationship of the isolates (86 SNPs and 661 allele difference), thus suggesting possible circulation of CR bacteria between swine and humans.
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Affiliation(s)
- Silvia Bonardi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Clotilde Silvia Cabassi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Gerardo Manfreda
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, 40064 Ozzano dell’Emilia, Italy; (G.M.); (C.C.); (F.P.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 70017 Putignano, Italy;
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University-Hospital, Department of Medicine and Surgery, Parma University, 43126 Parma, Italy; (E.F.); (A.S.)
| | - Alice Sabatino
- Nephrology Unit, Parma University-Hospital, Department of Medicine and Surgery, Parma University, 43126 Parma, Italy; (E.F.); (A.S.)
| | - Sandro Cavirani
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Cristina Bacci
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Martina Rega
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Costanza Spadini
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Mattia Iannarelli
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Cecilia Crippa
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, 40064 Ozzano dell’Emilia, Italy; (G.M.); (C.C.); (F.P.)
| | | | - Frédérique Pasquali
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, 40064 Ozzano dell’Emilia, Italy; (G.M.); (C.C.); (F.P.)
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11
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Cheng Y, Chen M, Zhang B, Lin H, Li X, Cai Y, Zhang H, Que W, Liu M, Qiu H. Rapid, simple, and economical LC-MS/MS method for simultaneous determination of ceftazidime and avibactam in human plasma and its application in therapeutic drug monitoring. J Clin Pharm Ther 2022; 47:1426-1437. [PMID: 35633089 DOI: 10.1111/jcpt.13693] [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: 02/20/2022] [Revised: 04/11/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Carbapenem-resistant Gram-negative bacterial pathogens continue to threaten public health. Avibactam (AVI), a novel non-β-lactam β-lactamase inhibitor, has been approved for use with ceftazidime (CAZ) mainly against carbapenem-resistant Enterobacteriaceae. Therapeutic drug monitoring (TDM) is urgently needed to optimize dosage regimens to maximize efficacy, minimize toxicity, and delay the emergence of resistance. This study aims to develop and validate a rapid, simple, and economical LC-MS/MS method for simultaneous determination of CAZ/AVI in human plasma. METHODS Samples were processed by simple protein precipitation, and gradient elution strategy was applied to separate CAZ and AVI on a reverse-phase C18 column; with subsequent detection by the mass spectrometer in a positive and negative ion switching mode. Plasma samples from patients were analysed. RESULTS AND DISCUSSION A 4-min run of LC-MS/MS was developed. The precision, trueness, matrix effect, extraction recovery, carry-over, dilution integrity, and stability were all acceptable for a bioanalytical method. The method was successfully applied to the determination of CAZ and AVI in patients, and a considerable PK variability of CAZ/AVI was observed among patients. WHAT IS NEW AND CONCLUSION A robust, rapid, simple, and economical LC-MS/MS method for the simultaneous determination of CAZ and AVI was developed. The considerable PK variability of CAZ/AVI among patients demonstrates the clinical significance of TDM.
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Affiliation(s)
- Yu Cheng
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China.,College of Pharmacy, Fujian Medical University, Fuzhou, People's Republic of China.,Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Maohua Chen
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China
| | - Bingqing Zhang
- College of Pharmacy, Fujian Medical University, Fuzhou, People's Republic of China
| | - Hailin Lin
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China
| | - Xueyong Li
- College of Pharmacy, Fujian Medical University, Fuzhou, People's Republic of China
| | - Yipeng Cai
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China
| | - Hui Zhang
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China
| | - Wancai Que
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China
| | - Maobai Liu
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China
| | - Hongqiang Qiu
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, People's Republic of China.,College of Pharmacy, Fujian Medical University, Fuzhou, People's Republic of China
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12
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In-Human Multiyear Evolution of Carbapenem-Resistant Klebsiella pneumoniae Causing Chronic Colonization and Intermittent Urinary Tract Infections: A Case Study. mSphere 2022; 7:e0019022. [PMID: 35531657 PMCID: PMC9241548 DOI: 10.1128/msphere.00190-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a frequent pathogen of the urinary tract, but how CRKP adapts in vivo over time is unclear. We examined 10 CRKP strains from a patient who experienced chronic colonization and recurrent urinary tract infections over a period of 4.5 years. We performed whole-genome sequencing and phenotypic assays to compare isolates that had evolved relative to the first isolate collected and to correlate genetic and phenotypic changes over time with the meropenem-containing regimen received. Phylogenetic analysis indicated that all 10 strains originated from the same sequence type 258 (ST258) clone and that three sublineages (SL) evolved over time; strains from two dominant sublineages were selected for detailed analysis. Up to 60 new mutations were acquired progressively in genes related to antibiotic resistance, cell metabolism, and biofilm production over time. Doubling of meropenem MICs, increases in biofilm production and blaKPC expression, and altered carbon metabolism occurred in the latter strains from the last sublineage compared to the initial strain. Subinhibitory meropenem exposure in vitro significantly induced or maintained high levels of biofilm production in colonizing isolates, but isolates causing infection were unaffected. Despite acquiring different mutations that affect carbon metabolism, overall carbon utilization was maintained across different strains. Together, these data showed that isolated urinary CRKP evolved through multiple adaptations affecting carbon metabolism, carbapenem resistance, and biofilm production to support chronic colonization and intermittent urinary tract infections. Our findings highlight the pliability of CRKP in adapting to repeated antibiotic exposure and should be considered when developing novel therapeutic and stewardship strategies. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) can cause a variety of infections such as recurrent urinary tract infections (rUTI) with the ability to change with the host environment over time. However, it is unclear how CRKP adapts to the urinary tract during chronic infections and colonization. Here, we studied the evolution of CRKP strains from a patient who experienced chronic colonization and recurrent UTIs over a period of 4.5 years despite multiple treatment courses with meropenem-containing regimens. Our findings show the flexibility of CRKP strains in developing changes in carbapenem resistance, biofilm production, and carbon metabolism over time, which could facilitate their persistence in the human body for long periods of time in spite of repeated antibiotic therapy.
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13
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Extensively Drug-Resistant Klebsiella pneumoniae Counteracts Fitness and Virulence Costs That Accompanied Ceftazidime-Avibactam Resistance Acquisition. Microbiol Spectr 2022; 10:e0014822. [PMID: 35435751 PMCID: PMC9241641 DOI: 10.1128/spectrum.00148-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ability of extensively drug-resistant (XDR) Klebsiella pneumoniae to rapidly acquire resistance to novel antibiotics is a global concern. Moreover, Klebsiella clonal lineages that successfully combine resistance and hypervirulence have increasingly occurred during the last years. However, the underlying mechanisms of counteracting fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we investigated whether and how an XDR sequence type (ST)307 K. pneumoniae strain developed resistance against the novel drug combination ceftazidime-avibactam (CAZ-AVI) using experimental evolution. In addition, we performed in vitro and in vivo assays, molecular modeling, and bioinformatics to identify resistance-conferring processes and explore the resulting decrease in fitness and virulence. The subsequent amelioration of the initial costs was also addressed. We demonstrate that distinct mutations of the major nonselective porin OmpK36 caused CAZ-AVI resistance that persists even upon following a second experimental evolution without antibiotic selection pressure and that the Klebsiella strain compensates the resulting fitness and virulence costs. Furthermore, the genomic and transcriptomic analyses suggest the envelope stress response regulator rpoE and associated RpoE-regulated genes as drivers of this compensation. This study verifies the crucial role of OmpK36 in CAZ-AVI resistance and shows the rapid adaptation of a bacterial pathogen to compensate fitness- and virulence-associated resistance costs, which possibly contributes to the emergence of successful clonal lineages. IMPORTANCE Extensively drug-resistant Klebsiella pneumoniae causing major outbreaks and severe infections has become a significant challenge for health care systems worldwide. Rapid resistance development against last-resort therapeutics like ceftazidime-avibactam is a significant driver for the accelerated emergence of such pathogens. Therefore, it is crucial to understand what exactly mediates rapid resistance acquisition and how bacterial pathogens counteract accompanying fitness and virulence costs. By combining bioinformatics with in vitro and in vivo phenotypic approaches, this study revealed the critical role of mutations in a particular porin channel in ceftazidime-avibactam resistance development and a major metabolic regulator for ameliorating fitness and virulence costs. These results highlight underlying mechanisms and contribute to the understanding of factors important for the emergence of successful bacterial pathogens.
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14
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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: 1] [Impact Index Per Article: 0.5] [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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15
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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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16
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Stepwise Evolution of a Klebsiella pneumoniae Clone within a Host Leading to Increased Multidrug Resistance. mSphere 2021; 6:e0073421. [PMID: 34817239 PMCID: PMC8612250 DOI: 10.1128/msphere.00734-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five blaCTX-M-14-positive Klebsiella pneumoniae isolates (KpWEA1, KpWEA2, KpWEA3, KpWEA4-1, and KpWEA4-2) were consecutively obtained from a patient with relapsed acute myeloid leukemia who was continuously administered antimicrobials. Compared with KpWEA1 and KpWEA2, KpWEA3 showed decreased susceptibility to antimicrobials, and KpWEA4-1 and KpWEA4-2 (isolated from a single specimen) showed further-elevated multidrug-resistance (MDR) phenotypes. This study aims to clarify the clonality of the five isolates and their evolutionary processes leading to MDR by comparison of these complete genomes. The genome comparison revealed KpWEA1 was the antecedent of the other four isolates, and KpWEA4-1 and KpWEA4-2 independently emerged from KpWEA3. Increasing levels of MDR were acquired by gradual accumulation of genetic alterations related to outer membrane protein expression: the loss of OmpK35 and upregulation of AcrAB-TolC occurred in KpWEA3 due to ramA overexpression caused by a mutation in ramR; then OmpK36 was lost in KpWEA4-1 and KpWEA4-2 by different mechanisms. KpWEA4-2 further acquired colistin resistance by the deletion of mgrB. In addition, we found that exuR and kdgR, which encode repressors of hexuronate metabolism-related genes, were disrupted in different ways in KpWEA4-1 and KpWEA4-2. The two isolates also possessed different amino acid substitutions in AtpG, which occurred at very close positions. These genetic alterations related to metabolisms may compensate for the deleterious effects of major porin loss. Thus, our present study reveals the evolutionary process of a K. pneumoniae clone leading to MDR and also suggests specific survival strategies in the bacteria that acquired MDR by the genome evolution. IMPORTANCE Within-host evolution is a survival strategy that can occur in many pathogens and is often associated with the emergence of novel antimicrobial-resistant (AMR) bacteria. To analyze this process, suitable sets of clinical isolates are required. Here, we analyzed five Klebsiella pneumoniae isolates which were consecutively isolated from a patient and showed a gradual increase in the AMR level. By genome sequencing and other analyses, we show that the first isolate was the antecedent of the later isolates and that they gained increased levels of antimicrobial resistance leading to multidrug resistance (MDR) by stepwise changes in the expression of outer membrane proteins. The isolates showing higher levels of MDR lost major porins but still colonized the patient’s gut, suggesting that the deleterious effects of porin loss were compensated for by the mutations in hexuronate metabolism-related genes and atpG, which were commonly detected in the MDR isolates.
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17
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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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18
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Genomic Features Associated with the Degree of Phenotypic Resistance to Carbapenems in Carbapenem-Resistant Klebsiella pneumoniae. mSystems 2021; 6:e0019421. [PMID: 34519526 PMCID: PMC8547452 DOI: 10.1128/msystems.00194-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae strains cause severe infections that are difficult to treat. The production of carbapenemases such as the K. pneumoniae carbapenemase (KPC) is a common mechanism by which these strains resist killing by the carbapenems. However, the degree of phenotypic carbapenem resistance (MIC) may differ markedly between isolates with similar carbapenemase genes, suggesting that our understanding of the underlying mechanisms of carbapenem resistance remains incomplete. To address this problem, we determined the whole-genome sequences of 166 K. pneumoniae clinical isolates resistant to meropenem, imipenem, or ertapenem. Multiple linear regression analysis of this collection of largely blaKPC-3-containing sequence type 258 (ST258) isolates indicated that blaKPC copy number and some outer membrane porin gene mutations were associated with higher MICs to carbapenems. A trend toward higher MICs was also observed with those blaKPC genes carried by the d isoform of Tn4401. In contrast, ompK37 mutations were associated with lower carbapenem MICs, and extended spectrum β-lactamase genes were not associated with higher or lower MICs in carbapenem-resistant K. pneumoniae. A machine learning approach based on the whole-genome sequences of these isolates did not result in a substantial improvement in prediction of isolates with high or low MICs. These results build upon previous findings suggesting that multiple factors influence the overall carbapenem resistance levels in carbapenem-resistant K. pneumoniae isolates. IMPORTANCEKlebsiella pneumoniae can cause severe infections in the blood, urinary tract, and lungs. Resistance to carbapenems in K. pneumoniae is an urgent public health threat, since it can make these isolates difficult to treat. While individual contributors to carbapenem resistance in K. pneumoniae have been studied, few reports explore their combined effects in clinical isolates. We sequenced 166 clinical carbapenem-resistant K. pneumoniae isolates to evaluate the contribution of known genes to carbapenem MICs and to try to identify novel genes associated with higher carbapenem MICs. The blaKPC copy number and some outer membrane porin gene mutations were associated with higher carbapenem MICs. In contrast, mutations in one specific porin, ompK37, were associated with lower carbapenem MICs. Machine learning did not result in a substantial improvement in the prediction of carbapenem resistance nor did it identify novel genes associated with carbapenem resistance. These findings enhance our understanding of the many contributors to carbapenem resistance in K. pneumoniae.
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Matovina M, Abram M, Repac-Antić D, Knežević S, Bubonja-Šonje M. An outbreak of ertapenem-resistant, carbapenemase-negative and porin-deficient ESBL-producing Klebsiella pneumoniae complex. Germs 2021; 11:199-210. [PMID: 34422692 DOI: 10.18683/germs.2021.1257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 11/08/2022]
Abstract
Introduction Carbapenem-resistant Klebsiella pneumoniae is an emerging healthcare-associated pathogen with dynamic molecular epidemiology. This study presents a retrospective analysis of the distribution and antibiotic resistance patterns of ertapenem-resistant ESBL-producing K. pneumoniae strains recovered during an outbreak from 2012 to 2014 in a Croatian University hospital. Methods We aimed to estimate genetic relatedness of clinical isolates and underlying mechanisms that conferred the ertapenem-resistant phenotype. Results Expression analysis of genes involved in the antibiotic resistance showed reduced expression of major non-selective porin channel OmpK35. Reduced expression of OmpK36 porin channel in isolates resistant to at least one more carbapenem, apart from the ertapenem, was found to a lesser degree. Pulsed-field gel electrophoresis analysis of genomic DNA revealed that almost all isolates belonged to the same genetic clone. Conclusions Caution regarding ertapenem-resistant, carbapenemase-negative porin-deficient mutants of K. pneumoniae is required as they are widespread, and under selective pressure this could result in a local clonal outbreak.
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Affiliation(s)
- Mihaela Matovina
- PhD, Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Maja Abram
- MD, PhD, Department of Microbiology, Faculty of Medicine, University of Rijeka, Braće Branchetta 20, 51 000 Rijeka, Croatia and Department of Clinical Microbiology, Clinical Hospital Center Rijeka, Krešimirova 40, 51 000 Rijeka, Croatia
| | - Davorka Repac-Antić
- MD, Department of Microbiology, Faculty of Medicine, University of Rijeka, Braće Branchetta 20, 51 000 Rijeka, Croatia and Department of Clinical Microbiology, Clinical Hospital Center Rijeka, Krešimirova 40, 51 000 Rijeka, Croatia
| | - Samira Knežević
- MD, Department of Infectology, Clinical Hospital Center Rijeka, Krešimirova 40, 51 000 Rijeka, Croatia
| | - Marina Bubonja-Šonje
- MD, PhD, Department of Microbiology, Faculty of Medicine, University of Rijeka, Braće Branchetta 20, 51 000 Rijeka, Croatia and Department of Clinical Microbiology, Clinical Hospital Center Rijeka, Krešimirova 40, 51 000 Rijeka, Croatia
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Serek P, Lewandowski Ł, Dudek B, Pietkiewicz J, Jermakow K, Kapczyńska K, Krzyżewska E, Bednarz-Misa I. Klebsiella pneumoniae enolase-like membrane protein interacts with human plasminogen. Int J Med Microbiol 2021; 311:151518. [PMID: 34237624 DOI: 10.1016/j.ijmm.2021.151518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/14/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022] Open
Abstract
Many models assessing the risk of sepsis utilize the knowledge of the constituents of the plasminogen system, as it is proven that some species of bacteria can activate plasminogen, as a result of interactions with bacterial outer membrane proteins. However, much is yet to be discovered about this interaction since there is little information regarding some bacterial species. This study is aimed to check if Klebsiella pneumoniae, one of the major factors of nosocomial pneumonia and a factor for severe sepsis, has the ability to bind to human plasminogen. The strain used in this study, PCM 2713, acted as a typical representative of the species. With use of various methods, including: electron microscopy, 2-dimensional electrophoresis, immunoblotting and peptide fragmentation fingerprinting, it is shown that Klebsiella pneumoniae binds to human plasminogen, among others, due to plasminogen-bacterial enolase-like protein interaction, occurring on the outer membrane of the bacterium. Moreover, the study reveals, that other proteins, such as: phosphoglucomutase, and phosphoenolpyruvate carboxykinase act as putative plasminogen-binding factors. These information may virtually act as a foundation for future studies investigating: the: pathogenicity of Klebsiella pneumoniae and means for prevention from the outcomes of Klebsiella-derived sepsis.
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Affiliation(s)
- Paweł Serek
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland
| | - Łukasz Lewandowski
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland
| | - Bartłomiej Dudek
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63-77, 51-148, Wroclaw, Poland
| | - Jadwiga Pietkiewicz
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland
| | - Katarzyna Jermakow
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, Chałubińskiego 4, 50-368, Wrocław, Poland
| | - Katarzyna Kapczyńska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Eva Krzyżewska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Iwona Bednarz-Misa
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland.
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21
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Indrajith S, Mukhopadhyay AK, Chowdhury G, Farraj DAA, Alkufeidy RM, Natesan S, Meghanathan V, Gopal S, Muthupandian S. Molecular insights of Carbapenem resistance Klebsiella pneumoniae isolates with focus on multidrug resistance from clinical samples. J Infect Public Health 2020; 14:131-138. [PMID: 33234410 DOI: 10.1016/j.jiph.2020.09.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/19/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Carbapenem are the last-line antibiotic, defence against Gram-negative extended spectrum ß-lactamases producers (ESBLs). Carbapenem resistance Enterobacteriaceae especially Carbapenem resistant-Klebsiella pneumoniae (CR-KP) is recognized as one of the well-known public health problem, which is increasingly being reported around the world. The present study was focused to analyse the prevalence and characterization of antibiotic resistance K. pneumoniae in centre region of Tamil Nadu, India. METHODOLOGY Totally 145 suspected K. pneumoniae isolates [Urine, Pus, Sputum, Blood and Biopsy] obtained from hospitals of Central South India. The isolates were subjected to biochemical and molecular identification technique, following with antibiotic resistance pattern by standard antibiotic sensitivity test. Multidrug resistance (MDR) with β-lactamase producing Carbapenem resistant K. pneumoniae (CR-KP) strains were screened by classical sensitivity method and also drug resistance encoded gene. Also, molecular typing of the MDR strains were characterized by Pulsed-Field Gel Electrophoresis (PFGE). Further, the outer membrane protein (OmpK35 and 36) related Carbapenem resistance were characterized. RESULTS Totally, 61% of isolates were confirmed as K. pneumoniae, 75 % of isolates were MDR including 58% carbapenem and 97% ESBL antibiotics and grouped into 17 distinct resistant patterns. The MDR KP isolates shows positive for blaCTXM-1 (92 %) gene followed by blaSHV (43 %), blaTEM (36 %), blaNDM-1 (26 %), blaGES (20 %) and blaIMP-1 (8 %). Moreover, 62 % CR-KP isolates loses OmpK36 and 33% isolates loses OmpK35. CONCLUSIONS Loss of OmpK36 were highly an influence the cefoxitin and carbapenem resistance. Sixteen different PFGE patterns have been observed among the 18 MDR isolates. Eventually, ESBL as well as CR-KP were diverse in genetic makeup and often associated with hyper virulence hvKP should be of serious concern.
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Affiliation(s)
- Sureka Indrajith
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Asish Kumar Mukhopadhyay
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Goutam Chowdhury
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Dunia A Al Farraj
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia
| | - Roua M Alkufeidy
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia
| | - Sivakumar Natesan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
| | - Velmurugan Meghanathan
- Department of Cellular and Molecular Biology Lab, University of Texas Health Science Center at Tyler, United States
| | - Selvakumar Gopal
- Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu 630003, India
| | - Saravanan Muthupandian
- Department of Microbiology and Immunology, Division of Biomedical Science, School of Medicine, College of Health Science, Mekelle University, PO. Box: 1871, Mekelle, Ethiopia
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22
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Reduced Susceptibility to Carbapenems in a Klebsiella pneumoniae Clinical Isolate Producing SCO-1 and CTX-M-15 β-Lactamases Together with OmpK35 and OmpK36 Porin Deficiency. Antimicrob Agents Chemother 2020; 64:AAC.00556-20. [PMID: 32423955 PMCID: PMC7526818 DOI: 10.1128/aac.00556-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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23
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Zhang H, Zhang J, Kang Y, Yang Q, Xu Y. Analysis of Susceptibilities of Carbapenem Resistant Enterobacterales to Colistin in Intra-Abdominal, Respiratory and Urinary Tract Infections from 2015 to 2017. Infect Drug Resist 2020; 13:1937-1948. [PMID: 32606842 PMCID: PMC7320917 DOI: 10.2147/idr.s250384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/28/2020] [Indexed: 12/30/2022] Open
Abstract
Purpose To evaluate the susceptibility rates of carbapenem-resistant (CR)-Enterobacterales strains from Chinese intra-abdominal infections (IAI), respiratory tract infections (RTI) and urinary tract infections (UTI) between 2015 and 2017 to colistin. Methods In total, 7138 Enterobacterales including 1074 CR-Enterobacterales strains were isolated from IAI+UTI+RTI samples and collected in 21 hospitals across 7 regions of China. Antimicrobial susceptibilities were determined at a central laboratory using CLSI broth microdilution and interpretive standards. Results From 2015 to 2017, E. coli (51.4%) and K. pneumoniae (30.0%) accounted for the majority of Enterobacterales isolated from IAIs, UTIs and RTIs. The percentage of CR strains within the species was highest for S. marcescens (27.9%), followed by K. pneumoniae (24.8%), P. mirabilis (22.6), K. oxytoca (19.5%), E. cloacae (17.7%), C. freundii (12.5%), K. aerogenes (11.0%) and lowest for E. coli (6.9%). Colistin susceptibilities were generally higher in CS than in CR isolates and were 83.5% for CR-E. coli, 88.6% for CR-K. pneumoniae, 79.2% for CR-E. cloacae and 87.5% for CR-K. aerogenes. For IAI and UTI isolates in particular, CR-E. coli and CR-K. pneumoniae showed a trend of decreasing susceptibility, which was especially noted for CR-E. coli in UTI isolates, and for both organisms in IAI isolates susceptibility dropped markedly in 2017. Conclusion Colistin was a last resort antibiotics for empirical CR-Enterobacterales treatments, since especially the percentage of CR-K. pneumoniae was 30.0% of all IAI, UTI and RTI isolates, with an incidence of 24.8% CR strains, of which 88.6% were susceptible to colistin. Also other analyzed CR-Enterobacterales showed colistin susceptibilities of ≥80.0%. However, resistance rates of IAI derived CR-K. pneumoniae and CR-E. coli, and CR-K. pneumoniae UTI isolates to colistin increased between 2015 and 2017, which should further be closely monitored.
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Affiliation(s)
- Hui Zhang
- Division of Microbiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Jingjia Zhang
- Division of Microbiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Yue Kang
- MRL Global Medical Affairs, MSD China, Shanghai, People's Republic of China
| | - Qiwen Yang
- Division of Microbiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Yingchun Xu
- Division of Microbiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, People's Republic of China
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Venditti C, Nisii C, Ballardini M, Meledandri M, Di Caro A. Identification of L169P mutation in the omega loop of KPC-3 after a short course of ceftazidime/avibactam. J Antimicrob Chemother 2020; 74:2466-2467. [PMID: 31086956 PMCID: PMC6640308 DOI: 10.1093/jac/dkz201] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Carolina Venditti
- 'L. Spallanzani' National Institute for Infectious Diseases, Rome, Italy
| | - Carla Nisii
- 'L. Spallanzani' National Institute for Infectious Diseases, Rome, Italy
| | - Milva Ballardini
- U.O.C. of Microbiology and Virology, San Filippo Neri Hospital, Rome, Italy
| | | | - Antonino Di Caro
- 'L. Spallanzani' National Institute for Infectious Diseases, Rome, Italy
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Ceftazidime-Avibactam Resistance Associated with Increased bla KPC-3 Gene Copy Number Mediated by pKpQIL Plasmid Derivatives in Sequence Type 258 Klebsiella pneumoniae. Antimicrob Agents Chemother 2020; 64:AAC.01816-19. [PMID: 31964792 DOI: 10.1128/aac.01816-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/12/2020] [Indexed: 12/11/2022] Open
Abstract
This study reports on the characterization of two ceftazidime-avibactam (CZA)-resistant KPC-producing Klebsiella pneumoniae strains (KP-14159 and KP-8788) sequentially isolated from infections occurred in a patient never treated with CZA. Whole-genome sequencing characterization using a combined short- and long-read sequencing approach showed that both isolates belonged to the same ST258 strain, had altered outer membrane porins (a truncated OmpK35 and an Asp137Thr138 duplication in the L3 loop of OmpK36), and carried novel pKpQIL plasmid derivatives (pIT-14159 and pIT-8788, respectively) harboring two copies of the Tn4401a KPC-3-encoding transposon. Plasmid pIT-8788 was a cointegrate of pIT-14159 with a ColE replicon (that was also present in KP-14159) apparently evolved in vivo during infection. pIT-8788 was maintained at a higher copy number than pIT-14159 and, upon transfer to Escherichia coli DH10B, was able to increase the CZA MIC by 32-fold. The present findings provide novel insights about the mechanisms of acquired resistance to CZA, underscoring the role that the evolution of broadly disseminated pKpQIL plasmid derivatives may have in increasing the bla KPC gene copy number and KPC-3 expression in bacterial hosts. Although not self-transferable, similar elements, with multiple copies of Tn4401 and maintained at a high copy number, could mediate transferable CZA resistance upon mobilization.
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26
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Moubareck CA, Hammoudi Halat D, Sartawi M, Lawlor K, Sarkis DK, Alatoom A. Assessment of the performance of CHROMagar KPC and Xpert Carba-R assay for the detection of carbapenem-resistant bacteria in rectal swabs: First comparative study from Abu Dhabi, United Arab Emirates. J Glob Antimicrob Resist 2020; 20:147-152. [DOI: 10.1016/j.jgar.2019.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/07/2019] [Accepted: 07/17/2019] [Indexed: 11/30/2022] Open
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Abstract
β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics. Critical β-lactamases are those enzymes whose genes are encoded on mobile elements that are transferable among species. Major β-lactamase families include plasmid-mediated extended-spectrum β-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases now appearing globally, with geographic preferences for specific variants. CTX-M enzymes include the most common ESBLs that are prevalent in all areas of the world. In contrast, KPC serine carbapenemases are present more frequently in the Americas, the Mediterranean countries, and China, whereas NDM metallo-β-lactamases are more prevalent in the Indian subcontinent and Eastern Europe. As selective pressure from β-lactam use continues, multiple β-lactamases per organism are increasingly common, including pathogens carrying three different carbapenemase genes. These organisms may be spread throughout health care facilities as well as in the community, warranting close attention to increased infection control measures and stewardship of the β-lactam-containing drugs in an effort to control selection of even more deleterious pathogens.
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28
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Pinet E, Franceschi C, Collin V, Davin-Regli A, Zambardi G, Pagès JM. A simple phenotypic test for detecting the contribution of outer membrane permeability to carbapenem resistance. J Med Microbiol 2020; 69:63-71. [PMID: 31904320 DOI: 10.1099/jmm.0.001129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Introduction. The worldwide emergence of carbapenem resistance in Gram-negative bacteria makes the development of simple tests mandatory to identify antimicrobial resistance mechanisms. Enzymatic and membrane barriers are the prominent resistance mechanisms described in these bacteria. Several tests are currently used to detect carbapenemase activities.Aim. However, a simple test for the identification of membrane-associated mechanisms of resistance is not yet available and this mechanism is often inferred after the exclusion of a carbapenemase in carbapenem-resistant Gram-negative bacteria.Methodology. Different media (liquid and solid) containing a membrane permeabilizer were tested to identify the existence of a membrane barrier. Here, polymyxin B nonapeptide (PMBN) was selected to bypass the role of impermeability in clinical carbapenem-resistant Enterobacteriaceae, including Escherichia coli, Enterobacter cloacae , Klebsiella pneumoniae and Klebsiella aerogenes isolates. In parallel, the expression of porins (OmpC and OmpF types) was checked in the various bacterial strains in order to search for a correlation between the restoration of susceptibility and the expression of porin.Results. Using a large number of clinical isolates, PMBN associated with a carbapenem allowed us to detect porin-deficient isolates with a sensitivity ranging from 89 to 93 % and a specificity ranging from 86 to 100 %.Conclusion. This paves the way for a diagnostic assay allowing the detection of this membrane-associated mechanism of resistance in Enterobacteriaceae.
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Affiliation(s)
- Elizabeth Pinet
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, SSA, IRBA, MCT, Marseille, France
| | | | - Valérie Collin
- R&D Microbiology Innovation, BIOMÉRIEUX, La Balme les Grottes, France
| | - Anne Davin-Regli
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Gilles Zambardi
- R&D Microbiology Innovation, BIOMÉRIEUX, La Balme les Grottes, France
| | - Jean Marie Pagès
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, SSA, IRBA, MCT, Marseille, France
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OmpK36-mediated Carbapenem resistance attenuates ST258 Klebsiella pneumoniae in vivo. Nat Commun 2019; 10:3957. [PMID: 31477712 PMCID: PMC6718652 DOI: 10.1038/s41467-019-11756-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
Carbapenem-resistance in Klebsiella pneumoniae (KP) sequence type ST258 is mediated by carbapenemases (e.g. KPC-2) and loss or modification of the major non-selective porins OmpK35 and OmpK36. However, the mechanism underpinning OmpK36-mediated resistance and consequences of these changes on pathogenicity remain unknown. By solving the crystal structure of a clinical ST258 OmpK36 variant we provide direct structural evidence of pore constriction, mediated by a di-amino acid (Gly115-Asp116) insertion into loop 3, restricting diffusion of both nutrients (e.g. lactose) and Carbapenems. In the presence of KPC-2 this results in a 16-fold increase in MIC to Meropenem. Additionally, the Gly-Asp insertion impairs bacterial growth in lactose-containing medium and confers a significant in vivo fitness cost in a murine model of ventilator-associated pneumonia. Our data suggests that the continuous selective pressure imposed by widespread Carbapenem utilisation in hospital settings drives the expansion of KP expressing Gly-Asp insertion mutants, despite an associated fitness cost. Carbapenem-resistance in Klebsiella pneumoniae sequence type ST258 can be enhanced by modification of the porins OmpK35 and OmpK36. Here, Wong et al. solve the crystal structure of a clinical ST258 OmpK36 variant, elucidating the mechanism of resistance and consequences on pathogenicity in vivo.
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30
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Bhagirath AY, Li Y, Patidar R, Yerex K, Ma X, Kumar A, Duan K. Two Component Regulatory Systems and Antibiotic Resistance in Gram-Negative Pathogens. Int J Mol Sci 2019; 20:E1781. [PMID: 30974906 PMCID: PMC6480566 DOI: 10.3390/ijms20071781] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/17/2022] Open
Abstract
Gram-negative pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa are the leading cause of nosocomial infections throughout the world. One commonality shared among these pathogens is their ubiquitous presence, robust host-colonization and most importantly, resistance to antibiotics. A significant number of two-component systems (TCSs) exist in these pathogens, which are involved in regulation of gene expression in response to environmental signals such as antibiotic exposure. While the development of antimicrobial resistance is a complex phenomenon, it has been shown that TCSs are involved in sensing antibiotics and regulating genes associated with antibiotic resistance. In this review, we aim to interpret current knowledge about the signaling mechanisms of TCSs in these three pathogenic bacteria. We further attempt to answer questions about the role of TCSs in antimicrobial resistance. We will also briefly discuss how specific two-component systems present in K. pneumoniae, A. baumannii, and P. aeruginosa may serve as potential therapeutic targets.
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Affiliation(s)
- Anjali Y Bhagirath
- Department of Oral Biology, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada.
| | - Yanqi Li
- Department of Oral Biology, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada.
| | - Rakesh Patidar
- Department of Microbiology, Faculty of Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Katherine Yerex
- Department of Oral Biology, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada.
| | - Xiaoxue Ma
- Department of Oral Biology, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada.
| | - Ayush Kumar
- Department of Microbiology, Faculty of Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Kangmin Duan
- Department of Oral Biology, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada.
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada.
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31
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Fajardo-Lubián A, Ben Zakour NL, Agyekum A, Qi Q, Iredell JR. Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen. PLoS Pathog 2019; 15:e1007218. [PMID: 30875398 PMCID: PMC6436753 DOI: 10.1371/journal.ppat.1007218] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 03/27/2019] [Accepted: 01/16/2019] [Indexed: 12/19/2022] Open
Abstract
As human population density and antibiotic exposure increase, specialised bacterial subtypes have begun to emerge. Arising among species that are common commensals and infrequent pathogens, antibiotic-resistant 'high-risk clones' have evolved to better survive in the modern human. Here, we show that the major matrix porin (OmpK35) of Klebsiella pneumoniae is not required in the mammalian host for colonisation, pathogenesis, nor for antibiotic resistance, and that it is commonly absent in pathogenic isolates. This is found in association with, but apparently independent of, a highly specific change in the co-regulated partner porin, the osmoporin (OmpK36), which provides enhanced antibiotic resistance without significant loss of fitness in the mammalian host. These features are common in well-described 'high-risk clones' of K. pneumoniae, as well as in unrelated members of this species and similar adaptations are found in other members of the Enterobacteriaceae that share this lifestyle. Available sequence data indicate evolutionary convergence, with implications for the spread of lethal antibiotic-resistant pathogens in humans.
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Affiliation(s)
- Alicia Fajardo-Lubián
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
- * E-mail: (AFL); (JRI)
| | - Nouri L. Ben Zakour
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Alex Agyekum
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Qin Qi
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
- * E-mail: (AFL); (JRI)
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32
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Bean DC, Agarwal A, Cherian BP, Wareham DW. Hypermucoviscous polymyxin-resistant Klebsiella pneumoniae from Kolkata, India: Genomic and phenotypic analysis. J Glob Antimicrob Resist 2019; 17:1-2. [PMID: 30825699 DOI: 10.1016/j.jgar.2019.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVES Here we report the draft genome sequence of a colistin-resistant hypermucoviscous Klebsiella pneumoniae isolated from a hospitalised patient with acute kidney injury in Kolkata, India. METHODS Whole genomic DNA was sequenced using an Illumina HiSeq platform. The generated reads were de novo assembled using SPAdes v.3.7.1. Genome annotation was performed using the NCBI Prokaryote Genome Annotation Pipeline (PGAP) v.4.6. The sequence type (ST), capsular type, antimicrobial resistance and virulence-related genes were predicted from the genome sequence. RESULTS Klebsiella pneumoniae KP26 belonged to ST147. The assembly comprised 63 contigs (>1000 bp) with a total read length of 5 560 935 bp and a total of 5399 coding sequences. The isolate was resistant to most β-lactams, aminoglycosides, quinolones, fosfomycin, trimethoprim, sulphonamides and polymyxins. No mcr genes were detected in the genome. CONCLUSION Isolate KP26 is a hypermucoviscous, multidrug-resistant K. pneumoniae strain that may represent an emerging high-risk clone associated with severe infections in India.
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Affiliation(s)
- David C Bean
- School of Health & Life Sciences, Federation University Australia, P.O. Box 663, Ballarat, VIC, Australia
| | - Anuradha Agarwal
- Clinical Microbiology & Hospital Infection Control, Belle Vue Clinic, 9U N Brahmachari Street, Kolkata 17, India
| | | | - David W Wareham
- Division of Infection, Barts Health NHS Trust, London, UK; Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK.
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Abstract
The transport of small molecules across membranes is essential for the import of nutrients and other energy sources into the cell and, for the export of waste and other potentially harmful byproducts out of the cell. While hydrophobic molecules are permeable to membranes, ions and other small polar molecules require transport via specialized membrane transport proteins . The two major classes of membrane transport proteins are transporters and channels. With our focus here on porins-major class of non-specific diffusion channel proteins , we will highlight some recent structural biology reports and functional assays that have substantially contributed to our understanding of the mechanism that mediates uptake of small molecules, including antibiotics, across the outer membrane of Enterobacteriaceae . We will also review advances in the regulation of porin expression and porin biogenesis and discuss these pathways as new therapeutic targets.
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Affiliation(s)
- Muriel Masi
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | | | - Jean-Marie Pagès
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France.
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34
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Laolerd W, Akeda Y, Preeyanon L, Ratthawongjirakul P, Santanirand P. Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae from Bangkok, Thailand, and Their Detection by the Carba NP and Modified Carbapenem Inactivation Method Tests. Microb Drug Resist 2018; 24:1006-1011. [DOI: 10.1089/mdr.2018.0080] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Warawut Laolerd
- Microbiology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Yukihiro Akeda
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Division of Infection Control and Prevention, Osaka University Hospital, Osaka University, Osaka, Japan
- Department of Infection Control and Prevention, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Likit Preeyanon
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Panan Ratthawongjirakul
- Research Group of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Pitak Santanirand
- Microbiology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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