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Adekanmbi AO, Rabiu AG, Ajose DJ, Akinlabi OC, Bolarinwa KA, Farinu EP, Olaposi AV, Adeyemi AO. Solid waste dumpsite leachate and contiguous surface water contain multidrug-resistant ESBL-producing Escherichia coli carrying Extended Spectrum β-Lactamase (ESBL) genes. BMC Microbiol 2024; 24:308. [PMID: 39164664 PMCID: PMC11334489 DOI: 10.1186/s12866-024-03444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
Dumpsites generate leachates containing bacteria that may carry antibiotic resistance genes, such as extended spectrum β-lactamase (ESBL). However, the contribution of dumpsite leachates in the environmental spread of ESBL genes has not been investigated in greater detail. This study aimed to quantify the impact of Ajakanga dumpsite leachate on the spread of ESBL genes through surface water. The susceptibility of Escherichia coli isolated from dumpsite leachate and the accompanying surface water to selected antibiotics was assessed by the standardized disc diffusion method. The isolates were evaluated for phenotypic ESBL production using the double disc synergy test (DDST). The detection of ESBL genes in the isolates was carried out using a primer-specific polymerase chain reaction (PCR). Escherichia coli isolates from leachate (n = 26/32) and surface water (n = 9/12) expressed ESBL phenotype. The ESBL-producing isolates showed the highest level of resistance to the 3rd generation cephalosporin antibiotics: cefotaxime (100%), cefpodoxime (97%), ceftazidime (97%), with low resistance observed to imipenem (6%) and azithromycin (3%). All the isolates were multidrug-resistant, showing resistance to three or more classes of antibiotics. All the ESBL-producing E. coli obtained carried blaCTX-M, 21/35 (60%) carried blaTEM while none of the isolates bore blaSHV. This study found that ESBL-producing Escherichia coli from dumpsite leachate and nearby surface water had identical resistance signatures indicating the relatedness of the isolates, and that dumpsite leachate could contribute to the transfer of ESBL-producing bacteria and their genes to receiving surface water. This study has necessitated the need for a review of the guidelines and operational procedures of dumpsites to forestall a potential public health challenge.
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Affiliation(s)
- Abimbola O Adekanmbi
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria.
- Molecular Biology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria.
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands.
| | - Akeem G Rabiu
- Department of Microbiology, Federal University of Health Sciences, Ila-Orangun, Osun State, Nigeria.
| | - Daniel J Ajose
- Antimicrobial Resistance and Phage Biocontrol Research Group (AREPHABREG), Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa.
- Food Security and Safety Focus Area, Faculty and Natural Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, 2735, South Africa.
| | - Olabisi C Akinlabi
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Kehinde A Bolarinwa
- Department of Education (Biology unit), Distance Learning Institute, University of Lagos, Akoka, Lagos State, Nigeria
| | - Esther P Farinu
- Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria
| | - Adedolapo V Olaposi
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
- Molecular Biology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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Gelalcha BD, Kerro Dego O. Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health. Antibiotics (Basel) 2022; 11:antibiotics11101313. [PMID: 36289970 PMCID: PMC9598938 DOI: 10.3390/antibiotics11101313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.
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Baunoch D, Luke N, Wang D, Vollstedt A, Zhao X, Ko DSC, Huang S, Cacdac P, Sirls LT. Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections. Infect Drug Resist 2021; 14:3275-3286. [PMID: 34447256 PMCID: PMC8382965 DOI: 10.2147/idr.s323095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/28/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Studies have shown that multiple genes influence antibiotic susceptibility, but the relationship between genotypic and phenotypic antibiotic susceptibility is unclear. We sought to analyze the concordance between the presence of antibiotic resistance (ABR) genes and antibiotic susceptibility results in urine samples collected from patients with symptomatic urinary tract infection (UTI). PATIENTS AND METHODS Urine samples were collected from patients presenting to 37 geographically disparate urology clinics across the United States from July 2018 to February 2019. Multiplex polymerase chain reaction was used to detect 27 ABR genes. In samples containing at least one culturable organism at a concentration of ≥ 104 cells per mL, pooled antibiotic susceptibility testing (P-AST), which involves simultaneous growing all detected bacteria together in the presence of antibiotic and then measure susceptibility, was performed against 14 antibiotics. The concordance rate between the ABR genes and the P-AST results was generated for the overall group. The concordance rates for each antibiotic between monomicrobial and polymicrobial infection were compared using chi-square test. RESULTS Results from ABR gene detection and P-AST of urine samples from 1155 patients were included in the concordance analysis. Overall, there was a 60% concordance between the presence or absence of ABR genes and corresponding antimicrobial susceptibility with a range of 49-78% across antibiotic classes. Vancomycin, meropenem, and piperacillin/tazobactam showed significantly lower concordance rates in polymicrobial infections than in monomicrobial infections. CONCLUSION Given the 40% discordance rate, the detection of ABR genes alone may not provide reliable data to make informed clinical decisions in UTI management. However, when used in conjunction with susceptibility testing, ABR gene data can offer valuable clinical information for antibiotic stewardship.
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Affiliation(s)
- David Baunoch
- Research/Development, Pathnostics, Irvine, CA, USA
- Clinical Affairs, Pathnostics, Irvine, CA, USA
| | | | - Dakun Wang
- Medical Writing, Stat4ward, Pittsburgh, PA, USA
| | - Annah Vollstedt
- Women’s Urology and Pelvic Health Center, Beaumont Hospital, Royal Oak, MI, USA
| | | | - Dicken S C Ko
- Department of Bio Med Surgery, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | | | | | - Larry T Sirls
- Women’s Urology and Pelvic Health Center, Beaumont Hospital, Royal Oak, MI, USA
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Jeong SH, Kwon JY, Shin SB, Choi WS, Lee JH, Kim SJ, Ha KS. Antibiotic resistance in shellfish and major inland pollution sources in the drainage basin of Kamak Bay, Republic of Korea. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:471. [PMID: 34226964 DOI: 10.1007/s10661-021-09201-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Shellfish-growing areas in marine environments are affected by pollutants that mainly originate from land, including streams, domestic wastewater, and the effluents of wastewater treatment plants (WWTPs), which may function as reservoirs of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The objective of this study was to identify the occurrence and distribution of antibiotic resistance at five oyster sampling sites and 11 major inland pollution sources in the drainage basin of Kamak Bay, Republic of Korea. Culture-based methods were used to estimate the diversity and abundance of antibiotic-resistant Escherichia coli strains isolated from oysters and major inland pollution sources. The percentages of ARB and multiple antibiotic resistance index values were significantly high in discharge water from small fishing villages without WWTPs. However, the percentages of antibiotic-resistant E. coli isolates from oysters were low, as there was no impact from major inland pollutants. Fourteen ARGs were also quantified from oysters and major inland pollution sources. Although most ARGs except for quinolones were widely distributed in domestic wastewater discharge and effluent from WWTPs, macrolide resistance genes (ermB and msrA) were detected mainly from oysters in Kamak Bay. This study will aid in tracking the sources of antibiotic contamination in shellfish to determine the correlation between shellfish and inland pollution sources.
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Affiliation(s)
- Sang Hyeon Jeong
- Southeast Sea Fisheries Research Institute (53085), National Institute of Fisheries Science, 397-68, Sanyangilju-ro, Sanyang-eup, Tongyeong-si, Gyeongsangnam-do, Republic of Korea.
| | - Ji Young Kwon
- Southeast Sea Fisheries Research Institute (53085), National Institute of Fisheries Science, 397-68, Sanyangilju-ro, Sanyang-eup, Tongyeong-si, Gyeongsangnam-do, Republic of Korea
| | - Soon Bum Shin
- South Sea Fisheries Research Institute (59780), National Institute of Fisheries Science, 22, Sepodangmeori-gil, Hwayang-myeon, Yeosu-si, Jeollanam-do, Republic of Korea
| | - Woo Suk Choi
- South Sea Fisheries Research Institute (59780), National Institute of Fisheries Science, 22, Sepodangmeori-gil, Hwayang-myeon, Yeosu-si, Jeollanam-do, Republic of Korea
| | - Ji Hee Lee
- South Sea Fisheries Research Institute (59780), National Institute of Fisheries Science, 22, Sepodangmeori-gil, Hwayang-myeon, Yeosu-si, Jeollanam-do, Republic of Korea
| | - Seon-Jae Kim
- Department of Marine Bio Food Science, Chonnam National University (59626), 50, Daehak-ro, Yeosu-si, Jeollanam-do, Republic of Korea
| | - Kwang Soo Ha
- Southeast Sea Fisheries Research Institute (53085), National Institute of Fisheries Science, 397-68, Sanyangilju-ro, Sanyang-eup, Tongyeong-si, Gyeongsangnam-do, Republic of Korea
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A Genotype-Phenotype Correlation Study of SHV β-Lactamases Offers New Insight into SHV Resistance Profiles. Antimicrob Agents Chemother 2020; 64:AAC.02293-19. [PMID: 32284385 DOI: 10.1128/aac.02293-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/03/2020] [Indexed: 01/09/2023] Open
Abstract
The SHV β-lactamases (BLs) have undergone strong allele diversification that has changed their substrate specificities. Based on 147 NCBI entries for SHV alleles, in silico mathematical models predicted 5 positions as relevant for the β-lactamase inhibitor (BLI)-resistant (2br) phenotype, 12 positions as relevant for the extended-spectrum BL (ESBL) (2be) phenotype, and 2 positions as related solely to the narrow-spectrum (2b) phenotype. These positions and six additional positions described in other studies (including one promoter mutation) were systematically substituted and investigated for their substrate specificities in a BL-free Escherichia coli background, representing, to our knowledge, the most comprehensive substrate and substitution analysis for SHV alleles to date. An in vitro analysis confirmed the essentiality of positions 238 and 179 for the 2be phenotype and of position 69 for the 2br phenotype. The E240K and E240R substitutions, which do not occur alone in known 2br SHV variants, led to a 2br phenotype, indicating a latent BLI resistance potential of these substitutions. The M129V, A234G, S271I, and R292Q substitutions conferred latent resistance to cefotaxime. In addition, seven positions that were found not always to be associated with the ESBL phenotype resulted in increased resistance to ceftaroline. We also observed that coupling of a strong promoter (IS26) to an A146V mutant with the 2b phenotype resulted in highly increased resistance to BLIs, cefepime, and ceftaroline but not to third-generation cephalosporins, indicating that SHV enzymes represent an underestimated risk for empirical therapies that use piperacillin-tazobactam or cefepime to treat different infectious diseases caused by Gram-negative bacteria.
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Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol 2018; 45:131-139. [PMID: 29723841 DOI: 10.1016/j.mib.2018.04.004] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 04/15/2018] [Indexed: 11/18/2022]
Abstract
Klebsiella pneumoniae is an opportunistic bacterial pathogen known for its high frequency and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant clinical problem in its own right, K. pneumoniae is the species within which several new AMR genes were first discovered before spreading to other pathogens (e.g. carbapenem-resistance genes KPC, OXA-48 and NDM-1). Whilst K. pneumoniae's contribution to the overall AMR crisis is impossible to quantify, current evidence suggests it has a wider ecological distribution, significantly more varied DNA composition, greater AMR gene diversity and a higher plasmid burden than other Gram negative opportunists. Hence we propose it plays a key role in disseminating AMR genes from environmental microbes to clinically important pathogens.
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Affiliation(s)
- Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia.
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia
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Analysis and comparative genomics of R997, the first SXT/R391 integrative and conjugative element (ICE) of the Indian Sub-Continent. Sci Rep 2017; 7:8562. [PMID: 28819148 PMCID: PMC5561048 DOI: 10.1038/s41598-017-08735-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/12/2017] [Indexed: 12/24/2022] Open
Abstract
The aim of this study was to analyse R997, the first integrative and conjugative element (ICE) isolated from the Indian Sub-Continent, and to determine its relationship to the SXT/R391 family of ICEs. WGS of Escherichia coli isolate AB1157 (which contains R997) was performed using Illumina sequencing technology. R997 context was assessed by de novo assembly, gene prediction and annotation tools, and compared to other SXT/R391 ICEs. R997 has a size of 85 Kb and harbours 85 ORFs. Within one of the variable regions a HMS-1 β-lactamase resistance gene is located. The Hotspot regions of the element contains restriction digestion systems and insertion sequences. R997 is very closely related to the SXT-like elements from widely dispersed geographic areas. The sequencing of R997 increases the knowledge of the earliest isolated SXT/R391 elements and may provide insight on the emergence of these elements on the Indian sub-continent.
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Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. mSphere 2017; 2:mSphere00290-17. [PMID: 28776045 PMCID: PMC5541162 DOI: 10.1128/mspheredirect.00290-17] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. K. variicola and K. quasipneumoniae are closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome sequencing to investigate infections caused by these organisms in our hospital system. We discovered that K. variicola and K. quasipneumoniae isolates are often misidentified as K. pneumoniae by routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar to K. pneumoniae. The presence of KPC in K. variicola and K. quasipneumoniae strains as well as NDM-1 metallo-beta-lactamase in one K. variicola strain is particularly concerning because these genes confer resistance to many different beta-lactam antibiotics. The sharing of plasmids, as well as evidence of homologous recombination, between these three species of Klebsiella is cause for additional concern. Klebsiella pneumoniae is a major threat to public health, causing significant morbidity and mortality worldwide. The emergence of highly drug-resistant strains is particularly concerning. There has been a recognition and division of Klebsiella pneumoniae into three distinct phylogenetic groups: Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. K. variicola and K. quasipneumoniae have often been described as opportunistic pathogens that have less virulence in humans than K. pneumoniae does. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates recovered from human infections and discovered that 28 strains were phylogenetically related to K. variicola and K. quasipneumoniae. Whole-genome sequencing of 95 additional non-ESBL-producing K. pneumoniae isolates recovered from patients found 12 K. quasipneumoniae strains. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis initially identified all patient isolates as K. pneumoniae, suggesting a potential pitfall in conventional clinical microbiology laboratory identification methods. Whole-genome sequence analysis revealed extensive sharing of core gene content and plasmid replicons among the Klebsiella species. For the first time, strains of both K. variicola and K. quasipneumoniae were found to carry the Klebsiella pneumoniae carbapenemase (KPC) gene, while another K. variicola strain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene. K. variicola and K. quasipneumoniae infections were not less virulent than K. pneumoniae infections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in one K. variicola strain, as well as one strain from a novel Klebsiella species, which challenge the current understanding of interrelationships between clades of Klebsiella. IMPORTANCEKlebsiella pneumoniae is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. K. variicola and K. quasipneumoniae are closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome sequencing to investigate infections caused by these organisms in our hospital system. We discovered that K. variicola and K. quasipneumoniae isolates are often misidentified as K. pneumoniae by routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar to K. pneumoniae. The presence of KPC in K. variicola and K. quasipneumoniae strains as well as NDM-1 metallo-beta-lactamase in one K. variicola strain is particularly concerning because these genes confer resistance to many different beta-lactam antibiotics. The sharing of plasmids, as well as evidence of homologous recombination, between these three species of Klebsiella is cause for additional concern.
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Brandt C, Braun SD, Stein C, Slickers P, Ehricht R, Pletz MW, Makarewicz O. In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species. Sci Rep 2017; 7:43232. [PMID: 28233789 PMCID: PMC5324141 DOI: 10.1038/srep43232] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/20/2017] [Indexed: 12/30/2022] Open
Abstract
The secretion of antimicrobial compounds is an ancient mechanism with clear survival benefits for microbes competing with other microorganisms. Consequently, mechanisms that confer resistance are also ancient and may represent an underestimated reservoir in environmental bacteria. In this context, β-lactamases (BLs) are of great interest due to their long-term presence and diversification in the hospital environment, leading to the emergence of Gram-negative pathogens that are resistant to cephalosporins (extended spectrum BLs = ESBLs) and carbapenems (carbapenemases). In the current study, protein sequence databases were used to analyze BLs, and the results revealed a substantial number of unknown and functionally uncharacterized BLs in a multitude of environmental and pathogenic species. Together, these BLs represent an uncharacterized reservoir of potentially transferable resistance genes. Considering all available data, in silico approaches appear to more adequately reflect a given resistome than analyses of limited datasets. This approach leads to a more precise definition of BL clades and conserved motifs. Moreover, it may support the prediction of new resistance determinants and improve the tailored development of robust molecular diagnostics.
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Affiliation(s)
- Christian Brandt
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Sascha D Braun
- InfectoGnostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Claudia Stein
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Peter Slickers
- InfectoGnostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Ralf Ehricht
- InfectoGnostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Mathias W Pletz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Oliwia Makarewicz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
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Antibiotic resistance and virulence genes in coliform water isolates. Int J Hyg Environ Health 2016; 219:823-831. [DOI: 10.1016/j.ijheh.2016.07.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 11/23/2022]
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12
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Liakopoulos A, Mevius D, Ceccarelli D. A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous. Front Microbiol 2016; 7:1374. [PMID: 27656166 PMCID: PMC5011133 DOI: 10.3389/fmicb.2016.01374] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/19/2016] [Indexed: 12/29/2022] Open
Abstract
β-lactamases are the primary cause of resistance to β-lactams among members of the family Enterobacteriaceae. SHV enzymes have emerged in Enterobacteriaceae causing infections in health care in the last decades of the Twentieth century, and they are now observed in isolates in different epidemiological settings both in human, animal and the environment. Likely originated from a chromosomal penicillinase of Klebsiella pneumoniae, SHV β-lactamases currently encompass a large number of allelic variants including extended-spectrum β-lactamases (ESBL), non-ESBL and several not classified variants. SHV enzymes have evolved from a narrow- to an extended-spectrum of hydrolyzing activity, including monobactams and carbapenems, as a result of amino acid changes that altered the configuration around the active site of the β -lactamases. SHV-ESBLs are usually encoded by self-transmissible plasmids that frequently carry resistance genes to other drug classes and have become widespread throughout the world in several Enterobacteriaceae, emphasizing their clinical significance.
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Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen UR Lelystad, Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen URLelystad, Netherlands; Faculty of Veterinary Medicine, Utrecht UniversityUtrecht, Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen UR Lelystad, Netherlands
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Graham DW, Knapp CW, Christensen BT, McCluskey S, Dolfing J. Appearance of β-lactam Resistance Genes in Agricultural Soils and Clinical Isolates over the 20th Century. Sci Rep 2016; 6:21550. [PMID: 26878889 PMCID: PMC4754643 DOI: 10.1038/srep21550] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/26/2016] [Indexed: 01/14/2023] Open
Abstract
Debate exists about whether agricultural versus medical antibiotic use drives increasing antibiotic resistance (AR) across nature. Both sectors have been inconsistent at antibiotic stewardship, but it is unclear which sector has most influenced acquired AR on broad scales. Using qPCR and soils archived since 1923 at Askov Experimental Station in Denmark, we quantified four broad-spectrum β-lactam AR genes (ARG; bla(TEM), bla(SHV), bla(OXA) and bla(CTX-M)) and class-1 integron genes (int1) in soils from manured (M) versus inorganic fertilised (IF) fields. "Total" β-lactam ARG levels were significantly higher in M versus IF in soils post-1940 (paired-t test; p < 0.001). However, dominant individual ARGs varied over time; bla(TEM) and bla(SHV) between 1963 and 1974, bla(OXA) slightly later, and bla(CTX-M) since 1988. These dates roughly parallel first reporting of these genes in clinical isolates, suggesting ARGs in animal manure and humans are historically interconnected. Archive data further show when non-therapeutic antibiotic use was banned in Denmark, bla(CTX-M) levels declined in M soils, suggesting accumulated soil ARGs can be reduced by prudent antibiotic stewardship. Conversely, int1 levels have continued to increase in M soils since 1990, implying direct manure application to soils should be scrutinized as part of future stewardship programs.
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Affiliation(s)
- David W Graham
- School of Civil Engineering &Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom, NE1 7RU
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom, G1 1XJ
| | - Bent T Christensen
- Department of Agroecology, Aarhus University, AU-Foulum, DK-8830 Tjele, Denmark
| | - Seánín McCluskey
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom, G1 1XJ
| | - Jan Dolfing
- School of Civil Engineering &Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom, NE1 7RU
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Wand ME, Baker KS, Benthall G, McGregor H, McCowen JWI, Deheer-Graham A, Sutton JM. Characterization of pre-antibiotic era Klebsiella pneumoniae isolates with respect to antibiotic/disinfectant susceptibility and virulence in Galleria mellonella. Antimicrob Agents Chemother 2015; 59:3966-72. [PMID: 25896708 PMCID: PMC4468732 DOI: 10.1128/aac.05009-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/13/2015] [Indexed: 01/24/2023] Open
Abstract
The EGD Murray collection consists of approximately 500 clinical bacterial isolates, mainly Enterobacteriaceae, isolated from around the world between 1917 and 1949. A number of these "Murray" isolates have subsequently been identified as Klebsiella pneumoniae. Antimicrobial susceptibility testing of these isolates showed that over 30% were resistant to penicillins due to the presence of diverse blaSHV β-lactamase genes. Analysis of susceptibility to skin antiseptics and triclosan showed that while the Murray isolates displayed a range of MIC/minimal bactericidal concentration (MBC) values, the mean MIC value was lower than that for more modern K. pneumoniae isolates tested. All Murray isolates contained the cation efflux gene cepA, which is involved in disinfectant resistance, but those that were more susceptible to chlorhexidine were found to have a 9- or 18-bp insertion in this gene. Susceptibility to other disinfectants, e.g., H2O2, in the Murray isolates was comparable to that in modern K. pneumoniae isolates. The Murray isolates were also less virulent in Galleria and had a different complement of putative virulence factors than the modern isolates, with the exception of an isolate related to the modern lineage CC23. More of the modern isolates (41% compared to 8%) are classified as good/very good biofilm formers, but there was overlap in the two populations. This study demonstrated that a significant proportion of the Murray Klebsiella isolates were resistant to penicillins before their routine use. This collection of pre-antibiotic era isolates may provide significant insights into adaptation in K. pneumoniae in relation to biocide susceptibility.
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Affiliation(s)
- Matthew E Wand
- Public Health England, Microbiology Services Division, Salisbury, Wiltshire, United Kingdom
| | - Kate S Baker
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Gabriel Benthall
- Public Health England, Microbiology Services Division, Salisbury, Wiltshire, United Kingdom
| | - Hannah McGregor
- National Collection of Type Cultures, Culture Collections, Public Health England, Salisbury, Wiltshire, United Kingdom
| | - James W I McCowen
- Public Health England, Microbiology Services Division, Salisbury, Wiltshire, United Kingdom
| | - Ana Deheer-Graham
- National Collection of Type Cultures, Culture Collections, Public Health England, Salisbury, Wiltshire, United Kingdom
| | - J Mark Sutton
- Public Health England, Microbiology Services Division, Salisbury, Wiltshire, United Kingdom
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15
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Rubin JE, Pitout JD. Extended-spectrum β-lactamase, carbapenemase and AmpC producing Enterobacteriaceae in companion animals. Vet Microbiol 2014; 170:10-8. [DOI: 10.1016/j.vetmic.2014.01.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 12/22/2022]
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16
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First Report of OXA-4, an ESBL Isolated from Pseudomonas aeruginosa a South Indian Strain. Indian J Microbiol 2014; 53:308-14. [PMID: 24426128 DOI: 10.1007/s12088-012-0326-3] [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: 11/04/2009] [Accepted: 03/22/2010] [Indexed: 10/27/2022] Open
Abstract
The OXA-type β-lactamases are so named because of their oxacillin-hydrolyzing abilities. In this study we characterize an extended spectrum β-lactamase, designated OXA-4, produced by a clinical isolate of Pseudomonas aeruginosa. ESBL production was detected by double disk synergy test. The P. aeruginosa isolate was obtained from endotracheal suction tip of 84 years old male patient diagnosed with CVA and hypertension. ESBL producing OXA β-lactamases was detected by PCR with primers specific to the conserved regions of the coding genes. Iso electric focusing was done to confirm the significance, sequencing the amplified product was also done. In the phenotypic identification, the strain was highly resistant to third generation cephalosporins and also to imipenem. The PCR amplified product for OXA β-lactamase was viewed at 919 bp. The pI point for the same was identified at 7.2. With the help of sequencing the amplified OXA β-lactamase was identified as OXA-4 gene. Here we report P. aeruginosa producing OXA-4 ESBL for the first time in the Indian subcontinent.
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Filip R, Chihu-Amparan L, Coman G, Velázquez ME, Silva J. Molecular Characterization of β-lactam Resistance ofSalmonellaIsolates from Pediatric Patients in Romania. J Chemother 2013; 16:337-42. [PMID: 15332707 DOI: 10.1179/joc.2004.16.4.337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The molecular characterization of 16 clinical isolates of Salmonella enterica (14 serotype Typhimurium and 2 serotype Kingston) obtained between January and June 1999 from feces of children hospitalized in Iasi, Romania were genotypically compared by pulse field gel electrophoresis of XbaI restricted bacterial DNA. The majority of the clinical isolates (12/16) belonged to cluster A and (4/16) to unrelated strains, correlating to the OMP profile. Two major different patterns of beta-lactamases were identified: the first with pI of 5.4, 8.2 in 6/16 strains and the second with pI of 5.4 in 5/16. The blaTEM beta-lactamase was identified in 14/16 of the clinical isolates and the blaSHV-5 gene in one strain. We concluded that extended spectrum beta-lactamase (ESBL) with pIs of 8.2 was the most frequent enzyme produced by serotype Typhimurium isolates which were related.
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Affiliation(s)
- R Filip
- Department of Microbiology, Faculty of Medicine, University of Medicine and Pharmacy Gr.T. Popa Iasi, Romania
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18
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Kurz SG, Bonomo RA. Reappraising the use of β-lactams to treat tuberculosis. Expert Rev Anti Infect Ther 2013; 10:999-1006. [PMID: 23106275 DOI: 10.1586/eri.12.96] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The emergence of multidrug-resistant and extensively drug-resistant tuberculosis calls for novel approaches to treatment. Recent studies have shown that BlaC, the β-lactamase of Mycobacterium tuberculosis, is the major determinant of β-lactam resistance. This review invites the reader to explore evidence in order to answer the questions: can β-lactam and β-lactamase inhibitors adequately treat M. tuberculosis infection and are they a viable option in the management of resistant tuberculosis today?
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Affiliation(s)
- Sebastian G Kurz
- Division of Pulmonary, Critical Care and Sleep Medicine, University Hospitals Case Medical Center and Louis Stokes Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
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Toleman MA, Walsh TR. Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 2011; 35:912-35. [DOI: 10.1111/j.1574-6976.2011.00294.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Chromosomally encoded blaCMY-2 located on a novel SXT/R391-related integrating conjugative element in a Proteus mirabilis clinical isolate. Antimicrob Agents Chemother 2010; 54:3545-50. [PMID: 20566768 DOI: 10.1128/aac.00111-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrating conjugative elements (ICEs) are mobile genetic elements that can transfer from the chromosome of a host to the chromosome of a new host through the process of excision, conjugation, and integration. Although SXT/R391-related ICEs, originally demonstrated in Vibrio cholerae O139 isolates, have become prevalent among V. cholerae isolates in Asia, the prevalence of the ICEs among gram-negative bacteria other than Vibrio spp. remains unknown. In addition, SXT/R391-related ICEs carrying genes conferring resistance to extended-spectrum cephalosporins have never been described. Here we carried out a genetic analysis of a cefoxitin-resistant Proteus mirabilis clinical isolate, TUM4660, which revealed the presence of a novel SXT/R391-related ICE, ICEPmiJpn1. ICEPmiJpn1 had a core genetic structure showing high similarity to that of R391 and carried xis and int genes completely identical to those of R391, while an IS10-mediated composite transposon carrying bla(CMY-2) was integrated into the ICE. A nucleotide sequence identical to the 3' part of ISEcp1 was located upstream of the bla(CMY-2) gene, and other genes observed around bla(CMY-2) in earlier studies were also present. Furthermore, the nucleotide sequences of hot spot 2 and hot spot 4 in ICEPmiJpn1 showed high similarity to that of hot spot 2 in SXT(MO10) and with a part of the nucleotide sequence found in P. mirabilis ATCC 29906, respectively. ICEPmiJpn1 was successfully transferred to Escherichia coli, Klebsiella pneumoniae, Salmonella enterica serovar Typhimurium, and Citrobacter koseri in conjugation experiments. These observations suggest that ICEs may contribute to the dissemination of antimicrobial resistance genes among clinically relevant Enterobacteriaceae, which warrants careful observation of the prevalence of ICEs, including SXT/R391-related ICEs.
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21
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Zhao WH, Hu ZQ. β-Lactamases identified in clinical isolates ofPseudomonas aeruginosa. Crit Rev Microbiol 2010; 36:245-58. [DOI: 10.3109/1040841x.2010.481763] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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Abstract
Since the introduction of penicillin, beta-lactam antibiotics have been the antimicrobial agents of choice. Unfortunately, the efficacy of these life-saving antibiotics is significantly threatened by bacterial beta-lactamases. beta-Lactamases are now responsible for resistance to penicillins, extended-spectrum cephalosporins, monobactams, and carbapenems. In order to overcome beta-lactamase-mediated resistance, beta-lactamase inhibitors (clavulanate, sulbactam, and tazobactam) were introduced into clinical practice. These inhibitors greatly enhance the efficacy of their partner beta-lactams (amoxicillin, ampicillin, piperacillin, and ticarcillin) in the treatment of serious Enterobacteriaceae and penicillin-resistant staphylococcal infections. However, selective pressure from excess antibiotic use accelerated the emergence of resistance to beta-lactam-beta-lactamase inhibitor combinations. Furthermore, the prevalence of clinically relevant beta-lactamases from other classes that are resistant to inhibition is rapidly increasing. There is an urgent need for effective inhibitors that can restore the activity of beta-lactams. Here, we review the catalytic mechanisms of each beta-lactamase class. We then discuss approaches for circumventing beta-lactamase-mediated resistance, including properties and characteristics of mechanism-based inactivators. We next highlight the mechanisms of action and salient clinical and microbiological features of beta-lactamase inhibitors. We also emphasize their therapeutic applications. We close by focusing on novel compounds and the chemical features of these agents that may contribute to a "second generation" of inhibitors. The goal for the next 3 decades will be to design inhibitors that will be effective for more than a single class of beta-lactamases.
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Affiliation(s)
- Sarah M. Drawz
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Robert A. Bonomo
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
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23
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Pyrosequencing using the single-nucleotide polymorphism protocol for rapid determination of TEM- and SHV-type extended-spectrum beta-lactamases in clinical isolates and identification of the novel beta-lactamase genes blaSHV-48, blaSHV-105, and blaTEM-155. Antimicrob Agents Chemother 2008; 53:977-86. [PMID: 19075050 DOI: 10.1128/aac.01155-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
TEM- and SHV-type extended-spectrum beta-lactamases (ESBLs) are the most common ESBLs found in the United States and are prevalent throughout the world. Amino acid substitutions at a number of positions in TEM-1 lead to the ESBL phenotype, although substitutions at residues 104 (E to K), 164 (R to S or H), 238 (G to S), and 240 (E to K) appear to be particularly important in modifying the spectrum of activity of the enzyme. The SHV-1-derived ESBLs are a less diverse collection of enzymes; however, the majority of amino acid substitutions resulting in an ESBL mirror those seen in the TEM-1-derived enzymes. Pyrosequencing by use of the single-nucleotide polymorphism (SNP) protocol was applied to provide sequence data at positions critical for the ESBL phenotype spanning the bla(TEM) and bla(SHV) genes. Three novel beta-lactamases are described: the ESBLs TEM-155 (Q39K, R164S, E240K) and SHV-105 (I8F, R43S, G156D, G238S, E240K) and a non-ESBL, SHV-48 (V119I). The ceftazidime, ceftriaxone, and aztreonam MICs for an Escherichia coli isolate expressing bla(SHV-105) were >128, 128, and >128 microg/ml, respectively. Likewise, the ceftazidime, ceftriaxone, and aztreonam MICs for an E. coli isolate expressing bla(TEM-155) were >128, 64, and > 128 microg/ml, respectively. Pyrosequence analysis determined the true identity of the beta-lactamase on plasmid R1010 to be SHV-11 rather than SHV-1, as previously reported. Pyrosequencing is a real-time sequencing-by-synthesis approach that was applied to SNP detection for TEM- and SHV-type ESBL identification and represents a robust tool for rapid sequence determination that may have a place in the clinical setting.
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Harada S, Ishii Y, Yamaguchi K. Extended-spectrum β-Lactamases: Implications for the Clinical Laboratory and Therapy. Ann Lab Med 2008; 28:401-12. [DOI: 10.3343/kjlm.2008.28.6.401] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sohei Harada
- Department of Microbiology and Infectious Diseases, School of Medicine, Faculty of Medicine, Toho University, Tokyo, Japan
- Division of Infectious Diseases2, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, School of Medicine, Faculty of Medicine, Toho University, Tokyo, Japan
| | - Keizo Yamaguchi
- Department of Microbiology and Infectious Diseases, School of Medicine, Faculty of Medicine, Toho University, Tokyo, Japan
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Mosqueda-Gómez JL, Montaño-Loza A, Rolón AL, Cervantes C, Bobadilla-del-Valle JM, Silva-Sánchez J, Garza-Ramos U, Villasís-Keever A, Galindo-Fraga A, Palacios GMR, Ponce-de-León A, Sifuentes-Osornio J. Molecular epidemiology and risk factors of bloodstream infections caused by extended-spectrum beta-lactamase-producing Klebsiella pneumoniae A case-control study. Int J Infect Dis 2008; 12:653-9. [PMID: 18511321 DOI: 10.1016/j.ijid.2008.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 03/05/2008] [Accepted: 03/14/2008] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES To study the prevalence, risk factors, outcome, and molecular epidemiology in patients with bacteremia caused by extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae (Kp) (cases), in comparison with patients with bacteremia caused by a susceptible Kp (controls). METHODS This was a retrospective case-control study including all episodes of Kp bacteremia for the period 1993 to 2002 at a referral hospital for adults in Mexico. ESBL production was tested for by E-test. All isolates were typed by pulsed field gel electrophoresis (PFGE). A subset of isolates underwent plasmid analysis, conjugal transfer of cefotaxime resistance to Escherichia coli J53-2, isoelectric focusing bioassay, colony-blot hybridization, PCR, and sequencing. RESULTS Of the 121 patients with bacteremia due to Kp included in the study, 17 (14.0%) had an ESBL-Kp isolate (cases). Multivariate analysis identified prior use of cephalosporins (OR 7.6, 95% CI 1.1-53.5; p=0.039) and stay in the intensive care unit (ICU; OR 5.6, 95% CI 1.1-27.9; p=0.033) as significant risk factors. No differences were observed in hospital stay or mortality after the event. Multi-drug resistance was more frequent in ESBL-Kp. There was no clonal predominance. A distinct beta-lactamase profile was identified, which included a combination of TEM-1 (pI 5.4) and SHV-5 (pI 8.2) in 13/17 ESBL-Kp isolates. Cefotaxime resistance was transferred by conjugation in 14/17 isolates with a >120-kb plasmid encoding ESBL. CONCLUSIONS The prevalence of ESBL-Kp was found to be lower than that previously reported in Latin America. ESBL-Kp bacteremia was not associated with a worse clinical outcome. We were able to identify a plasmid-mediated horizontal dissemination over the 10-year period.
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O'Halloran JA, McGrath BM, Pembroke JT. Theorf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE. FEMS Microbiol Lett 2007; 272:99-105. [PMID: 17504243 DOI: 10.1111/j.1574-6968.2007.00747.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Conjugation, Genetic/genetics
- Conserved Sequence/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Enterobacteriaceae/genetics
- Enterobacteriaceae/physiology
- Enterobacteriaceae/radiation effects
- Gene Deletion
- Gene Expression Regulation, Bacterial
- Gene Transfer, Horizontal/genetics
- Interspersed Repetitive Sequences
- Isoelectric Point
- Molecular Sequence Data
- Molecular Weight
- Mutagenesis, Insertional
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Recombination, Genetic
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology
- Ultraviolet Rays
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Affiliation(s)
- John A O'Halloran
- Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland
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27
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Marrero J, Waldor MK. The SXT/R391 family of integrative conjugative elements is composed of two exclusion groups. J Bacteriol 2007; 189:3302-5. [PMID: 17307849 PMCID: PMC1855829 DOI: 10.1128/jb.01902-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conjugative elements often encode entry exclusion systems that convert host cells into poor recipients for identical or similar elements. The diversity of exclusion systems within families of conjugative elements has received little attention. We report here the most comprehensive study to date of the diversity of exclusion determinants within a single family of conjugative elements. Unexpectedly, our analyses indicate that there are only two exclusion groups among the diverse members of the SXT/R391 family of integrative conjugative elements.
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Affiliation(s)
- Joeli Marrero
- Channing Lab, Harvard Medical School, 181 Longwood Ave, Boston MA, 02115, USA
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28
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Pembroke JT, Piterina AV. A novel ICE in the genome of Shewanella putrefaciens W3-18-1: comparison with the SXT/R391 ICE-like elements. FEMS Microbiol Lett 2006; 264:80-8. [PMID: 17020552 DOI: 10.1111/j.1574-6968.2006.00452.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A novel R391-like ICE (integrating conjugative element) has been detected in the 4.2 MB genome of Shewanella putrefaciens W3-18-1 located on three different contigs. Assembly of the ICE encoding contigs based on similarity with R391 revealed a mosaic element of plasmid, phage and transposon-like sequences typical of SXT/R391 ICE-like elements. The element, which is 110 057 bp in length, was highly similar to R391 sequences, with most related ORFs showing >96% amino acid sequence identity. The element, designated ICESpuPO1, contained a number of inserts determining resistance to copper and other heavy metals and a broad-spectrum RND efflux pump similar to antibiotic efflux systems. The element was integrated into the Shewanella prfC gene in a manner similar to related ICE-like elements. The chromosomal element junctions contained a 17-bp SXT/R391-like attL and attR site and an unannotated ORF between attL and the ICE integrase encoding a putative recombinational directional factor necessary for excision, with 100% amino acid identity to the R391 ORF4 product.
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Affiliation(s)
- J Tony Pembroke
- Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.
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30
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Burrus V, Marrero J, Waldor MK. The current ICE age: biology and evolution of SXT-related integrating conjugative elements. Plasmid 2006; 55:173-83. [PMID: 16530834 DOI: 10.1016/j.plasmid.2006.01.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 12/30/2005] [Accepted: 01/07/2006] [Indexed: 11/18/2022]
Abstract
SXT is an integrating conjugative element (ICE) that was initially isolated from a 1992 Vibrio cholerae O139 clinical isolate from India. This approximately 100-kb ICE encodes resistance to multiple antibiotics. SXT or closely related ICEs are now present in most clinical and some environmental V. cholerae isolates from Asia and Africa. SXT-related ICEs are not limited to V. cholerae. It is now clear that so-called IncJ elements such as R391 are closely related to SXT. More than 25 members of the SXT/R391 family of ICEs have now been identified in environmental and clinical isolates of diverse species of gamma-proteobacteria worldwide. In this review, we discuss the diversity, evolution and biology of this family of ICEs.
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Affiliation(s)
- Vincent Burrus
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Howard Hughes Medical Institute Boston, MA 02111, USA
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31
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McGrath BM, O'Halloran JA, Piterina AV, Pembroke JT. Molecular tools to detect the IncJ elements: a family of integrating, antibiotic resistant mobile genetic elements. J Microbiol Methods 2005; 66:32-42. [PMID: 16316703 DOI: 10.1016/j.mimet.2005.10.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 10/04/2005] [Accepted: 10/13/2005] [Indexed: 11/20/2022]
Abstract
The IncJ group of enterobacterial mobile genetic elements, which include R391, R392, R705, R997 and pMERPH, have been shown to be site-specific integrating elements encoding variable antibiotic and heavy metal resistance genes. They insert into a specific 17-bp site located in the prfC gene, encoding peptide release factor 3, in Escherichia coli and other hosts. A key feature of known IncJ elements is the presence of a site-specific recombination module consisting of an attachment site on the element and an integrase-encoding gene of the tyrosine recombinase class, which promotes integration between the attachment site on the element and a similar site on the host chromosome. We have cloned and sequenced the integrases from a number of known IncJ elements and designed PCR primers for specific amplification of this gene. Using conserved regions of enterobacterial prfC genes upstream and downstream of the insertion site, and conserved sequences at the ends of the integrated IncJ elements, we have designed specific primers to amplify across the integrated IncJ attL and attR junction fragments. Alignment of over 30 enterobacterial prfC-like genes indicates that the primers designed to amplify attR junction would amplify IncJ element: host junctions from a wide variety of hosts. The IncJ elements have been shown to sensitise recA(+)E. coli K12 strains to UV irradiation. A simple and rapid procedure for demonstrating this effect is described. These tools should enable the rapid detection of such elements in clinical and environmental settings.
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Affiliation(s)
- Barry M McGrath
- Molecular Biochemistry Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland
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Pembroke JT, McGrath BM. Pulsed field gel electrophoresis to rapidly detect the presence of IncJ conjugative transposon-like elements. Lett Appl Microbiol 2005; 41:258-61. [PMID: 16108917 DOI: 10.1111/j.1472-765x.2005.01747.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To develop a screening method to detect the presence of the IncJ group of integrating conjugative transposon-like elements upon transfer to Escherichia coli. METHODS AND RESULTS The unique insertion site of known IncJ elements, the prfC gene, is located in a region of the E. coli chromosome between 98.5 and 100 min on the E. coli genetic map. Using pulsed field gel electrophoresis and the rare cutting restriction enzymes SfiI and XbaI insertions of IncJ elements and an estimate of their size could be determined physically. CONCLUSIONS This method allows initial screening of putative IncJ conjugative transposon-like elements by physical determination of their integration. SIGNIFICANCE AND IMPACT OF THE STUDY IncJ-like elements, which appear to be highly homologous to the prototype IncJ element R391, have been found associated with recent epidemic outbreaks of cholera in a number of locations worldwide. Because of their integrative biology this method provides the first initial screening method to physically determine their presence upon transfer to E. coli.
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Affiliation(s)
- J T Pembroke
- Molecular Biochemistry Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.
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McGrath BM, O'Halloran JA, Pembroke JT. Pre-exposure to UV irradiation increases the transfer frequency of the IncJ conjugative transposon-like elements R391, R392, R705, R706, R997 and pMERPH and isrecA+dependent. FEMS Microbiol Lett 2005; 243:461-5. [PMID: 15686850 DOI: 10.1016/j.femsle.2005.01.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Accepted: 01/07/2005] [Indexed: 11/20/2022] Open
Abstract
The enteric conjugative transposon-like IncJ elements R391, R392, R705, R706 and pMERPH, all demonstrated increased conjugative transfer upon UV irradiation. The transfer frequency increased on average from its basal rate of 10(-5) to 10(-3) per recipient, upon pre-exposure to UV irradiation. However, the transfer frequency of R997, which was higher than the other IncJ elements at 10(-3) per donor, showed a smaller increase. This effect was shown to be recA+ dependent in all cases. Using PCR primers directed outwards from the ends of the integrated R391 element it was observed that a circular intermediate of the element forms within the host, which has been proposed to be a transfer intermediate. Using real-time PCR, it was determined that the amount of the circular intermediate produced increased substantially upon UV irradiation.
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Affiliation(s)
- Barry M McGrath
- Molecular Biochemistry Laboratory, Department of Chemical and Environmental Sciences, Industrial Biochemistry Programme, University of Limerick, Limerick, Ireland
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McGrath BM, Pembroke J. Detailed analysis of the insertion site of the mobile elements R997, pMERPH, R392, R705 and R391 inE. coliK12. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09673.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Miranda G, Castro N, Leaños B, Valenzuela A, Garza-Ramos U, Rojas T, Solórzano F, Chihu L, Silva J. Clonal and horizontal dissemination of Klebsiella pneumoniae expressing SHV-5 extended-spectrum beta-lactamase in a Mexican pediatric hospital. J Clin Microbiol 2004; 42:30-5. [PMID: 14715728 PMCID: PMC321705 DOI: 10.1128/jcm.42.1.30-35.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One hundred eighty-four clinical isolates of Klebsiella pneumoniae were recovered from August 1996 to October 1997 at the Pediatric Hospital of the Instituto Mexicano del Seguro Social in Mexico City, Mexico. Most of the isolates were collected from the neonatal intensive care unit and infant wards, which are located on the same floor of the hospital. Isolates were genotypically compared by pulsed-field gel electrophoresis with XbaI restriction of chromosomal DNA. Of 184 clinical isolates, 91 belonged to cluster A and comprised three subtypes (A1, A2, and A3), while 93 isolates, comprising two minor clones, B (10 isolates) and C (7 isolates), and 76 unique patterns, were considered unrelated isolates (URI). Susceptibility patterns were indistinguishable in both groups. Fifty extended-spectrum beta-lactamase-producing isolates, including 34 from clone A and 16 from URI, were examined for further studies. Molecular and genetic analysis showed that 47 of 50 clinical isolates expressed the SHV-5 beta-lactamase. This enzyme, in combination with TEM-1, was encoded in a >or=170-kb conjugative plasmid. Results indicate that dissemination of this resistance was due to clonal and horizontal spread.
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Affiliation(s)
- Guadalupe Miranda
- Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City
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36
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Böltner D, Osborn AM. Structural comparison of the integrative and conjugative elements R391, pMERPH, R997, and SXT. Plasmid 2004; 51:12-23. [PMID: 14711525 DOI: 10.1016/j.plasmid.2003.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
R391 and SXT are members of a group of eleven chromosome-borne conjugative elements found in the gamma-proteobacteria, whose members carry different antibiotic resistance traits. Recent genomic analysis of R391 and SXT revealed a highly conserved 'backbone' encoding integration/excision, conjugative transfer, and regulation functions, augmented by an array of phenotypic traits and transposable elements. In this study, PCR amplification and sequence analysis were employed to investigate the genomic structure of two further MGE of the R391 family, pMERPH (HgR) and R997 (ApR, SmR, SuR). R997 and pMERPH were found to be structurally related to R391 and SXT and share a number of virtually identical regions with them-including putative integration, conjugative transfer, and regulatory determinants-interrupted by variable DNA segments and transposable elements. The presence of a highly conserved backbone in the four elements strongly suggests their origin in a common ancestral element, which itself was a mosaic of sequences related to phages and plasmids. Subsequent genetic recombination and the acquisition of transposable elements resulted in the possession of variable phenotypic traits among the four MGE, and diversification into two distinct lineages, the first one including R391 and pMERPH, the second one containing SXT and R997.
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Affiliation(s)
- Dietmar Böltner
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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Osborn AM, Böltner D. When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum. Plasmid 2002; 48:202-12. [PMID: 12460536 DOI: 10.1016/s0147-619x(02)00117-8] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plasmids and bacteriophage represent the classical vectors for gene transfer within the horizontal gene pool. However, the more recent discovery of an increasing array of other mobile genetic elements (MGE) including genomic islands (GIs), conjugative transposons (CTns), and mobilizable transposons (MTns) which each integrate within the chromosome, offer an increasingly diverse assemblage contributing to bacterial adaptation and evolution. Molecular characterisation of these elements has revealed that they are comprised of functional modules derived from phage, plasmids, and transposons, and further that these modules are combined to generate a continuum of mosaic MGE. In particular, they are comprised of any one of three distinct types of recombinase, together with plasmid-derived transfer and mobilisation gene functions. This review highlights both the similarities and distinctions between these integrating transferable elements resulting from combination of the MGE toolbox.
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Affiliation(s)
- A Mark Osborn
- Department of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK.
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38
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Böltner D, MacMahon C, Pembroke JT, Strike P, Osborn AM. R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. J Bacteriol 2002; 184:5158-69. [PMID: 12193633 PMCID: PMC135318 DOI: 10.1128/jb.184.18.5158-5169.2002] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.
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Affiliation(s)
- Dietmar Böltner
- Department of Biological Sciences, University of Essex, Colchester, United Kingdom
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39
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Chaves J, Ladona MG, Segura C, Coira A, Reig R, Ampurdanés C. SHV-1 beta-lactamase is mainly a chromosomally encoded species-specific enzyme in Klebsiella pneumoniae. Antimicrob Agents Chemother 2001; 45:2856-61. [PMID: 11557480 PMCID: PMC90742 DOI: 10.1128/aac.45.10.2856-2861.2001] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nature of the SHV-1 beta-lactamase gene was analyzed in 97 epidemiologically unrelated Klebsiella pneumoniae strains isolated from clinical samples. beta-Lactamase bands that focused at a pI of 7.6 (SHV-1-type) in 74 strains, at a pI of 7.1 (LEN-1-type) in 13 strains, and at a pI of 5.4 (TEM-1-type) in 10 strains were detected by analytical isoelectric focusing (IEF). Among the 74 SHV-1-producing strains, 40 had, in addition to the pI 7.6 band, an additional band on IEF: 20 had a band with a pI of 7.1 and 20 had a band with a pI of 5.4. Most of the 74 SHV-1-producing strains (76.7%) carried plasmids. Transfer of beta-lactam resistance by conjugation was possible in only 9.3% of the strains tested. SHV-1 gene-specific PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the chromosomal DNA was positive for 93 of the 97 strains and negative for only 4 of the 10 samples with K. pneumoniae TEM-1 producers. In an attempt to approximate the location of the SHV gene locus by endonuclease restriction analysis, RFLP analysis with Southern blotting of chromosomal DNA with a labeled SHV-1 fragment as a probe was used to study the 97 strains. A trial with EcoRI showed at least one positive hybridization band for 96 strains; two bands were detected for 8 strains. The hybridization was negative for only one TEM-1 beta-lactamase-producing strain. DNA sequence analysis showed no differences in promoter regions or extra stop-triplet sequences; only point mutations determined different allelic variants. The novel SHV-type variants are designated SHV-32 and SHV-33. As a result of the RFLP and sequencing analyses, it can be postulated that the loci for SHV-1 and LEN-1 genes are arranged in tandem. Our results strongly support the hypothesis that the ancestor of the SHV-1 beta-lactamase originated from the K. pneumoniae chromosome.
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Affiliation(s)
- J Chaves
- Department of Pharmacology, Municipal Institute of Medical Investigation, 08003 Barcelona, Spain
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40
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Silva J, Gatica R, Aguilar C, Becerra Z, Garza-Ramos U, Velázquez M, Miranda G, Leaños B, Solórzano F, Echániz G. Outbreak of infection with extended-spectrum beta-lactamase-producing Klebsiella pneumoniae in a Mexican hospital. J Clin Microbiol 2001; 39:3193-6. [PMID: 11526149 PMCID: PMC88317 DOI: 10.1128/jcm.39.9.3193-3196.2001] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirty-one strains of Klebsiella pneumoniae (including 10 duplicates) from 21 septicemic pediatric patients (age, <2 months) were studied during a 4-month period (June to October 1996) in which the fatality rate was 62% (13 of 21). These isolates identified by the API 20E system yielded the same biotype. Pulsed-field gel electrophoresis experiments revealed the same clone in 31 strains. The isolates were multidrug-resistant but were still susceptible to ciprofloxacin, imipenem, and cefoxitin. A 135-kb plasmid was harbored in all of the isolates. No transconjugants were obtained that were resistant to ampicillin, cefotaxime, tetracycline, or gentamicin. Isoelectric focusing for beta-lactamases was performed on all strains, and three bands with pIs of 5.4, 7.6, and 8.2 were obtained. Of these, the pI 8.2 beta-lactamase had an extended-spectrum beta-lactamase phenotype. PCR amplification of both TEM- and SHV-type genes was obtained. The sequence analysis of the SHV PCR product indicated a mutation corresponding to the SHV-5 beta-lactamase.
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Affiliation(s)
- J Silva
- Department of Bacterial Resistance, National Institute of Public Health, Center for Research on Infectious Diseases, Cuernavaca, Morelos, Mexico.
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Hochhut B, Beaber JW, Woodgate R, Waldor MK. Formation of chromosomal tandem arrays of the SXT element and R391, two conjugative chromosomally integrating elements that share an attachment site. J Bacteriol 2001; 183:1124-32. [PMID: 11157923 PMCID: PMC94984 DOI: 10.1128/jb.183.4.1124-1132.2001] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2000] [Accepted: 11/17/2000] [Indexed: 11/20/2022] Open
Abstract
The SXT element, a conjugative, self-transmissible, integrating element (a constin) originally derived from a Vibrio cholerae O139 isolate from India, and IncJ element R391, originally derived from a South African Providencia rettgeri isolate, were found to be genetically and functionally related. Both of these constins integrate site specifically into the Escherichia coli chromosome at an identical attachment site within the 5' end of prfC. They encode nearly identical integrases, which are required for chromosomal integration, excision, and extrachromosomal circularization of these elements, and they have similar tra genes. Therefore, these closely related constins have virtually identical mechanisms for chromosomal integration and dissemination. The presence of either element in a recipient cell did not significantly reduce its ability to acquire the other element, indicating that R391 and SXT do not encode surface exclusion determinants. In cells harboring both elements, SXT and R391 were integrated in tandem fashion on the chromosome, and homologous recombination appeared to play little or no role in the formation of these arrays. Interference between R391 and SXT was detected by measuring the frequency of loss of an unselected resident element upon introduction of a second selected element. In these assays, R391 was found to have a stronger effect on SXT stability than vice versa. The level of expression and/or activity of the donor and recipient integrases may play a role in the interference between these two related constins.
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Affiliation(s)
- B Hochhut
- Division of Geographic Medicine/Infectious Diseases, New England Medical Center and Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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42
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Pembroke JT, Murphy DB. Isolation and analysis of a circular form of the IncJ conjugative transposon-like elements, R391 and R997: implications for IncJ incompatibility. FEMS Microbiol Lett 2000; 187:133-8. [PMID: 10856646 DOI: 10.1111/j.1574-6968.2000.tb09149.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The incompatibility between the chromosomally integrating, conjugative transposon-like, IncJ elements R997 (ampicillin resistant) and R391 (kanamycin resistant) was examined by constructing strains harbouring both elements. Unusually, recA(+) strains harbouring the resistance determinants of both elements could be isolated but all strains lacked detectable extrachromosomal DNA. The phenotypic characteristics and transfer patterns observed suggested the formation of recombinant hybrids rather than strains harbouring both elements independently. Formation of strains harbouring two IncJ elements in a recA background was thus examined and resulted in the visualisation of extrachromosomal DNA. When R391 was transferred to a recA strain containing integrated R997, both elements co-existed stably and resulted in the isolation of a plasmid of 93.9 kb. When R997 was transferred to a recA strain harbouring an integrated R391, a plasmid of 85 kb was isolated. Comparison of restriction patterns for both elements revealed many common and several distinct fragments indicating a close physical relationship. These data suggest that although IncJ elements normally integrate at a unique site in the Escherichia coli chromosome, they possess the ability for autonomous replication which becomes manifest in a recA background when this site is occupied. This observation has implications for the nature of the incompatibility associated with IncJ elements and also provides a reliable method for isolating IncJ elements for molecular characterisation.
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Affiliation(s)
- J T Pembroke
- Molecular Biochemistry Group, University of Limerick, Limerick, Ireland.
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43
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Silva J, Aguilar C, Ayala G, Estrada MA, Garza-Ramos U, Lara-Lemus R, Ledezma L. TLA-1: a new plasmid-mediated extended-spectrum beta-lactamase from Escherichia coli. Antimicrob Agents Chemother 2000; 44:997-1003. [PMID: 10722503 PMCID: PMC89804 DOI: 10.1128/aac.44.4.997-1003.2000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli R170, isolated from the urine of an infected patient, was resistant to expanded-spectrum cephalosporins, aztreonam, ciprofloxacin, and ofloxacin but was susceptible to amikacin, cefotetan, and imipenem. This particular strain contained three different plasmids that encoded two beta-lactamases with pIs of 7.0 and 9.0. Resistance to cefotaxime, ceftazidime, aztreonam, trimethoprim, and sulfamethoxazole was transferred by conjugation from E. coli R170 to E. coli J53-2. The transferred plasmid, RZA92, which encoded a single beta-lactamase, was 150 kb in length. The cefotaxime resistance gene that encodes the TLA-1 beta-lactamase (pI 9.0) was cloned from the transconjugant by transformation to E. coli DH5alpha. Sequencing of the bla(TLA-1) gene revealed an open reading frame of 906 bp, which corresponded to 301 amino acid residues, including motifs common to class A beta-lactamases: (70)SXXK, (130)SDN, and (234)KTG. The amino acid sequence of TLA-1 shared 50% identity with the CME-1 chromosomal class A beta-lactamase from Chryseobacterium (Flavobacterium) meningosepticum; 48.8% identity with the VEB-1 class A beta-lactamase from E. coli; 40 to 42% identity with CblA of Bacteroides uniformis, PER-1 of Pseudomonas aeruginosa, and PER-2 of Salmonella typhimurium; and 39% identity with CepA of Bacteroides fragilis. The partially purified TLA-1 beta-lactamase had a molecular mass of 31.4 kDa and a pI of 9.0 and preferentially hydrolyzed cephaloridine, cefotaxime, cephalothin, benzylpenicillin, and ceftazidime. The enzyme was markedly inhibited by sulbactam, tazobactam, and clavulanic acid. TLA-1 is a new extended-spectrum beta-lactamase of Ambler class A.
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Affiliation(s)
- J Silva
- Departamento de Resistencia Bacteriana, Instituto Nacional de Salud Pública, Centro de Investigaciones Sobre Enfermedades Infecciosas, Cuernavaca, Morelos, México.
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44
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Silva J, Aguilar C, Becerra Z, López-Antuñano F, García R. Extended-spectrum beta-lactamases in clinical isolates of enterobacteria in Mexico. Microb Drug Resist 2000; 5:189-93. [PMID: 10566868 DOI: 10.1089/mdr.1999.5.189] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Resistance to extended-spectrum cephalosporins within members of the family Enterobacteriaceae occurs virtually world-wide. Nevertheless, nothing was known about this problem among isolates from Mexico. To address this issue, we studied oximino-cephalosporin resistant isolates of Klebsiella pneumoniae (13), Escherichia coli (7), and Enterobacter cloacae (23) recovered from patients in Mexico City hospitals during 1990 to 1992. In the presence of clavulanic acid, these strains increased susceptibility to cefotaxime and ceftazidime (MIC90 64 and >256 microg/ml, respectively). The ability of these isolates to transfer resistance to both antibiotics by conjugation was most successfully demonstrated by K. pneumoniae. In all the clinical isolates tested, the largest plasmid coded for the extended-spectrum beta-lactamases (ESBL). Characteristics of pI, by isoelectric focusing (IEF)/bioassay and DNA hybridization with specific probes of TEM and SHV, indicated that in most of the clinical isolates and all transconjugates, the most frequent beta-lactamase coded were SHV-derived (20 strains as 41% of isolates) and a plasmid-encoded beta-lactamase (12 strains as 25% of isolates) (with a pI of >8.2), which is not related to TEM/SHV. Apparently, isolates from Mexico show characteristics similar to isolates from other geographic areas. The type of beta-lactamases coded in these resistant isolates is documented for the first time in Mexico.
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Affiliation(s)
- J Silva
- Bacterial Genetics Department, Instituto Nacional de Salud Pública, Centro de Investigaciones Sobre Enfermedades Infecciosas, Cuernavaca, Mor., Mexico.
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45
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Heritage J, M'Zali FH, Gascoyne-Binzi D, Hawkey PM. Evolution and spread of SHV extended-spectrum beta-lactamases in gram-negative bacteria. J Antimicrob Chemother 1999; 44:309-18. [PMID: 10511397 DOI: 10.1093/jac/44.3.309] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Resistance to beta-lactam antibiotics has been a problem for as long as these drugs have been used in clinical practice. In clinically significant bacteria the most important mechanism of resistance is the production of one or more beta-lactamases, enzymes that hydrolyse the beta-lactam bond characteristic of this family of antibiotics. Prominent among the beta-lactamases produced by the Enterobacteriaceae is the SHV family. The first reported SHV beta-lactamase had a narrow spectrum of activity. By the accumulation of point mutations at sites that affect the active site of the enzyme, a family of derivatives of SHV-1 has evolved. Derivatives of SHV-1 either have an extended spectrum of activity, capable of inactivating third-generation cephalosporins, or are resistant to beta-lactamase inhibitors. This review describes the evolution and spread of the SHV family of beta-lactamases, introducing the structure-function analysis made possible by DNA sequence analysis. It also reviews the methods used to characterize members of this family of beta-lactamases, indicating some of the difficulties involved.
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Affiliation(s)
- J Heritage
- Division of Microbiology, School of Biochemistry and Molecular Biology, and Antimicrobial Research Centre, University of Leeds, UK.
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46
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Murphy DB, Pembroke JT. Monitoring of chromosomal insertions of the IncJ elements R391 and R997 in Escherichia coli K-12. FEMS Microbiol Lett 1999; 174:355-61. [PMID: 10339829 DOI: 10.1111/j.1574-6968.1999.tb13590.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The integration site(s) of the IncJ element, R391, was localised to a specific region of the Escherichia coli chromosome, between the uxuA and serB loci (98.0-99.5 min), using classical Hfr mapping techniques. F-prime plasmid hosts, diploid for regions spanning the E. coli chromosome, were used as recipients in R391 and R997 conjugal transfer assays. Analysis of transconjugants revealed the integration of R391 and R997 into specific F-primes that contain the uxuA to serB region, but not F-primes that contain other regions of the chromosome. A comparison of the electrophoretic mobility of the original F-primes with those containing inserts demonstrated the integration of large elements, in excess of 85 kb. Linear integration of the IncJ elements into chromosomal DNA was demonstrated in recombination-deficient (recA) backgrounds in the absence of detectable autonomous stages. These observations account for the inability to isolate plasmid DNA from IncJ hosts, and suggests that the elements exhibit a conjugative transposon-like biology in E. coli.
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Affiliation(s)
- D B Murphy
- Department of Chemical and Environmental Science, University of Limerick, Ireland
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47
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Fournier B, Gravel A, Hooper DC, Roy PH. Strength and regulation of the different promoters for chromosomal beta-lactamases of Klebsiella oxytoca. Antimicrob Agents Chemother 1999; 43:850-5. [PMID: 10103190 PMCID: PMC89216 DOI: 10.1128/aac.43.4.850] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The two groups of chromosomal beta-lactamases from Klebsiella oxytoca (OXY-1 and OXY-2) can be overproduced 73- to 223-fold, due to point mutations in the consensus sequences of their promoters. The different versions of promoters from blaOXY-1 and blaOXY-2 were cloned upstream of the chloramphenicol acetyltransferase (CAT) gene of pKK232-8, and their relative strengths were determined in Escherichia coli and in K. oxytoca. The three different mutations in the OXY beta-lactamase promoters resulted in a 4- to 31-fold increase in CAT activity compared to that of the wild-type promoter. The G-->T transversion in the first base of the -10 consensus sequence caused a greater increase in the promoter strength of the wild-type promoter than the two other principal mutations (a G-to-A transition of the fifth base of the -10 consensus sequence and a T-to-A transversion of the fourth base of the -35 sequence). The strength of the promoter carrying a double mutation (transition in the Pribnow box and the transversion in the -35 hexamer) was increased 15- to 61-fold in comparison to that of the wild-type promoter. A change from 17 to 16 bp between the -35 and -10 consensus sequences resulted in a ninefold decrease of the promoter strength. The expression of the blaOXY promoter in E. coli differs from that in K. oxytoca, particularly for promoters carrying strong mutations. Furthermore, the blaOXY promoter appears not to be controlled by DNA supercoiling or an upstream curved DNA, but it is dependent on the gene copy number.
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Affiliation(s)
- B Fournier
- Laboratoire et Service d'Infectiologie, Centre Hospitalier de l'Université Laval, Sainte-Foy Québec, Canada.
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Ling JM, Koo IC, Kam KM, Cheng AF. Antimicrobial susceptibilities and molecular epidemiology of Salmonella enterica serotype enteritidis strains isolated in Hong Kong from 1986 to 1996. J Clin Microbiol 1998; 36:1693-9. [PMID: 9620402 PMCID: PMC104902 DOI: 10.1128/jcm.36.6.1693-1699.1998] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/1997] [Accepted: 03/17/1998] [Indexed: 02/07/2023] Open
Abstract
The incidence of salmonellosis has been increasing in Hong Kong since 1989. The most common Salmonella enterica serotype isolated in 1994 was S. enteritidis. The antimicrobial susceptibilities and molecular epidemiology of 275 S. enteritidis strains isolated in this locality between 1986 and 1996 were studied. Over 99% of the isolates were susceptible to 17 of the 19 antimicrobial agents tested. One isolate harbored an autotransferring plasmid that confers resistance to tetracycline and trimethoprim-sulfamethoxazole. Another isolate harbored a mobilizable plasmid that confers resistance to ampicillin and cephalothin. This isolate was found to produce a beta-lactamase with a pI of 5.2. A total of 264 isolates (96%) were found to harbor one to five plasmids, and the majority (254) harbored a 60-kb plasmid. Of these isolates, 94% contained identical 60-kb plasmids. Based on plasmid profiles, plasmid and chromosomal fingerprints, ribotypes, and randomly amplified polymorphic DNA (RAPD) patterns, 170 (62%) isolates were allocated to group 1b. About 90% of isolates had identical or similar DNA fingerprints, ribotypes, and RAPD patterns, suggesting that a predominant clone of S. enteritidis was circulating in Hong Kong during the period being studied.
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Affiliation(s)
- J M Ling
- Department of Microbiology, The Chinese University of Hong Kong, The Prince of Wales Hospital, Shatin, New Territories
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Haeggman S, Löfdahl S, Burman LG. An allelic variant of the chromosomal gene for class A beta-lactamase K2, specific for Klebsiella pneumoniae, is the ancestor of SHV-1. Antimicrob Agents Chemother 1997; 41:2705-9. [PMID: 9420042 PMCID: PMC164192 DOI: 10.1128/aac.41.12.2705] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Fecal Klebsiella isolates from neonates in 22 Swedish special care units were examined by a PCR we developed for detection of the SHV-1 beta-lactamase gene. All 105 K. pneumoniae isolates and all 11 K. pneumoniae reference strains (including the K. pneumoniae subsp. pneumoniae, ozaenae, and rhinoscleromatis type strains) tested were positive, whereas all 67 K. oxytoca isolates and the K. oxytoca, K. planticola, and K. terrigena type strains tested were negative. Resistance to beta-lactams in K. pneumoniae was not transferable by conjugation, and the beta-lactamase gene was never found on a plasmid. Southern blot analysis showed that the gene had a defined chromosomal location. Isoelectric focusing and sequencing of 231-bp PCR amplicons from different isolates revealed many variants of the enzyme, with the two main groups being SHV-1 like (pI 7.6; 68 isolates) and LEN-1 like (pI 7.1; 14 isolates). Clavulanic acid markedly reduced the MICs of ampicillin for all the K. pneumoniae isolates tested. This fact, MIC profiles (penicillin rather than cephalosporin resistance), pIs, and sequence data showed that the chromosomal beta-lactamase of K. pneumoniae is a class A, group 2 enzyme distinct from the chromosomal AmpC enzymes found in several other gram-negative bacteria and from the chromosomal beta-lactamase K1 of K. oxytoca. We propose that the chromosomal beta-lactamase of K. pneumoniae be designated K2 and suggest that an allelic pI 7.6 variant of this enzyme is the ancestor of the SHV family of plasmid-mediated beta-lactamases.
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Affiliation(s)
- S Haeggman
- Swedish Institute for Infectious Disease Control, Stockholm.
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Murphy DB, Pembroke JT. Transfer of the IncJ plasmid R391 to recombination deficient Escherichia coli K12: evidence that R391 behaves as a conjugal transposon. FEMS Microbiol Lett 1995; 134:153-8. [PMID: 8586262 DOI: 10.1111/j.1574-6968.1995.tb07930.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A study of the IncJ plasmid R391 confirmed a low frequency of transfer between recombination proficient (recA+) Escherichia coli (10(-5) donor -1). Reanalysis of its transfer to recombination deficient (recA) E. coli revealed an equivalent transfer frequency to and from all mutants tested. Extrachromosomal DNA could not be detected in either recA+ or recA transconjugants, while R391 proved refractory to curing in both backgrounds implying a high degree of stability. The integration of R391 into a specific region of the chromosome was demonstrated by its transfer as part of the exogenote mobilised from the transfer origins of Hfr strains BW6165 and JC158. Transfer of R391 coupled to recA independent chromosomal integration has significant implications as to the nature and classification of the element. We propose that R391 behaves like a conjugal transposon.
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Affiliation(s)
- D B Murphy
- Department of Chemical and Environment Science, University of Limerick, Ireland
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