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Labid A, Benouagueni S, Mehainaoui A, Gacemi Kirane D, Touati A. Antimicrobial Resistance Among Gram-Negative Bacteria Isolated in the Newborn Intensive Care Unit at ABDERREZAK-BOUHARA Hospital of Skikda, Algeria. Microb Drug Resist 2023. [PMID: 36812465 DOI: 10.1089/mdr.2022.0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Background: This study aimed to determine the epidemiology of gram-negative bacteria (GNB) isolated in the newborn intensive care unit (NICU) population, to assess their antibiotic susceptibility patterns and possible associated risk factors. Methods: All neonates admitted to the NICU of ABDERREZAK-BOUHARA hospital (Skikda, Algeria) with a clinical diagnosis of neonatal infections from March to May 2019 were included in the study. The extended-spectrum β-lactamase (ESBLs), plasmidic cephalosporinase (pAmpC), and carbapenemases genes were screened by polymerase chain reaction (PCR) and sequencing. PCR amplification of oprD among carbapenem-resistant Pseudomonas aeruginosa isolates was also performed. The clonal relatedness of the ESBLs isolates was studied using multilocus sequence typing (MLST). Results: Among 148 clinical specimens, 36 (24.3%) GNB strains were isolated from urine (n = 22), wound (n = 8), stool (n = 3), and blood (n = 3) samples. The bacterial species identified were Escherichia coli (n = 13), Klebsiella pneumoniae (n = 5), Enterobacter cloacae (n = 3), Serratia marcescens (n = 3), Salmonella spp. (n = 3), Proteus mirabilis (n = 1), P. aeruginosa (n = 5), and Acinetobacter baumannii (n = 3). PCR and sequencing showed that eleven Enterobacterales isolates harbored the blaCTX-M-15 gene, two E. coli isolates harbored the blaCMY-2 gene, and three A. baumannii isolates harbored both blaOXA-23 and blaOXA-51 genes. Also, five strains of P. aeruginosa were found to harbor mutations in the oprD gene. MLST showed that the K. pneumoniae strains belonged to ST13 and ST189, E. coli belonged to ST69, and E. cloacae belonged to ST214. Different risk factors that could predict positive GNB cultures were found, including female sex, Apgar score <8 at 5 min of life, enteral nutrition, antibiotic use, and extended length of hospitalization. Conclusion: Our study highlights the importance of determining the epidemiology of pathogens causing neonatal infections, their sequence types (ST), and their antibiotic susceptibility patterns to address rapidly a correct antibiotic treatment regimen.
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Affiliation(s)
- Asma Labid
- Research Laboratory of Interactions, Biodiversity, Ecosystems, and Biotechnology, Department of Nature and Life Sciences, University 20 August 1955, Skikda, Algeria
| | - Sarah Benouagueni
- Department of Biochemistry, Badji Mokhtar University, Annaba, Algeria
| | - Aida Mehainaoui
- Department of Biochemistry, Badji Mokhtar University, Annaba, Algeria
| | | | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
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Nabti LZ, Sahli F, Olowo-Okere A, Benslama A, Harrar A, Lupande-Mwenebitu D, Diene SM, Rolain JM. Molecular Characterization of Clinical Carbapenem-Resistant Enterobacteriaceae Isolates from Sétif, Algeria. Microb Drug Resist 2021; 28:274-279. [PMID: 34860598 DOI: 10.1089/mdr.2021.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study aimed to determine the incidence and the molecular mechanisms of carbapenem-resistant Enterobacteriaceae in patients from the Sétif University Hospital, Algeria. Nonduplicate clinical bacterial isolates recovered from patients attending the University Hospital of Sétif were collected between April and October 2018. Species identification was performed by MALDI-TOF/MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) method. The susceptibility of the isolates to carbapenems was determined using the disc diffusion method. The carbapenem resistant isolates were screened for the presence of common carbapenemase genes (blaKPC, blaOXA-48, blaVIM, blaIMP, and blaNDM) and extended-spectrum β-lactamase (blaCTX, blaTEM, and blaSHV) using PCR and sequencing technique. A total of 123 nonrepetitive Enterobacteriaceae isolates were obtained. Klebsiella pneumoniae (n = 52/42.28%), Escherichia coli (n = 24/19.51%), and Enterobacter cloacae (n = 19/15.45%) were the most prevalent species. The Carba-NP test showed that 6 out of 123 isolates carried carbapenemase enzymes. OXA-48 was found in five isolates (four K. pneumoniae and one E. coli) and NDM-5 in one E. cloacae isolate. We reported for the first time in Algeria the presence of NDM-5 carbapenemase enzyme in a clinical E. cloacae isolate.
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Affiliation(s)
- Larbi Zakaria Nabti
- Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria.,Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) de Sétif, Sétif, Algérie.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Farida Sahli
- Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) de Sétif, Sétif, Algérie
| | - Ahmed Olowo-Okere
- Department of Pharmaceutical Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Abderrahim Benslama
- Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria
| | - Abdenassar Harrar
- Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria
| | - David Lupande-Mwenebitu
- Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Seydina M Diene
- Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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Giraud-Gatineau A, Texier G, Fournier PE, Raoult D, Chaudet H. Using MALDI-TOF spectra in epidemiological surveillance for the detection of bacterial subgroups with a possible epidemic potential. BMC Infect Dis 2021; 21:1109. [PMID: 34711189 PMCID: PMC8554970 DOI: 10.1186/s12879-021-06803-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background For the purpose of epidemiological surveillance, the Hospital University Institute Méditerranée infection has implemented since 2013 a system named MIDaS, based on the systematic collection of routine activity materials, including MALDI-TOF spectra, and results. The objective of this paper is to present the pipeline we use for processing MALDI-TOF spectra during epidemiological surveillance in order to disclose proteinic cues that may suggest the existence of epidemic processes in complement of incidence surveillance. It is illustrated by the analysis of an alarm observed for Streptococcus pneumoniae. Methods The MALDI-TOF spectra analysis process looks for the existence of clusters of spectra characterized by a double time and proteinic close proximity. This process relies on several specific methods aiming at contrasting and clustering the spectra, presenting graphically the results for an easy epidemiological interpretation, and for determining the discriminating spectra peaks with their possible identification using reference databases. Results The use of this pipeline in the case of an alarm issued for Streptococcus pneumoniae has made it possible to reveal a cluster of spectra with close proteinic and temporal distances, characterized by the presence of three discriminant peaks (5228.8, 5917.8, and 8974.3 m/z) and the absence of peak 4996.9 m/z. A further investigation on UniProt KB showed that peak 5228.8 is possibly an OxaA protein and that the absent peak may be a transposase. Conclusion This example shows this pipeline may support a quasi-real time identification and characterization of clusters that provide essential information on a potentially epidemic situation. It brings valuable information for epidemiological sensemaking and for deciding on the continuation of the epidemiological investigation, in particular the involving of additional costly resources to confirm or invalidate the alarm. Clinical trials registration NCT03626987. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06803-3.
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Affiliation(s)
- Audrey Giraud-Gatineau
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Gaetan Texier
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France
| | - Pierre-Edouard Fournier
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - Hervé Chaudet
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France. .,Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France.
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Watthanaworawit W, Roberts T, Hopkins J, Gassiep I, Norton R, Robinson MT, Silisouk J, Sar P, Sao S, Amornchai P, Limmathurotsakul D, Wuthiekanun V, Nosten F, Simpson AJH, Turner P, Ling CL. A multi-country study using MALDI-TOF mass spectrometry for rapid identification of Burkholderia pseudomallei. BMC Microbiol 2021; 21:213. [PMID: 34266382 PMCID: PMC8283998 DOI: 10.1186/s12866-021-02276-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Background Burkholderia pseudomallei is the bacterial causative agent of melioidosis, a difficult disease to diagnose clinically with high mortality if not appropriately treated. Definitive diagnosis requires isolation and identification of the organism. With the increased adoption of MALDI-TOF MS for the identification of bacteria, we established a method for rapid identification of B. pseudomallei using the Vitek MS, a system that does not currently have B. pseudomallei in its in-vitro diagnostic database. Results A routine direct spotting method was employed to create spectra and SuperSpectra. An initial B. pseudomallei SuperSpectrum was created at Shoklo Malaria Research Unit (SMRU) from 17 reference isolates (46 spectra). When tested, this initial SMRU SuperSpectrum was able to identify 98.2 % (54/55) of Asian isolates, but just 46.7 % (35/75) of Australian isolates. Using spectra (430) from different reference and clinical isolates, two additional SMRU SuperSpectra were created. Using the combination of all SMRU SuperSpectra with seven existing SuperSpectra from Townsville, Australia 119 (100 %) Asian isolates and 31 (100 %) Australian isolates were correctly identified. In addition, no misidentifications were obtained when using these 11 SuperSpectra when tested with 34 isolates of other bacteria including the closely related species Burkholderia thailandensis and Burkholderia cepacia. Conclusions This study has established a method for identification of B. pseudomallei using Vitek MS, and highlights the impact of geographical differences between strains for identification using this technique. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02276-1.
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Affiliation(s)
- Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Gassiep
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Robert Norton
- Pathology, Townsville Hospital, Townsville, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Matthew T Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joy Silisouk
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sena Sao
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Premjit Amornchai
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J H Simpson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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5
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Fang L, Xu H, Ren X, Li X, Ma X, Zhou H, Hong G, Liang X. Epidemiology and Risk Factors for Carbapenem-Resistant Klebsiella Pneumoniae and Subsequent MALDI-TOF MS as a Tool to Cluster KPC-2-Producing Klebsiella Pneumoniae, a Retrospective Study. Front Cell Infect Microbiol 2020; 10:462. [PMID: 33042858 PMCID: PMC7521130 DOI: 10.3389/fcimb.2020.00462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/28/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) appeared recently and now presents a particularly critical problem to hospitalized patients worldwide. We aim to investigate the epidemiology and the risk factors for CRKP colonization and infections, and to evaluate the application performance of MALDI-TOF MS in clustering CRKP. Results: CRKP colonization and infections incidence was 2.7 (35/1,319,427) per 100,000 patient-days. Inpatients in CRKP group had higher medical expense than CSKP group. Inpatients with underlying conditions, particularly with pulmonary diseases, and with antimicrobial use prior to culture within 30 days, especially with carbapenem use, were risk factors for CRKP acquisition. All CRKP isolates were detected producing KPC-2. The MALDI-TOF MS system and PFGE system provided similar results, with a good concordance between the two methods (adjusted Rand's coefficient, 0.846) and a high probability of MALDI-TOF MS to predict PFGE results (Wallace coefficient, 0.908). Conclusions: Underlying conditions, particularly pulmonary diseases, and antimicrobial use prior to culture within 30 days, especially carbapenem use, are risk factors for CRKP acquisition. BlaKPC−2 is the mainstream gene of CRKP in our geographic area of analysis. As only simple sample preparation is needed and the results can be obtained in a short time, MALDI-TOF MS may be considered a probable alternative to PFGE in clustering KPC-2-producing CRKP.
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Affiliation(s)
- Lili Fang
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Heping Xu
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xiaoying Ren
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xun Li
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xiaobo Ma
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Guolin Hong
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xianming Liang
- Center of Clinical Laboratory, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China.,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
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López-Ramos I, Hernández M, Rodríguez-Lázaro D, Gutiérrez MP, Zarzosa P, Orduña A, March GA. Quick identification and epidemiological characterization of Francisella tularensis by MALDI-TOF mass spectrometry. J Microbiol Methods 2020; 177:106055. [PMID: 32918935 DOI: 10.1016/j.mimet.2020.106055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Currently, Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is being evaluated for its efficacy as a fast bacterial typing tool due to its great speed compared to other molecular methods. In this study, we evaluated MALDI-TOF as a tool for quick identification and typing of Francisella tularensis. MATERIALS AND METHODS This study encompassed 86 strains from two different geographical origins (Spain and the Czech Republic), which were previously characterised by Pulsed-Field Gel Electrophoresis (PFGE) and Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA). The direct colony method was used for microbial identification. High-quality spectra of the 86 strains were obtained and their main spectra profiles (MSPs) were created for epidemiological typing using MALDI-TOF. Based on the MSPs, principal components were generated and a dendrogram was constructed. An in-house MALDI-TOF library entry was created for each group of PFGE and MLVA strains based on their high-quality spectra. Two dendrograms were obtained using these entries and the unique peaks in each entry were searched. RESULTS All strains were correctly identified to the species level. No clear divisions were found in the 86-strain dendrogram; however, Spanish and Czech strains appeared separately in dendrograms created using MLVA and PFGE entries. Entries from our in-house MALDI-TOF library revealed 2-4 biomarker peaks for the detection of the five PFGE groups and 1-12 biomarker peaks for the detection of the seven MLVA groups. Finally, two and one specific biomarkers were found in the Czech and Spanish strains, respectively. CONCLUSION MALDI-TOF can be used to accurately identify F. tularensis strains in less than 15 min. Moreover, data on geographical origin and PFGE and MLVA groups could be obtained in less than one hour after colony growing.
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Affiliation(s)
- Irene López-Ramos
- Servicio de Análisis Clínicos, Departamento de Microbiología, Complejo Asistencial Universitario de Palencia, Avenida Donantes de Sangre s/n, 34005 Palencia, Spain.
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain; Área de Microbiología, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - David Rodríguez-Lázaro
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, 47071 Valladolid, Spain; Área de Microbiología, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - María P Gutiérrez
- Área de Microbiología, Facultad de Medicina, Av. Ramón y Cajal, s/n, 47003 Valladolid, Spain
| | - Pilar Zarzosa
- Área de Microbiología, Facultad de Medicina, Av. Ramón y Cajal, s/n, 47003 Valladolid, Spain
| | - Antonio Orduña
- Área de Microbiología, Facultad de Medicina, Av. Ramón y Cajal, s/n, 47003 Valladolid, Spain; Servicio de Microbiología e Inmunología, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 3, 47003 Valladolid, Spain
| | - Gabriel A March
- Servicio de Microbiología e Inmunología, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 3, 47003 Valladolid, Spain
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Giraud-Gatineau A, Texier G, Garnotel E, Raoult D, Chaudet H. Insights Into Subspecies Discrimination Potentiality From Bacteria MALDI-TOF Mass Spectra by Using Data Mining and Diversity Studies. Front Microbiol 2020; 11:1931. [PMID: 32903575 PMCID: PMC7438549 DOI: 10.3389/fmicb.2020.01931] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/22/2020] [Indexed: 12/25/2022] Open
Abstract
Bacterial identification at subspecies level is critical in clinical care and epidemiological investigations due to the different epidemic potentialities of a species. For this purpose, matrix-assisted laser desorption ionization – time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed in place of molecular genotyping, but with some result discrepancies. The aim of this work is to methodically mine the expression diversities of MALDI-TOF bacterial species spectra and their possible latent organization in order to evaluate their subspecies specific expression. Peak expression diversities of MALDI-TOF spectra coming from routine identifications have been analyzed using Hill numbers, rarefaction curves, and peak clustering. Some size effect critical thresholds were estimated using change point analyses. We included 167,528 spectra corresponding to 405 species. Species spectra diversities have a broad size-dependent variability, which may be influenced by the kind of sampling. Peak organization is characterized by the presence of a main cluster made of the most frequently co-occurring peaks and around 20 secondary clusters grouping less frequently co-occurring peaks. The 35 most represented species in our sample are distributed in two groups depending on the focusing of their protein synthesis activity on the main cluster or not. Our results may advocate some analogy with genomics studies of bacteria, with a main species-related cluster of co-occurring peaks and several secondary clusters, which may host peaks able to discriminate bacterial subgroups. This systematic study of the expression diversities of MALDI-TOF spectra shows that latent organization of co-occurring peaks supports subspecies discrimination and may explain why studies on MALDI-TOF-based typing exhibit some result divergences.
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Affiliation(s)
- Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
| | - Gaetan Texier
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France
| | - Eric Garnotel
- Hôpital d'Instruction des Armées Laveran, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
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Angeletti S, Ciccozzi M. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiology: An updating review. INFECTION GENETICS AND EVOLUTION 2019; 76:104063. [DOI: 10.1016/j.meegid.2019.104063] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/29/2019] [Accepted: 10/05/2019] [Indexed: 12/17/2022]
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Casanova C, Lo Priore E, Egli A, Seth-Smith HMB, Räber L, Ott D, Pflüger V, Droz S, Marschall J, Sommerstein R. Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing. Antimicrob Resist Infect Control 2019; 8:171. [PMID: 31700617 PMCID: PMC6829841 DOI: 10.1186/s13756-019-0619-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/01/2019] [Indexed: 11/10/2022] Open
Abstract
Background A number of episodes of nosocomial Agrobacterium spp. bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation. Methods Cases of Agrobacterium spp. bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates. Results We describe a total of eight bacteremia episodes due to A. radiobacter (n = 2), Agrobacterium genomovar G3 (n = 5) and A. pusense (n = 1). Two tight clusters were observed by WGS typing, representing the two A. radiobacter isolates (cluster I, isolated in 2015) and four of the Agrobacterium genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering. Conclusions We report clinical and epidemiological characteristics of two outbreak clusters with Agrobacterium. spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.
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Affiliation(s)
- Carlo Casanova
- 1Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
| | - Elia Lo Priore
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3001 Bern, Switzerland
| | - Adrian Egli
- 3Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.,4Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Helena M B Seth-Smith
- 3Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.,4Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Lorenz Räber
- Department of Cardiology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Daniel Ott
- Department of Radiology, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Sara Droz
- 1Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3001 Bern, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3001 Bern, Switzerland
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10
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Izdebski R, Baraniak A, Zabicka D, Sekowska A, Gospodarek-Komkowska E, Hryniewicz W, Gniadkowski M. VIM/IMP carbapenemase-producing Enterobacteriaceae in Poland: epidemic Enterobacter hormaechei and Klebsiella oxytoca lineages. J Antimicrob Chemother 2019; 73:2675-2681. [PMID: 29986025 DOI: 10.1093/jac/dky257] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/06/2018] [Indexed: 12/23/2022] Open
Abstract
Objectives To analyse VIM/IMP-type MBL-producing Enterobacteriaceae isolates identified in Poland during 2006-12. Methods Isolates were typed by PFGE, followed by MLST. blaVIM/IMP genes were amplified and sequenced within class 1 integrons. Their plasmidic versus chromosomal location was assessed by nuclease S1 and I-CeuI plus hybridization experiments. Plasmids were characterized by transfer assays and PCR-based replicon typing. Results One hundred and nineteen VIM/IMP-positive Enterobacteriaceae cases were reported in Poland from the first case in 2006 until 2012. The patients were in 54 hospitals and were infected or colonized by 121 organisms, including Enterobacter cloacae complex (n = 64), Klebsiella oxytoca (n = 23), Serratia marcescens (n = 20) and Klebsiella pneumoniae (n = 11). The isolates represented numerous pulsotypes and mainly original STs, and carried eight integrons with blaVIM-1-like genes (blaVIM-1/-4/-28/-37/-40; n = 101), three with blaVIM-2 variants (blaVIM-2/-20; n = 17) and one with blaIMP-19 (n = 3). Six integrons were new, and five and two formed prevalent families of In238-like (n = 96) and In1008-like (n = 16) elements, respectively. In238 (aacA4-blaVIM-4rpt) and In1008 (blaVIM-2-aacA4) had been originally observed in Polish Pseudomonas aeruginosa, suggestive of their transfer to enterobacteria, followed by spread and diversification. Four organisms have disseminated inter-regionally, i.e. Enterobacter hormaechei ST90 with plasmidic In238/In238a integrons (n = 36), K. oxytoca ST145 with a chromosomal In237-like element (n = 18) and two subclones of E. hormaechei ST89 with In1008- or In238-type variants (n = 8 and n = 7, respectively). Conclusions The epidemiology of VIM/IMP-producing Enterobacteriaceae in Poland has revealed a remarkable number of specific or novel characteristics of the organisms, with some possible links to other mid-southern European countries.
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Affiliation(s)
- R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - D Zabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - A Sekowska
- Department of Microbiology, Nicolas Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - E Gospodarek-Komkowska
- Department of Microbiology, Nicolas Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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Davin-Regli A, Lavigne JP, Pagès JM. Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin Microbiol Rev 2019; 32:e00002-19. [PMID: 31315895 PMCID: PMC6750132 DOI: 10.1128/cmr.00002-19] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.
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Affiliation(s)
- Anne Davin-Regli
- INSERM, SSA, IRBA, MCT, Aix Marseille University, Marseille, France
| | - Jean-Philippe Lavigne
- Department of Microbiology, U1047, INSERM, University Montpellier and University Hospital Nîmes, Nîmes, France
| | - Jean-Marie Pagès
- INSERM, SSA, IRBA, MCT, Aix Marseille University, Marseille, France
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12
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Boudjemaa H, Allem R, Fonkou MDM, Zouagui S, Khennouchi NCEH, Kerkoud M. Molecular drivers of emerging multidrug resistance in Proteus mirabilis clinical isolates from Algeria. J Glob Antimicrob Resist 2019; 18:249-256. [PMID: 30797091 DOI: 10.1016/j.jgar.2019.01.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/04/2019] [Accepted: 01/26/2019] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVES The aim of this study was to characterise the molecular drivers of multidrug resistance in Proteus mirabilis isolated from Algerian community and hospital patients. METHODS A total of 166 P. mirabilis isolates were collected from two hospitals and eight private laboratories from four cities (Khemis Miliana, Aïn Defla, Oran and Chlef) located in northwestern Algeria. All isolates were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antimicrobial susceptibility testing was performed by the disk diffusion and Etest methods. Genes encoding AmpC β-lactamases, extended-spectrum β-lactamases (ESBLs), quinolone resistance and aminoglycoside-modifying enzymes (AMEs) as well as plasmid replicon typing were characterised by PCR. Clonal relationships were also determined by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) typing and were compared with MALDI-TOF/MS proteomic typing. RESULTS Of the 166 P. mirabilis isolates, 14 (8.4%) exhibited resistance to important antibiotics, including amoxicillin, amoxicillin/clavulanic acid, cefotaxime, gentamicin and ciprofloxacin, of which 4/14 (28.6%) had an ESBL genotype (blaCTX-M-2) and 10 (71.4%) had an AmpC/ESBL genotype (blaCMY-2/blaTEM-1). AME genes were detected in all isolates, including ant(2'')-I, aac(3)-I, aac(6')-Ib-cr and aac(3)-IV. The qnrA gene was identified in 13 isolates (7.8%). ERIC-PCR showed one predominant clone, with eight blaCMY-2-producing isolates from UHC Oran belonging to profile A clustering together in the MALDI-TOF/MS dendrogram. CONCLUSION Here we report the first description of AME and plasmid-mediated quinolone resistance genes among ESBL- and/or AmpC β-lactamase-producing P. mirabilis isolates from community- and hospital-acquired infections in northwestern Algeria.
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Affiliation(s)
- Hadjer Boudjemaa
- Laboratory of Natural Bioresources, Department of Biology, Faculty of Natural Sciences and Life, University of Hassiba Benbouali Chlef, Box 151, 02000 Chlef, AlgeriaAlgeria.
| | - Rachida Allem
- Laboratory of Natural Bioresources, Department of Biology, Faculty of Natural Sciences and Life, University of Hassiba Benbouali Chlef, Box 151, 02000 Chlef, AlgeriaAlgeria
| | - Maxime Descartes Mbogning Fonkou
- MEPHI, UMR, IRD, Aix-Marseille Université, Marseille, France; INSERM U1095, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Souad Zouagui
- Laboratoire Central de Microbiologie du CHU d'Oran, 76 boulevard docteur Benzerdjeb (Ex Plateau), Oran, Algeria
| | - Nour Chems El Houda Khennouchi
- Laboratoire de Microbiologie et Biochimie Appliquée, Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algeria
| | - Mohamed Kerkoud
- Laboratory of Natural Bioresources, Department of Biology, Faculty of Natural Sciences and Life, University of Hassiba Benbouali Chlef, Box 151, 02000 Chlef, AlgeriaAlgeria; Laboratoire de diag-gene, 8 rue lenotre, Angers, France
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13
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Rödel J, Mellmann A, Stein C, Alexi M, Kipp F, Edel B, Dawczynski K, Brandt C, Seidel L, Pfister W, Löffler B, Straube E. Use of MALDI-TOF mass spectrometry to detect nosocomial outbreaks of Serratia marcescens and Citrobacter freundii. Eur J Clin Microbiol Infect Dis 2019; 38:581-591. [PMID: 30680577 DOI: 10.1007/s10096-018-03462-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/26/2018] [Indexed: 12/13/2022]
Abstract
MALDI-TOF mass spectrometry (MS) may be used as a rapid typing method for nosocomial pathogens. Here, we evaluated MALDI-TOF MS for discrimination of hospital outbreak-related clusters of Serratia marcescens and carbapenemase-producing Citrobacter freundii. Thirty-three S. marcescens isolates collected from neonatal intensive care unit (NICU) patients, and 23 C. freundii isolates including VIM-positive isolates from a hospital colonization outbreak were measured by Vitek MS. Consensus spectra of each isolate were clustered using SARAMIS software. Genotyping was performed by whole-genome sequencing (WGS). First, a set of 21 S. marcescens isolates from 2014 with seven genotypes including three monoclonal clusters was used for the evaluation of MALDI-TOF typing. MS clustering was largely in agreement with genotyping results when the similarity cut-off for clonal identity was set on 90%. MALDI-TOF cluster analysis was then investigated for the surveillance of S. marcescens in the NICU in 2017 and demonstrated the introduction of new strains into the hospital and nosocomial transmissions. MS analysis of the C. freundii outbreak in 2016 revealed a monoclonal cluster of VIM-positive isolates and the separation of epidemiologically non-related VIM-positive and negative isolates. Two additional VIM-positive Citrobacter isolates from food samples were closely related to the large monoclonal cluster. WGS confirmed the MS results. MALDI-TOF MS may be used as a first-line typing tool for S. marcescens and C. freundii to detect transmission events in the hospital because isolates of an identical WGS type were grouped into the same MS cluster.
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Affiliation(s)
- Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany.
| | | | - Claudia Stein
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Monika Alexi
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Frank Kipp
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Birgit Edel
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Kristin Dawczynski
- Unit Neonatology, Department of Paediatrics, Jena University Hospital, Jena, Germany
| | - Christian Brandt
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | | | - Wolfgang Pfister
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Eberhard Straube
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
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14
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond. Clin Microbiol Rev 2018; 32:32/1/e00037-18. [PMID: 30487165 DOI: 10.1128/cmr.00037-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied in recent years for first-line identification of pathogens in clinical microbiology because it is simple to use, rapid, and accurate and has economic benefits in hospital management. The range of clinical applications of MALDI-TOF MS for bacterial isolates is increasing constantly, from species identification to the two most promising applications in the near future: detection of antimicrobial resistance and strain typing for epidemiological studies. The aim of this review is to outline the contribution of previous MALDI-TOF MS studies in relation to detection of antimicrobial resistance and to discuss potential future challenges in this field. Three main approaches are ready (or almost ready) for clinical use, including the detection of antibiotic modifications due to the enzymatic activity of bacteria, the detection of antimicrobial resistance by analysis of the peak patterns of bacteria or mass peak profiles, and the detection of resistance by semiquantification of bacterial growth in the presence of a given antibiotic. This review provides an expert guide for MALDI-TOF MS users to new approaches in the field of antimicrobial resistance detection, especially possible applications as a routine diagnostic tool in microbiology laboratories.
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15
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Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains. BMC Microbiol 2018; 18:175. [PMID: 30466389 PMCID: PMC6251167 DOI: 10.1186/s12866-018-1325-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The antimicrobial resistance (AMR) phenotypic properties, multiple drug resistance (MDR) gene profiles, and genes related to potential virulence and pathogenic properties of five Enterobacter bugandensis strains isolated from the International Space Station (ISS) were carried out and compared with genomes of three clinical strains. Whole genome sequences of ISS strains were characterized using the hybrid de novo assembly of Nanopore and Illumina reads. In addition to traditional microbial taxonomic approaches, multilocus sequence typing (MLST) analysis was performed to classify the phylogenetic lineage. Agar diffusion discs assay was performed to test antibiotics susceptibility. The draft genomes after assembly and scaffolding were annotated with the Rapid Annotations using Subsystems Technology and RNAmmer servers for downstream analysis. RESULTS Molecular phylogeny and whole genome analysis of the ISS strains with all publicly available Enterobacter genomes revealed that ISS strains were E. bugandensis and similar to the type strain EB-247T and two clinical isolates (153_ECLO and MBRL 1077). Comparative genomic analyses of all eight E. bungandensis strains showed, a total of 4733 genes were associated with carbohydrate metabolism (635 genes), amino acid and derivatives (496 genes), protein metabolism (291 genes), cofactors, vitamins, prosthetic groups, pigments (275 genes), membrane transport (247 genes), and RNA metabolism (239 genes). In addition, 112 genes identified in the ISS strains were involved in virulence, disease, and defense. Genes associated with resistance to antibiotics and toxic compounds, including the MDR tripartite system were also identified in the ISS strains. A multiple antibiotic resistance (MAR) locus or MAR operon encoding MarA, MarB, MarC, and MarR, which regulate more than 60 genes, including upregulation of drug efflux systems that have been reported in Escherichia coli K12, was also observed in the ISS strains. CONCLUSION Given the MDR results for these ISS Enterobacter genomes and increased chance of pathogenicity (PathogenFinder algorithm with > 79% probability), these species pose important health considerations for future missions. Thorough genomic characterization of the strains isolated from ISS can help to understand the pathogenic potential, and inform future missions, but analyzing them in in-vivo systems is required to discern the influence of microgravity on their pathogenicity.
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Fournier PE, Drancourt M, Raoult D. New Laboratory Tools for Emerging Bacterial Challenges. Clin Infect Dis 2018; 65:S39-S49. [PMID: 28859351 DOI: 10.1093/cid/cix405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since its creation, the Méditerranée-Infection foundation has aimed at optimizing the management of infectious diseases and surveying the local and global epidemiology. This pivotal role was permitted by the development of rational sampling, point-of-care tests, and extended automation as well as new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and the development of versatile and permissive culture systems. By identifying and characterizing emerging microbial pathogens, these developments provided significant breakthroughs in infectious diseases.
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Affiliation(s)
- Pierre-Edouard Fournier
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Michel Drancourt
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
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Dandachi I, Sokhn ES, Dahdouh EA, Azar E, El-Bazzal B, Rolain JM, Daoud Z. Prevalence and Characterization of Multi-Drug-Resistant Gram-Negative Bacilli Isolated From Lebanese Poultry: A Nationwide Study. Front Microbiol 2018; 9:550. [PMID: 29628921 PMCID: PMC5876231 DOI: 10.3389/fmicb.2018.00550] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Currently, antimicrobial resistance is one of the most prominent public health issues. In fact, there is increasing evidence that animals constitute a reservoir of antimicrobial resistance. In collaboration with the Lebanese Ministry of Agriculture, the aim of this study was to determine the prevalence of intestinal carriage of multi-drug-resistant Gram-negative Bacilli in poultry farms at the national level. Between August and December 2015, 981 fecal swabs were obtained from 49 poultry farms distributed across Lebanon. The swabs were subcultured on MacConkey agar supplemented with cefotaxime (2 μg/ml). Isolated strains were identified using MALDI-TOF mass spectrometry. Multilocus sequence typing analysis was performed for Escherichia coli. Phenotypic detection of extended spectrum β-lactamases (ESBL) and AmpC production was performed using double disk synergy and the ampC disk test, respectively. β-lactamase encoding genes blaCTX-M, blaTEM, blaSHV, blaFOX, blaMOX, blaEBC, blaACC, blaDHA, and blaCMY using PCR amplification. Out of 981 fecal swabs obtained, 203 (20.6%) showed bacterial growth on the selective medium. Of the 235 strains isolated, 217 were identified as E. coli (92%), eight as Klebsiella pneumoniae (3%), three as Proteus mirabilis (1%) and three as Enterobacter cloacae (1%). MLST analysis of E. coli isolates showed the presence of ST156, ST5470, ST354, ST155, and ST3224. The phenotypic tests revealed that 43.5, 28.5, and 20.5% of the strains were ampC, ESBL, and ampC/ESBL producers, respectively. The putative TEM gene was detected in 83% of the isolates, SHV in 20%, CTX-M in 53% and CMY ampC β-lactamase gene in 65%. Our study showed that chicken farms in Lebanon are reservoirs of ESBL and AmpC producing Gram-negative bacilli. The level of antibiotic consumption in the Lebanese veterinary medicine should be evaluated. Future studies should focus on the risk factors associated with the acquisition of multi-drug-resistant organisms in farm animals in Lebanon.
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Affiliation(s)
- Iman Dandachi
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon.,IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Elie S Sokhn
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Elias A Dahdouh
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Eid Azar
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | | | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Ziad Daoud
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
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Chen HM, Zheng PX, Wang LR, Wu JJ, Yan JJ. Multilocus sequence typing of carbapenemase-producing Enterobacter cloacae bloodstream isolates between 2002 and 2013 in a Taiwanese university hospital. J Glob Antimicrob Resist 2017; 9:135-137. [PMID: 28576741 DOI: 10.1016/j.jgar.2017.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/14/2017] [Accepted: 05/21/2017] [Indexed: 11/29/2022] Open
Affiliation(s)
- Hung-Mo Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Po-Xing Zheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Li-Rong Wang
- Center for Infection Control, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Jing-Jou Yan
- Department of Pathology, Cheng Ching Hospital, Taichung, Taiwan; Department of Pathology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Raclavsky V, Stromerova N, Safarova D, Bardon J, Zatloukal J, Zapalka M, Jakubec P, Navratilova L, Novotny R. McRAPD unlike MALDI-TOF MS is a suitable candidate for routine discrimination of new Haemophilus influenzae strain acquisition in chronic obstructive pulmonary disease (COPD) and cystic fibrosis. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2016; 160:503-511. [PMID: 27752148 DOI: 10.5507/bp.2016.050] [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: 01/22/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND AND AIMS Haemophilus influenzae new strain acquisition has been demonstrated to increase the relative risk of acute exacerbation fourfold in contrast to colonisation or chronic infection by the same strain in chronic obstructive pulmonary disease (COPD). Unfortunately, molecular typing techniques are not suitable for routine use due to cost, labour-intensity and need for special expertise. We tested two techniques potentially useful for routine typing, namely the newly available MALDI-TOF MS and the modified McRAPD compared to MLST as the gold standard. METHODS In 10 patients (10.8%) suffering from COPD or cystic fibrosis, H. influenzae isolates were recovered repeatedly at different timepoints from the same patient during the study period. This allowed for thirteen pairwise comparisons of typing results in isolates recovered consecutively from the same patient to test the ability of the techniques to uncover new strain acquisition. RESULTS MLST detected 9 cases of new strain acquisition among the 13 pairwise comparisons. However, MALDI-TOF MS reported all 13 pairs as different and thus new. In contrast, McRAPD was able to differentiate all the new strain acquisitions from pre-existing ones, both by visual inspection of melting profiles and by Relative Significant Difference values. CONCLUSIONS Unlike MALDI-TOF MS, McRAPD appears to be a suitable candidate for routine discrimination of new strain acquisitions because of its accuracy and, rapid, easy and economic performance.
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Affiliation(s)
- Vladislav Raclavsky
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | | | - Dana Safarova
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University Olomouc, Czech Republic
| | - Jan Bardon
- State Veterinary Institute Olomouc, Czech Republic
| | - Jaromir Zatloukal
- Department of Respiratory Medicine, University Hospital Olomouc, Czech Republic
| | - Martin Zapalka
- Department of Pediatrics, University Hospital Olomouc, Czech Republic
| | - Petr Jakubec
- Department of Respiratory Medicine, University Hospital Olomouc, Czech Republic
| | - Lucie Navratilova
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Radko Novotny
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
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Cimmino T, Le Page S, Raoult D, Rolain JM. Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease. Expert Rev Mol Diagn 2016; 16:1163-1175. [PMID: 27690721 DOI: 10.1080/14737159.2016.1244005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.
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Affiliation(s)
- Teresa Cimmino
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Stéphanie Le Page
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Didier Raoult
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Jean-Marc Rolain
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
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Ayad A, Drissi M, de Curraize C, Dupont C, Hartmann A, Solanas S, Siebor E, Amoureux L, Neuwirth C. Occurence of ArmA and RmtB Aminoglycoside Resistance 16S rRNA Methylases in Extended-Spectrum β-Lactamases Producing Escherichia coli in Algerian Hospitals. Front Microbiol 2016; 7:1409. [PMID: 27672380 PMCID: PMC5018485 DOI: 10.3389/fmicb.2016.01409] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/25/2016] [Indexed: 01/14/2023] Open
Abstract
The aim of this study, was to characterize the extended-spectrum-β-lactamases (ESBLs) producing clinical strains of Escherichia coli isolated between January 2009 and June 2012 from Algerian hospitals and to determine the prevalence of 16S rRNA methylase among them. Sixty-seven ESBL-producers were detected among the 239 isolates included: 52 CTX-M-15-producers, 5 CTX-M-3-producers, 5 CTX-M-1-producers, 2 CTX-M-14-producers, 2 SHV-12-producers and one TEM-167-producer. Among the ESBL–producing strains twelve harbored 16S rRNA methylase genes: 8 rmtB and 4 armA. rmtB was located on a IncFIA plasmid and armA was located either on a IncL/M or a IncFIA plasmid. RmtB-producing isolates were genotypically related and belonged to the sequence type ST 405 whereas ArmA-producing isolates belonged to ST10, ST 167, and ST 117. This first description of 16S rRNA methylases among E. coli in Algerian hospitals pointed out the necessity to establish control measures to avoid their dissemination.
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Affiliation(s)
- Amel Ayad
- Laboratoire de Bactériologie Médicale, Plateau Technique de Biologie, Centre Hospitalier Universitaire de Dijon, DijonFrance; Laboratoire Antibiotiques, Antifongiques: Physico-chimie, Synthèse et Activité Biologique, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre et de l'Univers, Université Abou Bekr Belkaid, TlemcenAlgérie; Département de Biologie, Faculté des Sciences de la Nature et de la Vie, Université Hassiba Benbouali, ChlefAlgérie
| | - Mourad Drissi
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre et de l'Univers, Université Abou Bekr Belkaid, Tlemcen Algérie
| | - Claire de Curraize
- Laboratoire de Bactériologie Médicale, Plateau Technique de Biologie, Centre Hospitalier Universitaire de Dijon, Dijon France
| | - Chloé Dupont
- UMR 5569, Equipe "Pathogénes hydriques, Santé, Environnements" PHySE, Université de Montpellier France
| | | | | | - Eliane Siebor
- Laboratoire de Bactériologie Médicale, Plateau Technique de Biologie, Centre Hospitalier Universitaire de Dijon, Dijon France
| | - Lucie Amoureux
- Laboratoire de Bactériologie Médicale, Plateau Technique de Biologie, Centre Hospitalier Universitaire de Dijon, Dijon France
| | - Catherine Neuwirth
- Laboratoire de Bactériologie Médicale, Plateau Technique de Biologie, Centre Hospitalier Universitaire de Dijon, Dijon France
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Fan L, Ke M, Yuan M, Pu J, Li J, Lu J, Xu J, Zhang M, Xu W. Rapid determination of bacterial aminoglycoside resistance in environmental samples using membrane electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30 Suppl 1:202-207. [PMID: 27539439 DOI: 10.1002/rcm.7648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RATIONALE Antibiotic resistance in pathogenic bacteria is becoming a global public health problem, such as aminoglycoside resistance encoded by the armA gene. Although many methods have been reported, rapid analysis of environmental samples is still challenging. METHOD A rapid analytical method was developed in this study to determine bacterial aminoglycoside resistance using membrane electrospray ionization mass spectrometry (MESI-MS). Precursor/product-ion pairs of ArmA unique peptides were detected with minimal sample preparation. Standard peptides were synthesized and used for developing and validating the methodology, and then the method was verified by both ArmA positive and ArmA negative simulated environmental samples. RESULTS A rapid method for determination of bacterial aminoglycoside resistance was developed using MESI-MS/MS. The bacterial cultural time was optimized to 2 hours, and the precision, accuracy and recovery of this method were investigated. The peptide IHSSTNER (IR-8) unique to ArmA in simulated environmental samples can be successfully identified within 3 hours. CONCLUSIONS The novel assay offered a rapid method to determine bacterial aminoglycoside resistance with high sensitivity, accuracy and precision in simulated environmental samples. This method could also be applied to identify other drug-resistance proteins in clinical/environmental samples. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Liusheng Fan
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ming Ke
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Min Yuan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Juan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jinxing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Mei Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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Bardou M, Honnorat E, Dubourg G, Couderc C, Fournier PE, Seng P, Stein A. Meningitis caused by Pasteurella multocida in a dog owner without a dog bite: clonal lineage identification by MALDI-TOF mass spectrometry. BMC Res Notes 2015; 8:626. [PMID: 26521235 PMCID: PMC4628311 DOI: 10.1186/s13104-015-1615-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022] Open
Abstract
Background Pasteurella multocida meningitis in an immunocompetent patient is rare and commonly occurs after animal bite. To our knowledge, only 48 cases have been reported in the literature since 1989. P. multocida meningitis is commonly linked to animal contagion. Here we report on a new case of P. multocida meningitis in an immunocompetent patient who is a dog owner without a dog bite. We used the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry to investigate the clonal lineage between animal and human isolates. Case presentation In our case, a 25-year-old immunocompetent French Caucasian woman with nothing notable in her medical history was admitted for meningitis caused by P. multocida. Clonal lineage of P. multocida strains from cerebrospinal fluid and blood culture and her dog’s oral cavity has been recognized by MALDI-TOF mass spectrometry dendrograms and clustering of the 21 P. multocida isolates in our centres. She was treated by a combination of intravenous ceftriaxone (2 g/day) and oral levofloxacin (1 g/day). She was discharged on the 6th day of admission. The antimicrobial therapy was conducted for 15 days. The dog was treated by clavulanic-acid amoxicillin for 3 weeks by the veterinarian. The evolution of the patient at the 5th month after the end of the antimicrobial therapy was normal without any neurological after-effects. Conclusion The meningitis caused by P. multocida could be considered a cause of human meningitis in dog lovers without an animal bite. MALDI-TOF mass spectrometry should be considered as it is an accurate tool to identify clonal lineage between animal and human isolates.
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Affiliation(s)
- Matthieu Bardou
- Service de maladies infectieuses, Hôpital de la conception, Assistance publique-hôpitaux de marseille, 147, Boulevard baille, Marseille, France. .,Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France.
| | - Estelle Honnorat
- Service de maladies infectieuses, Hôpital de la conception, Assistance publique-hôpitaux de marseille, 147, Boulevard baille, Marseille, France. .,Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France.
| | - Gregory Dubourg
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France.
| | - Carine Couderc
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France.
| | - Pierre Edouard Fournier
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France.
| | - Piseth Seng
- Service de maladies infectieuses, Hôpital de la conception, Assistance publique-hôpitaux de marseille, 147, Boulevard baille, Marseille, France. .,Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France.
| | - Andreas Stein
- Service de maladies infectieuses, Hôpital de la conception, Assistance publique-hôpitaux de marseille, 147, Boulevard baille, Marseille, France. .,Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385, Marseille, France.
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