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Park PH, Keith K, Calendo G, Jelinek J, Madzo J, Gharaibeh RZ, Ghosh J, Sapienza C, Jobin C, Issa JPJ. Association between gut microbiota and CpG island methylator phenotype in colorectal cancer. Gut Microbes 2024; 16:2363012. [PMID: 38860458 PMCID: PMC11174071 DOI: 10.1080/19490976.2024.2363012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
The intestinal microbiota is an important environmental factor implicated in CRC development. Intriguingly, modulation of DNA methylation by gut microbiota has been reported in preclinical models, although the relationship between tumor-infiltrating bacteria and CIMP status is currently unexplored. In this study, we investigated tumor-associated bacteria in 203 CRC tumor cases and validated the findings using The Cancer Genome Atlas datasets. We assessed the abundance of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae through qPCR analysis and observed enrichment of all four bacterial species in CRC samples. Notably, except for E. coli, all exhibited significant enrichment in cases of CIMP. This enrichment was primarily driven by a subset of cases distinguished by high levels of these bacteria, which we labeled as "Superhigh". The bacterial Superhigh status showed a significant association with CIMP (odds ratio 3.1, p-value = 0.013) and with MLH1 methylation (odds ratio 4.2, p-value = 0.0025). In TCGA CRC cases (393 tumor and 45 adj. normal), bacterial taxa information was extracted from non-human whole exome sequencing reads, and the bacterial Superhigh status was similarly associated with CIMP (odds ratio 2.9, p < 0.001) and MLH1 methylation (odds ratio 3.5, p < 0.001). Finally, 16S ribosomal RNA gene sequencing revealed high enrichment of Bergeyella spp. C. concisus, and F. canifelinum in CIMP-Positive tumor cases. Our findings highlight that specific bacterial taxa may influence DNA methylation, particularly in CpG islands, and contribute to the development and progression of CIMP in colorectal cancer.
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Affiliation(s)
- Pyoung Hwa Park
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Gennaro Calendo
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
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Saputro S, Saepuloh U, Darusman HS, Putriyani W, Permanawati, Ayuningsih ED, Prabandari SA, Setyawati D, Pamungkas J. Klebsiella pneumoniae infection in cynomolgus monkeys at primate research center facility in Indonesia. J Med Primatol 2023; 52:361-368. [PMID: 37525379 DOI: 10.1111/jmp.12665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/05/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Klebsiella pneumoniae infection in nonhuman primates has been widely reported and causes significant morbidity and mortality. Animal deaths occur routinely at the Primate Research Center of IPB University. The results of necropsy and culture suggested a K. pneumoniae infection. METHODS A mass health assessment of Cynomolgus monkeys (n = 429) was carried out by physical examination and molecular targeting K. pneumoniae (n = 96), family of Coronaviridae (n = 148) and Paramyxoviridae (n = 148). RESULTS A total of 49.18% of the animals had clinical symptoms of respiratory disorders, abscesses, trauma, and others. PCR results indicated that 28.57% were positive for K. pneumoniae with 35.71% mortality, while all samples were negative for both virus families. CONCLUSIONS There have been outbreaks caused by K. pneumoniae and/or K. pneumoniae subsp. pneumoniae. This disease is chronic, infects all of the buildings, and no tendency for disease transmission according to gender and age class.
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Affiliation(s)
- Suryo Saputro
- Primate Research Center, IPB University, Bogor, Indonesia
- Primatology Graduate Study Program, IPB University, Bogor, Indonesia
| | - Uus Saepuloh
- Primate Research Center, IPB University, Bogor, Indonesia
- Primatology Graduate Study Program, IPB University, Bogor, Indonesia
| | - Huda Shalahudin Darusman
- Primate Research Center, IPB University, Bogor, Indonesia
- Primatology Graduate Study Program, IPB University, Bogor, Indonesia
- School of Veterinary Medicine and Biomedical Science, IPB University, Bogor, Indonesia
| | | | - Permanawati
- Primate Research Center, IPB University, Bogor, Indonesia
| | | | | | - Dyah Setyawati
- Primate Research Center, IPB University, Bogor, Indonesia
| | - Joko Pamungkas
- Primate Research Center, IPB University, Bogor, Indonesia
- Primatology Graduate Study Program, IPB University, Bogor, Indonesia
- School of Veterinary Medicine and Biomedical Science, IPB University, Bogor, Indonesia
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Guo Y, Liu F, Zhang Y, Wang X, Gao W, Xu B, Li Y, Song N. Virulence, antimicrobial resistance, and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae in a hospital in Shijiazhuang City from China. Int Microbiol 2023; 26:1073-1085. [PMID: 37097488 PMCID: PMC10622345 DOI: 10.1007/s10123-023-00357-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), as one of the most common drug-resistant bacteria threatening human health, is hyper-resistant to multiple antimicrobial drugs and carbapenems, which can be dealt with only limited clinical treatment options. This study described the epidemiological characteristics of CRKP in this tertiary care hospital from 2016 to 2020. Specimen sources included blood, sputum, alveolar lavage fluid, puncture fluid, secretions from a burn wound, and urine. Among the 87 carbapenem-resistant strains, ST11 was the predominant isolate, followed by ST15, ST273, ST340, and ST626. These STs were in broad agreement with the STs defined by pulsed-field gel electrophoresis clustering analysis in discriminating clusters of related strains. Most CRKP isolates contained the blaKPC-2 gene, some isolates carried the blaOXA-1, blaNDM-1, and blaNDM-5 genes, and the isolates carrying carbapenem resistance genes were more resistant to the antimicrobials of β-lactams, carbapenems, macrolides, and fluoroquinolone. The OmpK35 and OmpK37 genes were detected in all CRKP strains, and the Ompk36 gene was detected in some CRKP strains. All detected OmpK37 had 4 mutant sites, and OmpK36 had 11 mutant sites, while no mutant sites were found in OmpK35. More than half of the CRKP strains contained the OqxA and OqxB efflux pump genes. The virulence genes were most commonly combined with urea-wabG-fimH-entB-ybtS-uge-ycf. Only one CRKP isolate was detected with the K54 podoconjugate serotype. This study elucidated the clinical epidemiological features and molecular typing of CRKP, and grasped the distribution of drug-resistant genotypes, podocyte serotypes, and virulence genes of CRKP, providing some guidance for the subsequent treatment of CRKP infection.
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Affiliation(s)
- Yumei Guo
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Faqiang Liu
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
- Department of Infectious Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yulan Zhang
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Xiaoli Wang
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Weili Gao
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Baohong Xu
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yuxue Li
- Department of Clinical Laboratory, Shijiazhuang People's Hospital, Shijiazhuang, China.
| | - Ning Song
- Department of Infectious Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
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4
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Guo Y, Liu F, Zhang Y, Wang X, Gao W, Xu B, Li Y, Song N. Virulence, antimicrobial resistance, and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae in a hospital in Shijiazhuang City from China. Int Microbiol 2023; 26:1073-1085. [PMID: 37097488 PMCID: PMC10622345 DOI: 10.1007/s10123-023-00357-x 10.1007/s10123-023-00357-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 03/27/2024]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), as one of the most common drug-resistant bacteria threatening human health, is hyper-resistant to multiple antimicrobial drugs and carbapenems, which can be dealt with only limited clinical treatment options. This study described the epidemiological characteristics of CRKP in this tertiary care hospital from 2016 to 2020. Specimen sources included blood, sputum, alveolar lavage fluid, puncture fluid, secretions from a burn wound, and urine. Among the 87 carbapenem-resistant strains, ST11 was the predominant isolate, followed by ST15, ST273, ST340, and ST626. These STs were in broad agreement with the STs defined by pulsed-field gel electrophoresis clustering analysis in discriminating clusters of related strains. Most CRKP isolates contained the blaKPC-2 gene, some isolates carried the blaOXA-1, blaNDM-1, and blaNDM-5 genes, and the isolates carrying carbapenem resistance genes were more resistant to the antimicrobials of β-lactams, carbapenems, macrolides, and fluoroquinolone. The OmpK35 and OmpK37 genes were detected in all CRKP strains, and the Ompk36 gene was detected in some CRKP strains. All detected OmpK37 had 4 mutant sites, and OmpK36 had 11 mutant sites, while no mutant sites were found in OmpK35. More than half of the CRKP strains contained the OqxA and OqxB efflux pump genes. The virulence genes were most commonly combined with urea-wabG-fimH-entB-ybtS-uge-ycf. Only one CRKP isolate was detected with the K54 podoconjugate serotype. This study elucidated the clinical epidemiological features and molecular typing of CRKP, and grasped the distribution of drug-resistant genotypes, podocyte serotypes, and virulence genes of CRKP, providing some guidance for the subsequent treatment of CRKP infection.
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Affiliation(s)
- Yumei Guo
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Faqiang Liu
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
- Department of Infectious Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yulan Zhang
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Xiaoli Wang
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Weili Gao
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Baohong Xu
- Hebei Provincial Key Research Laboratory of Intractable Bacteria, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yuxue Li
- Department of Clinical Laboratory, Shijiazhuang People's Hospital, Shijiazhuang, China.
| | - Ning Song
- Department of Infectious Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
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M Shafik S, Abbas HA, Yousef N, Saleh MM. Crippling of Klebsiella pneumoniae virulence by metformin, N-acetylcysteine and secnidazole. BMC Microbiol 2023; 23:229. [PMID: 37608306 PMCID: PMC10464179 DOI: 10.1186/s12866-023-02969-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
INTRODUCTION The emergence of multidrug-resistant Klebsiella pneumoniae in hospitals represents a serious threat to public health. Infections caused by Klebsiella pneumoniae are widespread in healthcare institutions, mainly pneumonia, bloodstream infections, and infections affecting neonates in intensive care units; so, it is necessary to combat this pathogen with new strategies. Targeting virulence factors necessary to induce host damage and disease is a new paradigm for antimicrobial therapy with several potential benefits that could lead to decreased resistance. BACKGROUND The influence of metformin, N-acetylcysteine, and secnidazole on Klebsiella pneumoniae virulence factors production was tested. The production of Klebsiella pneumoniae virulence factors such as biofilm formation, urease, proteases, hemolysins, and tolerance to oxidative stress was evaluated phenotypically using sub-inhibitory concentration (1/8 MIC) of metformin, N-acetylcysteine, and secnidazole. For more confirmation, qRT-PCR was used to assess the relative expression level of rmpA, wcaG, fimH-1, mrkD, ureA, and khe genes regulating virulence factors production. RESULTS Metformin, N-acetylcysteine, and secnidazole were all found to have a powerful inhibitory effect on the production of virulence factors phenotypically. Our results showed a significant reduction in the expression level of rmpA, wcaG, fimH-1, mrkD, ureA, and khe genes. Furthermore, the tested drugs were investigated in vivo to inform their ability to protect mice against Klebsiella pneumoniae pathogenesis. CONCLUSIONS Metformin, N-acetylcysteine, and secnidazole inhibited the virulence of Klebsiella pneumoniae. Besides combating resistant Klebsiella pneumoniae, the tested drugs could also serve as an adjuvant to traditional antibiotics.
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Affiliation(s)
- Shokri M Shafik
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig City, Egypt
| | - Hisham A Abbas
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig City, Egypt
| | - Nehal Yousef
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig City, Egypt
| | - Moustafa M Saleh
- Microbiology and Immunology Department, Faculty of Pharmacy, Port Said University, Port Said City, Egypt.
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6
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Feng J, Cui X, Du B, Zhao H, Feng Y, Cui J, Yan C, Gan L, Fan Z, Fu T, Xu Z, Yu Z, Zhang R, Du S, Tian Z, Zhang Q, Xue G, Yuan J. Detection and Quantification of Klebsiella pneumoniae in Fecal Samples Using Digital Droplet PCR in Comparison with Real-Time PCR. Microbiol Spectr 2023; 11:e0424922. [PMID: 37306605 PMCID: PMC10433836 DOI: 10.1128/spectrum.04249-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/18/2023] [Indexed: 06/13/2023] Open
Abstract
This study aimed to develop a rapid and sensitive droplet digital PCR (ddPCR) assay for the specific detection of Klebsiella pneumoniae in fecal samples, and to evaluate its application in the clinic by comparison with real-time PCR assay and conventional microbial culture. Specific primers and a probe targeting the K. pneumoniae hemolysin (khe) gene were designed. Thirteen other pathogens were used to evaluate the specificity of the primers and probe. A recombinant plasmid containing the khe gene was constructed and used to assess the sensitivity, repeatability, and reproducibility of the ddPCR. Clinical fecal samples (n = 103) were collected and tested by the ddPCR, real-time PCR, and conventional microbial culture methods. The detection limit of ddPCR for K. pneumoniae was 1.1 copies/μL, about a 10-fold increase in sensitivity compared with real-time PCR. The ddPCR was negative for the 13 pathogens other than K. pneumoniae, confirming its high specificity. Clinical fecal samples gave a higher rate of positivity in the K. pneumoniae ddPCR assay than in analysis by real-time PCR or conventional culture. ddPCR also showed less inhibition by the inhibitor in fecal sample than real-time PCR. Thus, we established a sensitive and effective ddPCR-based assay method for K. pneumoniae. It could be a useful tool for K. pneumoniae detection in feces and may serve as a reliable method to identify causal pathogens and help guide treatment decisions. IMPORTANCE Klebsiella pneumoniae can cause a range of illnesses and has a high colonization rate in the human gut, making it crucial to develop an efficient method for detecting K. pneumoniae in fecal samples.
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Affiliation(s)
- Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Qun Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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Tohda M, Oinuma KI, Sakiyama A, Tsubouchi T, Niki M, Namikawa H, Yamane K, Yamada K, Watanabe T, Asai K, Kakeya H, Kaneko Y, Kawaguchi T. Rifampicin exerts anti-mucoviscous activity against hypervirulent Klebsiella pneumoniae via binding to the RNA polymerase β subunit. J Glob Antimicrob Resist 2023; 32:21-28. [PMID: 36572148 DOI: 10.1016/j.jgar.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES In hypervirulent Klebsiella pneumoniae (hvKP), the hypermucoviscous capsule is known to be a major virulence determinant. We previously discovered that rifampicin (RFP), a bactericidal drug that binds to and inhibits the β subunit of RNA polymerase (RpoB), elicits anti-mucoviscous activity against hvKP by suppressing rmpA, a regulator of capsule production. Here, we aimed to determine whether RFP exerts this effect at sub-growth-inhibitory concentrations via its binding to RpoB. METHODS Five spontaneous RFP-resistant mutants (R1-R5) were prepared from an hvKP clinical isolate and subjected to whole genome sequencing and mucoviscosity analyses. Subsequently, a two-step allelic exchange procedure was used to create a rpoB mutant R6 and revertants with wild-type rpoB from R1-R5 (named R1'-R5'). Transcription levels of rmpA and the capsular polysaccharide polymerase gene magA and capsule thickness of R1-R5 and R1'-R5' grown without or with RFP were evaluated by quantitative reverse transcription polymerase chain reaction and microscopic observation using India ink staining. RESULTS R1-R5 all had non-synonymous point mutations in rpoB and were highly resistant to the bactericidal effects and anti-mucoviscous activity of RFP. While the properties of R6 were similar to those of R1-R5, the responses of R1'-R5' to RFP were identical to those of the wild type. rmpA and magA transcription levels and capsule thickness correlated well with the mucoviscosity levels. CONCLUSIONS RFP exerts anti-mucoviscous activity by binding to RpoB. The mechanism of how this causes rmpA suppression remains to be explored.
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Affiliation(s)
- Mitsunori Tohda
- Department of Respiratory Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Ken-Ichi Oinuma
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan.
| | - Arata Sakiyama
- Department of Bacteriology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Taishi Tsubouchi
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Mamiko Niki
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Hiroki Namikawa
- Department of Medical Education and General Practice, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Kenshi Yamane
- Department of Respiratory Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Koichi Yamada
- Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan; Department of Infection Control Science, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Tetsuya Watanabe
- Department of Respiratory Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Kazuhisa Asai
- Department of Respiratory Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Kakeya
- Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan; Department of Infection Control Science, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Yukihiro Kaneko
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Tomoya Kawaguchi
- Department of Respiratory Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
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Braun P, Raab R, Bugert JJ, Braun S. Recombinant Reporter Phage rTUN1:: nLuc Enables Rapid Detection and Real-Time Antibiotic Susceptibility Testing of Klebsiella pneumoniae K64 Strains. ACS Sens 2023; 8:630-639. [PMID: 36719711 PMCID: PMC9972469 DOI: 10.1021/acssensors.2c01822] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The emergence of multi-drug-resistant Klebsiella pneumoniae (Kp) strains constitutes an enormous threat to global health as multi-drug resistance-associated treatment failure causes high mortality rates in nosocomial infections. Rapid pathogen detection and antibiotic resistance screening are therefore crucial for successful therapy and thus patient survival. Reporter phage-based diagnostics offer a way to speed up pathogen identification and resistance testing as integration of reporter genes into highly specific phages allows real-time detection of phage replication and thus living host cells. Kp-specific phages use the host's capsule, a major virulence factor of Kp, as a receptor for adsorption. To date, 80 different Kp capsule types (K-serotypes) have been described with predominant capsule types varying between different countries and continents. Therefore, reporter phages need to be customized according to the locally prevailing variants. Recently, we described the autographivirus vB_KpP_TUN1 (TUN1), which specifically infects Kp K64 strains, the most predominant capsule type at the military hospital in Tunis (MHT) that is also associated with high mortality rates. In this work, we developed the highly specific recombinant reporter phage rTUN1::nLuc, which produces nanoluciferase (nLuc) upon host infection and thus enables rapid detection of Kp K64 cells in clinical matrices such as blood and urine. At the same time, rTUN1::nLuc allows for rapid antibiotic susceptibility testing and therefore identification of suitable antibiotic treatment in less than 3 h.
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Affiliation(s)
- Peter Braun
- Bundeswehr Institute of Microbiology, 80937Munich, Germany
| | - Rene Raab
- Bundeswehr Institute of Microbiology, 80937Munich, Germany
| | | | - Simone Braun
- Bundeswehr Institute of Microbiology, 80937Munich, Germany
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9
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Aggarwal N, Liang Y, Foo JL, Ling H, Hwang IY, Chang MW. FELICX: A robust nucleic acid detection method using flap endonuclease and CRISPR-Cas12. Biosens Bioelectron 2023; 222:115002. [PMID: 36527830 DOI: 10.1016/j.bios.2022.115002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Nucleic acid detection is crucial for monitoring diseases for which rapid, sensitive, and easy-to-deploy diagnostic tools are needed. CRISPR-based technologies can potentially fulfill this need for nucleic acid detection. However, their widespread use has been restricted by the requirement of a protospacer adjacent motif in the target and extensive guide RNA optimization. In this study, we developed FELICX, a technique that can overcome these limitations and provide a useful alternative to existing technologies. FELICX comprises flap endonuclease, Taq ligase and CRISPR-Cas for diagnostics (X) and can be used for detecting nucleic acids and single-nucleotide polymorphisms. This method can be deployed as a point-of-care test, as only two temperatures are needed without thermocycling for its functionality, with the result generated on lateral flow strips. As a proof-of-concept, we showed that up to 0.6 copies/μL of DNA and RNA could be detected by FELICX in 60 min and 90 min, respectively, using simulated samples. Additionally, FELICX could be used to probe any base pair, unlike other CRISPR-based technologies. Finally, we demonstrated the versatility of FELICX by employing it for virus detection in infected human cells, the identification of antibiotic-resistant bacteria, and cancer diagnostics using simulated samples. Based on its unique advantages, we envision the use of FELICX as a next-generation CRISPR-based technology in nucleic acid diagnostics.
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Affiliation(s)
- Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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10
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Karaliute I, Ramonaite R, Bernatoniene J, Petrikaite V, Misiunas A, Denkovskiene E, Razanskiene A, Gleba Y, Kupcinskas J, Skieceviciene J. Reduction of gastrointestinal tract colonization by Klebsiella quasipneumoniae using antimicrobial protein KvarIa. Gut Pathog 2022; 14:17. [PMID: 35473598 PMCID: PMC9040220 DOI: 10.1186/s13099-022-00492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/09/2022] [Indexed: 12/03/2022] Open
Abstract
Background Klebsiella quasipneumoniae is an opportunistic pathogen causing antibiotic-resistant infections of the gastrointestinal tract in many clinical cases. Orally delivered bioactive Klebsiella-specific antimicrobial proteins, klebicins, could be a promising method to eradicate Klebsiella species infecting the gut. Methods Mouse infection model was established based on infection of antibiotic-treated BALB/C mice with K. quasipneumoniae strain DSM28212. Four study groups were used (3 animals/group) to test the antimicrobial efficacy of orally delivered klebicin KvarIa: vehicle-only group (control, phosphate-buffered saline), and other three groups with bacteria, antibiotic therapy and 100 µg of uncoated Kvarla, 100 µg coated KvarIa, 1000 µg coated-KvarIa. Because of the general sensitivity of bacteriocins to gastroduodenal proteases, Kvarla doses were coated with Eudragit®, a GMP-certified formulation agent that releases the protein at certain pH. The coating treatment was selected based on measurements of mouse GI tract pH. The quantity of Klebsiella haemolysin gene (khe) in faecal samples of the study animals was used to quantify the presence of Klebsiella. Results GI colonization of K. quasipneumoniae was achieved only in the antibiotic-treated mice groups. Significant changes in khe marker quantification were found after the use of Eudragit® S100 formulated klebicin KvarIa, at both doses, with a significant reduction of K. quasipneumoniae colonization compared to the vehicle-only control group. Conclusions Mouse GI tract colonization with K. quasipneumoniae can be achieved if natural gut microbiota is suppressed by prior antibiotic treatment. The study demonstrates that GI infection caused by K. quasipneumoniae can be significantly reduced using Eudragit®-protected klebicin KvarIa.
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Affiliation(s)
- Indre Karaliute
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania
| | - Rima Ramonaite
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania
| | - Jurga Bernatoniene
- Department of Drug Technology and Social Pharmacy, Lithuanian University of Health Sciences, Sukileliu Pr. 13, 50161, Kaunas, Lithuania
| | - Vilma Petrikaite
- Laboratory of Drug Targets Histopathology, Institute of Cardiology, Lithuanian University of Health Sciences, 50162, Kaunas, Lithuania
| | | | | | | | - Yuri Gleba
- Nomad Bioscience GmbH, Biozentrum Halle, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Juozas Kupcinskas
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania.,Department of Gastroenterology, Lithuanian University of Health Sciences, 44307, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania.
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11
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Karami-Zarandi M, Ghale HE, Ranjbar R. Characterization of virulence factors and antibacterial activity of curcumin in hypervirulent Klebsiella pneumoniae. Future Microbiol 2022; 17:529-540. [PMID: 35322691 DOI: 10.2217/fmb-2021-0222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Klebsiella pneumoniae is a threat to human health due to its carbapenem-resistance and hypervirulent phenotype. Curcumin is a well-known antimicrobial agent. Hence, it is important to investigate the antivirulence activity of curcumin against hypervirulent K. pneumoniae isolates. Materials & methods: Carbapenemase presence and prevalence of hypervirulent isolates were determined. Inhibition of biofilm formation and expression of virulence genes were analyzed by colorimetry and real-time PCR tests. Results: Sixteen hypervirulent K. pneumoniae isolates were identified. The optimum activity of curcumin was detected at 1/2 minimum inhibitory concentration. Curcumin possessed appropriate antibiofilm, anti-efflux and anticapsule activities. Conclusion: According to the crucial role of biofilm, capsule and efflux systems in the pathogenesis of hypervirulent K. pneumoniae, curcumin may be used to improve anti-Klebsiella treatment.
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Affiliation(s)
- Morteza Karami-Zarandi
- Molecular Biology Research Center, Systems Biology & Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, 14359-16471, Iran
| | - Hadi Eg Ghale
- Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, 14359-16471, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology & Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, 14359-16471, Iran
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12
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Barnes NM, Wu H. Mechanisms regulating the airborne survival of Klebsiella pneumoniae under different relative humidity and temperature levels. INDOOR AIR 2022; 32:e12991. [PMID: 35225398 DOI: 10.1111/ina.12991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/23/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
In this study, Klebsiella pneumoniae was suspended in synthetic saliva in a nebulizer (N0 ) and nebulized for 5 min (N5 ) into an aerosol chamber and further prolonged in the aerosolization phase for 15 min (A15 ) under four different conditions: 20°C, 50% relative humidity (RH); 20°C, 80% RH; 30°C, 50% RH; and 30°C, 80% RH. Samples were collected at N0 , N5 , and A15 , then subjected to survival analysis and comparative transcriptomic analysis in order to help elucidate the underlying mechanisms of airborne survival. Survival analysis shows that a higher humidity and lower temperature were favorable for the airborne survival of K. pneumoniae, and the effect of RH was more remarkable at 20°C than that at 30°C. The RNA-seq results show that during the nebulization phase (N0 vs. N5 ), a total number of 201 differentially expressed genes (DEGs) were identified (103 downregulated and 98 upregulated). Comparison between nebulization and aerosolization phases (N5 vs. A15 ) indicates up to 132 DEGs, with 46 downregulated and 86 upregulated. The most notable groups of genes are those involved in cellular remodeling, metabolism and energy processes. Alarmingly, the mbl gene, which encodes antibiotic resistance in K. pneumoniae, was upregulated during the suspension phase under all the tested conditions. This study provides insights into the control of airborne transmitted diseases.
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Affiliation(s)
- Natasha Maria Barnes
- Department of Biology, Hong Kong Special Administrative Region, Hong Kong Baptist University, Hong Kong, China
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India
| | - Haoxiang Wu
- Department of Biology, Hong Kong Special Administrative Region, Hong Kong Baptist University, Hong Kong, China
- Institute of Bioresource and Agriculture, Hong Kong Special Administrative Region, Hong Kong Baptist University, Hong Kong, China
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13
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Lin WH, Chiu HC, Chen KF, Tsao KC, Chen YY, Li TH, Huang YC, Hsieh YC. Molecular detection of respiratory pathogens in community-acquired pneumonia involving adults. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 55:829-837. [PMID: 34969624 DOI: 10.1016/j.jmii.2021.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 11/10/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Community-acquired pneumonia (CAP) causes substantial morbidity and mortality in adults worldwide. The etiology of CAP often remains uncertain, and therapy is empirical. Thus, there is still room for improvement in the diagnosis of pneumonia. METHODS Adults aged >20 years who presented at the outpatient or emergency departments of Linkou and Keelung Chang Gung Memorial Hospital with CAP were prospectively included between November 2016 and December 2018. We collected respiratory specimens for culture and molecular testing and calculated the incidence rates of CAP according to pathogens. RESULTS Of 212 hospitalized adult patients with CAP, 69.3% were male, and the median age of the patients was 67.8 years. Bacterial pathogens were detected in 106 (50%) patients, viruses in 77 (36.3%), and fungal pathogens in 1 patient (0.5%). The overall detection rate (culture and molecular testing method) was 70.7% (n = 150). Traditional microbial culture yielded positive results in 36.7% (n = 78), molecular testing in 61.3% (n = 130). The most common pathogens were influenza (16.1%), followed by Klebsiella pneumoniae (14.1%), Pseudomonas aeruginosa (13.6%), human rhinovirus (11.8%), and Streptococcus pneumoniae (9.9%). Multiple pathogen co-infections accounted for 28.7% (n = 61), of which co-infection with K. pneumoniae and human rhinovirus comprised the largest proportion. CONCLUSIONS Molecular diagnostic testing could detect 23.6% more pathogens than traditional culture techniques. However, despite the current diagnostic tests, there is still the possibility that no pathogen was detected.
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Affiliation(s)
- Wei-Hsuan Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Han-Cheng Chiu
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Kuan-Fu Chen
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Ting-Hsuan Li
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Yhu-Chering Huang
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Taipei, Taoyuan, Taiwan.
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Taipei, Taoyuan, Taiwan.
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14
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Contamination of Hospital Surfaces with Bacterial Pathogens under the Current COVID-19 Outbreak. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18179042. [PMID: 34501634 PMCID: PMC8431522 DOI: 10.3390/ijerph18179042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 pandemic remains a global health issue for several reasons, such as the low vaccination rates and a lack of developed herd immunity to the evolution of SARS-CoV-2, as well as its potential inclination to elude neutralizing antibodies. It should be noted that the severity of the COVID-19 disease is significantly affected by the presence of co-infections. Comorbid conditions are caused not only by pathogenic and opportunistic microorganisms but also by some representatives of the environmental microbiome. The presence of patients with moderate and severe forms of the disease in hospitals indicates the need for epidemiological monitoring of (1) bacterial pathogens circulating in hospitals, especially the ESKAPE group pathogens, and (2) the microbiome of various surfaces in hospitals. In our study, we used combined methods based on PCR and NGS sequencing, which are widely used for epidemiological monitoring. Through this approach, we identified the DNA of pathogenic bacteria (Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, CoNS, and Achromobacter spp.) on various surfaces. We also estimated the microbiome diversity of surfaces and identified the potential reservoirs of infections using 16S rRNA profiling. Although we did not assess the viability of identified microorganisms, our results indicate the possible risks of insufficient regular disinfection of surfaces, regardless of department, at the Infectious Diseases Hospital. Controlling the transmission of nosocomial diseases is critical to the successful treatment of COVID-19 patients, the rational use of antimicrobial drugs, and timely decontamination measures.
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15
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An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. Sci Rep 2021; 11:10590. [PMID: 34012005 PMCID: PMC8134577 DOI: 10.1038/s41598-021-89881-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/23/2021] [Indexed: 11/08/2022] Open
Abstract
Despite the advent of whole genome metagenomics, targeted approaches (such as 16S rRNA gene amplicon sequencing) continue to be valuable for determining the microbial composition of samples. Amplicon microbiome sequencing can be performed on clinical samples from a normally sterile site to determine the aetiology of an infection (usually single pathogen identification) or samples from more complex niches such as human mucosa or environmental samples where multiple microorganisms need to be identified. The methodologies are frequently applied to determine both presence of micro-organisms and their quantity or relative abundance. There are a number of technical steps required to perform microbial community profiling, many of which may have appreciable precision and bias that impacts final results. In order for these methods to be applied with the greatest accuracy, comparative studies across different laboratories are warranted. In this study we explored the impact of the bioinformatic approaches taken in different laboratories on microbiome assessment using 16S rRNA gene amplicon sequencing results. Data were generated from two mock microbial community samples which were amplified using primer sets spanning five different variable regions of 16S rRNA genes. The PCR-sequencing analysis included three technical repeats of the process to determine the repeatability of their methods. Thirteen laboratories participated in the study, and each analysed the same FASTQ files using their choice of pipeline. This study captured the methods used and the resulting sequence annotation and relative abundance output from bioinformatic analyses. Results were compared to digital PCR assessment of the absolute abundance of each target representing each organism in the mock microbial community samples and also to analyses of shotgun metagenome sequence data. This ring trial demonstrates that the choice of bioinformatic analysis pipeline alone can result in different estimations of the composition of the microbiome when using 16S rRNA gene amplicon sequencing data. The study observed differences in terms of both presence and abundance of organisms and provides a resource for ensuring reproducible pipeline development and application. The observed differences were especially prevalent when using custom databases and applying high stringency operational taxonomic unit (OTU) cut-off limits. In order to apply sequencing approaches with greater accuracy, the impact of different analytical steps needs to be clearly delineated and solutions devised to harmonise microbiome analysis results.
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16
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The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples. Appl Environ Microbiol 2020; 86:AEM.02711-19. [PMID: 32005732 PMCID: PMC7082575 DOI: 10.1128/aem.02711-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 11/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources. Klebsiella pneumoniae is of growing public health concern due to the emergence of strains that are multidrug resistant, virulent, or both. Taxonomically, the K. pneumoniae complex (“Kp”) includes seven phylogroups, with Kp1 (K. pneumoniaesensu stricto) being medically prominent. Kp can be present in environmental sources such as soils and vegetation, which could act as reservoirs of animal and human infections. However, the current lack of screening methods to detect Kp in complex matrices limits research on Kp ecology. Here, we analyzed 1,001 genome sequences and found that existing molecular detection targets lack specificity for Kp. A novel real-time PCR method, the ZKIR (zur-khe intergenic region) assay, was developed and used to detect Kp in 96 environmental samples. The results were compared to a culture-based method using Simmons citrate agar with 1% inositol medium coupled to matrix-assisted laser desorption ionization–time of flight mass spectrometry identification. Whole-genome sequencing of environmental Kp was performed. The ZKIR assay was positive for the 48 tested Kp reference strains, whereas 88 non-Kp strains were negative. The limit of detection of Kp in spiked soil microcosms was 1.5 × 10−1 CFU g−1 after enrichment for 24 h in lysogeny broth supplemented with ampicillin, and it was 1.5 × 103 to 1.5 × 104 CFU g−1 directly after soil DNA extraction. The ZKIR assay was more sensitive than the culture method. Kp was detected in 43% of environmental samples. Genomic analysis of the isolates revealed a predominance of phylogroups Kp1 (65%) and Kp3 (32%), a high genetic diversity (23 multilocus sequence types), a quasi-absence of antibiotic resistance or virulence genes, and a high frequency (50%) of O-antigen type 3. This study shows that the ZKIR assay is an accurate, specific, and sensitive novel method to detect the presence of Kp in complex matrices and indicates that Kp isolates from environmental samples differ from clinical isolates. IMPORTANCE The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.
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17
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Fakunle AG, Olusola B, Jafta N, Faneye A, Heederik D, Smit LA, Naidoo RN. Home Assessment of Indoor Microbiome (HAIM) in Relation to Lower Respiratory Tract Infections among Under-Five Children in Ibadan, Nigeria: The Study Protocol. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17061857. [PMID: 32183028 PMCID: PMC7143126 DOI: 10.3390/ijerph17061857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/22/2020] [Accepted: 03/03/2020] [Indexed: 12/15/2022]
Abstract
The association between household air pollution and lower respiratory tract infections (LRTI) among children under five years of age has been well documented; however, the extent to which the microbiome within the indoor environment contributes to this association is uncertain. The home assessment of indoor microbiome (HAIM) study seeks to assess the abundance of indoor microbiota (IM) in the homes of under-five children (U-5Cs) with and without LRTI. HAIM is a hospital- and community-based study involving 200 cases and 200 controls recruited from three children’s hospitals in Ibadan, Nigeria. Cases will be hospital-based patients with LRTI confirmed by a pediatrician, while controls will be community-based participants, matched to cases on the basis of sex, geographical location, and age (±3 months) without LRTI. The abundance of IM in houses of cases and controls will be investigated using active and passive air sampling techniques and analyzed by qualitative detection of bacterial 16SrRNA gene (V3–V4), fungal ITS1 region, and viral RNA sequencing. HAIM is expected to elucidate the relationship between exposure to IM and incidence of LRTI among U-5Cs and ultimately provide evidence base for strategic interventions to curtail the burgeoning burden of LRTI on the subcontinent.
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Affiliation(s)
- Adekunle G. Fakunle
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban 4041, South Africa;
- Department of Environmental Health Sciences, Faculty of Public Health, University of Ibadan, Ibadan 200212, Nigeria
- Correspondence: (A.G.F.); (R.N.N.); Tel.: +234-90-9395-6165 (A.G.F.); +27-824-379-333 (R.N.N.)
| | - Babatunde Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria; (B.O.); (A.F.)
| | - Nkosana Jafta
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban 4041, South Africa;
| | - Adedayo Faneye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria; (B.O.); (A.F.)
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Environmental Epidemiology Division (IRAS-EEPI), Utrecht University, 80177 Utrecht, The Netherlands; (D.H.)
| | - Lidwien A.M. Smit
- Institute for Risk Assessment Sciences, Environmental Epidemiology Division (IRAS-EEPI), Utrecht University, 80177 Utrecht, The Netherlands; (D.H.)
| | - Rajen N. Naidoo
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban 4041, South Africa;
- Correspondence: (A.G.F.); (R.N.N.); Tel.: +234-90-9395-6165 (A.G.F.); +27-824-379-333 (R.N.N.)
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18
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Abram TJ, Cherukury H, Ou CY, Vu T, Toledano M, Li Y, Grunwald JT, Toosky MN, Tifrea DF, Slepenkin A, Chong J, Kong L, Del Pozo DV, La KT, Labanieh L, Zimak J, Shen B, Huang SS, Gratton E, Peterson EM, Zhao W. Rapid bacterial detection and antibiotic susceptibility testing in whole blood using one-step, high throughput blood digital PCR. LAB ON A CHIP 2020; 20:477-489. [PMID: 31872202 PMCID: PMC7250044 DOI: 10.1039/c9lc01212e] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sepsis due to antimicrobial resistant pathogens is a major health problem worldwide. The inability to rapidly detect and thus treat bacteria with appropriate agents in the early stages of infections leads to excess morbidity, mortality, and healthcare costs. Here we report a rapid diagnostic platform that integrates a novel one-step blood droplet digital PCR assay and a high throughput 3D particle counter system with potential to perform bacterial identification and antibiotic susceptibility profiling directly from whole blood specimens, without requiring culture and sample processing steps. Using CTX-M-9 family ESBLs as a model system, we demonstrated that our technology can simultaneously achieve unprecedented high sensitivity (10 CFU per ml) and rapid sample-to-answer assay time (one hour). In head-to-head studies, by contrast, real time PCR and BioRad ddPCR only exhibited a limit of detection of 1000 CFU per ml and 50-100 CFU per ml, respectively. In a blinded test inoculating clinical isolates into whole blood, we demonstrated 100% sensitivity and specificity in identifying pathogens carrying a particular resistance gene. We further demonstrated that our technology can be broadly applicable for targeted detection of a wide range of antibiotic resistant genes found in both Gram-positive (vanA, nuc, and mecA) and Gram-negative bacteria, including ESBLs (blaCTX-M-1 and blaCTX-M-2 families) and CREs (blaOXA-48 and blaKPC), as well as bacterial speciation (E. coli and Klebsiella spp.) and pan-bacterial detection, without requiring blood culture or sample processing. Our rapid diagnostic technology holds great potential in directing early, appropriate therapy and improved antibiotic stewardship in combating bloodstream infections and antibiotic resistance.
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Affiliation(s)
- Timothy J Abram
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Hemanth Cherukury
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chen-Yin Ou
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Tam Vu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Michael Toledano
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Yiyan Li
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Physics and Engineering, Fort Lewis College, Durango, CO 81301, USA
| | | | - Melody N Toosky
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Anatoly Slepenkin
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Jonathan Chong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Lingshun Kong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Domenica Vanessa Del Pozo
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Kieu Thai La
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Louai Labanieh
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Byron Shen
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Susan S Huang
- Division of Infectious Diseases, UCI School of Medicine, Irvine, CA 92697, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA and Laboratory for Fluorescence Dynamics, University of California, Irvine, CA 92697, USA
| | - Ellena M Peterson
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA and Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA and Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, USA and Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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19
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Discovery of anti-mucoviscous activity of rifampicin and its potential as a candidate antivirulence agent against hypervirulent Klebsiella pneumoniae. Int J Antimicrob Agents 2019; 54:167-175. [DOI: 10.1016/j.ijantimicag.2019.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/13/2019] [Accepted: 05/25/2019] [Indexed: 11/21/2022]
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20
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HYPERMUCOVISCOUS KLEBSIELLA PNEUMONIAE ISOLATES FROM STRANDED AND WILD-CAUGHT MARINE MAMMALS OF THE US PACIFIC COAST: PREVALENCE, PHENOTYPE, AND GENOTYPE. J Wildl Dis 2018; 54:659-670. [PMID: 29733766 DOI: 10.7589/2017-07-178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Emergent hypermucoviscous (HMV) strains of Klebsiella pneumoniae have been reported in multiple marine mammal species; however, there is limited information regarding the epidemiology and pathogenesis of this infection in these species. We determined the prevalence of HMV K. pneumoniae in wild-caught and stranded marine mammal populations on the US Pacific Coast. Samples were collected from 270 free-ranging California sea lions (CSLs; Zalophus californianus) captured at three discrete sampling sites and from 336 stranded marine mammals of various species. We recovered HMV K. pneumoniae only from CSLs, with a prevalence of 1.5% (4 of 275) in stranded animals, compared with 1.1% (3 of 270) in wild-caught animals. We assessed the phenotypic and genotypic variability of recovered HMV K. pneumoniae isolates recovered from CSLs ( n=11) and of archival HMV and non-HMV isolates from stranded marine mammals ( n=19). All but two HMV isolates were of the K2 serotype, whereas none of the non-HMV isolates belonged to this serotype. Of the HMV isolates, 96% (24 of 25) were PCR positive for the HMV-associated gene p- rmpA, whereas 92% (23 of 25) were PCR positive for p- rmpA2. Genetic fingerprinting by repetitive extragenic palindromic PCR showed four discrete clusters, demonstrating genotypic variability that loosely correlated with phenotype. Antimicrobial susceptibility testing revealed all isolates from stranded CSLs were susceptible to ceftiofur, indicating this antimicrobial agent is an appropriate choice for treatment of HMV K. pneumoniae infections in stranded CSLs. Our culture assay could reliably detect HMV K. pneumoniae from concentrations as low as 102 colony-forming units per milligram of feces. We identified the presence of HMV K. pneumoniae in both wild-caught and stranded CSLs from the US Pacific Coast and highlight the need for further studies to evaluate the potential impact of this pathogen on marine mammal health.
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Tominaga T. Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays. J Microbiol Methods 2018. [DOI: 10.1016/j.mimet.2018.02.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Edwards T, Sasaki S, Williams C, Hobbs G, Feasey NA, Evans K, Adams ER. Speciation of common Gram-negative pathogens using a highly multiplexed high resolution melt curve assay. Sci Rep 2018; 8:1114. [PMID: 29348433 PMCID: PMC5773611 DOI: 10.1038/s41598-017-18915-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/18/2017] [Indexed: 11/23/2022] Open
Abstract
The identification of the bacterial species responsible for an infection remains an important step for the selection of antimicrobial therapy. Gram-negative bacteria are an important source of hospital and community acquired infections and frequently antimicrobial resistant. Speciation of bacteria is typically carried out by biochemical profiling of organisms isolated from clinical specimens, which is time consuming and delays the initiation of tailored treatment. Whilst molecular methods such as PCR have been used, they often struggle with the challenge of detecting and discriminating a wide range of targets. High resolution melt analysis is an end-point qPCR detection method that provides greater multiplexing capability than probe based methods. Here we report the design of a high resolution melt analysis assay for the identification of six common Gram-negative pathogens; Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Pseudomonas aeruginosa, Salmonella Sp, and Acinetobacter baumannii, and a generic Gram-negative specific 16S rRNA control. The assay was evaluated using a well characterised collection of 113 clinically isolated Gram-negative bacteria. The agreement between the HRM assay and the reference test of PCR and sequencing was 98.2% (Kappa 0.96); the overall sensitivity and specificity of the assay was 97.1% (95% CI: 90.1-99.7%) and 100% (95% CI: 91.78-100%) respectively.
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Affiliation(s)
- Thomas Edwards
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Shugo Sasaki
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Christopher Williams
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Glyn Hobbs
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Katie Evans
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Emily R Adams
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
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23
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Gozalo AS, Elkins WR, Lambert LE, Stock F, Thomas ML, Woodward RA. Genetic diversity of Klebsiella pneumoniae isolates during an outbreak in a non-human primate research colony. J Med Primatol 2016; 45:312-317. [PMID: 27477611 DOI: 10.1111/jmp.12229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND Klebsiella pneumoniae can be a serious pathogen in non-human primates, particularly Neotropical monkeys. METHODS During a K. pneumoniae outbreak in an owl monkey research colony, 13 K. pneumoniae isolates were DNA fingerprinted by automated repetitive extragenic palindromic-polymerase chain reaction and the profiles compared to isolates obtained from other non-human primate species during the same time period and isolates from previous outbreaks. RESULTS Eleven different types of K. pneumoniae were circulating in the owl monkey colony at the time of the outbreak. When comparing owl monkey isolates relatedness to previous colony outbreak isolates and squirrel monkey and capuchin monkey isolates, all were different. CONCLUSIONS These results agree with recent reports where K. pneumoniae nosocomial isolates in hospital settings can have high genetic diversity, and multiple strains can be circulating simultaneously. This potential genetic diversity should be considered when designing strategies for controlling K. pneumoniae outbreaks in captive non-human primate colonies.
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Affiliation(s)
- Alfonso S Gozalo
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - William R Elkins
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lynn E Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,SoBran Inc, Bethesda, MD, USA
| | - Frida Stock
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Marvin L Thomas
- Division of Veterinary Resources, National Institutes of Health, Bethesda, MD, USA
| | - Ruth A Woodward
- Research Animal Medicine Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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24
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Kumade E, Furusyo N, Takeshima N, Kishihara Y, Mitsumoto-Kaseida F, Etoh Y, Murata M, Hayashi J. A case of lobar pneumonia and sepsis with death caused by invasive Klebsiella rhinoscleromatis infection. J Infect Chemother 2016; 22:707-11. [PMID: 27184935 DOI: 10.1016/j.jiac.2016.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 03/03/2016] [Accepted: 03/10/2016] [Indexed: 11/17/2022]
Abstract
Klebsiella pneumoniae often causes pneumonia and other infections in heavy drinkers and patients with diabetes. Pneumonia caused by Klebsiella rhinoscleromatis, a subspecies of K. pneumoniae, has not been previously reported. We report a case of pneumonia caused by K. rhinoscleromatis. A 68-year-old man with type 2 diabetes visited our department complaining fever and fatigue for 10 days and cough and bloody sputum for two days. His Japan Coma Scale score was I-1, body temperature 38.3 °C, blood pressure 85/51 mmHg, pulse 135 bpm, and peripheral capillary oxygen saturation level 92% (room air). He had no abnormal breathing sounds. His white blood cell count had decreased to 2600/μL, and his C-reactive protein level was high, at 35.9 mg/dL. Chest computed tomography revealed lobar pneumonia in the right upper lobe and pneumonia in the left upper division. Klebsiella was suspected based on the result of a sputum smear examination. He was diagnosed with septic shock due to pneumonia and was immediately admitted. Intravenous antibacterial (levofloxacin) treatment was initiated, however, he died 13 h after presenting at the hospital. Subsequently, K. rhinoscleromatis was detected in sputum and blood culture. Additional testing determined the bacteria to be a highly pathogenic hypermucoviscosity phenotype and the cause of the fatal lobar pneumonia. Although cases of rhinoscleroma and bacteremia caused by K. rhinoscleromatis infection have been reported, this is the first report of a case with sepsis caused by fulminant pneumonia.
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MESH Headings
- Aged
- Anti-Bacterial Agents/therapeutic use
- Blood Culture
- C-Reactive Protein/analysis
- Diabetes Mellitus, Type 2/complications
- Fatal Outcome
- Humans
- Klebsiella Infections/microbiology
- Klebsiella pneumoniae/isolation & purification
- Klebsiella pneumoniae/pathogenicity
- Leukocyte Count
- Levofloxacin/therapeutic use
- Lung/diagnostic imaging
- Lung/pathology
- Male
- Pneumonia, Bacterial/complications
- Pneumonia, Bacterial/diagnostic imaging
- Pneumonia, Bacterial/drug therapy
- Pneumonia, Bacterial/microbiology
- Shock, Septic/blood
- Shock, Septic/drug therapy
- Shock, Septic/etiology
- Shock, Septic/microbiology
- Tomography, X-Ray Computed
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Affiliation(s)
- Eri Kumade
- Department of General Internal Medicine, National Kyushu Medical Center, Fukuoka, Japan; Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Norihiro Furusyo
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan.
| | - Norito Takeshima
- Department of General Internal Medicine, National Kyushu Medical Center, Fukuoka, Japan
| | - Yasuhiro Kishihara
- Department of General Internal Medicine, National Kyushu Medical Center, Fukuoka, Japan
| | | | - Yoshitaka Etoh
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Masayuki Murata
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Jun Hayashi
- Kyushu General Internal Medicine Center, Haradoi Hospital, Fukuoka, Japan
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25
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Soto E, Marchi S, Beierschmitt A, Kearney M, Francis S, VanNess K, Vandenplas M, Thrall M, Palmour R. Interaction of non-human primate complement and antibodies with hypermucoviscous Klebsiella pneumoniae. Vet Res 2016; 47:40. [PMID: 26951091 PMCID: PMC4782414 DOI: 10.1186/s13567-016-0325-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/17/2016] [Indexed: 01/31/2023] Open
Abstract
Emergent hypermucoviscosity (HMV) phenotypes of Klebsiella pneumoniae have been associated with increased invasiveness and pathogenicity in primates. In this study, we investigated the interaction of African green monkeys (AGM) (Chlorocebus aethiops sabaeus) complement and antibody with HMV and non-HMV isolates as in vitro models of primate infection. Significantly greater survival of HMV isolates was evident after incubation in normal serum or whole blood (p < 0.05) of AGM donors when compared to non-HMV strains. Greater survival of HMV strains (p < 0.05) was found after incubation in whole blood and serum from seropositive donors when compared to seronegative donor samples. Additionally, significantly greater amounts of K. pneumoniae were phagocytozed by AGM leukocytes when complement was active (p < 0.05), but no difference in uptake was observed when serum from seropositive or seronegative animals was used in challenged cells utilizing flow cytometry. Results demonstrate that interaction of cellular and humoral immune elements play a role in the in vitro killing of K. pneumoniae, particularly HMV isolates. Neither AGM serum, nor washed whole blood effectively killed HMV isolates; however, assays using heparinized whole blood of seronegative donors significantly reduced viability of HMV and non-HMV strains. The lack of bacterial killing observed in seropositive donors treatments could be at least partially associated with low IgG2 present in these animals. A better understanding of the pathogenesis of klebsiellosis in primates and host immune response is necessary to identify surface molecules that can induce both opsonizing and bactericidal antibody facilitating killing of Klebsiella, and the development of vaccines in human and animals.
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Affiliation(s)
- Esteban Soto
- Department of Epidemiology and Medicine, University of California, Davis-School of Veterinary Medicine, Davis, CA, USA. .,Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies.
| | - Sylvia Marchi
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies.
| | - Amy Beierschmitt
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies. .,Behavioural Science Foundation, Estridge Estate, Basseterre, St. Kitts, West Indies.
| | - Michael Kearney
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Stewart Francis
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies.
| | - Kimberly VanNess
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies.
| | - Michel Vandenplas
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies.
| | - MaryAnna Thrall
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies.
| | - Roberta Palmour
- Behavioural Science Foundation, Estridge Estate, Basseterre, St. Kitts, West Indies.
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26
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Wang H, Gu X, Weng Y, Xu T, Fu Z, Peng W, Yu W. Quantitative analysis of pathogens in the lower respiratory tract of patients with chronic obstructive pulmonary disease. BMC Pulm Med 2015; 15:94. [PMID: 26286268 PMCID: PMC4543462 DOI: 10.1186/s12890-015-0094-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/05/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Bacterial infection of the lower respiratory tract is believed to play a major role in the pathogenesis of chronic obstructive pulmonary disease (COPD) and acute exacerbations of COPD (AECOPD). This study investigates the potential relationship between AECOPD and the load of six common bacterial pathogens in the lower respiratory tract using real-time quantitative PCR (RT-qPCR) in COPD patients. METHODS Protected specimen brush (PSB) and bronchoalveolar lavage fluid (BALF) samples from the lower respiratory tract of 66 COPD patients and 33 healthy subjects were collected by bronchoscopy. The load of Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Pseudomonos aeruginosa, Haemophilus influenzeae, and Moraxella catarrhalis were detected by RT-qPCR. RESULTS High Klebsiella pneumoniae, Pseudomonos aeruginosa, Haemophilus influenzeae and Moraxella catarrhalis burden were detected by RT-qPCR in both PSB and BALF samples obtained from stable COPD and AECOPD patients compared with healthy subjects. The load of the above four pathogenic strains in PSB and BALF samples obtained from AECOPD patients were significantly higher compared with stable COPD patients. Finally, positive correlations between bacterial loads and inflammatory mediators such as neutrophil count and cytokine levels of IL-1β, IL-6 and IL-8, as well as negative correlations between bacterial loads and the forced expiratory volume in one second (FEV1) % predicted, forced vital capacity (FVC) % predicted, and FEV1/FVC ratio, were detected. CONCLUSIONS These findings suggest that increased bacterial loads mediated inflammatory response in the lower respiratory tract and were associated with AECOPD. In addition, these results provide guidance for antibiotic therapy of AECOPD patients.
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Affiliation(s)
- Huaying Wang
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Xiao Gu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Yuesong Weng
- Clinical Laboratory, First Hospital, 58 Liuting Road, Ningbo City, Zhejiang Province, 315010, P. R. China
| | - Tao Xu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Zhongming Fu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Weidong Peng
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Wanjun Yu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China.
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27
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Wong YP, Chua KH, Thong KL. One-step species-specific high resolution melting analysis for nosocomial bacteria detection. J Microbiol Methods 2015; 107:133-7. [PMID: 25307691 DOI: 10.1016/j.mimet.2014.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/09/2014] [Accepted: 10/02/2014] [Indexed: 11/25/2022]
Abstract
Nosocomial infections are a major public health concern worldwide. Early and accurate identification of nosocomial pathogens which are often multidrug resistant is crucial for prompt treatment. Hence, an alternative real-time polymerase chain reaction coupled with high resolution melting-curve analysis (HRMA) was developed for identification of five nosocomial bacteria. This assay targets species-specific regions of each nosocomial bacteria and produced five distinct melt curves with each representing a particular bacterial species. The melting curves were characterized by peaks of 78.8 ± 0.2 °C for Acinetobacter baumannii, 82.7 ± 0.2 °C for Escherichia coli, 86.3 ± 0.3 °C for Klebsiella pneumoniae, 88.8 ± 0.2 °C for Pseudomonas aeruginosa and 74.6 ± 02 °C for methicillin-resistant Staphylococcus aureus. The assay was able to specifically detect the five bacterial species with an overall detection limit of 2 × 10(-2) ng/μL. In conclusion, the HRM assay developed is a simple and rapid method for identification of the selected nosocomial pathogens.
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Affiliation(s)
- Yeng Pooi Wong
- Microbiology Unit, Institute of Biological Science, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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28
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Pankhurst L, Macfarlane-Smith L, Buchanan J, Anson L, Davies K, O'Connor L, Ashwin H, Pike G, Dingle KE, Peto TE, Wordsworth S, Walker AS, Wilcox MH, Crook DW. Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study. Health Technol Assess 2015; 18:1-167. [PMID: 25146932 DOI: 10.3310/hta18530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Every year approximately 5000-9000 patients are admitted to a hospital with diarrhoea, which in up to 90% of cases has a non-infectious cause. As a result, single rooms are 'blocked' by patients with non-infectious diarrhoea, while patients with infectious diarrhoea are still in open bays because of a lack of free side rooms. A rapid test for differentiating infectious from non-infectious diarrhoea could be very beneficial for patients. OBJECTIVE To evaluate MassCode multiplex polymerase chain reaction (PCR) for the simultaneous diagnosis of multiple enteropathogens directly from stool, in terms of sensitivity/specificity to detect four common important enteropathogens: Clostridium difficile, Campylobacter spp., Salmonella spp. and norovirus. DESIGN A retrospective study of fixed numbers of samples positive for C. difficile (n = 200), Campylobacter spp. (n = 200), Salmonella spp. (n = 100) and norovirus (n = 200) plus samples negative for all these pathogens (n = 300). Samples were sourced from NHS microbiology laboratories in Oxford and Leeds where initial diagnostic testing was performed according to Public Health England methodology. Researchers carrying out MassCode assays were blind to this information. A questionnaire survey, examining current practice for infection control teams and microbiology laboratories managing infectious diarrhoea, was also carried out. SETTING MassCode assays were carried out at Oxford University Hospitals NHS Trust. Further multiplex assays, carried out using Luminex, were run on the same set of samples at Leeds Teaching Hospitals NHS Trust. The questionnaire was completed by various NHS trusts. MAIN OUTCOME MEASURES Sensitivity and specificity to detect C. difficile, Campylobacter spp., Salmonella spp., and norovirus. RESULTS Nucleic acids were extracted from 948 clinical samples using an optimised protocol (200 Campylobacter spp., 199 C. difficile, 60 S. enterica, 199 norovirus and 295 negative samples; some samples contained more than one pathogen). Using the MassCode assay, sensitivities for each organism compared with standard microbiological testing ranged from 43% to 94% and specificities from 95% to 98%, with particularly poor performance for S. enterica. Relatively large numbers of unexpected positives not confirmed with quantitative PCR were also observed, particularly for S. enterica, Giardia lamblia and Cryptosporidium spp. As the results indicated that S. enterica detection might provide generic challenges to other multiplex assays for gastrointestinal pathogens, the Luminex xTag(®) gastrointestinal assay was also run blinded on the same extracts (937/948 remaining) and on re-extracted samples (839/948 with sufficient material). For Campylobacter spp., C. difficile and norovirus, high sensitivities (> 92%) and specificities (> 96%) were observed. For S. enterica, on the original MassCode/Oxford extracts, Luminex sensitivity compared with standard microbiological testing was 84% [95% confidence interval (CI) 73% to 93%], but this dropped to 46% on a fresh extract, very similar to MassCode, with a corresponding increase in specificity from 92% to 99%. Overall agreement on the per-sample diagnosis compared with combined microbiology plus PCR for the main four/all pathogens was 85.6%/64.7%, 87.0%/82.9% and 89.8%/86.8% for the MassCode assay, Luminex assay/MassCode extract and Luminex assay/fresh extract, respectively. Luminex assay results from fresh extracts implied that 5% of samples did not represent infectious diarrhoea, even though enteropathogens were genuinely present. Managing infectious diarrhoea was a significant burden for infection control teams (taking 21% of their time) and better diagnostics were identified as having major potential benefits for patients. CONCLUSIONS Overall, the Luminex xTag gastrointestinal panel showed similar or superior sensitivity and specificity to the MassCode assay. However, on fresh extracts, this test had low sensitivity to detect a key enteric pathogen, S. enterica; making it an unrealistic option for most microbiology laboratories. Extraction efficiency appears to be a major obstacle for nucleic acid-based tests for this organism, and possibly the whole Enterobacteriaceae family. To improve workflows in service microbiology laboratories, to reduce workload for infection control practitioners, and to improve outcomes for NHS patients, further research on deoxyribonucleic acid-based multiplex gastrointestinal diagnostics is urgently needed. FUNDING The Health Technology Assessment programme of the National Institute for Health Research.
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Affiliation(s)
- Louise Pankhurst
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Luke Anson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Lily O'Connor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Helen Ashwin
- University of Leeds, Microbiology, Leeds General Infirmary Old Medical School, Leeds, UK
| | - Graham Pike
- Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Timothy Ea Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Mark H Wilcox
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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29
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Bueno MG, Iovine RO, Torres LN, Catão-Dias JL, Pissinatti A, Kierulff MCM, Carvalho VM. Pneumonia and bacteremia in a golden-headed lion tamarin (Leontopithecus chrysomelas) caused by Klebsiella pneumoniae subsp. pneumoniae during a translocation program of free-ranging animals in Brazil. J Vet Diagn Invest 2015; 27:387-91. [PMID: 25943130 DOI: 10.1177/1040638715584792] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Klebsiella pneumoniae is an important emerging pathogen in humans, particularly the invasive hypermucoviscosity (HMV) phenotype. In addition, the organism is an important public health concern because of nosocomial infections and antimicrobial resistance. Nonhuman primates in captivity are susceptible to Klebsiella, particularly when a stress factor is involved. Infections vary depending on the species but can cause significant morbidity and mortality in these animals. The objective of this study was to describe a case of bronchopneumonia and bacteremia caused by Klebsiella pneumoniae in a free-ranging golden-headed lion tamarin (Leontopithecus chrysomelas) caught and maintained in quarantine during a translocation program for conservation purposes. An adult male, that had showed emaciation and apathy, was clinically examined and, despite being provided supportive therapy, died 2 days after onset of clinical signs. At postmortem examination, generalized bilateral pneumonia and pericarditis were observed. Tissue samples were fixed in 10% formalin for histology, and pulmonary tissues and cardiac blood were collected for microbiologic diagnostic procedures. Bacteria that were shown to be HMV K. pneumoniae subsp. pneumoniae strains were isolated from the pulmonary fluids and cardiac blood in pure cultures. Severe bronchopneumonia was the main pathological finding. The consequences of the confirmed presence of the HMV phenotype of K. pneumoniae subsp. pneumoniae in this wildlife species for human, animal, and ecosystem health should be determined. These results demonstrate the importance of quarantine and potential pathogen screening during wildlife translocation procedures.
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Affiliation(s)
- Marina G Bueno
- Pri-Matas for Biodiversity Conservation Institute, Belo Horizonte, Brazil (Bueno, Kierulff)Molecular and Cell Biology Laboratory, Institute of Health Sciences, Paulista University, São Paulo, Brazil (Iovine)Laboratory of Wildlife Comparative Pathology, LAPCOM, School of Veterinary Medicine and Animal Sciences, Pathology Department, São Paulo University, São Paulo, Brazil (Torres, Catão-Dias, Carvalho)Rio de Janeiro Primatology Center-CPRJ/INEA and Serra dos Órgãos University-UNIFESO, Rio de Janeiro, Brazil (Pissinatti)Post-Graduation Program for Tropical Biodiversity, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil (Kierulff)
| | - Renata O Iovine
- Pri-Matas for Biodiversity Conservation Institute, Belo Horizonte, Brazil (Bueno, Kierulff)Molecular and Cell Biology Laboratory, Institute of Health Sciences, Paulista University, São Paulo, Brazil (Iovine)Laboratory of Wildlife Comparative Pathology, LAPCOM, School of Veterinary Medicine and Animal Sciences, Pathology Department, São Paulo University, São Paulo, Brazil (Torres, Catão-Dias, Carvalho)Rio de Janeiro Primatology Center-CPRJ/INEA and Serra dos Órgãos University-UNIFESO, Rio de Janeiro, Brazil (Pissinatti)Post-Graduation Program for Tropical Biodiversity, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil (Kierulff)
| | - Luciana N Torres
- Pri-Matas for Biodiversity Conservation Institute, Belo Horizonte, Brazil (Bueno, Kierulff)Molecular and Cell Biology Laboratory, Institute of Health Sciences, Paulista University, São Paulo, Brazil (Iovine)Laboratory of Wildlife Comparative Pathology, LAPCOM, School of Veterinary Medicine and Animal Sciences, Pathology Department, São Paulo University, São Paulo, Brazil (Torres, Catão-Dias, Carvalho)Rio de Janeiro Primatology Center-CPRJ/INEA and Serra dos Órgãos University-UNIFESO, Rio de Janeiro, Brazil (Pissinatti)Post-Graduation Program for Tropical Biodiversity, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil (Kierulff)
| | - José L Catão-Dias
- Pri-Matas for Biodiversity Conservation Institute, Belo Horizonte, Brazil (Bueno, Kierulff)Molecular and Cell Biology Laboratory, Institute of Health Sciences, Paulista University, São Paulo, Brazil (Iovine)Laboratory of Wildlife Comparative Pathology, LAPCOM, School of Veterinary Medicine and Animal Sciences, Pathology Department, São Paulo University, São Paulo, Brazil (Torres, Catão-Dias, Carvalho)Rio de Janeiro Primatology Center-CPRJ/INEA and Serra dos Órgãos University-UNIFESO, Rio de Janeiro, Brazil (Pissinatti)Post-Graduation Program for Tropical Biodiversity, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil (Kierulff)
| | - Alcides Pissinatti
- Pri-Matas for Biodiversity Conservation Institute, Belo Horizonte, Brazil (Bueno, Kierulff)Molecular and Cell Biology Laboratory, Institute of Health Sciences, Paulista University, São Paulo, Brazil (Iovine)Laboratory of Wildlife Comparative Pathology, LAPCOM, School of Veterinary Medicine and Animal Sciences, Pathology Department, São Paulo University, São Paulo, Brazil (Torres, Catão-Dias, Carvalho)Rio de Janeiro Primatology Center-CPRJ/INEA and Serra dos Órgãos University-UNIFESO, Rio de Janeiro, Brazil (Pissinatti)Post-Graduation Program for Tropical Biodiversity, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil (Kierulff)
| | - Maria C M Kierulff
- Pri-Matas for Biodiversity Conservation Institute, Belo Horizonte, Brazil (Bueno, Kierulff)Molecular and Cell Biology Laboratory, Institute of Health Sciences, Paulista University, São Paulo, Brazil (Iovine)Laboratory of Wildlife Comparative Pathology, LAPCOM, School of Veterinary Medicine and Animal Sciences, Pathology Department, São Paulo University, São Paulo, Brazil (Torres, Catão-Dias, Carvalho)Rio de Janeiro Primatology Center-CPRJ/INEA and Serra dos Órgãos University-UNIFESO, Rio de Janeiro, Brazil (Pissinatti)Post-Graduation Program for Tropical Biodiversity, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil (Kierulff)
| | - Vania M Carvalho
- Pri-Matas for Biodiversity Conservation Institute, Belo Horizonte, Brazil (Bueno, Kierulff)Molecular and Cell Biology Laboratory, Institute of Health Sciences, Paulista University, São Paulo, Brazil (Iovine)Laboratory of Wildlife Comparative Pathology, LAPCOM, School of Veterinary Medicine and Animal Sciences, Pathology Department, São Paulo University, São Paulo, Brazil (Torres, Catão-Dias, Carvalho)Rio de Janeiro Primatology Center-CPRJ/INEA and Serra dos Órgãos University-UNIFESO, Rio de Janeiro, Brazil (Pissinatti)Post-Graduation Program for Tropical Biodiversity, Federal University of Espírito Santo, São Mateus, Espírito Santo, Brazil (Kierulff)
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Cox BL, Schiffer H, Dagget G, Beierschmitt A, Sithole F, Lee E, Revan F, Halliday-Simmonds I, Beeler-Marfisi J, Palmour R, Soto E. Resistance of Klebsiella pneumoniae to the innate immune system of African green monkeys. Vet Microbiol 2015; 176:134-42. [PMID: 25614101 DOI: 10.1016/j.vetmic.2015.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 01/01/2015] [Accepted: 01/03/2015] [Indexed: 11/28/2022]
Abstract
In recent years, an emergent Klebsiella pneumoniae hypermucoviscosity (HMV) phenotype has been associated with increased invasiveness and pathogenicity in primates. In this project, bacteria recovered from infected African green monkeys (AGM) (Chlorocebus aethiops sabaeus) were screened for HMV phenotype, and were compared to non-HMV isolates in in vitro, serum, and oxidative-mediated killing assays. Complement-mediated killing was assessed utilizing freshly collected serum from healthy AGM. Oxidative-mediated killing was investigated utilizing sodium hypochlorite and hydrogen peroxide. Compared to non-HMV isolates, HMV isolates were more resistant to serum-mediated and oxidative killing (p<0.05). Phagocytosis resistance was evaluated using AGM peripheral blood monocytes (PBMC), and results indicated that non-HMV isolates associated with the AGM PBMC to a greater extent than HMV isolates (p<0.001). Measurement of lactate dehydrogenase release showed that HMV isolates were more cytotoxic to AGM PBMC than non-HMV isolates (p<0.001). Thus, the hypermucoid phenotype appears to be an important virulence factor that promotes evasion of innate immune defenses.
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Affiliation(s)
- Brandi L Cox
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Holly Schiffer
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Gregory Dagget
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Amy Beierschmitt
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis; Behavioural Science Foundation, Estridge Estate, Saint Kitts and Nevis
| | - Fortune Sithole
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Elise Lee
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Floyd Revan
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Iona Halliday-Simmonds
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Janet Beeler-Marfisi
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis; Gribbles Veterinary Pathology, Christchurch, New Zealand
| | - Roberta Palmour
- Behavioural Science Foundation, Estridge Estate, Saint Kitts and Nevis
| | - Esteban Soto
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Saint Kitts and Nevis.
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31
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Eischeid AC, Kasko SM. Quantitative multiplex real-time PCR assay for shrimp allergen: comparison of commercial master mixes and PCR platforms in rapid cycling. J Food Prot 2015; 78:230-4. [PMID: 25581202 DOI: 10.4315/0362-028x.jfp-14-203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Real-time PCR has been used widely in numerous fields. In food safety, it has been applied to detection of microbes and other contaminants, including food allergens. Interest in rapid (fast) cycling real-time PCR has grown because it yields results in less time than does conventional cycling. However, fast cycling can adversely affect assay performance. Here we report on tests of commercial master mixes specifically designed for fast real-time PCR using a shrimp allergen assay we previously developed and validated. The objective of this work was to determine whether specialized commercial master mixes lead to improved assay performance in rapid cycling. Real-time PCR assays were carried out using four different master mixes and two different rapid cycling protocols. Results indicated that specialized master mixes did yield quality results. In many cases, linear ranges spanned up to 7 orders of magnitude, R(2) values were at least 0.95, and reaction efficiencies were within or near the optimal range of 90 to 110%. In the faster of the two rapid cycling protocols tested, assay performance and PCR amplification were markedly better for the shorter PCR product. In conclusion, specialized commercial master mixes were effective as part of rapid cycling protocols, but conventional cycling as used in our previous work is more reliable for the shrimp assay tested.
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Affiliation(s)
- Anne C Eischeid
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5100 Paint Branch Parkway, College Park, Maryland 20740, USA.
| | - Sasha M Kasko
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5100 Paint Branch Parkway, College Park, Maryland 20740, USA
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32
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Interleukin 10 overexpression alters survival in the setting of gram-negative pneumonia following lung contusion. Shock 2014; 41:301-10. [PMID: 24430542 DOI: 10.1097/shk.0000000000000123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Lung contusion injury produces a vulnerable window within the inflammatory defenses of the lung that predisposes the patient to pneumonia. Interleukin 10 (IL-10) is a known anti-inflammatory mediator produced by macrophages and capable of downregulating acute lung inflammation. We investigated the impact of increased levels of IL-10 within the lung on survival and the host response to trauma in the setting of lung contusion (LC) and gram-negative pneumonia. DESIGN A bitransgenic, tetracycline-inducible, lung-specific human IL-10 overexpression (IL-10 OE) mouse model and single transgenic (TG-) control mice were used. Mice underwent LC injury or sham injury (sham) at time -6 h. At time 0, animals were inoculated intratracheally with 500 colony-forming units of Klebsiella pneumoniae (pneu). Bronchoalveolar lavage fluid, lung tissue specimens, or purified macrophages were collected. Lung tissue and blood bacteria levels were quantified. Cytokine levels were assayed by enzyme-linked immunosorbent assay, and gene expression levels were evaluated by real-time polymerase chain reaction. Cell-type identification and quantification were done using real-time polymerase chain reaction and flow cytometry. MAIN RESULTS Interleukin 10 OE mice demonstrated decreased 5-day survival compared with TG- mice following LC + pneu (0 vs. 30%, P < 0.0001). Interleukin 10 OE mice had significantly higher lung bacteria counts (P = 0.02) and levels of bacteremia (P = 0.001) at 24 h. The IL-10 OE mice recruited more neutrophils into the alveoli as measured in bronchoalveolar lavage fluid compared with TG- mice. Alveolar macrophages from IL-10 OE mice displayed increased alternative activation (M2 macrophages, P = 0.046), whereas macrophages from TG- mice exhibited classic activation (M1 macrophages) and much higher intracellular bacterial killing potential (P = 0.03). Interleukin 6, keratinocyte-derived chemokine, and macrophage inflammatory protein 2 levels were significantly elevated in IL-10 OE LC + pneu animals (P < 0.05). CONCLUSIONS Lung-specific IL-10 overexpression induces alternative activation of alveolar macrophages. This shift in macrophage phenotype decreases intracellular bacterial killing, resulting in a more pronounced bacteremia and accelerated mortality in a model of LC and pneumonia.
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O'Sullivan DM, Laver T, Temisak S, Redshaw N, Harris KA, Foy CA, Studholme DJ, Huggett JF. Assessing the accuracy of quantitative molecular microbial profiling. Int J Mol Sci 2014; 15:21476-91. [PMID: 25421243 PMCID: PMC4264237 DOI: 10.3390/ijms151121476] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/11/2014] [Accepted: 11/14/2014] [Indexed: 01/04/2023] Open
Abstract
The application of high-throughput sequencing in profiling microbial communities is providing an unprecedented ability to investigate microbiomes. Such studies typically apply one of two methods: amplicon sequencing using PCR to target a conserved orthologous sequence (typically the 16S ribosomal RNA gene) or whole (meta)genome sequencing (WGS). Both methods have been used to catalog the microbial taxa present in a sample and quantify their respective abundances. However, a comparison of the inherent precision or bias of the different sequencing approaches has not been performed. We previously developed a metagenomic control material (MCM) to investigate error when performing different sequencing strategies. Amplicon sequencing using four different primer strategies and two 16S rRNA regions was examined (Roche 454 Junior) and compared to WGS (Illumina HiSeq). All sequencing methods generally performed comparably and in good agreement with organism specific digital PCR (dPCR); WGS notably demonstrated very high precision. Where discrepancies between relative abundances occurred they tended to differ by less than twofold. Our findings suggest that when alternative sequencing approaches are used for microbial molecular profiling they can perform with good reproducibility, but care should be taken when comparing small differences between distinct methods. This work provides a foundation for future work comparing relative differences between samples and the impact of extraction methods. We also highlight the value of control materials when conducting microbial profiling studies to benchmark methods and set appropriate thresholds.
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Affiliation(s)
| | - Thomas Laver
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - Sasithon Temisak
- Molecular Biology, LGC Ltd., Queens Road, Teddington TW11 0LY, UK.
| | - Nicholas Redshaw
- Molecular Biology, LGC Ltd., Queens Road, Teddington TW11 0LY, UK.
| | - Kathryn A Harris
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK.
| | - Carole A Foy
- Molecular Biology, LGC Ltd., Queens Road, Teddington TW11 0LY, UK.
| | - David J Studholme
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - Jim F Huggett
- Molecular Biology, LGC Ltd., Queens Road, Teddington TW11 0LY, UK.
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Multiplex PCR for identification of two capsular types in epidemic KPC-producing Klebsiella pneumoniae sequence type 258 strains. Antimicrob Agents Chemother 2014; 58:4196-9. [PMID: 24733470 DOI: 10.1128/aac.02673-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a multiplex PCR assay capable of identifying two capsular polysaccharide synthesis sequence types (sequence type 258 [ST258] cps-1 and cps-2) in epidemic Klebsiella pneumoniae ST258 strains. The assay performed with excellent sensitivity (100%) and specificity (100%) for identifying cps types in 60 ST258 K. pneumoniae sequenced isolates. The screening of 419 ST258 clonal isolates revealed a significant association between cps type and K. pneumoniae carbapenemase (KPC) variant: cps-1 is largely associated with KPC-2, while cps-2 is primarily associated with KPC-3.
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35
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Babu L, Reddy P, Murali HS, Batra HV. Optimization and evaluation of a multiplex PCR for simultaneous detection of prominent foodborne pathogens of Enterobacteriaceae. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0622-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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36
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Clifford RJ, Milillo M, Prestwood J, Quintero R, Zurawski DV, Kwak YI, Waterman PE, Lesho EP, Mc Gann P. Detection of bacterial 16S rRNA and identification of four clinically important bacteria by real-time PCR. PLoS One 2012; 7:e48558. [PMID: 23139793 PMCID: PMC3490953 DOI: 10.1371/journal.pone.0048558] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/26/2012] [Indexed: 12/26/2022] Open
Abstract
Within the paradigm of clinical infectious disease research, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa represent the four most clinically relevant, and hence most extensively studied bacteria. Current culture-based methods for identifying these organisms are slow and cumbersome, and there is increasing need for more rapid and accurate molecular detection methods. Using bioinformatic tools, 962,279 bacterial 16S rRNA gene sequences were aligned, and regions of homology were selected to generate a set of real-time PCR primers that target 93.6% of all bacterial 16S rRNA sequences published to date. A set of four species-specific real-time PCR primer pairs were also designed, capable of detecting less than 100 genome copies of A. baumannii, E. coli, K. pneumoniae, and P. aeruginosa. All primers were tested for specificity in vitro against 50 species of Gram-positive and –negative bacteria. Additionally, the species-specific primers were tested against a panel of 200 clinical isolates of each species, randomly selected from a large repository of clinical isolates from diverse areas and sources. A comparison of culture and real-time PCR demonstrated 100% concordance. The primers were incorporated into a rapid assay capable of positive identification from plate or broth cultures in less than 90 minutes. Furthermore, our data demonstrate that current targets, such as the uidA gene in E.coli, are not suitable as species-specific genes due to sequence variation. The assay described herein is rapid, cost-effective and accurate, and can be easily incorporated into any research laboratory capable of real-time PCR.
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Affiliation(s)
- Robert J. Clifford
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Michael Milillo
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jackson Prestwood
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Reyes Quintero
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Daniel V. Zurawski
- Department of Wound Infections, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Yoon I. Kwak
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Paige E. Waterman
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Emil P. Lesho
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Patrick Mc Gann
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail:
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Saha R, Bechanko R, Bestervelt LL, Donofrio RS. Evaluation of molecular techniques for identification and enumeration of Raoultella terrigena ATCC 33257 in water purifier efficacy testing. J Ind Microbiol Biotechnol 2010; 38:1337-44. [PMID: 21132347 DOI: 10.1007/s10295-010-0917-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/18/2010] [Indexed: 10/18/2022]
Abstract
Raoultella terrigena ATCC 33257, a representative of the coliform group, is commonly used as a challenge organism in water purifier efficacy testing. In addition to being time consuming, traditional culturing techniques and metabolic identification systems (including automated systems) also fail to accurately differentiate this organism from its closely related neighbors belonging to the Enterobacteriaceae group. Molecular-based techniques, such as real-time quantitative polymerase chain reaction (qPCR) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting, are preferred methods of detection because of their accuracy, reproducibility, specificity, and sensitivity, along with shorter turnaround time. ERIC-PCR performed with the 1R primer set demonstrated stable unique banding patterns (~800, ~300 bp) for R. terrigena ATCC 33257 different from patterns observed for R. planticola and R. ornithinolytica. The primer pair developed from gyraseA (gyrA) sequence of R. terrigena for the SYBR Green qPCR assay using the AlleleID(®) 7.0 primer probe design software was highly specific and sensitive for the target organism. The sensitivity of the assay was 10(1) colony forming units (CFU)/ml for whole cells and 4.7 fg with genomic DNA. The primer pair was successful in determining the concentration (5.5 ± 0.3 × 10(6) CFU/ml) of R. terrigena from water samples spiked with equal concentration of Escherichia coli and R. terrigena. Based on these results from the ERIC-PCR and the SYBR Green qPCR assay, these molecular techniques can be efficiently used for rapid identification and quantification of R. terrigena during water purifier testing.
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Affiliation(s)
- Ratul Saha
- NSF International, Microbiology Division, 789 Dixboro Road, Ann Arbor, MI 48105, USA.
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Burke RL, Whitehouse CA, Taylor JK, Selby EB. Epidemiology of invasive Klebsiella pneumoniae with hypermucoviscosity phenotype in a research colony of nonhuman primates. Comp Med 2009; 59:589-597. [PMID: 20034435 PMCID: PMC2798845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 08/30/2009] [Accepted: 09/05/2009] [Indexed: 05/28/2023]
Abstract
Invasive Klebsiella pneumoniae with hypermucoviscosity phenotype (HMV K. pneumoniae) is an emerging human pathogen that, over the past 20 y, has resulted in a distinct clinical syndrome characterized by pyogenic liver abscesses sometimes complicated by bacteremia, meningitis, and endophthalmitis. Infections occur predominantly in Taiwan and other Asian countries, but HMV K. pneumoniae is considered an emerging infectious disease in the United States and other Western countries. In 2005, fatal multisystemic disease was attributed to HMV K. pneumoniae in African green monkeys (AGM) at our institution. After identification of a cluster of subclinically infected macaques in March and April 2008, screening of all colony nonhuman primates by oropharyngeal and rectal culture revealed 19 subclinically infected rhesus and cynomolgus macaques. PCR testing for 2 genes associated with HMV K. pneumoniae, rmpA and magA, suggested genetic variability in the samples. Random amplified polymorphic DNA analysis on a subset of clinical isolates confirmed a high degree of genetic diversity between the samples. Environmental testing did not reveal evidence of aerosol or droplet transmission of the organism in housing areas. Further research is needed to characterize HMV K. pneumoniae, particularly with regard to genetic differences among bacterial strains and their relationship to human disease and to the apparent susceptibility of AGM to this organism.
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Affiliation(s)
- Robin L Burke
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA.
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