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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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Zhang S, Yang G, Ye Q, Wu Q, Zhang J, Huang Y. Phenotypic and Genotypic Characterization of Klebsiella pneumoniae Isolated From Retail Foods in China. Front Microbiol 2018; 9:289. [PMID: 29545778 PMCID: PMC5839057 DOI: 10.3389/fmicb.2018.00289] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 02/07/2018] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae is not only a major hospital-acquired pathogen but also an important food-borne pathogen that can cause septicaemia, liver abscesses, and diarrhea in humans. The phenotypic and genotypic characteristics of K. pneumoniae in retail foods have not been thoroughly investigated in China. The objective of this study was to characterize K. pneumoniae isolates through biotyping, serotyping, determination of virulence factors, antibiotic resistance testing, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and (GTG)5-PCR molecular typing. From May 2013 to April 2014, a total of 61 K. pneumoniae isolates were collected from retail foods in China. Using API 20E test strips, five different biotype profiles were identified among these isolates. The majority of isolates belonged to biochemical profile “5215773” (50 isolates, 80.6%). The capsular serotypes of the 61 K. pneumoniae isolates and one reference strain were determined by PCR. Of the seven capsular serotypes tested, four different capsular serotypes were identified. Serotypes K1, K20, K57, and K2 were detected in two, three, two, and one isolates, respectively. Serotypes K3, K5, and K54 were not detected. The presence of 11 virulence genes was assessed by PCR. The most common virulence genes were fimH (85.5%), ureA (79.0%), wabG (77.4%), uge (56.5%), and kfuBC (29.0%). ERIC-PCR and (GTG)5-PCR molecular typing indicated high genetic diversity among K. pneumoniae isolates. We identified 60 different ERIC patterns and 56 distinct (GTG)5 patterns. Genotypic results indicated that isolates carrying similar virulence factors were generally genetically related. Some isolates from the same geographic area have a closer relationship. The isolates showed high levels of resistance to ampicillin (51/62, 82.2%). Resistance to streptomycin (11/62, 17.7%) and piperacillin (10/62, 16.1%) was also common. The presence of virulent and antibiotic-resistant K. pneumoniae in foods poses a potential health hazard for consumers. Our findings highlight the importance of surveillance of K. pneumoniae in foods.
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Affiliation(s)
- Shuhong Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Guangzhu Yang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qinghua Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yuanbin Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
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53
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Higgins D, Pal C, Sulaiman IM, Jia C, Zerwekh T, Dowd SE, Banerjee P. Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area - A pilot study. Food Res Int 2017; 105:29-40. [PMID: 29433218 DOI: 10.1016/j.foodres.2017.10.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/26/2017] [Accepted: 10/28/2017] [Indexed: 01/08/2023]
Abstract
With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA. For high-throughput sequencing, microbial genomic DNA was directly extracted from the food products and subjected to genetic sequencing. Aerobic plate count of all food samples was also performed. Foods from small stores (such as corner stores) were found to contain higher bacterial counts as compared to large stores (such as supermarkets). High-throughput pyrosequencing in tandem with bioinformatics analyses revealed a comprehensive picture of the bacterial ecology of foods at different taxonomic levels. Firmicutes and Proteobacteria were the most abundant phyla across all products. At the genus level, Enterobacter and Pantoea in vegetables, and Bacillus and Aeromonas in animal products were found to be the most abundant. The bacterial predicted metabolic pathways such as inosine-5'-phosphate biosynthesis I, methylglyoxal (MG) degradation pathways, urea cycle, dTDP-l-rhamnose biosynthesis I, and mevalonate pathway I differed in foods procured from small stores as compared to large groceries or supermarkets. The results from this study revealed that the bacterial ecology (both in terms of numbers and types of bacteria) of food commodities might differ based on the vending outlet type (large vs. small) of retail stores. The overall estimation bacterial communities in foods by high-throughput sequencing method may be useful to identify potential taxa responsible for food spoilage. Moreover, the data from pyrosequencing of 16S rRNA genes can also be applied to infer major metabolic pathways in bacteria inhabiting different foods. This may reflect the role of these pathways in food-bacteria interaction and adaptation.
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Affiliation(s)
- Daleniece Higgins
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Chandan Pal
- Department of Infectious Diseases, Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Irshad M Sulaiman
- Southeast Regional Laboratory, U.S. Food and Drug Administration, Atlanta, GA, USA
| | - Chunrong Jia
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | | | - Scot E Dowd
- Molecular Research LP (MR DNA), Shallowater, TX, USA
| | - Pratik Banerjee
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA.
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54
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Ostria-Hernandez ML, Juárez-de la Rosa KC, Arzate-Barbosa P, Lara-Hernández A, Sakai F, Ibarra JA, Castro-Escarpulli G, Vidal JE. Nosocomial, Multidrug-Resistant Klebsiella pneumoniae Strains Isolated from Mexico City Produce Robust Biofilms on Abiotic Surfaces but Not on Human Lung Cells. Microb Drug Resist 2017; 24:422-433. [PMID: 28915364 DOI: 10.1089/mdr.2017.0073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae (Kpn) strains are a leading cause of hospital-acquired infections, including ventilator-associated pneumonia. Resistance to antibiotics, biofilm formation, and the production of certain fimbriae play an important role in the pathogenesis. AIM We investigated the genetic relatedness, antibiotic resistance, virulence potential, and ability to form biofilms of Kpn strains isolated from hospital-acquired infections (n = 76). Strains were isolated at three major hospitals serving the largest metropolitan urban area in Mexico City, Mexico. RESULTS Enterobacterial repetitive intergenic consensus (ERIC)-PCR demonstrated that clonal groups predominate in each hospital. Selected strains chosen from clonal groups (n = 47) were multidrug resistant (MDR, 83%), although the majority (∼70%) were susceptible to carbapenems. All strains produced robust biofilms on abiotic surfaces, and ∼90% harbored adhesin genes fimH, mrkA, and ecpA. The ultrastructure of biofilms was further studied by high-resolution confocal microscopy. The average height of Kpn biofilms on abiotic surfaces was ∼40 μm. We then assessed formation of biofilms on human lung cells, as a surrogate of lung infection. While Kpn strains formed robust biofilms on abiotic surfaces, studies on lung cells revealed attachment to human cells but scarce formation of biofilms. Gene expression studies revealed a differential temporal expression of an adhesin (ecpA) and a capsule (galF) gene when biofilms were formed on different substrates. CONCLUSIONS Kpn strains isolated from nosocomial infections in Mexico City are MDR, although the majority are still susceptible to carbapenems and form more robust biofilms on polystyrene in comparison to those formed on human cells.
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Affiliation(s)
- Martha Lorena Ostria-Hernandez
- 1 Laboratorio de Bacteriología Médica, Departamento de Microbiología Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional , Ciudad de México, México
| | - Karla Cecilia Juárez-de la Rosa
- 1 Laboratorio de Bacteriología Médica, Departamento de Microbiología Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional , Ciudad de México, México
| | - Patricia Arzate-Barbosa
- 2 Laboratorio de Bacteriología, Departamento de Análisis Clínicos, Instituto Nacional de Pediatría , Ciudad de México, México
| | - Antonino Lara-Hernández
- 2 Laboratorio de Bacteriología, Departamento de Análisis Clínicos, Instituto Nacional de Pediatría , Ciudad de México, México
| | - Fuminori Sakai
- 3 Hubert Department of Global Health, Rollins School of Public Health, Emory University , Atlanta, Georgia
| | - J Antonio Ibarra
- 4 Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional , Ciudad de México, México
| | - Graciela Castro-Escarpulli
- 1 Laboratorio de Bacteriología Médica, Departamento de Microbiología Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional , Ciudad de México, México
| | - Jorge E Vidal
- 3 Hubert Department of Global Health, Rollins School of Public Health, Emory University , Atlanta, Georgia
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55
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Anzai EK, de Souza Júnior JC, Peruchi AR, Fonseca JM, Gumpl EK, Pignatari ACC, Hirano ZMB, Silveira ACDO. First case report of non-human primates (Alouatta clamitans) with the hypervirulent Klebsiella pneumoniae serotype K1 strain ST 23: A possible emerging wildlife pathogen. J Med Primatol 2017; 46:337-342. [PMID: 28809435 DOI: 10.1111/jmp.12296] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND Hypervirulent strain of Klebsiella pneumoniae genotype K1 isolates have recently emerged, causing severe pyogenic liver abscess complicated by devastating metastatic infections in humans. METHODS We describe a short outbreak of the non-human primate (NHP) research center, associated with a hypervirulent K. pneumoniae. The genetic similarity of the strains was evaluated by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) techniques, and virulence encoding genes were detected by polymerase chain reaction (PCR). RESULTS The isolates were phenotypically like strains causing community-acquired invasive liver abscess syndrome in humans. All strains exhibited identical PFGE patterns and were found to belong to ST23 and presented a hypermucovisity phenotype and possessed magA and rmpA gene. CONCLUSION This is the first case report of NHPs caused by K. pneumoniae displaying a hypermucoviscosity phenotype and belonging to capsular serotypes K1 and ST23.
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Affiliation(s)
- Eleine Kuroki Anzai
- Departamento de Medicina Veterinária, Universidade Regional de Blumenau (FURB), Blumenau, SC, Brazil
| | | | - Amanda Rezende Peruchi
- Departamento de Ciências Naturais, Universidade Regional de Blumenau (FURB), Blumenau, SC, Brazil
| | - Juliana Mello Fonseca
- Laboratório Especial de Microbiologia Clínica (LEMC), Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Elke Kreuscher Gumpl
- Laboratório Especial de Microbiologia Clínica (LEMC), Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Antônio Carlos Campos Pignatari
- Laboratório Especial de Microbiologia Clínica (LEMC), Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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56
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Mulder M, Kiefte-de Jong JC, Goessens WHF, de Visser H, Hofman A, Stricker BH, Verbon A. Risk factors for resistance to ciprofloxacin in community-acquired urinary tract infections due to Escherichia coli in an elderly population. J Antimicrob Chemother 2016; 72:281-289. [PMID: 27655855 DOI: 10.1093/jac/dkw399] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/15/2016] [Accepted: 08/22/2016] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Antimicrobial resistance to ciprofloxacin is rising worldwide, especially in bacteria causing urinary tract infections (UTIs). Prudent use of current antibiotic drugs is therefore necessary. OBJECTIVES We analysed (modifiable) risk factors for ciprofloxacin-resistant Escherichia coli. METHODS Urinary cultures of UTIs caused by E. coli were collected from participants in the Rotterdam Study, a prospective cohort study in an elderly population, and analysed for susceptibility to ciprofloxacin. Multivariate logistic regression was performed to investigate several possible risk factors for resistance. RESULTS Ciprofloxacin resistance in 1080 E. coli isolates was 10.2%. Multivariate analysis showed that higher age (OR 1.03; 95% CI 1.00-1.05) and use of two (OR 5.89; 95% CI 3.45-10.03) and three or more (OR 3.38; 95% CI 1.92-5.97) prescriptions of fluoroquinolones were associated with ciprofloxacin resistance, while no association between fluoroquinolone use more than 1 year before culture and ciprofloxacin resistance could be demonstrated. Furthermore, a high intake of pork (OR 3.68; 95% CI 1.36-9.99) and chicken (OR 2.72; 95% CI 1.08-6.85) and concomitant prescription of calcium supplements (OR 2.51; 95% CI 1.20-5.22) and proton pump inhibitors (OR 2.04; 95% CI 1.18-3.51) were associated with ciprofloxacin resistance. CONCLUSIONS Ciprofloxacin resistance in community-acquired UTI was associated with a high intake of pork and chicken and with concomitant prescription of calcium supplements and proton pump inhibitors. Modification of antibiotic use in animals as well as temporarily stopping the prescription of concomitant calcium and proton pump inhibitors need further evaluation as strategies to prevent ciprofloxacin resistance.
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Affiliation(s)
- Marlies Mulder
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.,Inspectorate of Health Care, PO Box 2518, 6401 DA Heerlen, The Netherlands
| | - Jessica C Kiefte-de Jong
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.,Global Public Health, Leiden University College, PO Box 13228, 2501 EE The Hague, The Netherlands
| | - Wil H F Goessens
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Herman de Visser
- Star-Medisch Diagnostisch Centrum, PO Box 8661, 3009 AR Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands .,Inspectorate of Health Care, PO Box 2518, 6401 DA Heerlen, The Netherlands.,Department of Internal Medicine, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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