1
|
Pérez-Palacios P, Gual-de-Torrella A, Portillo-Calderón I, Recacha-Villamor E, Franco-Álvarez de Luna F, Lopez-Cerero L, Pascual A. Interhospital Spread of blaVIM-1- and blaCTX-M-15-Producing K. pneumoniae ST15 on an IncR Plasmid in Southern Spain. Antibiotics (Basel) 2023; 12:1727. [PMID: 38136761 PMCID: PMC10740488 DOI: 10.3390/antibiotics12121727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In 2014-2015, the main CTX-M-15- and OXA-48-producing clone in our region was ST15. Recently, K. pneumoniae ST15 isolates co-producing VIM-1 and CTX-M-15 were detected in several hospitals. The aim was to study the emergence and acquisition of this carbapenemase. Between 2017 and 2019, four hospitals submitted twenty-nine VIM-1- and CTX-M-15-producing K. pneumoniae ST15 isolates to our laboratory. Seven representatives of each XbaI PFGE pulsotype were sequenced using short- and long-read technologies. RAST, CGE databases, and Pathogenwatch were used for resistance determinants and capsule-type analysis. Plasmid comparison was performed with Easyfig2.1. Phylogenetic analysis included other contemporary ST15 isolates from Spain. The 29 isolates were clustered into seven different pulsotypes. The selected genomes, from three hospitals in two different provinces, were clustered together (fewer than 35 alleles) and differed by more than 100 alleles from other ST15 isolates obtained in the region. These seven isolates harbored one IncR plasmid (200-220 kb) with a common backbone and four regions flanked by IS26: one contained blaVIM-1, another contained blaCTX-M-15, the third contained blaOXA-1, and the fourth harbored heavy-metal-tolerance genes. The two initial plasmids, from two different centers, were identical, and rearrangement of four regions was observed in the five subsequent plasmids. Our findings showed the first intercenter dissemination of IncR plasmids carrying blaVIM-1, blaCTX-M-15, and metal-tolerance genes mediated by a new lineage of K. pneumoniae ST15. Two different capture events of the blaVIM-1 gene or different IS26-mediated plasmid rearrangements from a common ancestor may explain plasmid variations.
Collapse
Affiliation(s)
- Patricia Pérez-Palacios
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
| | - Ana Gual-de-Torrella
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
| | - Ines Portillo-Calderón
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
| | - Esther Recacha-Villamor
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Lorena Lopez-Cerero
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Alvaro Pascual
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| |
Collapse
|
2
|
Wu YL, Hu XQ, Wu DQ, Li RJ, Wang XP, Zhang J, Liu Z, Chu WW, Zhu X, Zhang WH, Zhao X, Guan ZS, Jiang YL, Wu JF, Cui Z, Zhang J, Li J, Wang RM, Shen SH, Cai CY, Zhu HB, Jiang Q, Zhang J, Niu JL, Xiong XP, Tian Z, Zhang JS, Zhang JL, Tang LL, Liu AY, Wang CX, Ni MZ, Jiang JJ, Yang XY, Yang M, Zhou Q. Prevalence and risk factors for colonisation and infection with carbapenem-resistant Enterobacterales in intensive care units: A prospective multicentre study. Intensive Crit Care Nurs 2023; 79:103491. [PMID: 37480701 DOI: 10.1016/j.iccn.2023.103491] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/24/2023]
Abstract
OBJECTIVES This study aimed to investigate the prevalence and risk factors for carbapenem-resistant Enterobacterales colonisation/infection at admission and acquisition among patients admitted to the intensive care unit. RESEARCH METHODOLOGY/DESIGN A prospective and multicentre study. SETTING This study was conducted in 24 intensive care units in Anhui, China. MAIN OUTCOME MEASURES Demographic and clinical data were collected, and rectal carbapenem-resistant Enterobacterales colonisation was detected by active screening. Multivariate logistic regression models were used to analyse factors associated with colonisation/infection with carbapenem-resistant Enterobacterales at admission and acquisition during the intensive care unit stay. RESULTS There were 1133 intensive care unit patients included in this study. In total, 5.9% of patients with carbapenem-resistant Enterobacterales colonisation/infection at admission, and of which 56.7% were colonisations. Besides, 8.5% of patients acquired carbapenem-resistant Enterobacterales colonisation/infection during the intensive care stay, and of which 67.6% were colonisations. At admission, transfer from another hospital, admission to an intensive care unit within one year, colonisation/infection/epidemiological link with carbapenem-resistant Enterobacterales within one year, and exposure to any antibiotics within three months were risk factors for colonisation/infection with carbapenem-resistant Enterobacterales. During the intensive care stay, renal disease, an epidemiological link with carbapenem-resistant Enterobacterales, exposure to carbapenems and beta-lactams/beta-lactamase inhibitors, and intensive care stay of three weeks or longer were associated with acquisition. CONCLUSION The prevalence of colonisation/infection with carbapenem-resistant Enterobacterales in intensive care units is of great concern and should be monitored systematically. Particularly for the 8.5% prevalence of carbapenem-resistant Enterobacterales acquisition during the intensive care stay needs enhanced infection prevention and control measures in these setting. Surveillance of colonisation/infection with carbapenem-resistant Enterobacterales at admission and during the patient's stay represents an early identification tool to prevent further transmission of carbapenem-resistant Enterobacterales. IMPLICATIONS FOR CLINICAL PRACTICE Carbapenem-resistant Enterobacterales colonization screening at admission and during the patient's stay is an important tool to control carbapenem-resistant Enterobacterales spread in intensive care units.
Collapse
Affiliation(s)
- Yi-Le Wu
- Department of Hospital Infection Prevention and Control, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Qian Hu
- Department of Hospital Infection Prevention and Control, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - De-Quan Wu
- Department of Hospital Infection Prevention and Control, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ruo-Jie Li
- Department of Hospital Infection Prevention and Control, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xue-Ping Wang
- Department of Hospital Infection Prevention and Control, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jin Zhang
- The Second Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhou Liu
- Department of Clinical Laboratory, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Wen-Wen Chu
- Department of Clinical Laboratory, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xi Zhu
- Department of Pharmacology, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Wen-Hui Zhang
- The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xue Zhao
- The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zi-Shu Guan
- Anhui No.2 Provincial People's Hospital, Hefei, Anhui, China
| | - Yun-Lan Jiang
- Department of Hospital Infection Prevention and Control, the First People's Hospital of Anqing, Anqing, Anhui, China
| | - Jin-Feng Wu
- Department of Hospital Infection Prevention and Control, Anqing Municipal Hospital, Anqing, Anhui, China
| | - Zhuo Cui
- Department of Hospital Infection Prevention and Control, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Ju Zhang
- Department of Hospital Infection Prevention and Control, The First People's Hospital of Bengbu, Bengbu, Anhui, China
| | - Jia Li
- Department of Hospital Infection Prevention and Control, The Third People's Hospital of Bengbu, Bengbu, Anhui, China
| | - Ru-Mei Wang
- Department of Hospital Infection Prevention and Control, The First People's Hospital of Chuzhou, Chuzhou, Anhui, China
| | - Shi-Hua Shen
- Department of Hospital Infection Prevention and Control, Fuyang People's Hospital, Fuyang, Anhui, China
| | - Chao-Yang Cai
- Department of Hospital Infection Prevention and Control, The Second People's Hospital of Hefei, Hefei, Anhui, China
| | - Hai-Bin Zhu
- Department of Hospital Infection Prevention and Control, The First People's Hospital of Huainan City, Huainan, Anhui, China
| | - Quan Jiang
- Department of Clinical Laboratory Medicine, Huainan Xinhua Medical Group, Huainan, Anhui, China
| | - Jing Zhang
- Department of Hospital Infection Prevention and Control, Huaibei People's Hospital, Huaibei, Anhui, China
| | - Jia-Lan Niu
- Department of Hospital Infection Prevention and Control, The First People's Hospital of Huoqiu County, Huoqiu, Anhui, China
| | - Xian-Peng Xiong
- Department of Hospital Infection Prevention and Control, Lu'an People's Hospital, Lu'an, Anhui, China
| | - Zhen Tian
- Department of Hospital Infection Prevention and Control, Suzhou Municipal Hospital, Suzhou, Anhui, China
| | - Jian-She Zhang
- Department of Hospital Infection Prevention and Control, Taihe County People's Hospital, Taihe, Anhui, China
| | - Jun-Lin Zhang
- Department of Hospital Infection Prevention and Control, Tongling People's Hospital, Tongling, Anhui, China
| | - Li-Ling Tang
- Department of Hospital Infection Prevention and Control, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - An-Yun Liu
- Department of Hospital Infection Prevention and Control, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Cheng-Xiang Wang
- Department of Hospital Infection Prevention and Control, The First People's Hospital of Wuhu, Wuhu, Anhui, China
| | - Ming-Zhu Ni
- Department of Hospital Infection Prevention and Control, The Second People's Hospital of Wuhu, Wuhu, Anhui, China
| | - Jing-Jing Jiang
- Department of Hospital Infection Prevention and Control, Xuancheng People's Hospital, Xuancheng, Anhui, China
| | - Xi-Yao Yang
- Department of Hospital Infection Prevention and Control, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
| | - Min Yang
- The Second Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
| | - Qiang Zhou
- Department of Clinical Laboratory, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
| |
Collapse
|
3
|
Legouge C, Bidet P, Gits-Muselli M, Cointe A, Courroux C, Birgy A, Bonacorsi S. Rapid, simple multi-locus variable number tandem repeat analysis: a reliable tool for Klebsiella pneumoniae outbreak screening. J Hosp Infect 2023; 141:41-48. [PMID: 37634603 DOI: 10.1016/j.jhin.2023.08.010] [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: 07/03/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Klebsiella pneumoniae causing nosocomial infections is increasingly multi-drug-resistant. Rapid and efficient typing tools are required for monitoring. AIM To assess a simple, rapid (<5 h) multiplex polymerase chain reaction method based on multi-locus variable number tandem repeat analysis (MLVA) as a screening tool to determine whether or not K. pneumoniae strains are related. METHODS The global discriminatory power of the method was assessed on 72 unrelated K. pneumoniae isolates, including community carriage isolates, highly virulent strains causing liver abscess, and extended-spectrum beta-lactamase- and carbapenemase-producing strains. Suspected related strains from a suspected outbreak and a relapsed meningitis case were also studied. MLVA results were compared with whole-genome sequencing (WGS) analysis and multi-locus sequence typing (MLST). FINDINGS MLVA and MLST had similar discriminatory power, each distinguishing 54 profiles among the 72 unrelated isolates (Hunter-Gaston index 0.989). Each strain belonging to one sequence type (ST) or ST complex had its own MLVA type, with few exceptions. Two strains of ST268 and ST1119 shared the same MLVA profile, and two unrelated strains of ST307, ST86, ST45 and ST37 exhibited two different MLVA types each. Moreover, investigation of seven grouped cases of K. pneumoniae neonatal sepsis pointed to strong suspicion of a common source for five isolates, while two isolates with a different MLVA profile were excluded from this cluster. CONCLUSION The MLVA approach is a useful, rapid and reliable tool for epidemiological investigation requiring only basic molecular biology equipment, and permits identification of sporadic isolates that are not part of an outbreak. However, analysis of strains sharing the same MLVA type by a highly discriminatory technique, such as WGS, remains necessary.
Collapse
Affiliation(s)
- C Legouge
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - P Bidet
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France.
| | - M Gits-Muselli
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
| | - A Cointe
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
| | - C Courroux
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - A Birgy
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
| | - S Bonacorsi
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
| |
Collapse
|
4
|
Zhang Y, Jiang Q, Sun F, Wang J, Wu J, Yao H, Li S, Jiang N, Liu Q, Liu Q, Zhang Y, Zhao Y, Chen C, Cui P, Jin J, Zhang W. Genomic tracking and precise control of Klebsiella pneumoniae transmission in a newly established hospital: a prospective molecular epidemiological study. Int J Antimicrob Agents 2023; 62:106910. [PMID: 37422097 DOI: 10.1016/j.ijantimicag.2023.106910] [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: 02/06/2023] [Revised: 06/27/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
OBJECTIVES Carbapenem-resistant Klebsiella pneumoniae (CRKP) pose an emerging clinical threat. We investigated its introduction and transmission in a new hospital, evaluating the effect of whole-genome sequencing (WGS) as an infection control measure. METHODS Based on WGS of identified K. pneumoniae (Kpn) strains, a prospective molecular epidemiological study of nosocomial transmission of CRKP in a newly established Chinese hospital was conducted. RESULTS Between September 2018 and August 2020, 206 Kpn strains were isolated, including 180 CRKP, from 152 patients. The first imported and nosocomial transmission cases were recorded in December 2018 and April 2019, respectively. Overall, 22 nosocomial transmission clusters involving 85 patients were identified, among which 5 were large-size clusters comprising 5-18 patients. Index cases of the large-size clusters were more likely associated with lower Glasgow Coma Scale scores than those of small-size clusters. Furthermore, results of multivariable logistic regression indicated that Kpn tended to transmit more among patients in the ICU [adjusted odds ratio (aOR) = 4.96, 95% confidence interval (CI) 1.97-13.47] and those infected with a ST11 strain (aOR = 8.04, 95% CI 2.51-29.53) or tetracycline-resistant strains (aOR = 17.63, 95% CI 6.32-57.32). However, transmission was less likely in strains bearing the rmpA gene (aOR = 0.12, 95% CI 0.03-0.37). The rate of nosocomial CRKP cases decreased by 2.25 with the intervention of WGS-based infection control. CONCLUSIONS Kpn transmission in the newly established hospital originated from several imported cases. Rates of nosocomial CRKP infection were reduced considerably through precise infection control measures.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, China
| | - Feng Sun
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Wang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haijun Yao
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Shirong Li
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Ning Jiang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Qihui Liu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yilin Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuanhan Zhao
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chen Chen
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jialin Jin
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| |
Collapse
|
5
|
Permana B, Beatson SA, Forde BM. GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach. BMC Bioinformatics 2023; 24:209. [PMID: 37208588 DOI: 10.1186/s12859-023-05332-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/11/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. RESULTS GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings. CONCLUSIONS GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com .
Collapse
Affiliation(s)
- Budi Permana
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
- Herston Infectious Diseases Institute, Metro North Health, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
| | - Brian M Forde
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia.
| |
Collapse
|
6
|
Gomes MZR, de Lima EM, Martins Aires CA, Pereira PS, Yim J, Silva FH, Rodrigues CAS, Oliveira TRTE, da Silva PP, Eller CM, de Souza CMR, Rybak MJ, Albano RM, de Miranda AB, Machado E, Catanho M. Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes. Sci Rep 2023; 13:6238. [PMID: 37069157 PMCID: PMC10110528 DOI: 10.1038/s41598-023-31901-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients' comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.
Collapse
Affiliation(s)
- Marisa Zenaide Ribeiro Gomes
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
- Hospital Federal Servidores do Estado, Ministry of Health, Rio de Janeiro, Brazil.
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
- Hospital Infection Control Committee, Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Caio Augusto Martins Aires
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
- Departamento de Ciência da Saúde, Universidade Federal Rural do Semi-Árido (UFERSA), Mossoró, Rio Grande do Norte, Brazil
| | - Polyana Silva Pereira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Juwon Yim
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Fernando Henrique Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Priscila Pinho da Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Cristiane Monteiro Eller
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Claudio Marcos Rocha de Souza
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Michael J Rybak
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, IBRAG, Universidade do Estado do Rio de Janeiro,, Rio de Janeiro, Brazil
| | - Antonio Basílio de Miranda
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Edson Machado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
| |
Collapse
|
7
|
Rong F, Liu Z, Yang P, Wu F, Sun Y, Sun X, Zhou J. Epidemiological and Molecular Characteristics of bla NDM-1 and bla KPC-2 Co-Occurrence Carbapenem-Resistant Klebsiella pneumoniae. Infect Drug Resist 2023; 16:2247-2258. [PMID: 37090038 PMCID: PMC10120834 DOI: 10.2147/idr.s400138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/01/2023] [Indexed: 04/25/2023] Open
Abstract
Objective Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged and spread worldwide. It can usually cause a serious threat complicating treatment options in clinical settings. However, treatment options are limited. The present study investigates the prevalence and genetic characteristics of bla NDM-1 and bla KPC-2 co-harboring clinical isolates of Klebsiella pneumoniae. Methods In this study, Multiplex polymerase chain reaction (PCR) was performed to detect the carbapenem-resistant genes, and the broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) of antibacterial drugs. The transferability of carbapenem-resistant phenotypes was examined using filter mating assays. Overall, we used Illumina sequencing to evaluate the epidemiological and molecular characteristics of bla NDM-1 and bla KPC-2 (genes encoding carbapenemase) co-occurrence in CRKP strains. Results All strains exhibited resistance to carbapenems and other antibiotics. However, they were still susceptible to polymyxin E. Among them, 18 isolates were positive for bla KPC-2, bla NDM-1, and multiple virulence determinants, such as genes encoding the virulence factor aerobactin, yersiniabactin, and the regulator of the mucoid phenotype (rmpA and rmpA2). Whole genome sequencing revealed that the 18 CRKP strains belonged to ST11 and capsular serotype KL64, and could be grouped into two evolutionary branches. Furthermore, these strains displayed hypervirulence potential since all of them carried pLVPK-like plasmid. Conclusion These findings suggested that ST11-KL64 CRKP strains are major threats in terms of nosocomial infections in this hospital. Hence, new strategies should be urgently developed to monitor, diagnose, and treat this high-risk CRKP clone.
Collapse
Affiliation(s)
- Fang Rong
- Department of General Practice, The Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Graduate School Department of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
| | - Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Pengbin Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Feng Wu
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Yu Sun
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Xuewei Sun
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Jun Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Correspondence: Jun Zhou, Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou, Jiangsu, 225009, People’s Republic of China, Email
| |
Collapse
|
8
|
Santos-Marques C, Ferreira H, Gonçalves Pereira S. Infection prevention and control strategies against carbapenem resistant Enterobacteriaceae - a systematic review. J Infect Prev 2022; 23:167-185. [PMID: 37256160 PMCID: PMC10226056 DOI: 10.1177/17571774211066762] [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: 11/04/2020] [Accepted: 11/17/2021] [Indexed: 09/20/2023] Open
Abstract
Background Antimicrobial resistance is exponentially worsening, and the spread of prevalent carbapenem resistant Enterobacteriaceae (CRE) is a major contributor to this global concern. Infection prevention and control strategies are increasingly consolidated key tools to control this worldwide problem. Aim To identify, collect and analyse available evidence regarding the impact of infection prevention and control strategies on prevalent CRE dissemination. Methods Pubmed®, Scopus® and Web of Science® were searched systematically for articles published between 1th January 2017 and 30th June 2020, guided by the research question 'What are the most effective and efficient strategies to prevent and control infection/colonisation caused by Carbapenem resistant Escherichia coli and Carbapenem resistant Klebsiella pneumoniae?'. Findings Eleven thousand six hundred and thirty-five publications were found, but after applying the inclusion and exclusion criteria, only 30 were selected. The majority of reviewed studies (n = 24) were performed in outbreak situations, 26 studies occurred in acute care units and of those, 17 in intensive care units . From the set of implemented infection prevention and control measures, in 29 studies surveillance cultures were applied, in 23 studies patients were isolated or cohorted and, in general, all described the implementation of standard and contact precaution measures. Conclusion This systematic review underlines the importance of infection prevention and control strategies in CRE dissemination, standing out the need of further studies outside outbreak and intensive care units contexts. Investment increments and training and educating of all involved are also important contributors to shift this problem, but still with relevant gaps in their implementation, in all types of care units, that need to be addressed.
Collapse
Affiliation(s)
- Catarina Santos-Marques
- Center for Innovative Care and
Health Technology – ciTechCare, Polytechnic of Leiria, Portugal
- Microbiology Laboratory, Biological
Sciences Department, Faculty of Pharmacy of University of Porto, Portugal
- Research Unit on Applied Molecular
Biosciences – UCIBIO, Portugal
| | - Helena Ferreira
- Microbiology Laboratory, Biological
Sciences Department, Faculty of Pharmacy of University of Porto, Portugal
- Research Unit on Applied Molecular
Biosciences – UCIBIO, Portugal
| | - Sónia Gonçalves Pereira
- Center for Innovative Care and
Health Technology – ciTechCare, Polytechnic of Leiria, Portugal
| |
Collapse
|
9
|
Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales. Nat Commun 2022; 13:3052. [PMID: 35650193 PMCID: PMC9160272 DOI: 10.1038/s41467-022-30637-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Carbapenemase-producing Enterobacterales (CPE) infection control practices are based on the paradigm that detected carriers in the hospital transmit to other patients who stay in the same ward. The role of plasmid-mediated transmission at population level remains largely unknown. In this retrospective cohort study over 4.7 years involving all multi-disciplinary public hospitals in Singapore, we analysed 779 patients who acquired CPE (1215 CPE isolates) detected by clinical or surveillance cultures. 42.0% met putative clonal transmission criteria, 44.8% met putative plasmid-mediated transmission criteria and 13.2% were unlinked. Only putative clonal transmissions associated with direct ward contact decreased in the second half of the study. Both putative clonal and plasmid-mediated transmission associated with indirect (no temporal overlap in patients’ admission period) ward and hospital contact did not decrease during the study period. Indirect ward and hospital contact were identified as independent risk factors associated with clonal transmission. In conclusion, undetected CPE reservoirs continue to evade hospital infection prevention measures. New measures are needed to address plasmid-mediated transmission, which accounted for 50% of CPE dissemination. Carbapenemase-producing Enterobacterales cause healthcare-associated infections but modes of transmission are not well understood. Here, the authors find evidence of transmission without direct patient contact, indicating presence of undetected environmental reservoirs, whilst half of the transmission events are likely due to plasmid-mediated transmission.
Collapse
|
10
|
Sequence-Based Genomic Analysis Reveals Transmission of Antibiotic Resistance and Virulence among Carbapenemase-Producing Klebsiella pneumoniae Strains. mSphere 2022; 7:e0014322. [PMID: 35546482 PMCID: PMC9241541 DOI: 10.1128/msphere.00143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenemase-producing Klebsiella pneumoniae (CP-Kpn) are a major concern for nosocomial infections. We previously reported an intensive care unit (ICU) outbreak of CP-Kpn. This study investigated the transmission pattern and genetic characteristic of CP-Kpn in the hospital during the outbreak period. Whole-genome sequencing was retrospectively performed on 173 CP-Kpn isolates. Pairwise single-nucleotide polymorphism (SNP) distances were calculated to determine SNP thresholds for clustering. Plasmids and mobile genome elements (MGEs) were identified through short- and long-read sequencing. Strains were classified into three groups, sequence type 11 (ST11) (86.12%), ST15 (9.83%), and other ST. An SNP threshold of 16 revealed a 66.47% clustering rate. ICU admission and meropenem use proportions were significantly higher in clustered patients than in unique patients. MGE distribution was consistent with the phylogenetic tree. Of the isolates, 53.18% were CP-Kpn with hypervirulence genes. We identified five plasmids carrying virulence genes, and four of them have not been previously reported. Clonal transmission was the main cause of CP-Kpn infections in the hospital. Multidrug resistance genes and MGE variations were correlated with clustering. Finally, four novel plasmids carrying virulence genes were identified. The findings highlight the control of CR-Kpn transmission through prevention measures to reduce nosocomial infections. IMPORTANCE In this study, we combined genomic and epidemiological analyses and defined an optimal cutoff value for SNP difference that could be used to aid investigation in tertiary hospital in China. We revealed clonal transmission was the main cause of CP-Kpn infections in the hospital and identified four novel plasmids carrying virulence genes. Our results strongly suggested that dominant CP K. pneumoniae strains lead to outbreaks and described different evolutionary patterns of plasmids carrying multidrug resistance and virulence genes.
Collapse
|
11
|
Lázaro-Perona F, Dahdouh E, Sotillo A, Pérez-Blanco V, Villa J, Viedma E, Ruiz-Carrascoso G, Mingorance J. Dissemination of a single ST11 clone of OXA-48-producing Klebsiella pneumoniae within a large polyclonal hospital outbreak determined by genomic sequencing. Microb Genom 2022; 8. [PMID: 35394416 PMCID: PMC9453077 DOI: 10.1099/mgen.0.000808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The population structure of a set of OXA-48-producing Klebsiella pneumoniae isolates belonging to sequence type 11 (ST11 Kp-OXA) and obtained from two hospitals in Madrid in the period from 2012 to 2015 was studied by genome sequencing. Overall, 97 ST11 Kp-OXA isolates were sequenced and their population structure and demography were studied by Bayesian phylodynamic analysis using core-genome SNVs. In total, 92 isolates were from Hospital La Paz, 57 of them from two selected units. The remaining five isolates were from different units of Hospital Doce de Octubre. Altogether, 96 out of the 97 ST11 Kp-OXA isolates could be ascribed to a single lineage that evolved into three sublineages. Demographic inference showed an expansion of the ST11 Kp-OXA in the first half of 2013 in agreement with the registered incidences. Dated phylogeny showed transmission clusters within hospital wards, between wards and between hospitals. The ST11 Kp-OXA outbreak in Hospital La Paz was largely due to the expansion of a single clone that was transmitted between different units and to Hospital Doce de Octubre. This clone diverged into three sub-lineages and spread out following a mixed mode of neutral core-genome evolution with some features of antibiotic selection, frequent large deletions and plasmid loss and gain events.
Collapse
Affiliation(s)
- Fernando Lázaro-Perona
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Elias Dahdouh
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Alma Sotillo
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Verónica Pérez-Blanco
- Servicio de Medicina Preventiva, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Jennifer Villa
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Imas12, Avenida de Córdoba sn, Madrid 28041, Spain
| | - Esther Viedma
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Imas12, Avenida de Córdoba sn, Madrid 28041, Spain
| | - Guillermo Ruiz-Carrascoso
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| |
Collapse
|
12
|
Yin C, Yang W, Lv Y, Zhao P, Wang J. Clonal spread of carbapenemase-producing Enterobacteriaceae in a region, China. BMC Microbiol 2022; 22:81. [PMID: 35350977 PMCID: PMC8962535 DOI: 10.1186/s12866-022-02497-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
Background The increasing number of carbapenemase-producing Enterobacterales (CPE) has become a serious problem globally. This study aimed to elucidate their geographically epidemiological characteristics. Methods Resistance genes were identified by polymerase chain reaction (PCR) and sequencing. Bacterial genotyping was studied using multilocus sequence typing (MLST) and wzi typing. The transferability of carbapenemase genes was determined by a broth mating method. The relationships between the rates of antimicrobial consumption and the prevalence of CRE were performed by Pearson's or Spearman's correlation analyses. Results A total of 930 phenotypically confirmed carbapenem-resistant Enterobacterales (CRE) isolates collected from 19 hospitals were genotypically characterized. K. pneumoniae (KP) and E. coli isolates were 785 (85.14%) and 96 (10.41%) among 922 CPE isolates. Two major carbapenemase genes blaKPC-2 and blaNDM in CPE isolates accounted for 84.6% (n = 780) and 13.77% (n = 127). ST11 comprised 86.83% (633/729) of KPC-2 KP isolates. Different combinations of extended spectrum-β-lactamase (ESBL) genes of blaSHV, blaCTX, and blaTEM were found in KPC-2 producing KP isolates, and blaCTM-M-14/15, blaSHV-11/12 and blaTEM-1 were common ESBL genotypes. The wzi typing method could further subdivide ST11 KP group into at least five subgroups, among which wzi209 (69.83%, 442/633) was the most frequently isolated, followed by wzi141 (25.28%, 160/633). Conjugation assays showed that high conjugation rates were observed in CPE (15.24%, 32/210) for NDM plasmids, but relatively low (8.1%, 17/210) for KPC-2 plasmids. Different STs, different wzis and temperature could influence plasmid conjugation efficiency. No associations between the rates of antibiotics consumption and CPE prevalence were observed. The number of intra-hospital and inter-hospital transfers of CPE patients increased gradually from 18 (17.82%, 101) and 12 (11.88%, 101) in 2015 to 63 (30.73%, 205) and 51 (24.88%, 205) in 2018 (p = 0.016 and p = 0.008), respectively. Evidence-based measures could effectively reduce the prevalence of ST11-wzi209 clone but failed to control the dissemination of ST11-wzi141 KP clone. Conclusions Clonal spread of CPE, especially KPC-2 ST11 KP was the key factor contributing to the CPE increase in the region. Continued vigilance for the importations should be maintained. Coordinated regional interventions are urgently needed to reduce CPE threat.
Collapse
|
13
|
Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:pathogens11020252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
Collapse
|
14
|
Kong Y, Sun Q, Chen H, Draz MS, Xie X, Zhang J, Ruan Z. Transmission Dynamics of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 Strains Carrying Capsular Loci KL64 and rmpA/ rmpA2 Genes. Front Microbiol 2021; 12:736896. [PMID: 34690977 PMCID: PMC8529244 DOI: 10.3389/fmicb.2021.736896] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022] Open
Abstract
The presence and dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) often cause life-threatening infections worldwide, but the therapeutic option is limited. In this study, whole-genome sequencing (WGS) was applied to assess the epidemiological characteristics and transmission dynamics of CRKP isolates recovered from two fetal outbreaks of nosocomial infections. Between April 2016 and March 2018, a total of 70 isolates of K. pneumoniae were collected from sterile samples in a tertiary hospital in Hangzhou, China. The minimal inhibitory concentrations (MICs) of 21 antimicrobial agents were determined using the broth microdilution methods. Pulsed-field gel electrophoresis (PFGE) was performed on 47 CRKP isolates, and 16 clonally related isolates were further characterized by Illumina sequencing. In addition, the complete genome sequences of three representative isolates (KP12, KP36, and KP37) were determined by Oxford Nanopore sequencing. The K. pneumoniae isolates were recovered from patients diagnosed with pulmonary infection, cancer, or encephalopathy. For all CRKP isolates, PFGE separated three clusters among all strains. The most predominant PFGE cluster contained 16 isolates collected from patients who shared close hospital units and represented a potential outbreak. All 16 isolates showed an extremely high resistance level (≥87.5%) to 18 antimicrobials tested but remain susceptible to colistin (CST). Multiple antimicrobial resistance and virulence determinants, such as the carbapenem resistance gene blaKPC-2, and genes encoding the virulence factor aerobactin and the regulator of the mucoid phenotype (rmpA and rmpA2), were observed in the 16 CRKP isolates. These isolates belonged to sequence type 11 (ST11) and capsular serotype KL64. A core genome single nucleotide polymorphism (cgSNP)-based phylogenetic analysis indicated that the 16 CRKP isolates could be partitioned into two separate clades (≤15 SNPs), suggesting the two independent transmission scenarios co-occurred. Moreover, a high prevalence of IncFIB/IncHI1B type virulence plasmid with the iroBCDN locus deleted, and an IncFII/IncR type blaKPC-2-bearing plasmid was co-harbored in ST11-KL64 CRKP isolates. In conclusion, our data indicated that the nosocomial dissemination of ST11-KL64 CRKP clone is a potential threat to anti-infective therapy. The development of novel strategies for surveillance, diagnosis, and treatment of this high-risk CRKP clone is urgently needed.
Collapse
Affiliation(s)
- Yingying Kong
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingyang Sun
- Department of Clinical Laboratory, No. 903 Hospital of PLA Joint Logistic Support Force, Hangzhou, China
| | - Hangfei Chen
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
15
|
da Silva KE, Rossato L, Jorge S, de Oliveira NR, Kremer FS, Campos VF, da Silva Pinto L, Dellagostin OA, Simionatto S. Three challenging cases of infections by multidrug-resistant Serratia marcescens in patients admitted to intensive care units. Braz J Microbiol 2021; 52:1341-1345. [PMID: 33829377 PMCID: PMC8324748 DOI: 10.1007/s42770-021-00477-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/26/2021] [Indexed: 11/28/2022] Open
Abstract
The occurrence of multidrug-resistant Serratia marcescens strains represents a serious public health threat. The purpose here is to report three cases of carbapenem-resistant S. marcescens infections with unfavorable clinical outcomes and provide a molecular description of the antibiotic resistance determinants at a genomic level. We performed bacterial identification by VITEK 2 and MALDI-TOF. The minimal inhibitory concentrations of antimicrobials were determined according to the Clinical and Laboratory Standards Institute guidelines, except for tigecycline, for which they were determined using Etest strips. Preliminary screening for the presence of carbapenemases was performed by ertapenem hydrolysis using MALDI-TOF MS. Whole-genome sequencing was provided to identify genes responsible for virulence and antimicrobial resistance. Here we report three challenging cases of S. marcescens that were resistant to the most commonly used antibiotics. Otherwise, we performed a genome description, which includes several genes involved in the resistance and virulence. These cases illustrate serious infection due to multidrug-resistant organisms and the complexity of treatment. Our results highlight the need to evaluate isolates regularly during long-term hospital stay to achieve optimal quality of clinical care and thus improve patient outcomes.
Collapse
Affiliation(s)
- Kesia Esther da Silva
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados - UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Luana Rossato
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados - UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Sérgio Jorge
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Natasha Rodrigues de Oliveira
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Frederico Schmitt Kremer
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Vinícius Farias Campos
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Luciano da Silva Pinto
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Odir Antonio Dellagostin
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Simone Simionatto
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados - UFGD, Dourados, Mato Grosso do Sul, Brazil.
- Cidade Universitária, Rodovia Dourados - Itahum km 12, Dourados, Mato Grosso do Sul, CEP: 79804970, Brazil.
| |
Collapse
|
16
|
Büdel T, Kuenzli E, Campos-Madueno EI, Mohammed AH, Hassan NK, Zinsstag J, Hatz C, Endimiani A. On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat. J Antimicrob Chemother 2021; 75:2432-2441. [PMID: 32562537 DOI: 10.1093/jac/dkaa198] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES Intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacterales (Ent) can be driven by contact with colonized animals and/or contamination of the food chain. We studied the ESC-R-Ent and COL-R-Ent colonizing poultry as well as contaminating chicken meat in Zanzibar (Tanzania). Results were compared with recently published data obtained from rectal swabs of people in the community. METHODS During June and July 2018, we collected poultry faecal material (n = 62) and retail chicken meat (n = 37) samples. ESC-R and CST-R strains were isolated implementing selective approaches and characterized with different molecular methods, including WGS coupled with core-genome analyses. RESULTS The prevalence of ESC-R-Ent and CST-R-Ent, respectively, were: 88.7% and 48.4% in poultry; and 43.2% and 18.9% in chicken meat. Overall, the following strains and main resistance mechanisms were found in the two settings: 69 ESC-R Escherichia coli (CTX-M-15 subgroup, 75%), 34 ESC-R Klebsiella pneumoniae (CTX-M-9 group, 54.5%), 24 non-ESC-R but CST-R E. coli (mcr-1, 95.8%) and 17 non-ESC-R but CST-R K. pneumoniae (D150G substitution in PhoQ). Several clones (differing by only 0-13 single nucleotide variants) were concomitantly and frequently found in human and non-human settings: mcr-1-carrying E. coli ST46; CTX-M-15-producing E. coli ST361; CTX-M-14-producing K. pneumoniae ST17; and CTX-M-15-producing K. pneumoniae ST1741. CONCLUSIONS This is one of the few studies that have assessed the occurrence of identical MDR Enterobacterales in human and non-human settings. The frequent human gut colonization observed in the community might be favoured by the spread of ESC-R-Ent and CST-R-Ent in poultry and chicken meat. Further studies with a One Health approach should be carried out to better investigate this phenomenon.
Collapse
Affiliation(s)
- Thomas Büdel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | | | | | | | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christoph Hatz
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| |
Collapse
|
17
|
Taylor YJ, Kowalkowski M, Spencer MD, Evans SM, Hall MN, Rissmiller S, Shrestha R, McWilliams A. Realizing a learning health system through process, rigor and culture change. HEALTHCARE-THE JOURNAL OF DELIVERY SCIENCE AND INNOVATION 2021; 8 Suppl 1:100478. [PMID: 34175095 DOI: 10.1016/j.hjdsi.2020.100478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 07/28/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022]
Abstract
While many healthcare organizations strive to achieve the patient care benefits of being a learning health system (LHS), myriad challenges stand in the way of successful implementation. The reality of creating a true LHS requires top-to-bottom commitment to culture change with the necessary vision, leadership, and investment. The Center for Outcomes Research and Evaluation (CORE) is a multidisciplinary research unit embedded within a large, vertically integrated healthcare system in the southeastern United States. We used a two-pronged approach to: a) methodically recruit a team of experts, while generating early wins that demonstrated real success; and b) build relationships and buy-in across organizational leadership. Building out a team with diverse expertise created the ability to deploy pragmatic, data-driven research designs that fit seamlessly into real-world care delivery, resulting in agile study execution that aligns with health system timelines. Case study examples from hospital readmissions and antibiotic stewardship illustrate how our LHS operationalizes practice-informed research and research-informed practice. Lessons from this experience can serve as a blueprint for other healthcare systems or networks seeking to expand the promise of the LHS framework to improve health for patients and communities.
Collapse
Affiliation(s)
| | - Marc Kowalkowski
- Center for Outcomes Research and Evaluation, Atrium Health, USA.
| | | | - Susan M Evans
- Center for Outcomes Research and Evaluation, Atrium Health, USA.
| | - Mary N Hall
- Division of Medical Education and Research, Atrium Health, USA; Medical Group Division, Atrium Health, USA.
| | | | | | - Andrew McWilliams
- Center for Outcomes Research and Evaluation, Atrium Health, USA; Medical Group Division, Atrium Health, USA; Department of Internal Medicine, Hospital Medicine, Atrium Health, USA.
| |
Collapse
|
18
|
O'Hara LM, Nguyen MH, Calfee DP, Miller LG, Pineles L, Magder LS, Johnson JK, Morgan DJ, Rasko DA, Harris AD. Risk factors for transmission of carbapenem-resistant Enterobacterales to healthcare personnel gloves and gowns in the USA. J Hosp Infect 2021; 109:58-64. [PMID: 33358930 DOI: 10.1016/j.jhin.2020.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Hospitals are sources for acquisition of carbapenem-resistant Entero-bacterales (CRE), and it is believed that the contamination of healthcare personnel (HCP) hands and clothing play a major role in patient-to-patient transmission of antibiotic-resistant bacteria. AIM The aim of this study was to determine which HCP types, HCP-patient interactions, and patient characteristics are associated with greater transmission of CRE to HCP gloves and gowns in the hospital. METHODS This was a prospective observational cohort study that enrolled patients with recent surveillance or clinical cultures positive for CRE at five hospitals in four states in the USA. HCP gloves and gown were cultured after patient care. Samples were also obtained from patients' stool, perianal area, and skin of the chest and arm to assess bacterial burden. FINDINGS Among 313 CRE-colonized patients and 3070 glove and gown cultures obtained after patient care, HCP gloves and gowns were found to be contaminated with CRE 7.9% and 4.3% of the time, respectively. Contamination of either gloves or gowns occurred in 10.0% of interactions. Contamination was highest (15.3%) among respiratory therapists (odds ratio: 3.79; 95% confidence interval: 1.61-8.94) and when any HCP touched the patient (1.52; 1.10-2.12). Associations were also found between CRE transmission to HCP gloves or gown and: being in the intensive care unit, having a positive clinical culture, and increasing bacterial burden on the patient. CONCLUSION CRE transmission to HCP gloves and gown occurred frequently. These findings may inform evidence-based policies about what situations and for which patients contact precautions are most important.
Collapse
Affiliation(s)
- L M O'Hara
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - M H Nguyen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - D P Calfee
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - L G Miller
- LA BioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - L Pineles
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - L S Magder
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - J K Johnson
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - D J Morgan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - D A Rasko
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - A D Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | | |
Collapse
|
19
|
Ernst CM, Braxton JR, Rodriguez-Osorio CA, Zagieboylo AP, Li L, Pironti A, Manson AL, Nair AV, Benson M, Cummins K, Clatworthy AE, Earl AM, Cosimi LA, Hung DT. Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nat Med 2020; 26:705-711. [PMID: 32284589 PMCID: PMC9194776 DOI: 10.1038/s41591-020-0825-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022]
Abstract
Among the most urgent public health threats is the worldwide emergence of carbapenem-resistant Enterobacteriaceae1-4, which are resistant to the antibiotic class of 'last resort'. In the United States and Europe, carbapenem-resistant strains of the Klebsiella pneumoniae ST258 (ref. 5) sequence type are dominant, endemic6-8 and associated with high mortality6,9,10. We report the global evolution of pathogenicity in carbapenem-resistant K. pneumoniae, resulting in the repeated convergence of virulence and carbapenem resistance in the United States and Europe, dating back to as early as 2009. We demonstrate that K. pneumoniae can enhance its pathogenicity by adopting two opposing infection programs through easily acquired gain- and loss-of-function mutations. Single-nucleotide polymorphisms in the capsule biosynthesis gene wzc lead to hypercapsule production, which confers phagocytosis resistance, enhanced dissemination and increased mortality in animal models. In contrast, mutations disrupting capsule biosynthesis genes impair capsule production, which enhances epithelial cell invasion, in vitro biofilm formation and persistence in urinary tract infections. These two types of capsule mutants have emerged repeatedly and independently in Europe and the United States, with hypercapsule mutants associated with bloodstream infections and capsule-deficient mutants associated with urinary tract infections. In the latter case, drug-tolerant K. pneumoniae can persist to yield potentially untreatable, persistent infection.
Collapse
Affiliation(s)
- Christoph M Ernst
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Julian R Braxton
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Carlos A Rodriguez-Osorio
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Anna P Zagieboylo
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Li Li
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | - Anil V Nair
- Center for Systems Biology, Program in Membrane Biology, Division of Nephrology, Massachusetts General Hospital, Boston, MA, USA
| | - Maura Benson
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Kaelyn Cummins
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Anne E Clatworthy
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ashlee M Earl
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa A Cosimi
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Deborah T Hung
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
20
|
Choi M, Tennant SM, Simon R, Cross AS. Progress towards the development of Klebsiella vaccines. Expert Rev Vaccines 2019; 18:681-691. [PMID: 31250679 DOI: 10.1080/14760584.2019.1635460] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Klebsiella pneumoniae (KP) are a leading cause of healthcare-associated infections. The dramatic increase in microbial resistance to third-generation cephalosporin and carbapenem 'front line' antimicrobial agents and the paucity of new antimicrobials have left clinicians with few therapeutic options and resulted in increased morbidity and mortality. Vaccines may reduce the incidence of infections thereby reducing the necessity for antimicrobials and are not subject to antimicrobial resistance mechanisms. Areas covered: We review whole cell, subunit, capsular polysaccharide (CPS), O polysaccharide (OPS) and conjugate vaccines against KP infection, as well as alternative KP vaccine platforms. Expert opinion: Vaccine-induced antibodies to KP CPS have been protective in preclinical studies, but the number of CPS types (>77) makes vaccines against this virulence factor less feasible. Since four OPS serotypes account of ~80% of invasive KP infections and anti-OPS antibodies are also protective in preclinical studies, both OPS-based conjugate and multiple antigen presenting system (MAPS) vaccines are in active development. Vaccines based on other KP virulence factors, such as outer membrane proteins, type 3 fimbriae (MrkA) and siderophores are at earlier stages of development. Novel strategies for the clinical testing of KP vaccines need to be developed.
Collapse
Affiliation(s)
- Myeongjin Choi
- a Center for Vaccine Development and Global Health, University of Maryland School of Medicine , Baltimore , MD , USA
| | - Sharon M Tennant
- a Center for Vaccine Development and Global Health, University of Maryland School of Medicine , Baltimore , MD , USA
| | - Raphael Simon
- a Center for Vaccine Development and Global Health, University of Maryland School of Medicine , Baltimore , MD , USA
| | - Alan S Cross
- a Center for Vaccine Development and Global Health, University of Maryland School of Medicine , Baltimore , MD , USA
| |
Collapse
|
21
|
Heinz E, Brindle R, Morgan-McCalla A, Peters K, Thomson NR. Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors. Microb Genom 2019; 5:e000266. [PMID: 31038449 PMCID: PMC6562249 DOI: 10.1099/mgen.0.000266] [Citation(s) in RCA: 15] [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: 02/05/2019] [Accepted: 03/21/2019] [Indexed: 12/14/2022] Open
Abstract
The surveillance of antimicrobial-resistant isolates has proven to be one of the most valuable tools to understand the global rise of multidrug-resistant bacterial pathogens. We report the first insights into the current situation in the Caribbean, where a pilot project to monitor antimicrobial resistance (AMR) through phenotypic resistance measurements combined with whole-genome sequencing was set up in collaboration with the Caribbean Public Health Agency (CARPHA). Our first study focused on Klebsiella pneumoniae, a highly relevant organism amongst the Gram-negative opportunistic pathogens worldwide causing hospital- and community-acquired infections. Our results show that not only carbapenem resistance, but also hypervirulent strains, are circulating in patients in the Caribbean. Our current data does not allow us to infer their prevalence in the population. We argue for the urgent need to further support AMR surveillance and stewardship in this almost uncharted territory, which can make a significant impact on the reduction of antimicrobial usage. This article contains data hosted by Microreact (https://microreact.org).
Collapse
Affiliation(s)
- Eva Heinz
- Wellcome Trust Sanger Institute, Hinxton, UK
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Richard Brindle
- Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago
- University of Bristol, Bristol, UK
| | - Andrina Morgan-McCalla
- Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago
- University of the West Indies, Mona, Jamaica
| | - Keisha Peters
- Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago
| | - Nicholas R. Thomson
- Wellcome Trust Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| |
Collapse
|