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Luo Q, Lu P, Chen Y, Shen P, Zheng B, Ji J, Ying C, Liu Z, Xiao Y. ESKAPE in China: epidemiology and characteristics of antibiotic resistance. Emerg Microbes Infect 2024; 13:2317915. [PMID: 38356197 PMCID: PMC10896150 DOI: 10.1080/22221751.2024.2317915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
The escalation of antibiotic resistance and the diminishing antimicrobial pipeline have emerged as significant threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria, demanding urgently effective therapies. Despite the introduction of various new antibiotics and antibiotic adjuvants, such as innovative β-lactamase inhibitors, these organisms continue to pose substantial therapeutic challenges. People's Republic of China, as a country facing a severe bacterial resistance situation, has undergone a series of changes and findings in recent years in terms of the prevalence, transmission characteristics and resistance mechanisms of antibiotic resistant bacteria. The increasing levels of population mobility have not only shaped the unique characteristics of antibiotic resistance prevalence and transmission within People's Republic of China but have also indirectly reflected global patterns of antibiotic-resistant dissemination. What's more, as a vast nation, People's Republic of China exhibits significant variations in the levels of antibiotic resistance and the prevalence characteristics of antibiotic resistant bacteria across different provinces and regions. In this review, we examine the current epidemiology and characteristics of this important group of bacterial pathogens, delving into relevant mechanisms of resistance to recently introduced antibiotics that impact their clinical utility in China.
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Affiliation(s)
- Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jinru Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Chaoqun Ying
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Zhiying Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
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Puljko A, Barišić I, Dekić Rozman S, Križanović S, Babić I, Jelić M, Maravić A, Udiković-Kolić N. Molecular epidemiology and mechanisms of carbapenem and colistin resistance in Klebsiella and other Enterobacterales from treated wastewater in Croatia. ENVIRONMENT INTERNATIONAL 2024; 185:108554. [PMID: 38479059 DOI: 10.1016/j.envint.2024.108554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/30/2024] [Accepted: 03/02/2024] [Indexed: 03/26/2024]
Abstract
Among the most problematic bacteria with clinical relevance are the carbapenem-resistant Enterobacterales (CRE), as there are very limited options for their treatment. Treated wastewater can be a route for the release of these bacteria into the environment and the population. The aim of this study was to isolate CRE from treated wastewater from the Zagreb wastewater treatment plant and to determine their phenotypic and genomic characteristics. A total of 200 suspected CRE were isolated, 148 of which were confirmed as Enterobacterales by MALDI-TOF MS. The predominant species was Klebsiella spp. (n = 47), followed by Citrobacter spp. (n = 40) and Enterobacter cloacae complex (cplx.) (n = 35). All 148 isolates were carbapenemase producers with a multidrug-resistant phenotype. Using multi-locus sequence typing and whole-genome sequencing (WGS), 18 different sequence types were identified among these isolates, 14 of which were associated with human-associated clones. The virulence gene analysis of the sequenced Klebsiella isolates (n = 7) revealed their potential pathogenicity. PCR and WGS showed that the most frequent carbapenemase genes in K. pneumoniae were blaOXA-48 and blaNDM-1, which frequently occurred together, while blaKPC-2 together with blaNDM-1 was mainly detected in K. oxytoca, E. cloacae cplx. and Citrobacter spp. Colistin resistance was observed in 40% of Klebsiella and 57% of Enterobacter isolates. Underlying mechanisms identified by WGS include known and potentially novel intrinsic mechanisms (point mutations in the pmrA/B, phoP/Q, mgrB and crrB genes) and acquired mechanisms (mcr-4.3 gene). The mcr-4.3 gene was identified for the first time in K. pneumoniae and is probably located on the conjugative IncHI1B plasmid. In addition, WGS analysis of 13 isolates revealed various virulence genes and resistance genes to other clinically relevant antibiotics as well as different plasmids possibly associated with carbapenemase genes. Our study demonstrates the important role that treated municipal wastewater plays in harboring and spreading enterobacterial pathogens that are resistant to last-resort antibiotics.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210 Vienna, Austria
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000 Split, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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Golikova MV, Alieva KN, Strukova EN, Kondratieva DA, Petrova NF, Petrova MA, Zinner SH. Comparative Meropenem Pharmacodynamics and Emergence of Resistance against Carbapenem-Susceptible Non-Carbapenemase-Producing and Carbapenemase-Producing Enterobacterales: A Pharmacodynamic Study in a Hollow-Fiber Infection Model. Antibiotics (Basel) 2023; 12:1717. [PMID: 38136751 PMCID: PMC10740541 DOI: 10.3390/antibiotics12121717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Resistance to carbapenems has become a problem due to Klebsiella pneumoniae (K. pneumoniae), harboring carbapenemases. Among them, there are isolates that are recognized as carbapenem-susceptible; however, these carbapenemase-producing strains with low meropenem minimal inhibitory concentrations (MICs) may pose a threat to public health. We aimed to investigate the impact of the ability to produce carbapenemases by a bacterial isolate on the effectiveness of meropenem in the hollow-fiber infection model. K. pneumoniae and Escherichia coli (E. coli) strains with equal meropenem MICs but differing in their ability to produce carbapenemases were used in pharmacodynamic simulations with meropenem. In addition to standard MIC determination, we assessed the MICs against tested strains at high inoculum density to test if the inoculum effect occurs. According to pharmacodynamic data, the carbapenemase-producing strains were characterized with a relatively decreased meropenem effectiveness compared to non-producers. Meanwhile, the effect of meropenem perfectly correlated with the meropenem exposure expressed as the DOSE/MIC ratio when high-inoculum (HI) MICs but not standard-inoculum (SI) MICs were used for regression analysis. It could be concluded that meropenem-susceptible carbapenemase-producing strains may not respond to meropenem therapy; the antibiotic inoculum effect (IE) may have a prognostic value to reveal the meropenem-susceptible Enterobacterales that harbor carbapenemase genes.
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Affiliation(s)
- Maria V. Golikova
- Department of Pharmacokinetics & Pharmacodynamics, Gause Institute of New Antibiotics, 11 Bolshaya Pirogovskaya Street, 119021 Moscow, Russia; (K.N.A.); (E.N.S.); (D.A.K.)
| | - Kamilla N. Alieva
- Department of Pharmacokinetics & Pharmacodynamics, Gause Institute of New Antibiotics, 11 Bolshaya Pirogovskaya Street, 119021 Moscow, Russia; (K.N.A.); (E.N.S.); (D.A.K.)
| | - Elena N. Strukova
- Department of Pharmacokinetics & Pharmacodynamics, Gause Institute of New Antibiotics, 11 Bolshaya Pirogovskaya Street, 119021 Moscow, Russia; (K.N.A.); (E.N.S.); (D.A.K.)
| | - Daria A. Kondratieva
- Department of Pharmacokinetics & Pharmacodynamics, Gause Institute of New Antibiotics, 11 Bolshaya Pirogovskaya Street, 119021 Moscow, Russia; (K.N.A.); (E.N.S.); (D.A.K.)
| | - Nika F. Petrova
- National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (N.F.P.); (M.A.P.)
| | - Mayya A. Petrova
- National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (N.F.P.); (M.A.P.)
| | - Stephen H. Zinner
- Harvard Medical School, Department of Medicine, Mount Auburn Hospital, 330 Mount Auburn Street., Cambridge, MA 02138, USA;
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Vásquez-Ponce F, Bispo J, Becerra J, Fontana H, Pariona JGM, Esposito F, Fuga B, Oliveira FA, Brunetti F, Power P, Gutkind G, Schreiber AZ, Lincopan N. Emergence of KPC-113 and KPC-114 variants in ceftazidime-avibactam-resistant Klebsiella pneumoniae belonging to high-risk clones ST11 and ST16 in South America. Microbiol Spectr 2023; 11:e0037423. [PMID: 37671877 PMCID: PMC10580961 DOI: 10.1128/spectrum.00374-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/18/2023] [Indexed: 09/07/2023] Open
Abstract
Two novel variants of Klebsiella pneumoniae carbapenemase (KPC) associated with resistance to ceftazidime-avibactam (CZA) and designated as KPC-113 and KPC-114 by NCBI were identified in 2020, in clinical isolates of Klebsiella pneumoniae in Brazil. While K. pneumoniae of ST16 harbored the blaKPC-113 variant on an IncFII-IncFIB plasmid, K. pneumoniae of ST11 carried the blaKPC-114 variant on an IncN plasmid. Both isolates displayed resistance to broad-spectrum cephalosporins, β-lactam inhibitors, and ertapenem and doripenem, whereas K. pneumoniae producing KPC-114 showed susceptibility to imipenem and meropenem. Whole-genome sequencing and in silico analysis revealed that KPC-113 presented a Gly insertion between Ambler positions 264 and 265 (R264_A265insG), whereas KPC-114 displayed two amino acid insertions (Ser-Ser) between Ambler positions 181 and 182 (S181_P182insSS) in KPC-2, responsible for CZA resistance profiles. Our results confirm the emergence of novel KPC variants associated with resistance to CZA in international clones of K. pneumoniae circulating in South America. IMPORTANCE KPC-2 carbapenemases are endemic in Latin America. In this regard, in 2018, ceftazidime-avibactam (CZA) was authorized for clinical use in Brazil due to its significant activity against KPC-2 producers. In recent years, reports of resistance to CZA have increased in this country, limiting its clinical application. In this study, we report the emergence of two novel KPC-2 variants, named KPC-113 and KPC-114, associated with CZA resistance in Klebsiella pneumoniae strains belonging to high-risk clones ST11 and ST16. Our finding suggests that novel mutations in KPC-2 are increasing in South America, which is a critical issue deserving active surveillance.
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Affiliation(s)
- Felipe Vásquez-Ponce
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Jessica Bispo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Johana Becerra
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Jesus G. M. Pariona
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Flavio A. Oliveira
- School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Florencia Brunetti
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriologia y Virología Molecular, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo Power
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriologia y Virología Molecular, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gabriel Gutkind
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriologia y Virología Molecular, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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Guo H, Wu Y, Li L, Wang J, Xu J, He F. Global emergence of carbapenem-resistant Klebsiella pneumoniae co-carrying multiple carbapenemases. Comput Struct Biotechnol J 2023; 21:3557-3563. [PMID: 37501706 PMCID: PMC10368534 DOI: 10.1016/j.csbj.2023.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) co-carrying multiple carbapenemases is complicating clinical treatment. This study aimed to investigate the global dissemination trends of CRKP strains that co-carry multiple carbapenemases. The CRKP isolate KP424 co-carrying blaNDM-1 and blaKPC-2, recovered from a stool specimen, was identified by the NG-Test Carba 5 test, and the genome sequence was further determined by using Nanopore MinION and Illumina NovaSeq 6000 technologies. The genome sequences of the CRKP strains carrying multiple carbapenemase genes were further retrieved from the NCBI GenBank database. Thirteen antimicrobial resistance genes, including blaNDM-1 and blaKPC-2, have been identified in KP424, with blaNDM-1 and blaKPC-2 located on different plasmids. In total, 832 genome sequences of CRKP strains co-carrying two carbapenemase genes were retrieved from the NCBI database. Strains carrying both blaNDM and blaOXA-48-like accounted for 665 (79.9 %) of the total strains, ranking first, and those carrying both blaKPC and blaNDM accounted for 103 (12.4 %), ranking second. The prevalence of CRKP strains co-carrying two carbapenemase genes increased significantly over time, from 0.40 % in 2010 to 9.67 % in 2021. The proportion of strains carrying both blaKPC and blaNDM has also increased, from 0.00 % in 2010 to 4.40 % in 2021. The strains carrying both blaKPC and blaNDM had the highest prevalence (66.7 %, 52/78) in China, while those carrying both blaNDM and blaOXA-48-like had the highest prevalence worldwide. Multiple-carbapenemase producers pose a great threat to public health; further research on the mechanisms underlying multiple carbapenemase gene occurrence is required to prevent their global dissemination.
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Affiliation(s)
- Hao Guo
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Lirong Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Jianfeng Wang
- Department of Respiratory and Critical Care Medicine, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, Zhejiang 310003, China
| | - Juan Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
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Caliskan-Aydogan O, Alocilja EC. A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques. Microorganisms 2023; 11:1491. [PMID: 37374993 DOI: 10.3390/microorganisms11061491] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.
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Affiliation(s)
- Oznur Caliskan-Aydogan
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lansing, MI 48824, USA
| | - Evangelyn C Alocilja
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lansing, MI 48824, USA
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Morgado S, Fonseca E, Vicente AC. Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources. Microorganisms 2022; 10:2281. [PMID: 36422351 PMCID: PMC9697336 DOI: 10.3390/microorganisms10112281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/03/2023] Open
Abstract
The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environment to humans. We therefore performed a genomic surveillance analysis of the KpSC using every public genome in Brazil, aiming to show their local and global relationships, and the connectivity of antibiotic resistance and virulence considering human, animal, and environmental sources. The 390 genomes from distinct sources encompassed the K. pneumoniae, Klebsiella quasipneumoniae subsp. quasipneumoniae, Klebsiella quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, Klebsiella variicola subsp. tropica, and Klebsiella grimontii species and subspecies. K. pneumoniae harbored dozens of antibiotic resistance genes, while most of the genomes belong to the high-risk pandemic CC258 occurring in humans, animals, and the environment. In K. pneumoniae ST11, a high prevalence of the virulence determinants yersiniabactin, colibactin, and T6SS was revealed in association with multi-drug resistance (MDR), including carbapenem resistance. A diversity of resistance genes is carried by plasmids, some shared between strains from different STs, regions, and sources. Therefore, here were revealed some factors driving the success of KpSC as a pathogen.
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Affiliation(s)
| | | | - Ana Carolina Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Av. Brasil, 4365—Manguinhos, Rio de Janeiro 21040-900, Brazil
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Koreň J, Andrezál M, Drahovská H, Hubenáková Z, Liptáková A, Maliar T. Next-Generation Sequencing of Carbapenem-Resistant Klebsiella pneumoniae Strains Isolated from Patients Hospitalized in the University Hospital Facilities. Antibiotics (Basel) 2022; 11:1538. [PMID: 36358193 PMCID: PMC9686475 DOI: 10.3390/antibiotics11111538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 07/30/2023] Open
Abstract
Carbapenem-resistant (CR) Klebsiella pneumoniae represents an urgent worldwide threat. We focused on CR K. pneumoniae in selected facilities of the University Hospital Bratislava (UHB) to investigate sequence types (STs), clonal relatedness, and antimicrobial resistance. Suspected carbapenem-nonsusceptible K. pneumoniae strains were obtained from hospitalized patients. Further examination included carbapenemase confirmation, cgMLST, and quantitative susceptibility testing. Of the total 41 CR K. pneumoniae strains, 26 (63.4%) were determined as ST11 in hospital No. 1; of these ST11, 22 (84.6%) were found in the first internal clinic. Six (14.6%) ST258 and three (7.3%) ST584 occurred in hospital No. 2; the most, i.e., four (66.7%), ST258 were detected in the geriatric clinic. In hospital No. 3, we found two (4.8%) ST584 and one (2.4%) ST258. Of the ST11 set, 24 (92.3%) produced NDM-1. Furthermore, seven (87.5) ST258 and five (100%) ST584 strains generated KPC-2. Antimicrobial resistance was as follows: ertapenem 97.6%, meropenem 63.4%, tigecycline 7.3%, eravacycline 7.3%, and colistin 2.5%. We revealed a presumably epidemiological association of ST11 with transmission, particularly in the first internal clinic of hospital No. 1, while ST258 and ST584 were related to interhospital dissemination between medical facilities No. 2 and No. 3. It is essential to prevent the circulation of these pathogens within and between healthcare facilities.
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Affiliation(s)
- Ján Koreň
- Institute of Microbiology, Faculty of Medicine, Comenius University, University Hospital Bratislava, 81108 Bratislava, Slovakia
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Zuzana Hubenáková
- Institute of Microbiology, Faculty of Medicine, Comenius University, University Hospital Bratislava, 81108 Bratislava, Slovakia
| | - Adriána Liptáková
- Institute of Microbiology, Faculty of Medicine, Comenius University, University Hospital Bratislava, 81108 Bratislava, Slovakia
| | - Tibor Maliar
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius in Trnava, 91701 Trnava, Slovakia
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Ribeiro ÁCDS, Santos FF, Moses IB, Minarini LADR, Gales AC. Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones. Microb Drug Resist 2022; 28:1037-1042. [DOI: 10.1089/mdr.2022.0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ághata Cardoso da Silva Ribeiro
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Ikechukwu Benjamin Moses
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
- Department of Applied Microbiology, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - Luciene Andrade da Rocha Minarini
- Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), Diadema, São Paulo, Brazil
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
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Martins WMBS, Cino J, Lenzi MH, Sands K, Portal E, Hassan B, Dantas PP, Migliavacca R, Medeiros EA, Gales AC, Toleman MA. Diversity of lytic bacteriophages against XDR Klebsiella pneumoniae sequence type 16 recovered from sewage samples in different parts of the world. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156074. [PMID: 35623509 DOI: 10.1016/j.scitotenv.2022.156074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Bacteriophages (phages) are viruses considered to be natural bacterial predators and widely detected in aquatic environments. Sewage samples are an important source of phage isolation since high density and diversity of bacterial cells are present, due to human, animal and household fluids. This study aims to investigate and characterise phages against an extremely drug-resistant (XDR) lineage, Klebsiella pneumoniae ST16, using sewage samples from different parts of the World. Sewage samples from Brazil, Bangladesh, Saudi Arabia, Thailand and the United Kingdom were collected and used to investigate phages against ten K. pneumoniae ST16 (hosts) recovered from infection sites. The phages were microbiological and genetically characterised by double-agar overlay (DLA), transmission electron microscopy and Illumina WGS. The host range against K. pneumoniae belonging to different sequence types was evaluated at different temperatures by spot test. Further phage characterisation, such as efficiency of plating, optimal phage temperature, and pH/temperature susceptibility, were conducted. Fourteen lytic phages were isolated, belonging to Autographiviridae, Ackermannviridae, Demerecviridae, Drexlerviridae, and Myoviridae families, from Brazil, Bangladesh, Saudi Arabia and Thailand and demonstrated a great genetic diversity. The viruses had good activity against our collection of clinical K. pneumoniae ST16 at room temperature and 37 °C, but also against other important Klebsiella clones such as ST11, ST15, and ST258. Temperature assays showed lytic activity in different temperatures, except for PWKp18 which only had activity at room temperature. Phages were stable between pH 5 and 10 with minor changes in phage activity, and 70 °C was the temperature able to kill all phages in this study. Using sewage from different parts of the World allowed us to have a set of highly efficient phages against an K. pneumoniae ST16 that can be used in the future to develop new tools to combat infections in humans or animals caused by this pathogen.
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Affiliation(s)
- Willames M B S Martins
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom; Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil.
| | - Juliana Cino
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Michael H Lenzi
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom; Department of Zoology, University of Oxford, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Brekhna Hassan
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Priscila P Dantas
- Universidade Federal de São Paulo, Hospital Epidemiology Committee, Hospital São Paulo, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, São Paulo, Brazil
| | - Roberta Migliavacca
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, 27100 Pavia, Italy
| | - Eduardo A Medeiros
- Universidade Federal de São Paulo, Hospital Epidemiology Committee, Hospital São Paulo, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, São Paulo, Brazil
| | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Mark A Toleman
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom.
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11
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Migliorini LB, Leaden L, de Sales RO, Correa NP, Marins MM, Koga PCM, Toniolo ADR, de Menezes FG, Martino MDV, Mingorance J, Severino P. The Gastrointestinal Load of Carbapenem-Resistant Enterobacteriacea Is Associated With the Transition From Colonization to Infection by Klebsiella pneumoniae Isolates Harboring the blaKPC Gene. Front Cell Infect Microbiol 2022; 12:928578. [PMID: 35865821 PMCID: PMC9294314 DOI: 10.3389/fcimb.2022.928578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 01/15/2023] Open
Abstract
Background Healthcare-associated infections by carbapenem-resistant Klebsiella pneumoniae are difficult to control. Virulence and antibiotic resistance genes contribute to infection, but the mechanisms associated with the transition from colonization to infection remain unclear. Objective We investigated the transition from carriage to infection by K. pneumoniae isolates carrying the K. pneumoniae carbapenemase–encoding gene blaKPC (KpKPC). Methods KpKPC isolates detected within a 10-year period in a single tertiary-care hospital were characterized by pulsed-field gel electrophoresis (PFGE), multilocus sequencing typing, capsular lipopolysaccharide and polysaccharide typing, antimicrobial susceptibility profiles, and the presence of virulence genes. The gastrointestinal load of carbapenem-resistant Enterobacteriaceae and of blaKPC-carrying bacteria was estimated by relative quantification in rectal swabs. Results were evaluated as contributors to the progression from carriage to infection. Results No PGFE type; ST-, K-, or O-serotypes; antimicrobial susceptibility profiles; or the presence of virulence markers, such yersiniabactin and colibactin, were associated with carriage or infection, with ST437 and ST11 being the most prevalent clones. Admission to intensive and semi-intensive care units was a risk factor for the development of infections (OR 2.79, 95% CI 1.375 to 5.687, P=0.005), but higher intestinal loads of carbapenem-resistant Enterobacteriaceae or of blaKPC-carrying bacteria were the only factors associated with the transition from colonization to infection in this cohort (OR 8.601, 95% CI 2.44 to 30.352, P<0.001). Conclusion The presence of resistance and virulence mechanisms were not associated with progression from colonization to infection, while intestinal colonization by carbapenem-resistant Enterobacteriacea and, more specifically, the load of gastrointestinal carriage emerged as an important determinant of infection.
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Affiliation(s)
- Letícia Busato Migliorini
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Laura Leaden
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Romário Oliveira de Sales
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | - Maryana Mara Marins
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | | | | | | | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
- *Correspondence: Patricia Severino,
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12
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Wang-Wang JH, Bordoy AE, Martró E, Quesada MD, Pérez-Vázquez M, Guerrero-Murillo M, Tiburcio A, Navarro M, Castellà L, Sopena N, Casas I, Saludes V, Giménez M, Cardona PJ. Evaluation of Fourier Transform Infrared Spectroscopy as a First-Line Typing Tool for the Identification of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Outbreaks in the Hospital Setting. Front Microbiol 2022; 13:897161. [PMID: 35756036 PMCID: PMC9218594 DOI: 10.3389/fmicb.2022.897161] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/19/2022] [Indexed: 12/20/2022] Open
Abstract
Early detection of pathogen cross-transmission events and environmental reservoirs is needed to control derived nosocomial outbreaks. Whole-genome sequencing (WGS) is considered the gold standard for outbreak confirmation, but, in most cases, it is time-consuming and has elevated costs. Consequently, the timely incorporation of WGS results to conventional epidemiology (CE) investigations for rapid outbreak detection is scarce. Fourier transform infrared spectroscopy (FTIR) is a rapid technique that establishes similarity among bacteria based on the comparison of infrared light absorption patterns of bacterial polysaccharides and has been used as a typing tool in recent studies. The aim of the present study was to evaluate the performance of the FTIR as a first-line typing tool for the identification of extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) outbreaks in the hospital setting in comparison with CE investigations using WGS as the gold standard method. Sixty-three isolates of ESBL-Kp collected from 2018 to 2021 and classified according to CE were typed by both FTIR and WGS. Concordance was measured using the Adjusted Rand index (AR) and the Adjusted Wallace coefficient (AW) for both CE and FTIR clustering considering WGS as the reference method. Both AR and AW were significantly higher for FTIR clustering than CE clustering (0.475 vs. 0.134, p = 0.01, and 0.521 vs. 0.134, p = 0.009, respectively). Accordingly, FTIR inferred more true clustering relationships than CE (38/42 vs. 24/42, p = 0.001). However, a similar proportion of genomic singletons was detected by both FTIR and CE (13/21 vs. 12/21, p = 1). This study demonstrates the utility of the FTIR method as a quick, low-cost, first-line tool for the detection of ESBL-Kp outbreaks, while WGS analyses are being performed for outbreak confirmation and isolate characterization. Thus, clinical microbiology laboratories would benefit from integrating the FTIR method into CE investigations for infection control measures in the hospital setting.
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Affiliation(s)
- Jun Hao Wang-Wang
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Antoni E Bordoy
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Elisa Martró
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Dolores Quesada
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Pérez-Vázquez
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mercedes Guerrero-Murillo
- Clinical Genomics Research Unit, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Badalona, Spain.,Clinical Genomics Unit, Clinical Genetics Service, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Can Ruti Campus, Badalona, Spain
| | - Andrea Tiburcio
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Marina Navarro
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Laia Castellà
- Enfermería Control de Infección, Dirección Enfermería, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Nieves Sopena
- Infectious Diseases Department, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Irma Casas
- Preventive Medicine Department, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Verónica Saludes
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Montserrat Giménez
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pere-Joan Cardona
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Germans Trias i Pujol University Hospital, Badalona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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13
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Camargo CH. Current status of NDM-producing Enterobacterales in Brazil: a narrative review. Braz J Microbiol 2022; 53:1339-1344. [PMID: 35690653 DOI: 10.1007/s42770-022-00779-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/03/2022] [Indexed: 01/05/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales was first detected in Brazil in 2014, in a Providencia rettgeri isolate recovered from surveillance swabs in the Southern region. Since then, an increasing number of NDM enzymes have been reported in different species. Nevertheless, comprehensive data on the current epidemiology of NDM-producing Enterobacterales in Brazil are lacking. Therefore, this study reviewed the available information on the status of NDM-producing bacteria in Brazil. The main finding was the diversity of bacteria producing NDM, including Klebsiella, Enterobacter, Morganella, Proteus, Escherichia, and Providencia. Limited data on clonality are available, but a few studies report different clonal backgrounds in NDM-producing K. pneumoniae, likely indicating local outbreaks. Over the years, a rise in the number of reported strains in different locations has been verified; however, different biases may have contributed to this finding. Therefore, a national surveillance study is warranted to identify the actual prevalence and incidence of NDM-producing Enterobacterales in Brazil and their role in patient management and outcome.
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Affiliation(s)
- Carlos Henrique Camargo
- Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 9º Andar, 351, São Paulo, CEP 01246-902, Brazil.
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14
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Tsilipounidaki K, Athanasakopoulou Z, Müller E, Burgold-Voigt S, Florou Z, Braun SD, Monecke S, Gatselis NK, Zachou K, Stefos A, Tsagalas I, Sofia M, Spyrou V, Billinis C, Dalekos GN, Ehricht R, Petinaki E. Plethora of Resistance Genes in Carbapenem-Resistant Gram-Negative Bacteria in Greece: No End to a Continuous Genetic Evolution. Microorganisms 2022; 10:microorganisms10010159. [PMID: 35056608 PMCID: PMC8781379 DOI: 10.3390/microorganisms10010159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/02/2022] Open
Abstract
Carbapenem-resistant Gram-negative bacteria are a public health threat that requires urgent action. The fact that these pathogens commonly also harbor resistance mechanisms for several other antimicrobial classes further reduces patient treatment options. The present study aimed to provide information regarding the multidrug resistance genetic background of carbapenem-resistant Gram-negative bacteria in Central Greece. Strains from a tertiary care hospital, collected during routine practice, were characterized using a DNA microarray-based assay. Various different resistance determinants for carbapenems, other beta-lactams, aminoglycosides, quinolones, trimethoprim, sulfonamides and macrolides were detected among isolates of the same sequence type. Eighteen different multidrug resistance genomic profiles were identified among the twenty-four K. pneumoniae ST258, seven different profiles among the eight K. pneumoniae ST11, four profiles among the six A. baumannii ST409 and two among the three K. oxytoca. This report describes the multidrug resistance genomic background of carbapenem-resistant Gram-negative bacteria from a tertiary care hospital in Central Greece, providing evidence of their continuous genetic evolution.
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Affiliation(s)
- Katerina Tsilipounidaki
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
| | - Zoi Athanasakopoulou
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (C.B.)
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.B.-V.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sindy Burgold-Voigt
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.B.-V.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Zoi Florou
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.B.-V.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.B.-V.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institut fuer Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Dresden, 01307 Dresden, Germany
| | - Nikolaos K. Gatselis
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
| | - Kalliopi Zachou
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
| | - Aggelos Stefos
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
| | - Ilias Tsagalas
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (C.B.)
| | - Vassiliki Spyrou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece;
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (C.B.)
- Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece
| | - George N. Dalekos
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.B.-V.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Efthymia Petinaki
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (Z.F.); (N.K.G.); (K.Z.); (A.S.); (I.T.); (G.N.D.)
- Correspondence:
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15
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The Spread of NDM-1 and NDM-7-Producing Klebsiella pneumoniae Is Driven by Multiclonal Expansion of High-Risk Clones in Healthcare Institutions in the State of Pará, Brazilian Amazon Region. Antibiotics (Basel) 2021; 10:antibiotics10121527. [PMID: 34943739 PMCID: PMC8698286 DOI: 10.3390/antibiotics10121527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Carbapenem resistance among Klebsiella pneumoniae isolates is often related to carbapenemase genes, located in genetic transmissible elements, particularly the blaKPC gene, which variants are spread in several countries. Recently, reports of K. pneumoniae isolates harboring the blaNDM gene have increased dramatically along with the dissemination of epidemic high-risk clones (HRCs). In the present study, we report the multiclonal spread of New Delhi metallo-beta-lactamase (NDM)-producing K. pneumoniae in different healthcare institutions in the state of Pará, Northern Brazil. A total of 23 NDM-producing isolates were tested regarding antimicrobial susceptibility testing features, screening of carbapenemase genes, and genotyping by multilocus sequencing typing (MLST). All K. pneumoniae isolates were determined as multidrug-resistant (MDR), being mainly resistant to carbapenems, cephalosporins, and fluoroquinolones. The blaNDM-7 (60.9%-14/23) and blaNDM-1 (34.8%-8/23) variants were detected. MLST genotyping revealed the predomination of HRCs, including ST11/CC258, ST340/CC258, ST15/CC15, ST392/CC147, among others. To conclude, the present study reveals the contribution of HRCs and non-HRCs in the spread of NDM-1 and NDM-7-producing K. pneumoniae isolates in Northern (Amazon region) Brazil, along with the first detection of NDM-7 variant in Latin America and Brazil, highlighting the need for surveillance and control of strains that may negatively impact healthcare and antimicrobial resistance.
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16
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Stallbaum LR, Pruski BB, Amaral SC, de Freitas SB, Wozeak DR, Hartwig DD. Phenotypic and molecular evaluation of biofilm formation in Klebsiella pneumoniae carbapenemase (KPC) isolates obtained from a hospital of Pelotas, RS, Brazil. J Med Microbiol 2021; 70. [PMID: 34779756 DOI: 10.1099/jmm.0.001451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. A significant cause of mortality in the intensive care unit (ICU) is multidrug-resistant (MDR) Gram-negative bacteria, such as Klebsiella pneumoniae carbapenemase (KPC). Biofilm production is a key factor in KPC colonization and persistence in the host, making the treatment difficult.Gap Statement. The aim of this study was to evaluate the antibiotic resistance, molecular and phenotypic biofilm profiles of 12 KPC isolates associated with nosocomial infection in a hospital in Pelotas, Rio Grande do Sul, Brazil.Methodology. Clinical isolates were obtained from different sources, identified and characterized by antibiotic resistance and carbapenemase synthesis following the Clinical and Laboratory Standards Institute (CLSI) guidelines. Polymerase chain reaction (PCR) was used to evaluate the presence of carbapenemase (blaKPC) and biofilm formation-associated genes (fimA, fimH, rmpA, ecpA, mrkD and wabG). Additionally, phenotypic evaluation of in vitro biofilm formation capacity was evaluated by Congo red agar (CRA) assay and the crystal violet staining method.Results. The 12 isolates evaluated in this study presented the blaKPC gene and were positive for synthesizing carbapenemases in vitro. In the carbapenem class, 83.3 % isolates were resistant and 16.7 % intermediately resistant to imipenem and meropenem. Molecular analyses found that the fimA and wabG genes were detected in 75 % of isolates, while fimH and ecpA were detected in 42 % and mrkD were detected in 8.3 % (1). The CRA assay demonstrated that all isolates were slime producers and 91.7 % (11) of isolates were classified as strong and 8.3 % (1) as moderate biofilm producers by the crystal violet staining method. The optical density (OD540nm) for strong biofilm formers ranged from 0.80±0.05 to 2.47±0.28 and was 0.55±0.12 for moderate biofilm formers.Conclusion. Our study revealed a high level of antibiotic resistance and biofilm formation in KPC isolates obtained from a hospital in Pelotas, RS, Brazil.
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Affiliation(s)
- Letícia Roloff Stallbaum
- Laboratory of Bacteriology and Bioassays (LaBBio), Department of Microbiology and Parasitology, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Beatriz Bohns Pruski
- Laboratory of Bacteriology and Bioassays (LaBBio), Department of Microbiology and Parasitology, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Suelen Cavalheiro Amaral
- Laboratory of Bacteriology and Bioassays (LaBBio), Department of Microbiology and Parasitology, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Stella Buchhorn de Freitas
- Laboratory of Bacteriology and Bioassays (LaBBio), Department of Microbiology and Parasitology, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Daniela Rodriguero Wozeak
- Laboratory of Bacteriology and Bioassays (LaBBio), Department of Microbiology and Parasitology, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Daiane Drawanz Hartwig
- Laboratory of Bacteriology and Bioassays (LaBBio), Department of Microbiology and Parasitology, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
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17
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Prevalence of carbapenemases and ESBL encoding genes among K. pneumoniae isolates obtained from an educational hospital in Ahvaz, Southwestern Iran. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Silveira MC, Rocha-de-Souza CM, de Oliveira Santos IC, Pontes LDS, Oliveira TRTE, Tavares-Teixeira CB, Cossatis NDA, Pereira NF, da Conceição-Neto OC, da Costa BS, Rodrigues DCS, Albano RM, da Silva FAB, Marques EA, Leão RS, Carvalho-Assef APD. Genetic Basis of Antimicrobial Resistant Gram-Negative Bacteria Isolated From Bloodstream in Brazil. Front Med (Lausanne) 2021; 8:635206. [PMID: 33791325 PMCID: PMC8005515 DOI: 10.3389/fmed.2021.635206] [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: 11/30/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant microorganisms are a well-known global problem, and gram-negative bacilli are top-ranking. When these pathogens are associated with bloodstream infections (BSI), outcomes become even worse. Here we applied whole-genome sequencing to access information about clonal distribution, resistance mechanism diversity and other molecular aspects of gram-negative bacilli (GNB) isolated from bloodstream infections in Brazil. It was possible to highlight international high-risk clones circulating in the Brazilian territory, such as CC258 for Klebsiella pneumoniae, ST79 for Acinetobacter baumannii and ST233 for Pseudomonas aeruginosa. Important associations can be made such as a negative correlation between CRISPR-Cas and K. pneumoniae CC258, while the genes blaTEM, blaKPC and blaCTX−M are highly associated with this clone. Specific relationships between A. baumannii clones and blaOXA−51 variants were also observed. All P. aeruginosa ST233 isolates showed the genes blaVIM and blaOXA486. In addition, some trends could be identified, where a new P. aeruginosa MDR clone (ST3079), a novel A. baumannii clonal profile circulating in Brazil (ST848), and important resistance associations in the form of blaVIM−2 and blaIMP−56 being found together in one ST233 strain, stand out. Such findings may help to develop approaches to deal with BSI and even other nosocomial infections caused by these important GNB.
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Affiliation(s)
- Melise Chaves Silveira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | - Leilane da Silva Pontes
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | - Nataly de Almeida Cossatis
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | - Natacha Ferreira Pereira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Bianca Santos da Costa
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Rodolpho Mattos Albano
- Departamento de Bioquímica, Instituto de Biologia Roberto de Alcântara Gome, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
| | | | - Elizabeth Andrade Marques
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
| | - Robson Souza Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
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Roch M, Sierra R, Sands K, Martins WMBS, Schrenzel J, Walsh TR, Gales AC, Andrey DO. Vertical and horizontal dissemination of an IncC plasmid harbouring rmtB 16S rRNA methylase gene, conferring resistance to plazomicin, among invasive ST258 and ST16 KPC-producing Klebsiella pneumoniae. J Glob Antimicrob Resist 2020; 24:183-189. [PMID: 33373732 DOI: 10.1016/j.jgar.2020.12.006] [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: 08/29/2020] [Revised: 11/13/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES Carbapenem resistance in Klebsiella pneumoniae is a major clinical challenge. Aminoglycosides remain an important asset in the current therapeutic arsenal to treat these infections. We examined aminoglycoside resistance phenotypes and genomics in a collection of 100 invasive KPC-producing K. pneumoniae isolates sequentially collected in a Brazilian tertiary hospital between 2014 and 2016. METHODS Aminoglycoside susceptibility testing was performed. We used a combined long-read (MinION) and short-read (Illumina) whole-genome sequencing strategy to provide a genomic picture of aminoglycoside resistance genes, with particular emphasis on 16S rRNA methyltransferases and related plasmids. RESULTS 68% of the strains were resistant to gentamicin and 42% to amikacin, with 35% resistant to both of these commonly used aminoglycosides. We identified the 16S rRNA methyltransferase gene rmtB in 30% of these isolates: 97% (29/30) belonged to sequence type 258 (ST258) and a single isolate to the emergent ST16 clone. In ST258 and ST16 the rmtB gene was located on large IncC plasmids of 177 kb and 174 kb, respectively, highly similar to a plasmid previously identified in Proteus mirabilis in the same hospital. Moreover, 99% of the isolates remained susceptible to the veterinary-approved drug apramycin, currently under clinical development for human medicine. CONCLUSION Such findings in geographically and temporally related isolates suggest a combination of vertical clonal spread as well as horizontal interspecies and intraspecies plasmid transfer. This broad rmtB dissemination in an endemic setting for KPC-producing clones is worrisome since it provides resistance to most clinically available aminoglycosides, including the novel aminoglycoside-modifying enzyme-resistant plazomicin.
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Affiliation(s)
- Mélanie Roch
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Roberto Sierra
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Willames M B S Martins
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK; Universidade Federal de São Paulo (UNIFESP), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Jacques Schrenzel
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Timothy R Walsh
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Ana C Gales
- Universidade Federal de São Paulo (UNIFESP), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Diego O Andrey
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.
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Taggar G, Attiq Rheman M, Boerlin P, Diarra MS. Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment. Antibiotics (Basel) 2020; 9:antibiotics9100693. [PMID: 33066205 PMCID: PMC7602032 DOI: 10.3390/antibiotics9100693] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
The Enterobacteriales order consists of seven families including Enterobacteriaceae, Erwiniaceae, Pectobacteriaceae, Yersiniaceae, Hafniaceae, Morganellaceae, and Budviciaceae and 60 genera encompassing over 250 species. The Enterobacteriaceae is currently considered as the most taxonomically diverse among all seven recognized families. The emergence of carbapenem resistance (CR) in Enterobacteriaceae caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. Carbapenem-resistant Enterobacteriaceae (CRE) isolates have been reported not only in nosocomial and community-acquired pathogens but also in food-producing animals, companion animals, and the environment. The reported carbapenemases in Enterobacteriaceae from different sources belong to the Ambler class A (blaKPC), class B (blaIMP, blaVIM, blaNDM), and class D (blaOXA-48) β-lactamases. The carbapenem encoding genes are often located on plasmids or associated with various mobile genetic elements (MGEs) like transposons and integrons, which contribute significantly to their spread. These genes are most of the time associated with other antimicrobial resistance genes such as other β-lactamases, as well as aminoglycosides and fluoroquinolones resistance genes leading to multidrug resistance phenotypes. Control strategies to prevent infections due to CRE and their dissemination in human, animal and food have become necessary. Several factors involved in the emergence of CRE have been described. This review mainly focuses on the molecular epidemiology of carbapenemases in members of Enterobacteriaceae family from humans, animals, food and the environment.
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Affiliation(s)
- Gurleen Taggar
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Muhammad Attiq Rheman
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Moussa Sory Diarra
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
- Correspondence:
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