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Hamzaoui Z, Ferjani S, Medini I, Charaa L, Landolsi I, Ben Ali R, Khaled W, Chammam S, Abid S, Kanzari L, Ferjani A, Fakhfakh A, Kebaier D, Bouslah Z, Ben Sassi M, Trabelsi S, Boutiba-Ben Boubaker I. Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing. IJID Reg 2024; 11:100356. [PMID: 38655560 PMCID: PMC11035039 DOI: 10.1016/j.ijregi.2024.100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Objectives This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs). Methods SARS-CoV-2 genomic sequences and metadata from the EpiCoV database via the Global Initiative on Sharing All Influenza Data platform were analyzed. Data analysis included cases, deaths, demographics, patient status, sequencing technologies, and variant analysis. Results A comprehensive analysis of 10,783 viral genomic sequences from six North African countries revealed notable insights. SARS-CoV-2 sampling methods lack standardization, with a majority of countries lacking clear strategies. Over 59% of analyzed genomes lack essential clinical and demographic metadata, including patient age, sex, underlying health conditions, and clinical outcomes, which are essential for comprehensive genomic analysis and epidemiological studies, as submitted to the Global Initiative on Sharing All Influenza Data. Morocco reported the highest number of confirmed COVID-19 cases (1,272,490), whereas Tunisia leads in reported deaths (29,341), emphasizing regional variations in the pandemic's impact. The GRA clade emerged as predominant in North African countries. The lineage analysis showcased a diversity of 190 lineages in Egypt, 26 in Libya, 121 in Tunisia, 90 in Algeria, 146 in Morocco, and 10 in Mauritania. The temporal dynamics of SARS-CoV-2 variants revealed distinct waves driven by different variants. Conclusions This study contributes valuable insights into the genomic landscape of SARS-CoV-2 in North Africa, highlighting the importance of genomic surveillance in understanding viral dynamics and informing public health strategies.
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Affiliation(s)
- Zaineb Hamzaoui
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sana Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ines Medini
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Latifa Charaa
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ichrak Landolsi
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Roua Ben Ali
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Wissal Khaled
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Sarra Chammam
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Salma Abid
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Lamia Kanzari
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Asma Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ahmed Fakhfakh
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Dhouha Kebaier
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Zoubeir Bouslah
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Mouna Ben Sassi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Sameh Trabelsi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
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Haddad-Boubaker S, Arbi M, Souiai O, Chouikha A, Fares W, Edington K, Sims S, Camma C, Lorusso A, Diagne MM, Diallo A, Boubaker IBB, Ferjani S, Mastouri M, Mhalla S, Karray H, Gargouri S, Bahri O, Trabelsi A, Kallala O, Hannachi N, Chaabouni Y, Smaoui H, Meftah K, Bouhalila SB, Foughali S, Zribi M, Lamari A, Touzi H, Safer M, Alaya NB, Kahla AB, Gdoura M, Triki H. The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage. Front Public Health 2023; 10:990832. [PMID: 36684874 PMCID: PMC9846204 DOI: 10.3389/fpubh.2022.990832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction The Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated. Methods Viral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs. Results The age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country. Discussion This study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.
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Affiliation(s)
- Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Marwa Arbi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Wasfi Fares
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kate Edington
- New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom
| | - Sam Sims
- New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom
| | - Cesare Camma
- Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy
| | - Alessio Lorusso
- Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy
| | | | - Amadou Diallo
- Department of Virology, Pasteur Institute of Dakar, Dakar, Senegal
| | - Ilhem Boutiba Ben Boubaker
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
- Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Sana Ferjani
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
- Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Maha Mastouri
- Laboratory of Microbiology, Fattouma Bourguiba Hospital, Monastir, Tunisia
- Laboratory Research Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Salma Mhalla
- Laboratory of Microbiology, Fattouma Bourguiba Hospital, Monastir, Tunisia
- Laboratory Research Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Hela Karray
- Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Saba Gargouri
- Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Olfa Bahri
- Laboratory of Microbiology and Biochemistry, Aziza Othmana Hospital, Tunis, Tunisia
| | | | - Ouafa Kallala
- Laboratory of Virology, Sahloul Hospital of Sousse, Sousse, Tunisia
| | - Naila Hannachi
- Laboratory of Microbiology, Farhat Hached Hospital of Sousse, Sousse, Tunisia
| | - Yassine Chaabouni
- Laboratory of Medical Biology, Ibn El Jazzar Hospital, Kairouan, Tunisia
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanen Smaoui
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Khaoula Meftah
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Sophia Besbes Bouhalila
- Laboratory of Medical Biology and Blood Bank, Institute Mohamed Kassab d'orthopédie, Manouba, Tunisia
| | - Soumaya Foughali
- Laboratory of Medical Biology, Menzel Bourguiba Hospital, Bizerte, Tunisia
| | - Mariem Zribi
- Laboratory of Microbiology, La Rabta Hospital, Tunis, Tunisia
| | - Asma Lamari
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mouna Safer
- National Observatory of New and Emergent Diseases, Tunis, Tunisia
| | - Nissaf Ben Alaya
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- National Observatory of New and Emergent Diseases, Tunis, Tunisia
| | - Alia Ben Kahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Virology, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
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Ferjani S, Maamar E, Ferjani A, Meftah K, Battikh H, Mnif B, Hamdoun M, Chebbi Y, Kanzari L, Achour W, Bahri O, Hammami A, Zribi M, Smaoui H, Boubaker IBB. Tunisian Multicenter Study on the Prevalence of Colistin Resistance in Clinical Isolates of Gram Negative Bacilli: Emergence of Escherichia coli Harbouring the mcr-1 Gene. Antibiotics (Basel) 2022; 11:antibiotics11101390. [PMID: 36290048 PMCID: PMC9598684 DOI: 10.3390/antibiotics11101390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/12/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Actually, no data on the prevalence of plasmid colistin resistance in Tunisia are available among clinical bacteria. Objectives: This study aimed to investigate the current epidemiology of colistin resistance and the spread of the mcr gene in clinical Gram-negative bacteria (GNB) isolated from six Tunisian university hospitals. Methods: A total of 836 GNB strains were inoculated on COL-R agar plates with selective screening agar for the isolation of GNB resistant to colistin. For the selected isolates, mcr genes, beta-lactamases associated-resistance genes and molecular characterisation were screened by PCRs and sequencing. Results: Colistin-resistance was detected in 5.02% (42/836) of the isolates and colistin-resistant isolates harboured an ESBL (blaCTX-M-15) and/or a carbapenemase (blaOXA-48, blaVIM) encoding gene in 45.2% of the cases. The mcr-1 gene was detected in four E. coli isolates (0.59%) causing urinary tract infections and all these isolates also contained the blaTEM-1 gene. The blaCTX-M-15 gene was detected in three isolates that also carried the IncY and IncFIB replicons. The genetic environment surrounding the mcr-carrying plasmid indicated the presence of pap-2 gene upstream mcr-1 resistance marker with unusual missing of ISApl1 insertion sequence. The Conclusions: This study reports the first description of the mcr-1 gene among clinical E. coli isolates in Tunisia and provides an incentive to conduct routine colistin susceptibility testing in GNB clinical isolates.
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Affiliation(s)
- Sana Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis Rue Djebal Lakhdar 1006, Tunisia
- Correspondence: ; Tel.: +216-515-47301
| | - Elaa Maamar
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis Rue Djebal Lakhdar 1006, Tunisia
| | - Asma Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis Rue Djebal Lakhdar 1006, Tunisia
- Charles Nicolle Hospital, Laboratory of Microbiology, Boulevard 9 April, Tunis 1006, Tunisia
| | - Khaoula Meftah
- Laboratory of Microbiology, Children’s Hospital of Tunis, Boulevard 9 April, Tunis 1006, Tunisia
| | - Hager Battikh
- Microbiology Laboratory, Rabta University Hospital, Rue Jabbari, Tunis 1007, Tunisia
| | - Besma Mnif
- Laboratory of Microbiology, Habib Bourguiba University Hospital, Route de l’Ain, Sfax 3000, Tunisia
- Research Laboratory for Microorganisms and Human Disease, University of Sfax, Avenue Majida Boulila, Sfax 3029, Tunisia
| | - Manel Hamdoun
- Aziza Othmana Hospital, Laboratoire de Microbiologie-Biochimie, Bab Menara Tunis 1008, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR16SP01, Tunis Rue Djebal Lakhdar 1006, Tunisia
| | - Yosra Chebbi
- National Bone Marrow Transplant Center, Laboratory Ward, Tunis Rue Djebal Lakhdar 1006, Tunisia
- Faculty of Medicine of Tunis, Tunis El Manar University, LR18ES39, Tunis Rue Djebal Lakhdar 1006, Tunisia
| | - Lamia Kanzari
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis Rue Djebal Lakhdar 1006, Tunisia
- Charles Nicolle Hospital, Laboratory of Microbiology, Boulevard 9 April, Tunis 1006, Tunisia
| | - Wafa Achour
- National Bone Marrow Transplant Center, Laboratory Ward, Tunis Rue Djebal Lakhdar 1006, Tunisia
- Faculty of Medicine of Tunis, Tunis El Manar University, LR18ES39, Tunis Rue Djebal Lakhdar 1006, Tunisia
| | - Olfa Bahri
- Aziza Othmana Hospital, Laboratoire de Microbiologie-Biochimie, Bab Menara Tunis 1008, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR16SP01, Tunis Rue Djebal Lakhdar 1006, Tunisia
| | - Adenene Hammami
- Laboratory of Microbiology, Habib Bourguiba University Hospital, Route de l’Ain, Sfax 3000, Tunisia
- Research Laboratory for Microorganisms and Human Disease, University of Sfax, Avenue Majida Boulila, Sfax 3029, Tunisia
| | - Meriam Zribi
- Microbiology Laboratory, Rabta University Hospital, Rue Jabbari, Tunis 1007, Tunisia
| | - Hanen Smaoui
- Laboratory of Microbiology, Children’s Hospital of Tunis, Boulevard 9 April, Tunis 1006, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis Rue Djebal Lakhdar 1006, Tunisia
- Charles Nicolle Hospital, Laboratory of Microbiology, Boulevard 9 April, Tunis 1006, Tunisia
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Ferjani S, Kanzari L, Maamar E, Hamzaoui Z, Rehaiem A, Ferjani A, Boutiba-Ben Boubaker I. Extensively drug-resistant Acinetobacter baumannii co-producing VIM-2 and OXA-23 in intensive care units: Results of a one-day point prevalence in a Tunisian hospital. Infect Dis Now 2022; 52:426-431. [DOI: 10.1016/j.idnow.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022]
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Harbaoui S, Ferjani S, Abbassi M, Saidani M, Gargueh T, Ferjani M, Hammi Y, Boutiba‐Ben Boubaker I. Genetic heterogeneity and predominance of
bla
CTX‐M
‐15
in cefotaxime‐resistant
Enterobacteriaceae
isolates colonizing hospitalized children in Tunisia. Lett Appl Microbiol 2022; 75:1460-1474. [DOI: 10.1111/lam.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Affiliation(s)
- S. Harbaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - S. Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - M.S. Abbassi
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie Tunis Tunisie
| | - M. Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
| | - T. Gargueh
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - M. Ferjani
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - Y. Hammi
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - I. Boutiba‐Ben Boubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
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Sassi MB, Ferjani S, Mkada I, Arbi M, Safer M, Elmoussi A, Abid S, Souiai O, Gharbi A, Tejouri A, Gaies E, Eljabri H, Ayed S, Hechaichi A, Daghfous R, Gouider R, Khelil JB, Kharrat M, Kacem I, Alya NB, Benkahla A, Trabelsi S, Boubaker IBB. Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia. Infection, Genetics and Evolution 2022; 102:105300. [PMID: 35552003 PMCID: PMC9085353 DOI: 10.1016/j.meegid.2022.105300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022]
Abstract
Since the beginning of the Coronavirus disease-2019 pandemic, there has been a growing interest in exploring SARS-CoV-2 genetic variation to understand the origin and spread of the pandemic, improve diagnostic methods and develop the appropriate vaccines. The objective of this study was to identify the SARS-CoV-2s lineages circulating in Tunisia and to explore their amino acid signature in order to follow their genome dynamics. Whole genome sequencing and genetic analyses of fifty-eight SARS-CoV-2 samples collected during one-year between March 2020 and March 2021 from the National Influenza Center were performed using three sampling strategies.. Multiple lineage introductions were noted during the initial phase of the pandemic, including B.4, B.1.1, B.1.428.2, B.1.540 and B.1.1.189. Subsequently, lineages B1.160 (24.2%) and B1.177 (22.4%) were dominant throughout the year. The Alpha variant (B.1.1.7 lineage) was identified in February 2021 and firstly observed in the center of our country. In addition, A clear diversity of lineages was observed in the North of the country. A total of 335 mutations including 10 deletions were found. The SARS-CoV-2 proteins ORF1ab, Spike, ORF3a, and Nucleocapsid were observed as mutation hotspots with a mutation frequency exceeding 20%. The 2 most frequent mutations, D614G in S protein and P314L in Nsp12 appeared simultaneously and are often associated with increased viral infectivity. Interestingly, deletions in coding regions causing consequent deletions of amino acids and frame shifts were identified in NSP3, NSP6, S, E, ORF7a, ORF8 and N proteins. These findings contribute to define the COVID-19 outbreak in Tunisia. Despite the country's limited resources, surveillance of SARS-CoV-2 genomic variation should be continued to control the occurrence of new variants.
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Affiliation(s)
- Mouna Ben Sassi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Sana Ferjani
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007 Tunis, Tunisia.
| | - Imen Mkada
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Mouna Safer
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Awatef Elmoussi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Salma Abid
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Alya Gharbi
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Asma Tejouri
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Emna Gaies
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Hanene Eljabri
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia
| | - Samia Ayed
- Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia; Abderrahmen Mami Hospital, Department of Medical Intensive Care, 2080 Ariana, Tunisia
| | - Aicha Hechaichi
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Riadh Daghfous
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Riadh Gouider
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Jalila Ben Khelil
- Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia; Abderrahmen Mami Hospital, Department of Medical Intensive Care, 2080 Ariana, Tunisia
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Imen Kacem
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Nissaf Ben Alya
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Sameh Trabelsi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007 Tunis, Tunisia
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7
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Ferjani S, Maamar E, Ferjani A, Kanzari L, Boubaker IBB. Evaluation of Three Carbapenemase-Phenotypic Detection Methods and Emergence of Diverse VIM and GES Variants among Pseudomonas aeruginosa Isolates in Tunisia. Antibiotics (Basel) 2022; 11:antibiotics11070858. [PMID: 35884112 PMCID: PMC9311584 DOI: 10.3390/antibiotics11070858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Since 2012, few reports on the molecular epidemiology of Pseudomonas aeruginosa were reported in Tunisia. Objectives: This study aimed to evaluate carbapenem-resistance determinants and molecular epidemiology and to compare the carbapenemase-phenotypic detection methods of multidrug-resistant P. aeruginosa isolates. Methods: During a period of four years (2014 to 2017), all imipenem-ceftazidime-resistant P. aeruginosa isolates were retrospectively selected at the microbial laboratory of Charles Nicolle hospital of Tunis. These isolates were examined by the modified Hodge test, modified carbapenem inactivation method (mCIM), and another mCIM, called CIMTris, and their performance was evaluated using PCR analysis as the gold standard. Results: A total of 35 isolates were recovered among patients hospitalized in different units. All strains were colistin-susceptible.All carbapenem-resistant isolates showed a high-level resistance to carbapenems. CIMTris and mCIM showed 96.15% and 46.15% sensitivity and 44.44% and 100% specificity, respectively, for detecting carbapenemase production.Conclusions: CIMTris is a promising approach for detecting carbapenemase activity in P. aeruginosa and merits further testing. Moreover, this study described the first detection of GES-5- and GES-9-producing P. aeruginosa in Tunisia as well as the co-occurrence of the blaGES-5 and blaVIM-11 carbapenemase genes in one isolate. These findings are of great concern because the rapid dissemination of MDR strains represents a major therapeutic and epidemiological threat.
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Affiliation(s)
- Sana Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis 1007, Tunisia; (E.M.); (A.F.); (L.K.); (I.B.B.B.)
- Correspondence: ; Tel.: +216-515-473-01
| | - Elaa Maamar
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis 1007, Tunisia; (E.M.); (A.F.); (L.K.); (I.B.B.B.)
| | - Asma Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis 1007, Tunisia; (E.M.); (A.F.); (L.K.); (I.B.B.B.)
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis 1006, Tunisia
| | - Lamia Kanzari
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis 1007, Tunisia; (E.M.); (A.F.); (L.K.); (I.B.B.B.)
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis 1006, Tunisia
| | - Ilhem Boutiba Ben Boubaker
- Faculty of Medicine of Tunis, University of Tunis El Manar, LR99ES09, Tunis 1007, Tunisia; (E.M.); (A.F.); (L.K.); (I.B.B.B.)
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis 1006, Tunisia
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8
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Miloud SB, Dziri O, Ferjani S, Ali MM, Mysara M, Boutiba I, Houdt RVAN, Chouchani C. First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia. Pol J Microbiol 2021; 70:161-174. [PMID: 34335797 PMCID: PMC8318066 DOI: 10.33073/pjm-2021-012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 01/11/2023] Open
Abstract
Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, Hg, and Cu), and antibiotics. In an initial screening, 80 isolates were selected on ampicillin, and 39 isolates, retained for further analysis, could grow on a Tris-buffered mineral medium with gluconate as carbon source. Isolates were identified based on their 16S rRNA gene sequence. Results showed the prevalence of antibiotic resistance genes, especially all isolates harbored the blaTEM gene. Some of them (15.38%) harbored blaSHV. Moreover, several were even ESBLs and MBLs-producers, which can threaten the human health. On the other hand, 92.30%, 56.41%, and 51.28% of the isolates harbored the heavy metals resistance genes silE, cusA, and merA, respectively. These genes confer resistance to silver, copper, and mercury. A cross-resistance between antibiotics and heavy metals was detected in 97.43% of our isolates.
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Affiliation(s)
- Samar Ben Miloud
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia.,Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Olfa Dziri
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia
| | - Sana Ferjani
- Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Muntasir Md Ali
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ilhem Boutiba
- Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Rob VAN Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Chedly Chouchani
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia
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9
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Abid S, Ferjani S, El Moussi A, Ferjani A, Nasr M, Landolsi I, Saidi K, Gharbi H, Letaief H, Hechaichi A, Safer M, Ben Alaya NBE, Boubaker IBB. Assessment of sample pooling for SARS-CoV-2 molecular testing for screening of asymptomatic persons in Tunisia. Diagn Microbiol Infect Dis 2020; 98:115125. [PMID: 32768876 PMCID: PMC7335417 DOI: 10.1016/j.diagmicrobio.2020.115125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/03/2022]
Abstract
The aim of this study is to test a pooling approach for the RT-PCR test to detect low viral loads of SARS-CoV-2. We found that a single positive specimen can still be detected in pools of up to 10. Each laboratory should conduct its own evaluation and validation of pooling protocols according to its specific context.
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Affiliation(s)
- Salma Abid
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia.
| | - Awatef El Moussi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Asma Ferjani
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Mejda Nasr
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Ichrak Landolsi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Karima Saidi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hanène Gharbi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hajer Letaief
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Aicha Hechaichi
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Mouna Safer
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | | | - Ilhem Boutiba-Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
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10
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Ferjani S, Sassi I, Saidani M, Mhiri E, Ghariani A, Boutiba Ben Boubaker I, Slim L, Amine S. Polymorphism of ftsI gene in Haemophilus influenzae and emergence of cefotaxime resistance in two Tunisian hospitals. New Microbes New Infect 2020; 36:100690. [PMID: 32489667 PMCID: PMC7262452 DOI: 10.1016/j.nmni.2020.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 03/19/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
The decreased affinity to β-lactams in Haemophilus influenzae is usually caused by specific alterations in penicillin-binding protein 3 due to varieties of substitutions in ftsI gene. This study aimed to characterize the polymorphism of ftsI gene in 19 H. influenzae strains, isolated between 2014 and 2016 (different resistance phenotypes to β-lactams (n = 9) and susceptible strains (n = 10) used for comparative purposes). All strains were characterized for capsular type by PCR and agglutination tests and for β-lactam resistance by amplification and sequencing of ftsI. Biotyping and clonality were performed by API-NH and pulsed-field gel electrophoresis, respectively. Four strains were β-lactamase-negative ampicillin-resistant and five were β-lactamase-positive clavulanic-acid-resistant. One strain from each group was resistant to cefotaxime. Our isolates belonged mainly to biotype IV and I and were non-typeable and genetically unrelated. According to mutation profiles of their ftsI, strains were classified as group I (n = 3), group II (n = 4), group–III–like (n = 1) and group III (n = 1). All group II strains were further classified as subgroup IIb, except for one strain, which harboured a new mutation (N422I). Ampicillin MICs of β-lactamase-negative ampicillin-resistant strains were 6 to 12 times the MICs of susceptible strains. Only blaTEM-1 was detected in β-lactamase-positive clavulanic-acid-resistant strains, and was responsible for high MICs for ampicillin (>256 mg/L), whatever the ftsI mutational resistance group. The emergence of cefotaxime-resistant isolates in our country is a matter of concern and requires strict surveillance and rationalization of antibiotic use to preserve these molecules.
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Affiliation(s)
- S Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Laboratory of Research 'Resistance to Antimicrobial Agents, Tunis, Tunisia
| | - I Sassi
- Charles Nicolle Hospital, Laboratory of Microbiology, Tunis, Tunisia
| | - M Saidani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Laboratory of Research 'Resistance to Antimicrobial Agents, Tunis, Tunisia.,Charles Nicolle Hospital, Laboratory of Microbiology, Tunis, Tunisia
| | - E Mhiri
- Abderrahmen Mami Hospital, Laboratory of Microbiology, Ariana, Tunisia
| | - A Ghariani
- Abderrahmen Mami Hospital, Laboratory of Microbiology, Ariana, Tunisia
| | - I Boutiba Ben Boubaker
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Laboratory of Research 'Resistance to Antimicrobial Agents, Tunis, Tunisia.,Charles Nicolle Hospital, Laboratory of Microbiology, Tunis, Tunisia
| | - L Slim
- Abderrahmen Mami Hospital, Laboratory of Microbiology, Ariana, Tunisia
| | - S Amine
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Laboratory of Research 'Resistance to Antimicrobial Agents, Tunis, Tunisia.,Charles Nicolle Hospital, Laboratory of Microbiology, Tunis, Tunisia
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11
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Kilani H, Ferjani S, Mansouri R, Boutiba-Benboubaker I, Abbassi MS. Occurrence of plasmid-mediated quinolone resistance determinants among Escherichia coli strains isolated from animals in Tunisia: Specific pathovars acquired qnr genes. J Glob Antimicrob Resist 2019; 20:50-55. [PMID: 31365855 DOI: 10.1016/j.jgar.2019.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES The aim of this study was to characterise Escherichia coli strains harbouring plasmid-mediated quinolone resistance (PMQR) genes recovered from various samples (n = 116) from healthy and diarrhoeic animals in Tunisia. METHODS All nalidixic acid-resistant E. coli isolates were screened for the presence of PMQR genes. Isolates positive for PMQR genes were investigated by PCR for chromosomal mutations in the quinolone resistance-determining regions (QRDRs) of GyrA and ParC, the presence of class 1 and class 2 integrons, genes encoding tetracycline and sulfonamide resistance, genes encoding virulence factors, and phylogenetic group. Genetic relationships was determined by pulsed-field gel electrophoresis (PFGE). RESULTS Amongst 51 nalidixic acid-resistant isolates, 9 harboured PMQR genes (5 co-harbouredqnrS1 and qnrB1, 3 harboured qnrS1 and 1 harboured qnrB1). Two types of mutation in the QRDR of GyrA were observed: S83L and D87N (eight isolates) and S83L (one isolate). For the QRDR of ParC, the substitution S80I was observed in four isolates. A class 1 integron was found in six isolates. The tetA or tetB gene was observed in six isolates and both tetA and tetB were co-harboured by two isolates. The sul1, sul2 and sul3 genes were detected in six, four and one isolates, respectively. According to the presence of specific virulence genes, the nine strains were classified as UPEC (5), EAEC (3) and EPEC (1). Three isolates from turkey faeces were clonally related by PFGE. CONCLUSION These findings highlight the plausible role of the avian industry as a reservoir of human pathogenic E. coli strains.
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Affiliation(s)
- Hajer Kilani
- Université de Tunis El Manar, Institut de la Recherché Vétérinaire de Tunisie, Tunis 1006, Tunisia; Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Recherche 'Résistance aux Antimicrobiens', Tunis 1007, Tunisia
| | - Sana Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Recherche 'Résistance aux Antimicrobiens', Tunis 1007, Tunisia
| | - Riadh Mansouri
- Université de Tunis El Manar, Institut de la Recherché Vétérinaire de Tunisie, Tunis 1006, Tunisia
| | - Ilhem Boutiba-Benboubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Recherche 'Résistance aux Antimicrobiens', Tunis 1007, Tunisia; Hôpital Charles Nicolle, Service de Microbiologie, Tunis 1006, Tunisia
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherché Vétérinaire de Tunisie, Tunis 1006, Tunisia; Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Recherche 'Résistance aux Antimicrobiens', Tunis 1007, Tunisia.
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12
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Hamzaoui Z, Ocampo-Sosa A, Maamar E, Fernandez Martinez M, Ferjani S, Hammami S, Harbaoui S, Genel N, Arlet G, Saidani M, Slim A, Boutiba-Ben Boubaker I, Martinez-Martinez L. An Outbreak of NDM-1-ProducingKlebsiella pneumoniae, Associated with OmpK35 and OmpK36 Porin Loss in Tunisia. Microb Drug Resist 2018; 24:1137-1147. [DOI: 10.1089/mdr.2017.0165] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Zaineb Hamzaoui
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
- Faculty of Sciences of Bizerte, University of Carthage, Tunis, Tunisia
| | - Alain Ocampo-Sosa
- Service of Microbiology, University Hospital Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Elaa Maamar
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
| | | | - Sana Ferjani
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
- Faculty of Sciences of Bizerte, University of Carthage, Tunis, Tunisia
| | - Samia Hammami
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
- Faculty of Sciences of Bizerte, University of Carthage, Tunis, Tunisia
| | - Sarra Harbaoui
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
| | - Nathalie Genel
- Department of Bacteriology, Medical School, University Pierre et Marie Curie, Paris, France
| | - Guillaume Arlet
- Department of Bacteriology, Medical School, University Pierre et Marie Curie, Paris, France
| | - Mabrouka Saidani
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Amine Slim
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Faculty of Medicine of Tunis—LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Luis Martinez-Martinez
- Service of Microbiology, University Hospital Marqués de Valdecilla-IDIVAL, Santander, Spain
- Department of Molecular Biology, School of Medicine, University of Cantabria, Santander, Spain
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13
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Ferjani S, Saidani M, Maamar E, Harbaoui S, Hamzaoui Z, Hosni H, Amine FS, Boubaker IBB. Escherichia coli colonizing healthy children in Tunisia: High prevalence of extra-intestinal pathovar and occurrence of non-extended-spectrum-β-lactamase-producing ST131 clone. Int J Antimicrob Agents 2018; 52:878-885. [PMID: 30036576 DOI: 10.1016/j.ijantimicag.2018.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 11/16/2022]
Abstract
This study was performed to investigate the distribution of antimicrobial resistance genes and extra-intestinal virulence determinants in a collection of 98 Escherichia coli strains isolated from rectal swabs of healthy children. Forty-six isolated strains were resistant to at least one of the tested antibiotics (usually active against enterobacteria). They were mainly resistant to ampicillin and ticarcillin (42.97%), tetracyclin (26.5%), and trimethoprim/sulfamethoxazole (18.4%). No resistance to the third generation of cephalosporins, carbapenems, aminoglycosides and colistin was found. Resistance to penicillins was encoded by blaTEM-1 (n=34) and blaSHV-1 genes (n=4). Tetracyclin resistance was encoded by tetB (n=12), tetA (n= 5), and tetC (n=1) genes. Amongst resistant quinolones isolated (n=5), chromosomal mutations in gyrA and parC genes were detected in four isolates and qnrS1 gene in two strains. Nine plasmid replicon types were detected; IncFIB (n=36) and IncI1 (n=7) were the most frequent ones. Isolates frequently belonged to phylogenetic groups A (51.1%) and D (27.5%). Extra-intestinal pathovar (n=38) occurred mainly in B2 phylogroup (P=0.0002). Amongst them, two isolates (non-extended-spectrum-β-lactamase (ESBL)-producers) belonged to the pandemic clone ST131. A significant distribution of virulence determinants and pathogenicity island marker was observed within strains belonging to B2 and D phylogroups. Interestingly, our results showed that ExPEC strains, including ST131 pandemic clone, are present within fecal isolates in healthy children. These findings highlight the importance of intestinal microbiota as a reservoir for virulent and resistant strains. Thus, reinforcing hand hygiene and antibiotic rational use is imperative to avoid the diffusion of these pathogens in the community.
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Affiliation(s)
- Sana Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche «Résistance aux antimicrobiens» 1007, Tunis, Tunisia.
| | - Mabrouka Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche «Résistance aux antimicrobiens» 1007, Tunis, Tunisia; CHU Charles Nicolle, Service de Microbiologie, 1006, Tunis, Tunisia
| | - Elaa Maamar
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche «Résistance aux antimicrobiens» 1007, Tunis, Tunisia
| | - Sarra Harbaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche «Résistance aux antimicrobiens» 1007, Tunis, Tunisia
| | - Zeineb Hamzaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche «Résistance aux antimicrobiens» 1007, Tunis, Tunisia
| | - Houda Hosni
- CHU Charles Nicolle, Service de Microbiologie, 1006, Tunis, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche «Résistance aux antimicrobiens» 1007, Tunis, Tunisia; CHU Charles Nicolle, Service de Microbiologie, 1006, Tunis, Tunisia
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Kanzari L, Ferjani S, Saidani M, Hamzaoui Z, Jendoubi A, Harbaoui S, Ferjani A, Rehaiem A, Boutiba Ben Boubaker I, Slim A. First report of extensively-drug-resistant Proteus mirabilis isolate carrying plasmid-mediated bla NDM-1 in a Tunisian intensive care unit. Int J Antimicrob Agents 2018; 52:906-909. [PMID: 29958975 DOI: 10.1016/j.ijantimicag.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 05/15/2018] [Accepted: 06/16/2018] [Indexed: 10/28/2022]
Abstract
Emergence of the New Delhi metallo-β-lactamase (NDM-1), an Ambler class B metallo-β-lactamase able to hydrolyse all β-lactams except monobactams, constitutes a critical and increasingly important medical issue. The acquisition of blaNDM-1 is of particular concern for Proteus mirabilis, which is intrinsically resistant to tetracycline, tigecycline and colistin, as this will make clinical treatment extremely difficult. To the authors' knowledge, this is the first report of the blaNDM-1 gene in an extensively-drug-resistant P. mirabilis clinical isolate carrying plasmid-mediated resistance to carbapenems (blaNDM-1), cephalosporins (blaCMY-4), aminoglycosides (aph3 VIa and aph3 Ia) and fluoroquinolones (qnrA6).
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Affiliation(s)
- Lamia Kanzari
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie; Hôpital Charles Nicolle, Laboratoire de microbiologie, Tunis, Tunisie.
| | - Sana Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie
| | - Mabrouka Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie; Hôpital Charles Nicolle, Laboratoire de microbiologie, Tunis, Tunisie
| | - Zeineb Hamzaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie
| | - Ali Jendoubi
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie; Hôpital Charles Nicolle, Unité de réanimation médico-chirurgicale, Tunis, Tunisie
| | - Sarra Harbaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie
| | - Asma Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie; Hôpital Charles Nicolle, Laboratoire de microbiologie, Tunis, Tunisie
| | - Amel Rehaiem
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie; Hôpital Charles Nicolle, Laboratoire de microbiologie, Tunis, Tunisie
| | - Ilhem Boutiba Ben Boubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie; Hôpital Charles Nicolle, Laboratoire de microbiologie, Tunis, Tunisie
| | - Amine Slim
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de Recherche "Résistance aux antibiotiques" LR99ES09, 1007, Tunis, Tunisie; Hôpital Charles Nicolle, Laboratoire de microbiologie, Tunis, Tunisie
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15
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Maamar E, Alonso CA, Ferjani S, Jendoubi A, Hamzaoui Z, Jebri A, Saidani M, Ghedira S, Torres C, Boubaker IBB. NDM-1- and OXA-23-producing Acinetobacter baumannii isolated from intensive care unit patients in Tunisia. Int J Antimicrob Agents 2018; 52:910-915. [PMID: 29665444 DOI: 10.1016/j.ijantimicag.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/23/2018] [Accepted: 04/07/2018] [Indexed: 10/17/2022]
Abstract
Gastrointestinal colonisation by carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical step before nosocomial infection. This study evaluated CRAB intestinal carriage in patients admitted to a Tunisian ICU and determined the antimicrobial resistance mechanisms involved. From December 2014 to February 2015, all 63 patients admitted to the ICU were screened for rectal CRAB colonisation upon admission and once weekly thereafter. ICU patients who acquired a CRAB nosocomial infection were also included. β-Lactamases and associated resistance genes were screened by PCR sequencing, and molecular typing was performed by PFGE and MLST. The CRAB faecal carriage rate at admission was 4.8% (3/63). The CRAB acquisition rate during ICU stay was analysed in 39 of the remaining 60 patients and the rate of acquired CRAB faecal carriage was 15.4% (6/39); 4 patients also showed an ICU-acquired CRAB infection (one patient was a faecal carrier and suffered infection). Overall, 13 CRAB isolates were collected from 12 patients, of which 11 isolates showed resistance to all antibiotics tested except colistin. blaOXA-23 and blaNDM-1 were detected in 11 and 2 isolates, respectively. All OXA-23-producing strains carried armA, tetB, sul1 and catB, and some of them carried aph(3')-VIa, blaTEM-1, aph(3')-Ia and ant(2'')-Ia. The blaNDM-1-positive isolates harboured aph(3')-VIa and catB. Three PFGE patterns and two STs were identified [ST195 (n = 11), ST1089 (n = 2, NDM-1-positive)]. Whether imported or acquired during ICU stay, CRAB colonisation is a major risk factor for the occurrence of serious nosocomial infection. Systematic screening of faecal carriage is mandatory to prevent their spread.
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Affiliation(s)
- Elaa Maamar
- University of Tunis El Manar, Faculty of Medicine of Tunis-LR99ES09 Research Laboratory 'Antimicrobial resistance', 15 Rue Djebel Akhdhar, La Rabta, 1007 Tunis, Tunisia.
| | - Carla Andrea Alonso
- Universidad de La Rioja, Area de Bioquímica y Biología Molecular, Logroño, Spain
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis-LR99ES09 Research Laboratory 'Antimicrobial resistance', 15 Rue Djebel Akhdhar, La Rabta, 1007 Tunis, Tunisia
| | - Ali Jendoubi
- Charles Nicolle Hospital, Intensive Care Unit, 1006 Tunis, Tunisia
| | - Zaineb Hamzaoui
- University of Tunis El Manar, Faculty of Medicine of Tunis-LR99ES09 Research Laboratory 'Antimicrobial resistance', 15 Rue Djebel Akhdhar, La Rabta, 1007 Tunis, Tunisia
| | - Alia Jebri
- Charles Nicolle Hospital, Intensive Care Unit, 1006 Tunis, Tunisia
| | - Mabrouka Saidani
- University of Tunis El Manar, Faculty of Medicine of Tunis-LR99ES09 Research Laboratory 'Antimicrobial resistance', 15 Rue Djebel Akhdhar, La Rabta, 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
| | - Salma Ghedira
- Charles Nicolle Hospital, Intensive Care Unit, 1006 Tunis, Tunisia
| | - Carmen Torres
- Universidad de La Rioja, Area de Bioquímica y Biología Molecular, Logroño, Spain
| | - Ilhem Boutiba-Ben Boubaker
- University of Tunis El Manar, Faculty of Medicine of Tunis-LR99ES09 Research Laboratory 'Antimicrobial resistance', 15 Rue Djebel Akhdhar, La Rabta, 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
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16
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Hamzaoui Z, Ocampo-Sosa A, Fernandez Martinez M, Landolsi S, Ferjani S, Maamar E, Saidani M, Slim A, Martinez-Martinez L, Boutiba-Ben Boubaker I. Role of association of OmpK35 and OmpK36 alteration and bla ESBL and/or bla AmpC genes in conferring carbapenem resistance among non-carbapenemase-producing Klebsiella pneumoniae. Int J Antimicrob Agents 2018; 52:898-905. [PMID: 29621592 DOI: 10.1016/j.ijantimicag.2018.03.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/01/2018] [Accepted: 03/28/2018] [Indexed: 12/16/2022]
Abstract
In Klebsiella pneumoniae, loss of the two major outer membrane porins (OMPs) OmpK35 and OmpK36 confers resistance to carbapenems in strains producing extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC-type β-lactamases. This study investigated mechanisms responsible for carbapenem resistance in non-carbapenemase-producing K. pneumoniae (NCPK). All carbapenem-resistant Enterobacteriaceae (CRE) at Charles Nicolle Hospital (Tunis, Tunisia) were collected over a 6-year period (2010-2015). Among the 334 CRE strains collected, 44 (13.2%) were NCPK. MIC ranges for ertapenem, imipenem and meropenem were 1 to >32 mg/L, 0.125-8 mg/L and 0.125-32 mg/L, respectively. All strains showed a multidrug-resistant (MDR) phenotype and were negative for carbapenemase activity. None of the carbapenemase genes searched for were found. ESBL production was confirmed in all isolates except one [CTX-M-15 (n = 39) and SHV-5 (n = 4)]. Three isolates produce DHA-1 (associated with CTX-M-15 in two strains). Molecular fingerprints grouped the 44 NCPK isolates into seven clusters. In seven representative strains of these clusters, SDS-PAGE results showed that four isolates lacked the OmpK35 porin, one isolate lacked OmpK36 and two isolates lacked both OmpK35 and OmpK36. Sequencing of the corresponding porin genes showed amino acid insertions and deletions leading to early termination of translation, point mutations in the promoter region, or insertion sequences disrupting the gene coding sequence. Loss or deficiency of OMPs, coupled with ESBL and/or AmpC production, plays an important role in conferring carbapenem resistance in K. pneumoniae. Dissemination of these MDR bacteria in our hospital may create serious therapeutic problems in the future.
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Affiliation(s)
- Zaineb Hamzaoui
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisia.
| | - Alain Ocampo-Sosa
- Service of Microbiology, University Hospital Marqués de Valdecilla-IDIVAL, Santander 39008, Spain
| | - Marta Fernandez Martinez
- Service of Microbiology, University Hospital Marqués de Valdecilla-IDIVAL, Santander 39008, Spain
| | - Sarrah Landolsi
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisia
| | - Elaa Maamar
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia
| | - Mabrouka Saidani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
| | - Amine Slim
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
| | - Luis Martinez-Martinez
- Clinical Unit of Microbiology, University Hospital Reina Sofía, Córdoba, Spain; Department of Microbiology, University of Córdoba, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Ilhem Boutiba-Ben Boubaker
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
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Maamar E, Alonso CA, Hamzaoui Z, Dakhli N, Abbassi MS, Ferjani S, Saidani M, Boutiba-Ben Boubaker I, Torres C. Emergence of plasmid-mediated colistin-resistance in CMY-2-producing Escherichia coli of lineage ST2197 in a Tunisian poultry farm. Int J Food Microbiol 2018; 269:60-63. [PMID: 29421359 DOI: 10.1016/j.ijfoodmicro.2018.01.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 01/14/2023]
Abstract
Our study aimed to investigate colistin resistance and the mechanisms involved in a collection of 35 extended-spectrum beta-lactamase (ESBL) and 13 CMY-2-producing E. coli strains which were previously recovered from chicken gut microbiota in Tunisia, as well as to determine the genetic location of mcr genes. Forty-eight ESBL and CMY-2-producing E. coli strains were obtained from 137 fecal samples of healthy chickens during 2013. These strains were tested for colistin resistance by the broth microdilution method, and screened for mcr-1 and mcr-2 genes by PCR. Two of these strains were colistin-resistant (MIC = 8 mg/L). Both harbored the mcr-1 gene, were CMY-2 producers, and were additionally resistant to tetracycline, ciprofloxacin, chloramphenicol, gentamicin, tobramycin and trimethoprim-sulfamethoxazole. They shared phylogroup A, the same pulsed-field gel electrophoresis (PFGE)-pattern, and were typed as ST2197. In both strains, ISApl1 and pap2 were detected upstream and downstream of mcr-1 gene, respectively. The analysis of the two mcr-1-positive strains and their transconjugants by PCR-based replicon typing and S1-PFGE, demonstrated that mcr-1 gene is linked to an IncP plasmid (~242 kb), and blaCMY-2 to an IncI1 plasmid (97 kb). The occurrence of E. coli harboring mcr-1 gene among intestinal microbiota in poultry and its location on a conjugative plasmid could represent a risk for public health. The evolution of this type of resistant microorganisms should be evaluated in the future.
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Affiliation(s)
- Elaa Maamar
- University of Tunis El Manar, Faculty of Medicine of Tunis- LR99ES09 Research Laboratory «Antimicrobial resistance», 1007 Tunis, Tunisia.
| | - Carla Andrea Alonso
- Universidad de La Rioja, Area de Bioquímica y Biología Molecular, Logroño, Spain
| | - Zaineb Hamzaoui
- University of Tunis El Manar, Faculty of Medicine of Tunis- LR99ES09 Research Laboratory «Antimicrobial resistance», 1007 Tunis, Tunisia
| | - Nouha Dakhli
- University of Tunis El Manar, Faculty of Medicine of Tunis- LR99ES09 Research Laboratory «Antimicrobial resistance», 1007 Tunis, Tunisia
| | - Mohamed Salah Abbassi
- University of Tunis El Manar, Faculty of Medicine of Tunis- LR99ES09 Research Laboratory «Antimicrobial resistance», 1007 Tunis, Tunisia; University of Tunis El Manar, Institute of Veterinary Research of Tunisia-Laboratory of bacteriological research, Tunis, Tunisia
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis- LR99ES09 Research Laboratory «Antimicrobial resistance», 1007 Tunis, Tunisia
| | - Mabrouka Saidani
- University of Tunis El Manar, Faculty of Medicine of Tunis- LR99ES09 Research Laboratory «Antimicrobial resistance», 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- University of Tunis El Manar, Faculty of Medicine of Tunis- LR99ES09 Research Laboratory «Antimicrobial resistance», 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
| | - Carmen Torres
- Universidad de La Rioja, Area de Bioquímica y Biología Molecular, Logroño, Spain
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Ajmi H, Abid D, Milouchi S, Choura D, Louati D, Ferjani S, Chaaben K, Kammoun S. P6131Speckle tracking as an early detection parameter of subclinical cardiac dysfunction in pregnant women with hypertensive disorder. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx493.p6131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Kilani H, Abbassi MS, Ferjani S, Ben Salem R, Mansouri R, Ben Chehida N, Boutiba-Ben Boubaker I. Diverse Escherichia coli pathovars of phylogroups B2 and D isolated from animals in Tunisia. J Infect Dev Ctries 2017; 11:549-556. [DOI: 10.3855/jidc.8579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/06/2016] [Indexed: 10/31/2022] Open
Abstract
Introduction: The virulent Escherichia coli strains responsible for extraintestinal infections were mainly belonged to B2 and D phylogroups. However, no past studies have determinate via the presence of virulence genes the frequency of E. coli pathovars recovered from animals housed in farms in Tunisia. The aims of this study were to investigate 26 E. coli isolated from healthy and diarrheic animals and to determinate via the presence of virulence genes the frequency of pathovars.
Methodology: Twenty-six E. coli isolates of phylogroups B2 (n = 14), B22 (n = 9), B23 (n = 5), and D2 (n = 12) were characterized. Genes encoding virulence factors (fimH,eaeA,aggC,papC, papG allele III, hlyA, east1, cnf1, exhA,stx1, stx2, iutA, fyuA, ibeA,and ipaH), and antibiotic resistance as well as class 1 and 2 integrons were searched by polymerase chain reaction (PCR). The genetic relationship of isolates was done by PFGE.
Results: According to the occurrence of specific genes the 26 isolates were classified as:9 EAEC, 2 EHEC, 4 UPEC, 3 EPEC/EHEC and 1 NTEC. Therefore, 2 Ex-PEC and 5 APEC were presented amongst our strains. Some isolates (12) were clonal and the remaining was unrelated.
Conclusions: Higher diversity of pathovars which carried diverse combinations of virulence genes in healthy isolates. In addition, it seems that the infections were caused by different mechanisms.
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Maamar E, Ferjani S, Jendoubi A, Hammami S, Hamzaoui Z, Mayonnove-Coulange L, Saidani M, Kammoun A, Rehaiem A, Ghedira S, Houissa M, Boutiba-Ben Boubaker I, Slim A, Dubois V. High Prevalence of Gut Microbiota Colonization with Broad-Spectrum Cephalosporin Resistant Enterobacteriaceae in a Tunisian Intensive Care Unit. Front Microbiol 2016; 7:1859. [PMID: 27965626 PMCID: PMC5126703 DOI: 10.3389/fmicb.2016.01859] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/04/2016] [Indexed: 11/15/2022] Open
Abstract
Healthcare-associated infections due to cefotaxime-resistant (CTX-R) Enterobacteriaceae have become a major public health threat, especially in intensive care units (ICUs). Often acquired nosocomially, CTX-R Enterobacteriaceae can be introduced initially by patients at admission. This study aimed to determine the prevalence and genetic characteristics of CTX-R Enterobacteriaceae-intestinal carriage in ICU patients, to evaluate the rate of acquisition of these organisms during hospitalization, and to explore some of the associated risk factors for both carriage and acquisition. Between December 2014 and February 2015, the 63 patients admitted in the ICU of Charles Nicolle hospital were screened for rectal CTX-R Enterobacteriaceae colonization at admission and once weekly thereafter to identify acquisition. CTX-R Enterobacteriaceae fecal carriage rate was 20.63% (13/63) at admission. Among the 50 non-carriers, 35 were resampled during their hospitalization and the acquisition rate was 42.85% (15/35). Overall, 35 CTX-R Enterobacteriaceae isolates were collected from 28 patients (25 Klebsiella pneumoniae, seven Escherichia coli, and three Enterobacter cloacae strains). Seven patients were simultaneously colonized with two CTX-R Enterobacteriaceae isolates. CTX-M-15 was detected in most of the CTX-R Enterobacteriaceae isolates (30/35, 88.23%). Three strains co-produced CMY-4 and 22 strains were carbapenem-resistant and co-produced a carbapenemase [OXA-48 (n = 13) or NDM-1 (n = 6)]. Molecular typing of K. pneumoniae strains, revealed eight Pulsed field gel electrophoresis (PFGE) patterns and four sequence types (ST) [ST101, ST147, ST429, and ST336]. However, E. coli isolates were genetically unrelated and belonged to A (n = 2), B1 (n = 2) and B2 (n = 3) phylogenetic groups and to ST131 (two strains), ST572 (two strains), ST615 (one strain) and ST617 (one strain). Five colonized patients were infected by CTX-R Enterobacteriaceae (four with the same strain identified from their rectal swab and one with a different strain). Whether imported or acquired during the stay in the ICU, colonization by CTX-R Enterobacteriaceae is a major risk factor for the occurrence of serious nosocomial infections. Their systematic screening in fecal carriage is mandatory to prevent the spread of these multidrug resistant bacteria.
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Affiliation(s)
- Elaa Maamar
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El ManarTunis, Tunisia; Faculty of Sciences of Tunis, University of Tunis El ManarTunis, Tunisia
| | - Sana Ferjani
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar Tunis, Tunisia
| | - Ali Jendoubi
- Intensive Care Unit, Charles Nicolle Hospital Tunis, Tunisia
| | - Samia Hammami
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El ManarTunis, Tunisia; Faculty of Sciences of Gafsa, University of GafsaGafsa, Tunisia
| | - Zaineb Hamzaoui
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El Manar Tunis, Tunisia
| | | | - Mabrouka Saidani
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El ManarTunis, Tunisia; Laboratory of Microbiology, Charles Nicolle HospitalTunis, Tunisia
| | - Aouatef Kammoun
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El ManarTunis, Tunisia; Laboratory of Microbiology, Charles Nicolle HospitalTunis, Tunisia
| | - Amel Rehaiem
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El ManarTunis, Tunisia; Laboratory of Microbiology, Charles Nicolle HospitalTunis, Tunisia
| | - Salma Ghedira
- Intensive Care Unit, Charles Nicolle Hospital Tunis, Tunisia
| | - Mohamed Houissa
- Intensive Care Unit, Charles Nicolle Hospital Tunis, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El ManarTunis, Tunisia; Laboratory of Microbiology, Charles Nicolle HospitalTunis, Tunisia
| | - Amine Slim
- Faculty of Medicine of Tunis - LR99ES09 Research Laboratory of Antimicrobial Resistance, University of Tunis El ManarTunis, Tunisia; Laboratory of Microbiology, Charles Nicolle HospitalTunis, Tunisia
| | - Veronique Dubois
- University Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR5234 Bordeaux, France
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Amoush A, Aletan M, Ferjani S, Rabatic B, Madden N, Al-Basheer A, Marascio J, Zaenger D, Huang K, Green A, Shaaban S, Pishgou M, Marchan E, Giller C, Forseen S, Choudhri H, Ferguson C, Vender J, Alleyne C, Mourad W. Dosimetric Study of the Effect of the 6-Dimensional Calypso-Compatible Couch Top and Rails for Spine Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.2233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ferjani S, Saidani M, Hamzaoui Z, Alonso CA, Torres C, Maamar E, Slim AF, Boutiba BBI. Community fecal carriage of broad-spectrum cephalosporin-resistant Escherichia coli in Tunisian children. Diagn Microbiol Infect Dis 2016; 87:188-192. [PMID: 27856044 DOI: 10.1016/j.diagmicrobio.2016.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/04/2016] [Accepted: 03/05/2016] [Indexed: 10/22/2022]
Abstract
The spread of extended spectrum β-lactamases (ESBL) and plasmid mediated AmpC β-lactamases (pAmpC) was evaluated in Escherichia coli strains collected from the intestinal microbiota of healthy children in Tunisia. The carriage rate of CTXRE. coli was 6.6% (7 of 105 samples) and one strain/sample was further characterized (7 isolates). These isolates harbored blaCTX-M-1 (n = 4), blaCTX-M-15 (n = 2), and blaCMY-2 gene (n = 1), which were usually located on FIB replicon type and carried class 1 integrons. The acc(6')-Ib-cr variant was identified in one isolate that harbored blaCTX-M-15. CTXRE. coli isolates were genetically unrelated and belonged to B1 (n = 3/ST155/ST398/ST58), D (n = 2/ST117/ST493), B2 (n = 1/ST127), and A (n = 1/ST746) phylogroups. Strain virulence scores varied from 3 to 12, and frequently harbored the pathogenicity island PAI IV536. The intestinal tract of healthy children constitute an important reservoir of ESBL producing E. coli. Thus, improvement of hygiene measures mainly in the school environment and rational use of antibiotics would be of great help in preventing selection and diffusion of resistant strains from intestinal microbiota.
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Affiliation(s)
- Sana Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Résistance aux antimicrobiens, 1007, Tunis, Tunisie.
| | - Mabrouka Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Résistance aux antimicrobiens, 1007, Tunis, Tunisie; CHU Charles Nicolle, Service de Microbiologie, 1006, Tunis, Tunisie
| | - Zeineb Hamzaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Résistance aux antimicrobiens, 1007, Tunis, Tunisie
| | - Carla Andrea Alonso
- Area Bioquímica y Biología Molecular, Universidad de La Rioja, Logrono, Spain
| | - Carmen Torres
- Area Bioquímica y Biología Molecular, Universidad de La Rioja, Logrono, Spain
| | - Elaa Maamar
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Résistance aux antimicrobiens, 1007, Tunis, Tunisie
| | | | - Ben Boubaker Ilhem Boutiba
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de Résistance aux antimicrobiens, 1007, Tunis, Tunisie; CHU Charles Nicolle, Service de Microbiologie, 1006, Tunis, Tunisie
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El Ghoul J, Ferjani S, Sanaii S. Étiologies actuelles des hémoptysies chez le sujet jeune : étude comparative à propos de 50 cas. Rev Mal Respir 2016. [DOI: 10.1016/j.rmr.2015.10.365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Maamar E, Hammami S, Ferjani S, Hamzaoui Z, Jlizi A, Saidani M, Slim A, Boubaker IBB. Molecular characterization of extended spectrum β-lactamases, ampccephalosporinases and carbapenemases in klebsiellapneumoniae causing bacteremia at charles nicolle Hospital of Tunisia. Acta Med Int 2016. [DOI: 10.5530/ami.2016.2.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Saleh H, Ferjani S, Masssey V, Howlin T, Pokhrel D. SU-E-T-815: In Vivo Dosimetry and Daily Arc Junction Verification Using EBT3 Gafchromic Film for Pediatric Cranio-Spinal Irradiation. Med Phys 2015. [DOI: 10.1118/1.4925179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Kilani H, Abbassi MS, Ferjani S, Mansouri R, Sghaier S, Ben Salem R, Jaouani I, Douja G, Brahim S, Hammami S, Ben Chehida N, Boubaker IBB. Occurrence of bla CTX-M-1, qnrB1 and virulence genes in avian ESBL-producing Escherichia coli isolates from Tunisia. Front Cell Infect Microbiol 2015; 5:38. [PMID: 26000252 PMCID: PMC4419849 DOI: 10.3389/fcimb.2015.00038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/13/2015] [Indexed: 11/20/2022] Open
Abstract
Avian ESBL-producing Escherichia coli isolates have been increasingly reported worldwide. Animal to human dissemination, via food chain or direct contact, of these resistant bacteria has been reported. In Tunisia, little is known about avian ESBL- producing E. coli and further studies are needed. Seventeen ESBL-producing Escherichia coli isolates from poultry feces from two farms (Farm 1 and farm 2) in the North of Tunisia have been used in this study. Eleven of these isolates (from farm 1) have the same resistance profile to nalidixic acid, sulfonamides, streptomycin, tetracycline, and norfloxacine (intermediately resistant). Out of the six isolates recovered from farm 2, only one was co-resistant to tetracycline. All isolates, except one, harbored blaCTX-M-1 gene, and one strain co-harbored the blaTEM-1 gene. The genes tetA and tetB were carried, respectively, by 11 and 1 amongst the 12 tetracycline-resistant isolates. Sulfonamides resistance was encoded by sul1, sul2, and sul3 genes in 3, 17, and 5 isolates, respectively. The qnrB1 was detected in nine strains, one of which co-harbored qnrS1 gene. The search for the class 1 and 2 integrons by PCR showed that in farm 1, class 1 and 2 integrons were found in one and ten isolates, respectively. In farm 2, class 1 integron was found in only one isolate, class 2 was not detected. Only one gene cassette arrangement was demonstrated in the variable regions (VR) of the 10 int2-positive isolates: dfrA1- sat2-aadA1. The size of the VR of the class 1 integron was approximately 250 bp in one int1-positive isolate, whereas in the second isolate, no amplification was observed. All isolates of farm 1 belong to the phylogroup A (sub-group A0). However, different types of phylogroups in farm 2 were detected. Each of the phylogroups A1, B22, B23 was detected in one strain, while the D2 phylogroup was found in 3 isolates. The virulence genes iutA, fimH, and traT were detected in 3, 7, and 3 isolates, respectively. Two types of gene combination were detected: iutA+fimH+traT in 3 isolates and iutA+fimH in one isolate. The isolates recovered in farm 1 showed the same profile of PFGE macro-restriction, while isolates of farm 2 presented unrelated PFGE patterns. We conclude that these avian ESBL-producing E. coli isolates show homo- and heterogenic genetic background and that plasmids harboring ESBL genes could be involved in the dissemination of this resistance phenotype.
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Affiliation(s)
- Hajer Kilani
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia ; LR99ES09 Laboratoire de Résistance aux Antimicrobiens, Faculté de Médecine de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Mohamed Salah Abbassi
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia ; LR99ES09 Laboratoire de Résistance aux Antimicrobiens, Faculté de Médecine de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Sana Ferjani
- LR99ES09 Laboratoire de Résistance aux Antimicrobiens, Faculté de Médecine de Tunis, Université de Tunis El Manar Tunis, Tunisia ; Hôpital Charles Nicolle, Service de Microbiologie Tunis, Tunisia
| | - Riadh Mansouri
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia ; Regional Animal Health Center for North Africa (RAHC-NA) Tunis, Tunisia
| | - Senda Sghaier
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Rakia Ben Salem
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Imen Jaouani
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Gtari Douja
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Sana Brahim
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Salah Hammami
- École Nationale de Médecine Vétérinaire de Sidi Thabet Sidi Thabet, Tunisia
| | - Noureddine Ben Chehida
- Laboratory of Bacteriological Research, Institut de la Recherche Vétérinaire de Tunis, Université de Tunis El Manar Tunis, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- LR99ES09 Laboratoire de Résistance aux Antimicrobiens, Faculté de Médecine de Tunis, Université de Tunis El Manar Tunis, Tunisia ; Hôpital Charles Nicolle, Service de Microbiologie Tunis, Tunisia
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Ferjani S, Saidani M, Amine FS, Boutiba-Ben Boubaker I. Prevalence and characterization of plasmid-mediated quinolone resistance genes in extended-spectrum β-lactamase-producing Enterobacteriaceae in a Tunisian hospital. Microb Drug Resist 2014; 21:158-66. [PMID: 25247633 DOI: 10.1089/mdr.2014.0053] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The objective of the study was to assess the prevalence of plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB, qnrC, qnrD, qnrS, aac(6')-Ib-cr, qepA, and oqxAB) in a collection of 120 extended-spectrum β-lactamases (ESBLs)-producing enterobacteria and to characterize them. Overall, PMQR determinants were detected in 72 (60%) isolates (20 Escherichia coli, 32 Klebsiella pneumoniae, and 20 Enterobacter cloacae). PMQR frequencies were as follows: qnr genes (25.8%), oqxAB (21.6%), and aac(6')-Ib-cr variant (19.2%). Four qnr alleles were identified as qnrB1 (83.8%), qnrB4 (6.4%), qnrB2 (3.2%), and qnrS1 (6.4%). qnr genes were mainly detected in E. cloacae (50%), aac(6')-Ib-cr in E. coli (47.5%), and oqxAB in K. pneumoniae (65%). Overall, blaCTX-M-15 (90.3%) was the most prevalent blaESBL type followed by blaSHV-12 (6.4%) and blaSHV-27 (2.7%). Rates of mutations in gyrA and parC genes were 75% for E. coli, 72.8% for K. pneumoniae, and 50% for E. cloacae. Isolates with mutations in their quinolone resistance-determining regions exhibited high fluoroquinolones resistance levels compared to those with wild ones. Genetic study of PMQR-harboring isolates revealed a great genomic diversity among each Enterobacteriaceae species. Our findings indicate the high prevalence of PMQR determinants among ESBL-producing Enterobacteriaceae isolates from our hospital and their diffusion in various unrelated CTX-M-15-producing clones.
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Affiliation(s)
- Sana Ferjani
- 1 LR99ES09 Laboratoire de Résistance aux antimicrobiens, Faculté de Médecine de Tunis, Université de Tunis El Manar , Tunis, Tunisie
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Ferjani S, Saidani M, Ennigrou S, Hsairi M, Slim AF, Boutiba Ben Boubaker I. Multidrug resistance and high virulence genotype in uropathogenic Escherichia coli due to diffusion of ST131 clonal group producing CTX-M-15: an emerging problem in a Tunisian hospital. Folia Microbiol (Praha) 2013; 59:257-62. [DOI: 10.1007/s12223-013-0292-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 11/08/2013] [Indexed: 10/26/2022]
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Ferjani S, Stephans K, Tendulkar R, Xia P. SU-E-T-649: Planning Margins Validation for Concurrent Treatment of Prostate and Pelvic Lymph Nodes Under Daily Image Guided Delivery. Med Phys 2013. [DOI: 10.1118/1.4815076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Ferjani S, Huang G, Shang Q, Xia P. TU-C-213CD-10: Shifting MLC to Follow the Prostate Movements While Concurrently Treating Pelvic Lymph Nodes. Med Phys 2012. [DOI: 10.1118/1.4735937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Ferjani S, Huang G, Shang Q, Xia P. SU-E-J-30: Using Shifting Planned Dose Matrix to Evaluate Daily Dose Changes for IMRT Prostate Treatment. Med Phys 2012; 39:3659. [PMID: 28517603 DOI: 10.1118/1.4734863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Summation of daily DVH from KV-cone beam CT (KV-CBCT) to obtain a composite dose volume histogram (DVH) is challenging. Directly translating the planned dose matrix according to measured daily prostate displacements provided a common reference frame for a composite DVH from daily DVHs. The purpose of this study is to evaluate the shifting planned dose matrix method compared to the dose recalculation method using daily KV-CBCT. METHODS Six patients, who received concurrent IMRT treatment for prostate and pelvic lymph nodes with 124 daily CBCTs, were selected for this study. Contours for CBCT's were transferred from the planning CT after soft tissue registration for prostate and bony registration for pelvic lymph nodes. Using the same planning beam configurations, we re-calculated doses for these CBCTs after shifting to corrected treatment isocenters. The planned dose matrix translation was performed by an in-house program written in MATLAB and incorporated with Computational Environment for Radiotherapy Research (CERR) software. The corresponding daily DVH was obtained by shifting the planned dose matrix according to shifts of treatment iso-centers. To compare these two methods, selected endpoint doses for tumor targets and sensitive structures were extracted from DVHs. RESULTS For prostate displacement less then 1.5 cm, the dose matrix shifting method resulted in 93% and 98% fractions within 5% differences from the recalculation method for D95 of prostate and pelvic lymph nodes, respectively. These numbers decreased to 58% and 71% when 2% dose difference criterion was used. CONCLUSIONS Allowing 5% daily dose difference, shifting planned dose matrix provides effective means to evaluating daily dose changes for concurrent IMRT treatment for prostate and pelvic lymph nodes. The utility of this tool is to provide a common coordinate frame to obtain composite dose distributions.
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Affiliation(s)
- S Ferjani
- The Cleveland Clinic Foundation, Cleveland, OH
| | - G Huang
- The Cleveland Clinic Foundation, Cleveland, OH
| | - Q Shang
- The Cleveland Clinic Foundation, Cleveland, OH
| | - P Xia
- The Cleveland Clinic Foundation, Cleveland, OH
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Ferjani S, Saidani M, Ennigrou S, Hsairi M, Ben Redjeb S. Virulence determinants, phylogenetic groups and fluoroquinolone resistance in Escherichia coli isolated from cystitis and pyelonephritis. ACTA ACUST UNITED AC 2011; 60:270-4. [PMID: 21872408 DOI: 10.1016/j.patbio.2011.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 07/22/2011] [Indexed: 12/17/2022]
Abstract
AIM OF THE STUDY The aim of this study is to assess the relation between virulence genotype, phylogenetic group and susceptibility to fluoroquinolones and the urinary tract infection type including pyelonephritis and cystitis due to Escherichia coli. MATERIALS AND METHODS Between 2006 and 2007, 129 non-duplicate E. coli isolates from pyelonephritis (n=56) and cystitis (n=73) were prospectively collected. The antibiotic susceptibility was done by disk diffusion method. The phylogenetic groups, A, B1, B2 and D and 18 virulence genes were determined by multiplex PCR. Statistical analysis was done with the Pearson χ2 test, Mann-Whitney U-test, Kruskal-Wallis test and stepwise multivariable logistic regression analysis, P values below 0.05 were considered statistically significant. RESULTS For the pyelonephritis group, sex ratio was 0.3, the median age for women was 30 years and for men it was 54 years. For the cystitis group, sex ratio was 0.4, the median age for women was 41.5 years and for men it was 67.8 years. Significant statistical correlations were found between pyelonephritis isolates and susceptibility to ciprofloxacin (P=4 10(-5)), papG allele II (P=2 10(-6)), hlyA (P=10(-03)), iroN (P=0.04), iha (P=0.03) and ompT (P=0.03) virulence genes, high virulence score (P=0.008) and B2 phylogenetic group (P=0.03). In multivariate logistic regression analysis, papG II as predictor of pyelonephritis, no correlation could be established for the cystitis group. CONCLUSION Our findings argue for a direct link between pyelonephritis, virulence factors, susceptibility to fluroquinolones and B2 phylogenetic group among uropthogenic E. coli.
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Affiliation(s)
- S Ferjani
- Laboratoire de recherche resistance aux antimicrobiens, hôpital Charles-Nicolle de Tunis, boulevard 9-Avril, 1006 Tunis, Tunisia.
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Ferjani S, De Luca A, Barna V, Versace C, Strangi G. Thermo-recurrent nematic random laser. Opt Express 2009; 17:2042-2047. [PMID: 19189035 DOI: 10.1364/oe.17.002042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This experimental work is aimed to investigate the thermal behavior of random laser action in dye doped nematic liquid crystals. The study evidenced an important temperature dependence of the random lasing characteristics in the nematic phase and in close proximity of the nematicisotropic (N-I) phase transition. A lowering of the laser emission intensity as the temperature increases is strictly related to the shift of the lasing threshold as function of the temperature even though the pump energy is kept fixed. The optical losses increasing owing to the thermal fluctuation enhanced scattering drive the input-output smoother behavior until the system stops to lase, because below threshold. The unexpected reoccurrence of random lasing at higher temperature, in proximity of N-I transition is found to be related to a different scattering mechanism, the micro-droplets nucleation and critical opalescence.
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Affiliation(s)
- S Ferjani
- LICRYL CNR-INFM and Center of Excellence CEMIF.CAL, Department of Physics, University of Calabria, Rende (CS), Italy
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Strangi G, Ferjani S, Barna V, De Luca A, Versace C, Scaramuzza N, Bartolino R. Random lasing and weak localization of light in dye-doped nematic liquid crystals. Opt Express 2006; 14:7737-7744. [PMID: 19529143 DOI: 10.1364/oe.14.007737] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The first observation of random laser action in a partially ordered, optically anisotropic nematic liquid crystal with long-range dielectric tensor fluctuations is reported. Above a given pump power the fluorescence curve collapses and the typical narrowing and explosion effect leads to discrete sharp peaks. The unexpected surviving of interference effects in recurrent multiple scattering provide the required optical feedback for lasing in nematics. Coherent backscattering of light waves in orientationally ordered nematic liquid crystals manifests a weak localization of light which strongly supports diffusive laser action in presence of gain medium. Intensity fluctuations of the speckle-like emission pattern indicate the typical spatio-temporal randomness of diffusive laser emission. A comparison of the laser action is reported for systems with different order degree: fully disordered semiconductor powders, self-ordered cholesterics and partially ordered nematic liquid crystals.
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