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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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ESBL/AmpC-Producing Enterobacteriaceae Fecal Colonization in Dogs after Elective Surgery. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The purpose of this study was to evaluate the presence and load of ESBL/AmpC-producing Enterobacteriaceae fecal carriage in healthy dogs. Fecal samples were collected from dogs submitted to surgical procedures (n = 25). Fecal samples were collected before surgery (BS) and after surgery (AS). β-lactamases were detected by PCR. Statistical analyses were performed with SAS software (v.9.4); a p value ≤ 0.05 was considered statistically significant. The ESBL/AmpC-producing Enterobacteriaceae bacteria species detected in this study were E. coli, K. pneumoniae and E. cloacae. TEM, and CTX-M-1 group genes were the most frequent β-lactamases detected. The number of dogs colonized with 3GC-resistant Enterobacteriaceae bacteria was significantly higher in the AS (63.6%, n = 14/22) group compared to in the BS group (20.0%, n = 5/25, p = 0.0033). The ESBL/AmpC-producing bacteria fecal load was significantly higher in the AS group compared to in the BS (p = 0.025) group. This study shows that 3GC-resistant Enterobacteriaceae and ESBLs/AmpC producers in the veterinary clinical practice are a concern and highlights the need to implement preventive measures to minimize their spread.
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Barani M, Zeeshan M, Kalantar-Neyestanaki D, Farooq MA, Rahdar A, Jha NK, Sargazi S, Gupta PK, Thakur VK. Nanomaterials in the Management of Gram-Negative Bacterial Infections. NANOMATERIALS 2021; 11:nano11102535. [PMID: 34684977 PMCID: PMC8540672 DOI: 10.3390/nano11102535] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 01/10/2023]
Abstract
The exploration of multiplexed bacterial virulence factors is a major problem in the early stages of Escherichia coli infection therapy. Traditional methods for detecting Escherichia coli (E. coli), such as serological experiments, immunoassays, polymerase chain reaction, and isothermal microcalorimetry have some drawbacks. As a result, detecting E. coli in a timely, cost-effective, and sensitive manner is critical for various areas of human safety and health. Intelligent devices based on nanotechnology are paving the way for fast and early detection of E. coli at the point of care. Due to their specific optical, magnetic, and electrical capabilities, nanostructures can play an important role in bacterial sensors. Another one of the applications involved use of nanomaterials in fighting microbial infections, including E. coli mediated infections. Various types of nanomaterials, either used directly as an antibacterial agent such as metallic nanoparticles (NPs) (silver, gold, zinc, etc.), or as a nanocarrier to deliver and target the antibiotic to the E. coli and its infected area. Among different types, polymeric NPs, lipidic nanocarriers, metallic nanocarriers, nanomicelles, nanoemulsion/ nanosuspension, dendrimers, graphene, etc. proved to be effective vehicles to deliver the drug in a controlled fashion at the targeted site with lower off-site drug leakage and side effects.
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Affiliation(s)
- Mahmood Barani
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman 7616913555, Iran; (M.B.); (D.K.-N.)
| | - Mahira Zeeshan
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Davood Kalantar-Neyestanaki
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman 7616913555, Iran; (M.B.); (D.K.-N.)
- Department of Medical Microbiology (Bacteriology and virology), Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman 7616913555, Iran
| | - Muhammad Asim Farooq
- Faculty of Pharmacy, Department of Pharmaceutics, The University of Lahore, Lahore 54000, Pakistan;
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol 9861335856, Iran
- Correspondence: (A.R.); (P.K.G.); (V.K.T.)
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida 201310, India;
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran;
| | - Piyush Kumar Gupta
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201310, India
- Correspondence: (A.R.); (P.K.G.); (V.K.T.)
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Center, SRUC, Edinburgh EH9 3JG, UK
- Department of Mechanical Engineering, School of Engineering, Shiv Nadar University, Greater Noida 201314, India
- School of Engineering, University of Petroleum & Energy Studies (UPES), Dehradun 248007, India
- Correspondence: (A.R.); (P.K.G.); (V.K.T.)
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Comparative in vitro activity of plazomicin and older aminoglyosides against Enterobacterales isolates; prevalence of aminoglycoside modifying enzymes and 16S rRNA methyltransferases. Diagn Microbiol Infect Dis 2020; 97:115092. [PMID: 32569921 DOI: 10.1016/j.diagmicrobio.2020.115092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 11/20/2022]
Abstract
Comparative in vitro activity of plazomicin and 4 older aminoglycosides was evaluated with broth microdilution in 714 blood isolates from 14 hospitals in Turkey. Isolates included Escherichia coli (n=320), Klebsiella spp. (n=294), Enterobacter spp. (n=69), Serratia marcescens (n=20), and Citrobacter spp. (n=11). Isolates resistant to older aminoglycosides (n=240) were screened for aminoglycoside modifying enzyme genes: aac(6')-Ib, aac(3)-Ia, aac(3)-IIa, ant(2″)-Ia. Isolates with high MICs for plazomicin (n=41) were screened for 16S rRNA methyltransferase genes (armA, rmtA, rmtB, rmtC, rmtD, rmtE, rmtF, rmtG, rmtH, npmA) and 2 carbapenemase genes (blaOXA-48, blaNDM-1). Overall, resistance to plazomicin, amikacin, netilmicin, gentamicin, and tobramycin was 7.7%, 7.4%, 31.5%, 32.9%, and 34.7%, respectively. aac(6')-Ib and aac(3)-IIa were the most common AME genes. Co-occurrence of blaNDM-1 with armA and rmtC and blaOXA-48 with armA was striking. Enterobacter cloacae carrying rmtC+blaNDM-1, S. marcescens with armA+blaOXA-48, and rmtF+ blaOXA-48 in K. pneumoniae were reported for the first time.
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Brons JK, Vink SN, de Vos MGJ, Reuter S, Dobrindt U, van Elsas JD. Fast identification of Escherichia coli in urinary tract infections using a virulence gene based PCR approach in a novel thermal cycler. J Microbiol Methods 2019; 169:105799. [PMID: 31790780 DOI: 10.1016/j.mimet.2019.105799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 01/20/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common causal agent of urinary tract infections (UTIs) in humans. Currently, clinical detection methods take hours (dipsticks) to days (culturing methods), limiting rapid intervention. As an alternative, the use of molecular methods could improve speed and accuracy, but their applicability is complicated by high genomic variability within UPEC strains. Here, we describe a novel PCR-based method for the identification of E. coli in urine. Based on in silico screening of UPEC genomes, we selected three UPEC-specific genes predicted to be involved in pathogenesis (c3509, c3686 (yrbH) and chuA), and one E. coli-specific marker gene (uidA). We validated the method on 128 clinical (UTI) strains. Despite differential occurrences of these genes in uropathogenic E. coli, the method, when using multi-gene combinations, specifically detected the target organism across all samples. The lower detection limit, assessed with model UPEC strains, was approximately 104 CFU/ml. Additionally, the use of this method in a novel ultrafast PCR thermal cycler (Nextgen PCR) allowed a detection time from urine sampling to identification of only 52 min. This is the first study that uses such defined sets of marker genes for the detection of E. coli in UTIs. In addition, we are the first to demonstrate the potential of the Nextgen thermal cycler. Our E. coli identification method has the potential to be a rapid, reliable and inexpensive alternative for traditional methods.
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Affiliation(s)
- Jolanda K Brons
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
| | - Stefanie N Vink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Marjon G J de Vos
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Stefan Reuter
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital of Münster, Münster, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Jan Dirk van Elsas
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
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Evidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting Humans. J Clin Microbiol 2019; 57:JCM.01537-18. [PMID: 30944193 DOI: 10.1128/jcm.01537-18] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/22/2019] [Indexed: 12/12/2022] Open
Abstract
This study aimed to characterize the fecal colonization and sharing of Klebsiella pneumoniae strains between companion animals and humans living in close contact. Fecal samples were collected from 50 healthy participants (24 humans, 18 dogs, and 8 cats) belonging to 18 households. Samples were plated onto MacConkey agar (MCK) plates with and without cefotaxime or meropenem supplementation. Up to five K. pneumoniae colonies per participant were compared by pulsed-field gel electrophoresis (PFGE) after XbaI restriction. K. pneumoniae strains with unique pulse types from each participant were characterized for antimicrobial susceptibility, virulence genes, and multilocus sequence type (MLST). Fecal K. pneumoniae pulse types were compared to those of clinical K. pneumoniae strains from animal and human patients with urinary tract infections (n = 104). K. pneumoniae colonization was detected in nonsupplemented MCK in around 38% of dogs (n = 7) and humans (n = 9). K. pneumoniae strains isolated from dogs belonged to sequence type 17 (ST17), ST188, ST252, ST281, ST423, ST1093, ST1241, ST3398, and ST3399. None of the K. pneumoniae strains were multidrug resistant or hypervirulent. Two households included multiple colonized participants. Notably, two colonized dogs within household 15 (H15) shared a strain each (ST252 and ST1241) with one coliving human. One dog from H16 shared one PFGE-undistinguishable K. pneumoniae ST17 strain with two humans from different households; however, the antimicrobial susceptibility phenotypes of these three strains differed. Two main virulence genotypes were detected, namely fimH-1 mrkD ycfM entB kfu and fimH-1 mrkD ycfM entB kpn These results highlight the potential role of dogs as a reservoir of K. pneumoniae to humans and vice versa. Furthermore, to our best knowledge, this is the first report of healthy humans and dogs sharing K. pneumoniae strains that were undistinguishable by PFGE/MLST.
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Marques C, Belas A, Franco A, Aboim C, Gama LT, Pomba C. Increase in antimicrobial resistance and emergence of major international high-risk clonal lineages in dogs and cats with urinary tract infection: 16 year retrospective study. J Antimicrob Chemother 2019; 73:377-384. [PMID: 29136156 DOI: 10.1093/jac/dkx401] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022] Open
Abstract
Objectives To evaluate temporal trends in antimicrobial resistance, over 16 years, in bacteria isolated from dogs and cats with urinary tract infection (UTI) and the clonal lineages of bacteria harbouring critical antimicrobial resistance mechanisms. Methods Antimicrobial susceptibility testing was conducted for 948 bacteria isolated from dogs and cats with UTI (1999-2014). Resistance mechanisms were detected by PCR, namely ESBL/AmpC in third-generation cephalosporin (3GC)-resistant Escherichia coli and Proteus mirabilis, mecA in methicillin-resistant staphylococci, and aac(6')-Ieaph(2″)-Ia and aph(2″)-1d in high-level gentamicin-resistant (HLGR) enterococci. Resistant bacteria were typed by MLST, and temporal trends in E. coli and Enterobacteriaceae antimicrobial resistance were determined by logistic regression. Results Enterobacteriaceae had a significant temporal increase in resistance to amoxicillin/clavulanate, 3GCs, trimethoprim/sulfamethoxazole, fluoroquinolones, gentamicin and tetracycline (P < 0.001). An increase in MDR was also detected (P < 0.0001). 3GC resistance was mainly caused by the presence of blaCTX-M-15 and blaCMY-2 in E. coli and the presence of blaCMY-2 in P. mirabilis. Two major 3GC-resistant E. coli clonal lineages were detected: O25b:H4-B2-ST131 and ST648. The mecA gene was detected in 9.2% (n = 11/119) of Staphylococcus spp., including MRSA clonal complex (CC) 5 (n = 2) and methicillin-resistant Staphylococcus epidermidis CC5 (n = 4). A temporal increase in MDR methicillin-resistant Staphylococcus pseudintermedius was detected (P = 0.0069). Some ampicillin-resistant and/or HLGR Enterococcus spp. were found to belong to hospital-adapted CCs, namely Enterococcus faecalis ST6-CC6 (n = 1) and Enterococcus faecium CC17 (n = 8). Conclusions The temporal increase in antimicrobial resistance and in MDR bacteria causing UTI in dogs and cats creates important therapeutic limitations in veterinary medicine. Furthermore, the detection of MDR high-risk clonal lineages raises public health concerns since companion animals with UTI may contribute to the spread of such bacteria.
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Affiliation(s)
- Cátia Marques
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Adriana Belas
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Andreia Franco
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Catarina Aboim
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Luís Telo Gama
- Animal Genetic Resources, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Constança Pomba
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
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Montenegro DA, Borda LF, Neuta Y, Gómez LA, Castillo DM, Loyo D, Lafaurie GI. Oral and uro-vaginal intra-amniotic infection in women with preterm delivery: A case-control study. ACTA ACUST UNITED AC 2019; 10:e12396. [PMID: 30663264 DOI: 10.1111/jicd.12396] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/04/2018] [Accepted: 11/12/2018] [Indexed: 01/11/2023]
Abstract
AIM The aim of the present study was to establish the association between the presence of oral and uro-vaginal microorganisms in the placental membrane and preterm delivery (PTD), the premature rupture of membranes (PRM), and the clinical signs of intra-amniotic infection. METHODS Eighty-four women with PTD and 127 women with delivery at term were assessed for the PRM, clinical signs of intra-amniotic infection, and the presence of periodontitis. Twenty-seven microorganisms were identified in the placental tissue using nested polymerase chain reaction (PCR). Porphyromonas gingivalis (P. gingivalis) was quantified by droplet digital PCR. RESULTS The prevalence of microorganisms was 9.47% (20/211). P. gingivalis was the most prevalent (12/211, 5.68%). Mycoplasma hominis, Ureaplasma urealyticum, Staphylococcus spp, and Fusobacterium nucleatum were isolated at a very low frequency in the placenta. Candida albicans was associated with PTD (P = 0.027). Periodontitis was associated with clinical signs of infection (odds ratio [OR] = 3.8, 95% confidence interval [CI]: 1.28-13.5) and with PTD (OR = 1.99; 95% CI: 1.07-3.72). CONCLUSION The presence of P. gingivalis in the placenta was not associated with perinatal complications. Detecting microorganisms in the placenta by nested PCR is not relevant, as it has a poor association with clinical variables that establish the diagnosis of chorioamnionitis. However, periodontitis was associated with the clinical signs of intra-amniotic infection and PTD.
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Affiliation(s)
- Daniel A Montenegro
- Obstetrics and Gynecology Service, Hospital Simón Bolivar, Bogotá, Colombia.,School of Medicine, Universidad El Bosque, Bogotá, Colombia
| | - Luis F Borda
- School of Medicine, Universidad El Bosque, Bogotá, Colombia
| | - Yineth Neuta
- Unit of Oral Basic Investigation-UIBO, School of Dentistry, Universidad El Bosque, Bogotá, Colombia
| | - Luz A Gómez
- Unit of Oral Basic Investigation-UIBO, School of Dentistry, Universidad El Bosque, Bogotá, Colombia
| | - Diana M Castillo
- Unit of Oral Basic Investigation-UIBO, School of Dentistry, Universidad El Bosque, Bogotá, Colombia
| | - Daniela Loyo
- Unit of Oral Basic Investigation-UIBO, School of Dentistry, Universidad El Bosque, Bogotá, Colombia
| | - Gloria I Lafaurie
- Unit of Oral Basic Investigation-UIBO, School of Dentistry, Universidad El Bosque, Bogotá, Colombia
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Marques C, Menezes J, Belas A, Aboim C, Cavaco-Silva P, Trigueiro G, Telo Gama L, Pomba C. Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: population structure, antimicrobial resistance and virulence genes. J Antimicrob Chemother 2018; 74:594-602. [DOI: 10.1093/jac/dky499] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/17/2018] [Accepted: 11/08/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Cátia Marques
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Juliana Menezes
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Adriana Belas
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Catarina Aboim
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Patrícia Cavaco-Silva
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Caparica, Portugal
- Technophage, Lisboa, Portugal
| | - Graça Trigueiro
- Laboratório de Análises Clínicas Dr. Joaquim Chaves, Lisboa, Portugal
| | - Luís Telo Gama
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Constança Pomba
- CIISA - Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
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Harada T, Taguchi M, Kawahara R, Kanki M, Kawatsu K. Prevalence and Antimicrobial Susceptibility of Bacterial Pathogens in Ready-to-Eat Foods Retailed in Osaka Prefecture, Japan. J Food Prot 2018; 81:1450-1458. [PMID: 30080122 DOI: 10.4315/0362-028x.jfp-18-035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The potential human health risk of Japanese ready-to-eat (RTE) foods was investigated by determining the contamination by foodborne bacterial pathogens, the prevalence of opportunistic and nosocomial pathogens, and the antibiotic susceptibility of the isolates recovered from 96 samples of lightly pickled vegetables, 88 samples of Western-style desserts, and 98 samples of RTE fish and seafood products sold at retail in Osaka, Japan. Staphylococcus aureus, including isolates producing staphylococcal enterotoxin (SE), were isolated from six lightly pickled vegetable products, seven Western-style dessert products, and three RTE fish and seafood products. Of these isolates, one SEC-producing isolate from a cake was identified as community-acquired methicillin-resistant S. aureus, which was multilocus sequence type 8 and staphylococcal cassette chromosome mec type IV. Enterobacteriaceae species, including Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, Proteus mirabilis, Serratia marcescens, Citrobacter freundii-Citrobacter braakii, and/or the Enterobacter cloacae complex, were isolated from 92 (95.8%) of the lightly pickled vegetable products, 39 (44.3%) of the Western-style dessert products, and 74 (75.5%) of the RTE fish and seafood products. On the basis of the antimicrobial susceptibility profiles of the opportunistic and nosocomial Enterobacteriaceae pathogens, the third-generation cephalosporin, fosfomycin, and quinolone resistance determinants were investigated. We detected AmpC products of the CIT group and a qnrB9 product in 5 and 1 C. freundii-C. braakii isolates, respectively, and fosA gene products in 15 E. cloacae complex isolates. Because RTE foods are consumed without a heating process, the spread of bacterial pathogens from contaminated food to human consumers is possible. RTE foods must be handled using hygienic procedures from the processing steps to the table to reduce the prevalence of potentially pathogenic or pathogenic bacteria and to prevent bacterial growth.
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Affiliation(s)
- Tetsuya Harada
- Osaka Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Masumi Taguchi
- Osaka Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Ryuji Kawahara
- Osaka Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Masashi Kanki
- Osaka Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Kentaro Kawatsu
- Osaka Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
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Gond DP, Singh S, Agrawal NK. Norepinephrine augmented in vitro growth of uropathogenic E. coli in Type 2 diabetes mellitus and its suppression by silodosin (alpha blocker). Diagn Microbiol Infect Dis 2018; 92:85-89. [PMID: 29934070 DOI: 10.1016/j.diagmicrobio.2018.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 03/16/2018] [Accepted: 05/06/2018] [Indexed: 12/18/2022]
Abstract
Norepinephrine is secreted under conditions of stress in humans. The ability of bacteria to sense mammalian hormone may have a role in propagation of infection. The present study investigated the effect of norepinephrine on in vitro growth of uropathogenic E. coli (UPEC) and the effect of silodosin on norepinephrine-induced changes. The spot urine samples were collected from 56 individuals (14 diabetic patients with UTI, 14 diabetic without UTI, 14 non-diabetic UTI and 14 healthy volunteer controls) for the measurement of urinary norepinephrine concentrations. The concentration of norepinephrine, as found in urine of human subjects, was reproduced in artificial urine medium to study the growth of UPEC. The norepinephrine concentration showing maximum growth response was selected to study the effect of silodosin on the growth inhibition of UPEC. Result showed significantly elevated urinary norepinephrine in diabetic patients with and without UTI and also in nondiabetic UTI groups. The norepinephrine concentration equivalent to that in diabetic UTI patients enhanced the growth of UPEC. Furthermore, silodosin (0.32 μM) inhibited the growth of the UPEC.
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Affiliation(s)
- Dinesh Prasad Gond
- Department of Endocrinology and Metabolism, Institute of Medical Sciences Banaras Hindu University Varanasi, India
| | - Shivendra Singh
- Department of Nephrology, Institute of Medical Sciences Banaras Hindu University Varanasi, India
| | - N K Agrawal
- Department of Endocrinology and Metabolism, Institute of Medical Sciences Banaras Hindu University Varanasi, India.
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Khan IUH, Cloutier M, Libby M, Lapen DR, Wilkes G, Topp E. Enhanced Single-tube Multiplex PCR Assay for Detection and Identification of Six Arcobacter Species. J Appl Microbiol 2017; 123:1522-1532. [PMID: 28960631 DOI: 10.1111/jam.13597] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 11/30/2022]
Abstract
AIM A single-tube multiplex PCR (mPCR) assay was developed for rapid, sensitive and simultaneous detection and identification of six Arcobacter species including two new species, A. lanthieri and A. faecis, along with A. butzleri, A. cibarius, A. cryaerophilus and A. skirrowii on the basis of differences in the lengths of their PCR products. Previously designed monoplex, mPCR and RFLP assays do not detect or differentiate A. faecis and A. lanthieri from other closely related known Arcobacter spp. METHODS AND RESULTS Primer pairs for each target species (except A. skirrowii) and mPCR protocol were newly designed and optimized using variable regions of housekeeping including cpn60, gyrA, gyrB and rpoB genes. The accuracy and specificity of the mPCR assay was assessed using DNA templates from six targets and 11 other Arcobacter spp. as well as 50 other bacterial reference species and strains. Tests on the DNA templates of target Arcobacter spp. were appropriately identified, whereas all 61 other DNA templates from other bacterial species and strains were not amplified. Sensitivity and specificity of the mPCR assay was 10 pg μl-1 of DNA concentration per target species. The optimized assay was further evaluated, validated and compared with other mPCR assays by testing Arcobacter cultures isolated from various faecal and water sources. CONCLUSIONS Study results confirm that the newly developed mPCR assay is rapid, accurate, reliable, simple, and valuable for the simultaneous detection and routine diagnosis of six human- and animal-associated Arcobacter spp. SIGNIFICANCE AND IMPACT OF THE STUDY The new mPCR assay is useful not only for pure but also mixed cultures. Moreover, it has the ability to rapidly detect six species which enhances the value of this technology for aetiological and epidemiological studies.
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Affiliation(s)
- I U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - M Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - M Libby
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - D R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - G Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - E Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada
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13
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Felt JR, Yurkovich C, Garshott DM, Kamat D, Farooqi A, Fribley AM, Callaghan MU, Hebert K. The Utility of Real-Time Quantitative Polymerase Chain Reaction Genotype Detection in the Diagnosis of Urinary Tract Infections in Children. Clin Pediatr (Phila) 2017; 56:912-919. [PMID: 28436231 DOI: 10.1177/0009922817706144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Urinary tract infections (UTIs) are the most common serious bacterial infection in children with significant morbidity with delayed diagnosis. Polymerase chain reaction (PCR) is very accurate in detecting bacteria and widely available, but has never been evaluated to detect UTIs in children. To assess the utility of PCR as a rapid diagnostic tool, we conducted a prospective cohort study of 193 urine samples from children younger than 36 months undergoing evaluation for UTI in the emergency department over a 10-month period. A quantification cycle (Cq) threshold of 26.15 identified all Escherichia coli positive samples with sensitivity and specificity of 100% and 99.5%, respectively (95% CI = 71.5%-100% and 97.9%-99.5%, respectively). A Cq threshold of 19.03 identified E coli infections >100 000 colony forming units/mL with sensitivity and specificity of 100% (95% CI = 72.2%-100% and 98.6%-100%, respectively). PCR is very accurate in diagnosing E coli UTIs in young children and could be useful as a rapid diagnostic tool.
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Affiliation(s)
- Jon R Felt
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Chelsey Yurkovich
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | | | - Deepak Kamat
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Ahmad Farooqi
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Andrew M Fribley
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | | | - Katherine Hebert
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
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14
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Williams MR, Stedtfeld RD, Waseem H, Stedtfeld T, Upham B, Khalife W, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA. Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:1229-1241. [PMID: 29657581 PMCID: PMC5898395 DOI: 10.1039/c6ay03405e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.
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Affiliation(s)
- M R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - R D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - H Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - T Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - B Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - W Khalife
- Department of Microbiology, Sparrow Laboratories, Sparrow Health System, Lansing, MI 48912, USA
| | - B Etchebarne
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - M Hughes
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - J M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - S A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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15
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Dubourg G, Fournier PE. Advances in Diagnostic Microbiology. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00161-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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16
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Xu B, Du Y, Lin J, Qi M, Shu B, Wen X, Liang G, Chen B, Liu D. Simultaneous Identification and Antimicrobial Susceptibility Testing of Multiple Uropathogens on a Microfluidic Chip with Paper-Supported Cell Culture Arrays. Anal Chem 2016; 88:11593-11600. [PMID: 27934103 DOI: 10.1021/acs.analchem.6b03052] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Banglao Xu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Yan Du
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Jinqiong Lin
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Mingyue Qi
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Bowen Shu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Xiaoxia Wen
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Guangtie Liang
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Bin Chen
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Dayu Liu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
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17
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Fritzenwanker M, Imirzalioglu C, Chakraborty T, Wagenlehner FM. Modern diagnostic methods for urinary tract infections. Expert Rev Anti Infect Ther 2016; 14:1047-1063. [DOI: 10.1080/14787210.2016.1236685] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Kumar M, Ghosh S, Nayak S, Das A. Recent advances in biosensor based diagnosis of urinary tract infection. Biosens Bioelectron 2016; 80:497-510. [DOI: 10.1016/j.bios.2016.02.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/06/2016] [Accepted: 02/08/2016] [Indexed: 12/16/2022]
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19
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Harada T, Yamane R, Dang VC, Nguyen DP, Nguyen TAD, Jinnai M, Yonogi S, Kawahara R, Kanki M, Kawai T, Kawatsu K, Kumeda Y, Isegawa Y, Yamamoto Y. Prevalence and Antimicrobial Susceptibility of Enterobacteriaceae Isolated from Retail Pepper in Vietnam. J Food Prot 2016; 80:716-724. [PMID: 28350183 DOI: 10.4315/0362-028x.jfp-16-501] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/06/2017] [Indexed: 11/11/2022]
Abstract
To investigate the microbial quality of retail pepper in Vietnam, the enumeration and detection of Enterobacteriaceae and the screening of cefotaxime (CTX)-resistant coliforms were performed by using 84 commercial samples. Although Enterobacteriaceae were isolated from 78 samples, the number of Enterobacteriaceae was lower than 1.0 log CFU/g in 46 samples. For the detection of Enterobacteriaceae with the International Organization for Standardization methods, Salmonella spp., Escherichia coli, Klebsiella pneumoniae, Cronobacter sakazakii, and Enterobacter cloacae complex were isolated from 5, 12, 36, 19, and 30 samples, respectively. During screening of CTX-resistant coliforms, K. pneumoniae, C. sakazakii, and E. cloacae complex were isolated from 8, 1, and 21 samples, respectively. Seven K. pneumoniae and seven E. cloacae complex isolates obtained in the screening of CTX-resistant coliforms were resistant to at least one of the three third-generation cephalosporins (CTX, ceftazidime, and cefpodoxime). Moreover, one E. cloacae complex cluster IV and all K. pneumoniae isolates were positive for extended-spectrum β-lactamase genes or plasmid-mediated AmpC β-lactamase genes or both. Additionally, two extended-spectrum β-lactamase-producing K. pneumoniae isolates and one AmpC β-lactamase-producing E. cloacae complex cluster IV isolate were positive for the plasmid-mediated quinolone resistance determinants and also had amino acid alterations in the quinolone resistance-determining regions of GyrA and ParC. Furthermore, 10 E. cloacae complex isolates were positive for the plasmid-mediated fosfomycin resistance gene fosA. As pepper is often consumed without a heating process, the possible spread to humans of foodborne, opportunistic, and nosocomial infection pathogens or resistance genes from foods prepared or seasoned with pepper cannot be excluded. Therefore, it is necessary to handle pepper by using hygienic conditions during the cultivation, harvesting and processing steps.
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Affiliation(s)
- Tetsuya Harada
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Ryoko Yamane
- Mukogawa Women's University, 6-46 Ikebiraki, Nishinomiya, Hyogo 663-8558, Japan
| | - Van Chinh Dang
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City 751301, Vietnam; and
| | - Do Phuc Nguyen
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City 751301, Vietnam; and
| | - Thi Anh Dao Nguyen
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City 751301, Vietnam; and
| | - Michio Jinnai
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Shinya Yonogi
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Ryuji Kawahara
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Masashi Kanki
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Takao Kawai
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Kentaro Kawatsu
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Yuko Kumeda
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan
| | - Yuji Isegawa
- Mukogawa Women's University, 6-46 Ikebiraki, Nishinomiya, Hyogo 663-8558, Japan
| | - Yoshimasa Yamamoto
- Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka 537-0025, Japan.,Global Collaboration Center, Osaka University, 2-7 Yamadaoka, Suita, Osaka 565-0871, Japan
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20
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Cui Z, Ojaghian M, Tao Z, Kakar K, Zeng J, Zhao W, Duan Y, Vera Cruz C, Li B, Zhu B, Xie G. Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J Appl Microbiol 2016; 120:1357-67. [DOI: 10.1111/jam.13094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Z. Cui
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - M.R. Ojaghian
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - Z. Tao
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - K.U. Kakar
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - J. Zeng
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - W. Zhao
- Chinese Academy of Inspection and Quarantine; Beijing China
| | - Y. Duan
- USDA-ARS-USHRL; Fort Pierce FL USA
| | - C.M. Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division; International Rice Research Institute; Metro Manila Philippines
| | - B. Li
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - B. Zhu
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation; College of Life Science; Zhejiang Sci-Tech University; Hangzhou China
| | - G. Xie
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
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21
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Ahmed S, Kawaguchiya M, Ghosh S, Paul SK, Urushibara N, Mahmud C, Nahar K, Hossain MA, Kobayashi N. Drug resistance and molecular epidemiology of aerobic bacteria isolated from puerperal infections in Bangladesh. Microb Drug Resist 2015; 21:297-306. [PMID: 25555043 DOI: 10.1089/mdr.2014.0219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Puerperal infection is a common complication during postnatal period in developing countries. Bacterial species, drug resistance, and genetic characteristics were investigated for a total of 470 isolates from puerperal infections in Bangladesh for a 2-year period (2010-2012). The most common species was Escherichia coli (n=98), followed by Enterococcus faecalis (n=54), Staphylococcus haemolyticus (n=33), Proteus mirabilis (n=32), Staphylococcus aureus (n=27), Klebsiella pneumoniae (n=22), and Enterobacter cloacae (n=21). S. aureus and Acinetobacter baumannii were isolated at a higher frequency from wound infections after cesarean section, while E. coli, E. cloacae, and K. pneumoniae were isolated from community-acquired endometritis and urinary tract infections. Resistance to third-generation cephalosporins was frequent for Enterobacteriacae, and was mainly mediated by blaCTX-M-1 group beta-lactamases. The CTX-M gene in E. coli from the four phylogroups was identified as blaCTX-M-15, and phylogroup B2 isolates with blaCTX-M-15 were classified into ST131 with O25b allele, harboring aac(6')-Ib-cr and various virulence factors. Carbapenemase genes blaNDM-1 and blaNDM-7 were identified in one isolate each of phylogroup A E. coli. Methicillin-resistant S. aureus isolates had type IV or V SCCmec, including isolates of ST361 (CC672), which is related to an emerging ST672 clone in the Indian subcontinent. This study revealed the recent epidemiological status of aerobic bacteria causing puerperal infections in Bangladesh, providing useful information to improve clinical practice and infection control.
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Affiliation(s)
- Salma Ahmed
- 1Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Mitsuyo Kawaguchiya
- 2Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Souvik Ghosh
- 2Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan.,3Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts, West Indies
| | - Shyamal Kumar Paul
- 1Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Noriko Urushibara
- 2Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Chand Mahmud
- 1Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Kamrun Nahar
- 4Department of Gynecology and Obstetrics, Mymensingh Medical College, Mymensingh, Bangladesh
| | | | - Nobumichi Kobayashi
- 2Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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22
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Levy PY, Fournier PE, Fenollar F, Raoult D. Systematic PCR detection in culture-negative osteoarticular infections. Am J Med 2013; 126:1143.e25-33. [PMID: 24135511 DOI: 10.1016/j.amjmed.2013.04.027] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/29/2013] [Accepted: 04/30/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Identification of microorganisms is crucial for the successful treatment of osteoarticular infections. Molecular methods are more sensitive than culture-dependent methods but may suffer from lack of specificity. METHODS We studied a large series of 3840 bone and joint culture-negative samples collected from 2308 patients hospitalized in Marseille University Hospitals from November 2007 to October 2009. The samples were systematically cultured for 15 days, and conventional broad-range polymerase chain reaction (PCR) (16S rDNA and 18S rDNA) as well as real-time PCR assays targeting human Bglobin, Staphylococcus aureus, and Kingella kingae were realized on one culture-negative specimen. RESULTS Specimens from 741 patients (32.1%) tested positive by culture, including 38 in which bacteria grew only after 6 days of incubation. PCR was positive in 141 (9%) culture-negative specimens. Microorganisms identified by PCR were classified into 2 groups: fastidious bacteria (n = 35), mostly anaerobes in adult patients, and K. kingae in children; and nonfastidious bacteria (n = 106), mostly S. aureus (32.7%). A discrepancy between a positive PCR result for S. aureus and a negative culture were explained by previous antibiotherapy in 31.4% of cases. Our study highlights the usefulness of systematic 16S rDNA gene PCR for the diagnosis of bone and joint infections in culture-negative patients, thus enabling the administration of specific antibiotic treatments. CONCLUSIONS We recommend the use of conventional broad-range PCR for culture-negative bone and joint specimens, as well as S. aureus-specific PCR for adults and K. kingae-specific PCR for children. 18S rDNA PCR should be reserved only for specific cases.
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Affiliation(s)
- Pierre-Yves Levy
- Faculté de Médecine, Aix-Marseille Université, Marseille, France
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23
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Fournier PE, Drancourt M, Colson P, Rolain JM, Scola BL, Raoult D. Modern clinical microbiology: new challenges and solutions. Nat Rev Microbiol 2013; 11:574-85. [PMID: 24020074 PMCID: PMC7097238 DOI: 10.1038/nrmicro3068] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
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