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Bertrans-Tubau L, Martínez-Campos S, Lopez-Doval J, Abril M, Ponsá S, Salvadó V, Hidalgo M, Pico-Tomàs A, Balcazar JL, Proia L. Nature-based bioreactors: Tackling antibiotic resistance in urban wastewater treatment. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 22:100445. [PMID: 39055482 PMCID: PMC11269294 DOI: 10.1016/j.ese.2024.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide (sul1 and sul2) and tetracycline (tet(C), tet(G), and tetR) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges.
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Affiliation(s)
- Lluís Bertrans-Tubau
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Martínez-Campos
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Julio Lopez-Doval
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Meritxell Abril
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Ponsá
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Victoria Salvadó
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Manuela Hidalgo
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Anna Pico-Tomàs
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
| | - Jose Luis Balcazar
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
- University of Girona, 17004, Girona, Spain
| | - Lorenzo Proia
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
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Ding L, Shen S, Chen J, Tian Z, Shi Q, Han R, Guo Y, Hu F. Klebsiella pneumoniae carbapenemase variants: the new threat to global public health. Clin Microbiol Rev 2023; 36:e0000823. [PMID: 37937997 PMCID: PMC10732083 DOI: 10.1128/cmr.00008-23] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/31/2023] [Indexed: 11/09/2023] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC) variants, which refer to the substitution, insertion, or deletion of amino acid sequence compared to wild blaKPC type, have reduced utility of ceftazidime-avibactam (CZA), a pioneer antimicrobial agent in treating carbapenem-resistant Enterobacterales infections. So far, more than 150 blaKPC variants have been reported worldwide, and most of the new variants were discovered in the past 3 years, which calls for public alarm. The KPC variant protein enhances the affinity to ceftazidime and weakens the affinity to avibactam by changing the KPC structure, thereby mediating bacterial resistance to CZA. At present, there are still no guidelines or expert consensus to make recommendations for the diagnosis and treatment of infections caused by KPC variants. In addition, meropenem-vaborbactam, imipenem-relebactam, and other new β-lactam-β-lactamase inhibitor combinations have little discussion on KPC variants. This review aims to discuss the clinical characteristics, risk factors, epidemiological characteristics, antimicrobial susceptibility profiles, methods for detecting blaKPC variants, treatment options, and future perspectives of blaKPC variants worldwide to alert this new great public health threat.
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Affiliation(s)
- Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Jing Chen
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang, China
| | - Zhen Tian
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, Zhejiang, China
| | - Qingyu Shi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Yan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
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Huang X, Shen S, Chang F, Liu X, Yue J, Xie N, Yin L, Hu F, Xiao D. Emergence of KPC-134, a KPC-2 variant associated with ceftazidime-avibactam resistance in a ST11 Klebsiella pneumoniae clinical strain. Microbiol Spectr 2023; 11:e0072523. [PMID: 37772834 PMCID: PMC10580995 DOI: 10.1128/spectrum.00725-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023] Open
Abstract
The emergence of various new Klebsiella pneumoniae carbapenemase (KPC) variants leading to ceftazidime-avibactam treatment failure is a new challenge in current clinical anti-infection treatment. Here, we report a ceftazidime-avibactam-resistant K. pneumoniae 1072-2 clinical strain carrying a novel KPC variant, KPC-134, which differs from KPC-2 by both single mutation (D178A) and 8-amino acid insertions (asp-asp-asn-arg-ala-pro-asn-lys). The results of antimicrobial susceptibility testing showed that the isolate was resistant to meropenem (MIC = 4 mg/L), ceftazidime (MIC ≥ 32 mg/L), cefepime (MIC ≥128 mg/L), aztreonam (MIC ≥128 mg/L), and ceftazidime-avibactam (MIC ≥128 mg/L) but sensitive to imipenem (MIC = 0.5 mg/L), imepenem-relebactam (MIC = 0.5 mg/L), meropenem-vaborbactam (MIC = 2 mg/L), and aztreonam-avibactam (MIC = 4 mg/L). The plasmid containing blaKPC-134 was isolated from K. pneumoniae, and the blaKPC-134 gene was cloned into plasmid pHSG398 and transformed into an Escherichia coli DH5α to observe changes in antimicrobial resistance. The results indicated that the transformant was positive for blaKPC-134 and increased MICs of ceftazidime-avibactam, ceftazidime, cefepime, and aztreonam by 512-fold, 256-fold, 16-fold, and 4-fold, respectively, compared with the recipient. The results of third-generation sequencing showed that the blaKPC-134 gene was carried by a 133,789 bp IncFII-IncR plasmid, and many common resistance genes (including blaCTX-M-65, blaTEM-1B, blaSHV-12, rmtB, and catB4) along with the IS26, tnpR, ISkpn8, ISkpn6-like, and Tn1721 elements were identified. IMPORTANCE The emergence of various new KPC variants leading to ceftazidime-avibactam treatment failure is a new challenge for clinical anti-infection treatment. Here, we describe the characterization of a ceftazidime-avibactam-resistant blaKPC-134-positive Klebsiella pneumoniae clinical strain for the first time. K. pneumoniae bearing with KPC variant often mislead clinical anti-infection treatment because of their unique antimicrobial susceptibility profile and the tendency of conventional carbapenemase assays to give false negative results. Therefore, timely identification of KPC variants and effective anti-infective therapy are key to saving infected patients.
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Affiliation(s)
- Xiangning Huang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Fan Chang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin Liu
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jinxi Yue
- Department of Laboratory Medicine, Affiliated Hospital, North Sichuan Medical College, Nanchong, China
| | - Ning Xie
- Department of Laboratory Medicine, Affiliated Hospital, North Sichuan Medical College, Nanchong, China
| | - Lin Yin
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Daiwen Xiao
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
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Identification of KPC-112 from an ST15 Klebsiella pneumoniae Strain Conferring Resistance to Ceftazidime-Avibactam. mSphere 2022; 7:e0048722. [PMID: 36374086 PMCID: PMC9769832 DOI: 10.1128/msphere.00487-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Ceftazidime-avibactam is an effective antibiotic combination of a β-lactam and a β-lactamase inhibitor against Klebsiella pneumoniae-carbapenemase (KPC)-producing Enterobacterales. Despite a relatively low resistance rate, reports of resistance to ceftazidime-avibactam mainly caused by the mutations in KPC have increased in recent years. Here, we report a ceftazidime-avibactam-resistant and carbapenem-susceptible Klebsiella pneumoniae strain carrying a novel KPC variant, KPC-112, which differs from KPC-2 by 4-amino-acid deletions at Ambler positions 166L/167E and 242G/243T. The isolate was identified as K. pneumoniae by a Vitek mass spectrometer (bioMérieux, France). The MICs of antimicrobial agents were determined using broth microdilution susceptibility method. The result showed that the isolate was resistant to ceftazidime-avibactam (MIC = >128 mg/L) but susceptible to imipenem (MIC = 0.5 mg/L), meropenem (MIC = 1 mg/L), and tigecycline (MIC = 2 mg/L). The carbapenemase genes were confirmed by PCR-based sequencing. Plasmid transformation assay showed that the blaKPC-112-positive transformant increased MICs of ceftazidime-avibactam, ceftazidime, and cefepime by at least 256-fold, 128-fold, and 128-fold, respectively, compared with the recipient Escherichia coli DH5α. According to the whole-genome sequencing analysis, many common resistance genes were identified, including blaKPC-112, blaOXA-1, blaCTX-M-15, blaTEM-1B, blaSHV-28, aac(6')Ib-cr, aac(3)-IId, qnrS1, catA2, catB4, and fosA6, and mutations of GyrA (GyrA-83F and GyrA-87A) and ParC (ParC-80I) were also found. Overall, our study highlights the importance of monitoring susceptibility during ceftazidime-avibactam treatment and accurate detection of KPC variants. IMPORTANCE Carbapenem-resistant Enterobacterales (CRE) are one of the most serious antimicrobial resistance problems in the world, listed as an "urgent" threat by the U.S. Centers for Disease Control and Prevention. Among CRE, K. pneumoniae-carbapenemase-producing Klebsiella pneumoniae (KPC-KP) has become a significant health threat due to its rapid transmissibility and high mortality. With the wider clinical use of ceftazidime-avibactam, reports of resistance have increased in recent years even though the overall resistance rate remains relatively low. Among the reported resistance mechanisms are mainly mutations derived from the blaKPC-2 or blaKPC-3 gene. Here, we describe the characterization of a ceftazidime-avibactam-resistant blaKPC-112-positive K. pneumoniae clinical isolate for the first time. A number of Enterobacteriaceae isolates producing these kinds of KPC variants might be missed by conventional antimicrobial susceptibility testing (AST) methods and lead to irrational drug use. So, this study of KPC-112 will help to establish the diversity of KPCs and remind researchers of the challenge of drug resistance and detection brought by the KPC variants.
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Clinical and Molecular Characterizations of Carbapenem-Resistant Klebsiella pneumoniae Causing Bloodstream Infection in a Chinese Hospital. Microbiol Spectr 2022; 10:e0169022. [PMID: 36190403 PMCID: PMC9603270 DOI: 10.1128/spectrum.01690-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Bloodstream infection (BSI) caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious and urgent threat for hospitalized patients. This study aims to describe the clinical and molecular characteristics of CRKP causing BSI in a tertiary-care hospital in Beijing, China. A total of 146 CRKP strains and 39 carbapenem-susceptible K. pneumoniae (CSKP) strains collected in the hospital from 2017 to 2020 were sent for whole-genome sequencing. Univariate and multivariate analyses were used to evaluate risk factors for in-hospital mortality of CRKP-BSI cases. Thirty (20.5%) of 146 CRKP-BSI patients and three (7.7%) of 39 CSKP-BSI patients died at discharge (χ2 = 3.471, P = 0.062). Multivariate logistic regression analysis indicated that age and use of urinary catheters were independent risk factors for the death of CRKP-BSI. The 146 CRKP isolates belonged to 9 sequence types (STs) and 11 serotypes, while the 39 CSKP isolates belonged to 23 STs and 27 serotypes. The mechanism of carbapenem resistance for all the CRKP strains was the acquisition of carbapenemase, mainly KPC-2 (n = 127). There were 2 predominant serotypes for ST11 CRKP, namely, KL47 (n = 82) and KL64 (n = 42). Some virulent genes, including rmpA2, iucABCD and iutA, and repB gene, which was involved in plasmid replication, were detected in all ST11-KL64 strains. Evolutionary transmission analysis suggested that ST11 CRKP strains might have evolved from KL47 into KL64 and were accompanied by multiple outbreak events. This study poses an urgent need for enhancing infection control measures in the hospital, especially in the intensive care unit where the patients are at high-risk for acquiring CRKP-BSI. IMPORTANCE CRKP-BSI is demonstrated to cause high mortality. In this study, we demonstrated that ST11 CRKP strains might carry many virulent genes. Meanwhile, outbreak events occurred several times in the strains collected. Carbapenemase acquisition (mainly KPC-2 carbapenemase) was responsible for carbapenem resistance of all the 146 CRKP strains. As 2 predominant strains, all ST11-KL64 strains, but not ST11-KL47 strains, carried rmpA2, iucABCD, iutA, as well as a plasmid replication initiator (repB). Our study suggested that the occurrence of region-specific recombination events manifested by the acquisition of some virulence genes might contribute to serotype switching from ST11-KL47 to ST11-KL64. The accumulation of virulent genes in epidemic resistant strains poses a great challenge for the prevention and treatment of BSI caused by K. pneumoniae in high-risk patients.
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Cherak Z, Loucif L, Bendjama E, Moussi A, Benbouza A, Grainat N, Rolain JM. Dissemination of Carbapenemases and MCR-1 Producing Gram-Negative Bacteria in Aquatic Environments in Batna, Algeria. Antibiotics (Basel) 2022; 11:antibiotics11101314. [PMID: 36289972 PMCID: PMC9598638 DOI: 10.3390/antibiotics11101314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 12/02/2022] Open
Abstract
Antibiotic-resistant-bacteria are being considered as emerging environmental contaminants where the importance of the surrounding environment in their emergence and dissemination has been emphasized. The aim of this study was to screen for the presence and diversity of carbapenem- and colistin-resistant Gram-negative bacteria (GNBs) in different aquatic environments. Water samples were collected in Batna, Algeria. Carbapenem- and colistin-resistant GNBs were selectively isolated and then identified using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. After phenotypic antibiotic susceptibility testing, the molecular mechanisms of β-lactams and colistin-resistance were investigated by PCR and sequencing. The clonality of mcr-1 positive Escherichia coli was determined by multi-locus sequence typing. We noticed a high level of resistance in both tap water and wastewater. The most commonly found carbapenem-resistance mechanism was the OXA-48 enzyme, but other carbapenemases were also detected. In addition, the mcr-1 gene was detected in 18 E. coli of different sequence types. Our findings highlight the role of aquatic environments in the dissemination of resistant-bacteria, especially considering that water is a connecting medium between different ecological systems and can easily transmit resistant-bacteria and promote horizontal gene transfer. Thus, the development of effective treatment strategies for eliminating antibiotic-resistance is seriously needed.
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Affiliation(s)
- Zineb Cherak
- Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna 05078, Algeria
| | - Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna 05078, Algeria
- Correspondence: ; Tel.: +213-(0)5-40-92-54-00
| | - Esma Bendjama
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna 05078, Algeria
- Départements de Technologie Alimentaire, Instituts des Sciences Agronomiques et Vétérinaires, Université El Hadj Lakhdar-Batna 1, Batna 05000, Algeria
| | - Abdelhamid Moussi
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bioressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra 07000, Algeria
| | - Amel Benbouza
- Faculté de Médecine, Université de Batna 2, Batna 05078, Algeria
| | - Nadia Grainat
- Faculté de Médecine, Université de Batna 2, Batna 05078, Algeria
| | - Jean-Marc Rolain
- Faculté de Médecine et de Pharmacie, Aix Marseille Université, IRD, MEPHI, 13007 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique des Hôpitaux de Marseille, 13005 Marseille, France
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Within patient genetic diversity of bla KPC harboring Klebsiella pneumoniae in a Colombian hospital and identification of a new NTE KPC platform. Sci Rep 2021; 11:21409. [PMID: 34725422 PMCID: PMC8560879 DOI: 10.1038/s41598-021-00887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022] Open
Abstract
Resistance to carbapenems in Klebsiellapneumoniae has been mostly related with the worldwide dissemination of KPC, largely due to the pandemic clones belonging to the complex clonal (CC) 258. To unravel blaKPC post-endemic clinical impact, here we describe clinical characteristics of 68 patients from a high complexity hospital, and the molecular and genetic characteristics of their 139 blaKPC—K.pneumoniae (KPC-Kp) isolates. Of the 26 patients that presented relapses or reinfections, 16 had changes in the resistance profiles of the isolates recovered from the recurrent episodes. In respect to the genetic diversity of KPC-Kp isolates, PFGE revealed 45 different clonal complexes (CC). MLST for 12 representative clones showed ST258 was present in the most frequent CC (23.0%), however, remaining 11 representative clones belonged to non-CC258 STs (77.0%). Interestingly, 16 patients presented within-patient genetic diversity of KPC-Kp clones. In one of these, three unrelated KPC-Kp clones (ST258, ST504, and ST846) and a blaKPC—K.variicola isolate (ST182) were identified. For this patient, complete genome sequence of one representative isolate of each clone was determined. In K.pneumoniae isolates blaKPC was mobilized by two Tn3-like unrelated platforms: Tn4401b (ST258) and Tn6454 (ST504 and ST846), a new NTEKPC-IIe transposon for first time characterized also determined in the K.variicola isolate of this study. Genome analysis showed these transposons were harbored in different unrelated but previously reported plasmids and in the chromosome of a K.pneumoniae (for Tn4401b). In conclusion, in the blaKPC post-endemic dissemination in Colombia, different KPC-Kp clones (mostly non-CC258) have emerged due to integration of the single blaKPC gene in new genetic platforms. This work also shows the intra-patient resistant and genetic diversity of KPC-Kp isolates. This circulation dynamic could impact the effectiveness of long-term treatments.
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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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Kocer K, Klein S, Hildebrand D, Krall J, Heeg K, Boutin S, Nurjadi D. Pitfalls in genotypic antimicrobial susceptibility testing caused by low expression of blaKPC in Escherichia coli. J Antimicrob Chemother 2021; 76:2795-2801. [PMID: 34324652 DOI: 10.1093/jac/dkab267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND There is a growing interest in the rapid genotypic identification of antimicrobial resistance (AMR). In routine diagnostics, we detected multiple KPC-positive Escherichia coli (KPC-Ec) with discordant phenotypic meropenem susceptibility from a single patient's blood cultures, which prompted a more thorough investigation. OBJECTIVES We investigated the potential clinical relevance of, and the mechanism behind, discordant phenotypic and genotypic meropenem susceptibility in KPC-Ec. METHODS WGS was used to perform a comparative analysis of the isolates' genetic characteristics and their blaKPC-2 locus. Expression of blaKPC-2 was determined by quantitative PCR and the potency of meropenem hydrolysis was determined using a semi-quantitative carbapenem inactivation method. An in vivo infection assay using Galleria mellonella was performed to assess the potential clinical relevance of KPC expression in E. coli. RESULTS Despite the presence of blaKPC-2, three of five isolates were susceptible to meropenem (MICVITEK2 ≤ 0.25 mg/L), while two isolates were resistant (MICVITEK2 ≥ 16 mg/L). The isolates with high MICs had significantly higher blaKPC-2 expression, which corresponds to phenotypic meropenem inactivation. The genetic environment of blaKPC-2, which may impact KPC production, was identical in all isolates. In vivo infection assay with G. mellonella suggested that meropenem was effective in reducing mortality following infection with low-expressing KPC-Ec. CONCLUSIONS Our findings clearly highlight a limitation of genotypic AMR prediction for blaKPC. For the time being, genotypic AMR prediction requires additional analysis for accurate antibiotic therapy decision-making.
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Affiliation(s)
- Kaan Kocer
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Sabrina Klein
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Dagmar Hildebrand
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Johannes Krall
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Klaus Heeg
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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Detection of a New Resistance-Mediating Plasmid Chimera in a blaOXA-48-Positive Klebsiella pneumoniae Strain at a German University Hospital. Microorganisms 2021; 9:microorganisms9040720. [PMID: 33807212 PMCID: PMC8066831 DOI: 10.3390/microorganisms9040720] [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] [Received: 03/17/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
Mobile genetic elements, such as plasmids, facilitate the spread of antibiotic resistance genes in Enterobacterales. In line with this, we investigated the plasmid-resistome of seven blaOXA-48 gene-carrying Klebsiella pneumoniae isolates, which were isolated between 2013 and 2014 at the University Medical Center in Göttingen, Germany. All isolates were subjected to complete genome sequencing including the reconstruction of entire plasmid sequences. In addition, phenotypic resistance testing was conducted. The seven isolates comprised both disease-associated isolates and colonizers isolated from five patients. They fell into two clusters of three sequence type (ST)101 and two ST11 isolates, respectively; and ST15 and ST23 singletons. The seven isolates harbored various plasmids of the incompatibility (Inc) groups IncF, IncL/M, IncN, IncR, and a novel plasmid chimera. All blaOXA-48 genes were encoded on the IncL/M plasmids. Of note, distinct phenotypical resistance patterns associated with different sets of resistance genes encoded by IncL/M and IncR plasmids were observed among isolates of the ST101 cluster in spite of high phylogenetic relatedness of the bacterial chromosomes, suggesting nosocomial transmission. This highlights the importance of plasmid uptake and plasmid recombination events for the fast generation of resistance variability after clonal transmission. In conclusion, this study contributes a piece in the puzzle of molecular epidemiology of resistance gene-carrying plasmids in K. pneumoniae in Germany.
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Prevalence of blaKPC-2, blaKPC-3 and blaKPC-30-Carrying Plasmids in Klebsiella pneumoniae Isolated in a Brazilian Hospital. Pathogens 2021; 10:pathogens10030332. [PMID: 33809215 PMCID: PMC7998191 DOI: 10.3390/pathogens10030332] [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] [Received: 02/08/2021] [Revised: 02/22/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC) actively hydrolyzes carbapenems, antibiotics often used a last-line treatment for multidrug-resistant bacteria. KPC clinical relevance resides in its widespread dissemination. In this work, we report the genomic context of KPC coding genes blaKPC-2, blaKPC-3 and blaKPC-30 in multidrug-resistant Klebsiellapneumoniae isolates from Brazil. Plasmids harboring blaKPC-3 and blaKPC-30 were identified. Fifteen additional carbapenem-resistant K. pneumoniae isolates were selected from the same tertiary hospital, collected over a period of 8 years. Their genomes were sequenced in order to evaluate the prevalence and dissemination of blaKPC-harboring plasmids. We found that blaKPC genes were mostly carried by one of two isoforms of transposon Tn4401 (Tn4401a or Tn4401b) that were predominantly located on plasmids highly similar to the previously described plasmid pKPC_FCF3SP (IncN). The identified pKPC_FCF3SP-like plasmids carried either blaKPC-2 or blaKPC-30. Two K. pneumoniae isolates harbored pKpQIL-like (IncFII) plasmids, only recently identified in Brazil; one of them harbored blaKPC-3 in a Tn4401a transposon. Underlining the risk of horizontal spread of KPC coding genes, this study reports the prevalence of blaKPC-2 and the recent spread of blaKPC-3, and blaKPC-30, in association with different isoforms of Tn4401, together with high synteny of plasmid backbones among isolates studied here and in comparison with previous reports.
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Cui X, Shan B, Zhang X, Qu F, Jia W, Huang B, Yu H, Tang YW, Chen L, Du H. Reduced Ceftazidime-Avibactam Susceptibility in KPC-Producing Klebsiella pneumoniae From Patients Without Ceftazidime-Avibactam Use History - A Multicenter Study in China. Front Microbiol 2020; 11:1365. [PMID: 32655534 PMCID: PMC7324628 DOI: 10.3389/fmicb.2020.01365] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/27/2020] [Indexed: 12/19/2022] Open
Abstract
KPC-producing Klebsiella pneumoniae (KPC-KP) is the most widely spread carbapenem-resistant Enterobacteriaceae (CRE) in China. Avibactam is a novel non-β-lactam β-lactamase inhibitor which is highly active against KPC. Recently, ceftazidime-avibactam (CAZ-AVI) was approved for clinical treatment in China. Here we conducted a retrospective study to examine the antimicrobial susceptibility of CAZ-AVI prior to its usage in China, and evaluated the potential to develop resistance in KPC-KP. CAZ-AVI MICs were tested in 347 KPC-KP isolates collected from patients with no prior treatment with this combination from six medical centers in China. Almost all isolates (n = 346; 99.7%) were CAZ-AVI-susceptible, with only 12 (3.5%) which showed reduced susceptibility (MIC ≥ 4/4 μg/ml) or resistance. The 12 isolates belong to ST11 and half of them carry virulence genes. In comparison to susceptible isolates, these isolates demonstrated higher bla KPC-2 copy numbers and expressions, and demonstrated higher frequency of developing CAZ-AVI resistance.
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Affiliation(s)
- Xiaoyan Cui
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Bin Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xue Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fen Qu
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China.,Aviation General Hospital, China Medical University, Beijing, China
| | - Wei Jia
- Medical Laboratory Center, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hua Yu
- Sichuan Academy of Medical Sciences Sichuan Provincial People's Hospital, Chengdu, China
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States.,Cepheid, Shanghai, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States.,Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Genetic Factors Associated with Enhanced bla KPC Expression in Tn 3/Tn 4401 Chimeras. Antimicrob Agents Chemother 2020; 64:AAC.01836-19. [PMID: 31844015 DOI: 10.1128/aac.01836-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
The expression of the bla KPC gene plays a key role in carbapenem resistance in Enterobacteriaceae However, the genetic regulators of the bla KPC gene have not been completely elucidated, especially the genes in Tn3-Tn4401 chimeras. Two novel Tn3-Tn4401 chimera isoforms were characterized in our hospital, isoform A (CTA), which harbors a 121-bp deletion containing the PX promoter and was present in 22.6% (54/239) of isolates, and isoform C (CTC), which harbors a 624-bp insertion and a P1 promoter deletion and was present in only 1 isolate. The carbapenem MICs of both isoforms were 2-fold or more higher than those of the wild type (Tn3-Tn4401 chimera, CTB), and bla KPC was most highly expressed in CTA. Bioinformatics and 5' rapid amplification of cDNA ends (5' RACE) experiments indicated a novel strong putative promoter, PY, at the 3' end of the ISKpn8 gene. PY mutation nearly abrogated bla KPC expression (P < 0.01) and restored carbapenem susceptibility in all 3 isoforms. Although the mutation of PX or P1 halved bla KPC expression in CTB (P < 0.05), PX deletion caused a 68% increase in bla KPC expression (P = 0.037) in CTA. The level of bla KPC mRNA in CTC was 8-fold higher than that in InCTC, which harbors P1 (P = 0.011). These results suggest that PY is a core promoter of the bla KPC gene in the chimeras and that the deletion of the PX and P1 promoters enhanced gene expression in CTA and CTC, respectively.
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