51
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Castanheira M, Doyle TB, Deshpande LM, Mendes RE, Sader HS. Activity of ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam against carbapenemase-negative carbapenem-resistant Enterobacterales isolates from US hospitals. Int J Antimicrob Agents 2021; 58:106439. [PMID: 34547421 DOI: 10.1016/j.ijantimicag.2021.106439] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/31/2021] [Accepted: 09/12/2021] [Indexed: 12/25/2022]
Abstract
We investigated the prevalence, resistance mechanisms and activity of ceftazidime/avibactam, meropenem/vaborbactam, imipenem/relebactam and comparator agents against carbapenem-resistant Enterobacterales (CRE) that did not carry carbapenemase genes. Among 304 CRE isolates collected in US hospitals during 2016-2018 (1.1% of the overall Enterobacterales), 45 (14.8%) isolates did not carry carbapenemases. These isolates were mainly Klebsiella aerogenes (n = 11), Enterobacter cloacae (n = 11) and Klebsiella pneumoniae (n = 10). Isolates harboured one to six β-lactam resistance mechanisms (median, three mechanisms). Acquired β-lactamase genes were detected in 21 isolates; blaCTX-M-15 was the most common acquired β-lactamase gene found (14 isolates). All 11 K. aerogenes and 6 E. cloacae isolates overexpressed AmpC. Only one isolate belonging to these species carried acquired β-lactamase genes. Disruptions or reduced expression of both outer membrane proteins (ompC/ompK36 and ompF/ompK35) were detected among 20 isolates. AcrAB-TolC was modestly expressed or overexpressed among 19 isolates from six species. One E. coli isolate produced a CTX-M-15 variant that displayed an increased meropenem minimum inhibitory concentration (MIC) when expressed in a clean background. Most β-lactam agents had limited activity against CRE isolates that did not carry carbapenemases. Ceftazidime/avibactam inhibited all isolates, while imipenem/relebactam and meropenem/vaborbactam inhibited 93.0% (88.9% if Proteus mirabilis is included) and 93.3% of tested isolates at current breakpoints. The resistance mechanisms among CRE isolates that did not produce carbapenemases are complex; β-lactam/β-lactamase inhibitor combinations might have different activity against these isolates depending on their resistance mechanisms and the bacterial species.
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Affiliation(s)
- Mariana Castanheira
- JMI Laboratories, 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317, USA.
| | - Timothy B Doyle
- JMI Laboratories, 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317, USA
| | | | - Rodrigo E Mendes
- JMI Laboratories, 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317, USA
| | - Helio S Sader
- JMI Laboratories, 345 Beaver Kreek Centre, Suite A, North Liberty, IA 52317, USA
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Sanikhani R, Moeinirad M, Solgi H, Hadadi A, Shahcheraghi F, Badmasti F. The face of hypervirulent Klebsiella pneumoniae isolated from clinical samples of two Iranian teaching hospitals. Ann Clin Microbiol Antimicrob 2021; 20:58. [PMID: 34465335 PMCID: PMC8406009 DOI: 10.1186/s12941-021-00467-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/24/2021] [Indexed: 12/20/2022] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern. In this study, both phenotypic and genotypic tests were used to detect hvKp. Antimicrobial resistance profiles and clonal relatedness of clinical isolates were also determined. We found that 34.2% (163/477) of the isolates were tellurite resistant, and among them 102 hvKp isolates detected with iucA or iutA or peg-344 as molecular markers. The blaSHV (80.4%), followed by blaCTX-M-15 (76.5%) and blaTEM (67.6%), blaOXA-48 (53.9%), and blaNDM-1 (32.3%) were detected, while blaKPC-1 was not present in any hvKp isolates. It was found that the majority of hvKp isolates belonged to capsular serotype K20 and ompK36 group C, which is related to clonal group (CG) 23 (e.g. ST23). A high percentage of multidrug-resistant hvKp (76.6%) and high resistance to imipenem (67%) indicated a serious problem that should be addressed in the clinical setting.
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Affiliation(s)
| | - Mohammad Moeinirad
- Division of Bacteriology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Solgi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Amin Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azar Hadadi
- Sina Hospital, Internal Medicine Department, and Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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53
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McCreary EK, Heil EL, Tamma PD. New Perspectives on Antimicrobial Agents: Cefiderocol. Antimicrob Agents Chemother 2021; 65:e0217120. [PMID: 34031052 PMCID: PMC8373209 DOI: 10.1128/aac.02171-20] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacterial resistance to carbapenem agents has reached alarming levels. Accordingly, collaborative efforts between national and international organizations and the pharmaceutical industry have led to an impressive expansion of commercially available β-lactam agents in recent years. No available agent comes close to the broad range of activity afforded by cefiderocol, a novel siderophore-cephalosporin conjugate. The novelty of and need for cefiderocol are clear, but available clinical data are conflicting, leaving infectious diseases specialists puzzled as to when to prescribe this agent in clinical practice. After a brief overview of cefiderocol pharmacokinetics and pharmacodynamics, safety data, cefiderocol susceptibility testing, and putative mechanisms of cefiderocol resistance, this review focuses on determining cefiderocol's role in the management of specific pathogens, including carbapenem-resistant Acinetobacter baumannii complex, carbapenem-resistant Pseudomonas aeruginosa, carbapenem-resistant Enterobacterales, and less commonly identified glucose-nonfermenting organisms such as Stenotrophomonas maltophilia, Burkholderia species, and Achromobacter species. Available preclinical, clinical trial, and postmarketing data are summarized for each organism, and each section concludes with our opinions on where to position cefiderocol as a clinical therapeutic.
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Affiliation(s)
- Erin K. McCreary
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily L. Heil
- Department of Pharmacy Practice and Science, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Pranita D. Tamma
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Baltimore, Maryland, USA
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54
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Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study. Microbiol Spectr 2021; 9:e0005821. [PMID: 34259540 PMCID: PMC8552774 DOI: 10.1128/spectrum.00058-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The aim of this study was to determine the contribution of the contamination of the health care environment in the acquisition of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a CRKP-prevalent setting. We performed a 3-month prospective study in a 20-bed medical intensive care unit (ICU) by collecting rectal/oral swabs from patients within 3 days of ICU admission and weekly thereafter. We also comprehensively sampled the beds and rooms of patients and instruments for patient care every week. CRKP were detected, genome sequenced, and assigned to clones based on core genome analyses. The survival of four CRKP clones was determined under ICU conditions. Seventeen patients were in the ICU at the start of the study, and 99 were admitted afterwards. Six were positive patients, with four detected on initial screening and two during weekly monitoring. CRKP was detected from 76 of 3,699 (2.1%) environment samples, including from the immediate surroundings of 21 patients (five had CRKP from clinical samples and 16 did not). CRKP was not detected outside patient care areas. Among 49 CRKP sequenced isolates (nine from swabs, five from clinical samples, and 35 from environment) from 21 patients, 45 were ST11 and had blaKPC-2. These could be assigned to four clones, with either KL47 (n = 22) or KL64 (n = 23) capsular type. The two dominant clones survived >30 days under ICU conditions. In conclusion, environmental contamination of CRKP was extensive but usually transient. It had little impact on CRKP acquisition by ICU patients, highlighting the ability to control CRKP transmission through infection prevention efforts even in high-prevalence settings. IMPORTANCEKlebsiella pneumoniae can be an opportunistic pathogen with the oral cavity and gut the main origin. However, carbapenem-resistant Klebsiella pneumoniae (CRKP) can be found in patient surroundings and is a serious threat for human infections. Although the hospital environment, particularly sinks, has long been considered a potential reservoir of CRKP, the exact role of environmental contamination contributing to the acquisition and transmission of CRKP among patients remains largely unknown. To understand the link between environmental contamination in health care settings and colonization and infection of patients by CRKP, we performed a 3-month prospective study in a 20-bed medical ICU. Isolates were collected by active patient screening and were subsequently genome sequenced to describe the diversity of CRKP and the linkage of patients and environmental reservoirs. We found that the environmental contamination of CRKP was extensive, and CRKP clones were freely circulating in the ICU. Environmental contamination was not due to sharing the bed unit or sharing contaminated instruments but more likely resulted from the movement of health care workers. Very few patients acquired CRKP in the ICU, which is likely due to the fact that environmental contamination was usually transient when a routine cleaning protocol was complied. Although CRKP contamination in patient surroundings may be extensive, as long as routine environment cleaning protocols are appropriate and well implemented, the health care environment is unlikely to be a major source of CRKP colonization and infection in ICU patients. Reducing the high workload for ICU nurses may help minimize CRKP environmental contamination.
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Emergence and genomics of OXA-232-producing Klebsiella pneumoniae in a hospital in Yancheng, China. J Glob Antimicrob Resist 2021; 26:194-198. [PMID: 34146740 DOI: 10.1016/j.jgar.2021.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES The aims of this study were to infer the phylogenetic relationship of OXA-232-producing Klebsiella pneumoniae (OXA232Kp) strains collected from a Chinese hospital and to determine the composition and genetic background of antimicrobial resistance genes (ARGs) among these strains. METHODS Three non-duplicate OXA232Kp strains were collected from a Chinese hospital. Whole-genome sequencing was used to determine their genome sequences and then a genomic comparison of ARG-carrying genetic elements from the three strains with related sequences was performed. Phylogenetic analysis was conducted by constructing a maximum-likelihood phylogenetic tree. RESULTS Compared with other Chinese sequence type 15 (ST15)-OXA232Kp strains, the three ST15-OXA232Kp strains in this study could be divided into a single subgroup in phylogenetic relationship. The composition and genetic background of ARGs were identical in the three strains. Three ARG-carrying genetic elements or multidrug resistance (MDR) regions were determined, including a truncated Tn2013-like IS-based transposition unit, a unit transposition Tn6867b and a 40.9-kb MDR region. CONCLUSION This study reported clonal dissemination of ST15-OXA232Kp strains carrying multiple ARGs in a Chinese hospital. A comprehensive evolutionary and genomics analysis provided a deeper understanding of OXA232Kp. Further surveillance and study should be advocated to prevent the dissemination of OXA232Kp strains in China.
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Asenjo A, Oteo-Iglesias J, Alós JI. What's new in mechanisms of antibiotic resistance in bacteria of clinical origin? ACTA ACUST UNITED AC 2021; 39:291-299. [PMID: 34088451 DOI: 10.1016/j.eimce.2020.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/22/2020] [Indexed: 11/18/2022]
Abstract
The discovery, commercialization and administration of antibiotics revolutionized the world of medicine in the middle of the last century, generating a significant change in the therapeutic paradigm of the infectious diseases. Nevertheless, this great breakthrough was soon threatened due to the enormous adaptive ability that bacteria have, through which they are able to develop or acquire different mechanisms that allow them to survive the exposure to antibiotics. We are faced with a complex, multifactorial and inevitable but potentially manageable threat. To fight against it, a global and multidisciplinary approach is necessary, based on the support, guidance and training of the next generation of professionals. Nevertheless, the information published regarding the resistance mechanisms to antibiotics are abundant, varied and, unfortunately, not always well structured. The objective of this review is to structure the, in our opinion, most relevant and novel information regarding the mechanisms of resistance to antibiotics that has been published from January 2014 to September 2019, analysing their possible clinical and epidemiological impact.
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Affiliation(s)
- Alejandra Asenjo
- Servicio de Microbiología, Hospital Universitario de Getafe, Getafe, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Juan-Ignacio Alós
- Servicio de Microbiología, Hospital Universitario de Getafe, Getafe, Madrid, Spain.
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57
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Özad Düzgün A. From Turkey: First Report of KPC-3- and CTX-M-27-Producing Multidrug-Resistant Klebsiella pneumoniae ST147 Clone Carrying OmpK36 and Ompk37 Porin Mutations. Microb Drug Resist 2021; 27:1265-1270. [PMID: 33794115 DOI: 10.1089/mdr.2020.0274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aim: The aim of this study was to identify antimicrobial resistance genes, virulence factor genes, and porin loss or mutations exhibited by the multidrug-resistant Klebsiella pneumoniae strain. Materials and Methods: Whole-genome sequencing was done via the Illumina NovaSeq 6000 platform. Strain identification and antibiotic susceptibility testing of strains were performed by the Vitek 2 automated system. Multilocus sequence typing analysis was carried out using seven conserved housekeeping genes. Results: The strain was resistant to penicillins, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and trimethoprim/sulfamethoxazole. The isolate was found to carry KPC-3, CTX-M-27, SHV-11, SHV-67, and TEM-1 β-lactamases. The clonal subtype of the isolate was ST147, and it possessed wzi64 and wzc38 alleles. Fifteen different point mutations (N49S, L59V, R146H, V178P, G189T, F198Y, V202L, F207Y, A217S, T222L, D223G, H235N, A280V, N304E, and S346N) were detected in the OmpK36 porin. A frame shift was observed in OmpK35 and two different point mutations (I70M and I128M) were found in the OmpK37 porin, in addition to seven mutations observed on the AcrR. Conclusions: This study demonstrated for the first time that the ST147 clone produced CTX-M-27 as well as KPC-3. In addition, new mutations were detected in the outer membrane proteins. These mutations together with the production of extended-spectrum β-lactamase and carbapenemase were found to contribute to the resistance of the ST147 clone to carbapenem and other antibiotics.
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Affiliation(s)
- Azer Özad Düzgün
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gumushane University, Gümüşhane, Turkey
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58
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Chen CM, Tang HL, Chiou CS, Tung KC, Lu MC, Lai YC. Colonization dynamics of Klebsiella pneumoniae in the pet animals and human owners in a single household. Vet Microbiol 2021; 256:109050. [PMID: 33799228 DOI: 10.1016/j.vetmic.2021.109050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/19/2021] [Indexed: 12/23/2022]
Abstract
Klebsiella pneumoniae resides in the gastrointestinal (GI) microbiota of humans and animals. To characterize the population dynamics of GI-colonizing K. pneumoniae, we examined the clonality of K. pneumoniae isolates, which were longitudinally collected from the fecal samplings of a healthy married couple and their pet animals during Sep. 2015 to Oct. 2016. As revealed by XbaI-PFGE analysis, the K. pneumoniae populations detected in the male owner and in one of the dogs, consisted of clonally diverse K. pneumoniae isolates; whereas, a dominant clone persisted in the GI tract of the female owner who was prone to chronic diarrhea. Whole-genome sequencing analysis of a representative strain of this pathobiont clone revealed a sequence type (ST) 29 lineage with the carriage of KL54 cps locus and a 192,603 bp IncHIB-type virulence plasmid. After probiotics intervention, the pathobiont K. pneumoniae diminished. The vacant niche was transiently occupied by other clones of K. pneumoniae, one of which was also present in the male owner. Besides the dog, the fecal carriage of K. pneumoniae was also detected in a pet turtle. This turtle isolate was resistant to multiple antimicrobials, including carbapenems. Possible transmission of drug-resistant K. pneumoniae through human-pet bonds warrants our attention.
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Affiliation(s)
- Chih-Ming Chen
- Department of Internal Medicine, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan; Department of Health Food, Chung Chou University of Science and Technology, Changhua, Taiwan
| | - Hui-Ling Tang
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan; Institute of Medical Research, China Medical University, Taiwan
| | - Chien-Shun Chiou
- Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan
| | - Kwong-Chung Tung
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Min-Chi Lu
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan; Institute of Medical Research, China Medical University, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan.
| | - Yi-Chyi Lai
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan; Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.
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Characterization of an IncFIB/IncHI1B Plasmid Encoding Efflux Pump TMexCD1-TOprJ1 in a Clinical Tigecycline- and Carbapenem-Resistant Klebsiella pneumoniae Strain. Antimicrob Agents Chemother 2021; 65:AAC.02340-20. [PMID: 33468479 DOI: 10.1128/aac.02340-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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60
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Black CA, So W, Dallas SS, Gawrys G, Benavides R, Aguilar S, Chen CJ, Shurko JF, Lee GC. Predominance of Non-carbapenemase Producing Carbapenem-Resistant Enterobacterales in South Texas. Front Microbiol 2021; 11:623574. [PMID: 33643226 PMCID: PMC7902696 DOI: 10.3389/fmicb.2020.623574] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Carbapenem-resistant Enterobacterales (CRE) pose a significant global public health threat. Resistance among CRE is particularly complex, owing to numerous possible resistance mechanisms and broad definitions. We aimed to characterize the clinical and molecular profiles of CRE in the South Texas region. Materials and methods We compared the clinical, genotypic, and phenotypic profiles of carbapenemase producing Enterobacterales (CPE) with those of non-carbapenemase producers (NCPE) isolated from South Texas, United States between 2011 and 2019. Molecular characteristics and resistance mechanisms were analyzed using whole-genome sequences. Results The majority (59%) of the CRE isolates were NCPE while 41% of isolates harbored carbapenemases, predmonantly blaKPC-type. The most common CPE was Klebsiella pneumoniae while majority of Enterobacter cloacae and Escherichia coli were NCPE Among K. pneumoniae, the clonal group 307 has emerged as a predmoninant group and was associated with as many CRE infections as the previous common clonal group 258. Patients with NCPE compared to CPE infections were associated with higher antimicrobial exposure prior to culture collection (days of therapy, 795 vs. 242; p < 0.001) and emergency department visits within past 90 days (22% vs. 4%; p = 0.011). The all cause 30-day mortality was 21%. Conclusions This study highlights the diversity of resistance mechanisms underlying CRE in South Texas, with 59% not harboring a carbapenemase. Individuals with NCPE infections were more likely to have had prior antimicrobial therapy and emergency department visits compared to those with CPE. Identification and distinction of these mechanisms by rapid identification of species and carbapenemase would allow for optimal treatment and infection control efforts.
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Affiliation(s)
- Cody A Black
- The University of Texas at Austin, College of Pharmacy, Austin, TX, United States.,School of Medicine, The University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Pathology and Laboratory Medicine, The University of Texas Health San Antonio, University Health System, San Antonio, TX, United States
| | - Wonhee So
- School of Pharmacy, Long Island University, Brooklyn, US and Pharmacy, New York Presbyterian/Weill Cornell Medical Center, New York, NY, United States
| | - Steven S Dallas
- School of Medicine, The University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Pathology and Laboratory Medicine, The University of Texas Health San Antonio, University Health System, San Antonio, TX, United States
| | - Gerard Gawrys
- The University of Texas at Austin, College of Pharmacy, Austin, TX, United States.,Methodist Healthcare System, San Antonio, TX, United States
| | - Raymond Benavides
- The University of Texas at Austin, College of Pharmacy, Austin, TX, United States.,School of Medicine, The University of Texas Health San Antonio, San Antonio, TX, United States
| | - Samantha Aguilar
- The University of Texas at Austin, College of Pharmacy, Austin, TX, United States.,School of Medicine, The University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Pathology and Laboratory Medicine, The University of Texas Health San Antonio, University Health System, San Antonio, TX, United States
| | - Chang-Jui Chen
- The University of Texas at Austin, College of Pharmacy, Austin, TX, United States.,School of Medicine, The University of Texas Health San Antonio, San Antonio, TX, United States
| | - James F Shurko
- The University of Texas at Austin, College of Pharmacy, Austin, TX, United States.,School of Medicine, The University of Texas Health San Antonio, San Antonio, TX, United States
| | - Grace C Lee
- The University of Texas at Austin, College of Pharmacy, Austin, TX, United States.,School of Medicine, The University of Texas Health San Antonio, San Antonio, TX, United States
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61
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Batisti Biffignandi G, Gibbon MJ, Corbella M, Thorpe HA, Merla C, Castelli M, Kallonen T, Pegrum K, Brisse S, Corander J, Marone P, Feil EJ, Sassera D. Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae. G3-GENES GENOMES GENETICS 2021; 11:6130821. [PMID: 33615377 PMCID: PMC8022944 DOI: 10.1093/g3journal/jkab019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 11/14/2022]
Abstract
During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”
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Affiliation(s)
| | - Marjorie J Gibbon
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA 27AY, UK
| | - Marta Corbella
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo N-0317, Norway
| | - Cristina Merla
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku 20521, Finland
| | - Katie Pegrum
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA 27AY, UK
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris 75015, France
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo N-0317, Norway.,Parasites & Microbes, Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Piero Marone
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA 27AY, UK
| | - Davide Sassera
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia 27100, Italy
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Hernández M, López-Urrutia L, Abad D, De Frutos Serna M, Ocampo-Sosa AA, Eiros JM. First Report of an Extensively Drug-Resistant ST23 Klebsiella pneumoniae of Capsular Serotype K1 Co-Producing CTX-M-15, OXA-48 and ArmA in Spain. Antibiotics (Basel) 2021; 10:antibiotics10020157. [PMID: 33557209 PMCID: PMC7913926 DOI: 10.3390/antibiotics10020157] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
An extensively drug-resistant (XDR) Klebsiella pneumoniae isolate MS3802 from a tracheostomy exudate was whole-genome sequenced using MiSeq and Oxford Nanopore MinION platforms in order to identify the antimicrobial resistance and virulence determinates and their genomic context. Isolate MS3802 belonged to the clone ST23 and presented a capsular serotype K1, associated with hypervirulent K. pneumoniae (hvKp) isolates. The isolate harboured a chromosomally encoded blaCTX-M-15 gene and contained a large IncHI1B hybrid virulence/resistance plasmid carrying another copy of the blaCTX-M-15 and the virulence factors iucABCD-iutA, iroBCDN, rmpA and rmpA2. The carbapenemase gene blaOXA-48 was found in a Tn1999-like transposon and the 16S rRNA methylase armA gen located in the vicinity of other antibiotic-resistant genes on an IncM2 plasmid. This study represents, to the best of our knowledge, the first description of a blaCTX-M-15-, blaOXA-48- and armA-harbouring K. pneumoniae of ST23 and capsular serotype K1 in Spain. Our report emphasizes the importance of implementing new surveillance strategies to monitor the risk of emergence and spread of such XDR and hypervirulent K. pneumoniae isolates.
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Affiliation(s)
- Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain; (M.H.); (D.A.)
| | - Luis López-Urrutia
- Servicio de Microbiología, Hospital Universitario del Río Hortega, 47012 Valladolid, Spain; (L.L.-U.); (M.D.F.S.); (J.M.E.)
| | - David Abad
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain; (M.H.); (D.A.)
| | - Mónica De Frutos Serna
- Servicio de Microbiología, Hospital Universitario del Río Hortega, 47012 Valladolid, Spain; (L.L.-U.); (M.D.F.S.); (J.M.E.)
| | - Alain A. Ocampo-Sosa
- Laboratorio de Microbiología Clínica y Molecular, Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain
- Correspondence: ; Tel.: +34-942-944-382
| | - José María Eiros
- Servicio de Microbiología, Hospital Universitario del Río Hortega, 47012 Valladolid, Spain; (L.L.-U.); (M.D.F.S.); (J.M.E.)
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Liao Q, Yuan Y, Li Q, Wu S, Liu Y, Zhang W, Xiao Y, Kang M. Comparing three different phenotypic methods for accurate detection of carbapenemase-producing Enterobacterales. J Infect Chemother 2021; 27:794-799. [PMID: 33468425 DOI: 10.1016/j.jiac.2021.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/12/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Early identification of carbapenemase-producing Enterobacterales (CPE) is highly essential to prevent their dissemination within health care settings. OBJECTIVE This study aimed to compare 3 reported phenotypic assays for detecting carbapenemase-producing Enterobacterales (CPE). METHODS 151 Enterobacterales isolates were collected, the sensitivity and specificity of each test was determined, with molecular genotype serving as the gold standard. The phenotypic evaluations were performed using EDTA-synergistic carbapenem inactivation method (esCIM), EDTA-carbapenem inactivation method (eCIM), and enzyme inhibitor enhancement experiment (EIE). RESULTS The concordance rate was 98% for the EIE for the detection of KPC producer, and 100% for the esCIM and eCIM. Sensitivity differed among the 3 methods, and all assays had excellent sensitivity exceeding 90% for detecting metallo-β-lactamases (MBLs). The specificity of the eCIM, esCIM and EIE was 100%, 100% and 95%. Both eCIM and esCIM were unsatisfactory in detecting multi-enzyme strains (MBL and class A serine carbapenemase) (0/6). However, EIE increased the positive number to six (6/6). CONCLUSIONS The eCIM, esCIM and EIE can be used to accurately detect and distinguish carbapenemase and is suitable for routine use in most clinical microbiology laboratories.
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Affiliation(s)
- Quanfeng Liao
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Yu Yuan
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Qingrong Li
- The Second Affiliated Hospital of Kunming Medical University Kunming, Yunnan Province, China
| | - Siying Wu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Ya Liu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Weili Zhang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Yuling Xiao
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China.
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Shropshire WC, Aitken SL, Pifer R, Kim J, Bhatti MM, Li X, Kalia A, Galloway-Peña J, Sahasrabhojane P, Arias CA, Greenberg DE, Hanson BM, Shelburne SA. IS26-mediated amplification of blaOXA-1 and blaCTX-M-15 with concurrent outer membrane porin disruption associated with de novo carbapenem resistance in a recurrent bacteraemia cohort. J Antimicrob Chemother 2021; 76:385-395. [PMID: 33164081 PMCID: PMC7816169 DOI: 10.1093/jac/dkaa447] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/28/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Approximately half of clinical carbapenem-resistant Enterobacterales (CRE) isolates lack carbapenem-hydrolysing enzymes and develop carbapenem resistance through alternative mechanisms. OBJECTIVES To elucidate development of carbapenem resistance mechanisms from clonal, recurrent ESBL-positive Enterobacterales (ESBL-E) bacteraemia isolates in a vulnerable patient population. METHODS This study investigated a cohort of ESBL-E bacteraemia cases in Houston, TX, USA. Oxford Nanopore Technologies long-read and Illumina short-read sequencing data were used for comparative genomic analysis. Serial passaging experiments were performed on a set of clinical ST131 Escherichia coli isolates to recapitulate in vivo observations. Quantitative PCR (qPCR) and qRT-PCR were used to determine copy number and transcript levels of β-lactamase genes, respectively. RESULTS Non-carbapenemase-producing CRE (non-CP-CRE) clinical isolates emerged from an ESBL-E background through a concurrence of primarily IS26-mediated amplifications of blaOXA-1 and blaCTX-M-1 group genes coupled with porin inactivation. The discrete, modular translocatable units (TUs) that carried and amplified β-lactamase genes mobilized intracellularly from a chromosomal, IS26-bound transposon and inserted within porin genes, thereby increasing β-lactamase gene copy number and inactivating porins concurrently. The carbapenem resistance phenotype and TU-mediated β-lactamase gene amplification were recapitulated by passaging a clinical ESBL-E isolate in the presence of ertapenem. Clinical non-CP-CRE isolates had stable carbapenem resistance phenotypes in the absence of ertapenem exposure. CONCLUSIONS These data demonstrate IS26-mediated mechanisms underlying β-lactamase gene amplification with concurrent outer membrane porin disruption driving emergence of clinical non-CP-CRE. Furthermore, these amplifications were stable in the absence of antimicrobial pressure. Long-read sequencing can be utilized to identify unique mobile genetic element mechanisms that drive antimicrobial resistance.
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Affiliation(s)
- William C Shropshire
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Samuel L Aitken
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Division of Pharmacy, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Reed Pifer
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School at Houston, Houston, TX 77030, USA
| | - Jiwoong Kim
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah M Bhatti
- Department of Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiqi Li
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jessica Galloway-Peña
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Cesar A Arias
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX 77030, USA
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Ak. 9#131a2, Colombia
| | - David E Greenberg
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Internal Medicine, UT Southwestern, Dallas, TX 75390, USA
- Department of Microbiology, UT Southwestern, Dallas, TX 75390, USA
| | - Blake M Hanson
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Samuel A Shelburne
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
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Cefoperazone/sulbactam: New composites against multiresistant gram negative bacteria? INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 88:104707. [PMID: 33418147 DOI: 10.1016/j.meegid.2021.104707] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/27/2020] [Accepted: 12/31/2020] [Indexed: 01/29/2023]
Abstract
Sulbactam, a class A β-lactamase inhibitor, added to cefoperazone either at a fixed 8 mg/L level of sulbactam or at a level of fixed cefoperazone: sulbactam ratio (2:1) would constitute a combination form of cefoperazone/sulbactam, which has better activities against Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii than cefoperazone alone. Cefoperazone/sulbactam (1:1 or 1:2) has greater in-vitro activity against most multidrug-resistant organisms (ESBL- and AmpC-producing Enterobacteriaceae and carbapenem-resistant A. baumannii except for carbapenem-resistant P. aeruginosa) than a 2:1 ratio. However, increased sulbactam concentration may induce AmpC production. Besides, sulbactam concentration might not be readily achievable in serum if the susceptibility rates were defined by the breakpoints of higher sulbactam composites, such as ≤16/16 (1:1) or 16/32 (1:2) mg/L. Carbapenemases (KPC-, OXA-type enzymes and metallo-β-lactamases) can't be inhibited by sulbactam. Some in-vitro studies showed that increasing sulbactam composites of cefoperazone/sulbactam had no effect on carbapenem-resistant P. aeruginosa, suggesting the presence of carbapenemases or AmpC overproduction that could not be overcome by increasing sulbactam levels to recover cefoperazone activity. Sulbactam alone has good intrinsic activity against carbapenem-resistant Acinetobacter strains sometimes even in the presence of carbapenemase genes, suggesting unsteady levels of carbapenemases. In conclusion, appropriate composites of cefoperazone and β-lactamase inhibitor sulbactam may expand the clinical use if the pharmacokinetic optimization could be achieved in the human serum.
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Chuang C, Su CF, Lin JC, Lu PL, Huang CT, Wang JT, Chuang YC, Siu LK, Fung CP, Lin YT. Does Antimicrobial Therapy Affect Mortality of Patients with Carbapenem-Resistant Klebsiella pneumoniae Bacteriuria? A Nationwide Multicenter Study in Taiwan. Microorganisms 2020; 8:microorganisms8122035. [PMID: 33352662 PMCID: PMC7767250 DOI: 10.3390/microorganisms8122035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022] Open
Abstract
Few clinical studies have previously discussed patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) bacteriuria. This study aimed to assess the effect of antimicrobial therapy on the mortality of patients with CRKP bacteriuria. Hospitalized adults with CRKP bacteriuria were enrolled retrospectively from 16 hospitals in Taiwan during 2013 and 2014. Critically ill patients were defined as those with an Acute Physiology and Chronic Health Evaluation (APACHE) II score ≥ 20. Multivariate Cox regression analysis was used to determine independent risk factors for 14- and 28-day mortality. Of 107 patients with CRKP bacteriuria, the 14-day and 28-day mortality was 14.0% and 25.2%, respectively. Thirty-three patients received appropriate antimicrobial therapy. In the multivariate Cox regression analysis, the APACHE II score ≥ 20 was the only independent risk factor for 14-day mortality (hazard ratio [HR]: 6.15, p = 0.024). APACHE II score ≥ 20 (HR: 3.05, p = 0.018) and male sex (HR: 2.57, p = 0.037) were associated with 28-day mortality. Among critically ill patients with CRKP bacteriuria, appropriate antimicrobial therapy was not associated with 14-day or 28-day survival. In conclusion, in patients with CRKP bacteriuria, the use of appropriate antimicrobial therapy was not an independent factor associated with reduced mortality. Our findings may inform future antibiotic stewardship interventions for bacteriuria caused by multidrug resistant pathogens.
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Affiliation(s)
- Chien Chuang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, 11217 Taipei, Taiwan;
- Division of Infectious Diseases, Department of Internal Medicine, Chia-yi Branch, Taichung Veterans General Hospital, Chiayi 60090, Taiwan
| | - Chin-Fang Su
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Po-Liang Lu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan;
- College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Ching-Tai Huang
- Division of Infectious Diseases, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
| | - Jann-Tay Wang
- Division of Infectious Diseases, Department of Medicine, National Taiwan University Hospital, Taipei 10048, Taiwan;
| | - Yin-Ching Chuang
- Department of Internal Medicine and Medical Research, Chi Mei Medical Center, Tainan 71004, Taiwan;
| | - L. Kristopher Siu
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 35053, Taiwan;
| | - Chang-Phone Fung
- Division of Infectious Diseases, Sijhih Cathay General Hospital, New Taipei City 10630, Taiwan;
| | - Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, 11217 Taipei, Taiwan;
- Institute of Emergency and Critical Care Medicine, National Yang-Ming University, Taipei 11221, Taiwan
- Correspondence: ; Tel.: +886-2-28757494
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Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae: a Systematic Review of Current Reports. mSystems 2020; 5:5/6/e00783-20. [PMID: 33323413 PMCID: PMC7771540 DOI: 10.1128/msystems.00783-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. A systematic review of all studies published in PubMed database between 2015 to October 2020 was performed. Journal articles evaluating carbapenem and polymyxin resistance mechanisms, respectively, were included. The search identified 171 journal articles for inclusion. Different New Delhi metallo-β-lactamase (NDM) carbapenemase variants had different transcriptional and affinity responses to different carbapenems. Mutations within the Klebsiella pneumoniae carbapenemase (KPC) mobile transposon, Tn4401, affect its promoter activity and expression levels, increasing carbapenem resistance. Insertion of IS26 in ardK increased imipenemase expression 53-fold. ompCF porin downregulation (mediated by envZ and ompR mutations), micCF small RNA hyperexpression, efflux upregulation (mediated by acrA, acrR, araC, marA, soxS, ramA, etc.), and mutations in acrAB-tolC mediated clinical carbapenem resistance when coupled with β-lactamase activity in a species-specific manner but not when acting without β-lactamases. Mutations in pmrAB, phoPQ, crrAB, and mgrB affect phosphorylation of lipid A of the lipopolysaccharide through the pmrHFIJKLM (arnBCDATEF or pbgP) cluster, leading to polymyxin resistance; mgrB inactivation also affected capsule structure. Mobile and induced mcr, efflux hyperexpression and porin downregulation, and Ecr transmembrane protein also conferred polymyxin resistance and heteroresistance. Carbapenem and polymyxin resistance is thus mediated by a diverse range of genetic and transcriptional mechanisms that are easily activated in an inducing environment. The molecular understanding of these emerging mechanisms can aid in developing new therapeutics for multidrug-resistant Enterobacteriaceae isolates.
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Kopotsa K, Mbelle NM, Osei Sekyere J. Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains. Microb Genom 2020; 6:mgen000474. [PMID: 33170117 PMCID: PMC8116673 DOI: 10.1099/mgen.0.000474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio's SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both blaOXA-48 and blaNDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
| | - Nontombi M. Mbelle
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
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Hu H, Mao J, Chen Y, Wang J, Zhang P, Jiang Y, Yang Q, Yu Y, Qu T. Clinical and Microbiological Characteristics of Community-Onset Carbapenem-Resistant Enterobacteriaceae Isolates. Infect Drug Resist 2020; 13:3131-3143. [PMID: 32982328 PMCID: PMC7494230 DOI: 10.2147/idr.s260804] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/26/2020] [Indexed: 01/01/2023] Open
Abstract
Objective The aim of this study was to investigate the clinical and microbiological features of community-onset CRE (CO-CRE) obtained from outpatients at a tertiary hospital in China. Patients and Methods We isolated 64 CRE strains from outpatients and divided them into three groups: 36 hospital-acquired CRE (HA-CRE), 28 CO-CRE including 15 community-acquired CRE (CA-CRE) and 13 healthcare-associated CRE (HCA-CRE). Clinical information was collected. The antibiotic susceptibilities of the 28 CO-CRE strains were tested. Whole-genome sequencing (WGS) was conducted, and then drug resistance gene analysis was performed. CgMLST and SNP comparisons were used to analyze the genomic relationship with E. coli and K. pneumoniae strains, respectively. Results In this study, the 28 CO-CRE isolates included K. pneumoniae (53.6%), E. coli (28.6%), E. cloacae (7.1%), C. freundii (7.1%) and E. asburiae (3.6%). The CO-CRE isolates were mainly isolated from urine samples (75%). The ceftazidime/avibactam resistance rate of community-onset E. coli was significantly higher than that of community-onset K. pneumoniae, while the aztreonam, ciprofloxacin, levofloxacin, and chloramphenicol resistance rates were significantly lower (P<0.05). Thirteen of the 15 K. pneumoniae strains belonged to ST11 containing blaKPC-2. Correspondingly, 8 E. coli strains belonged to 7 STs, and they all were NDM producers. K. pneumoniae belonged to two major clusters, while E. coli was sporadic. The number of SNPs separating ST11 K. pneumoniae isolates ranged from 7 to 2154. Conclusion Community-onset CRE is not rare, and the dissemination of E. coli was sporadic while K. pneumoniae was clonal spread with similar STs as HA-CRE. Active surveillance of CRE in the community setting is in demand.
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Affiliation(s)
- Hangbin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Jinchao Mao
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China.,Infectious Disease Department, The First People's Hospital of Wenling, Wenling, Zhejiang Province, People's Republic of China
| | - Yiyi Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Jie Wang
- Respiratory Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Piaopiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Qing Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
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Wu LT, Guo MK, Ke SC, Lin YP, Pang YC, Nguyen HTV, Chen CM. Characterization of the Genetic Background of KPC-2-Producing Klebsiella pneumoniae with Insertion Elements Disrupting the ompK36 Porin Gene. Microb Drug Resist 2020; 26:1050-1057. [PMID: 32283046 DOI: 10.1089/mdr.2019.0410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Lii-Tzu Wu
- The Institute of Medical Science and Department of Microbiology, China Medical University Hospital, Taichung, Taiwan
| | - Ming-Kai Guo
- The Institute of Medical Science and Department of Microbiology, China Medical University Hospital, Taichung, Taiwan
| | - Se-Chin Ke
- Infection Control Office, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
- Department of Medical Technology, Jen-The Junior College of Medicine, Nursing and Management, Miaoli, Taiwan
| | - Yi-Pei Lin
- Department of Medical Research, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Yi-Chun Pang
- The Institute of Medical Science and Department of Microbiology, China Medical University Hospital, Taichung, Taiwan
| | - Hong-Thuy Vy Nguyen
- The Institute of Biomedical Sciences College of Medicine, China Medical University, Taichung, Taiwan
| | - Chih-Ming Chen
- Department of Internal Medicine, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
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Wang Y, Cong S, Zhang Q, Li R, Wang K. iTRAQ-Based Proteomics Reveals Potential Anti-Virulence Targets for ESBL-Producing Klebsiella pneumoniae. Infect Drug Resist 2020; 13:2891-2899. [PMID: 32903891 PMCID: PMC7445504 DOI: 10.2147/idr.s259894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/28/2020] [Indexed: 11/23/2022] Open
Abstract
Purpose Treatment of infections with Klebsiella pneumoniae strains producing extended-spectrum beta-lactamases (ESBLs) is challenging due to the coexistence of multiple resistance mechanisms and the hypervirulent variant. Therefore, new targets or more effective treatment options aimed at ESBL-producing Klebsiella pneumoniae are urgently needed. Materials and Methods Here, we collected ESBL-producing and non-ESBL Klebsiella pneumoniae isolates and studied their differences from a proteomic point of view. Results We revealed treA, wza, gnd, rmlA, rmlC, rmlD, galE, aceE, and sucD as important virulence-related proteins in ESBL-producing Klebsiella pneumoniae, distinct from those in non-ESBL strains. Conclusion Our findings provide plausible anti-virulence targets and suggest new therapeutic avenues against ESBL-producing Klebsiella pneumoniae.
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Affiliation(s)
- Yan Wang
- Department of Respiratory and Critical Care Medicine., The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Shan Cong
- Department of Respiratory and Critical Care Medicine., The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Qinghua Zhang
- Department of Respiratory and Critical Care Medicine., The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Ranwei Li
- Department of Urology, The Second Hospital of Jilin University, Changchun, People's Republic of China
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine., The Second Hospital of Jilin University, Changchun, People's Republic of China
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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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Tian X, Wang Q, Perlaza-Jiménez L, Zheng X, Zhao Y, Dhanasekaran V, Fang R, Li J, Wang C, Liu H, Lithgow T, Cao J, Zhou T. First description of antimicrobial resistance in carbapenem-susceptible Klebsiella pneumoniae after imipenem treatment, driven by outer membrane remodeling. BMC Microbiol 2020; 20:218. [PMID: 32689945 PMCID: PMC7372807 DOI: 10.1186/s12866-020-01898-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 07/12/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a looming threat to human health. Although there are numerous studies regarding porin alteration in association with the production of ESBLs and/or AmpC β-lactamase, a systematic study on the treatment-emergence of porins alteration in antibiotic resistance does not yet exist. The aim of this study was to investigate the underlying mechanism of resistance of K. pneumoniae during carbapenem treatment. RESULTS Here, we report three strains (FK-2624, FK-2723 and FK-2820) isolated from one patient before and after imipenem treatment during hospitalization. Antibiotic susceptibility testing indicated that that the first isolate, FK-2624, was susceptible to almost all tested antimicrobials, being resistant only to fosfomycin. The subsequent isolates FK-2723 and FK-2820 were multidrug resistant (MDR). After imipenem therapy, FK-2820 was found to be carbapenem-resistant. PCR and Genome Sequencing analysis indicated that oqxA, and fosA5, were identified in all three strains. In addition, FK-2624 also harbored blaSHV-187 and blaTEM-116. The blaSHV-187 and blaTEM-116 genes were not detected in FK-2723 and FK-2820. blaDHA-1, qnrB4, aac (6')-IIc, and blaSHV-12, EreA2, CatA2, SulI, and tetD, were identified in both FK-2723 and FK-2820. Moreover, the genes blaDHA-1, qnrB4, aac (6')-IIc were co-harbored on a plasmid. Of the virulence factors found in this study, ybtA, ICEKp6, mrkD, entB, iroN, rmpA2-6, wzi16 and capsular serotype K57 were found in the three isolates. The results of pairwise comparisons, multi-locus sequencing typing (MLST) and pulsed-field gel electrophoresis (PFGE) revealed high homology among the isolates. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) results showed that isolate FK-2820 lacked OmpK36, with genome sequence data validating that there was a premature stop codon in the ompK36 gene and real-time RT-PCR suggesting high turnover of the ompK36 non-sense transcript in FK-2820, with the steady-state mRNA level 0.007 relative to the initial isolate. CONCLUSION This study in China highlight that the alteration of outer membrane porins due to the 14-day use of imipenem play a potential role in leading to clinical presentation of carbapenem-resistance. This is the first description of increased resistance developing from a carbapenem-susceptible K. pneumoniae with imipenem treatment driven by outer membrane remodeling.
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Affiliation(s)
- Xuebin Tian
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qiongdan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Laura Perlaza-Jiménez
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Xiangkuo Zheng
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yajie Zhao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Vijay Dhanasekaran
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Renchi Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiahui Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Chong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Haiyang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia.
| | - Jianming Cao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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Chen Y, Brook TC, Soe CZ, O'Neill I, Alcon-Giner C, Leelastwattanagul O, Phillips S, Caim S, Clarke P, Hall LJ, Hoyles L. Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors. Microb Genom 2020; 6:e000377. [PMID: 32436839 PMCID: PMC7371107 DOI: 10.1099/mgen.0.000377] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/26/2020] [Indexed: 01/08/2023] Open
Abstract
Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella, as previous studies have focused on the recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. The aim of this study was to better characterize preterm-associated Klebsiella populations using phenotypic and genotypic approaches. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for Klebsiella spp., and virulence and antimicrobial resistance genes identified. Antibiotic susceptibility profiling and in vitro macrophage and iron assays were undertaken for the Klebsiella strains. Metapangenome analyses with a manually curated genome dataset were undertaken to examine the diversity of Klebsiella oxytoca and related bacteria in a publicly available shotgun metagenome dataset. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. 'healthy') encoded multiple β-lactamases. No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut. There is little difference in the phenotypic and genomic characteristics of Klebsiella isolates recovered from healthy and sick infants. Identification of β-lactamases in all isolates may prove problematic when defining treatment regimens for NEC or sepsis, and suggests that healthy preterm infants contribute to the resistome. Refined analyses with curated sequence databases are required when studying closely related species present in metagenomic data.
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Affiliation(s)
- Yuhao Chen
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Thomas C. Brook
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Cho Zin Soe
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ian O'Neill
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Cristina Alcon-Giner
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Onnicha Leelastwattanagul
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian Campus), Bangkok, Thailand
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Shabhonam Caim
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J. Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lesley Hoyles
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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Abstract
The discovery, commercialization and administration of antibiotics revolutionized the world of medicine in the middle of the last century, generating a significant change in the therapeutic paradigm of the infectious diseases. Nevertheless, this great breakthrough was soon threatened due to the enormous adaptive ability that bacteria have, through which they are able to develop or acquire different mechanisms that allow them to survive the exposure to antibiotics. We are faced with a complex, multifactorial and inevitable but potentially manageable threat. To fight against it, a global and multidisciplinary approach is necessary, based on the support, guidance and training of the next generation of professionals. Nevertheless, the information published regarding the resistance mechanisms to antibiotics are abundant, varied and, unfortunately, not always well structured. The objective of this review is to structure the, in our opinion, most relevant and novel information regarding the mechanisms of resistance to antibiotics that has been published from January 2014 to September 2019, analysing their possible clinical and epidemiological impact.
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The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9040186. [PMID: 32316342 PMCID: PMC7235769 DOI: 10.3390/antibiotics9040186] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups.
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Global Trends in Proteome Remodeling of the Outer Membrane Modulate Antimicrobial Permeability in Klebsiella pneumoniae. mBio 2020; 11:mBio.00603-20. [PMID: 32291303 PMCID: PMC7157821 DOI: 10.1128/mbio.00603-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Klebsiella pneumoniae is a pathogen of humans with high rates of mortality and a recognized global rise in incidence of carbapenem-resistant K. pneumoniae (CRKP). The outer membrane of K. pneumoniae forms a permeability barrier that modulates the ability of antibiotics to reach their intracellular target. OmpK35, OmpK36, OmpK37, OmpK38, PhoE, and OmpK26 are porins in the outer membrane of K. pneumoniae, demonstrated here to have a causative relationship to drug resistance phenotypes in a physiological context. The data highlight that currently trialed combination treatments with a carbapenem and β-lactamase inhibitors could be effective on porin-deficient K. pneumoniae. Together with structural data, the results reveal the role of outer membrane proteome remodeling in antimicrobial resistance of K. pneumoniae and point to the role of extracellular loops, not channel parameters, in drug permeation. This significant finding warrants care in the development of phage therapies for K. pneumoniae infections, given the way porin expression will be modulated to confer phage-resistant—and collateral drug-resistant—phenotypes in K. pneumoniae. In Gram-negative bacteria, the permeability of the outer membrane governs rates of antibiotic uptake and thus the efficacy of antimicrobial treatment. Hydrophilic drugs like β-lactam antibiotics depend on diffusion through pore-forming outer membrane proteins to reach their intracellular targets. In this study, we investigated the distribution of porin genes in more than 2,700 Klebsiella isolates and found a widespread loss of OmpK35 functionality, particularly in those strains isolated from clinical environments. Using a defined set of outer-membrane-remodeled mutants, the major porin OmpK35 was shown to be largely responsible for β-lactam permeation. Sequence similarity network analysis characterized the porin protein subfamilies and led to discovery of a new porin family member, OmpK38. Structure-based comparisons of OmpK35, OmpK36, OmpK37, OmpK38, and PhoE showed near-identical pore frameworks but defining differences in the sequence characteristics of the extracellular loops. Antibiotic sensitivity profiles of isogenic Klebsiella pneumoniae strains, each expressing a different porin as its dominant pore, revealed striking differences in the antibiotic permeability characteristics of each channel in a physiological context. Since K. pneumoniae is a nosocomial pathogen with high rates of antimicrobial resistance and concurrent mortality, these experiments elucidate the role of porins in conferring specific drug-resistant phenotypes in a global context, informing future research to combat antimicrobial resistance in K. pneumoniae.
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MCR-8 mediated colistin resistance in a carbapenem-resistant Klebsiella pneumoniae isolated from a repatriated patient from Morocco. Int J Antimicrob Agents 2020; 55:105920. [DOI: 10.1016/j.ijantimicag.2020.105920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/13/2020] [Accepted: 02/08/2020] [Indexed: 11/17/2022]
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Chiotos K, Hayes M, Gerber JS, Tamma PD. Treatment of Carbapenem-Resistant Enterobacteriaceae Infections in Children. J Pediatric Infect Dis Soc 2020; 9:56-66. [PMID: 31872226 PMCID: PMC7047006 DOI: 10.1093/jpids/piz085] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 11/27/2019] [Indexed: 12/15/2022]
Abstract
Infections due to carbapenem-resistant Enterobacteriaceae (CRE) are increasingly prevalent in children and are associated with poor clinical outcomes. Optimal treatment strategies for CRE infections continue to evolve. A lack of pediatric-specific comparative effectiveness data, uncertain pediatric dosing regimens for several agents, and a relative lack of new antibiotics with pediatric indications approved by the US Food and Drug Administration (FDA) collectively present unique challenges for children. In this review, we provide a framework for antibiotic treatment of CRE infections in children, highlighting relevant microbiologic considerations and summarizing available data related to the evaluation of FDA-approved antibiotics (as of September 2019) with CRE activity, including carbapenems, ceftazidime-avibactam, meropenem-vaborbactam, imipenem/cilastatin-relebactam, polymyxins, tigecycline, eravacycline, and plazomicin.
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Affiliation(s)
- Kathleen Chiotos
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Critical Care Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Antimicrobial Stewardship Program, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Molly Hayes
- Antimicrobial Stewardship Program, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Antimicrobial Stewardship Program, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Pranita D Tamma
- Division of Pediatric Infectious Diseases, Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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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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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond. Clin Microbiol Rev 2018; 32:32/1/e00037-18. [PMID: 30487165 DOI: 10.1128/cmr.00037-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied in recent years for first-line identification of pathogens in clinical microbiology because it is simple to use, rapid, and accurate and has economic benefits in hospital management. The range of clinical applications of MALDI-TOF MS for bacterial isolates is increasing constantly, from species identification to the two most promising applications in the near future: detection of antimicrobial resistance and strain typing for epidemiological studies. The aim of this review is to outline the contribution of previous MALDI-TOF MS studies in relation to detection of antimicrobial resistance and to discuss potential future challenges in this field. Three main approaches are ready (or almost ready) for clinical use, including the detection of antibiotic modifications due to the enzymatic activity of bacteria, the detection of antimicrobial resistance by analysis of the peak patterns of bacteria or mass peak profiles, and the detection of resistance by semiquantification of bacterial growth in the presence of a given antibiotic. This review provides an expert guide for MALDI-TOF MS users to new approaches in the field of antimicrobial resistance detection, especially possible applications as a routine diagnostic tool in microbiology laboratories.
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First Description of Colistin and Tigecycline-Resistant Acinetobacter baumannii Producing KPC-3 Carbapenemase in Portugal. Antibiotics (Basel) 2018; 7:antibiotics7040096. [PMID: 30404152 PMCID: PMC6315367 DOI: 10.3390/antibiotics7040096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 02/07/2023] Open
Abstract
Herein, we describe a case report of carbapenem-resistant Acinetobacter baumannii and Klebsiella pneumoniae isolates that were identified from the same patient at a Tertiary University Hospital Centre in Portugal. Antimicrobial susceptibility and the molecular characterization of resistance and virulence determinants were performed. PCR screening identified the presence of the resistance genes blaKPC-3, blaTEM-1 and blaSHV-1 in both isolates. The KPC-3 K. pneumoniae isolate belonged to the ST-14 high risk clone and accumulated an uncommon resistance and virulence profile additional to a horizontal dissemination capacity. In conclusion, the molecular screening led to the first identification of the A. baumannii KPC-3 producer in Portugal with a full antimicrobial resistance profile including tigecycline and colistin.
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