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Wilhelm CM, Antochevis LC, Magagnin CM, Arns B, Vieceli T, Pereira DC, Lutz L, de Souza ÂC, Dos Santos JN, Guerra RR, Medeiros GS, Santoro L, Falci DR, Rigatto MH, Barth AL, Martins AF, Zavascki AP. Susceptibility evaluation of novel beta-lactam/beta-lactamase inhibitor combinations against carbapenem-resistant Klebsiella pneumoniae from bloodstream infections in hospitalized patients in Brazil. J Glob Antimicrob Resist 2024:S2213-7165(24)00118-8. [PMID: 38936472 DOI: 10.1016/j.jgar.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/13/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
Novel beta-lactams/beta-lactamase inhibitors (BIBLI) combinations are commercially available and they have been used for treating carbapenem-resistant Klebsiella pneumoniae (CRKP) infections. Continuous surveillance of susceptibility profile and resistance mechanisms identification are necessary to monitor the evolution of resistance as these agents are used. The purpose of this study was to evaluate susceptibility rates to ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam in CRKP isolates from patients with bloodstream infection screened for a randomized clinical trial in Brazil. Minimum inhibitory concentration (MIC) was determined by gradient diffusion strip method for meropenem, ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam. Carbapenemase genes were detected by multiplex qPCR. KPC-producing isolates showing resistance to any BLBLI and NDM-producing isolates showing susceptibility to any BLBLI were further submitted to whole genome sequencing. From a total of 69 CRKP isolates, 39 were positive for blaKPC, 19 for blaNDM and 11 for blaKPC and blaNDM. KPC-producing isolates demonstrated susceptibility rates above 94% for all BLBLI. Two isolates with resistance to meropenem/vaborbactam showed a Gly and Asp duplication at OmpK36 protein and truncated ompK35 genes. All NDM-producing isolates, including KPC and NDM coproducers, demonstrated susceptibility rates for ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam of 0%, 9.1 to 21.1% and 9.1 to 26.3%, respectively. Five NDM-producing isolates that presented susceptibility to BLBLI also demonstrated alterations in porins. This study demonstrated that, although high susceptibility rates to the BLBLI were found, KPC-2 isolates can also demonstrate resistance due to porin mutations. Additionally, NDM-1 isolates can demonstrate susceptibility in vitro to the BLBLI.
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Affiliation(s)
- Camila Mörschbächer Wilhelm
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, Brazil.
| | - Laura Czerkster Antochevis
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, Brazil
| | - Cibele Massotti Magagnin
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, Brazil
| | - Beatriz Arns
- Hospital de Clínicas de Porto Alegre, Infectious Diseases Service, Porto Alegre, Brazil
| | - Tarsila Vieceli
- Hospital de Clínicas de Porto Alegre, Infectious Diseases Service, Porto Alegre, Brazil
| | - Dariane Castro Pereira
- Hospital de Clínicas de Porto Alegre, Serviço de Diagnóstico Laboratorial - Unidade de Microbiologia, Porto Alegre, Brasil
| | - Larissa Lutz
- Hospital de Clínicas de Porto Alegre, Serviço de Diagnóstico Laboratorial - Unidade de Microbiologia, Porto Alegre, Brasil
| | - Ândrea Celestino de Souza
- Pontifícia Universidade Católica do Rio Grande do Sul, Hospital São Lucas - Setor de Microbiologia, Porto Alegre, Brasil
| | - Jéssica Nesello Dos Santos
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, Brazil
| | - Rafaela Ramalho Guerra
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, Brazil
| | | | - Lucas Santoro
- Pontifícia Universidade Católica do Rio Grande do Sul, Department of Clinical Medicine, Porto Alegre, Brazil
| | - Diego R Falci
- Hospital de Clínicas de Porto Alegre, Infectious Diseases Service, Porto Alegre, Brazil; Pontifícia Universidade Católica do Rio Grande do Sul, Department of Clinical Medicine, Porto Alegre, Brazil
| | - Maria Helena Rigatto
- Hospital de Clínicas de Porto Alegre, Infectious Diseases Service, Porto Alegre, Brazil; Universidade Federal do Rio Grande do Sul, Department of Internal Medicine, Porto Alegre, Brazil
| | - Afonso Luís Barth
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, Brazil
| | - Andreza Francisco Martins
- Hospital de Clínicas de Porto Alegre, Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Porto Alegre, Brazil
| | - Alexandre Prehn Zavascki
- Hospital de Clínicas de Porto Alegre, Infectious Diseases Service, Porto Alegre, Brazil; Universidade Federal do Rio Grande do Sul, Department of Internal Medicine, Porto Alegre, Brazil
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Silva JTP, Santos FF, Valiatti TB, Valêncio A, Ribeiro ÁCDS, Oliveira LFV, Cay R, Pignatari ACC, Gales AC. Unraveling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying bla NDM-1. J Glob Antimicrob Resist 2024:S2213-7165(24)00110-3. [PMID: 38852850 DOI: 10.1016/j.jgar.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024] Open
Abstract
OBJECTIVE Despite the increasing reports of blaNDM in Enterobacterales in Brazil, comprehensive whole genome sequencing (WGS) data remains scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae (KQPN) clinical strain isolated in Brazil. METHODS The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the BrCAST/EUCAST recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome. RESULTS The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (blaNDM-1, blaCTX-M-15, blaOXA-9, blaOKP-A-5, blaTEM-1), aminoglycosides [aph(3')-VI, aadA1, aac(6')-Ib], and fluoroquinolones (oqxAB, qnrS1, aac(6')-Ib-cr]. Additionally, it was verified the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes: fimABCDEFGHIK (type 1 fimbria), pilW (type IV pili), iutA (aerobactin), entABCDEFS/fepABCDG/fes (Ent siderophores), iroE (salmochelin), and allABCDRS (allantoin utilization). Furthermore, we found that A-73.113 strain belongs to ST1040. CONCLUSION Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood culture in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of blaNDM-1 in Brazilian nosocomial settings.
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Affiliation(s)
- Juliana Thalita P Silva
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Fernanda F Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
| | - Tiago B Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - André Valêncio
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | | | - Rodrigo Cay
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório de Bacteriologia e Imunologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema SP, Brazil
| | - Antônio Carlos C Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
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3
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Takei S, Tabe Y, Miida T, Hishinuma T, Khasawneh A, Kirikae T, Sherchand JB, Tada T. Multidrug-resistant Klebsiella pneumoniae clinical isolates producing NDM- and OXA-type carbapenemase in Nepal. J Glob Antimicrob Resist 2024; 37:233-243. [PMID: 38759919 DOI: 10.1016/j.jgar.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/13/2024] [Accepted: 04/19/2024] [Indexed: 05/19/2024] Open
Abstract
OBJECTIVES The emergence of multidrug-resistant Klebsiella pneumoniae has become a serious problem in medical settings worldwide. METHODS A total of 46 isolates of multidrug-resistant K. pneumoniae were obtained from 2 hospitals in Nepal from October 2018 to April 2019. RESULTS Most of these isolates were highly resistant to carbapenems, aminoglycosides, and fluoroquinolones with the minimum inhibitory concentrations (MICs) of more than 64 µg/mL. These isolates harboured carbapenemase-encoding genes, including blaNDM-1, blaNDM-5, blaOXA-181 and blaOXA-232, and 16S rRNA methyltransferase-encoding genes, including armA, rmtB, rmtC, and rmtF. Multilocus sequence typing revealed that 44 of 46 isolates were high-risk clones such as ST11 (2%), ST14 (4%), ST15 (11%), ST37 (2%), ST101 (2%), ST147 (28%), ST231 (13%), ST340 (4%), and ST395 (28%). In particular, ST395 isolates, which spread across medical settings in Nepal, co-harboured blaNDM-5 and rmtB on IncFII plasmids and co-harboured blaOXA-181/-232 and rmtF on ColKP3 plasmids. Several isolates harboured blaOXA-181 or blaNDM-5 on their chromosomes and multi-copies of blaNDM-1 or genes encoding 16S rRNA methyltransferases on their plasmids. CONCLUSIONS The presented study demonstrates that the high-risk clones of multidrug-resistant K. pneumoniae spread in a clonal manner across hospitals in Nepal.
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Affiliation(s)
- Satomi Takei
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoko Tabe
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomomi Hishinuma
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Abdullah Khasawneh
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Teruo Kirikae
- Department of Microbiome Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Jeevan B Sherchand
- Department of Medical Microbiology, Tribhuvan University, Maharajgunj, Kathmandu, Nepal
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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Kakaraskoska Boceska B, Vilken T, Xavier BB, Kostyanev T, Lin Q, Lammens C, Ellis S, O'Brien S, da Costa RMA, Cook A, Russell N, Bielicki J, Riddell A, Stohr W, Walker AS, Berezin EN, Roilides E, De Luca M, Romani L, Ballot D, Dramowski A, Wadula J, Lochindarat S, Boonkasidecha S, Namiiro F, Ngoc HTB, Tran MD, Cressey TR, Preedisripipat K, Berkley JA, Musyimi R, Zarras C, Nana T, Whitelaw A, da Silva CB, Jaglal P, Ssengooba W, Saha SK, Islam MS, Mussi-Pinhata MM, Carvalheiro CG, Piddock LJV, Heath PT, Malhotra-Kumar S, Sharland M, Glupczynski Y, Goossens H. Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries. Nat Commun 2024; 15:3947. [PMID: 38729951 PMCID: PMC11087563 DOI: 10.1038/s41467-024-48296-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Gram-negative bacteria (GNB) are a major cause of neonatal sepsis in low- and middle-income countries (LMICs). Although the World Health Organization (WHO) reports that over 80% of these sepsis deaths could be prevented through improved treatment, the efficacy of the currently recommended first- and second-line treatment regimens for this condition is increasingly affected by high rates of drug resistance. Here we assess three well known antibiotics, fosfomycin, flomoxef and amikacin, in combination as potential antibiotic treatment regimens by investigating the drug resistance and genetic profiles of commonly isolated GNB causing neonatal sepsis in LMICs. The five most prevalent bacterial isolates in the NeoOBS study (NCT03721302) are Klebsiella pneumoniae, Acinetobacter baumannii, E. coli, Serratia marcescens and Enterobacter cloacae complex. Among these isolates, high levels of ESBL and carbapenemase encoding genes are detected along with resistance to ampicillin, gentamicin and cefotaxime, the current WHO recommended empiric regimens. The three new combinations show excellent in vitro activity against ESBL-producing K. pneumoniae and E. coli isolates. Our data should further inform and support the clinical evaluation of these three antibiotic combinations for the treatment of neonatal sepsis in areas with high rates of multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Biljana Kakaraskoska Boceska
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Tuba Vilken
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tomislav Kostyanev
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sally Ellis
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Seamus O'Brien
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | | | - Aislinn Cook
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Neal Russell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Julia Bielicki
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
- Paediatric Research Centre, University of Basel Children's Hospital, Basel, Switzerland
| | - Amy Riddell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Wolfgang Stohr
- MRC Clinical Trials Unit, University College London, London, UK
| | | | | | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Dept Paediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Maia De Luca
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Lorenza Romani
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Daynia Ballot
- Department of Pediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | | | | | - Flavia Namiiro
- Mulago Specialized Women's and Neonatal Hospital, Kampala, Uganda
| | | | | | - Tim R Cressey
- AMS-PHPT Research Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | | | - James A Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Robert Musyimi
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charalampos Zarras
- Microbiology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Cely Barreto da Silva
- Infection Control and Prevention Service, Santa Casa de Sao Paulo, Sao Paulo, Brazil
| | - Prenika Jaglal
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Willy Ssengooba
- Makerere University, Department of Medical Microbiology, Kampala, Uganda
| | - Samir K Saha
- Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | | | | | | | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Paul T Heath
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Michael Sharland
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Parker EM, Mollenkopf DF, Ballash GA, Li C, Wittum TE. Transcontinental Dissemination of Enterobacterales Harboring blaNDM-1 in Retail Frozen Shrimp. Foodborne Pathog Dis 2024. [PMID: 38563789 DOI: 10.1089/fpd.2023.0161] [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: 04/04/2024] Open
Abstract
The global food trade provides a means of disseminating antimicrobial resistant (AMR) bacteria and genes. Using selective media, carbapenem-resistant species of Enterobacterales (Providencia sp. and Citrobacter sp.), were detected in a single package of imported frozen shrimp purchased from a grocery store in Ohio, USA. Polymerase chain reaction confirmed that both isolates harbored blaNDM-1 genes. Following PacBio long read sequencing, the sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline. The blaNDM-1 genes were found in IncC plasmids, each with different antimicrobial resistance island configuration. We found that the blaNDM-1 AMR islands had close relationships with previously reported environmental, food, and clinical isolates detected in Asia and the United States, highlighting the importance of the food chain in the global dissemination of antimicrobial resistance.
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Affiliation(s)
- Elizabeth M Parker
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Dixie F Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Gregory A Ballash
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Cong Li
- Center for Veterinary Medicine, Office of Applied Science, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Thomas E Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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Al Fadhli AH, Mouftah SF, Jamal WY, Rotimi VO, Ghazawi A. Cracking the Code: Unveiling the Diversity of Carbapenem-Resistant Klebsiella pneumoniae Clones in the Arabian Peninsula through Genomic Surveillance. Antibiotics (Basel) 2023; 12:1081. [PMID: 37508177 PMCID: PMC10376398 DOI: 10.3390/antibiotics12071081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
The rise of antimicrobial resistance is a global challenge that requires a coordinated effort to address. In this study, we examined the genetic similarity of carbapenem-resistant Klebsiella pneumoniae (CRKP) in countries belonging to the Gulf Cooperation Council (GCC) to gain a better understanding of how these bacteria are spreading and evolving in the region. We used in silico genomic tools to investigate the occurrence and prevalence of different types of carbapenemases and their relationship to specific sequence types (STs) of CRKP commonly found in the region. We analyzed 720 publicly available genomes of multi-drug resistant K. pneumoniae isolates collected from six GCC countries between 2011 and 2020. Our findings showed that ST-14 and ST-231 were the most common STs, and 51.7% of the isolates carried blaOXA-48-like genes. Additionally, we identified rare carbapenemase genes in a small number of isolates. We observed a clonal outbreak of ST-231 in Oman, and four Saudi isolates were found to have colistin resistance genes. Our study offers a comprehensive overview of the genetic diversity and resistance mechanisms of CRKP isolates in the GCC region that could aid in developing targeted interventions to combat this pressing global issue.
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Affiliation(s)
- Amani H Al Fadhli
- Laboratory Sciences, Department of Medical, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Jabriya 24923, Kuwait
| | - Shaimaa F Mouftah
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
- Department of Biomedical Sciences, University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Wafaa Y Jamal
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya 24923, Kuwait
| | - Vincent O Rotimi
- Center for Infection Control and Patient Safety, College of Medicine University of Lagos, Idi-Araba 102215, Nigeria
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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7
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Regional transmission patterns of carbapenemase-producing Enterobacterales: A healthcare network analysis. Infect Control Hosp Epidemiol 2023; 44:453-459. [PMID: 35450553 DOI: 10.1017/ice.2022.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Carbapenem-resistant Enterobacterales (CRE) pose a serious public health threat and spread rapidly between healthcare facilities (HCFs) during interfacility patient movement. We examined patterns of transmission of CRE associated with network clustering and positions during patient interfacility transfer. METHODS A retrospective cohort study was conducted in the Greater Houston region ofTexas, , and social network analysis was performed by constructing facility-to-facility patient transfer network using CRE surveillance data. The network method (community detection algorithm) was used to detect clustering patterns of CRE in the network. In addition, network measures of centrality and local connectivity (clustering coefficient) were computed for each healthcare facility. Zero-inflated negative binomial regression analysis was applied to test the association between network measures and facility-specific incidence rate of CRE. RESULTS A network of 268 healthcare facilities was identified, in which 10 acute-care hospitals (ACHs) alone accounted for 63% of identified CRE cases. Transmission of New Delhi metallo-β-lactamase-producing CRE occurred in 3 clusters, yet all cases were traced to patients who had had medical care abroad. The incidence rate of CRE attributed to ACHs was >4-fold (adjusted rate ratio, 4.5; 95% confidence interval [CI], 3.02-6.72) higher than that of long-term care facilities. Each additional patient shared with another HCF conferred a 3% (95% CI, 2%-4%) increase in the incidence rate of CRE at that HCF. CONCLUSIONS The incidence rates of CRE at a given HCF was predicted by the healthcare network metrics. Increased surveillance and selective targeting of high-risk facilities are warranted.
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Traglia GM, Pasteran F, Escalante J, Nishimura B, Tuttobene MR, Subils T, Nuñez MR, Rivollier MG, Corso A, Tolmasky ME, Ramirez MS. Genomic Comparative Analysis of Two Multi-Drug Resistance (MDR) Acinetobacter baumannii Clinical Strains Assigned to International Clonal Lineage II Recovered Pre- and Post-COVID-19 Pandemic. BIOLOGY 2023; 12:358. [PMID: 36979049 PMCID: PMC10045941 DOI: 10.3390/biology12030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND After the emergence of COVID-19, numerous cases of A. baumannii/SARS-CoV-2 co-infection were reported. Whether the co-infecting A. baumannii strains have distinctive characteristics remains unknown. METHODS AND RESULTS A. baumannii AMA_NO was isolated in 2021 from a patient with COVID-19. AMA166 was isolated from a mini-BAL used on a patient with pneumonia in 2016. Both genomes were similar, but they possessed 337 (AMA_NO) and 93 (AMA166) unique genes that were associated with biofilm formation, flagellar assembly, antibiotic resistance, secretion systems, and other functions. The antibiotic resistance genes were found within mobile genetic elements. While both strains harbored the carbapenemase-coding gene blaOXA-23, only the strain AMA_NO carried blaNDM-1. Representative functions coded for by virulence genes are the synthesis of the outer core of lipooligosaccharide (OCL5), biosynthesis and export of the capsular polysaccharide (KL2 cluster), high-efficiency iron uptake systems (acinetobactin and baumannoferrin), adherence, and quorum sensing. A comparative phylogenetic analysis including 239 additional sequence type (ST) 2 representative genomes showed high similarity to A. baumannii ABBL141. Since the degree of similarity that was observed between A. baumannii AMA_NO and AMA166 is higher than that found among other ST2 strains, we propose that they derive from a unique background based on core-genome phylogeny and comparative genome analysis. CONCLUSIONS Acquisition or shedding of specific genes could increase the ability of A. baumannii to infect patients with COVID-19.
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Affiliation(s)
- German Matias Traglia
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo 11200, Uruguay
| | - Fernando Pasteran
- National Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires 1282, Argentina
| | - Jenny Escalante
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Brent Nishimura
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Marisel R. Tuttobene
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario 2000, Argentina
| | - Tomás Subils
- Instituto de Procesos Biotecnológicos y Químicos de Rosario (IPROBYQ, CONICET-UNR), Rosario 2000, Argentina
| | - Maria Rosa Nuñez
- Laboratorio de Microbiología, Hospital Provincial Neuquén Dr. Castro Rendón, Neuquén 8300, Argentina
| | | | - Alejandra Corso
- National Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires 1282, Argentina
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
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Shukla S, Desai S, Bagchi A, Singh P, Joshi M, Joshi C, Patankar J, Maheshwari G, Rajni E, Shah M, Gajjar D. Diversity and Distribution of β-Lactamase Genes Circulating in Indian Isolates of Multidrug-Resistant Klebsiella pneumoniae. Antibiotics (Basel) 2023; 12:antibiotics12030449. [PMID: 36978316 PMCID: PMC10044340 DOI: 10.3390/antibiotics12030449] [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: 01/16/2023] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/30/2023] Open
Abstract
Klebsiella pneumoniae (Kp) has gained prominence in the last two decades due to its global spread as a multidrug-resistant (MDR) pathogen. Further, carbapenem-resistant Kp are emerging at an alarming rate. The objective of this study was (1) to evaluate the prevalence of β-lactamases, especially carbapenemases, in Kp isolates from India, and (2) determine the most prevalent sequence type (ST) and plasmids, and their association with β-lactamases. Clinical samples of K. pneumoniae (n = 65) were collected from various pathology labs, and drug susceptibility and minimum inhibitory concentrations (MIC) were detected. Whole genome sequencing (WGS) was performed for n = 22 resistant isolates, including multidrug-resistant (MDR) (n = 4), extensively drug-resistant (XDR) (n = 15), and pandrug-resistant (PDR) (n = 3) categories, and genomic analysis was performed using various bioinformatics tools. Additional Indian MDRKp genomes (n = 187) were retrieved using the Pathosystems Resource Integration Center (PATRIC) database. Detection of β-lactamase genes, location (on chromosome or plasmid), plasmid replicons, and ST of genomes was carried out using CARD, mlplasmids, PlasmidFinder, and PubMLST, respectively. All data were analyzed and summarized using the iTOL tool. ST231 was highest, followed by ST147, ST2096, and ST14, among Indian isolates. blaampH was detected as the most prevalent gene, followed by blaCTX-M-15 and blaTEM-1. Among carbapenemase genes, blaOXA-232 was prevalent and associated with ST231, ST2096, and ST14, which was followed by blaNDM-5, which was observed to be prevalent in ST147, ST395, and ST437. ST231 genomes were most commonly found to carry Col440I and ColKP3 plasmids. ST16 carried mainly ColKP3, and Col(BS512) was abundantly present in ST147 genomes. One Kp isolate with a novel MLST profile was identified, which carried blaCTX-M-15, blaOXA-1, and blaTEM-1. ST16 and ST14 are mostly dual-producers of carbapenem and ESBL genes and could be emerging high-risk clones in India.
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Affiliation(s)
- Suraj Shukla
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Siddhi Desai
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Ashutosh Bagchi
- Amity Institute of Biotechnology, Amity University of Noida, Noida 201313, Uttar Pradesh, India
| | - Pushpendra Singh
- ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, Madhya Pradesh, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, Gujarat, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, Gujarat, India
| | | | | | - Ekadashi Rajni
- Department of Microbiology, Mahatma Gandhi University of Medical Sciences & Technology, Jaipur 302015, Rajasthan, India
| | - Manali Shah
- Desai Metropolis Health Service Pvt. Ltd., Surat 395001, Gujarat, India
| | - Devarshi Gajjar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
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Monteiro J, Abboud CS, Inoue FM, Tufik S, Kiffer CRV. NDM-producing Enterobacterales prevalence associated to COVID-19 in a tertiary hospital. Braz J Infect Dis 2022; 27:102735. [PMID: 36586722 PMCID: PMC9790865 DOI: 10.1016/j.bjid.2022.102735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/20/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Colonizations/Infections caused by carbapenem-resistant Enterobacterales are of great clinical and epidemiological importance due to their rapid dissemination and high mortality rates. In this scenario, the use of antibiotics intensified by the COVID-19 pandemic has brought about a great warning on the real impact that this pandemic could have on antimicrobial management programs and long-term antimicrobial resistance rates. The objective of this study was to evaluate the increase of New Delhi Metallo β-Lactamase (NDM)-producing Enterobacterales cases in COVID-19 units of a complex Brazilian tertiary hospital. This retrospective observational study included all patients admitted to the hospital identified as colonized or infected by NDM-producing Gram negative bacilli (GNB), from January 2017 to April 2021. Forty-two NDM-producing Enterobacterales were identified in 39 patients. The rate of NDM cases per total surveillance cultures increased progressively between 2017 and 2021 (chi-2 for trend, p < 0.0001) and was associated with a higher occurrence specifically in COVID units (Fisher exact, p < 0.0001). The molecular investigation of the NDM-producing Klebsiella pneumoniae strains revealed the emergence of diverse clones during the COVID-19 period, also with possible evidence of horizontal transmission among patients within COVID units. NDM-producing Enterobacterales with multiple and different clonalities in the COVID-19 units also raised questions about the importance of other factors besides horizontal clonal transfer, including the increase of antimicrobial consumption by these patients.
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Affiliation(s)
- Jussimara Monteiro
- Associação Fundo de Incentivo a Pesquisa (AFIP - Medicina Diagnóstica), Departamento de Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
| | - Cely S Abboud
- Instituto Dante Pazzanese de Cardiologia, Divisão de Doenças Infecciosas, São Paulo, SP, Brazil
| | - Fernanda M Inoue
- Associação Fundo de Incentivo a Pesquisa (AFIP - Medicina Diagnóstica), Departamento de Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
| | - Sergio Tufik
- Associação Fundo de Incentivo a Pesquisa (AFIP - Medicina Diagnóstica), Departamento de Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
| | - Carlos R V Kiffer
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Medicina Interna, Divisão de Doenças Infecciosas, São Paulo, SP, Brazil.
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11
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Kempf M, Arhin FF, Stone G, Utt E. Ceftazidime-avibactam activity against Gram-negative respiratory isolates collected between 2018 and 2019. J Glob Antimicrob Resist 2022; 31:239-247. [PMID: 36208850 DOI: 10.1016/j.jgar.2022.09.012] [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: 03/08/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES The objective of this study was to assess the in vitro activity of ceftazidime-avibactam (CAZ-AVI) and a panel of comparator agents against isolates of Enterobacter spp., Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa collected in 2018 and 2019 by different centres worldwide from patients with respiratory tract infections. METHODS Susceptibility and minimum inhibitory concentration (MIC) of all organisms were determined using broth microdilution methodology for CAZ-AVI, and a panel of comparator antimicrobial agents by a central reference laboratory according to Clinical and Laboratory Standards Institute guidelines and European Committee on Antimicrobial Susceptibility Testing guidelines. RESULTS CAZ-AVI demonstrated potent antimicrobial activity against isolates of Enterobacter spp. (97.6% susceptibility, MIC90, 1 µg/ml), E. coli (98.5% susceptibility, MIC90, 0.25 µg/ml), K. pneumoniae (94.7% susceptibility, MIC90 2 µg/ml), and P. aeruginosa (91.2% susceptibility, MIC90 8 µg/ml). CAZ-AVI was also active (susceptibility >85%) against MDR isolates for all organisms except P. aeruginosa. Only a small proportion (<10%) of all isolates of Enterobacter spp. and E. coli were identified as XDR compared to isolates of K. pneumoniae and P. aeruginosa isolates (>20%). Susceptibility to CAZ-AVI was high (>70%) among XDR isolates of Enterobacter spp., K. pneumoniae, and E. coli, compared to P. aeruginosa (<70%). Among the comparator agents, only colistin showed consistent activity across all the organisms (>85%). CONCLUSION Gram-negative respiratory isolates collected in 2018-2019 showed high susceptibility to CAZ-AVI; CAZ-AVI represents a potential treatment option against infection caused by these organisms.
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Affiliation(s)
- Marie Kempf
- University Hospital Angers, Laboratory of Bacteriology, France; CRCINA, INSERM U1232, Université d'Angers, Angers, France
| | | | | | - Eric Utt
- Pfizer, Inc., Groton, Connecticut.
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12
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Ahmed N, Tahir K, Aslam S, Cheema SM, Rabaan AA, Turkistani SA, Garout M, Halwani MA, Aljeldah M, Al Shammari BR, Sabour AA, Alshiekheid MA, Alshamrani SA, Azmi RA, Al-Absi GH, Zeb S, Yean CY. Heavy Metal (Arsenic) Induced Antibiotic Resistance among Extended-Spectrum β-Lactamase (ESBL) Producing Bacteria of Nosocomial Origin. Pharmaceuticals (Basel) 2022; 15:1426. [PMID: 36422556 PMCID: PMC9692669 DOI: 10.3390/ph15111426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 08/26/2023] Open
Abstract
Antimicrobial resistance (AMR) is a leading cause of treatment failure for many infectious diseases worldwide. Improper overdosing and the misuse of antibiotics contributes significantly to the emergence of drug-resistant bacteria. The co-contamination of heavy metals and antibiotic compounds existing in the environment might also be involved in the spread of AMR. The current study was designed to test the efficacy of heavy metals (arsenic) induced AMR patterns in clinically isolated extended-spectrum β-lactamase (ESBL) producing bacteria. A total of 300 clinically isolated ESBL-producing bacteria were collected from a tertiary care hospital in Lahore, Pakistan, with the demographic characteristics of patients. After the collection of bacterial isolates, these were reinoculated on agar media for reidentification purposes. Direct antimicrobial sensitivity testing (AST) for bacterial isolates by disk diffusion methods was used to determine the AST patterns with and without heavy metal. The heavy metal was concentrated in dilutions of 1.25 g/mL. The collected bacterial isolates were isolated from wounds (n = 63, 21%), urine (n = 112, 37.3%), blood (n = 43, 14.3%), pus (n = 49, 16.3%), and aspirate (n = 33, 11%) samples. From the total 300 bacterial isolates, n = 172 were Escherichia coli (57.3%), 57 were Klebsiella spp. (19%), 32 were Pseudomonas aeruginosa (10.6%), 21 were Proteus mirabilis (7%) and 18 were Enterobacter spp. (6%). Most of the antibiotic drugs were found resistant to tested bacteria. Colistin and Polymyxin-B showed the highest sensitivity against all tested bacteria, but when tested with heavy metals, these antibiotics were also found to be significantly resistant. We found that heavy metals induced the resistance capability in bacterial isolates, which leads to higher AMR patterns as compared to without heavy metal tested isolates. The results of the current study explored the heavy metal as an inducer of AMR and may contribute to the formation and spread of AMR in settings that are contaminated with heavy metals.
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Affiliation(s)
- Naveed Ahmed
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Pakistan
| | - Kinza Tahir
- Department of Medical Education, Allama Iqbal Medical College, Lahore 54000, Pakistan
| | - Sara Aslam
- Department of Medical Education, Allama Iqbal Medical College, Lahore 54000, Pakistan
| | - Sara Masood Cheema
- Department of Pathology, Azra Naheed Medical College, Lahore 54000, Pakistan
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Safaa A. Turkistani
- Department of Medical Laboratory Sciences, Fakeeh College for Medical Science, Jeddah 21134, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Muhammad A. Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha 4781, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Amal A. Sabour
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Maha A. Alshiekheid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh A. Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Reyouf Al Azmi
- Infection Prevention and Control, Eastern Health Cluster, Dammam 32253, Saudi Arabia
| | - Ghadeer H. Al-Absi
- College of Pharmacy, Department of Pharmacy Practice, Alfaisal University, Riyadh 325476, Saudi Arabia
| | - Shah Zeb
- Department of Microbiology, Faculty of Biomedical and Health Science, The University of Haripur, Haripur 22610, Pakistan
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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13
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Tesfa T, Mitiku H, Edae M, Assefa N. Prevalence and incidence of carbapenem-resistant K. pneumoniae colonization: systematic review and meta-analysis. Syst Rev 2022; 11:240. [PMID: 36380387 PMCID: PMC9667607 DOI: 10.1186/s13643-022-02110-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/30/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a gram-negative rod belonging to the order Enterobacterales and having a wide distribution in the environment, including the human colon. Recently, the bacterium is one of the known problems in the healthcare setting as it has become resistant to last-resort drugs like carbapenems. The colonized person can serve as a reservoir for his/herself and others, especially in the healthcare setting leading to nosocomial and opportunistic infections. Therefore, we aimed to quantitatively estimate the rate of prevalence and incidence of colonization with carbapenem-resistant K. pneumoniae. METHODS A literature search was conducted on PubMed/MEDLINE, Google Scholar, Science Direct, Cochrane Library, WHO Index Medicus, and university databases. The study includes all published and unpublished papers that addressed the prevalence or incidence of K. pneumoniae colonization. Data were extracted onto format in Microsoft Excel and pooled estimates with a 95% confidence interval calculated using Der-Simonian-Laird random-effects model. With the use of I2 statistics and prediction intervals, the level of heterogeneity was displayed. Egger's tests and funnel plots of standard error were used to demonstrate the publication bias. RESULTS A total of 35 studies were included in the review and 32 records with 37,661 patients for assessment of prevalence, while ten studies with 3643 patients for incidence of colonization. The prevalence of carbapenem-resistant K. pneumoniae colonization varies by location and ranges from 0.13 to 22%, with a pooled prevalence of 5.43%. (3.73-7.42). Whereas the incidence of colonization ranges from 2 to 73% with a pooled incidence of 22.3% (CI 12.74-31.87), both prevalence and incidence reports are majorly from developed countries. There was a variation in the distribution of carbapenem resistance genes among colonizing isolates with KPC as a prominent gene reported from many studies and NDM being reported mainly by studies from Asian countries. A univariate meta-regression analysis indicated continent, patient type, study design, and admission ward do not affect the heterogeneity (p value>0.05). CONCLUSION The review revealed that colonization with K. pneumoniae is higher in a healthcare setting with variable distribution in different localities, and resistance genes for carbapenem drugs also have unstable distribution in different geographic areas.
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Affiliation(s)
- Tewodros Tesfa
- Department of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, P.O.Box 235, Harar, Ethiopia.
| | - Habtamu Mitiku
- Department of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, P.O.Box 235, Harar, Ethiopia
| | - Mekuria Edae
- Hiwot Fana Specialized University Hospital, College of Health and Medical Sciences, Haramaya University, P.O.Box 235, Harar, Ethiopia
| | - Nega Assefa
- School of Nursing Midwifery, College of Health and Medical Sciences, Haramaya University, P.O.Box 235, Harar, Ethiopia
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14
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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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Kiratisin P, Arhin FF, Stone G, Utt E. Antimicrobial Activity of Ceftazidime–Avibactam and Comparators Against Fluoroquinolone-Resistant Klebsiella pneumoniae Collected Globally from Antimicrobial Testing Leadership and Surveillance: 2018–2019. Microb Drug Resist 2022; 28:1019-1027. [DOI: 10.1089/mdr.2022.0104] [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)
- Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | | | - Gregory Stone
- Hospital Business Unit, Pfizer, Inc., Groton, Connecticut, USA
| | - Eric Utt
- Hospital Business Unit, Pfizer, Inc., Groton, Connecticut, USA
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16
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Genomic Diversity of NDM-Producing Klebsiella Species from Brazil, 2013–2022. Antibiotics (Basel) 2022; 11:antibiotics11101395. [PMID: 36290053 PMCID: PMC9598336 DOI: 10.3390/antibiotics11101395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Since its first report in the country in 2013, NDM-producing Enterobacterales have been identified in all the Brazilian administrative regions. In this study, we characterized by antimicrobial susceptibility testing and by molecular typing a large collection of NDM-producing Klebsiella isolates from different hospitals in Brazil, mainly from the state of Sao Paulo, over the last decade. Methods: Bacterial isolates positive for blaNDM-genes were identified by MALDI-TOF MS and submitted to antimicrobial susceptibility testing by disk diffusion or broth microdilution (for polymyxin B). All isolates were submitted to pulsed-field gel electrophoresis, and isolates belonging to different clusters were submitted to whole genome sequencing by Illumina technology and downstream analysis. Mating out assays were performed by conjugation, plasmid sizes were determined by S1-PFGE, and plasmid content was investigated by hybrid assembly after MinIon long reads sequencing. Results: A total of 135 NDM-producing Klebsiella were identified, distributed into 107 different pulsotypes; polymyxin B was the only antimicrobial with high activity against 88.9% of the isolates. Fifty-four isolates presenting diversified pulsotypes were distributed in the species K. pneumoniae (70%), K. quasipneumoniae (20%), K. variicola (6%), K. michiganensis (a K. oxytoca Complex species, 2%), and K. aerogenes (2%); blaNDM-1 was the most frequent allele (43/54, 80%). There was a predominance of Clonal Group 258 (ST11 and ST340) encompassing 35% of K. pneumoniae isolates, but another thirty-one different sequence types (ST) were identified, including three described in this study (ST6244 and ST6245 for K. pneumoniae, and ST418 for K. michiganensis). The blaNDM-1 and blaNDM-7 were found to be located into IncF and IncX3 type transferable plasmids, respectively. Conclusions: Both clonal (mainly driven by CG258) and non-clonal expansion of NDM-producing Klebsiella have been occurring in Brazil in different species and clones, associated with different plasmids, since 2013.
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Quezada-Aguiluz M, Opazo-Capurro A, Lincopan N, Esposito F, Fuga B, Mella-Montecino S, Riedel G, Lima CA, Bello-Toledo H, Cifuentes M, Silva-Ojeda F, Barrera B, Hormazábal JC, González-Rocha G. Novel Megaplasmid Driving NDM-1-Mediated Carbapenem Resistance in Klebsiella pneumoniae ST1588 in South America. Antibiotics (Basel) 2022; 11:antibiotics11091207. [PMID: 36139987 PMCID: PMC9494972 DOI: 10.3390/antibiotics11091207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) is a critical public health problem in South America, where the prevalence of NDM metallo-betalactamases has increased substantially in recent years. In this study, we used whole genome sequencing to characterize a multidrug-resistant (MDR) Klebsiella pneumoniae (UCO-361 strain) clinical isolate from a teaching hospital in Chile. Using long-read (Nanopore) and short-read (Illumina) sequence data, we identified a novel un-typeable megaplasmid (314,976 kb, pNDM-1_UCO-361) carrying the blaNDM-1 carbapenem resistance gene within a Tn3000 transposon. Strikingly, conjugal transfer of pNDM-1_UCO-361 plasmid only occurs at low temperatures with a high frequency of 4.3 × 10−6 transconjugants/receptors at 27 °C. UCO-361 belonged to the ST1588 clone, previously identified in Latin America, and harbored aminoglycoside, extended-spectrum β-lactamases (ESBLs), carbapenem, and quinolone-resistance determinants. These findings suggest that blaNDM-1-bearing megaplasmids can be adapted to carriage by some K. pneumoniae lineages, whereas its conjugation at low temperatures could contribute to rapid dissemination at the human–environmental interface.
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Affiliation(s)
- Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción 4030000, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 8320000, Chile
- Centro Regional de Telemedicina y Telesalud del Biobío (CRT Biobío), Concepción 4030000, Chile
| | - Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 8320000, Chile
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Sergio Mella-Montecino
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción 4030000, Chile
- Unidad de Infectología, Hospital Regional “Dr. Guillermo Grant Benavente”, Concepción 4030000, Chile
| | - Gisela Riedel
- Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción 4030000, Chile
- Unidad de Infectología, Hospital Regional “Dr. Guillermo Grant Benavente”, Concepción 4030000, Chile
| | - Celia A. Lima
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Marcela Cifuentes
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8320000, Chile
| | - Francisco Silva-Ojeda
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8320000, Chile
| | - Boris Barrera
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8320000, Chile
| | - Juan C. Hormazábal
- Subdepartamento de Enfermedades Infecciosas, Instituto de Salud Pública de Chile (ISP), Santiago 8320000, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 8320000, Chile
- Correspondence: ; Tel.: +56-41-2661527; Fax: +56-41-2245975
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Villinger D, Schultze TG, Musyoki VM, Inwani I, Aluvaala J, Okutoyi L, Ziegler AH, Wieters I, Stephan C, Museve B, Kempf VAJ, Masika M. Genomic transmission analysis of multidrug-resistant Gram-negative bacteria within a newborn unit of a Kenyan tertiary hospital: A four-month prospective colonization study. Front Cell Infect Microbiol 2022; 12:892126. [PMID: 36093198 PMCID: PMC9452910 DOI: 10.3389/fcimb.2022.892126] [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: 03/08/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Multidrug-resistant organisms (MDRO), especially carbapenem-resistant organisms (CRO), represent a threat for newborns. This study investigates the colonization prevalence of these pathogens in a newborn unit at a Kenyan tertiary hospital in an integrated approach combining routine microbiology, whole genome sequencing (WGS) and hospital surveillance data. Methods The study was performed in the Kenyatta National Hospital (KNH) in 2019 over a four-month period and included 300 mother-baby pairs. A total of 1,097 swabs from newborns (weekly), mothers (once) and the hospital environment were taken. Routine clinical microbiology methods were applied for surveillance. Of the 288 detected MDRO, 160 isolates were analyzed for antimicrobial resistance genes and phylogenetic relatedness using whole genome sequencing (WGS) and bioinformatic analysis. Results In maternal vaginal swabs, MDRO detection rate was 15% (n=45/300), including 2% CRO (n=7/300). At admission, MDRO detection rate for neonates was 16% (n=48/300), including 3% CRO (n=8/300) with a threefold increase for MDRO (44%, n=97/218) and a fivefold increase for CRO (14%, n=29/218) until discharge. Among CRO, K. pneumoniae harboring blaNDM-1 (n=20) or blaNDM-5 (n=16) were most frequent. WGS analysis revealed 20 phylogenetically related transmission clusters (including five CRO clusters). In environmental samples, the MDRO detection rate was 11% (n=18/164), including 2% CRO (n=3/164). Conclusion Our study provides a snapshot of MDRO and CRO in a Kenyan NBU. Rather than a large outbreak scenario, data indicate several independent transmission events. The CRO rate among newborns attributed to the spread of NDM-type carbapenemases is worrisome.
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Affiliation(s)
- David Villinger
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
| | - Tilman G. Schultze
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
| | - Victor M. Musyoki
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Irene Inwani
- Pediatrics Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Jalemba Aluvaala
- Pediatrics Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Lydia Okutoyi
- Quality Health Department, Kenyatta National Hospital, Nairobi, Kenya
| | - Anna-Henriette Ziegler
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Imke Wieters
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- Center of Internal Medicine/Infectious Diseases Unit, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Christoph Stephan
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- Center of Internal Medicine/Infectious Diseases Unit, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
| | - Beatrice Museve
- Department of Laboratory Medicine, Kenyatta National Hospital, Nairobi, Kenya
| | - Volkhard A. J. Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Hesse, Germany
- University Center of Competence for Infection Control, Frankfurt, Hesse, Germany
- *Correspondence: Volkhard A. J. Kempf, ; Moses Masika,
| | - Moses Masika
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- *Correspondence: Volkhard A. J. Kempf, ; Moses Masika,
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19
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Håkonsholm F, Hetland MA, Svanevik CS, Lunestad BT, Löhr IH, Marathe NP. Insights into the genetic diversity, antibiotic resistance and pathogenic potential of Klebsiella pneumoniae from the Norwegian marine environment using whole-genome analysis. Int J Hyg Environ Health 2022; 242:113967. [DOI: 10.1016/j.ijheh.2022.113967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/25/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023]
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20
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Rodrigues C, Hauser K, Cahill N, Ligowska-Marzęta M, Centorotola G, Cornacchia A, Garcia Fierro R, Haenni M, Nielsen EM, Piveteau P, Barbier E, Morris D, Pomilio F, Brisse S. High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods. Microbiol Spectr 2022; 10:e0237621. [PMID: 35196810 PMCID: PMC8865463 DOI: 10.1128/spectrum.02376-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/20/2022] [Indexed: 12/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices and to characterize food isolates phenotypically and genotypically. Chicken meat (n = 160) and salad (n = 145) samples were collected in five European countries and screened for the presence of KpSC using culture-based and zur-khe intergenic region (ZKIR) quantitative PCR (qPCR) methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44°C for 48 h) was defined as the most suitable selective culture method for KpSC recovery. A high prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and the culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). A total of 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples-same food type and same country (15 cases), different food types and same country (1), and same food type and two countries (1)-suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans. IMPORTANCE Bacteria of the Klebsiella pneumoniae species complex (KpSC) are ubiquitous, and K. pneumoniae is a leading cause of antibiotic-resistant infections in humans. Despite the urgent public health threat represented by K. pneumoniae, there is a lack of knowledge of the contribution of food sources to colonization and subsequent infection in humans. This is partly due to the absence of standardized methods for characterizing the presence of KpSC in food matrices. Our multicentric study provides and implements a novel isolation strategy for KpSC from food matrices and shows that KpSC members are highly prevalent in salads and chicken meat, reinforcing the view of food as a potential source of KpSC colonization in humans. Despite the large genetic diversity and the low levels of resistance detected, the occurrence of identical genotypes across samples suggests high rates of transmission of KpSC within the food sector, which need to be further explored to define possible control strategies.
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Affiliation(s)
- Carla Rodrigues
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathrin Hauser
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | | | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Raquel Garcia Fierro
- Unité Antibiorésistance et Virulence Bactériennes, Université Claude Bernard Lyon 1 - ANSES, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université Claude Bernard Lyon 1 - ANSES, Lyon, France
| | | | | | - Elodie Barbier
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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21
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Ruan Z, Zou S, Wang Z, Zhang L, Chen H, Wu Y, Jia H, Draz MS, Feng Y. Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids. Brief Bioinform 2022; 23:6519793. [PMID: 35108376 DOI: 10.1093/bib/bbac004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) enables comprehensive pathogen detection and has become increasingly popular in clinical diagnosis. The distinct pathogenic traits between strains require mNGS to achieve a strain-level resolution, but an equivocal concept of 'strain' as well as the low pathogen loads in most clinical specimens hinders such strain awareness. Here we introduce a metagenomic intra-species typing (MIST) tool (https://github.com/pandafengye/MIST), which hierarchically organizes reference genomes based on average nucleotide identity (ANI) and performs maximum likelihood estimation to infer the strain-level compositional abundance. In silico analysis using synthetic datasets showed that MIST accurately predicted the strain composition at a 99.9% average nucleotide identity (ANI) resolution with a merely 0.001× sequencing depth. When applying MIST on 359 culture-positive and 359 culture-negative real-world specimens of infected body fluids, we found the presence of multiple-strain reached considerable frequencies (30.39%-93.22%), which were otherwise underestimated by current diagnostic techniques due to their limited resolution. Several high-risk clones were identified to be prevalent across samples, including Acinetobacter baumannii sequence type (ST)208/ST195, Staphylococcus aureus ST22/ST398 and Klebsiella pneumoniae ST11/ST15, indicating potential outbreak events occurring in the clinical settings. Interestingly, contaminations caused by the engineered Escherichia coli strain K-12 and BL21 throughout the mNGS datasets were also identified by MIST instead of the statistical decontamination approach. Our study systemically characterized the infected body fluids at the strain level for the first time. Extension of mNGS testing to the strain level can greatly benefit clinical diagnosis of bacterial infections, including the identification of multi-strain infection, decontamination and infection control surveillance.
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Affiliation(s)
- Zhi Ruan
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shengmei Zou
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Zeyu Wang
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Luhan Zhang
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Hangfei Chen
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuye Wu
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huiqiong Jia
- Deparment of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
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22
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Huang W, Zhang J, Zeng L, Yang C, Yin L, Wang J, Li J, Li X, Hu K, Zhang X, Liu B. Carbapenemase Production and Epidemiological Characteristics of Carbapenem-Resistant Klebsiella pneumoniae in Western Chongqing, China. Front Cell Infect Microbiol 2022; 11:775740. [PMID: 35071036 PMCID: PMC8769044 DOI: 10.3389/fcimb.2021.775740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022] Open
Abstract
Background This study aimed to determine the molecular characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in a hospital in western Chongqing, southwestern China. Methods A total of 127 unique CRKP isolates were collected from the Yongchuan Hospital of Chongqing Medical University, identified using a VITEK-2 compact system, and subjected to microbroth dilution to determine the minimal inhibitory concentration. Enterobacteriaceae intergenic repeat consensus polymerase chain reaction and multilocus sequence typing were used to analyze the homology among the isolates. Genetic information, including resistance and virulence genes, was assessed using polymerase chain reaction. The genomic features of the CRKP carrying gene blaKPC-2 were detected using whole-genome sequencing. Results ST11 was the dominant sequence type in the homology comparison. The resistance rate to ceftazidime-avibactam in children was much higher than that in adults as was the detection rate of the resistance gene blaNDM (p < 0.0001). Virulence genes such as mrkD (97.6%), uge (96.9%), kpn (96.9%), and fim-H (84.3%) had high detection rates. IncF (57.5%) was the major replicon plasmid detected, and sequencing showed that the CRKP063 genome contained two plasmids. The plasmid carrying blaKPC-2, which mediates carbapenem resistance, was located on the 359,625 base pair plasmid IncFII, together with virulence factors, plasmid replication protein (rep B), stabilizing protein (par A), and type IV secretion system (T4SS) proteins that mediate plasmid conjugation transfer. Conclusion Our study aids in understanding the prevalence of CRKP in this hospital and the significant differences between children and adults, thus providing new ideas for clinical empirical use of antibiotics.
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Affiliation(s)
- Wan Huang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jisheng Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Lingyi Zeng
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Department of Microbiology, Jiaxing Maternity and Child Health Care Hospital, Jiaxing, China
| | - Chengru Yang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Department of Microbiology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Lining Yin
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Department of Microbiology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Jianmin Wang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Li
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xinhui Li
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Kewang Hu
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Department of Microbiology, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoli Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Department of Microbiology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Beizhong Liu
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing, China
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23
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Antibacterial and Anti-Biofilm Activities of Essential Oil Compounds against New Delhi Metallo-β-Lactamase-1-Producing Uropathogenic Klebsiella pneumoniae Strains. Antibiotics (Basel) 2022; 11:antibiotics11020147. [PMID: 35203751 PMCID: PMC8868355 DOI: 10.3390/antibiotics11020147] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
The World Health Organization points out that the opportunistic pathogen Klebsiella pneumoniae that causes various infections among others, urinary tract infections (UTIs), is one of the high-priority species due to a global problem of antimicrobial resistance. The aim of this study was to investigate antibacterial and anti-biofilm activities of chosen constituents of essential oils against NDM-1-producing, uropathogenic K. pneumoniae strains. The genes encoding lipopolysaccharide (uge, wabG), adhesin gene fimH (type I fimbriae) and gene encoding carbapenemase (blaNDM-1) for all tested strains were detected by PCR amplification. The K. pneumoniae ATCC BAA-2473 reference strain was uge- and blaNDM-1-positive. The effectiveness of fifteen essential oil compounds (EOCs) (linalool, β-citronellol, linalyl acetate, menthone, (−)-menthol, (+)-menthol, geraniol, eugenol, thymol, trans-anethole, farnesol, β-caryophyllene, (R)-(+)-limonene, 1,8-cineole, and carvacrol) was assessed by determining the MIC, MBC, MBC/MIC ratio against K. pneumoniae strains by the microdilution method. Anti-biofilm properties of these compounds were also investigated. Thymol, carvacrol and geraniol exhibited the best antibacterial and anti-biofilm activities against uropathogenic NDM-1-producing K. pneumoniae isolates. Results of our investigations provide a basis for more detailed studies of these phytochemicals on their application against uropathogenic K. pneumoniae.
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24
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Franklin-Alming FV, Kaspersen H, Hetland MAK, Bakksjø RJ, Nesse LL, Leangapichart T, Löhr IH, Telke AA, Sunde M. Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers. Front Microbiol 2021; 12:725414. [PMID: 34557173 PMCID: PMC8453068 DOI: 10.3389/fmicb.2021.725414] [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: 06/15/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Klebsiella pneumoniae is a well-studied human pathogen for which antimicrobial resistant and hypervirulent clones have emerged globally. K. pneumoniae is also present in a variety of environmental niches, but currently there is a lack of knowledge on the occurrence and characteristics of K. pneumoniae from non-human sources. Certain environmental niches, e.g., animals, may be associated with high K. pneumoniae abundance, and these can constitute a reservoir for further transmission of strains and genetic elements. The aim of this study was to explore and characterize K. pneumoniae from healthy broilers and turkeys. A total of 511 cecal samples (broiler n = 356, turkey n = 155), included in the Norwegian monitoring program for antimicrobial resistance (AMR) in the veterinary sector (NORM-VET) in 2018, were screened for K. pneumoniae by culturing on SCAI agar. K. pneumoniae was detected in 207 (40.5%) samples. Among the broiler samples, 25.8% were positive for K. pneumoniae, in contrast to turkey with 74.2% positive samples (p < 0.01). Antibiotic susceptibility testing was performed, in addition to investigating biofilm production. Whole genome sequencing was performed on 203 K. pneumoniae isolates, and analysis was performed utilizing comparative genomics tools. The genomes grouped into 66 sequence types (STs), with ST35, ST4710 and ST37 being the most prevalent at 13.8%, 7.4%, and 5.4%, respectively. The overall AMR occurrence was low, with only 11.3% of the isolates showing both pheno- and genotypic resistance. Genes encoding aerobactin, salmochelin or yersiniabactin were detected in 47 (23.2%) genomes. Fifteen hypervirulent genomes belonging to ST4710 and isolated from turkey were identified. These all encoded the siderophore virulence loci iuc5 and iro5 on an IncF plasmid. Isolates from both poultry species displayed good biofilm-forming abilities with an average of OD595 0.69 and 0.64. To conclude, the occurrence of K. pneumoniae in turkey was significantly higher than in broiler, indicating that turkey might be an important zoonotic reservoir for K. pneumoniae compared to broilers. Furthermore, our results show a highly diverse K. pneumoniae population in poultry, low levels of antimicrobial resistance, good biofilm-forming abilities and a novel hypervirulent ST4710 clone circulating in the turkey population.
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Affiliation(s)
- Fiona V Franklin-Alming
- Section for Microbiology, Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, Norway
| | - Håkon Kaspersen
- Research Section Food Safety and Animal Health, Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Marit A K Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway.,Department of Biological Sciences, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Ragna-Johanne Bakksjø
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Live L Nesse
- Research Section Food Safety and Animal Health, Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Thongpan Leangapichart
- Research Section Food Safety and Animal Health, Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Iren H Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Amar A Telke
- Research Section Food Safety and Animal Health, Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Marianne Sunde
- Research Section Food Safety and Animal Health, Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
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25
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Spaziante M, Venditti C, Butera O, Messina F, Di Caro A, Tonziello G, Lanini S, Cataldo MA, Puro V. Importance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy. Infect Drug Resist 2021; 14:3659-3665. [PMID: 34526785 PMCID: PMC8435879 DOI: 10.2147/idr.s318717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
Introduction New Delhi metallo-β-lactamase producing Klebsiella pneumoniae (NDM-Kpn) strains have been causing healthcare-associated infections worldwide. The aim of this study was to describe the molecular mechanisms of antimicrobial resistance and to analyze the clonality of NDM-Kpn isolates collected between January 2019 and June 2020 from patients admitted to hospitals from the Lazio region, Italy. Methods We performed a retrospective cohort study. Whole-genome sequencing (WGS) was performed on all NDM-Kpn strains; clonality and genetic relationships were further investigated. Results During the surveillance period, 17 NDM-Kpn isolates were obtained from 17 patients admitted to seven different hospitals. Eight different sequence types (STs) were detected: ST147 (n = 4), ST383 (n = 4), ST15 (n = 3), ST11 (n = 2), ST17 (n = 1), ST29 (n = 1), ST307 (n = 1) and the newly identified ST4853 (n = 1). Genetic relationships were further investigated by the WGS-based core genome MLST (cgMLST) scheme, and 5 cluster types (CTs) were identified. Whereas a substantial overall heterogeneity among isolates was detected (8 different STs were identified out of 17 isolates), the strains within each cluster showed a very high level of genome similarity. Discussion Our study highlights the key role of surveillance, which allowed taking a picture of a part of the NDM-Kpn strains circulating in Italy, adding further insight into their molecular features.
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Affiliation(s)
- Martina Spaziante
- Emerging Infection Unit and Regional Service for Surveillance and Control of Infectious Diseases (SeRESMI), National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Carolina Venditti
- Laboratory of Microbiology, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Ornella Butera
- Laboratory of Microbiology, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Francesco Messina
- Laboratory of Microbiology, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Antonino Di Caro
- Laboratory of Microbiology, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Gilda Tonziello
- Emerging Infection Unit and Regional Service for Surveillance and Control of Infectious Diseases (SeRESMI), National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Simone Lanini
- Emerging Infection Unit and Regional Service for Surveillance and Control of Infectious Diseases (SeRESMI), National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Maria Adriana Cataldo
- Emerging Infection Unit and Regional Service for Surveillance and Control of Infectious Diseases (SeRESMI), National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Vincenzo Puro
- Emerging Infection Unit and Regional Service for Surveillance and Control of Infectious Diseases (SeRESMI), National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
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26
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Feng Y, Xue G, Feng J, Yan C, Cui J, Gan L, Zhang R, Zhao H, Xu W, Li N, Liu S, Du S, Zhang W, Yao H, Tai J, Ma L, Zhang T, Qu D, Wei Y, Yuan J. Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children. Front Microbiol 2021; 12:691289. [PMID: 34367092 PMCID: PMC8339468 DOI: 10.3389/fmicb.2021.691289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/30/2021] [Indexed: 11/26/2022] Open
Abstract
New Delhi metallo-β-lactamase, a metallo-β-lactamase carbapenemase type, mediates resistance to most β-lactam antibiotics including penicillins, cephalosporins, and carbapenems. Therefore, it is important to detect blaNDM genes in children’s clinical samples as quickly as possible and analyze their characteristics. Here, a recombinase-aided amplification (RAA) assay, which operates in a single one-step reaction tube at 39°C in 5−15 min, was established to target blaNDM genes in children’s clinical samples. The analytical sensitivity of the RAA assay was 20 copies, and the various bacterial types without blaNDM genes did not amplify. This method was used to detect blaNDM genes in 112 children’s stool samples, 10 of which were tested positive by both RAA and standard PCR. To further investigate the characteristics of carbapenem-resistant bacteria carrying blaNDM in children, 15 carbapenem-resistant bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca, Acinetobacter junii, and Proteus mirabilis) were isolated from the 10 samples. Notably, more than one bacterial type was isolated from three samples. Most of these isolates were resistant to cephalosporins, cefoperazone-sulbactam, piperacillin-tazobactam, ticarcillin-clavulanic acid, aztreonam, co-trimoxazole, and carbapenems. blaNDM–1 and blaNDM–5 were the two main types in these samples. These data show that the RAA assay has potential to be a sensitive and rapid blaNDM gene screening test for clinical samples. The common existence of blaNDM and multi-drug resistance genes presents major challenges for pediatric treatment.
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Affiliation(s)
| | - Guanhua Xue
- Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Hanqin Zhao
- Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Nannan Li
- Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Capital Institute of Pediatrics, Beijing, China
| | | | - Hailan Yao
- Capital Institute of Pediatrics, Beijing, China
| | - Jun Tai
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Lijuan Ma
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Dong Qu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Yongxiang Wei
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Capital Institute of Pediatrics, Beijing, China
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